diff --git a/DB_restructuring_queries.sql b/DB_restructuring_queries.sql deleted file mode 100644 index d9c0ed3..0000000 --- a/DB_restructuring_queries.sql +++ /dev/null @@ -1,34 +0,0 @@ ----- Add cube extension to DB ---- -CREATE EXTENSION IF NOT EXISTS cube; - ----- CREATE INDICES ON MOLECULE_ID ---- -CREATE INDEX IF NOT EXISTS idx_molecule_molecule_id ON molecule (molecule_id); -CREATE INDEX IF NOT EXISTS idx_molecule_smiles ON molecule (smiles); -CREATE INDEX IF NOT EXISTS idx_molecule_umap_knn ON molecule USING gist (umap); -CREATE INDEX IF NOT EXISTS idx_pca_smiles ON pca (smiles); - ----- Set column pca in table molecule to a cube of all 4 pca component columns ---- -ALTER TABLE molecule ADD COLUMN pca cube; -UPDATE molecule -SET pca = cube(ARRAY[pca.pca1, pca.pca2, pca.pca3, pca.pca4]) -FROM pca -WHERE molecule.smiles = pca.smiles; - ---- Create indices on PCA --- -CREATE INDEX IF NOT EXISTS idx_molecule_pca ON molecule (pca); -CREATE INDEX IF NOT EXISTS idx_molecule_pca_knn ON molecule USING gist (pca); - ----- Query to make umap into cube data type on molecule table ---- -ALTER TABLE molecule RENAME umap TO umap_point; -ALTER TABLE molecule ADD COLUMN umap cube; -UPDATE molecule -SET umap = cube(ARRAY[umap_point[0], umap_point[1]]) -WHERE umap_point IS NOT NULL; - ---- Drop umap_point --- -ALTER TABLE molecule DROP COLUMN umap_point; - ----- Drop unneccessary tables ---- -DROP TABLE new_data; -DROP TABLE pca; -DROP TABLE temporary; \ No newline at end of file diff --git a/add_data_tables.sql b/add_data_tables.sql deleted file mode 100644 index 0e8ea7b..0000000 --- a/add_data_tables.sql +++ /dev/null @@ -1,68 +0,0 @@ -CREATE TABLE ml_data ( - molecule_id INTEGER, - property TEXT, - max DOUBLE PRECISION, - min DOUBLE PRECISION, - delta DOUBLE PRECISION, - vburminconf DOUBLE PRECISION, - boltzmann_average DOUBLE PRECISION -); - -ALTER TABLE ml_data -ADD CONSTRAINT fk_molecule_id -FOREIGN KEY (molecule_id) REFERENCES molecule(molecule_id); - -CREATE INDEX idx_ml_data_molecule_id ON ml_data(molecule_id); - -\COPY ml_data FROM 'ml_data_json_table.csv' DELIMITER ',' CSV HEADER; - -CREATE TABLE dft_data ( - molecule_id INTEGER, - property TEXT, - max DOUBLE PRECISION, - min DOUBLE PRECISION, - delta DOUBLE PRECISION, - vburminconf DOUBLE PRECISION, - boltzmann_average DOUBLE PRECISION -); - -ALTER TABLE dft_data -ADD CONSTRAINT fk_molecule_id -FOREIGN KEY (molecule_id) REFERENCES molecule(molecule_id); - -CREATE INDEX idx_dft_data_molecule_id ON dft_data(molecule_id); - -\COPY dft_data FROM 'dft_data_json_table.csv' DELIMITER ',' CSV HEADER; - -CREATE TABLE xtb_data ( - molecule_id INTEGER, - property TEXT, - max DOUBLE PRECISION, - min DOUBLE PRECISION, - boltzmann_average DOUBLE PRECISION -); - -ALTER TABLE xtb_data -ADD CONSTRAINT fk_molecule_id -FOREIGN KEY (molecule_id) REFERENCES molecule(molecule_id); - -CREATE INDEX idx_xtb_data_molecule_id ON xtb_data(molecule_id); - -\COPY xtb_data FROM 'xtb_data_json_table.csv' DELIMITER ',' CSV HEADER; - - -CREATE TABLE xtb_ni_data ( - molecule_id INTEGER, - property TEXT, - boltzmann_average DOUBLE PRECISION, - max DOUBLE PRECISION, - min DOUBLE PRECISION -); - -ALTER TABLE xtb_ni_data -ADD CONSTRAINT fk_molecule_id -FOREIGN KEY (molecule_id) REFERENCES molecule(molecule_id); - -CREATE INDEX idx_xtb_ni_data_molecule_id ON xtb_ni_data(molecule_id); - -\COPY xtb_ni_data FROM 'xtb_ni_data_json_table.csv' DELIMITER ',' CSV HEADER; diff --git a/backend/app/app/api/v2/endpoints/conformer.py b/backend/app/app/api/v2/endpoints/conformer.py index 4c64b3e..5734428 100644 --- a/backend/app/app/api/v2/endpoints/conformer.py +++ b/backend/app/app/api/v2/endpoints/conformer.py @@ -1,6 +1,6 @@ from fastapi import APIRouter, Depends from fastapi.responses import PlainTextResponse -from typing import List +from typing import List, Any from sqlalchemy import text from sqlalchemy.orm import Session @@ -18,11 +18,19 @@ def get_conformer_and_format(conformer_id, format, db): return "Not implemented yet" try: - coords, elements = ( - db.query(models.conformer.coords, models.conformer.elements) - .filter(models.conformer.conformer_id == conformer_id) - .one() - ) + query = text(""" + SELECT coords, elements + FROM conformer + WHERE conformer_id = :conformer_id + """) + + stmt = query.bindparams(conformer_id=conformer_id) + + result = db.execute(stmt).fetchone() + + coords = result.coords + elements = result.elements + except: return None @@ -38,7 +46,7 @@ def get_conformer_and_format(conformer_id, format, db): @router.get("/export/{format}/{conformer_id}", response_class=PlainTextResponse) def export_conformer( - conformer_id: int = 0, + conformer_id: int | str, format: str = "xyz", db: Session = Depends(deps.get_db), ): @@ -51,11 +59,29 @@ def format_for_ngl( db: Session = Depends(deps.get_db), ): conformer_id, format = filename.split(".") - return get_conformer_and_format(int(conformer_id), format, db) + return get_conformer_and_format(conformer_id, format, db) + +@router.get("/data/{conformer_id}", response_model=Any) +def get_conformer_data(conformer_id: int | str, db: Session = Depends(deps.get_db)): + + query = text(f""" + SELECT * + FROM conformer + WHERE conformer_id = :conformer_id + """) + + stmt = query.bindparams(conformer_id=conformer_id) + + result = db.execute(stmt).fetchone() + + # Hacky way to get each row as a dictionary. + # do this to generalize for different data sets - column names may vary. + data = { k:v for k, v in result._asdict().items() if k != "coords" and k != "elements" } + return data @router.get("/others_id/{conformer_id}") -def get_other_conformers_id(conformer_id: int = 0, db: Session = Depends(deps.get_db)): +def get_other_conformers_id(conformer_id: int | str, db: Session = Depends(deps.get_db)): sql = text( ( "select conformer_id from conformer " diff --git a/backend/app/app/api/v2/endpoints/molecule.py b/backend/app/app/api/v2/endpoints/molecule.py index 14b7cb6..f7e658e 100644 --- a/backend/app/app/api/v2/endpoints/molecule.py +++ b/backend/app/app/api/v2/endpoints/molecule.py @@ -50,22 +50,6 @@ def _pandas_to_buffer(df): return buffer -def _valid_molecule_id(molecule_id, db): - - # Generalized - get max molecule id. - query = text(f"SELECT MAX(molecule_id) FROM molecule;") - max_molecule_id = db.execute(query).fetchall()[0][0] - - # Check to see if the molecule_id is within range. - if molecule_id > max_molecule_id: - raise HTTPException(status_code=404, detail=f"Molecule with ID supplied not found, the maximum ID is {max_molecule_id}") - - # Check to see if the molecule_id is within range. - if molecule_id <= 0: - raise HTTPException(status_code=500) - - return - def valid_smiles(smiles): """Check to see if a smile string is valid to represent a molecule. @@ -100,8 +84,41 @@ def valid_smiles(smiles): return smiles -@router.get("/data/{molecule_id}", response_model=List[schemas.MoleculeData]) -async def get_molecule_data(molecule_id: int, +@router.get("/first_id", response_model=Any) +async def get_first_molecule_id(db: Session = Depends(deps.get_db)): + query = text("SELECT molecule_id FROM molecule ORDER BY molecule_id LIMIT 1;") + result = db.execute(query).fetchone() + return {"first_molecule_id": result[0]} + +@router.get("/data_types", response_model=Any) +async def get_data_types(db: Session = Depends(deps.get_db)): + query = text("SELECT table_name FROM information_schema.tables WHERE table_schema = 'public';") + results = db.execute(query).fetchall() + return {"available_types": [x[0] for x in results if "data" in x[0]] } + + +@router.get("/{molecule_id}/data_types", response_model=Any) +async def get_molecule_data_types(molecule_id: int | str, db: Session = Depends(deps.get_db)): + # First, fetch all table names that have 'data' in their name + query_tables = text("SELECT table_name FROM information_schema.tables WHERE table_schema = 'public' AND table_name LIKE '%data%';") + tables = db.execute(query_tables).fetchall() + + # Prepare a dictionary to store the results + results = {} + + # Loop through each table to check for the molecule_id + for table in tables: + table_name = table[0] + # Assuming the column storing molecule IDs is named 'molecule_id' in all tables. + # You might need to adjust this according to your database schema. + query_check = text(f"SELECT EXISTS(SELECT 1 FROM {table_name} WHERE molecule_id = :molecule_id) AS exists;") + exists = db.execute(query_check, {"molecule_id": molecule_id}).fetchone()[0] + results[table_name] = exists + + return results + +@router.get("/data/{molecule_id}", response_model=Any) +async def get_molecule_data(molecule_id: int | str, data_type: str="ml", db: Session = Depends(deps.get_db)): @@ -120,8 +137,12 @@ async def get_molecule_data(molecule_id: int, stmt = query.bindparams(molecule_id=molecule_id) results = db.execute(stmt).fetchall() + + # Hacky way to get each row as a dictionary. + # do this to generalize for different data sets - column names may vary. + list_of_dicts = [row._asdict() for row in results] - return results + return list_of_dicts @router.get("/data/export/batch") async def get_molecules_data(molecule_ids: str, @@ -130,14 +151,8 @@ async def get_molecules_data(molecule_ids: str, context: Optional[str]=None, db: Session = Depends(deps.get_db)): - - # Sanitize molecule ids - int_check = [x.strip().isdigit() for x in molecule_ids.split(",")] - if not all(int_check): - raise HTTPException(status_code=400, detail="Invalid molecule ids.") - - molecule_ids_list = [int(x) for x in molecule_ids.split(",")] + molecule_ids_list = [ x.strip() for x in molecule_ids.split(",")] first_molecule_id = molecule_ids_list[0] num_molecules = len(molecule_ids_list) @@ -145,9 +160,6 @@ async def get_molecules_data(molecule_ids: str, if context.lower() not in ["substructure", "pca_neighbors", "umap_neighbors"]: raise HTTPException(status_code=400, detail="Invalid context.") - # Check to see if all molecule ids are valid. - [ _valid_molecule_id(int(x), db) for x in molecule_ids.split(",") ] - # Check for valid data type. if data_type.lower() not in ["ml", "dft", "xtb", "xtb_ni"]: raise HTTPException(status_code=400, detail="Invalid data type.") @@ -158,14 +170,18 @@ async def get_molecules_data(molecule_ids: str, # Use pandas.read_sql_query to get the data. table_name = f"{data_type}_data" + # Generating a safe query with placeholders + placeholders = ', '.join([':id' + str(i) for i in range(len(molecule_ids_list))]) + query_parameters = {'id' + str(i): mid for i, mid in enumerate(molecule_ids_list)} + query = text(f""" SELECT t.*, m.SMILES FROM {table_name} t JOIN molecule m ON t.molecule_id = m.molecule_id - WHERE t.molecule_id IN ({molecule_ids}) + WHERE t.molecule_id IN ({placeholders}) """) - df = pd.read_sql_query(query, db.bind) + df = pd.read_sql_query(query, db.bind, params=query_parameters) df_wide = _pandas_long_to_wide(df) @@ -186,12 +202,10 @@ async def get_molecules_data(molecule_ids: str, return response @router.get("/data/export/{molecule_id}") -async def export_molecule_data(molecule_id: int, +async def export_molecule_data(molecule_id: int | str, data_type: str="ml", db: Session = Depends(deps.get_db)): - # Check to see if the molecule_id is valid. - _valid_molecule_id(molecule_id, db) # Check for valid data type. if data_type.lower() not in ["ml", "dft", "xtb", "xtb_ni"]: @@ -274,9 +288,8 @@ def get_molecule_umap( @router.get("/{molecule_id}", response_model=schemas.Molecule) -def get_a_single_molecule(molecule_id: int, db: Session = Depends(deps.get_db)): +def get_a_single_molecule(molecule_id: int | str, db: Session = Depends(deps.get_db)): - _valid_molecule_id(molecule_id, db) molecule = ( db.query(models.molecule) @@ -284,15 +297,29 @@ def get_a_single_molecule(molecule_id: int, db: Session = Depends(deps.get_db)): .one() ) + if not molecule: + raise HTTPException(status_code=404, detail="Molecule not found") + + # Attempt to fetch conformers associated with this molecule from the conformer view + try: + conformers = molecule.conformer_collection + except: + sql = text("SELECT * FROM conformer WHERE molecule_id = :molecule_id") + stmt = sql.bindparams(molecule_id=molecule_id) + conformers = db.execute(stmt).fetchall() + + # for databases where there are no compound names, set the compound name to None + try: + molecule.compound_name + except AttributeError: + molecule.compound_name = None + response = schemas.Molecule( molecule_id=molecule.molecule_id, smiles=molecule.smiles, molecular_weight=molecule.molecular_weight, - conformers_id=[c.conformer_id for c in molecule.conformer_collection], - dft_data=molecule.dft_data, - xtb_data=molecule.xtb_data, - xtb_ni_data=molecule.xtb_ni_data, - ml_data=molecule.ml_data, + compound_name=molecule.compound_name, + conformers_id=[c.conformer_id for c in conformers], ) return response @@ -335,7 +362,7 @@ def search_molecules( @router.get("/{molecule_id}/neighbors/", response_model=List[schemas.MoleculeNeighbors]) def search_neighbors( - molecule_id: int, + molecule_id: int | str, type: str = "pca", components: Optional[str] = None, skip: int = 1, @@ -344,8 +371,6 @@ def search_neighbors( ): type = type.lower() - - _valid_molecule_id(molecule_id, db) # Check for valid neighbor type. if type not in ["pca", "umap"]: @@ -353,7 +378,7 @@ def search_neighbors( # Set defaults for components if type == "pca" and components is None: - components = "1,2,3,4" + components = "1,2,3" # Set defaults for components if type == "umap" and components is None: @@ -462,7 +487,7 @@ def get_molecule_dimensions( # Set defaults for components if type == "pca" and components is None: - components = "1,2,3,4" + components = "1,2,3" # Set defaults for components if type == "umap" and components is None: diff --git a/backend/app/app/core/config.py b/backend/app/app/core/config.py index bd43801..c65ffab 100644 --- a/backend/app/app/core/config.py +++ b/backend/app/app/core/config.py @@ -5,7 +5,7 @@ from urllib.parse import quote class Settings(BaseSettings): - PROJECT_NAME: str = 'Phosphines' + PROJECT_NAME: str = 'Descriptor Libraries API' POSTGRES_SERVER: str POSTGRES_USER: str diff --git a/backend/app/app/main.py b/backend/app/app/main.py index 51bddeb..efb4c04 100644 --- a/backend/app/app/main.py +++ b/backend/app/app/main.py @@ -1,3 +1,6 @@ + +import os + from fastapi import FastAPI import api.v1.api @@ -5,19 +8,21 @@ import core.config +name = os.getenv("API_PREFIX") + app = FastAPI( - title=core.config.settings.PROJECT_NAME, - openapi_url="/api/openapi.json", - docs_url="/api/docs", + title=core.config.settings.PROJECT_NAME + " " + name, + openapi_url=f"/api/{name}/openapi.json", + docs_url=f"/api/{name}/docs", redoc=None ) # default API endpoints -app.include_router(api.v2.api.router, prefix="/api", tags=["current"]) +app.include_router(api.v2.api.router, prefix=f"/api/{name}", tags=["current"]) # versioned API endpoints -app.include_router(api.v2.api.router, prefix="/api/v2", tags=["v2"]) -app.include_router(api.v1.api.router, prefix="/api/v1", tags=["v1"]) +app.include_router(api.v2.api.router, prefix=f"/api/{name}/v2", tags=["v2"]) +app.include_router(api.v1.api.router, prefix=f"/api/{name}/v1", tags=["v1"]) diff --git a/backend/app/app/schemas/conformer.py b/backend/app/app/schemas/conformer.py index fc248d8..2921b09 100644 --- a/backend/app/app/schemas/conformer.py +++ b/backend/app/app/schemas/conformer.py @@ -11,6 +11,6 @@ class Atom(BaseModel): class Conformer(BaseModel): - id: int + id: int | str coords: List[Atom] property: float diff --git a/backend/app/app/schemas/molecule.py b/backend/app/app/schemas/molecule.py index 6a62426..c855920 100644 --- a/backend/app/app/schemas/molecule.py +++ b/backend/app/app/schemas/molecule.py @@ -1,17 +1,14 @@ -from typing import Dict, List, Optional +from typing import Dict, List, Optional, Any from pydantic import BaseModel class Molecule(BaseModel): - molecule_id: int + molecule_id: int | str smiles: str molecular_weight: Optional[float] = None - conformers_id: List[Optional[int]] - dft_data: Optional[Dict] = None - xtb_data: Optional[Dict] = None - xtb_ni_data: Optional[Dict] = None - ml_data: Optional[Dict] = None + conformers_id: List[Optional[int | str]] + compound_name: Optional[str] = None class MoleculeData(BaseModel): property: str @@ -23,7 +20,7 @@ class MoleculeData(BaseModel): vburminconf: Optional[float] = None class MoleculeSimple(BaseModel): - molecule_id: int + molecule_id: int | str umap1: Optional[float] = None umap2: Optional[float] = None pat: Optional[str] = None @@ -31,7 +28,7 @@ class MoleculeSimple(BaseModel): class MoleculeComponents(BaseModel): type: Optional[str] = None - molecule_id: int + molecule_id: int | str pat: Optional[str] = None smiles: str components: Optional[list[float]] = None diff --git a/backend/backend.dockerfile b/backend/backend.dockerfile deleted file mode 100644 index 972ca94..0000000 --- a/backend/backend.dockerfile +++ /dev/null @@ -1,12 +0,0 @@ -FROM mambaorg/micromamba - -COPY environment.yaml* /tmp/conda-tmp/ - -ARG MAMBA_DOCKERFILE_ACTIVATE=1 - -RUN micromamba install -f /tmp/conda-tmp/environment.yaml && \ - micromamba clean --all --yes - -WORKDIR /app/ -ADD ./app /app/ -RUN pip install -e . \ No newline at end of file diff --git a/docker-compose.local.yml b/docker-compose.local.yml deleted file mode 100644 index 5b51c42..0000000 --- a/docker-compose.local.yml +++ /dev/null @@ -1,132 +0,0 @@ -version: '3' - -services: - local_reverse-proxy: - # The official v2 Traefik docker image - image: traefik:v2.8 - # Enables the web UI and tells Traefik to listen to docker - container_name: local_reverse_proxy - command: - - --api.insecure=true - - --api.dashboard=true - - --api.debug=true - - --providers.docker - - --entrypoints.web.address=:80 - ports: - # The HTTP port - - "80:80" - # The Web UI (enabled by --api.insecure=true) - - "8080:8080" - # - volumes: - # So that Traefik can listen to the Docker events - - /var/run/docker.sock:/var/run/docker.sock - networks: - - local-web - - local-db - labels: - - "traefik.enable=true" - - "traefik.http.routers.api.service=api@internal" - - local_database: - image: 'mcs07/postgres-rdkit' - container_name: local_database - shm_size: '4gb' - environment: - POSTGRES_SERVER: database - POSTGRES_USER: postgres - POSTGRES_PASSWD: "$postgresPWD" - POSTGRES_DB: postgres - ports: - - "5432:5432" - volumes: - - "kraken-postgres:/var/lib/postgresql/data" - - "pr3:/home/db" - healthcheck: - test: ["CMD-SHELL", "psql -U postgres -d postgres -c 'SELECT molecule_id FROM molecule LIMIT 1;' || exit 1"] - interval: 5s - timeout: 2s - retries: 5 - environment: - POSTGRES_HOST_AUTH_METHOD: trust - POSTGRES_DB: postgres - networks: - - local-db - - local_backend: - image: 'phosphines-backend:latest' - container_name: local_backend - build: - context: ./backend - dockerfile: backend.dockerfile - volumes: - - "./backend/app:/app" - environment: - POSTGRES_SERVER: local_database - POSTGRES_USER: postgres - POSTGRES_PASSWD: testing-password - POSTGRES_DB: postgres - entrypoint: bash prestart.sh - depends_on: - local_database: - condition: service_healthy - networks: - - local-web - - local-db - labels: - - "traefik.enable=true" - - "traefik.http.routers.backend.rule=Host(`localhost`) && PathPrefix(`/api`)" - - "traefik.http.services.backend.loadbalancer.server.port=8080" - - local_cdk-depict: - image: 'simolecule/cdkdepict:latest' - container_name: local_cdk-depcit - networks: - - local-web - labels: - - "traefik.enable=true" - - "traefik.http.routers.cdk-depict.rule=Host(`localhost`) && PathPrefix(`/depict`)" - - local_frontend: - image: 'phosphines-frontend:latest' - container_name: local_frontend - volumes: - - "./frontend/src:/app/src" - build: - context: . - dockerfile: frontend.development.dockerfile - networks: - - local-web - entrypoint: npm start - labels: - - "traefik.enable=true" - - "traefik.http.routers.frontend.rule=Host(`localhost`)" - - "traefik.http.services.frontend.loadbalancer.server.port=3000" - - local_documentation: - image: "phosphines-docs:latest" - container_name: local_documentation - build: - context: ./docs - dockerfile: docs.dockerfile - entrypoint: bash start.sh - volumes: - - "./docs:/docs" - networks: - - local-web - labels: - - "traefik.enable=true" - - "traefik.http.routers.documentation.rule=Host(`localhost`) && PathPrefix(`/docs`)" - - "traefik.http.services.documentation.loadbalancer.server.port=5000" - - -networks: - local-web: - local-db: - -volumes: - kraken-postgres: - external: true - pr3: - external: true - diff --git a/docker-compose.yml b/docker-compose.yml index b077256..6476c7f 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,110 +1,107 @@ version: '3' services: - reverse-proxy: - image: traefik:v2.9 - container_name: reverse_proxy - command: - - --api.insecure=false + local_reverse-proxy: + # The official v2 Traefik docker image + image: traefik:v2.8 + # Enables the web UI and tells Traefik to listen to docker + container_name: local_reverse_proxy + command: + - --api.insecure=true + - --api.dashboard=true + - --api.debug=true - --providers.docker - - --providers.docker.exposedByDefault=false - --entrypoints.web.address=:80 - - # Uncomment below for SSL - - --entrypoints.web.http.redirections.entrypoint.to=websecure - - --entrypoints.web.http.redirections.entrypoint.scheme=https - - --entrypoints.websecure.address=:443 - - --entrypoints.websecure.http.tls=true - - --certificatesresolvers.le.acme.email=janash@vt.edu - - --certificatesresolvers.le.acme.httpchallenge.entrypoint=web - - --certificatesResolvers.le.acme.storage=/acme/acme.json ports: + # The HTTP port - "80:80" - - "443:443" + # The Web UI (enabled by --api.insecure=true) + - "8080:8080" volumes: + # So that Traefik can listen to the Docker events - /var/run/docker.sock:/var/run/docker.sock - - ./acme:/acme networks: - - web - - db + - local-web + - local-db labels: - "traefik.enable=true" - "traefik.http.routers.api.service=api@internal" - - database: - image: 'mcs07/postgres-rdkit' - container_name: database + descriptor_database: + image: 'rdkit-postgres:latest' + container_name: descriptor_database shm_size: '4gb' + environment: + POSTGRES_SERVER: database + POSTGRES_USER: postgres ports: - - "127.0.0.1:5432:5432" + - "5432:5432" volumes: - - "kraken-postgres:/var/lib/postgresql/data" - - "pr3:/home/db" - environment: - POSTGRES_HOST_AUTH_METHOD: trust - POSTGRES_DB: postgres + - "postgres16:/var/lib/postgresql/data" + healthcheck: + test: ["CMD-SHELL", "psql -U postgres -d kraken_data -c 'SELECT molecule_id FROM molecule LIMIT 1;' || exit 1"] + interval: 5s + timeout: 2s + retries: 5 networks: - - db + - local-db - backend: - image: 'phosphines-backend:latest' - container_name: backend - depends_on: - - database + descriptor_backend: + image: 'descriptor-backend:latest' + container_name: kraken_backend build: context: ./backend dockerfile: backend.dockerfile volumes: - "./backend/app:/app" environment: - POSTGRES_SERVER: database + POSTGRES_SERVER: descriptor_database POSTGRES_USER: postgres - POSTGRES_PASSWD: $postgresPWD - POSTGRES_DB: postgres + POSTGRES_DB: kraken_data + API_PREFIX: kraken entrypoint: bash prestart.sh + depends_on: + descriptor_database: + condition: service_healthy networks: - - web - - db + - local-web + - local-db labels: - "traefik.enable=true" - - "traefik.http.routers.backend.rule=Host(`kraken.molssi.org`) && PathPrefix(`/api`)" - - "traefik.http.services.backend.loadbalancer.server.port=8080" - - "traefik.http.routers.backend.tls=true" - - "traefik.http.routers.backend.tls.certresolver=le" + - "traefik.http.routers.kraken_backend.rule=Host(`localhost`) && PathPrefix(`/api/kraken`)" + - "traefik.http.services.kraken_backend.loadbalancer.server.port=8080" - cdk-depict: + local_cdk-depict: image: 'simolecule/cdkdepict:latest' - container_name: cdk_depict + container_name: local_cdk-depcit networks: - - web + - local-web labels: - "traefik.enable=true" - - "traefik.http.routers.cdk-depict.rule=Host(`kraken.molssi.org`) && PathPrefix(`/depict`)" - - "traefik.http.routers.cdk-depict.tls=true" - - "traefik.http.routers.cdk-depict.tls.certresolver=le" + - "traefik.http.routers.cdk-depict.rule=Host(`localhost`) && PathPrefix(`/depict`)" - frontend: - image: 'phosphines-frontend:latest' - container_name: frontend + descriptor_frontend: + image: 'descriptor-frontend:latest' + container_name: kraken_frontend volumes: - "./frontend/src:/app/src" + - "./frontend/public:/app/public" + environment: + - VITE_BASE_URL=/descriptor build: context: . - dockerfile: frontend.production.dockerfile + dockerfile: frontend.development.dockerfile networks: - - web - entrypoint: npm run serve + - local-web + entrypoint: npm run start labels: - "traefik.enable=true" - - "traefik.http.routers.frontend.rule=Host(`kraken.molssi.org`)" + - "traefik.http.routers.frontend.rule=Host(`localhost`) && PathPrefix(`/descriptor`)" - "traefik.http.services.frontend.loadbalancer.server.port=3000" - - "traefik.http.routers.frontend.tls=true" - - "traefik.http.routers.frontend.tls.certresolver=le" - documentation: + local_documentation: image: "phosphines-docs:latest" - container_name: documentation + container_name: local_documentation build: context: ./docs dockerfile: docs.dockerfile @@ -112,20 +109,18 @@ services: volumes: - "./docs:/docs" networks: - - web + - local-web labels: - "traefik.enable=true" - - "traefik.http.routers.documentation.rule=Host(`kraken.molssi.org`) && PathPrefix(`/docs`)" + - "traefik.http.routers.documentation.rule=Host(`localhost`) && PathPrefix(`/docs`)" - "traefik.http.services.documentation.loadbalancer.server.port=5000" - - "traefik.http.routers.documentation.tls=true" - - "traefik.http.routers.documentation.tls.certresolver=le" + networks: - web: - db: + local-web: + local-db: volumes: - kraken-postgres: - external: true - pr3: + postgres16: external: true + diff --git a/docker.compose.local.yml b/docker.compose.local.yml deleted file mode 100644 index fcea449..0000000 --- a/docker.compose.local.yml +++ /dev/null @@ -1,132 +0,0 @@ -version: '3' - -services: - local_reverse-proxy: - # The official v2 Traefik docker image - image: traefik:v2.8 - # Enables the web UI and tells Traefik to listen to docker - container_name: local_reverse_proxy - command: - - --api.insecure=true - - --api.dashboard=true - - --api.debug=true - - --providers.docker - - --entrypoints.web.address=:80 - ports: - # The HTTP port - - "80:80" - # The Web UI (enabled by --api.insecure=true) - - "8080:8080" - # - volumes: - # So that Traefik can listen to the Docker events - - /var/run/docker.sock:/var/run/docker.sock - networks: - - local-web - - local-db - labels: - - "traefik.enable=true" - - "traefik.http.routers.api.service=api@internal" - - local_database: - image: 'mcs07/postgres-rdkit' - container_name: local_database - shm_size: '4gb' - environment: - POSTGRES_SERVER: database - POSTGRES_USER: postgres - POSTGRES_PASSWD: $postgresPWD - POSTGRES_DB: postgres - ports: - - "5432:5432" - volumes: - - "kraken-postgres:/var/lib/postgresql/data" - - "pr3:/home/db" - healthcheck: - test: ["CMD-SHELL", "psql -U postgres -d postgres -c 'SELECT molecule_id FROM molecule LIMIT 1;' || exit 1"] - interval: 5s - timeout: 2s - retries: 5 - environment: - POSTGRES_HOST_AUTH_METHOD: trust - POSTGRES_DB: postgres - networks: - - local-db - - local_backend: - image: 'phosphines-backend:latest' - container_name: local_backend - build: - context: ./backend - dockerfile: backend.dockerfile - volumes: - - "./backend/app:/app" - environment: - POSTGRES_SERVER: local_database - POSTGRES_USER: postgres - POSTGRES_PASSWD: testing-password - POSTGRES_DB: postgres - entrypoint: bash prestart.sh - depends_on: - local_database: - condition: service_healthy - networks: - - local-web - - local-db - labels: - - "traefik.enable=true" - - "traefik.http.routers.backend.rule=Host(`localhost`) && PathPrefix(`/api`)" - - "traefik.http.services.backend.loadbalancer.server.port=8080" - - local_cdk-depict: - image: 'simolecule/cdkdepict:latest' - container_name: local_cdk-depcit - networks: - - local-web - labels: - - "traefik.enable=true" - - "traefik.http.routers.cdk-depict.rule=Host(`localhost`) && PathPrefix(`/depict`)" - - local_frontend: - image: 'phosphines-frontend:latest' - container_name: local_frontend - volumes: - - "./frontend/src:/app/src" - build: - context: . - dockerfile: frontend.development.dockerfile - networks: - - local-web - entrypoint: npm start - labels: - - "traefik.enable=true" - - "traefik.http.routers.frontend.rule=Host(`localhost`)" - - "traefik.http.services.frontend.loadbalancer.server.port=3000" - - local_documentation: - image: "phosphines-docs:latest" - container_name: local_documentation - build: - context: ./docs - dockerfile: docs.dockerfile - entrypoint: bash start.sh - volumes: - - "./docs:/docs" - networks: - - local-web - labels: - - "traefik.enable=true" - - "traefik.http.routers.documentation.rule=Host(`localhost`) && PathPrefix(`/docs`)" - - "traefik.http.services.documentation.loadbalancer.server.port=5000" - - -networks: - local-web: - local-db: - -volumes: - kraken-postgres: - external: true - pr3: - external: true - diff --git a/frontend.production.dockerfile b/frontend.production.dockerfile deleted file mode 100644 index bed53ec..0000000 --- a/frontend.production.dockerfile +++ /dev/null @@ -1,7 +0,0 @@ -FROM node:latest as react-build - -WORKDIR /app/ -ADD ./frontend /app/ -EXPOSE 3000 -RUN yarn install -RUN npm run build \ No newline at end of file diff --git a/frontend/index.html b/frontend/index.html index 4944a69..021e419 100644 --- a/frontend/index.html +++ b/frontend/index.html @@ -2,14 +2,12 @@ - + - Kraken v2 + Molecular Descriptors Library diff --git a/frontend/package.json b/frontend/package.json index efe835a..874b57e 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -12,6 +12,7 @@ "@testing-library/react": "^13.0.0", "@testing-library/user-event": "^13.2.1", "cors": "^2.8.5", + "dompurify": "^3.0.8", "ketcher-core": "^2.8.0", "ketcher-react": "^2.10.0", "ketcher-standalone": "^2.8.0", @@ -20,9 +21,12 @@ "plotly.js": "^2.14.0", "react": "^18.2.0", "react-dom": "^18.2.0", + "react-markdown": "^9.0.1", "react-plotly.js": "^2.6.0", "react-router-dom": "^6.4.1", "react-scripts": "^5.0.1", + "rehype-raw": "^7.0.0", + "remark-gfm": "^4.0.0", "serve": "^14.2.0", "web-vitals": "^2.1.0" }, diff --git a/frontend/public/favicon.ico b/frontend/public/brand/favicon.ico similarity index 100% rename from frontend/public/favicon.ico rename to frontend/public/brand/favicon.ico diff --git a/frontend/public/brand/logo.svg b/frontend/public/brand/logo.svg new file mode 100644 index 0000000..a6c9e7f --- /dev/null +++ b/frontend/public/brand/logo.svg @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + diff --git a/frontend/public/brand/names.json b/frontend/public/brand/names.json new file mode 100644 index 0000000..7e209dc --- /dev/null +++ b/frontend/public/brand/names.json @@ -0,0 +1,8 @@ +[ + { + "name": "KRAKEN", + "tagline": "Kolossal viRtual dAtabase for moleKular dEscriptors of orgaNophosphorus ligands.", + "title": "KRAKEN v2", + "prefix": "" + } +] \ No newline at end of file diff --git a/frontend/src/images/kraken-workflow.png b/frontend/public/content/kraken-workflow.png similarity index 100% rename from frontend/src/images/kraken-workflow.png rename to frontend/public/content/kraken-workflow.png diff --git a/frontend/public/content/library_details.md b/frontend/public/content/library_details.md new file mode 100644 index 0000000..aac8320 --- /dev/null +++ b/frontend/public/content/library_details.md @@ -0,0 +1,70 @@ +# Library Details + +
+ Kraken Workflow +
+ +## Conformational Searching + + Initial ligand geometries were generated using SMILES strings and converted to free ligands and [LNi(CO)3] complexes using RDKit, OpenBabel or Molconvert. +These guess geometries were optimized at the GFN2-xTB level of theory (xTB v6.2.2). +Optimized geometries were subjected to a conformational search using CREST (v2.8) at the GFN2-xTB level with toluene solvation (GBSA model). +For ligands containing ferrocene, conformational searches were performed at the GFN-FF level to avoid structural changes. + +## xTB Descriptors + + Molecular descriptors at the xTB level for the full conformational ensembles from CREST of the free ligands and the [NiCO3]-bound complexes were collected using MORFEUS. + +## Selection of conformers for DFT computations + + Conformers from both sets (free ligand and Ni complex) were selected based on the following two criteria: + +* Conformers that minimize or maximize any of the following xTB-level steric properties in any of the two conformer sets: +B1, B5, lval, far_vbur, far_vtot, max_delta_qvbur, max_delta_qvtot, near_vbur, near_vtot, ovbur_max, ovbur_min, ovtot_max, +ovtot_min, pyr_val, qvbur_max, qvbur_min, qvtot_max, qvtot_min, vbur. + +* Up to 20 conformers within 3 kcal/mol relative energy in the free ligand conformer set. If more than 20 conformers are in that range, the selection was made by RMSD pruning (using PyDP4). This enables structurally diverse selection of conformers in the relevant energy window. + +## DFT computations + +Prior to DFT computations, the [Ni(CO)3]-fragment was removed from the Ni complex conformer set to obtain free-ligand initial geometries. +All DFT optimizations (Gaussian 16, rev C.01) were performed at the PBE-D3(BJ)/6-31+G(d,p) level of theory. +The corresponding geometries were used for a series of single-point energy calculations at the PBE0-D3(BJ)/def2-TZVP and PBE0-D3(BJ)/def2-TZVP/SMD(CHCl3) levels of theory. +Additional single-points were also run for the radical cations and radical anions from the optimized geometry of the neutral free ligand. + +From the DFT calculations, steric, electronic, or full molecule/interaction-type descriptors were collected for each conformer. +The range of properties across the conformers of a single ligand was treated by using up to five condensed measures for each of the properties. + +| Condensed Properties | Description | For xTB | For DFT | For ML | +| ----------------------- | --------------------------------------------------------------------- | ---------| --------- | ---------| +| boltzmann | Boltzmann-weighted average of all conformers' properties (T=298.15 K) | ✔️ | ✔️ | ✔️ | +| max | highest value of a property of any conformer | ✔️ | ✔️ | ✔️ | +| min | lowest value of a property of any conformer | ✔️ | ✔️ | ✔️ | +| std | standard deviation of the value across all conformers | ✔️ | | | +| vburminconf | property value of the conformer with the smallest buried volume | | ✔️ | ✔️ | +| delta | difference between the maximum and minimum property values | | ✔️ | ✔️ | + + +## ML Descriptor Prediction + +The machine learning portion of the workflow aims to expand the total number of monophosphine ligands in the library from ~1500 (which is a fraction of the total possible space) to > 300,000 ligands. +The computational workflow used to calculate the set of ~1500 is too intensive to calculate all possible monophosphines, so descriptors were predicted using machine learning methods. + +New descriptors were predicted using the sum of contributions of each phosphorus substituent using the "Bag of Substituents" approach. +These contributions are made up of 576 unique substituents from the ~1500 set of ligands. + +For more details on the machine learning models used to predict descriptors, see the original publication supporting information. + +## Video Tutorial + +A video tutorial of Kraken which explains relevant background information and the computational workflow, and provides a walkthrough of this website: + +
+ +
+ +An extended explanation of the computational workflow used to build the monophosphine library, +as well as details on the collected and predicted descriptors can be found in the original publication supporting information. + +## Citation +Gensch, T.; dos Passos Gomes, G.; Friederich, P.; Peters, E.; Gaudin, T.; Pollice, R.; Jorner, K.; Nigam, A.; Lindner-D'Addario, M.; Sigman, M. S.; Aspuru-Guzik, A. A Comprehensive Discovery Platform for Organophosphorus Ligands for Catalysis. J. Am. Chem. Soc. 2022, 144, 3, 1205–1217. DOI: 10.1021/jacs.1c09718 diff --git a/frontend/public/content/stats.json b/frontend/public/content/stats.json new file mode 100644 index 0000000..69ecd9c --- /dev/null +++ b/frontend/public/content/stats.json @@ -0,0 +1,30 @@ +[{ + "number": "1,558", + "description": "DFT Calculated Ligands" + }, + + { + "number": "300,000+", + "description": "ML calculated Ligands" + }, + + { + "number": "576", + "description": "unique substituents" + }, + + { + "number": "190", + "description": "DFT-level descriptors" + }, + + { + "number": "21,437", + "description": "unique conformers" + }, + + { + "number": "13.8", + "description": "average conformers per ligand" + } +] \ No newline at end of file diff --git a/frontend/public/logo192.png b/frontend/public/logo192.png deleted file mode 100644 index fc44b0a..0000000 Binary files a/frontend/public/logo192.png and /dev/null differ diff --git a/frontend/public/logo512.png b/frontend/public/logo512.png deleted file mode 100644 index a4e47a6..0000000 Binary files a/frontend/public/logo512.png and /dev/null differ diff --git a/frontend/public/manifest.json b/frontend/public/manifest.json index b62564f..5041499 100644 --- a/frontend/public/manifest.json +++ b/frontend/public/manifest.json @@ -3,19 +3,9 @@ "name": "Kolossal viRtual dAtabase for moleKular dEscriptors of orgaNophosphorus ligands (kraken)", "icons": [ { - "src": "favicon.ico", + "src": "brand/favicon.ico", "sizes": "64x64 32x32 24x24 16x16", "type": "image/x-icon" - }, - { - "src": "logo192.png", - "type": "image/png", - "sizes": "192x192" - }, - { - "src": "logo512.png", - "type": "image/png", - "sizes": "512x512" } ], "start_url": ".", diff --git a/frontend/renameBase.sh b/frontend/renameBase.sh new file mode 100644 index 0000000..705a636 --- /dev/null +++ b/frontend/renameBase.sh @@ -0,0 +1,5 @@ +#/bin/bash + +find ./dist -type f -exec sed -i 's|/base_url|'"$VITE_BASE_URL"'|g' {} + + +node server.js diff --git a/frontend/server.js b/frontend/server.js new file mode 100644 index 0000000..4f8ac6a --- /dev/null +++ b/frontend/server.js @@ -0,0 +1,42 @@ +const express = require('express'); +const path = require('path'); +const fs = require('fs'); // File System module to check if file exists +const app = express(); + +const PORT = process.env.PORT || 3000; +const BASE_URL = process.env.VITE_BASE_URL || '/'; + +// Serve files from the public directory (with precedence) +app.use(BASE_URL, express.static(path.join(__dirname, 'public'), {fallthrough: true})); + +// Serve files from the pre-built dist directory only if not found in public +app.use(BASE_URL, express.static(path.join(__dirname, 'dist'))); + +// Handle fallback for SPA (Single Page Application) and return 404 for missing files +app.use((req, res, next) => { + // Try to find the file in the 'public' directory first + const publicFilePath = path.join(__dirname, 'public', req.path); + if (fs.existsSync(publicFilePath)) { + // If the file exists in the public folder, serve it + return res.sendFile(publicFilePath); + } + + // If not found in 'public', check the 'dist' directory + const distFilePath = path.join(__dirname, 'dist', req.path); + if (fs.existsSync(distFilePath)) { + // If the file exists in the dist folder, serve it + return res.sendFile(distFilePath); + } + + // For SPA: If it's a navigation request (no file extension), serve index.html from 'dist' + if (!path.extname(req.path)) { + return res.sendFile(path.join(__dirname, 'dist', 'index.html')); + } + + // If it's a file request but the file doesn't exist in both directories, return 404 + res.status(404).send('Not found'); +}); + +app.listen(PORT, () => { + console.log(`Server running on http://localhost:${PORT}${BASE_URL}`); +}); diff --git a/frontend/src/App.jsx b/frontend/src/App.jsx index 11d1739..7c21ea8 100644 --- a/frontend/src/App.jsx +++ b/frontend/src/App.jsx @@ -55,7 +55,7 @@ function App() { <> - + diff --git a/frontend/src/common/MoleculeUtils.jsx b/frontend/src/common/MoleculeUtils.jsx index c7d8080..777494e 100644 --- a/frontend/src/common/MoleculeUtils.jsx +++ b/frontend/src/common/MoleculeUtils.jsx @@ -17,7 +17,7 @@ const Item = styled(Paper)(({ theme }) => ({ async function substructureSearch(substructure, limit=48, skip=0, signal) { let encoded = encodeURIComponent(substructure); - const response = await fetch(`/api/molecules/search/?substructure=${encoded}&skip=${skip}&limit=${limit}`, {signal: signal}) + const response = await fetch(`/api/${document.location.pathname.split('/')[1]}/molecules/search/?substructure=${encoded}&skip=${skip}&limit=${limit}`, {signal: signal}) if (!response.ok) { throw new Error('Invalid SMILES') @@ -37,7 +37,7 @@ function moleculePage(molecule_id) { // website name. Need the first and third elements (0, 2) to redirect to the molecule endpoint below. This is so that regardless of which page we are on, we can redirect to the // molecule page. let og_url = window.location.href.split("/"); - let url = og_url[0] + "//" + og_url[2] + "/molecule/" + molecule_id; + let url = og_url[0] + "//" + og_url[2] + `/${document.location.pathname.split('/')[1]}/molecule/` + molecule_id; window.open(url, "_blank", "noreferrer"); } @@ -49,7 +49,7 @@ function neighborPage(molecule_id) { // Gets the original url for the window and splits it into its components. The first element will always be http(s):, second will always be empty, third will always be // website name. Need the first and third elements (0, 2) to redirect to the neighboar endpoint below. let og_url = window.location.href.split("/"); - let url = og_url[0] + "//" + og_url[2] + "/neighbors/" + molecule_id; + let url = og_url[0] + "//" + og_url[2] + `/${document.location.pathname.split('/')[1]}/neighbors/` + molecule_id; window.open(url, "_blank", "noreferrer"); } @@ -154,9 +154,9 @@ async function retrieveSVG(smiles, molecule_id, substructure = undefined, distan } -const downloadMoleculeData = (moleculeIDs, context=null) => { +const downloadMoleculeData = (moleculeIDs, data_type="ml", context=null) => { const a = document.createElement('a'); - let search_string = `/api/molecules/data/export/batch?molecule_ids=${moleculeIDs}`; + let search_string = `/api/${document.location.pathname.split('/')[1]}/molecules/data/export/batch?molecule_ids=${moleculeIDs}&data_type=${data_type}`; if (context) { search_string += `&context=${context}`; diff --git a/frontend/src/common/Navbar.jsx b/frontend/src/common/Navbar.jsx index 1f9f0f3..883ce2a 100644 --- a/frontend/src/common/Navbar.jsx +++ b/frontend/src/common/Navbar.jsx @@ -1,4 +1,4 @@ -import * as React from 'react'; +import React, { useEffect, useState } from 'react'; import PropTypes from 'prop-types'; import AppBar from '@mui/material/AppBar'; import Box from '@mui/material/Box'; @@ -18,13 +18,42 @@ import { NavLink, useLocation } from 'react-router-dom'; import { Link } from 'react-router-dom'; -import OriginalKraken from './OriginalKraken.js' - const drawerWidth = 240; +const Badge = ({display}) => { + const displayStyle = { + display: display, + mr: 1, + fontSize: '60px', + maxHeight: '70px', + }; + return ( + + ); +}; + +// Adapted from MUI documentation +// Responsive App Bbar with Drawer - https://mui.com/material-ui/react-app-bar/#responsive-app-bar-with-drawer function DrawerAppBar(props) { - const { window, pages } = props; + const { navwindow, pages } = props; const [mobileOpen, setMobileOpen] = React.useState(false); + const [name, setName] = useState(""); + + useEffect(() => { + fetch(`/${document.location.pathname.split('/')[1]}/brand/names.json`) + .then(response => { + if (!response.ok) { + throw new Error('Network response was not ok'); + } + return response.json(); + }) + .then(data => { + setName(data[0].name); + }) + .catch(error => { + console.error('Error fetching stats:', error); + }); +}, []); const handleDrawerToggle = () => { setMobileOpen(prevState => !prevState); @@ -41,7 +70,7 @@ function DrawerAppBar(props) { const drawer = ( - kraken + { name } @@ -60,25 +89,28 @@ function DrawerAppBar(props) { ); })} + {/*} - + + + */} ); - const container = window !== undefined ? () => window().document.body : undefined; + const container = navwindow !== undefined ? () => navwindow().document.body : undefined; return ( - + - kraken + { name } {Object.keys(pages).map(item => { @@ -110,11 +142,13 @@ function DrawerAppBar(props) { ); })} - + {/* + + */} @@ -141,7 +175,7 @@ function DrawerAppBar(props) { } DrawerAppBar.propTypes = { - window: PropTypes.func, // Injected by the documentation to work in an iframe. You won't need it on your project. + window: PropTypes.func, }; export default DrawerAppBar; \ No newline at end of file diff --git a/frontend/src/common/OriginalKraken.js b/frontend/src/common/OriginalKraken.js deleted file mode 100644 index 92b7452..0000000 --- a/frontend/src/common/OriginalKraken.js +++ /dev/null @@ -1,9 +0,0 @@ -import { jsx as _jsx } from "react/jsx-runtime"; -import createSvgIcon from "@mui/icons-material/utils/createSvgIcon.js"; - - -const OriginalKraken = createSvgIcon(_jsx("path", { - d:"M 12.214478,0 1.1895664,5.843998 1,17.843999 11.835433,24 22.860432,18.15609 23.049912,6.1560897 Z m 1.595477,3.2252694 c 0.01986,0.02621 0.168044,0.048257 0.431354,0.06413 0.255609,0.015409 0.302768,0.022588 0.403299,0.061748 0.06262,0.024389 0.155862,0.050997 0.207209,0.059101 l 0.09341,0.014732 v -0.044458 c 0,-0.042735 0.0031,-0.044546 0.07375,-0.044546 h 0.07383 l 0.0043,0.059543 c 0.0043,0.0557 0.009,0.060862 0.07189,0.079832 0.03695,0.011155 0.08739,0.028055 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-0.0043,0.1162235 0.0412,0.2018268 0.026811,0.050721 0.069052,0.113968 0.093945,0.1405209 0.024905,0.026554 0.093218,0.1024571 0.1519015,0.1686607 0.1165304,0.1314659 0.1175821,0.1319186 0.4459948,0.2242328 0.1472341,0.041386 0.1063531,0.040813 0.9336259,0.013848 0.2987369,-0.00973 0.3753016,-0.016837 0.4167985,-0.0389 0.027979,-0.014864 0.070244,-0.027082 0.093953,-0.027082 0.023739,-6e-7 0.069412,-0.014285 0.10162,-0.031755 0.03222,-0.01747 0.079026,-0.031755 0.1039989,-0.031755 0.024962,0 0.045443,-0.00714 0.045443,-0.015878 6e-6,-0.00873 0.018015,-0.015878 0.040029,-0.015878 0.028591,0 0.060941,-0.022986 0.1126503,-0.080007 0.039849,-0.04398 0.08063,-0.078086 0.090595,-0.075861 0.03628,0.00809 0.4871829,-0.2987854 0.6305303,-0.429148 0.049322,-0.044822 0.1265659,-0.1026115 0.1717509,-0.1284359 0.045202,-0.025824 0.1350408,-0.090265 0.1997071,-0.1431668 0.06468,-0.052903 0.1259824,-0.09615 0.1362028,-0.09615 0.010155,-1.48e-5 0.035608,-0.014317 0.05645,-0.031756 C 9.4243541,6.2501937 9.600186,6.1701272 9.809031,6.0930184 l 0.159662,-0.058925 0.213033,0.017026 c 0.261002,0.020879 0.33573,0.040715 0.541968,0.144137 0.08888,0.044574 0.167281,0.075116 0.174131,0.067834 0.0069,-0.00727 -0.02042,-0.064409 -0.06051,-0.1269361 -0.0401,-0.062528 -0.08378,-0.1359469 -0.09703,-0.1631908 -0.01403,-0.028837 -0.03112,-0.04499 -0.04077,-0.038637 -0.0098,0.00649 -0.01236,0.00374 -0.0063,-0.00679 0.01089,-0.018743 -0.03228,-0.118116 -0.125527,-0.2888916 -0.031,-0.056772 -0.06432,-0.1425871 -0.07409,-0.1906251 -0.0097,-0.048037 -0.02694,-0.1301933 -0.03801,-0.1825973 -0.03775,-0.1782265 -0.05577,-0.3573743 -0.04551,-0.4535826 0.01396,-0.1309476 0.07602,-0.3257515 0.1257,-0.3945687 0.06641,-0.091977 0.09389,-0.1442393 0.08442,-0.1605447 -0.0048,-0.00839 5.66e-4,-0.011322 0.01211,-0.00662 0.01205,0.00492 0.03148,-0.00849 0.04568,-0.031579 0.04864,-0.078966 0.445527,-0.3647907 0.552907,-0.3981858 0.103568,-0.032207 0.307795,-0.1387212 0.307948,-0.1606328 1.34e-4,-0.019436 0.0974,-0.060971 0.178983,-0.07639 0.02853,-0.0054 0.07897,-0.023185 0.112029,-0.039607 0.107029,-0.053173 0.336677,-0.1103823 0.499979,-0.1245543 0.04471,-0.00389 0.09605,-0.017383 0.114145,-0.029991 0.01993,-0.013884 0.105696,-0.029288 0.217442,-0.039078 0.101486,-0.00889 0.218172,-0.023253 0.259251,-0.031844 0.04108,-0.00859 0.111654,-0.022416 0.156839,-0.030785 0.04519,-0.00837 0.099,-0.023508 0.119525,-0.033608 0.03967,-0.0195 0.599446,-0.045624 0.612367,-0.028581 z m 1.911979,8.0189366 c 0.02386,-2e-6 0.07665,0.06319 0.06688,0.08001 -0.01107,0.01908 -0.02251,0.01869 -0.05565,-0.0018 -0.02773,-0.01717 -0.03646,-0.07814 -0.0112,-0.07814 z m 2.3451,5.613679 c 0.0082,-0.0054 0.01501,0.0012 0.01501,0.01491 0,0.01361 -0.0068,0.02478 -0.01501,0.02478 -0.0082,1.9e-5 -0.01488,-0.0068 -0.01488,-0.01491 -6e-6,-0.0082 0.0068,-0.01939 0.01488,-0.02478 z" -}), 'OriginalKraken'); - -export default OriginalKraken; \ No newline at end of file diff --git a/frontend/src/common/Routes.jsx b/frontend/src/common/Routes.jsx index 43d028c..1e5b686 100644 --- a/frontend/src/common/Routes.jsx +++ b/frontend/src/common/Routes.jsx @@ -10,7 +10,8 @@ export const AppRoutes = ({ pages }) => ( {Object.keys(pages).map((page, index) => ( ))} - } /> - } /> + } /> + } /> + ); \ No newline at end of file diff --git a/frontend/src/components/DFTTable.jsx b/frontend/src/components/DFTTable.jsx deleted file mode 100644 index f7ac33b..0000000 --- a/frontend/src/components/DFTTable.jsx +++ /dev/null @@ -1,63 +0,0 @@ -import { - Container, - Table, - TableHead, - TableContainer, - TableRow, - TableBody, - TableCell, - Paper, -} from '@mui/material'; - -function createData( - name, - description, - forXTB, - forDFT, - forML, -) { - return { name, description, forXTB, forDFT, forML } -}; - -const rows = [ - createData("boltz", "Boltzmann-weighted average of all conformers' properties (T=298.15 K)", true, true, true), - createData("max", "highest value of a property of any conformer", true, true, true), - createData("min", "lowest value of a property of any conformer", true, true,true), - createData("std", "standard deviation of the value across all conformers", true, false, false), - createData("vburminconf", "property value of the conformer with the smallest buried volume", false, true, true), - createData("delta", "difference between the maximum and minimum property values", false, true, true), -]; - -function DataTable() { - return ( - - - - - - Condensed Properties - Description - For xTB - For DFT - For ML - - - - {rows.map((row) => ( - - {row.name} - {row.description} - {row.forXTB ? '✔️' : ''} - {row.forDFT ? '✔️' : ''} - {row.forML ? '✔️' : ''} - - ))} - -
- - - ); -}; - -export default DataTable; - diff --git a/frontend/src/components/DataDownloadButton.jsx b/frontend/src/components/DataDownloadButton.jsx new file mode 100644 index 0000000..d867602 --- /dev/null +++ b/frontend/src/components/DataDownloadButton.jsx @@ -0,0 +1,97 @@ +import React from 'react'; +import { styled } from '@mui/material/styles'; +import Button from '@mui/material/Button'; +import Menu from '@mui/material/Menu'; +import MenuItem from '@mui/material/MenuItem'; +import KeyboardArrowDownIcon from '@mui/icons-material/KeyboardArrowDown'; + +import { downloadMoleculeData } from '../common/MoleculeUtils'; + +const StyledMenu = styled((props) => ( + +))(({ theme }) => ({ + '& .MuiPaper-root': { + borderRadius: 6, + marginTop: theme.spacing(1), + minWidth: 180, + color: + theme.palette.mode === 'light' ? 'rgb(55, 65, 81)' : theme.palette.grey[300], + boxShadow: + 'rgb(255, 255, 255) 0px 0px 0px 0px, rgba(0, 0, 0, 0.05) 0px 0px 0px 1px, rgba(0, 0, 0, 0.1) 0px 10px 15px -3px, rgba(0, 0, 0, 0.05) 0px 4px 6px -2px', + '& .MuiMenu-list': { + padding: '4px 0', + }, + }, +})); + +export default function DropDownButton({ molecule_ids, dataTypes }) { + const [anchorEl, setAnchorEl] = React.useState(null); + const open = Boolean(anchorEl); + + const dataTypeMapping = { + "ML Data": "ml", + "DFT Data": "dft", + "xTB Data": "xtb", + "xTB_Ni Data": "xtb_ni" +}; + + const handleClick = (event) => { + setAnchorEl(event.currentTarget); + }; + + const handleClose = () => { + setAnchorEl(null); + }; + + const handleMenuItemClick = (dataType) => { + console.log(`${dataTypeMapping[dataType]} data requested`); + downloadMoleculeData(molecule_ids, dataTypeMapping[dataType]) + handleClose(); // Close the menu + }; + + return ( +
+ + + + {dataTypes.map((dataType, index) => ( + handleMenuItemClick(dataType)} disableRipple> + {dataType} + + ))} + +
+ ); +} diff --git a/frontend/src/components/FileDownload.jsx b/frontend/src/components/FileDownload.jsx new file mode 100644 index 0000000..4da07bd --- /dev/null +++ b/frontend/src/components/FileDownload.jsx @@ -0,0 +1,36 @@ +import React, { useState, useEffect } from 'react'; +import Grid from '@mui/material/Grid'; +import DownloadIcon from '@mui/icons-material/Download'; +import IconLink from './IconLink'; + +const CheckFileAndDownloadIcon = () => { + const [isSpreadsheet, setIsSpreadsheet] = useState(false); + + useEffect(() => { + + async function isSpreadsheetEndpoint() { + const url = `/${document.location.pathname.split('/')[1]}/content/${document.location.pathname.split('/')[1]}_library.xlsx`; + const response = await fetch(url); + // Check if the request was successful + if (!response.ok) { + console.error('HTTP Error:', response.status); + return false; + } + else { + return true; + }; + + }; + + isSpreadsheetEndpoint().then(result => setIsSpreadsheet(result)); + }, []); + + return ( + + {isSpreadsheet && + } + + ); +}; + +export default CheckFileAndDownloadIcon; diff --git a/frontend/src/components/Graph.jsx b/frontend/src/components/Graph.jsx index 96d302b..768341b 100644 --- a/frontend/src/components/Graph.jsx +++ b/frontend/src/components/Graph.jsx @@ -87,7 +87,7 @@ export default function Graph({ molData, componentArray, type, neighborSearch, c // molecule page. let og_url = window.location.href.split("/"); let molecule_id = event.points[0].text.split(",")[1]; - let url = og_url[0] + "//" + og_url[2] + "/molecule/" + molecule_id; + let url = og_url[0] + "//" + og_url[2] + `/${document.location.pathname.split('/')[1]}/molecule/` + molecule_id; if (molecule_id !== undefined) { window.open(url, "_blank", "noreferrer"); } diff --git a/frontend/src/components/Graphv2.jsx b/frontend/src/components/Graphv2.jsx new file mode 100644 index 0000000..64ca373 --- /dev/null +++ b/frontend/src/components/Graphv2.jsx @@ -0,0 +1,184 @@ +import React, { useEffect, useState } from 'react'; +import Plot from 'react-plotly.js'; + +import { Container } from "@mui/material"; +import { TextField } from '@mui/material'; +import MenuItem from '@mui/material/MenuItem'; + + + +const Graphv2 = ({ molData, componentArray, type, neighborSearch, containerStyle=null }) => { + // Set the x and y indices to the first 2 values in the component array. + const [ xIndex, setXIndex ] = useState(0); + const [ yIndex, setYIndex ] = useState(1); + const [ patterns, setPatterns ] = useState({}); + const [ plotData, setPlotData ] = useState([]) + const [showLegend, setShowLegend] = useState(false); + + const symbols = [0, 1, 2, 13, 14, 15, 16, 17, 18]; + // Still need to be genericized + const axis_dict = {"pca1": "pc1", "pca2": "pc2", "pca3": "pc3", "pca4": "pc4", "umap1": "umap1", "umap2": "umap2"}; + + + useEffect(() => { + fetch(`/${document.location.pathname.split('/')[1]}/brand/patterns.json`) + .then(response => { + if (!response.ok) { + throw new Error('Network response was not ok'); + } + return response.json(); + }) + .then(data => { + const patterns_data = data[0]; + if (!patterns_data.hasOwnProperty('default')) { + patterns_data['default'] = { color: '#ADD8E6', name: 'default' }; + } + setPatterns(patterns_data); + }) + .catch(error => { + console.error('Error fetching patterns:', error); + }); + }, []); + + useEffect(() => { + // Group data by 'pat' + const groupedByPat = molData.reduce((acc, mol) => { + const pat = mol.pat || 'default'; // Use 'default' as a fallback + if (!acc[pat]) { + acc[pat] = []; + } + acc[pat].push(mol); + return acc; + }, {}); + + // Create a trace for each 'pat' + const newPlotData = Object.entries(groupedByPat).map(([pat, molArray], index) => { + return { + x: molArray.map(mol => mol.components[xIndex]), + y: molArray.map(mol => mol.components[yIndex]), + text: molArray.map(mol => encodeURIComponent(mol.smiles) + "," + mol.molecule_id), + hovertemplate: "( %{x}, %{y})", + hovermode: "closest", + mode: 'markers', + type: 'scatter', + marker: { + size: 10, + opacity: 0.75, + color: patterns[pat]?.color || patterns['default']?.color, + }, + name: patterns[pat]?.name || pat, + }; + }); + + setPlotData(newPlotData); + setShowLegend(newPlotData.length > 1); + }, [molData, patterns, xIndex, yIndex]); + + // Plotting functions to show molecules on hover + function showSVGWindow(svg, event) { + /** + * Creates SVG window on the molecule element when hovering of a point on the plotly graph. + * @param {string} svg Svg of the molecule. + * @param {event} event Hover event when hovering over a point on the plotly graph. + */ + + // remove in case existing + if (document.getElementById("molecule")) { + document.getElementById("molecule").remove() + } + + let mol = document.createElement("g") + mol.setAttribute("id", "molecule") + + let plotly_container = document.getElementsByClassName("plotly") + mol.innerHTML = svg; + + let xpos = event.event.clientX - 160; + let ypos = event.event.clientY - 160; + + plotly_container[0].appendChild(mol); + mol.style.position = "fixed"; + mol.style.left = `${xpos}px`; + mol.style.top = `${ypos}px`; + mol.style.border = "ridge #393536"; + mol.style.borderRadius = "5px"; + mol.style.height = "40mm"; + mol.style.width = "40mm"; + } + + function showSVG(event) { + /** + * Requests svg data for the molecule you are hovering on. + * @param {event} event Hover even when hovering over a point on the plotly graph. + */ + let smiles = event.points[0].text.split(",")[0]; + fetch(`/depict/cow/svg?smi=${smiles}&w=40&h=40`).then(response => + response.text() ).then( body => showSVGWindow(body, event) ); + } + + function hideSVG() { + /** + * Removes molecule element which holds its SVG, when you are no longer hovering. + */ + if (document.getElementById("molecule")) { + document.getElementById("molecule").remove() + } + } + + function moleculePage(event) { + /** + * Redirects to the molecule page for the molecule when clicking on a point on the graph. + * @param {event} event event when hovering over a point on the plotly graph. + */ + // Gets the original url for the window and splits it into its components. The first element will always be http(s):, second will always be empty, third will always be + // website name. Need the first and third elements (0, 2) to redirect to the molecule endpoint below. This is so that regardless of which page we are on, we can redirect to the + // molecule page. + + let og_url = window.location.href.split("/"); + let molecule_id = event.points[0].text.split(",")[1]; + let url = og_url[0] + "//" + og_url[2] + `/${document.location.pathname.split('/')[1]}/molecule/` + molecule_id; + if (molecule_id !== undefined) { + window.open(url, "_blank", "noreferrer"); + } + } + + return ( + + moleculePage(event)} + onHover={ (event) => showSVG(event) } + onUnhover={ (event)=> hideSVG(event) } + style={{'width': '100%', 'height': '100%' }} + useResizeHandler={true} + data={plotData} + layout={ { + autosize: true, + useResizeHandler: true, + showlegend: showLegend, + style: {width: '100%', height: '100%'}, + xaxis: { + title: { + text: 'umap1', + font: { + size: 18, + color: '#7f7f7f' + } + } + }, + + yaxis: { + title: { + text: 'umap2', + font: { + size: 18, + color: '#7f7f7f' + } + } + } + } } + /> + + ); + }; + +export default Graphv2; \ No newline at end of file diff --git a/frontend/src/components/IconLink.jsx b/frontend/src/components/IconLink.jsx index 0852a22..0d364fd 100644 --- a/frontend/src/components/IconLink.jsx +++ b/frontend/src/components/IconLink.jsx @@ -3,21 +3,29 @@ import { Link } from 'react-router-dom'; import { Typography, Box, IconButton } from "@mui/material"; import SearchIcon from '@mui/icons-material/Search'; -function IconLink({ IconElement, text, link, reloadDocument = false }) { - const linkProps = reloadDocument ? { to: link, reloadDocument } : { to: link }; +function IconLink({ IconElement, text, link, isDownload = false }) { + // Conditionally set props based on whether this is a download link + const linkAttributes = isDownload ? { + href: link, + download: true + } : { + to: link + }; + + const LinkComponent = isDownload ? 'a' : Link; return ( - + - {IconElement ? : } + {IconElement ? : } {text} - - ) + + ); } export default IconLink; diff --git a/frontend/src/components/KetcherPopup.jsx b/frontend/src/components/KetcherPopup.jsx index 104e74c..a574e21 100644 --- a/frontend/src/components/KetcherPopup.jsx +++ b/frontend/src/components/KetcherPopup.jsx @@ -3,6 +3,11 @@ import React, { useState } from 'react'; import Button from '@mui/material/Button'; import Dialog from '@mui/material/Dialog'; import Slide from '@mui/material/Slide'; +import CloseIcon from '@mui/icons-material/Close'; +import IconButton from '@mui/material/IconButton'; +import AppBar from '@mui/material/AppBar'; +import Toolbar from '@mui/material/Toolbar'; +import Typography from '@mui/material/Typography'; //import { convertStructToString } from 'ketcher-core' import { ChemicalMimeType } from 'ketcher-core'; @@ -41,13 +46,26 @@ export default function FullScreenDialog({ ketcherCallBack }) { + + + + + + + { - setSelectedDataType(event.target.value); + setSelectedDataType(event.target.value); }; - + return ( - - + + CSV} disabled={!download} @@ -96,104 +117,91 @@ function CustomFooter({ selectedDataType, setSelectedDataType, moleculeID, downl ); } +// Dynamically generate columns based on the keys of the first data item +const generateColumns = (data) => { + if (!data || data.length === 0) return []; + + return Object.keys(data[0]) + .filter(key => !key.toLowerCase().includes("id") && key.toLowerCase() !== "smiles") // Exclude columns with "id" or named "smiles" + .map(key => ({ + field: key, + headerName: key.charAt(0).toUpperCase() + key.slice(1).replace(/_/g, ' '), // Capitalize the first letter and replace underscores with spaces + flex: true, + filterable: true, + headerAlign: 'right', + align: 'right', + })); +}; + + export default function MoleculeDataTable({ molecule_id, initial_data_type }) { const [moleculeData, setMoleculeData] = useState(null); const [data_type, setDataType] = useState(initial_data_type); - const [selectedDataType, setSelectedDataType] = useState("ML Data"); // Set the default value to "ML Data" + const [selectedDataType, setSelectedDataType] = useState("DFT Data"); // Set the default value to "ML Data" const [moleculeID, setMoleculeID] = useState(molecule_id); const [download, setDownload] = useState(true); // Allow CSV download + const [availableDataTypes, setAvailableDataTypes] = useState([]); useEffect(() => { async function fetchData() { - let data = await retrieveData(moleculeID, dataTypeMapping["DFT Data"]); - - // If DFT data is empty, default to ML Data + let data = await retrieveData(moleculeID, dataTypeMapping[selectedDataType]); + if (!data || Object.keys(data).length === 0) { - setSelectedDataType("ML Data"); - data = await retrieveData(moleculeID, dataTypeMapping["ML Data"]); - } else { - setSelectedDataType("DFT Data"); + const fallbackDataType = selectedDataType === "ML Data" ? "DFT Data" : "ML Data"; + data = await retrieveData(moleculeID, dataTypeMapping[fallbackDataType]); + if (data && Object.keys(data).length !== 0) { + setSelectedDataType(fallbackDataType); + } else { + console.log(`No data available for ${selectedDataType} or ${fallbackDataType}`); + } } + setMoleculeData(data); + setDownload(data != null && Object.keys(data).length !== 0); } - + fetchData(); - }, [moleculeID]); + }, [moleculeID, selectedDataType]); useEffect(() => { async function fetchData() { - const data = await retrieveData(moleculeID, data_type); - // Check to see if the data is empty, set download to false. - if (data.length==0) { - setDownload(false); - } - else { - setDownload(true); - } - setMoleculeData(data); + const dataTypes = await retrieveMoleculeDataTypes(moleculeID); + console.log(dataTypes); + setAvailableDataTypes(dataTypes); } fetchData(); - - }, [data_type]); - - useEffect(() => { - setDataType(dataTypeMapping[selectedDataType]); - }, [selectedDataType]); - - const columns = [ - { field: 'property', headerName: 'Property', filterable: true, flex: true }, - { field: 'min', headerName: 'Min', filterable: true, headerAlign: 'right', align: 'right', flex: true }, - { field: 'max', headerName: 'Max', filterable: true, headerAlign: 'right', align: 'right', flex: true }, - { field: 'delta', headerName: 'Delta', filterable: true, headerAlign: 'right', align: 'right', flex: true }, - { field: 'vburminconf', headerName: 'vbur min conf', filterable: true, headerAlign: 'right', align: 'right', flex: true }, - { field: 'boltzmann_average', headerName: 'Boltz', filterable: true, headerAlign: 'right', align: 'right', flex: true }, - { field: 'std', headerName: 'std', filterable: true, headerAlign: 'right', align: 'right', flex: true} - ]; - - // Filter out delta and vburminconf columns for xTB data. - let displayColumns = columns; - if (selectedDataType === "xTB Data" || selectedDataType === "xTB_Ni Data") { - displayColumns = columns.filter(column => column.field !== 'delta' && column.field !== 'vburminconf'); + } + , [moleculeID]); - else { - displayColumns = columns.filter(column => column.field !== 'std'); - } + const columns = generateColumns(moleculeData); const rows = moleculeData ? moleculeData - .map(item => ({ - id: item.property, - property: item.property, - max: item.max, - min: item.min, - delta: item.delta, - boltzmann_average: item.boltzmann_average, - vburminconf: item.vburminconf, - std: item.std, + .map((item, index) => ({ + id: index, // Ensure each row has a unique id + ...item, })) : []; return ( ); -} \ No newline at end of file +} diff --git a/frontend/src/components/StatsGrid.jsx b/frontend/src/components/StatsGrid.jsx new file mode 100644 index 0000000..c43b98e --- /dev/null +++ b/frontend/src/components/StatsGrid.jsx @@ -0,0 +1,74 @@ +import { useState, useEffect } from 'react'; +import { Typography, Grid, Card, CardContent, Container, CircularProgress } from "@mui/material"; + + +function StatCard({number, caption, size}) { + /** + * Creates a card with a number and caption. + * + * + * @param {string} number Number to display in the card. + * @param {string} caption Caption to display in the card. + * @param {number} size Size of the card. + * + * @return {StatCard} Card with the number and caption. + **/ + + const cardStyle = { + height: size, + display: "flex", + justifyContent: "center", + alignItems: "center", + }; + + + return ( + + + + { number } + { caption } + + + + ) +} + +const StatsGrid = () => { + const [stats, setStats] = useState(null); + + useEffect(() => { + fetch(`/${document.location.pathname.split('/')[1]}/content/stats.json`) + .then(response => { + if (!response.ok) { + throw new Error('Network response was not ok'); + } + return response.json(); + }) + .then(data => { + setStats(data); + }) + .catch(error => { + console.error('Error fetching stats:', error); + }); + }, []); + + return ( + + {stats ? ( + + {stats.map((stat, index) => ( + + ))} + + ) : ( + <> + + + )} + + ); +}; + + +export default StatsGrid; \ No newline at end of file diff --git a/frontend/src/components/SummaryCard.jsx b/frontend/src/components/SummaryCard.jsx deleted file mode 100644 index 1a0122d..0000000 --- a/frontend/src/components/SummaryCard.jsx +++ /dev/null @@ -1,33 +0,0 @@ -import { Typography, Grid, Card, CardContent } from "@mui/material"; - -export default function StatCard({number, caption, size}) { - /** - * Creates a card with a number and caption. - * - * - * @param {string} number Number to display in the card. - * @param {string} caption Caption to display in the card. - * @param {number} size Size of the card. - * - * @return {StatCard} Card with the number and caption. - **/ - - const cardStyle = { - height: size, - display: "flex", - justifyContent: "center", - alignItems: "center", - }; - - - return ( - - - - { number } - { caption } - - - - ) -} \ No newline at end of file diff --git a/frontend/src/components/YouTube.jsx b/frontend/src/components/YouTube.jsx deleted file mode 100644 index a69e1fa..0000000 --- a/frontend/src/components/YouTube.jsx +++ /dev/null @@ -1,42 +0,0 @@ -import React, { useState, useEffect } from 'react'; - -const ResponsiveYouTube = ({ videoId }) => { - const [windowWidth, setWindowWidth] = useState(window.innerWidth); - - useEffect(() => { - const handleResize = () => { - setWindowWidth(window.innerWidth); - }; - - window.addEventListener('resize', handleResize); - - return () => { - window.removeEventListener('resize', handleResize); - }; - }, []); - - // Determine the size of the iframe based on the window width - const getIframeSize = () => { - if (windowWidth > 1024) { // Large screens - return { width: '800px', height: '450px' }; // 16:9 aspect ratio - } else if (windowWidth > 600) { // Medium screens - return { width: '600px', height: '338px' }; // 16:9 aspect ratio - } else { // Small screens - return { width: '100%', height: 'auto' }; // Full width, auto height - } - }; - - const iframeSize = getIframeSize(); - - return ( - - ); -}; - -export default ResponsiveYouTube; diff --git a/frontend/src/index.css b/frontend/src/index.css index 3948c87..5150e82 100644 --- a/frontend/src/index.css +++ b/frontend/src/index.css @@ -28,3 +28,13 @@ code { width: 100%; } +.centered-container { + text-align: center; +} + +.responsive-image { + width: 80%; + max-width: 100%; + height: auto; +} + diff --git a/frontend/src/index.jsx b/frontend/src/index.jsx index a488b59..b64b772 100644 --- a/frontend/src/index.jsx +++ b/frontend/src/index.jsx @@ -5,10 +5,43 @@ import "./index.css"; import App from "./App"; import reportWebVitals from "./reportWebVitals"; +function setLinkIcon() { + const link = document.createElement('link'); + link.rel = 'icon'; + link.href = `/${document.location.pathname.split('/')[1]}/brand/favicon.ico`; + document.head.appendChild(link); + +} + +function setSiteManifest() { + const link = document.createElement('link'); + link.rel = 'manifest'; + link.href = `/${document.location.pathname.split('/')[1]}/manifest.json`; +} + +function setAppBrand() { + fetch(`/${document.location.pathname.split('/')[1]}/brand/names.json`) + .then(response => response.json()) + .then(data => { + // Update the site title + document.title = data[0].title; + + // Update the site favicon + setLinkIcon(); + + // Update the site manifest + setSiteManifest(); + }) + .catch(error => console.error('Error loading site configuration:', error)); +} + + const container = document.getElementById('root'); const root = createRoot(container) +setAppBrand(); + root.render( diff --git a/frontend/src/pages/Home.jsx b/frontend/src/pages/Home.jsx index c1b5915..9427dd4 100644 --- a/frontend/src/pages/Home.jsx +++ b/frontend/src/pages/Home.jsx @@ -1,60 +1,59 @@ import React, { useEffect, useState } from 'react'; -import { Link } from "react-router-dom"; -import { Container, Typography, Box, Grid } from "@mui/material"; +import { Typography, Box, Grid } from "@mui/material"; import { useTheme } from '@mui/material/styles'; -import OriginalKraken from '../common/OriginalKraken'; import Graph from "../components/Graph"; +import Graphv2 from '../components/Graphv2'; import SearchIcon from '@mui/icons-material/Search'; import BubbleChartIcon from '@mui/icons-material/BubbleChart'; -//import DownloadIcon from '@mui/icons-material/Download'; -import AutoStoriesIcon from '@mui/icons-material/AutoStories'; +import DownloadIcon from '@mui/icons-material/Download'; +//import AutoStoriesIcon from '@mui/icons-material/AutoStories'; import InfoIcon from '@mui/icons-material/Info'; -import StatCard from '../components/SummaryCard'; +import StatsGrid from '../components/StatsGrid'; import IconLink from '../components/IconLink'; -const stats = [ - { - "number": "1,558", - "description": "DFT Calculated Ligands" - }, - - { - "number": "300,000+", - "description": "ML calculated Ligands" - }, - - { - "number": "576", - "description": "unique substituents" - }, - - { - "number": "190", - "description": "DFT-level descriptors" - }, - - { - "number": "21,437", - "description": "unique conformers" - }, - - { - "number": "13.8", - "description": "average conformers per ligand" - }, - -] +import CheckFileAndDownloadIcon from '../components/FileDownload'; + +import purify from 'dompurify'; + +const Badge = ({ isMobile }) => { + const displayStyle = { + maxWidth: isMobile ? '120px' : '240px', // This sets the maximum width of the image + height: '15vh' // Set the height of the image to 20% of the viewport height (box is 35% of vh) + }; + + return ( + logo + ); +}; + function Home() { const [ molData, setMolData ] = useState([]); - const [ components, setComponents ] = useState(["1", "2"]); - const [ type, setType ] = useState("umap"); const [isMobile, setIsMobile] = useState(window.innerWidth < 768); + const [name, setName] = useState(""); + const [tagline, setTagline] = useState(""); const theme = useTheme(); + useEffect(() => { + fetch(`/${document.location.pathname.split('/')[1]}/brand/names.json`) + .then(response => { + if (!response.ok) { + throw new Error('Network response was not ok'); + } + return response.json(); + }) + .then(data => { + setName(data[0].name); + setTagline(data[0].tagline); + }) + .catch(error => { + console.error('Error fetching stats:', error); + }); +}, []); + useEffect(() => { function checkMobile() { setIsMobile(window.innerWidth < 768); @@ -70,17 +69,14 @@ function Home() { }, []); // Empty array means this effect runs once on mount and cleanup on unmount - async function umap(type, components, limit=1000) { + async function umap() { /** * Requests general umap data from the backend. - * @param {string} type Type of dimensionality reduction. Can be one of PCA or UMAP. - * @param {string} components String of comma separated integers. - * @param {number} limit Limit of the search. * @return {json} The response json. */ - let encoded = encodeURIComponent(components); + let encoded = encodeURIComponent("1,2"); - const response = await fetch(`/api/molecules/dimensions/?type=${type}&components=${encoded}&limit=${limit}`) + const response = await fetch(`/api/${document.location.pathname.split('/')[1]}/molecules/dimensions/?type=umap&components=${encoded}&limit=10000`) if (!response.ok) { throw new Error('Invalid Molecule Id') @@ -97,7 +93,7 @@ function Home() { * */ const fetchData = async () => { - const molecule_data = await umap(type, components); + const molecule_data = await umap(); return molecule_data } @@ -111,7 +107,7 @@ function Home() { } useEffect(() => { loadData() - }, [type]); + }, []); return ( <> @@ -129,16 +125,13 @@ function Home() { flexDirection: isMobile ? 'column' : 'row', }} > - + - KRAKEN + { name } { - - Kolossal viRtual dAtabase - for moleKular dEscriptors of orgaNophosphorus - ligands. + } @@ -151,24 +144,15 @@ function Home() { - {/* Hide until we're ready to add - - - - */} + + {/* Hide until we're ready to add + */} - - - - {stats.map((stat, index) => ( - - ))} - - + - {!isMobile && } + {!isMobile && } ); diff --git a/frontend/src/pages/Library_Details.jsx b/frontend/src/pages/Library_Details.jsx index 904e97f..c657a52 100644 --- a/frontend/src/pages/Library_Details.jsx +++ b/frontend/src/pages/Library_Details.jsx @@ -1,112 +1,62 @@ +import { useEffect, useState, useContext } from 'react'; + import { Container, - Typography, - List, - ListItem, - Link, - Box, + Table, + TableBody, + TableCell, + TableHead, + TableRow, + Typography } from '@mui/material'; -import DataTable from '../components/DFTTable'; -import ResponsiveYouTube from '../components/YouTube'; - -import KrakenWorkflow from '../images/kraken-workflow.png'; - -function Library_Details() { +import ReactMarkdown from 'react-markdown'; + +// use rehype-raw to render HTML inside markdown +// https://stackoverflow.com/questions/70548725/any-way-to-render-html-in-react-markdown +// use remarkGfm to render markdown tables (gfm = GitHub Flavored Markdown) +import rehypeRaw from 'rehype-raw'; +import remarkGfm from 'remark-gfm'; + + +const MarkdownPage =({ markdown_file }) => { + const [content, setContent] = useState(""); + + useEffect(() => { + fetch(markdown_file) + .then((response) => response.text()) + .then((text) => { + setContent(text); + }); + }, [markdown_file]); + + const renderers = { + h1: ({ children }) => {children}, + h2: ({ children }) => {children}, + table: ({ children }) => {children}
, + thead: ({ children }) => {children}, + tbody: ({ children }) => {children}, + tr: ({ children }) => {children}, + th: ({ children, align }) => {children}, + td: ({ children, align }) => {children} + }; + return ( - - Library Details - - - Kraken Workflow - - - Conformational Searching - - Initial ligand geometries were generated using SMILES strings and converted to free ligands and [LNi(CO)3] complexes using RDKit, OpenBabel or Molconvert. - These guess geometries were optimized at the GFN2-xTB level of theory (xTB v6.2.2). - Optimized geometries were subjected to a conformational search using CREST (v2.8) at the GFN2-xTB level with toluene solvation (GBSA model). - For ligands containing ferrocene, conformational searches were performed at the GFN-FF level to avoid structural changes. - - - xTB Descriptors - - Molecular descriptors at the xTB level for the full conformational ensembles from CREST of the free ligands and the [NiCO3]-bound complexes were collected using MORFEUS. - - - Selection of conformers for DFT computations - - Conformers from both sets (free ligand and Ni complex) were selected based on the following two criteria: - - - - - Conformers that minimize or maximize any of the following xTB-level steric properties in any of the two conformer sets: - B1, B5, lval, far_vbur, far_vtot, max_delta_qvbur, max_delta_qvtot, near_vbur, near_vtot, ovbur_max, ovbur_min, ovtot_max, - ovtot_min, pyr_val, qvbur_max, qvbur_min, qvtot_max, qvtot_min, vbur. - - - - Up to 20 conformers within 3 kcal/mol relative energy in the free ligand conformer set. If more than 20 conformers are in that range, the selection was made by RMSD pruning (using PyDP4). - This enables structurally diverse selection of conformers in the relevant energy window. - - - - - DFT computations - - - Prior to DFT computations, the [Ni(CO)3]-fragment was removed from the Ni complex conformer set to obtain free-ligand initial geometries. - All DFT optimizations (Gaussian 16, rev C.01) were performed at the PBE-D3(BJ)/6-31+G(d,p) level of theory. - The corresponding geometries were used for a series of single-point energy calculations at the PBE0-D3(BJ)/def2-TZVP and PBE0-D3(BJ)/def2-TZVP/SMD(CHCl3) levels of theory. - Additional single-points were also run for the radical cations and radical anions from the optimized geometry of the neutral free ligand. - - - - From the DFT calculations, steric, electronic, or full molecule/interaction-type descriptors were collected for each conformer. - The range of properties across the conformers of a single ligand was treated by using up to five condensed measures for each of the properties. - - - - - - ML Descriptor Prediction - - - The machine learning portion of the workflow aims to expand the total number of monophosphine ligands in the library from ~1500 (which is a fraction of the total possible space) to {">"} 300,000 ligands. - The computational workflow used to calculate the set of ~1500 is too intensive to calculate all possible monophosphines, so descriptors were predicted using machine learning methods. - - - - New descriptors were predicted using the sum of contributions of each phosphorus substituent using the “Bag of Substituents” approach. - These contributions are made up of 576 unique substituents from the ~1500 set of ligands. - - - - For more details on the machine learning models used to predict descriptors, see the original publication supporting information. - - - Video Tutorial - A video tutorial of Kraken which explains relevant background information and the computational workflow, and provides a walkthrough of this website: - - - - - - An extended explanation of the computational workflow used to build the monophosphine library, - as well as details on the collected and predicted descriptors can be found in original publication supporting information. - - - Citation - - Gensch, T.; dos Passos Gomes, G.; Friederich, P.; Peters, E.; Gaudin, T.; Pollice, R.; Jorner, K.; Nigam, A.; Lindner-D’Addario, M.; Sigman, M. S.; Aspuru-Guzik, A. A Comprehensive Discovery Platform for Organophosphorus Ligands for Catalysis. J. Am. Chem. Soc. 2022, 144, 3, 1205–1217. DOI: 10.1021/jacs.1c09718 - - + + {content} + ) } +const Library_Details = () => { + return ( + + ); +}; + + export default Library_Details; \ No newline at end of file diff --git a/frontend/src/pages/Molecule.jsx b/frontend/src/pages/Molecule.jsx index 69a0219..d408a7e 100644 --- a/frontend/src/pages/Molecule.jsx +++ b/frontend/src/pages/Molecule.jsx @@ -12,13 +12,49 @@ import MoleculeDataTable from "../components/MoleculeDataTable"; import { neighborPage } from "../common/MoleculeUtils"; +const MoleculeCard = ({ molData, identifierData }) => { + // Merging molData and identifierData objects and removing 'conformers_id' + const combinedData = { + ...molData, + ...identifierData, + }; + delete combinedData.conformers_id; // Removing the 'conformers_id' key + + // Function to format keys to title case + const toTitleCase = (str) => { + return str.replace(/_/g, ' ').replace(/\w\S*/g, (txt) => { + return txt.charAt(0).toUpperCase() + txt.substr(1).toLowerCase(); + }); + }; + + // Conditionally formatting values (e.g., for molecular_weight) + const formattedValue = (key, value) => { + if (key === 'molecular_weight') { + return value.toFixed(2); + } + return value; + }; + + return ( +
+ {Object.entries(combinedData) + .filter(([key, value]) => value != null && value !== '') // Filtering out null or empty values + .map(([key, value]) => ( + + {toTitleCase(key)}: {formattedValue(key, value)} + + ))} +
+ ); +}; + async function molecule(molecule_id, signal) { /** * Requests general umap or pca data from the backend. * @param {number} molecule_id Id of the molecule to search on. * @param {AbortSignal} signal Abortsignal object. */ - const response = await fetch(`/api/molecules/${molecule_id}`, {signal: signal}) + const response = await fetch(`/api/${document.location.pathname.split('/')[1]}/molecules/${molecule_id}`, {signal: signal}) if (!response.ok) { throw new Error('Invalid Molecule Id') @@ -41,7 +77,7 @@ async function dimensionality(molecule_id, type, components, signal, limit=10) { */ let encoded = encodeURIComponent(components); - const response = await fetch(`/api/molecules/${molecule_id}/neighbors/?type=${type}&components=${encoded}&skip=0&limit=${limit}`, {signal: signal}) + const response = await fetch(`/api/${document.location.pathname.split('/')[1]}/molecules/${molecule_id}/neighbors/?type=${type}&components=${encoded}&skip=0&limit=${limit}`, {signal: signal}) if (!response.ok) { throw new Error('Invalid Molecule Id') @@ -61,7 +97,7 @@ async function identifiers(smiles, signal) { */ let encoded = encodeURIComponent(smiles); - const response = await fetch(`/api/molecules/identifiers/?smiles=${encoded}`, {signal: signal}) + const response = await fetch(`/api/${document.location.pathname.split('/')[1]}/molecules/identifiers/?smiles=${encoded}`, {signal: signal}) if (!response.ok) { throw new Error('Invalid Molecule Smiles') @@ -84,6 +120,7 @@ export default function MoleculeInfo() { const [ svg, setSvg ] = useState({}); const [ allConformers, setAllConformers ] = useState([]); const [ conformer, setConformer ] = useState(""); + const [ conformerCluster, setConformerCluster ] = useState([]); const [ width, setWidth ] = useState(window.innerWidth); useEffect(() => { @@ -121,7 +158,7 @@ export default function MoleculeInfo() { const fetchData = async () => { const molecule_data = await molecule(molid, signal); const umap_neighbor_data = await dimensionality(molid, "umap", ["1", "2"], signal); - const pca_neighbor_data = await dimensionality(molid, "pca", ["1", "2", "3", "4"], signal); + const pca_neighbor_data = await dimensionality(molid, "pca", ["1", "2", "3"], signal); const svg_data = await retrieveSVG(molecule_data.smiles, signal); const identifier_data = await identifiers(molecule_data.smiles, signal); return [ molecule_data, umap_neighbor_data, pca_neighbor_data, svg_data, identifier_data ] @@ -167,6 +204,22 @@ export default function MoleculeInfo() { [ params ] ); + useEffect(() => { + const controller = new AbortController(); + const signal = controller.signal; + fetch(`/api/${document.location.pathname.split('/')[1]}/conformers/data/` + conformer, {signal: signal}) + .then(response => response.json()) + .then(data => { + if (data.cluster) { + setConformerCluster(data.cluster); + } else { + setConformerCluster(false); + } + }) + + }, [conformer]); + + return ( @@ -182,11 +235,7 @@ export default function MoleculeInfo() { {Object.keys(molData).length > 0 && - SMILES: {molData.smiles} - kraken Ligand ID: {molData.molecule_id} - InChI: {identifierData.InChI} - InChIKey: {identifierData.InChIKey} - Molecular Weight: {molData.molecular_weight.toFixed(2)} + @@ -213,9 +262,12 @@ export default function MoleculeInfo() { ))} + + This conformer ensemble was clustered. + - + diff --git a/frontend/src/pages/Neighbors.jsx b/frontend/src/pages/Neighbors.jsx index ecf2c42..9f30318 100644 --- a/frontend/src/pages/Neighbors.jsx +++ b/frontend/src/pages/Neighbors.jsx @@ -7,11 +7,21 @@ import { useParams } from "react-router-dom"; import Button from '@mui/material/Button'; -import Graph from '../components/Graph' +import DropDownButton from '../components/DataDownloadButton'; -import { retrieveAllSVGs, dynamicGrid, extractIdsFromResults, downloadMoleculeData } from '../common/MoleculeUtils'; +import Graph from '../components/Graph' +import { retrieveAllSVGs, dynamicGrid, extractIdsFromResults } from '../common/MoleculeUtils'; +async function fetchInitialMoleculeId() { + const response = await fetch(`/api/${document.location.pathname.split('/')[1]}/molecules/first_id`); + if (!response.ok) { + throw new Error('Network response was not ok'); + } + const result = await response.json(); + const initial_id = result["first_molecule_id"]; + return initial_id; +} async function NeighborSearch(molecule_id, type="pca", components="1,2,3,4", limit=48, skip=0, signal) { @@ -27,7 +37,7 @@ async function NeighborSearch(molecule_id, type="pca", components="1,2,3,4", lim */ let encoded = encodeURIComponent(components); - const response = await fetch(`/api/molecules/${molecule_id}/neighbors/?type=${type}&components=${encoded}&skip=${skip}&limit=${limit}`, {signal: signal}) + const response = await fetch(`/api/${document.location.pathname.split('/')[1]}/molecules/${molecule_id}/neighbors/?type=${type}&components=${encoded}&skip=${skip}&limit=${limit}`, {signal: signal}) if (!response.ok) { throw new Error('Invalid Molecule Id') @@ -48,7 +58,7 @@ export default function NeighborSearchHook () { const params = useParams(); const interval = 15; - const [ moleculeid, setMoleculeID ] = useState(params.molid || 1); + const [ moleculeid, setMoleculeID ] = useState(); const [ skip, setSkip ] = useState(0); const [ validMolecule, setValidMolecule ] = useState(true); const [ svg_results, setSVGResults ] = useState([]) @@ -60,6 +70,43 @@ export default function NeighborSearchHook () { const [ searchToggle, setSearchToggle ] = useState(true); const [ isMobile, setIsMobile ] = useState(window.innerWidth < 768); const [ moleculeIDs, setMoleculeIDs ] = useState(""); + const [ availableDataTypes, setAvailableDataTypes ] = useState([]); + + const reverseMapping = { + "ml_data": "ML Data", + "dft_data": "DFT Data", + "xtb_data": "xTB Data", + "xtb_ni_data": "xTB_Ni Data" + }; + + useEffect(() => { + const init = async () => { + try { + // Check if there's a molid in the URL params + if (params.molid) { + setMoleculeID(params.molid); + } else { + // Fetch the initial molecule ID from the endpoint + const initialId = await fetchInitialMoleculeId(); + setMoleculeID(initialId); + } + } catch (error) { + console.error('Failed to initialize molecule ID:', error); + // Handle error (e.g., set state to show an error message) + } + }; + + init(); + }, [params.molid]); // Depend on params.molid so this effect re-runs if the URL parameter changes + + useEffect(() => { + fetch(`/api/${document.location.pathname.split('/')[1]}/molecules/data_types`) + .then(response => response.json()) + .then(data => { + const translatedDataTypes = data["available_types"].map(key => reverseMapping[key] || key); + setAvailableDataTypes(translatedDataTypes); + }); + }, []); // Extract the molecule ids from the results useEffect(() => { @@ -111,7 +158,7 @@ export default function NeighborSearchHook () { * @param {AbortSignal} signal Abortsignal object. */ const fetchData = async () => { - const molecule_data = await NeighborSearch(moleculeid, "pca", "1,2,3,4", interval, skip, signal); + const molecule_data = await NeighborSearch(moleculeid, "pca", "1,2,3", interval, skip, signal); const svg_data = await retrieveAllSVGs(molecule_data, signal); return [ molecule_data, svg_data ] @@ -170,14 +217,14 @@ export default function NeighborSearchHook () { } }, // eslint-disable-next-line react-hooks/exhaustive-deps - [ searchToggle ] + [ searchToggle, moleculeid ] ); return ( Neighbor Search - Neighbors are identified by Euclidian distance in 4 principal component space. + Neighbors are identified by Euclidian distance in 3 principal component space. @@ -185,7 +232,8 @@ export default function NeighborSearchHook () { style = {{width: 350}} sx={{ m: 0.5}} id="search-outline" - label="Enter a Molecule ID to Search" + label="" + helperText="Enter a molecule ID to search for neighbors." variant="outlined" value= {moleculeid} onKeyDown = { (e) => _handleKeyDown(e) } @@ -215,12 +263,7 @@ export default function NeighborSearchHook () { Load More - - + } diff --git a/frontend/src/pages/SearchHook.jsx b/frontend/src/pages/SearchHook.jsx index e69e629..6b05a63 100644 --- a/frontend/src/pages/SearchHook.jsx +++ b/frontend/src/pages/SearchHook.jsx @@ -12,11 +12,13 @@ import FullScreenDialog from '../components/KetcherPopup'; import { substructureSearch, retrieveAllSVGs, dynamicGrid, extractIdsFromResults, downloadMoleculeData } from '../common/MoleculeUtils'; +import DropDownButton from '../components/DataDownloadButton'; + export default function SearchHook () { const interval = 15; - const [ searchString, setSearch ] = useState('PC=C'); + const [ searchString, setSearch ] = useState('C=C'); const [ skip, setSkip ] = useState(0); const [ results, setResults ] = useState([]); const [ validSmiles, setValidSmiles ] = useState(true); @@ -33,6 +35,24 @@ export default function SearchHook () { const [ fromKetcher, setFromKetcher ] = useState(false); const [ updatedParameters, setUpdatedParameters ] = useState(false); const [ moleculeIDs, setMoleculeIDs ] = useState(""); + const [ availableDataTypes, setAvailableDataTypes ] = useState([]); + + const reverseMapping = { + "ml_data": "ML Data", + "dft_data": "DFT Data", + "xtb_data": "xTB Data", + "xtb_ni_data": "xTB_Ni Data" + }; + + + useEffect(() => { + fetch(`/api/${document.location.pathname.split('/')[1]}/molecules/data_types`) + .then(response => response.json()) + .then(data => { + const translatedDataTypes = data["available_types"].map(key => reverseMapping[key] || key); + setAvailableDataTypes(translatedDataTypes); + }); + }, []); // Extract the molecule ids from the results useEffect(() => { @@ -220,11 +240,7 @@ export default function SearchHook () { Load More - + } @@ -247,11 +263,7 @@ export default function SearchHook () { Load More - + } diff --git a/frontend/vite.config.js b/frontend/vite.config.js index efb817d..ab67461 100644 --- a/frontend/vite.config.js +++ b/frontend/vite.config.js @@ -5,6 +5,7 @@ import { nodePolyfills } from 'vite-plugin-node-polyfills'; // have to do this f // https://vitejs.dev/config/ export default defineConfig(({ mode }) => { return { + base: process.env.VITE_BASE_URL || '/base_url', plugins: [react(), nodePolyfills()], server: { host: '0.0.0.0', @@ -13,5 +14,6 @@ export default defineConfig(({ mode }) => { define: { 'process.env': process.env // have to do this for ketcher } - }; + } }); + diff --git a/frontend/yarn.lock b/frontend/yarn.lock index 3205580..04563a7 100644 --- a/frontend/yarn.lock +++ b/frontend/yarn.lock @@ -1,13406 +1,19955 @@ -# THIS IS AN AUTOGENERATED FILE. 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100644 index 1d2f166..0000000 --- a/install-pr3.sh +++ /dev/null @@ -1,20 +0,0 @@ -echo "Snapshotting filesystem" - -echo "Updating source" -git pull origin master - -echo "Building frontend" -cd frontend && yarn build - -echo "Installing frontend" -cp -fr build/* /zroot/iocage/jails/www/root/usr/local/www/nginx-dist/ -cd .. - -echo "Installing backend" -cd backend && cp -fr app /zroot/iocage/jails/backend/root/ -cd .. -iocage restart backend - -echo "Updating DB" -POSTGRES_SERVER=192.168.5.3 POSTGRES_USER=postgres POSTGRES_PASSWD='' POSTGRES_DB=phosphines alembic upgrade head -psql -U postgres -h 192.168.5.3 -d phosphines -c 'REINDEX index molecule_search_mol' ; diff --git a/move_std.sql b/move_std.sql deleted file mode 100644 index cdaa0ad..0000000 --- a/move_std.sql +++ /dev/null @@ -1,34 +0,0 @@ -ALTER TABLE xtb_data -ADD COLUMN std DOUBLE PRECISION; - -UPDATE xtb_data -SET std = x.boltzmann_average -FROM ( - SELECT - SUBSTRING(property FROM 1 FOR POSITION('_std' IN property) - 1) AS property_name, - boltzmann_average - FROM xtb_data - WHERE property LIKE '%_std%' -) AS x -WHERE xtb_data.property = x.property_name; - -DELETE FROM xtb_data -WHERE property LIKE '%_std%'; - ---------------------------------------------- -ALTER TABLE xtb_ni_data -ADD COLUMN std DOUBLE PRECISION; - -UPDATE xtb_ni_data -SET std = x.boltzmann_average -FROM ( - SELECT - SUBSTRING(property FROM 1 FOR POSITION('_std' IN property) - 1) AS property_name, - boltzmann_average - FROM xtb_ni_data - WHERE property LIKE '%_std%' -) AS x -WHERE xtb_ni_data.property = x.property_name; - -DELETE FROM xtb_ni_data -WHERE property LIKE '%_std%'; diff --git a/nginx.conf b/nginx.conf deleted file mode 100644 index 907fb31..0000000 --- a/nginx.conf +++ /dev/null @@ -1,17 +0,0 @@ -server { - listen 80; - location / { - root /usr/share/nginx/html; - index index.html index.htm; - try_files $uri /index.html; - } - location /api { - proxy_pass http://backend/api; - } - location /docs { - proxy_pass http://backend/docs; - } - location /depict { - proxy_pass http://cdk-depict:8080/depict; - } -} diff --git a/nginx.dockerfile b/nginx.dockerfile deleted file mode 100644 index 89c8e09..0000000 --- a/nginx.dockerfile +++ /dev/null @@ -1,12 +0,0 @@ -FROM node:16 as react-build -WORKDIR /app -COPY frontend/ . -#RUN yarn -#RUN yarn build - -#FROM nginx:alpine -#COPY nginx.conf /etc/nginx/conf.d/default.conf -#COPY --from=react-build /app/build /usr/share/nginx/html -#EXPOSE 80 -#CMD ["nginx", "-g", "daemon off;"] - diff --git a/scripts/fix_dft_data.py b/scripts/fix_dft_data.py deleted file mode 100644 index 39bc184..0000000 --- a/scripts/fix_dft_data.py +++ /dev/null @@ -1,30 +0,0 @@ -from glob import glob -import os -import yaml -from tqdm import tqdm - - -def main(smiles_filename, data_folder): - data_files = glob(os.path.join(data_folder, '*.yml')) - data_files.sort() - - raw_smiles_data = open(smiles_filename, 'r').read().split('\n')[:-1] - smiles_data = {} - for line in raw_smiles_data: - num, smiles = line.split(' ') - smiles_data[num] = smiles - - for filename in tqdm(data_files): - if not '_' in os.path.basename(filename): - continue - num = os.path.basename(filename).split('_')[0] - data = yaml.load(open(filename, 'r'), Loader=yaml.CLoader) - smiles = smiles_data[num] - data['smiles'] = smiles - with open(filename, 'w') as f: - yaml.dump(data, f, Dumper=yaml.CDumper) - - -if __name__ == '__main__': - main('/Users/tga/Downloads/dft_data_210125.smi', - './xtb/results_all_noNi/') diff --git a/scripts/fix_xtb_data.py b/scripts/fix_xtb_data.py deleted file mode 100644 index a86c9bc..0000000 --- a/scripts/fix_xtb_data.py +++ /dev/null @@ -1,39 +0,0 @@ -from glob import glob -import os -import yaml -from tqdm import tqdm - - -def main(data_folder): - data_files = glob(os.path.join(data_folder, '*.yml')) - data_files.sort() - - smiles = None - import ipdb; ipdb.set_trace() - for filename in tqdm(data_files): - if not '_' in os.path.basename(filename): - new_data = {} - data = yaml.load(open(filename, 'r'), Loader=yaml.CLoader) - for section_name, section in data.items(): - if isinstance(section, str) or isinstance(section, int) or isinstance(section, float): - new_data[section_name] = section - continue - new_data[section_name] = {} - if not isinstance(section, dict): - continue - for name, value in section.items(): - if isinstance(value, list): - continue - new_data[section_name][name] = value - smiles = data['smiles'] - with open(filename, 'w') as f: - yaml.dump(new_data, f, Dumper=yaml.CDumper) - continue - data = yaml.load(open(filename, 'r'), Loader=yaml.CLoader) - data['smiles'] = smiles - with open(filename, 'w') as f: - yaml.dump(data, f, Dumper=yaml.CDumper) - - -if __name__ == '__main__': - main('./xtb/results_all_noNi/') diff --git a/scripts/generate_pca_js.py b/scripts/generate_pca_js.py deleted file mode 100644 index 6f13159..0000000 --- a/scripts/generate_pca_js.py +++ /dev/null @@ -1,44 +0,0 @@ -import sys -from tqdm import tqdm -from rdkit import Chem - -sys.path.append('../backend/app') -from app.db.session import SessionLocal, models - - -def get_molecule_id(smiles, session): - # mol = Chem.MolFromSmiles(smiles) - # canonical_smiles = Chem.MolToSmiles(mol, canon=True) - out = ( - session.query(models.molecule) - .filter(models.molecule.smiles == smiles) - .one() - ) - return out.molecule_id - -def main(pca_file): - import ipdb; ipdb.set_trace() - data = open(pca_file, 'r').read().split('\n')[1:-1] - dst = open('plot_data.js', 'w') - - session = SessionLocal() - - custom_data = [] - x_list = [] - y_list = [] - for line in tqdm(data): - _, smiles, x, y = line.split(',') - molecule_id = get_molecule_id(smiles, session) - x_list.append(float(x)) - y_list.append(float(y)) - custom_data.append(f'{{ molecule_id: {molecule_id}, smiles: \"{smiles}\" }}') - - dst.write(f"x: {x_list},\n") - dst.write(f"y: {y_list},\n") - dst.write(f"customdata: [{', '.join(custom_data)}]\n") - dst.close() - - -if __name__ == "__main__": - main("/Users/tga/Downloads/PL_PC_210126.csv") - diff --git a/scripts/populate_db.py b/scripts/populate_db.py deleted file mode 100644 index faaf279..0000000 --- a/scripts/populate_db.py +++ /dev/null @@ -1,181 +0,0 @@ -import os -import sys -from argparse import ArgumentParser -from glob import glob - -import yaml -from tqdm import tqdm - -sys.path.append("../backend/app") -from app.db.session import SessionLocal, models - -parser = ArgumentParser() -parser.add_argument("--xtb", action="store_true", default=False) -parser.add_argument("--xtb-ni", action="store_true", default=False) -parser.add_argument("--ml", action="store_true", default=False) -parser.add_argument("--dft", action="store_true", default=False) - -parser.add_argument("--data-folder", type=str) - - -def extract_conformer_data(filename): - data = yaml.load(open(filename, "r"), Loader=yaml.CLoader) - data_to_store = [] - for key, conformer_data in data.items(): - if key == "smiles": - continue - conformer_data_to_store = {} - # naming is different in xtb file. - if "coords" in conformer_data.keys(): - conformer_data_to_store["coords"] = conformer_data["coords"] - else: - conformer_data_to_store["coords"] = conformer_data["coords_extended"] - if "elements" in conformer_data.keys(): - conformer_data_to_store["elements"] = conformer_data["elements"] - else: - conformer_data_to_store["elements"] = conformer_data["sterimol_parameters"][ - "elements_extended" - ] - data_to_store.append(conformer_data_to_store) - return data_to_store, data["smiles"] - - -def extract_molecule_data(filename, field): - data = yaml.load(open(filename, "r"), Loader=yaml.CLoader) - data_to_store = {field: {}} - keys = [ - "boltzmann_averaged_data", - "max_data", - "min_data", - "delta_data", - "vburminconf_data", - ] - - for key in keys: - if key in data.keys(): - data_to_store[field][key] = data[key] - - if "smi" in data.keys(): - data_to_store["smiles"] = data["smiv"] - elif "smiles" in data.keys(): - data_to_store["smiles"] = data["smiles"] - return data_to_store - - -def populate_ml_data(path, session): - data = open(path, "r").read().split("\n")[:-1] - headers = data[0].split(";")[1:] - for line in tqdm(data[1:]): - max_data = {} - min_data = {} - delta_data = {} - boltz_data = {} - vburminconf_data = {} - out = line.split(";") - smiles = out[0] - for name, value in zip(headers, out[1:]): - name = "".join(name) - if name.endswith("_boltz"): - name = name[: -len("_boltz")] - boltz_data[name] = value - elif name.endswith("_delta"): - name = name[: -len("_delta")] - delta_data[name] = value - elif name.endswith("_min"): - name = name[: -len("_min")] - min_data[name] = value - elif name.endswith("_max"): - name = name[: -len("_max")] - max_data[name] = value - elif name.endswith("_vburminconf"): - name = name[: -len("_vburminconf")] - vburminconf_data[name] = value - else: - raise ValueError("Something is wrong!") - ml_data = {} - ml_data["smiles"] = smiles - ml_data["ml_data"] = {} - ml_data["ml_data"]["max_data"] = max_data - ml_data["ml_data"]["min_data"] = min_data - ml_data["ml_data"]["vburminconf_data"] = vburminconf_data - ml_data["ml_data"]["delta_data"] = delta_data - ml_data["ml_data"]["boltzmann_averaged_data"] = boltz_data - - molecule = ( - session.query(models.molecule) - .filter(models.molecule.smiles == smiles) - .one_or_none() - ) - if molecule is None: - molecule = models.molecule(**ml_data) - session.add(molecule) - session.commit() - continue - setattr(molecule, "ml_data", ml_data["ml_data"]) - session.commit() - - -def main(args): - field = "" - if args.dft: - field = "dft_data" - elif args.xtb: - field = "xtb_data" - elif args.ml: - field = "ml_data" - elif args.xtb_ni: - field = "xtb_ni_data" - else: - raise ValueError("Datatype not set! Please set one of --dft/--ml/--xtb!") - - session = SessionLocal() - if field == "ml_data": - populate_ml_data(args.data_folder, session) - return - - data_files = glob(os.path.join(args.data_folder, "*.yml")) - # DFT naming convention is different - data_files.sort(reverse=True if args.dft else False) - - for i, filename in enumerate(tqdm(data_files)): - if filename.endswith("_combined.yml"): - continue - - elif filename.endswith("_confdata.yml") or filename.endswith("_confs.yml"): - if args.xtb or args.xtb_ni: - continue - data, smiles = extract_conformer_data(filename) - molecule = ( - session.query(models.molecule) - .filter(models.molecule.smiles == smiles) - .one_or_none() - ) - if molecule is None: - raise ValueError("Could not add conformer: molecule not found") - for confo in data: - confo["molecule_id"] = molecule.molecule_id - session.add(models.conformer(**confo)) - session.commit() - - else: - data = extract_molecule_data(filename, field) - molecule = ( - session.query(models.molecule) - .filter(models.molecule.smiles == data["smiles"]) - .one_or_none() - ) - if molecule is None: - molecule = models.molecule(**data) - session.add(molecule) - session.commit() - continue - setattr(molecule, field, data[field]) - session.add(molecule) - session.commit() - - -if __name__ == "__main__": - args = parser.parse_args() - if (args.dft and args.ml) or (args.dft and args.xtb) or (args.xtb and args.ml) or (args.xtb_ni and args.ml): - raise ValueError("only one of --dft/--xtb/--ml can be set at the same time!") - main(args) diff --git a/tests/db/test_db_small.sql b/tests/db/test_db_small.sql deleted file mode 100644 index b5a52aa..0000000 --- a/tests/db/test_db_small.sql +++ /dev/null @@ -1,694 +0,0 @@ --- --- PostgreSQL database dump --- - --- Dumped from database version 12.3 (Debian 12.3-1.pgdg100+1) --- Dumped by pg_dump version 12.14 (Ubuntu 12.14-0ubuntu0.20.04.1) - -SET statement_timeout = 0; -SET lock_timeout = 0; -SET idle_in_transaction_session_timeout = 0; -SET client_encoding = 'UTF8'; -SET standard_conforming_strings = on; -SELECT pg_catalog.set_config('search_path', '', false); -SET check_function_bodies = false; -SET xmloption = content; -SET client_min_messages = warning; -SET row_security = off; - --- --- Name: cube; Type: EXTENSION; Schema: -; Owner: - --- - -CREATE EXTENSION IF NOT EXISTS cube WITH SCHEMA public; - - --- --- Name: EXTENSION cube; Type: COMMENT; Schema: -; Owner: --- - -COMMENT ON EXTENSION cube IS 'data type for multidimensional cubes'; - - --- --- Name: pg_trgm; Type: EXTENSION; Schema: -; Owner: - --- - -CREATE EXTENSION IF NOT EXISTS pg_trgm WITH SCHEMA public; - - --- --- Name: EXTENSION pg_trgm; Type: COMMENT; Schema: -; Owner: --- - -COMMENT ON EXTENSION pg_trgm IS 'text similarity measurement and index searching based on trigrams'; - - --- --- Name: rdkit; Type: EXTENSION; Schema: -; Owner: - --- - -CREATE EXTENSION IF NOT EXISTS rdkit WITH SCHEMA public; - - --- --- Name: EXTENSION rdkit; Type: COMMENT; Schema: -; Owner: --- - -COMMENT ON EXTENSION rdkit IS 'Cheminformatics functionality for PostgreSQL.'; - - --- --- Name: rdk_add_mol(); Type: FUNCTION; Schema: public; Owner: postgres --- - -CREATE FUNCTION public.rdk_add_mol() RETURNS trigger - LANGUAGE plpgsql - AS $$ - declare - begin - if NEW.smiles is null then - raise exception 'smiles can not be null'; - end if; - if NEW.mol is null then - NEW.mol = (select mol_from_smiles(NEW.smiles::cstring)); - end if; - if NEW.molecular_weight is null then - NEW.molecular_weight = (select mol_amw(NEW.mol)); - end if; - return NEW; - end; - $$; - - -ALTER FUNCTION public.rdk_add_mol() OWNER TO postgres; - -SET default_tablespace = ''; - -SET default_table_access_method = heap; - --- --- Name: alembic_version; Type: TABLE; Schema: public; Owner: postgres --- - -CREATE TABLE public.alembic_version ( - version_num character varying(32) NOT NULL -); - - -ALTER TABLE public.alembic_version OWNER TO postgres; - --- --- Name: cmda_exec; Type: TABLE; Schema: public; Owner: postgres --- - -CREATE TABLE public.cmda_exec ( - cmda_output text -); - - -ALTER TABLE public.cmda_exec OWNER TO postgres; - --- --- Name: conformer; Type: TABLE; Schema: public; Owner: postgres --- - -CREATE TABLE public.conformer ( - conformer_id integer NOT NULL, - molecule_id integer, - coords double precision[] NOT NULL, - elements character varying[] NOT NULL, - data jsonb -); - - -ALTER TABLE public.conformer OWNER TO postgres; - --- --- Name: conformer_id_seq; Type: SEQUENCE; Schema: public; Owner: postgres --- - -CREATE SEQUENCE public.conformer_id_seq - START WITH 1 - INCREMENT BY 1 - NO MINVALUE - NO MAXVALUE - CACHE 1; - - -ALTER TABLE public.conformer_id_seq OWNER TO postgres; - --- --- Name: conformer_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: postgres --- - -ALTER SEQUENCE public.conformer_id_seq OWNED BY public.conformer.conformer_id; - - --- --- Name: molecule; Type: TABLE; Schema: public; Owner: postgres --- - -CREATE TABLE public.molecule ( - molecule_id integer NOT NULL, - smiles text NOT NULL, - molecular_weight double precision, - dft_data jsonb, - xtb_data jsonb, - ml_data jsonb, - mol public.mol, - xtb_ni_data jsonb, - fingerprint public.bfp, - morganbv public.bfp, - pat character varying, - pca public.cube, - umap public.cube -); - - -ALTER TABLE public.molecule OWNER TO postgres; - --- --- Name: molecule_id_seq; Type: SEQUENCE; Schema: public; Owner: postgres --- - -CREATE SEQUENCE public.molecule_id_seq - START WITH 1 - INCREMENT BY 1 - NO MINVALUE - NO MAXVALUE - CACHE 1; - - -ALTER TABLE public.molecule_id_seq OWNER TO postgres; - --- --- Name: molecule_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: postgres --- - -ALTER SEQUENCE public.molecule_id_seq OWNED BY public.molecule.molecule_id; - - --- --- Name: t_e; Type: TABLE; Schema: public; Owner: postgres --- - -CREATE TABLE public.t_e ( - docs text -); - - -ALTER TABLE public.t_e OWNER TO postgres; - --- --- Name: conformer conformer_id; Type: DEFAULT; Schema: public; Owner: postgres --- - -ALTER TABLE ONLY public.conformer ALTER COLUMN conformer_id SET DEFAULT nextval('public.conformer_id_seq'::regclass); - - --- --- Name: molecule molecule_id; Type: DEFAULT; Schema: public; Owner: postgres --- - -ALTER TABLE ONLY public.molecule ALTER COLUMN molecule_id SET DEFAULT nextval('public.molecule_id_seq'::regclass); - - --- --- Name: 1268888; Type: BLOB; Schema: -; Owner: postgres --- - -SELECT pg_catalog.lo_create('1268888'); - - -ALTER LARGE OBJECT 1268888 OWNER TO postgres; - --- --- Name: 2601034; Type: BLOB; Schema: -; Owner: postgres --- - -SELECT pg_catalog.lo_create('2601034'); - - -ALTER LARGE OBJECT 2601034 OWNER TO postgres; - --- --- Name: 5912902; Type: BLOB; Schema: -; Owner: postgres --- - -SELECT pg_catalog.lo_create('5912902'); - - -ALTER LARGE OBJECT 5912902 OWNER TO postgres; - --- --- Name: 7115235; Type: BLOB; Schema: -; Owner: postgres --- - -SELECT pg_catalog.lo_create('7115235'); - - -ALTER LARGE OBJECT 7115235 OWNER TO postgres; - --- --- Name: 7608663; Type: BLOB; Schema: -; Owner: postgres --- - -SELECT pg_catalog.lo_create('7608663'); - - -ALTER LARGE OBJECT 7608663 OWNER TO postgres; - --- --- Name: 8146173; Type: BLOB; Schema: -; Owner: postgres --- - -SELECT pg_catalog.lo_create('8146173'); - - -ALTER LARGE OBJECT 8146173 OWNER TO postgres; - --- --- Name: 8337475; Type: BLOB; Schema: -; Owner: postgres --- - -SELECT pg_catalog.lo_create('8337475'); - - -ALTER LARGE OBJECT 8337475 OWNER TO postgres; - --- --- Data for Name: alembic_version; Type: TABLE DATA; Schema: public; Owner: postgres --- - -COPY public.alembic_version (version_num) FROM stdin; -97fe717d2f34 -\. - - --- --- Data for Name: cmda_exec; Type: TABLE DATA; Schema: public; Owner: postgres --- - -COPY public.cmda_exec (cmda_output) FROM stdin; -\. - - --- --- Data for Name: conformer; Type: TABLE DATA; Schema: public; Owner: postgres --- - -COPY public.conformer (conformer_id, molecule_id, coords, elements, data) FROM stdin; -31646 1 {{-4.430332,-0.39481,-3.468906},{-4.914983,-0.121922,-2.031326},{-6.055908,-1.08218,-1.642317},{-3.765565,-0.179848,-1.034941},{-3.044337,-1.367333,-0.82188},{-1.977027,-1.437041,0.085645},{-1.251664,-2.761174,0.303462},{-2.082036,-3.685867,1.216811},{-0.881245,-3.462127,-1.015114},{-1.616593,-0.272314,0.815821},{-0.515685,-0.341548,1.833934},{-0.859096,-0.492614,3.192827},{0.12279,-0.564807,4.189915},{1.475947,-0.48608,3.831734},{1.831221,-0.346383,2.482485},{0.856471,-0.27524,1.464691},{1.261883,-0.142357,-0.35125},{1.493648,1.739136,-0.458923},{1.37634,2.236278,-1.915071},{1.419759,3.773086,-1.990312},{2.66628,4.340303,-1.292943},{2.753836,3.854157,0.162241},{2.735213,2.316567,0.239246},{3.007455,-0.85517,-0.395923},{2.937586,-2.358499,-0.048719},{4.316198,-3.032304,-0.145213},{4.939858,-2.832242,-1.534925},{5.013193,-1.340551,-1.894226},{3.635457,-0.662189,-1.792132},{-2.328115,0.938188,0.617474},{-1.984555,2.205219,1.397505},{-2.965527,2.414809,2.569759},{-1.944379,3.462624,0.508618},{-3.38917,0.957554,-0.307089},{-3.630584,0.30632,-3.758673},{-4.027938,-1.418434,-3.561783},{-5.261174,-0.292721,-4.188191},{-5.317412,0.908824,-2.001413},{-6.904468,-0.984536,-2.341145},{-5.716422,-2.132073,-1.671616},{-6.419887,-0.875742,-0.622414},{-3.320827,-2.266777,-1.382514},{-0.308063,-2.541092,0.83088},{-3.051058,-3.931255,0.747959},{-2.288377,-3.203308,2.186645},{-1.544404,-4.630661,1.408767},{-0.255413,-4.34805,-0.811612},{-1.774068,-3.810869,-1.562327},{-0.317438,-2.779682,-1.671817},{-1.918388,-0.565765,3.459452},{-0.167811,-0.687022,5.237872},{2.256047,-0.538242,4.597873},{2.893054,-0.299756,2.22255},{0.60211,2.11124,0.083721},{0.44306,1.851347,-2.363168},{2.206013,1.824136,-2.520264},{1.383158,4.099733,-3.045252},{0.516094,4.186195,-1.500869},{2.659042,5.444434,-1.331075},{3.572126,4.010533,-1.839903},{3.665627,4.246437,0.648252},{1.892659,4.254995,0.732678},{3.650518,1.926074,-0.246194},{2.764985,1.988317,1.293126},{3.662052,-0.349114,0.341466},{2.514353,-2.500778,0.960749},{2.239162,-2.851747,-0.753206},{4.225303,-4.108691,0.087357},{4.988089,-2.599099,0.622281},{4.319387,-3.356579,-2.288455},{5.94475,-3.289244,-1.578755},{5.716677,-0.834684,-1.203406},{5.421335,-1.207001,-2.912352},{2.95489,-1.088059,-2.555739},{3.734942,0.411846,-2.025172},{-0.977161,2.066353,1.830077},{-2.954923,1.557447,3.261118},{-2.702462,3.321413,3.141906},{-3.996792,2.533004,2.193885},{-1.313986,3.30868,-0.381941},{-1.53963,4.318418,1.075308},{-2.951673,3.747481,0.159864},{-3.943526,1.889056,-0.46901}} {C,C,C,C,C,C,C,C,C,C,C,C,C,C,C,C,P,C,C,C,C,C,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -31647 1 {{5.105637,0.171717,2.792114},{4.398414,-0.764291,1.792373},{4.014168,-2.097634,2.462737},{3.194632,-0.088339,1.150787},{3.155887,0.146601,-0.231758},{2.064223,0.776879,-0.855403},{2.115052,1.083157,-2.351879},{2.859103,2.412447,-2.603336},{2.750979,-0.039408,-3.191848},{0.955758,1.17155,-0.060177},{-0.162218,1.956541,-0.685388},{0.011101,3.359896,-0.680098},{-0.9283,4.233646,-1.239712},{-2.073642,3.704232,-1.848007},{-2.25298,2.316253,-1.876868},{-1.332284,1.412952,-1.287582},{-1.964901,-0.340718,-1.432238},{-0.490286,-1.53513,-1.451952},{-0.821646,-2.656892,-2.466787},{0.356835,-3.62513,-2.663155},{0.83568,-4.212451,-1.327241},{1.178075,-3.094334,-0.332511},{-0.009575,-2.138568,-0.119825},{-2.755851,-0.609474,0.265908},{-3.686529,0.554758,0.655091},{-4.390459,0.289801,1.997475},{-5.161896,-1.038807,1.985565},{-4.243311,-2.203282,1.585329},{-3.555113,-1.930128,0.236929},{0.974268,0.947773,1.34239},{-0.178204,1.405233,2.233054},{0.1408,2.767875,2.882766},{-0.551814,0.376627,3.316141},{2.094037,0.32414,1.919089},{4.442124,0.418809,3.638979},{6.010375,-0.307871,3.203363},{5.4022,1.118116,2.310849},{5.113725,-0.990396,0.978587},{3.303454,-1.933121,3.291213},{3.537413,-2.782058,1.742575},{4.906128,-2.596375,2.879048},{4.011449,-0.169498,-0.838849},{1.07458,1.215941,-2.699191},{2.372121,3.251158,-2.082223},{2.881759,2.645707,-3.68183},{3.900569,2.343768,-2.243579},{2.290189,-1.019209,-2.986009},{2.626432,0.178096,-4.265761},{3.834219,-0.129668,-3.001501},{0.917523,3.762839,-0.216035},{-0.757663,5.314212,-1.209886},{-2.817348,4.362144,-2.308007},{-3.136789,1.898381,-2.371598},{0.339398,-0.938137,-1.871246},{-1.121147,-2.211706,-3.431838},{-1.702648,-3.224137,-2.105312},{0.068344,-4.43118,-3.361939},{1.195912,-3.081402,-3.140819},{1.708358,-4.871615,-1.485475},{0.0326,-4.846366,-0.900922},{1.486929,-3.520972,0.639211},{2.041276,-2.512886,-0.708779},{-0.834221,-2.705698,0.352046},{0.278233,-1.342403,0.582428},{-1.958553,-0.689927,1.02794},{-3.122201,1.501364,0.705683},{-4.447406,0.690894,-0.139451},{-5.068682,1.129073,2.235813},{-3.630338,0.259428,2.802365},{-5.994302,-0.968957,1.257717},{-5.619503,-1.228062,2.973226},{-3.470022,-2.344355,2.366357},{-4.815042,-3.147382,1.532016},{-4.319529,-1.861163,-0.561839},{-2.902981,-2.779219,-0.032376},{-1.059515,1.546476,1.583485},{0.328661,3.540845,2.121165},{-0.700596,3.104298,3.512959},{1.038987,2.691474,3.520141},{-0.723142,-0.625014,2.888511},{-1.473326,0.690799,3.834257},{0.236855,0.284877,4.082439},{2.105406,0.15157,3.000326}} {C,C,C,C,C,C,C,C,C,C,C,C,C,C,C,C,P,C,C,C,C,C,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -31618 2 {{0.527355,-1.668199,2.733145},{0.378328,-0.321765,2.167452},{1.124854,0.653607,2.954468},{-0.964484,0.036865,1.835698},{-1.656364,1.007232,2.593428},{-2.98241,1.321313,2.284781},{-3.643893,0.663248,1.245219},{-2.97882,-0.313474,0.466118},{-3.705182,-1.044219,-0.509903},{-5.156766,-1.03344,-0.399512},{-3.281761,-1.029684,-1.910625},{-1.599817,-0.595051,0.730911},{-0.894195,-1.627338,-0.092916},{-1.404686,-2.942708,0.033311},{-0.902819,-4.015671,-0.708238},{0.121964,-3.781264,-1.636723},{0.619429,-2.483739,-1.791456},{0.161419,-1.383037,-1.020333},{1.109144,0.156135,-1.508707},{2.640515,0.056829,-0.377248},{3.832905,0.741497,-1.079238},{5.074794,0.772777,-0.171667},{5.466757,-0.640344,0.287161},{4.27925,-1.353943,0.951775},{3.038308,-1.367966,0.041982},{0.211866,1.654933,-0.805951},{1.121195,2.900401,-0.774033},{0.356247,4.126347,-0.241858},{-0.913151,4.408738,-1.059972},{-1.813903,3.166158,-1.118503},{-1.044949,1.94517,-1.648307},{1.600394,-1.91127,2.806409},{0.049045,-2.41568,2.086351},{0.081843,-1.737717,3.750694},{2.189108,0.364528,2.947657},{1.035691,1.654193,2.5023},{0.801362,0.713442,4.018932},{-1.166375,1.498362,3.436074},{-3.512136,2.080984,2.868407},{-4.678457,0.927452,1.018529},{-5.462096,-1.206169,0.643984},{-5.62543,-0.087368,-0.755658},{-5.555767,-1.854004,-1.019087},{-3.637223,-0.115507,-2.435168},{-2.190833,-1.083197,-1.999833},{-3.706181,-1.909654,-2.423086},{-2.227989,-3.103187,0.736291},{-1.319345,-5.018714,-0.573864},{0.51966,-4.596197,-2.249494},{1.39068,-2.295906,-2.547344},{2.386284,0.615552,0.542931},{4.064032,0.179388,-2.00521},{3.571289,1.763749,-1.401423},{5.917474,1.255615,-0.698914},{4.858349,1.398637,0.717302},{6.32924,-0.599679,0.976694},{5.792519,-1.227723,-0.594033},{4.554865,-2.388426,1.227139},{4.02834,-0.833238,1.897923},{2.195978,-1.86316,0.548288},{3.259503,-1.972303,-0.859478},{-0.097677,1.441486,0.229288},{1.498625,3.114203,-1.794221},{2.004682,2.722208,-0.136934},{0.071145,3.93862,0.812519},{1.020649,5.009585,-0.239144},{-1.462395,5.266983,-0.632445},{-0.623132,4.69828,-2.08959},{-2.697685,3.358792,-1.753855},{-2.195003,2.934546,-0.105721},{-1.706222,1.065667,-1.655184},{-0.73905,2.12114,-2.698761}} {C,N,C,C,C,C,C,C,N,C,C,C,C,C,C,C,C,C,P,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -31619 2 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{C,N,C,C,C,C,C,C,N,C,C,C,C,C,C,C,C,C,P,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -31595 3 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{{1.935645,2.652043,1.526529},{0.813995,1.70654,1.084007},{0.838255,1.419644,-0.35547},{0.732767,2.567827,-1.265762},{-0.569249,3.373152,-1.146041},{0.266536,-0.088207,-0.991967},{-1.372799,-0.37091,-0.1416},{-1.531383,-0.646118,1.232653},{-2.810789,-0.739279,1.798368},{-3.952037,-0.561432,0.997621},{-3.807622,-0.296232,-0.372858},{-2.52493,-0.204554,-0.935735},{1.249326,-1.181211,0.015078},{2.704081,-0.989238,-0.141676},{3.457752,-1.245061,1.16822},{0.836829,-2.598525,-0.03767},{0.898993,-3.277242,-1.417554},{1.817587,3.667742,1.114083},{1.93555,2.741124,2.625823},{2.919535,2.265868,1.210793},{0.939045,0.738611,1.595522},{-0.170406,2.112741,1.398852},{0.829367,2.170757,-2.291361},{1.601608,3.233512,-1.101282},{-1.44566,2.730956,-1.335276},{-0.686373,3.816441,-0.142951},{-0.57767,4.198599,-1.87815},{-0.640985,-0.801624,1.850895},{-2.920287,-0.952718,2.866822},{-4.95009,-0.635136,1.440813},{-4.692701,-0.167135,-1.004013},{-2.409323,-0.001381,-2.007398},{2.870697,0.055888,-0.452287},{3.118352,-1.631245,-0.948111},{3.110386,-0.555857,1.955497},{3.315185,-2.275943,1.53357},{4.540948,-1.091884,1.022543},{1.475817,-3.148738,0.676724},{-0.191758,-2.671699,0.353013},{1.907972,-3.222705,-1.85892},{0.627461,-4.342961,-1.329051},{0.197112,-2.804968,-2.124915}} {C,C,N,C,C,P,C,C,C,C,C,C,N,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -30496 58 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{C,C,C,N,C,C,C,P,C,C,C,C,C,C,N,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -29450 138 {{0.078522,2.2828,1.432529},{-0.061942,2.413029,0.007017},{0.009906,1.06629,-1.016353},{-1.425338,0.055281,-0.423424},{-2.577523,0.70413,0.068499},{-3.727489,-0.030173,0.393718},{-3.752265,-1.421834,0.211063},{-2.618917,-2.074315,-0.299902},{-1.464636,-1.342573,-0.615081},{1.428609,0.07219,-0.345883},{1.383943,-0.713893,0.826272},{2.526796,-1.391202,1.273963},{3.730876,-1.293814,0.556578},{3.789037,-0.517314,-0.610586},{2.64435,0.160992,-1.056499},{-0.116868,3.280768,1.853963},{-0.64639,1.560632,1.850699},{1.101418,1.964999,1.700238},{-2.567351,1.791673,0.196299},{-4.608466,0.487549,0.78623},{-4.650697,-1.99424,0.460903},{-2.63052,-3.158601,-0.449549},{-0.584969,-1.865871,-1.004673},{0.44589,-0.806059,1.382397},{2.478551,-1.996985,2.184441},{4.62076,-1.826504,0.906035},{4.723128,-0.443067,-1.175893},{2.68665,0.765459,-1.969424}} {C,O,P,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -9021 1290 {{1.602744,-1.225313,-0.039818},{0.809438,-1e-06,-0.191971},{1.60274,1.225315,-0.039835},{-0.75795,-5e-06,0.530461},{-1.357549,1.270726,-0.334215},{-1.357555,-1.270718,-0.334239},{2.368007,-1.251181,-0.834873},{0.963359,-2.111418,-0.16462},{2.121746,-1.284714,0.939968},{2.368004,1.251173,-0.834889},{2.12174,1.284732,0.939951},{0.963352,2.111416,-0.164651}} {C,N,C,P,F,F,H,H,H,H,H,H} \N -30497 58 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{C,C,C,N,C,C,C,P,C,C,C,C,C,C,N,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -30490 59 {{2.556633,-2.076974,-0.511517},{1.337678,-1.448418,-0.006636},{1.128606,-1.690014,1.419093},{0.831841,4e-06,-0.830646},{-0.953068,7e-06,-0.350517},{-1.667688,-1.213076,-0.250823},{-3.052249,-1.212901,-0.027581},{-3.749797,4e-06,0.088106},{-3.052247,1.212911,-0.027553},{-1.667685,1.213089,-0.250795},{1.337676,1.448434,-0.006653},{1.128641,1.689996,1.419087},{2.556654,2.076953,-0.511525},{2.499561,-3.173762,-0.375015},{2.664124,-1.865441,-1.586954},{3.471344,-1.719058,0.00927},{1.071997,-2.778705,1.610839},{1.952849,-1.280575,2.040851},{0.181563,-1.238409,1.749788},{-1.124435,-2.15865,-0.346551},{-3.587933,-2.164044,0.055186},{-4.830248,3e-06,0.261963},{-3.587929,2.164053,0.055238},{-1.12443,2.158663,-0.346501},{0.181564,1.238457,1.749774},{1.952857,1.28047,2.040823},{1.072121,2.778685,1.610869},{2.499627,3.173739,-0.374988},{3.471355,1.718985,0.009243},{2.664127,1.865448,-1.586969}} {C,N,C,P,C,C,C,C,C,C,N,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -30491 59 {{-1.519411,2.704926,-0.364183},{-1.46286,1.371786,0.230237},{-1.123853,1.381249,1.650701},{-0.882683,0.114096,-0.820385},{0.901873,-0.093238,-0.323855},{1.863799,0.484547,-1.177001},{3.226692,0.463419,-0.840954},{3.643382,-0.146005,0.352489},{2.693542,-0.731688,1.206985},{1.332309,-0.703512,0.872759},{-1.547585,-1.275756,0.072673},{-3.012184,-1.239209,0.165635},{-1.102106,-2.555741,-0.492893},{-0.554975,3.252608,-0.286442},{-2.292756,3.306837,0.148128},{-1.787328,2.624415,-1.429736},{-1.853843,2.008518,2.194197},{-1.181494,0.356234,2.047396},{-0.106276,1.782097,1.844556},{1.538032,0.948768,-2.115566},{3.96299,0.913908,-1.514127},{4.70565,-0.169515,0.615115},{3.016756,-1.211091,2.136907},{0.587593,-1.165277,1.529662},{-3.342426,-2.036949,0.85422},{-3.515707,-1.399945,-0.814756},{-3.3361,-0.267898,0.567615},{-1.41951,-3.372406,0.179272},{-1.527364,-2.75848,-1.501738},{-0.004132,-2.583965,-0.567374}} {C,N,C,P,C,C,C,C,C,C,N,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -29564 128 {{-1.203044,2.330096,-0.174958},{0.000667,1.527954,0.071975},{1.205153,2.328975,-0.174812},{-5.8e-05,-0.040771,-0.762715},{1.434324,-0.659492,-0.003596},{2.11616,-1.748506,-0.690922},{1.691304,-0.613312,1.430729},{-1.434963,-0.658228,-0.003527},{-1.691741,-0.611842,1.430827},{-2.117767,-1.746648,-0.690829},{-2.104899,1.725862,-0.001914},{-1.210738,3.186392,0.522926},{-1.247676,2.734842,-1.211311},{1.250311,2.733655,-1.211167},{1.21354,3.185282,0.523051},{2.106428,1.723925,-0.001623},{1.834648,-2.746824,-0.291024},{3.213471,-1.641438,-0.587511},{1.865707,-1.723208,-1.76401},{1.166425,0.247833,1.871135},{1.359752,-1.539616,1.946598},{2.776396,-0.493392,1.617802},{-1.360885,-1.538417,1.946659},{-2.77671,-0.491016,1.61802},{-1.166103,0.248879,1.871163},{-1.867513,-1.721438,-1.763964},{-3.214973,-1.638754,-0.587182},{-1.836898,-2.745211,-0.291092}} {C,N,C,P,N,C,C,N,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -29565 128 {{1.200538,2.331449,-0.174888},{-0.002292,1.527943,0.071978},{-1.207609,2.327677,-0.174953},{0.000153,-0.04077,-0.762718},{1.435865,-0.656594,-0.003647},{2.119317,-1.744708,-0.690827},{1.692523,-0.610051,1.430741},{-1.433603,-0.660978,-0.003534},{-2.114332,-1.750723,-0.690789},{-1.690632,-0.61497,1.430786},{2.103089,1.72831,-0.001693},{1.244797,2.73616,-1.211267},{1.207144,3.187818,0.522916},{-1.253065,2.732307,-1.211312},{-2.108268,1.72169,-0.001861},{-1.216972,3.183973,0.522905},{1.838967,-2.743377,-0.291007},{3.216449,-1.63619,-0.587118},{1.869105,-1.719719,-1.763975},{1.36232,-1.536886,1.946518},{2.777388,-0.488439,1.617992},{1.166229,0.250259,1.871083},{-3.211751,-1.644766,-0.587361},{-1.831788,-2.748734,-0.290862},{-1.863927,-1.72521,-1.763882},{-2.775845,-0.496107,1.61784},{-1.166623,0.246731,1.871136},{-1.358174,-1.540903,1.946729}} {C,N,C,P,N,C,C,N,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -29562 129 {{-0.754995,3.346038,-0.233853},{0.006466,2.170065,0.193584},{-0.137636,1.904863,1.625077},{-0.011857,0.848899,-0.949306},{1.493604,-0.075787,-0.414853},{2.593819,0.60292,0.148736},{3.784607,-0.08144,0.434742},{3.900253,-1.450973,0.149867},{2.815999,-2.131759,-0.427281},{1.623588,-1.450431,-0.709378},{-1.366952,-0.276414,-0.343704},{-1.272567,-1.122754,0.782017},{-2.382348,-1.8625,1.214575},{-3.605739,-1.766951,0.530463},{-3.714178,-0.929616,-0.5902},{-2.600959,-0.192509,-1.02328},{-1.846173,3.249589,-0.042404},{-0.392624,4.23467,0.314642},{-0.603745,3.51362,-1.311452},{0.528707,1.082365,1.927216},{-1.177428,1.63639,1.908831},{0.154176,2.807881,2.191143},{2.502637,1.672942,0.36194},{4.625675,0.458891,0.881007},{4.829535,-1.98414,0.372476},{2.896692,-3.199105,-0.656336},{0.783627,-1.994429,-1.154468},{-0.320712,-1.211912,1.315161},{-2.292945,-2.515875,2.088507},{-4.469841,-2.347288,0.868545},{-4.662184,-0.8566,-1.132463},{-2.681769,0.452939,-1.905413}} {C,N,C,P,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -29451 138 {{-0.767461,3.337819,0.319603},{0.132542,2.2237,0.413354},{0.001288,1.093784,-0.854972},{1.449575,0.071008,-0.348746},{1.513004,-1.28377,-0.736827},{2.646931,-2.053319,-0.443829},{3.731399,-1.48006,0.240588},{3.673637,-0.133001,0.629072},{2.542736,0.64339,0.331307},{-1.368082,0.001059,-0.245711},{-1.416209,-0.4651,1.084957},{-2.479475,-1.270168,1.51189},{-3.499192,-1.627766,0.611111},{-3.458594,-1.169683,-0.713757},{-2.399221,-0.349599,-1.137686},{-0.458916,4.055494,1.095031},{-1.811243,3.026403,0.512872},{-0.713105,3.823543,-0.672922},{0.664976,-1.74508,-1.254817},{2.680262,-3.105518,-0.743342},{4.615266,-2.08227,0.472039},{4.512224,0.318681,1.168598},{2.492157,1.690641,0.641942},{-0.614101,-0.191514,1.778231},{-2.512768,-1.628138,2.545877},{-4.325797,-2.262356,0.945605},{-4.253004,-1.443562,-1.415012},{-2.369909,0.022455,-2.168187}} {C,O,P,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -29438 139 {{-0.376602,3.75027,0.979488},{0.026908,2.306829,0.726537},{-0.101013,2.052612,-0.692544},{0.023417,0.491397,-1.329729},{-1.391488,-0.374225,-0.503152},{-1.395664,-1.776542,-0.343548},{-2.532349,-2.436447,0.145888},{-3.683585,-1.70652,0.48248},{-3.69379,-0.312644,0.315893},{-2.560924,0.34703,-0.182956},{1.460821,-0.253123,-0.416195},{1.42011,-0.721266,0.915192},{2.575185,-1.225291,1.529111},{3.788208,-1.269779,0.821535},{3.842491,-0.80979,-0.502831},{2.684996,-0.30547,-1.115557},{0.255291,4.438082,0.395187},{-1.427631,3.920256,0.69456},{-0.261231,3.993109,2.049299},{1.074208,2.125708,1.031982},{-0.618535,1.61002,1.295121},{-0.501449,-2.357419,-0.593679},{-2.516337,-3.524004,0.269113},{-4.568518,-2.221667,0.868189},{-4.588643,0.263965,0.570922},{-2.577481,1.43252,-0.327085},{0.476172,-0.701896,1.468805},{2.529604,-1.584376,2.56222},{4.687924,-1.666761,1.30186},{4.783447,-0.847976,-1.060335},{2.724133,0.050395,-2.151176}} {C,C,O,P,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -29439 139 {{0.576726,2.398781,1.6742},{-0.447986,2.582676,0.560566},{0.020455,2.175516,-0.747817},{-0.031582,0.591993,-1.346449},{-1.452485,-0.189954,-0.442178},{-1.406135,-0.666948,0.886057},{-2.550052,-1.20569,1.491225},{-3.758434,-1.276,0.778025},{-3.818997,-0.806802,-0.542886},{-2.672311,-0.268726,-1.147029},{1.409282,-0.241428,-0.527939},{2.587807,0.492231,-0.277855},{3.745528,-0.14893,0.184847},{3.752607,-1.539017,0.3836},{2.594009,-2.283061,0.110656},{1.433032,-1.641198,-0.345954},{0.830359,1.338959,1.829084},{1.507704,2.943822,1.450752},{0.163343,2.794993,2.618248},{-1.384775,2.048324,0.802657},{-0.69346,3.651553,0.43785},{-0.466169,-0.625685,1.444751},{-2.499154,-1.570851,2.521904},{-4.649696,-1.699459,1.251377},{-4.756332,-0.864734,-1.104698},{-2.715906,0.093208,-2.180302},{2.588175,1.574574,-0.439677},{4.646694,0.438771,0.387122},{4.656812,-2.039928,0.742462},{2.590611,-3.367845,0.257612},{0.536339,-2.235333,-0.551871}} {C,C,O,P,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -29425 140 {{-2.34274,2.662377,-0.177393},{-0.87171,2.927449,-0.501266},{-0.205009,3.888123,0.484276},{-0.116655,1.686769,-0.626946},{-0.042819,0.657353,0.724447},{1.564891,-0.136657,0.285979},{1.853953,-1.43433,0.758238},{3.107005,-2.014286,0.518961},{4.08839,-1.306702,-0.194958},{3.806492,-0.016175,-0.667982},{2.554118,0.569698,-0.425815},{-1.192123,-0.703616,0.210336},{-2.045265,-1.267443,1.17702},{-2.92815,-2.303884,0.829219},{-2.97189,-2.769372,-0.493012},{-2.129745,-2.202089,-1.466559},{-1.239924,-1.178902,-1.116155},{-2.92225,3.599153,-0.235583},{-2.454263,2.25845,0.844053},{-2.773239,1.936968,-0.885614},{-0.799698,3.349415,-1.520265},{0.852028,4.046293,0.216337},{-0.249119,3.489625,1.511899},{-0.716978,4.865143,0.471979},{1.08961,-2.001757,1.300518},{3.314906,-3.025118,0.883781},{5.065523,-1.761528,-0.384162},{4.563069,0.538623,-1.232177},{2.326625,1.569412,-0.806339},{-2.020067,-0.889075,2.205498},{-3.58535,-2.74011,1.588034},{-3.662973,-3.572148,-0.76834},{-2.164302,-2.566023,-2.498495},{-0.577767,-0.736904,-1.867598}} {C,C,C,O,P,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -29426 140 {{0.705398,3.492346,0.709958},{-0.174435,2.263606,0.490583},{-1.652183,2.572721,0.732453},{0.015093,1.848443,-0.897769},{0.044342,0.239672,-1.404807},{-1.339141,-0.576991,-0.465754},{-1.273454,-0.995319,0.880745},{-2.403173,-1.527563,1.517737},{-3.614644,-1.653767,0.817531},{-3.690596,-1.253366,-0.525362},{-2.558552,-0.721128,-1.160864},{1.50731,-0.454538,-0.50403},{1.622876,-1.844467,-0.281159},{2.797234,-2.386979,0.2598},{3.878058,-1.551534,0.585313},{3.779923,-0.171035,0.352444},{2.608739,0.37069,-0.197768},{1.771355,3.25612,0.569786},{0.568919,3.881276,1.733008},{0.428648,4.285879,-0.003884},{0.157851,1.445412,1.158514},{-2.282951,1.687591,0.565511},{-1.982719,3.372724,0.049091},{-1.804644,2.915333,1.770274},{-0.331926,-0.908895,1.431876},{-2.339256,-1.843138,2.564009},{-4.495295,-2.06938,1.316978},{-4.629239,-1.357991,-1.078263},{-2.615932,-0.406142,-2.208857},{0.786177,-2.508204,-0.523889},{2.865927,-3.465782,0.432193},{4.792337,-1.975139,1.011797},{4.620078,0.487663,0.594537},{2.54462,1.443984,-0.398183}} {C,C,C,O,P,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -29414 141 {{-4.941792,-0.852448,0.026594},{-4.260076,-1.837531,0.761934},{-2.860537,-1.861172,0.793048},{-2.13096,-0.887443,0.086237},{-0.755069,-0.964035,0.192624},{0.255177,-0.213838,-0.986414},{0.447563,1.475967,-0.261884},{0.371517,1.706934,1.126412},{0.511923,3.006175,1.631133},{0.740648,4.082674,0.756217},{0.816171,3.859544,-0.626863},{0.657431,2.560183,-1.135594},{1.80246,-1.014351,-0.377547},{1.833009,-2.41953,-0.250714},{3.01697,-3.072043,0.11784},{4.191015,-2.333459,0.339669},{4.17148,-0.937807,0.1995},{2.98357,-0.279215,-0.15338},{-2.802361,0.110347,-0.642804},{-4.206195,0.114976,-0.672846},{-6.035021,-0.838779,0.002613},{-4.82169,-2.598261,1.312928},{-2.313523,-2.622819,1.355556},{0.196549,0.863183,1.801379},{0.44671,3.181641,2.709518},{0.852967,5.09605,1.153739},{0.986416,4.69668,-1.310841},{0.695038,2.386178,-2.217212},{0.921004,-2.9996,-0.422922},{3.023969,-4.160884,0.22846},{5.116608,-2.844651,0.621334},{5.080706,-0.354839,0.376498},{2.973718,0.811679,-0.239298},{-2.237932,0.881404,-1.174405},{-4.723633,0.892076,-1.243828}} {C,C,C,C,O,P,C,C,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -29415 141 {{-1.985289,3.212444,-1.098473},{-2.732477,2.462705,-0.175461},{-2.084413,1.67728,0.787769},{-0.680161,1.643961,0.829843},{-0.061568,0.887385,1.819338},{0.444458,-0.742599,1.565809},{-0.835669,-1.410765,0.413794},{-1.030176,-0.967021,-0.913426},{-2.072761,-1.490222,-1.689058},{-2.931626,-2.464577,-1.153213},{-2.748022,-2.914544,0.163025},{-1.707609,-2.385603,0.942389},{1.884888,-0.517187,0.424215},{2.845244,0.466672,0.748265},{4.024731,0.588975,0.002383},{4.278615,-0.288718,-1.065013},{3.346134,-1.289146,-1.376318},{2.158115,-1.404825,-0.637132},{0.076798,2.399081,-0.082503},{-0.582667,3.179417,-1.044858},{-2.492772,3.823325,-1.85079},{-3.826167,2.483519,-0.207397},{-2.648523,1.076888,1.506431},{-0.367003,-0.207301,-1.336666},{-2.218534,-1.132627,-2.713061},{-3.744011,-2.872271,-1.762929},{-3.413463,-3.674952,0.583046},{-1.565111,-2.729272,1.972979},{2.657215,1.146776,1.586094},{4.750811,1.367097,0.258328},{5.201429,-0.196264,-1.645637},{3.537895,-1.980752,-2.202759},{1.437201,-2.186381,-0.895716},{1.167089,2.367015,-0.036645},{0.007678,3.767539,-1.754488}} {C,C,C,C,O,P,C,C,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -20913 565 {{-2.111883,-1.619012,0.246233},{-1.758501,0.020644,-0.500133},{-2e-06,0.545394,0.630934},{-0.000195,2.351472,0.164744},{1.758255,0.020695,-0.500574},{2.112481,-1.618392,0.246657},{-3.152031,-1.867453,-0.012038},{-1.44859,-2.394999,-0.163562},{-2.013032,-1.57828,1.341739},{0.897078,2.820851,0.59615},{-0.000517,2.510789,-0.925462},{-0.897238,2.820814,0.596669},{2.013593,-1.577069,1.342139},{1.449551,-2.394928,-0.16268},{3.152753,-1.866469,-0.011463}} {C,S,P,C,S,C,H,H,H,H,H,H,H,H,H} \N -20914 565 {{-2.112047,-1.61885,0.24631},{-1.758473,0.020691,-0.500217},{-3.1e-05,0.545395,0.630916},{-5e-05,2.351447,0.16466},{1.758399,0.020733,-0.500304},{2.112257,-1.618671,0.246389},{-1.449212,-2.395034,-0.163855},{-2.012563,-1.578144,1.34176},{-3.152418,-1.866953,-0.011379},{5.1e-05,2.51074,-0.925551},{-0.89727,2.820785,0.596217},{0.897059,2.820835,0.596389},{1.449469,-2.395007,-0.163559},{3.152627,-1.866654,-0.011428},{2.012945,-1.577834,1.341848}} {C,S,P,C,S,C,H,H,H,H,H,H,H,H,H} \N -29403 142 {{2.692379,-2.357738,0.928943},{3.064696,-0.777782,0.272071},{4.395474,-0.351358,0.194364},{4.696548,0.90972,-0.34219},{3.65987,1.739753,-0.791539},{2.325718,1.318359,-0.702785},{2.011614,0.051739,-0.176654},{0.733346,-0.419172,-0.035432},{-0.525313,0.102553,-1.097447},{-1.71629,-1.194961,-0.552169},{-1.27007,-2.477653,-0.175133},{-2.200334,-3.480992,0.135644},{-3.577374,-3.22181,0.058338},{-4.025233,-1.947354,-0.32473},{-3.101058,-0.937747,-0.627044},{-1.198638,1.551573,-0.16523},{-1.375969,1.527163,1.233503},{-1.872645,2.655234,1.897805},{-2.210903,3.810624,1.17051},{-2.041571,3.840319,-0.221427},{-1.526632,2.715351,-0.886689},{5.186739,-1.016547,0.549257},{5.737965,1.236579,-0.404194},{3.883256,2.726866,-1.20612},{1.51543,1.975146,-1.030702},{-0.197623,-2.678268,-0.101449},{-1.844198,-4.469626,0.441667},{-4.299389,-4.007931,0.299209},{-5.097292,-1.734083,-0.378668},{-3.460168,0.05925,-0.904309},{-1.11907,0.622059,1.79312},{-2.003639,2.634621,2.984197},{-2.60413,4.688557,1.692217},{-2.301304,4.739407,-0.788593},{-1.377306,2.739526,-1.972375}} {Cl,C,C,C,C,C,C,O,P,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -29404 142 {{-2.429129,2.511112,-0.593275},{-2.948825,0.920818,-0.079186},{-4.302703,0.567297,-0.162566},{-4.715475,-0.707367,0.251741},{-3.77628,-1.624958,0.747855},{-2.423602,-1.268534,0.829236},{-1.996396,0.005797,0.418778},{-0.674084,0.366955,0.564492},{0.358519,0.105051,-0.807035},{1.708352,1.209053,-0.216547},{3.049586,0.924617,-0.549257},{4.070388,1.821709,-0.204915},{3.764699,3.010421,0.476945},{2.431742,3.298749,0.808981},{1.405211,2.409495,0.458063},{1.069976,-1.5446,-0.367277},{1.642351,-1.813135,0.894611},{2.123188,-3.09402,1.191865},{2.046143,-4.117138,0.229112},{1.480806,-3.858636,-1.027961},{0.987277,-2.576553,-1.321985},{-5.021409,1.294045,-0.549625},{-5.773085,-0.977734,0.186158},{-4.095142,-2.619567,1.07234},{-1.670518,-1.962065,1.213578},{3.300453,-0.008855,-1.064107},{5.107887,1.586124,-0.461665},{4.562666,3.707631,0.749968},{2.186907,4.221325,1.344596},{0.367406,2.633426,0.719465},{1.706415,-1.012217,1.63818},{2.564321,-3.297467,2.172782},{2.42705,-5.116217,0.462675},{1.417532,-4.653981,-1.776923},{0.530983,-2.372849,-2.297111}} {Cl,C,C,C,C,C,C,O,P,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -29388 143 {{3.147408,-1.404145,-0.047883},{1.766404,-1.056535,0.160043},{1.161414,0.173735,-0.830989},{1.53621,1.589432,-0.007677},{1.179798,1.746875,1.383692},{-0.604753,-0.079969,-0.339423},{-1.528476,0.920406,-0.709609},{-2.891422,0.773584,-0.4167},{-3.348007,-0.383246,0.236346},{-2.436241,-1.387592,0.596912},{-1.070467,-1.23986,0.308832},{3.389068,-1.476661,-1.123947},{3.815705,-0.661179,0.422557},{3.302774,-2.383971,0.428612},{0.084728,1.812231,1.503469},{1.647177,2.684464,1.718874},{1.561242,0.903814,1.984436},{-1.175898,1.823804,-1.220802},{-3.598056,1.559544,-0.700855},{-4.412557,-0.50197,0.46061},{-2.789162,-2.290571,1.105257},{-0.354177,-2.015022,0.594683}} {C,O,P,O,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H} \N -29389 143 {{3.147537,-1.403854,-0.048524},{1.766475,-1.056551,0.15957},{1.161441,0.174125,-0.830966},{1.53618,1.589424,-0.006923},{1.179394,1.746209,1.384427},{-0.604732,-0.079885,-0.33957},{-1.528663,0.92007,-0.710369},{-2.89159,0.773127,-0.417408},{-3.347935,-0.38341,0.236328},{-2.435955,-1.387345,0.597514},{-1.070206,-1.239489,0.309375},{3.815738,-0.66078,0.421887},{3.303153,-2.383677,0.427899},{3.38909,-1.476266,-1.124621},{1.646983,2.683463,1.720249},{1.56037,0.902683,1.984824},{0.084304,1.811858,1.503899},{-1.176275,1.823236,-1.222111},{-3.598393,1.558758,-0.702064},{-4.412467,-0.502234,0.46064},{-2.788693,-2.2901,1.10639},{-0.353756,-2.014339,0.595679}} {C,O,P,O,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H} \N -29356 144 {{-2.095476,3.281166,0.052291},{-2.286566,1.772161,0.025528},{-1.02554,1.128843,0.316335},{-0.560256,-0.155779,-0.672221},{-0.911816,-1.569704,0.179667},{-2.088743,-2.308479,-0.223335},{-3.304355,-1.931965,0.614668},{1.216957,-0.098216,-0.202304},{1.969694,-1.286938,-0.121171},{3.348931,-1.235634,0.127882},{3.991321,0.0023,0.287948},{3.247907,1.190286,0.202532},{1.868728,1.141956,-0.046124},{-1.687603,3.6019,1.024394},{-3.060817,3.791739,-0.104603},{-1.399264,3.601509,-0.739975},{-3.015061,1.454919,0.79503},{-2.663967,1.437965,-0.96171},{-1.830569,-3.371917,-0.080634},{-2.284659,-2.144528,-1.30125},{-3.083592,-2.045443,1.688101},{-4.158244,-2.58371,0.36167},{-3.607034,-0.887572,0.432875},{1.464742,-2.251251,-0.228979},{3.922334,-2.165023,0.201815},{5.067934,0.04119,0.480737},{3.742421,2.157734,0.33499},{1.285656,2.066224,-0.094666}} {C,C,O,P,O,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -29357 144 {{2.054591,-3.429447,0.44455},{1.140622,-2.529096,-0.371944},{1.219463,-1.193827,0.169454},{0.64453,0.054316,-0.831533},{1.188327,1.333609,0.104386},{2.590077,1.673022,-0.039357},{2.801846,3.060185,0.543721},{-1.11243,0.153561,-0.275952},{-1.475525,-0.049993,1.070735},{-2.82142,0.019732,1.452884},{-3.813898,0.2876,0.493168},{-3.459638,0.482293,-0.850408},{-2.110676,0.411393,-1.233822},{3.099843,-3.087102,0.377321},{2.000077,-4.466086,0.071853},{1.755562,-3.424651,1.505126},{1.440153,-2.525111,-1.439665},{0.092481,-2.884973,-0.317441},{2.87361,1.643022,-1.110355},{3.195306,0.918818,0.496684},{2.504373,3.083532,1.604382},{2.204203,3.808653,-0.000776},{3.865985,3.34175,0.474321},{-0.694925,-0.264916,1.80706},{-3.101193,-0.134668,2.499959},{-4.86494,0.339441,0.794258},{-4.232108,0.68587,-1.598506},{-1.83,0.557943,-2.283393}} {C,C,O,P,O,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -29329 145 {{3.184625,3.498202,0.166942},{3.187415,2.136394,0.502671},{2.019462,1.366303,0.387253},{0.834275,1.977941,-0.055658},{-0.362575,1.294937,-0.223909},{-0.733636,-0.08567,0.709081},{-0.271022,-1.326926,-0.375858},{0.972504,-1.930533,-0.229297},{1.777468,-2.035336,-1.374989},{3.026198,-2.66598,-1.28568},{3.477418,-3.181064,-0.05919},{2.66423,-3.070929,1.079641},{1.407262,-2.451314,1.00167},{-2.505279,-0.121547,0.247672},{-3.450984,-0.145478,1.289743},{-4.823741,-0.170806,0.99654},{-5.251875,-0.171551,-0.338889},{-4.309382,-0.147446,-1.382392},{-2.939716,-0.122935,-1.093621},{0.819562,3.341928,-0.394369},{1.995571,4.095024,-0.285104},{4.100744,4.08927,0.25295},{4.107742,1.655919,0.848382},{2.041612,0.300135,0.630185},{1.413986,-1.612944,-2.315393},{3.653226,-2.746071,-2.178847},{4.454305,-3.668257,0.007571},{3.003329,-3.475968,2.038024},{0.764139,-2.372035,1.882427},{-3.113206,-0.144079,2.332207},{-5.555745,-0.189947,1.809517},{-6.321437,-0.191344,-0.569806},{-4.646206,-0.14852,-2.423701},{-2.202156,-0.106024,-1.900673},{-0.117125,3.789115,-0.7377},{1.980033,5.156461,-0.550878}} {C,C,C,C,O,P,O,C,C,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -14388 1012 {{0.015895,2.354182,0.856406},{-0.058296,1.481166,-0.570643},{1.397636,0.384939,-0.282181},{2.271771,0.567138,0.806164},{3.392708,-0.265613,0.955482},{3.651927,-1.278994,0.020817},{2.786358,-1.458462,-1.071409},{1.668754,-0.627756,-1.226034},{-1.418286,0.30647,-0.148801},{-1.294415,-0.717702,0.814193},{-2.382913,-1.551342,1.099109},{-3.600839,-1.378909,0.418113},{-3.731697,-0.367826,-0.54546},{-2.64408,0.473696,-0.82554},{2.068302,1.355925,1.535815},{4.064512,-0.120105,1.80726},{4.526733,-1.925426,0.139273},{2.983102,-2.246357,-1.804998},{0.998648,-0.775859,-2.080902},{-0.341738,-0.861425,1.333547},{-2.282076,-2.342239,1.848867},{-4.44727,-2.036636,0.638832},{-4.678475,-0.233733,-1.077376},{-2.741893,1.266897,-1.575048}} {F,P,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H} \N -29330 145 {{-3.185181,-3.497609,0.166838},{-1.996351,-4.094557,-0.28563},{-0.820145,-3.341744,-0.394705},{-0.834417,-1.977905,-0.055361},{0.362608,-1.295191,-0.22347},{0.733763,0.085614,0.709271},{0.271085,1.326609,-0.375857},{-0.972364,1.930376,-0.229361},{-1.777247,2.035206,-1.375099},{-3.025892,2.666033,-1.285898},{-3.477103,3.181276,-0.059474},{-2.663985,3.071122,1.079404},{-1.4071,2.451326,1.001545},{2.505362,0.121373,0.247713},{2.939693,0.12259,-1.093613},{4.309338,0.147043,-1.38249},{5.251911,0.171267,-0.339065},{4.823882,0.1707,0.996398},{3.451148,0.145422,1.28971},{-2.01938,-1.366146,0.387986},{-3.187536,-2.135958,0.503204},{-4.10146,-4.088454,0.252679},{-1.981148,-5.155873,-0.551907},{0.116364,-3.789036,-0.738382},{-1.413777,1.612684,-2.315448},{-3.652865,2.746138,-2.179101},{-4.453928,3.668605,0.007201},{-3.003074,3.476283,2.037738},{-0.764039,2.372009,1.882345},{2.202072,0.105594,-1.900606},{4.64608,0.147977,-2.423826},{6.321456,0.191017,-0.570068},{5.555948,0.18994,1.809316},{3.113452,0.144166,2.3322},{-2.04119,-0.300106,0.631518},{-4.107677,-1.65538,0.849262}} {C,C,C,C,O,P,O,C,C,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -29269 146 {{4.605086,-0.715271,-0.368209},{3.408847,-1.420552,0.280562},{2.48149,-2.0786,-0.749033},{1.212787,-2.682973,-0.14399},{0.439181,-1.712708,0.597136},{-0.46927,-0.611372,-0.323372},{-1.619732,-0.249878,0.844915},{-2.73457,-1.172738,0.947708},{-3.829126,-0.869845,-0.073799},{-4.425625,0.537039,0.063076},{-5.498886,0.831804,-0.990897},{0.511209,0.92973,-0.069237},{0.817147,1.422887,1.215629},{1.628606,2.55562,1.357219},{2.144272,3.202379,0.219514},{1.841775,2.717682,-1.061509},{1.025273,1.583791,-1.203829},{5.265173,-0.261409,0.389606},{5.21293,-1.416571,-0.967184},{4.264832,0.092681,-1.039395},{3.762581,-2.190097,0.993344},{2.825651,-0.693446,0.871464},{2.190697,-1.331369,-1.513734},{3.021041,-2.87951,-1.291866},{0.588101,-3.140038,-0.937424},{1.4646,-3.466276,0.592428},{-3.11303,-1.042247,1.976619},{-2.373269,-2.214176,0.853937},{-3.416641,-1.005253,-1.092258},{-4.625288,-1.631057,0.04395},{-3.610657,1.278721,-0.009953},{-4.855547,0.650266,1.077013},{-5.083739,0.757265,-2.011311},{-6.337159,0.116149,-0.921322},{-5.914125,1.846474,-0.872679},{0.41457,0.911823,2.095181},{1.864471,2.936406,2.356114},{2.781795,4.084602,0.334191},{2.239102,3.221403,-1.948214},{0.787641,1.201203,-2.203556}} {C,C,C,C,O,P,O,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -29270 146 {{2.183031,4.21508,-0.985308},{1.360379,3.434406,0.045719},{2.027299,2.116307,0.457591},{1.237691,1.313969,1.492264},{-0.107997,0.966312,1.083062},{-0.300542,0.117502,-0.355692},{0.297014,-1.37638,0.184106},{0.806141,-2.282236,-0.819776},{2.138919,-2.866475,-0.361475},{3.277031,-1.839088,-0.301147},{4.603597,-2.444495,0.171145},{-2.116888,-0.1136,-0.139217},{-2.67036,-0.648438,1.041914},{-4.05406,-0.837095,1.144919},{-4.895162,-0.495836,0.070109},{-4.350227,0.032661,-1.109299},{-2.962135,0.22035,-1.213426},{3.183777,4.467285,-0.592188},{2.327477,3.622926,-1.905956},{1.687004,5.158137,-1.268943},{1.197275,4.055107,0.947473},{0.357036,3.218282,-0.362736},{2.204061,1.492836,-0.440273},{3.026304,2.318008,0.891266},{1.776772,0.38752,1.7646},{1.093881,1.908592,2.410883},{0.930874,-1.748906,-1.785186},{0.057569,-3.082318,-0.97002},{1.997848,-3.331356,0.632508},{2.410037,-3.684801,-1.05671},{2.981793,-1.017157,0.374785},{3.408214,-1.38508,-1.302382},{5.405152,-1.687958,0.20562},{4.504985,-2.874775,1.183094},{4.935854,-3.254338,-0.50197},{-2.008441,-0.910557,1.872655},{-4.482316,-1.250663,2.06364},{-5.976269,-0.644904,0.15406},{-5.003511,0.297832,-1.946399},{-2.530918,0.631234,-2.133855}} {C,C,C,C,O,P,O,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -27388 238 {{-5.543963,-1.008514,-0.210339},{-4.314829,-1.897163,0.016138},{-3.0264,-1.087718,0.219058},{-1.805872,-1.978344,0.445234},{-0.595194,-1.224383,0.683984},{0.128523,-0.54403,-0.696799},{-0.05956,1.256865,-0.322485},{-0.659676,1.722373,0.862941},{-0.80481,3.10045,1.088957},{-0.350409,4.024993,0.13596},{0.247766,3.566502,-1.049937},{0.385277,2.190871,-1.280839},{1.900032,-0.784225,-0.222886},{2.560296,-0.007952,0.751284},{3.895298,-0.276359,1.083618},{4.587347,-1.3172,0.44198},{3.940993,-2.090885,-0.534218},{2.604339,-1.822684,-0.865977},{-6.457145,-1.609637,-0.353681},{-5.414733,-0.373727,-1.103969},{-5.713511,-0.338675,0.650474},{-4.483323,-2.545292,0.897482},{-4.1866,-2.578475,-0.846499},{-2.846936,-0.446934,-0.665864},{-3.140391,-0.406382,1.082603},{-1.663182,-2.659068,-0.417872},{-1.937322,-2.598737,1.349071},{-1.003461,0.994883,1.604295},{-1.27132,3.452181,2.014875},{-0.464642,5.098783,0.313313},{0.601158,4.282181,-1.798916},{0.845333,1.839295,-2.211817},{2.026808,0.809638,1.245827},{4.399274,0.330185,1.842811},{5.631267,-1.521048,0.700014},{4.47835,-2.898853,-1.040462},{2.099098,-2.420873,-1.632494}} {C,C,C,C,O,P,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -27389 238 {{4.915495,-1.865639,-0.836686},{4.634719,-1.00415,0.403431},{3.204159,-0.440384,0.469615},{2.133104,-1.515685,0.653931},{0.809599,-0.953535,0.815815},{0.043442,-0.459929,-0.620183},{-1.683404,-0.973871,-0.201242},{-2.516058,-0.267517,0.690476},{-3.801221,-0.743216,0.985444},{-4.271383,-1.924793,0.388399},{-3.452775,-2.631307,-0.506148},{-2.166488,-2.155064,-0.801031},{-0.085369,1.360649,-0.325149},{-0.624585,2.168573,-1.347438},{-0.728547,3.555928,-1.176771},{-0.280149,4.1544,0.012774},{0.267384,3.357185,1.029743},{0.363906,1.966437,0.863694},{4.303482,-2.782848,-0.852479},{5.972913,-2.1761,-0.873795},{4.697029,-1.305524,-1.762714},{4.838436,-1.592063,1.319302},{5.34369,-0.157013,0.423123},{3.122574,0.274882,1.307732},{2.986551,0.129978,-0.454344},{2.316057,-2.088794,1.580265},{2.13324,-2.226782,-0.193923},{-2.156424,0.658126,1.1503},{-4.439868,-0.189044,1.680631},{-5.27713,-2.291032,0.616943},{-3.817438,-3.548968,-0.978133},{-1.528207,-2.700685,-1.505013},{-0.968267,1.708494,-2.281341},{-1.153162,4.172336,-1.975387},{-0.354325,5.238351,0.143469},{0.617918,3.818282,1.958821},{0.781784,1.336346,1.654499}} {C,C,C,C,O,P,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -27137 247 {{3.3772,0.982853,0.63098},{2.637457,0.362163,-0.559074},{1.354973,-0.266213,-0.176192},{1.372015,-1.731847,-0.290526},{2.266528,-2.388977,0.765255},{-0.06368,0.498139,-0.959914},{0.098584,2.177419,-0.131082},{-1.067274,3.090605,-0.529927},{-1.356341,-0.204541,-0.071933},{-1.351774,-0.344468,1.387582},{-2.355885,0.56604,2.10858},{-2.463561,-0.826961,-0.804804},{-2.399468,-2.358685,-0.895243},{3.584867,0.223468,1.401767},{4.336689,1.42477,0.308077},{2.770446,1.774705,1.099087},{3.281834,-0.395546,-1.047687},{2.472473,1.137667,-1.335147},{1.692692,-2.05958,-1.307504},{0.337358,-2.087167,-0.154644},{3.32473,-2.102907,0.643625},{1.947181,-2.093965,1.778686},{2.208848,-3.487736,0.682639},{1.056325,2.628112,-0.444163},{0.151132,2.035887,0.963768},{-1.085115,3.264944,-1.619149},{-0.992302,4.07219,-0.032422},{-2.035928,2.643012,-0.250864},{-1.554519,-1.401151,1.655385},{-0.324645,-0.138328,1.736154},{-2.122894,1.628455,1.933533},{-2.328496,0.381271,3.196555},{-3.388668,0.384935,1.766443},{-2.467702,-0.399926,-1.822352},{-3.419373,-0.520783,-0.336164},{-3.298625,-2.751157,-1.400829},{-2.348687,-2.827592,0.101974},{-1.515784,-2.679235,-1.471616}} {C,C,N,C,C,P,C,C,N,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -27138 247 {{2.15368,-2.582674,-0.512397},{1.37085,-1.446782,-1.177966},{1.280913,-0.24177,-0.336544},{2.557291,0.486174,-0.210705},{3.236055,0.285647,1.150671},{-0.155391,0.742029,-0.734406},{-0.002227,2.041267,0.632842},{0.391624,3.431166,0.112934},{-1.354842,-0.348899,-0.140376},{-2.628686,-0.405892,-0.862426},{-3.729387,0.510807,-0.30707},{-1.335302,-0.815962,1.249912},{-1.716105,-2.293597,1.398664},{2.122857,-3.485635,-1.145991},{3.214143,-2.320089,-0.362842},{1.718861,-2.827558,0.471171},{0.338407,-1.787517,-1.367888},{1.826164,-1.211503,-2.167776},{2.402089,1.568366,-0.37499},{3.243275,0.165308,-1.021558},{3.432756,-0.780147,1.346077},{4.196527,0.829886,1.189717},{2.594656,0.658747,1.965935},{0.679027,1.696161,1.430097},{-1.012434,2.087931,1.078094},{0.357473,4.182533,0.920269},{-0.2914,3.762542,-0.687487},{1.412123,3.444386,-0.306701},{-2.415999,-0.131149,-1.910447},{-2.989639,-1.452551,-0.877787},{-4.652787,0.41001,-0.90286},{-3.41148,1.566916,-0.34211},{-3.979829,0.263874,0.738433},{-1.995475,-0.195979,1.894253},{-0.301514,-0.679073,1.609524},{-1.597928,-2.608511,2.449248},{-1.065269,-2.925205,0.771293},{-2.76299,-2.488419,1.112107}} {C,C,N,C,C,P,C,C,N,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -26826 267 {{-0.000505,2.48188,2.370169},{-1.339017,2.217365,1.684442},{-1.319551,2.628276,-0.126614},{-0.933494,0.863457,-1.246417},{-2.175054,-0.386034,-0.684935},{-1.936675,-1.749172,-0.963483},{-2.917085,-2.711123,-0.689291},{-4.154563,-2.325816,-0.148386},{-4.404991,-0.970439,0.110145},{-3.423996,-0.00392,-0.159839},{0.637159,0.157384,-0.523245},{0.771604,-0.568016,0.67636},{-0.292097,-0.796908,1.479592},{2.000517,-1.077884,1.113729},{2.087665,-1.764886,2.270789},{3.154753,-0.85431,0.350577},{4.340195,-1.331905,0.766055},{3.066992,-0.129647,-0.844816},{4.173786,0.085998,-1.581793},{1.821659,0.360329,-1.258992},{1.789206,1.050294,-2.420055},{0.291854,3.539787,2.276326},{-0.0718,2.23701,3.444348},{0.804799,1.871041,1.933841},{-1.667512,1.173541,1.798461},{-2.131681,2.862091,2.100558},{-0.977426,-2.065355,-1.388159},{-2.713313,-3.765457,-0.899804},{-4.918982,-3.078331,0.066276},{-5.367808,-0.659129,0.526996},{-3.626492,1.053597,0.03735}} {C,C,S,P,C,C,C,C,C,C,C,C,F,C,F,C,F,C,F,C,F,H,H,H,H,H,H,H,H,H,H} \N -26827 267 {{-0.90545,2.467952,1.867378},{-2.069495,2.416174,0.883345},{-1.605846,2.389719,-0.905597},{-0.949298,0.420264,-1.401379},{-2.061219,-0.59739,-0.330272},{-1.7595,-1.012773,0.98144},{-2.694583,-1.746782,1.725874},{-3.944335,-2.064707,1.172745},{-4.255306,-1.649025,-0.131856},{-3.31883,-0.922864,-0.880362},{0.716842,0.086506,-0.608145},{1.148893,-1.255595,-0.575217},{0.313117,-2.238924,-0.991453},{2.420544,-1.644055,-0.141213},{2.771547,-2.945449,-0.112752},{3.338627,-0.662564,0.254392},{4.569484,-1.011855,0.669791},{2.966346,0.685422,0.199955},{3.848917,1.637934,0.563506},{1.681477,1.042176,-0.236848},{1.418848,2.366076,-0.28913},{-0.297799,1.550843,1.817984},{-0.244068,3.324971,1.668682},{-1.294162,2.556414,2.897001},{-2.725254,1.550797,1.074451},{-2.692013,3.324904,0.955132},{-0.789458,-0.76725,1.424088},{-2.445367,-2.066122,2.742456},{-4.672572,-2.636932,1.755095},{-5.225617,-1.897823,-0.572001},{-3.561958,-0.604145,-1.8996}} {C,C,S,P,C,C,C,C,C,C,C,C,F,C,F,C,F,C,F,C,F,H,H,H,H,H,H,H,H,H,H} \N -26736 272 {{-5.068113,-0.527431,0.190819},{-3.746744,-1.215129,0.555086},{-2.560609,-0.710217,-0.279204},{-1.232954,-1.388993,0.078173},{0.220187,-0.683128,-0.876},{1.560698,-1.763157,-0.116459},{2.967522,-1.529544,-0.69777},{3.669563,-0.242271,-0.226012},{4.063588,-0.2619,1.256973},{0.404611,0.876326,-0.150393},{0.564164,2.030716,-1.04198},{-0.756301,2.618254,-1.558994},{0.569463,1.113402,1.280515},{-0.548956,1.94306,1.928965},{-5.002142,0.564213,0.342915},{-5.325632,-0.698381,-0.869061},{-5.904825,-0.901825,0.803971},{-3.846655,-2.309634,0.423676},{-3.52729,-1.055375,1.628547},{-2.458598,0.383144,-0.143047},{-2.773574,-0.863405,-1.354499},{-1.27985,-2.468656,-0.159692},{-1.043339,-1.315367,1.167822},{1.562534,-1.686851,0.987738},{1.236983,-2.795756,-0.348184},{3.610429,-2.393355,-0.437168},{2.895626,-1.520685,-1.8014},{4.580234,-0.097684,-0.83602},{3.018973,0.627353,-0.428153},{4.583685,0.666762,1.546123},{4.740586,-1.107121,1.474441},{3.184859,-0.363775,1.915761},{1.188205,1.739267,-1.908286},{1.135956,2.805111,-0.494373},{-1.308601,1.856501,-2.134291},{-0.567957,3.480498,-2.223081},{-1.401342,2.951258,-0.729796},{1.546418,1.612323,1.46385},{0.629778,0.135979,1.789246},{-1.528682,1.456446,1.792235},{-0.605626,2.953301,1.491444},{-0.363156,2.057612,3.01135}} {C,C,C,C,P,C,C,C,C,N,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -26737 272 {{0.569207,4.18085,1.265074},{0.421293,3.447522,-0.073583},{0.255308,1.929681,0.093156},{0.092054,1.195381,-1.242853},{0.081953,-0.682448,-1.222102},{-1.239091,-0.97167,0.081583},{-2.628074,-0.494478,-0.364788},{-3.742953,-0.909862,0.607516},{-5.127708,-0.411713,0.177296},{1.517147,-0.997602,-0.197351},{1.591534,-2.418624,0.214205},{1.515947,-2.597193,1.73389},{2.779154,-0.510769,-0.778717},{3.896243,-0.408174,0.264866},{1.447811,3.813181,1.823487},{0.692053,5.267532,1.122794},{-0.317749,4.0243,1.903772},{1.306741,3.647671,-0.707239},{-0.44769,3.853008,-0.626778},{-0.623539,1.733804,0.735695},{1.123781,1.513697,0.636315},{0.8801,1.504393,-1.954353},{-0.858048,1.477635,-1.735672},{-1.27247,-2.06061,0.267753},{-0.936943,-0.490377,1.029118},{-2.633011,0.608038,-0.462402},{-2.856685,-0.89307,-1.372555},{-3.752746,-2.013015,0.694585},{-3.504226,-0.524655,1.617222},{-5.151836,0.690349,0.114135},{-5.910331,-0.723351,0.888898},{-5.401095,-0.806773,-0.816699},{2.52927,-2.865585,-0.172333},{0.778322,-3.000101,-0.266752},{2.333884,-2.05457,2.234391},{1.587947,-3.66561,2.004959},{0.565348,-2.202407,2.126949},{2.603303,0.493087,-1.199583},{3.117245,-1.153961,-1.625085},{4.809568,0.005167,-0.195699},{4.154651,-1.393262,0.687233},{3.589544,0.249689,1.094965}} {C,C,C,C,P,C,C,C,C,N,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -26380 297 {{-0.786569,-2.686745,-0.452794},{-1.605615,-1.475719,0.03554},{-1.580035,-1.430555,1.571229},{-3.06531,-1.658099,-0.440187},{-0.927516,0.032219,-0.958666},{0.809655,-0.118813,-0.955488},{2.288586,-0.116474,0.025716},{2.06854,-0.798552,1.774717},{3.484527,-1.239768,-0.922689},{3.082556,1.604935,0.11945},{-1.262184,1.64079,0.0226},{-2.787079,1.799879,0.178935},{-0.578675,1.79112,1.390748},{-0.73956,2.755308,-0.911389},{-1.236397,-3.61779,-0.061184},{-0.777127,-2.752695,-1.554884},{0.259511,-2.634664,-0.113112},{-1.943314,-2.395802,1.973802},{-0.567109,-1.268681,1.966943},{-2.240614,-0.645359,1.972473},{-3.482311,-2.586683,-0.007518},{-3.71536,-0.826046,-0.125583},{-3.123214,-1.73531,-1.538587},{1.076993,-0.263526,-1.932721},{3.05746,-0.807981,2.266139},{1.689977,-1.83342,1.764249},{1.396763,-0.187152,2.396844},{3.639781,-0.883003,-1.955976},{4.472457,-1.264628,-0.431731},{3.101713,-2.272843,-0.974284},{4.070844,1.544801,0.608792},{3.233951,2.009843,-0.895897},{2.473836,2.332433,0.680277},{-3.312689,1.653228,-0.780486},{-3.205196,1.093225,0.913991},{-3.017289,2.82077,0.535784},{-0.787275,2.79894,1.797955},{-0.932573,1.055863,2.126725},{0.514067,1.699811,1.306321},{-0.932721,3.744423,-0.455959},{0.346309,2.660052,-1.076653},{-1.239102,2.725663,-1.894307}} {C,C,C,C,P,N,Si,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -26381 297 {{2.989481,1.536718,0.494264},{1.53874,1.57241,-0.015856},{1.513683,1.84449,-1.529053},{0.790818,2.721559,0.695794},{0.585926,-0.002616,0.549241},{-0.769455,0.013372,-0.527157},{-2.460048,-0.007052,-0.01055},{-2.881999,1.554527,0.969094},{-3.47178,-0.082319,-1.607437},{-2.819898,-1.506865,1.082595},{1.553867,-1.562849,-0.022549},{0.533631,-2.715504,0.085965},{2.113006,-1.526181,-1.452861},{2.68664,-1.831291,0.989302},{3.448445,2.535833,0.375878},{3.040811,1.272747,1.56502},{3.610324,0.821797,-0.069119},{0.479233,1.908547,-1.907},{2.05302,1.081454,-2.109786},{1.99391,2.819305,-1.735838},{1.263758,3.689007,0.443003},{0.8145,2.603086,1.792008},{-0.264236,2.767771,0.379806},{-0.587897,0.012572,-1.535182},{-2.767727,2.460048,0.34974},{-2.214262,1.652904,1.841725},{-3.921253,1.521023,1.339648},{-4.551854,-0.083081,-1.382677},{-3.24888,-0.998088,-2.181134},{-3.266514,0.788201,-2.253774},{-2.658729,-2.45164,0.53789},{-2.157525,-1.505925,1.96476},{-3.863318,-1.488407,1.442205},{-0.285856,-2.599128,-0.640651},{0.087013,-2.768622,1.093575},{1.042833,-3.676615,-0.112344},{2.934664,-0.800277,-1.559325},{2.515191,-2.520749,-1.724252},{1.332745,-1.279657,-2.194292},{3.489165,-1.080309,0.937811},{2.301059,-1.847964,2.023044},{3.142207,-2.817645,0.782891}} {C,C,C,C,P,N,Si,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -26259 307 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{C,O,C,C,C,C,C,C,C,C,C,C,C,C,C,C,N,P,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -26260 307 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{C,O,C,C,C,C,C,C,C,C,C,C,C,C,C,C,N,P,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -26011 316 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{C,C,C,C,C,C,C,C,C,C,C,C,C,C,C,N,P,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -26012 316 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{C,C,C,C,C,C,C,C,C,C,C,C,C,C,C,N,P,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -25925 318 {{1.703749,-3.290653,0.872796},{1.700585,-2.472766,-0.423334},{1.753485,-1.016212,-0.182809},{3.025253,-0.40748,-0.600141},{4.191659,-0.814868,0.305663},{0.312503,-0.128812,-0.77971},{-0.958869,-0.948169,0.316401},{-2.750546,-0.455861,-0.1177},{-2.943982,1.399861,-0.445828},{-3.252153,-1.40776,-1.677724},{-3.865097,-0.954409,1.334279},{0.55096,1.388232,-0.007156},{0.45722,2.613777,-0.802952},{1.787538,3.351334,-1.011649},{0.886377,1.519225,1.412765},{-0.236503,2.104827,2.280771},{1.680161,-4.373255,0.654221},{2.604857,-3.074441,1.468849},{0.827883,-3.04082,1.493258},{2.561912,-2.76824,-1.054813},{0.805424,-2.736151,-1.023443},{3.270181,-0.656727,-1.659353},{2.899099,0.686814,-0.551204},{4.390453,-1.898707,0.257148},{5.114314,-0.294472,-0.003329},{3.973711,-0.554185,1.354741},{-0.7215,-0.759421,1.379336},{-0.904653,-2.042415,0.168488},{-2.350301,1.709976,-1.321431},{-4.002008,1.637864,-0.651528},{-2.617472,2.007043,0.41362},{-3.211861,-2.498049,-1.511843},{-2.572058,-1.166983,-2.512583},{-4.278761,-1.151023,-1.99008},{-4.924754,-0.740368,1.112045},{-3.776386,-2.031892,1.554584},{-3.59458,-0.4005,2.249774},{0.040725,2.329469,-1.784901},{-0.280055,3.302056,-0.342437},{2.252351,3.646244,-0.056097},{1.62209,4.272767,-1.595802},{2.505106,2.721,-1.562755},{1.795799,2.144102,1.519697},{1.172383,0.516215,1.774226},{0.101121,2.202914,3.327006},{-0.541252,3.106925,1.935162},{-1.127603,1.456858,2.266378}} {C,C,N,C,C,P,C,Si,C,C,C,N,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -25926 318 {{1.494795,-3.397869,0.007457},{1.643802,-2.328391,1.108145},{1.729274,-0.925635,0.682143},{3.079368,-0.427728,0.390395},{3.76362,-0.916199,-0.900093},{0.452311,-0.270054,-0.38363},{-1.027407,-0.832041,0.608419},{-2.685921,-0.437145,-0.248941},{-2.935891,-1.723044,-1.618893},{-4.063768,-0.589659,1.046429},{-2.74212,1.292188,-1.018667},{0.562997,1.400137,0.026625},{0.716293,2.381042,-1.048948},{2.151396,2.88295,-1.267519},{0.673555,1.884851,1.403182},{-0.576945,2.612165,1.918254},{1.427715,-4.40314,0.459626},{0.579238,-3.236521,-0.587307},{2.344921,-3.391291,-0.691566},{0.800132,-2.427262,1.815176},{2.555551,-2.53739,1.698922},{3.016385,0.674432,0.363292},{3.713485,-0.677975,1.263121},{3.114177,-0.745921,-1.775342},{4.708832,-0.368257,-1.061281},{4.004145,-1.990683,-0.857704},{-0.979385,-0.426899,1.63611},{-1.004759,-1.933897,0.695777},{-2.983302,-2.745244,-1.20558},{-3.870504,-1.539854,-2.175889},{-2.099133,-1.686454,-2.337506},{-5.056128,-0.433035,0.589525},{-3.939504,0.160598,1.846368},{-4.061609,-1.587345,1.517608},{-2.529951,2.079787,-0.278476},{-2.003222,1.387303,-1.830974},{-3.742611,1.47994,-1.445647},{0.352075,1.91093,-1.978886},{0.044462,3.24024,-0.85348},{2.809023,2.057445,-1.586783},{2.576405,3.3265,-0.351285},{2.171116,3.659478,-2.051654},{1.549991,2.558982,1.487607},{0.905353,1.012482,2.040062},{-0.407775,2.989684,2.941771},{-0.835671,3.476322,1.283196},{-1.447306,1.93678,1.940482}} {C,C,N,C,C,P,C,Si,C,C,C,N,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -23597 449 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{{-3.528931,-0.266113,-0.454221},{-2.761982,-1.57126,-0.657263},{-1.294371,-1.766662,0.451642},{0.121782,-0.600324,-0.690794},{1.802188,-1.600212,0.277225},{3.171067,-0.708421,-0.585771},{3.645381,0.551932,0.136437},{0.032672,0.99659,-0.054141},{0.148688,1.321105,1.375361},{-1.192131,1.568837,2.079086},{0.256069,2.088384,-1.012654},{-0.820084,3.178813,-0.982504},{-2.889051,0.605808,-0.66264},{-4.401164,-0.227257,-1.130779},{-3.891732,-0.176339,0.58246},{-2.417523,-1.681204,-1.699338},{-3.394826,-2.444703,-0.427029},{3.985644,-1.44797,-0.661483},{2.839499,-0.485047,-1.615352},{4.488148,1.013056,-0.408964},{2.836847,1.295422,0.211037},{3.982826,0.317427,1.15872},{0.803207,2.210109,1.471248},{0.680073,0.488492,1.872184},{-1.75081,2.398124,1.617628},{-1.814456,0.662819,2.034189},{-1.017648,1.818889,3.140014},{0.296134,1.636643,-2.020151},{1.250591,2.550177,-0.83069},{-0.839499,3.705443,-0.014778},{-0.615438,3.928588,-1.765603},{-1.819794,2.75057,-1.162481}} {C,C,S,P,S,C,C,N,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -20774 577 {{1.805461,-2.649787,1.132954},{1.353619,-3.469008,0.0468},{0.729138,-2.639098,-0.865937},{0.775662,-1.333618,-0.369173},{-0.000468,-0.000109,-1.200598},{0.767007,1.338575,-0.369377},{1.920765,1.950741,-0.866718},{2.328188,2.906117,0.046015},{1.393498,2.887851,1.132772},{0.445567,1.917237,0.861411},{-1.543186,-0.004935,-0.368848},{-1.882661,-0.571296,0.862804},{-3.197487,-0.236694,1.134049},{-3.681793,0.561613,0.046305},{-2.651083,0.686323,-0.866866},{1.438202,-1.343798,0.861256},{2.356185,-2.979452,2.012942},{1.485597,-4.544573,-0.060016},{0.252861,-2.850295,-1.821649},{2.341224,1.643883,-1.822693},{3.193847,3.557893,-0.061175},{1.404413,3.529395,2.012917},{-0.439577,1.597214,1.406753},{-1.16193,-1.176146,1.408682},{-3.757983,-0.547352,2.01478},{-4.67958,0.984133,-0.061237},{-2.596418,1.202443,-1.823666},{1.603527,-0.416867,1.406029}} {C,C,C,N,P,N,C,C,C,C,N,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H} \N -20775 577 {{1.076626,3.019104,1.133612},{2.004329,3.137688,0.047173},{1.70132,2.144982,-0.866382},{0.619194,1.413022,-0.36988},{-0.000398,-8.1e-05,-1.201297},{-1.533732,-0.169886,-0.369399},{-2.708793,0.401179,-0.865799},{-3.72006,0.166449,0.047479},{-3.153451,-0.578103,1.133597},{-1.810712,-0.771211,0.861337},{0.913861,-1.242872,-0.369645},{1.006727,-2.546139,-0.865804},{1.716139,-3.304317,0.047292},{2.078039,-2.441082,1.13307},{1.573626,-1.181794,0.860831},{0.237598,1.95318,0.861247},{1.018883,3.657506,2.014233},{2.79559,3.878144,-0.059283},{2.152325,1.885343,-1.822436},{-2.709513,0.922047,-1.821603},{-4.757006,0.48128,-0.058949},{-3.677496,-0.947918,2.013936},{-1.029823,-1.297424,1.405988},{0.555673,-2.807365,-1.821408},{1.962078,-4.359733,-0.059084},{2.660794,-2.709773,2.013177},{1.639256,-0.242322,1.405316},{-0.60839,1.539971,1.406113}} {C,C,C,N,P,N,C,C,C,C,N,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H} \N -20645 586 {{-4.717703,-1.102104,-1.508706},{-4.36896,-1.966796,-0.458898},{-3.493643,-1.536485,0.548203},{-2.96687,-0.230789,0.504256},{-1.856614,0.326982,1.798371},{0.137313,-0.038714,1.019735},{0.201952,0.890486,-0.943607},{0.895811,2.475424,-0.464977},{0.189854,3.350043,0.384974},{0.746716,4.59256,0.722076},{1.990996,4.977537,0.199015},{2.687397,4.108878,-0.656602},{2.149769,2.855087,-0.980852},{-0.099864,-2.092772,0.376805},{1.642224,-2.428672,0.072355},{2.134555,-2.391402,-1.245538},{3.482094,-2.691625,-1.493495},{4.338485,-3.024147,-0.432146},{3.84537,-3.059792,0.882076},{2.498273,-2.766176,1.13789},{-3.318999,0.640314,-0.545064},{-4.192882,0.198913,-1.549378},{-5.400149,-1.44177,-2.293588},{-4.776228,-2.981728,-0.423491},{-3.21193,-2.204193,1.366991},{-0.787037,3.055486,0.779944},{0.199047,5.26477,1.389692},{2.417346,5.951303,0.457663},{3.660101,4.401287,-1.063873},{2.6971,2.163534,-1.627807},{1.461379,-2.119144,-2.062815},{3.862907,-2.661992,-2.518925},{5.389487,-3.25634,-0.628668},{4.509417,-3.319793,1.711982},{2.103504,-2.797125,2.157301},{-2.904389,1.650855,-0.571048},{-4.462753,0.875819,-2.365599}} {C,C,C,C,S,P,S,C,C,C,C,C,C,S,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -20646 586 {{-0.000967,4.72882,-0.807742},{1.214703,4.135082,-0.433454},{1.220156,2.949065,0.314427},{-0.000282,2.354558,0.693136},{0.000141,0.847297,1.654074},{0.000169,-0.748621,0.13805},{1.580112,-0.20939,-1.238604},{2.937077,-1.06276,-0.42507},{3.36878,-0.699235,0.86566},{4.459931,-1.363138,1.444947},{5.138077,-2.367686,0.736945},{4.714366,-2.717422,-0.554756},{3.609579,-2.076292,-1.133944},{-1.579937,-0.209564,-1.238464},{-2.936735,-1.063221,-0.424959},{-3.609364,-2.076497,-1.134076},{-4.714047,-2.717837,-0.55492},{-5.137521,-2.368573,0.736987},{-4.459245,-1.364283,1.445227},{-3.368202,-0.700162,0.865983},{-1.221064,2.948548,0.314722},{-1.216294,4.134569,-0.433158},{-0.001233,5.655005,-1.39025},{2.164257,4.593744,-0.725222},{2.163341,2.480299,0.606066},{2.847495,0.089643,1.415006},{4.785329,-1.084572,2.451921},{5.994266,-2.876029,1.190118},{5.235788,-3.502031,-1.111429},{3.260664,-2.358466,-2.13131},{-3.260625,-2.358319,-2.131603},{-5.235566,-3.502247,-1.111782},{-5.993624,-2.877084,1.190133},{-4.784457,-1.086082,2.452362},{-2.846832,0.088529,1.415518},{-2.16398,2.479383,0.60659},{-2.166113,4.592829,-0.724696}} {C,C,C,C,S,P,S,C,C,C,C,C,C,S,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -20614 587 {{-3.399937,3.262305,-0.771091},{-2.281442,4.041035,-0.435743},{-1.146912,3.441004,0.131144},{-1.137061,2.055908,0.381809},{0.306459,1.338992,1.178727},{0.876063,-0.085688,-0.35141},{0.617301,-2.049149,0.550209},{-1.128948,-2.254086,0.195617},{-1.610812,-2.30387,-1.127309},{-2.985168,-2.442187,-1.36461},{-3.883714,-2.547842,-0.289485},{-3.402102,-2.510958,1.028082},{-2.028826,-2.355171,1.274148},{2.726361,-0.033907,-0.212503},{3.47804,-1.133001,-0.688298},{4.877074,-1.069682,-0.735231},{5.549135,0.089664,-0.317486},{4.809666,1.187546,0.145964},{3.409045,1.130734,0.196378},{-2.264316,1.275497,0.061514},{-3.384864,1.880173,-0.525359},{-4.279832,3.730957,-1.221863},{-2.283275,5.1185,-0.627051},{-0.265006,4.040226,0.375162},{-0.909331,-2.220947,-1.962059},{-3.354458,-2.471045,-2.394306},{-4.955437,-2.659219,-0.479413},{-4.096391,-2.586833,1.87039},{-1.648201,-2.293878,2.297478},{2.968958,-2.045082,-1.013808},{5.442538,-1.933483,-1.098082},{6.641705,0.135838,-0.3527},{5.322583,2.096095,0.476391},{2.842155,1.99118,0.562828},{-2.266212,0.202949,0.270552},{-4.252218,1.263608,-0.780599}} {C,C,C,C,S,P,S,C,C,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -20615 587 {{-3.399941,3.262194,-0.771056},{-2.281317,4.040885,-0.43605},{-1.146785,3.440872,0.130851},{-1.137061,2.055839,0.381868},{0.306473,1.338942,1.178781},{0.876102,-0.085649,-0.351429},{0.617287,-2.049155,0.550065},{-1.128981,-2.25401,0.19552},{-1.610916,-2.303633,-1.127386},{-2.985284,-2.441899,-1.364631},{-3.883779,-2.547665,-0.289475},{-3.4021,-2.510946,1.028072},{-2.028808,-2.35521,1.274086},{2.726396,-0.033911,-0.212496},{3.409099,1.130658,0.196558},{4.809722,1.187446,0.146171},{5.549174,0.089612,-0.317422},{4.877093,-1.069661,-0.735338},{3.478058,-1.132955,-0.688436},{-2.264441,1.275471,0.061913},{-3.384995,1.880123,-0.524972},{-4.27984,3.73083,-1.221839},{-2.283054,5.118302,-0.627633},{-0.26478,4.040054,0.374613},{-0.909478,-2.220621,-1.962164},{-3.354627,-2.470627,-2.394312},{-4.955514,-2.659002,-0.479363},{-4.096345,-2.586916,1.870408},{-1.64813,-2.294052,2.297405},{2.842222,1.991064,0.563123},{5.322655,2.095938,0.476731},{6.641745,0.135767,-0.352614},{5.442543,-1.933423,-1.098302},{2.96896,-2.044979,-1.014081},{-2.266423,0.202973,0.27122},{-4.252448,1.263589,-0.779952}} {C,C,C,C,S,P,S,C,C,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -14391 1011 {{1.777152,-0.04496,1.520692},{1.566767,0.233818,0.023136},{1.564871,1.746149,-0.264242},{2.715258,-0.43064,-0.773528},{-0.000979,-0.544886,-0.736451},{0.025687,-1.979696,0.141771},{-1.565942,0.224411,0.027771},{-1.533394,0.531577,1.531534},{-2.66749,-0.823486,-0.256385},{-1.878952,1.499881,-0.783072},{2.792028,0.284716,1.810825},{1.059351,0.493389,2.155319},{1.695165,-1.120669,1.742715},{2.567779,2.160555,-0.05405},{1.333607,1.968081,-1.32152},{0.843869,2.286494,0.370083},{3.685167,-0.026099,-0.430351},{2.626843,-0.237503,-1.855795},{2.733328,-1.522918,-0.621012},{-0.850543,1.362896,1.768167},{-1.231522,-0.350284,2.119367},{-2.543676,0.830362,1.868632},{-3.64877,-0.406315,0.034668},{-2.716097,-1.085716,-1.327492},{-2.503101,-1.749651,0.316406},{-1.161002,2.311701,-0.587173},{-2.882552,1.86983,-0.504608},{-1.885987,1.301171,-1.868801}} {C,C,C,C,P,F,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -20459 591 {{-1.815736,3.043028,-1.451377},{-0.431953,3.070119,-1.211725},{0.105295,2.420405,-0.090988},{-0.745805,1.726902,0.792739},{-0.095974,0.864412,2.225753},{0.544227,-1.072354,1.476121},{1.924453,-0.666326,0.309923},{2.867504,0.330307,0.638184},{4.001455,0.533774,-0.160292},{4.221289,-0.264446,-1.294285},{3.301866,-1.274132,-1.616628},{2.165987,-1.479294,-0.819104},{-0.828218,-1.519136,0.324788},{-1.777635,-2.448393,0.800405},{-2.880603,-2.808456,0.012393},{-3.043487,-2.246338,-1.263778},{-2.104118,-1.320644,-1.745297},{-1.005338,-0.954007,-0.956165},{-2.13342,1.699633,0.550635},{-2.664586,2.361499,-0.565537},{-2.2306,3.55454,-2.32526},{0.234372,3.602838,-1.897322},{1.181339,2.439387,0.096256},{2.700153,0.957686,1.520044},{4.71572,1.319569,0.105542},{5.104963,-0.103526,-1.919087},{3.465247,-1.906574,-2.494888},{1.459526,-2.271778,-1.084687},{-1.646849,-2.888595,1.79493},{-3.608035,-3.532502,0.392105},{-3.901159,-2.529211,-1.882},{-2.23181,-0.870922,-2.734834},{-0.28566,-0.222004,-1.332874},{-2.783614,1.1455,1.233191},{-3.743136,2.33334,-0.748322}} {C,C,C,C,S,P,C,C,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -20460 591 {{-1.81709,3.042292,-1.451511},{-0.433265,3.069729,-1.212141},{0.104355,2.420302,-0.091417},{-0.746412,1.726736,0.792579},{-0.096135,0.86468,2.225649},{0.544592,-1.072006,1.476242},{1.924737,-0.665781,0.310012},{2.867423,0.33128,0.638008},{4.001335,0.5349,-0.160486},{4.221495,-0.263588,-1.294222},{3.30244,-1.273695,-1.616295},{2.166602,-1.479009,-0.818757},{-0.827698,-1.519241,0.324905},{-1.776956,-2.448629,0.800575},{-2.879774,-2.809044,0.012515},{-3.042654,-2.247159,-1.263758},{-2.103447,-1.321326,-1.745323},{-1.004829,-0.954328,-0.95614},{-2.134063,1.699103,0.550748},{-2.665604,2.360687,-0.565411},{-2.232244,3.55359,-2.325378},{0.2328,3.602505,-1.897945},{1.180432,2.439561,0.095607},{2.699819,0.958868,1.51967},{4.715311,1.321027,0.105137},{5.105136,-0.102548,-1.919037},{3.466078,-1.906346,-2.494355},{1.460425,-2.271814,-1.084133},{-1.646156,-2.888667,1.79517},{-3.607082,-3.533194,0.392264},{-3.900199,-2.53032,-1.882021},{-2.231146,-0.871778,-2.734937},{-0.285291,-0.222201,-1.332875},{-2.783994,1.144919,1.233512},{-3.744182,2.332248,-0.74798}} {C,C,C,C,S,P,C,C,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -19966 625 {{-0.886352,3.009841,-2.046273},{-1.218046,2.350141,-0.686294},{-1.823662,3.370981,0.288117},{-0.136014,1.534881,-0.083829},{1.036815,2.152679,0.55569},{1.656765,3.363659,-0.167732},{0.804806,2.470858,2.048671},{-0.018204,-0.039502,-0.905215},{-1.455375,-0.786625,-0.236057},{-1.987845,-0.532681,1.119108},{-3.359428,0.185036,1.161172},{-2.044729,-1.761014,2.045651},{-2.019987,-1.801783,-1.155941},{-3.552699,-1.785974,-1.262622},{-1.502429,-3.235484,-0.920107},{1.42939,-0.737968,-0.216563},{2.471564,-0.996333,-1.239118},{3.039628,-2.425165,-1.237449},{3.607241,0.048187,-1.26594},{1.587661,-1.103984,1.20859},{1.413721,-2.612454,1.497612},{2.893816,-0.623898,1.873595},{-0.247374,3.899617,-1.942724},{-0.38193,2.289115,-2.709997},{-1.821689,3.328057,-2.539689},{-2.012325,1.61193,-0.903672},{-1.128245,4.198894,0.50176},{-2.730561,3.813746,-0.157918},{-2.10266,2.89641,1.2417},{1.80386,1.364339,0.519028},{1.871237,3.133578,-1.223344},{2.608491,3.630149,0.323746},{1.011473,4.25636,-0.132116},{1.761857,2.729661,2.536279},{0.381819,1.597012,2.570319},{0.117379,3.318927,2.193712},{-1.265646,0.188606,1.543039},{-3.487487,0.66184,2.148759},{-3.434664,0.970778,0.396086},{-4.202076,-0.509939,1.023246},{-1.082395,-2.287287,2.097662},{-2.315955,-1.439096,3.066488},{-2.814922,-2.479327,1.71752},{-1.629372,-1.499599,-2.14888},{-3.933775,-0.769352,-1.445599},{-4.037585,-2.184764,-0.356375},{-3.861653,-2.426354,-2.105899},{-0.401603,-3.254148,-0.95376},{-1.877108,-3.908128,-1.711824},{-1.828497,-3.643719,0.049762},{1.925769,-0.876804,-2.195883},{3.692507,-2.615673,-0.36965},{2.233485,-3.175557,-1.240586},{3.651908,-2.573742,-2.143014},{4.240986,-0.111994,-2.155937},{3.196235,1.068559,-1.323985},{4.257987,-0.011702,-0.379646},{0.758146,-0.582622,1.718959},{1.241021,-2.767365,2.577129},{2.310463,-3.188554,1.223793},{0.558447,-3.025814,0.94653},{2.846754,-0.834803,2.955718},{3.064775,0.455663,1.747573},{3.768939,-1.162049,1.474691}} {C,C,C,N,C,C,C,P,N,C,C,C,C,C,C,N,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -19967 625 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{C,C,N,P,N,C,C,O,C,C,N,C,C,O,C,C,C,C,O,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -14387 1012 {{0.016173,2.354401,0.855864},{-0.058217,1.481059,-0.570958},{-1.418301,0.3066,-0.148791},{-2.643983,0.473467,-0.825809},{-3.731612,-0.367969,-0.545514},{-3.600875,-1.378579,0.418564},{-2.38306,-1.550636,1.099852},{-1.294551,-0.717098,0.814719},{1.397608,0.384728,-0.282294},{1.667845,-0.629091,-1.225196},{2.785424,-1.459796,-1.070477},{3.651838,-1.27926,0.020906},{3.393481,-0.264797,0.95462},{2.272588,0.568,0.805181},{-2.741697,1.26632,-1.575696},{-4.678307,-0.234164,-1.077645},{-4.447318,-2.036227,0.63946},{-2.282328,-2.341162,1.850013},{-0.341957,-0.860509,1.33431},{0.997065,-0.778078,-2.07938},{2.981477,-2.248555,-1.80332},{4.526611,-1.925719,0.13944},{4.06593,-0.118451,1.805743},{2.069808,1.357638,1.534099}} {F,P,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H} \N -19791 643 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{C,C,N,P,N,C,C,O,C,C,N,C,C,O,C,C,C,C,O,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -19716 645 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{C,C,C,N,C,C,C,P,N,C,C,C,C,C,C,N,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -19066 663 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{C,C,C,N,P,N,C,C,C,C,C,N,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -19067 663 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{{2.109018,0.714891,2.143625},{3.050502,0.717111,0.92979},{3.624787,2.121469,0.681514},{2.335209,-0.036894,-0.678761},{0.415264,-0.060186,-0.383339},{-0.333259,-1.260572,-0.21104},{-1.709678,-1.331406,-0.000704},{-2.319047,-2.594354,0.172605},{-3.686848,-2.698206,0.416136},{-4.470071,-1.529916,0.488894},{-3.872655,-0.281965,0.312304},{-2.485963,-0.1363,0.060916},{-1.84211,1.169201,-0.154267},{-2.589235,2.374844,-0.142626},{-1.981664,3.604805,-0.393102},{-0.604671,3.672944,-0.682844},{0.145231,2.497609,-0.69132},{-0.433874,1.235636,-0.409634},{2.94377,-1.832699,-0.536559},{2.479877,-2.640112,-1.761619},{2.694392,-2.579014,0.78452},{1.251852,1.388295,1.974684},{2.640001,1.071267,3.046001},{1.707356,-0.288292,2.357532},{3.905083,0.04479,1.141982},{4.178522,2.470891,1.57187},{4.309855,2.13506,-0.181282},{2.822756,2.854157,0.490343},{0.130053,-2.167866,-0.192066},{-1.696047,-3.494486,0.115861},{-4.14452,-3.682608,0.550415},{-5.544495,-1.597014,0.681187},{-4.503447,0.607963,0.370121},{-3.663766,2.357603,0.055405},{-2.585745,4.517553,-0.379356},{-0.133656,4.634951,-0.906698},{1.209473,2.537267,-0.94483},{4.040523,-1.709288,-0.634562},{2.737229,-2.122466,-2.700096},{1.387993,-2.802336,-1.772786},{2.958918,-3.635281,-1.773399},{1.622917,-2.72326,1.003905},{3.159883,-3.581362,0.750409},{3.127048,-2.044424,1.64499}} {C,C,C,P,B,N,C,C,C,C,C,C,C,C,C,C,C,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -14390 1011 {{1.777554,-0.045613,1.520476},{1.566778,0.233785,0.023095},{1.564567,1.746249,-0.263527},{2.715227,-0.430107,-0.774087},{-0.001027,-0.544904,-0.736465},{0.025578,-1.979711,0.141795},{-1.565925,0.224438,0.027781},{-1.533231,0.531686,1.531512},{-2.667489,-0.823481,-0.256215},{-1.879023,1.499832,-0.783149},{1.695828,-1.121434,1.742042},{2.792433,0.284147,1.810502},{1.059804,0.492311,2.155508},{1.33331,1.96868,-1.320697},{0.843421,2.286098,0.371061},{2.567375,2.160758,-0.053065},{2.733646,-1.522425,-0.621914},{3.685121,-0.025416,-0.431048},{2.62647,-0.236656,-1.856266},{-0.850265,1.362944,1.768031},{-1.231397,-0.350181,2.119354},{-2.543446,0.830608,1.868686},{-2.503031,-1.749622,0.316586},{-3.648739,-0.40631,0.034934},{-2.716216,-1.085736,-1.327308},{-2.882549,1.869855,-0.504523},{-1.886308,1.300966,-1.868845},{-1.161004,2.311649,-0.58753}} {C,C,C,C,P,F,C,C,C,C,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -14377 1015 {{-0.423592,4.156659,-0.446066},{-1.0587,4.083995,0.842339},{-1.430264,2.84237,1.461005},{-1.11891,1.635415,0.741049},{-0.48697,1.623102,-0.557582},{0.000235,-0.000278,-1.53189},{-1.162066,-1.233426,-0.557069},{-0.858363,-1.783724,0.743313},{-1.748263,-2.656328,1.46361},{-3.008053,-2.957751,0.843544},{-3.386875,-2.447159,-0.446572},{-2.441265,-1.594163,-1.112508},{1.649435,-0.38987,-0.557186},{1.976237,0.151553,0.741307},{3.177053,-0.182502,1.461414},{4.066048,-1.125918,0.843333},{3.811242,-1.712623,-0.444867},{2.599698,-1.320301,-1.110806},{-0.156892,2.9112,-1.111628},{-0.12998,5.21164,-0.946047},{-1.263101,4.951774,1.332435},{-1.970116,2.807029,2.536587},{-1.385021,0.74191,1.155791},{0.047822,-1.566121,1.158855},{-1.448977,-3.103752,2.540549},{-3.657641,-3.568173,1.333884},{-4.446279,-2.722382,-0.947657},{-2.680883,-1.227593,-2.031948},{1.336262,0.829649,1.15575},{3.416575,0.303186,2.536731},{4.919537,-1.383097,1.333666},{4.577663,-2.495068,-0.944421},{2.400691,-1.713449,-2.028953},{0.282833,2.935368,-2.0299}} 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{{0.94898,-4.03071,-0.09731},{2.136933,-3.855459,0.689984},{2.73415,-2.568447,0.926225},{2.08787,-1.427257,0.339658},{0.884523,-1.515204,-0.447319},{-0.000617,0.000233,-1.259688},{0.869776,1.524203,-0.447483},{0.192587,2.523856,0.338106},{0.858887,3.65327,0.925053},{2.272543,3.777331,0.690369},{3.017726,2.83465,-0.095642},{2.291289,1.717494,-0.639076},{-1.755575,-0.008504,-0.447287},{-2.63558,1.124151,-0.640704},{-3.966244,1.193457,-0.096941},{-4.407853,0.077549,0.691393},{-3.591695,-1.083002,0.927846},{-2.280607,-1.094225,0.340519},{0.343235,-2.843522,-0.640252},{0.47695,-5.119686,-0.299752},{2.581032,-4.678421,1.090422},{3.730206,-2.448922,1.591973},{2.472603,-0.502628,0.531834},{-0.80088,2.396191,0.529349},{0.257835,4.457278,1.589843},{2.76394,4.57277,1.091181},{4.197311,2.968279,-0.29661},{2.78997,1.08007,-1.257917},{-2.334369,1.874118,-1.261012},{-4.673479,2.146565,-0.29959},{-5.342409,0.10456,1.092287},{-3.985823,-2.004988,1.594354},{-1.671846,-1.889309,0.533244},{-0.457347,-2.957374,-1.259979}} {B,N,B,N,B,P,B,N,B,N,B,N,B,N,B,N,B,N,N,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H} \N -9044 1283 {{-1.406825,-0.772343,0.249917},{0,0.107016,-0.580226},{1.406822,-0.772348,0.249917},{3e-06,1.490713,0.365605},{-2.353621,-0.263151,0.011331},{-1.464512,-1.800128,-0.14887},{-1.278731,-0.81347,1.344509},{1.278729,-0.813474,1.344509},{1.464505,-1.800133,-0.148869},{2.353618,-0.263159,0.011329}} {C,P,C,F,H,H,H,H,H,H} \N -9043 1284 {{-1.561872,2.1e-05,0.212965},{0.115177,0,-0.549984},{0.741854,1.24893,0.328014},{0.741812,-1.248951,0.328013},{-2.111535,-0.895281,-0.122274},{-2.111548,0.895292,-0.122334},{-1.48633,5.8e-05,1.312325}} {C,P,F,F,H,H,H} \N -9031 1285 {{1.312736,1.602807,0.564818},{1.011857,0.830811,-0.72455},{0.091239,-0.787754,-0.579447},{1.089329,-1.537771,0.543599},{-1.285054,-0.313863,0.587974},{-2.280139,0.65425,-0.071111},{0.39301,1.976648,1.0437},{1.95343,2.47597,0.35538},{1.839893,0.965058,1.292454},{1.946848,0.579996,-1.257608},{0.422353,1.441498,-1.435924},{-1.791168,-1.256095,0.861528},{-0.861896,0.109332,1.51544},{-1.8227,1.638556,-0.266753},{-3.153618,0.81946,0.580563},{-2.655105,0.261807,-1.032259}} {C,C,P,F,C,C,H,H,H,H,H,H,H,H,H,H} \N -9032 1285 {{1.314088,1.602093,0.564793},{1.012476,0.830337,-0.724555},{0.090875,-0.787734,-0.579416},{1.088409,-1.538098,0.543585},{-1.285353,-0.313208,0.587948},{-2.280285,0.655119,-0.071108},{1.841205,0.964027,1.292228},{0.394646,1.976262,1.044027},{1.955086,2.475059,0.355314},{1.947223,0.578941,-1.257811},{0.423264,1.441417,-1.435863},{-1.791685,-1.255366,0.861452},{-0.862225,0.10984,1.515525},{-2.655295,0.26287,-1.03235},{-1.822768,1.639457,-0.266565},{-3.153809,0.820347,0.580551}} {C,C,P,F,C,C,H,H,H,H,H,H,H,H,H,H} \N -9028 1286 {{1.916576,-3e-06,-0.524954},{1.078527,0.000154,0.759538},{-0.761302,6e-06,0.538703},{-0.863406,-1.247681,-0.539508},{-0.863636,1.247523,-0.539685},{1.704228,0.890619,-1.136284},{2.991563,0.000198,-0.281469},{1.704465,-0.890929,-1.13592},{1.295977,0.884696,1.389043},{1.296062,-0.884167,1.389327}} {C,C,P,F,F,H,H,H,H,H} \N -9029 1286 {{2.238361,0.039359,0.036387},{0.941726,-0.710524,-0.307529},{-0.529103,0.029261,0.540275},{-1.688794,-0.826895,-0.265253},{-0.600945,1.424028,-0.342892},{3.104911,-0.454473,-0.431594},{2.206606,1.078513,-0.32803},{2.420652,0.065594,1.12437},{0.740342,-0.711478,-1.393527},{0.991157,-1.764279,0.024818}} {C,C,P,F,F,H,H,H,H,H} \N -9026 1287 {{-2.147155,0.411336,-1.229504},{-1.680293,-0.58816,-0.000295},{-2.147163,0.410103,1.229915},{0.110742,-0.202251,-0.00012},{1.004657,-1.290896,-0.000382},{2.389825,-1.064327,-0.000243},{2.879883,0.249947,0.000159},{1.990205,1.339864,0.000402},{0.608417,1.118046,0.000261},{0.617066,-2.316404,-0.000694},{3.083413,-1.910415,-0.000454},{3.959509,0.428983,0.000281},{2.378777,2.362843,0.000702},{-0.087879,1.962142,0.000436}} {F,P,F,C,C,C,C,C,C,H,H,H,H,H} \N -9027 1287 {{-2.1467,0.4111,-1.23051},{-1.680484,-0.587842,-0.000322},{-2.148218,0.409917,1.23025},{0.110854,-0.201768,0.000303},{1.004471,-1.290654,5.7e-05},{2.389646,-1.064568,-0.000207},{2.88014,0.249455,4e-06},{1.990826,1.339579,0.000404},{0.609002,1.118297,0.000526},{0.616413,-2.315908,-5.6e-05},{3.082872,-1.910847,-0.000516},{3.959739,0.428135,-0.000118},{2.379653,2.362374,0.000607},{-0.086787,1.962666,0.000728}} {F,P,F,C,C,C,C,C,C,H,H,H,H,H} \N -9025 1288 {{1.515567,1.266123,-0.519947},{0.83832,0,0.04386},{1.515571,-1.26612,-0.51995},{0.854687,-1e-06,1.579309},{-0.907892,-1e-06,-0.649994},{-1.53091,-1.246914,0.238545},{-1.530909,1.246914,0.238544},{1.473917,1.303956,-1.623207},{1.053543,2.185341,-0.12389},{2.581367,1.271327,-0.230102},{1.473908,-1.303959,-1.623209},{2.581374,-1.271317,-0.230117},{1.053558,-2.185341,-0.123884},{0.355645,-0.893016,1.987948},{1.900916,-2e-06,1.93498},{0.355647,0.893014,1.987949}} {C,C,C,C,P,F,F,H,H,H,H,H,H,H,H,H} \N -9022 1289 {{2.61998,0.103913,-0.693399},{1.343796,0.237551,0.004809},{1.442763,0.742134,1.373425},{0.006231,-0.602523,-0.615031},{-0.22667,-1.902061,0.439731},{-1.253074,0.375938,0.126941},{-2.575391,-0.258284,0.194811},{-1.335798,1.737308,-0.414765},{3.315233,-0.564623,-0.148215},{3.10244,1.093113,-0.801099},{2.451283,-0.312297,-1.699615},{1.86104,1.766107,1.372116},{2.101923,0.097093,1.985969},{0.438653,0.765111,1.821919},{-2.486207,-1.268054,0.617976},{-3.079517,-0.322168,-0.79515},{-3.219512,0.339154,0.863652},{-0.33569,2.195894,-0.443811},{-1.975745,2.345105,0.248979},{-1.771719,1.777108,-1.437518}} {C,N,C,P,F,N,C,C,H,H,H,H,H,H,H,H,H,H,H,H} \N -\. - - --- --- Data for Name: molecule; Type: TABLE DATA; Schema: public; Owner: postgres --- - -COPY public.molecule (molecule_id, smiles, molecular_weight, dft_data, xtb_data, ml_data, mol, xtb_ni_data, fingerprint, morganbv, pat, pca, umap) FROM stdin; -138 COP(c1ccccc1)c1ccccc1 216.22000122070312 {"max_data": {"pyr_P": 0.9564548294144979, 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-3.088460922241211, -9.500231742858888) (2.602943658828736, 9.179974555969238) -\. - - --- --- Data for Name: t_e; Type: TABLE DATA; Schema: public; Owner: postgres --- - -COPY public.t_e (docs) FROM stdin; -\. - - --- --- Name: conformer_id_seq; Type: SEQUENCE SET; Schema: public; Owner: postgres --- - -SELECT pg_catalog.setval('public.conformer_id_seq', 1, false); - - --- --- Name: molecule_id_seq; Type: SEQUENCE SET; Schema: public; Owner: postgres --- - -SELECT pg_catalog.setval('public.molecule_id_seq', 1, false); - - --- --- Data for Name: BLOBS; Type: BLOBS; Schema: -; Owner: - --- - -BEGIN; - -SELECT pg_catalog.lo_open('1268888', 131072); -SELECT pg_catalog.lo_close(0); - -SELECT pg_catalog.lo_open('2601034', 131072); -SELECT pg_catalog.lo_close(0); - -SELECT pg_catalog.lo_open('5912902', 131072); -SELECT pg_catalog.lo_close(0); - -SELECT pg_catalog.lo_open('7115235', 131072); -SELECT pg_catalog.lo_close(0); - -SELECT pg_catalog.lo_open('7608663', 131072); -SELECT pg_catalog.lo_close(0); - -SELECT pg_catalog.lo_open('8146173', 131072); -SELECT pg_catalog.lo_close(0); - -SELECT pg_catalog.lo_open('8337475', 131072); -SELECT pg_catalog.lo_close(0); - -COMMIT; - --- --- Name: alembic_version alembic_version_pkc; Type: CONSTRAINT; Schema: public; Owner: postgres --- - -ALTER TABLE ONLY public.alembic_version - ADD CONSTRAINT alembic_version_pkc PRIMARY KEY (version_num); - - --- --- Name: conformer conformer_pkey; Type: CONSTRAINT; Schema: public; Owner: postgres --- - -ALTER TABLE ONLY public.conformer - ADD CONSTRAINT conformer_pkey PRIMARY KEY (conformer_id); - - --- --- Name: molecule molecule_pkey; Type: CONSTRAINT; Schema: public; Owner: postgres --- - -ALTER TABLE ONLY public.molecule - ADD CONSTRAINT molecule_pkey PRIMARY KEY (molecule_id); - - --- --- Name: molecule molecule_smiles_key; Type: CONSTRAINT; Schema: public; Owner: postgres --- - -ALTER TABLE ONLY public.molecule - ADD CONSTRAINT molecule_smiles_key UNIQUE (smiles); - - --- --- Name: idx_molecule_molecule_id; Type: INDEX; Schema: public; Owner: postgres --- - -CREATE INDEX idx_molecule_molecule_id ON public.molecule USING btree (molecule_id); - - --- --- Name: idx_molecule_pca; Type: INDEX; Schema: public; Owner: postgres --- - -CREATE INDEX idx_molecule_pca ON public.molecule USING btree (pca); - - --- --- Name: idx_molecule_pca_knn; Type: INDEX; Schema: public; Owner: postgres --- - -CREATE INDEX idx_molecule_pca_knn ON public.molecule USING gist (pca); - - --- --- Name: idx_molecule_smiles; Type: INDEX; Schema: public; Owner: postgres --- - -CREATE INDEX idx_molecule_smiles ON public.molecule USING btree (smiles); - - --- --- Name: idx_molecule_umap; Type: INDEX; Schema: public; Owner: postgres --- - -CREATE INDEX idx_molecule_umap ON public.molecule USING btree (umap); - - --- --- Name: idx_molecule_umap_knn; Type: INDEX; Schema: public; Owner: postgres --- - -CREATE INDEX idx_molecule_umap_knn ON public.molecule USING gist (umap); - - --- --- Name: moelcule_fingerprint_idx; Type: INDEX; Schema: public; Owner: postgres --- - -CREATE INDEX moelcule_fingerprint_idx ON public.molecule USING gist (fingerprint); - - --- --- Name: molecule_dft; Type: INDEX; Schema: public; Owner: postgres --- - -CREATE INDEX molecule_dft ON public.molecule USING hash (dft_data) WHERE (dft_data IS NOT NULL); - - --- --- Name: molecule_ml; Type: INDEX; Schema: public; Owner: postgres --- - -CREATE INDEX molecule_ml ON public.molecule USING hash (ml_data) WHERE (ml_data IS NOT NULL); - - --- --- Name: molecule_mol; Type: INDEX; Schema: public; Owner: postgres --- - -CREATE INDEX molecule_mol ON public.molecule USING gist (mol); - - --- --- Name: molecule_xtb; Type: INDEX; Schema: public; Owner: postgres --- - -CREATE INDEX molecule_xtb ON public.molecule USING hash (xtb_data) WHERE (xtb_data IS NOT NULL); - - --- --- Name: morganbv_idx; Type: INDEX; Schema: public; Owner: postgres --- - -CREATE INDEX morganbv_idx ON public.molecule USING gist (morganbv); - - --- --- Name: mw_idx; Type: INDEX; Schema: public; Owner: postgres --- - -CREATE INDEX mw_idx ON public.molecule USING btree (molecular_weight); - - --- --- Name: smiles_trgm_gin_idx; Type: INDEX; Schema: public; Owner: postgres --- - -CREATE INDEX smiles_trgm_gin_idx ON public.molecule USING gin (smiles public.gin_trgm_ops); - - --- --- Name: smiles_trgm_idx; Type: INDEX; Schema: public; Owner: postgres --- - -CREATE INDEX smiles_trgm_idx ON public.molecule USING gist (smiles public.gist_trgm_ops); - - --- --- Name: molecule rdk_add_mol_trigger; Type: TRIGGER; Schema: public; Owner: postgres --- - -CREATE TRIGGER rdk_add_mol_trigger BEFORE INSERT ON public.molecule FOR EACH ROW EXECUTE FUNCTION public.rdk_add_mol(); - - --- --- Name: conformer conformer_molecule_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: postgres --- - -ALTER TABLE ONLY public.conformer - ADD CONSTRAINT conformer_molecule_id_fkey FOREIGN KEY (molecule_id) REFERENCES public.molecule(molecule_id); - - --- --- PostgreSQL database dump complete --- -