Merge branch 'main' into v131

results/v128/model_media/model_stats.csv

@@ -0,0 +1,11 @@
+run,cindex,pearson,spearman,mse,mae,rmse
+DGM_PDBbind1D_nomsaF_binaryE_64B_0.0001LR_0.4D_2000E_originalLF_binaryLE,0.6700303728768234,0.5066764643691913,0.4877355421142711,2.8944340651943885,1.3393119536913358,1.7013036369779466
+DGM_PDBbind0D_nomsaF_binaryE_64B_0.0001LR_0.4D_2000E_originalLF_binaryLE,0.6920256384153837,0.5521166195053873,0.5492833432385198,2.6901810056403943,1.2902274471429678,1.6401771263008134
+DGM_PDBbind2D_nomsaF_binaryE_64B_0.0001LR_0.4D_2000E_originalLF_binaryLE,0.6860817317553821,0.5349021289716281,0.5292561754408733,2.783316931934153,1.3007997966913076,1.668327585318349
+DGM_PDBbind4D_nomsaF_binaryE_64B_0.0001LR_0.4D_2000E_originalLF_binaryLE,0.6814616054321716,0.5209332896962908,0.5205006093028853,2.791164015918997,1.3129914098152748,1.6706777115646805
+DGM_PDBbind3D_nomsaF_binaryE_64B_0.0001LR_0.4D_2000E_originalLF_binaryLE,0.6886407871725875,0.5377497788348156,0.536984917834154,2.7892612584388665,1.3068153142929078,1.6701081577068195
+DGM_PDBbind0D_nomsaF_aflowE_128B_0.0009185598967356679LR_0.22880989869337157D_2000E_originalLF_binaryLE,0.6791215578161572,0.5426811555689641,0.5087142971057145,2.7253219488991136,1.2940673363869717,1.6508549145515827
+DGM_PDBbind2D_nomsaF_aflowE_128B_0.0009185598967356679LR_0.22880989869337157D_2000E_originalLF_binaryLE,0.6935974149775556,0.5590003871276702,0.5527753938595599,2.613210370957274,1.2817467006748329,1.616542721661656
+DGM_PDBbind1D_nomsaF_aflowE_128B_0.0009185598967356679LR_0.22880989869337157D_2000E_originalLF_binaryLE,0.6776316790562161,0.5208748506408137,0.5056665537333501,2.79682269540488,1.3061289907536988,1.672370382243383
+DGM_PDBbind3D_nomsaF_aflowE_128B_0.0009185598967356679LR_0.22880989869337157D_2000E_originalLF_binaryLE,0.6772535031619085,0.5129702979170532,0.5079117445737773,2.876293932539623,1.343678560827124,1.69596401274898
+DGM_PDBbind4D_nomsaF_aflowE_128B_0.0009185598967356679LR_0.22880989869337157D_2000E_originalLF_binaryLE,0.6803930344028177,0.5261288742927207,0.5152003489955188,2.7888457682850523,1.3061685765992026,1.669983762880661

results/v128/model_media/model_stats_val.csv

@@ -0,0 +1,11 @@
+run,cindex,pearson,spearman,mse,mae,rmse
+DGM_PDBbind1D_nomsaF_binaryE_64B_0.0001LR_0.4D_2000E_originalLF_binaryLE,0.6865570848103539,0.5217828035285198,0.5342788004080268,3.12362316791697,1.4128894441393012,1.7673774831418922
+DGM_PDBbind0D_nomsaF_binaryE_64B_0.0001LR_0.4D_2000E_originalLF_binaryLE,0.6856114868115144,0.5126870149038275,0.5317248936648343,3.3695982839888123,1.4536717794904257,1.8356465574801737
+DGM_PDBbind2D_nomsaF_binaryE_64B_0.0001LR_0.4D_2000E_originalLF_binaryLE,0.6727143444861741,0.5022869639192042,0.5008407950347942,3.421695656587546,1.4982888305121282,1.849782597114468
+DGM_PDBbind4D_nomsaF_binaryE_64B_0.0001LR_0.4D_2000E_originalLF_binaryLE,0.6923138709195878,0.5430234761140276,0.5501681361051465,2.9685919834473102,1.3589257854182952,1.7229602384986458
+DGM_PDBbind3D_nomsaF_binaryE_64B_0.0001LR_0.4D_2000E_originalLF_binaryLE,0.7221237704365324,0.5997226273753726,0.6282960957077218,3.071004525264972,1.3901743548518686,1.7524281797737025
+DGM_PDBbind0D_nomsaF_aflowE_128B_0.0009185598967356679LR_0.22880989869337157D_2000E_originalLF_binaryLE,0.6765066849227523,0.5001545914726073,0.5133105406519389,3.044526199847986,1.3962691384923704,1.7448570714668827
+DGM_PDBbind2D_nomsaF_aflowE_128B_0.0009185598967356679LR_0.22880989869337157D_2000E_originalLF_binaryLE,0.7083260415364561,0.5949781068309761,0.5895379695932953,2.563278684581813,1.274137923604572,1.601024261084701
+DGM_PDBbind1D_nomsaF_aflowE_128B_0.0009185598967356679LR_0.22880989869337157D_2000E_originalLF_binaryLE,0.6854165476207483,0.5218685304168357,0.535423559993022,2.837139616188374,1.326142185326017,1.6843810780783468
+DGM_PDBbind3D_nomsaF_aflowE_128B_0.0009185598967356679LR_0.22880989869337157D_2000E_originalLF_binaryLE,0.6752795639801628,0.5022118247529487,0.5077603820327848,3.2012135060951,1.425228337672172,1.7891935351143822
+DGM_PDBbind4D_nomsaF_aflowE_128B_0.0009185598967356679LR_0.22880989869337157D_2000E_originalLF_binaryLE,0.6843307790913993,0.5107948247428088,0.5298336871787266,2.9007170257795094,1.3341726068459485,1.7031491495989155

src/utils/pocket_alignment.py

@@ -3,20 +3,27 @@
 mask from a binding pocket sequence.
 """
 
+import json
+import os
+import shutil
+
 from Bio import Align
 from Bio.Align import substitution_matrices
+import pandas as pd
 import torch
 
+from src.data_prep.downloaders import Downloader
+
 
-def create_pocket_mask(target_seq: str, query_seq: str) -> list[bool]:
+def create_pocket_mask(target_seq: str, pocket_seq: str) -> list[bool]:
     """
     Return an index mask of a pocket on a protein sequence.
     
     Parameters
     ----------
     target_seq : str
         The protein sequence you want to query in
-    query_seq : str
+    pocket_seq : str
         The binding pocket sequence for the protein
 
     Returns
@@ -25,6 +32,8 @@ def create_pocket_mask(target_seq: str, query_seq: str) -> list[bool]:
         A boolean list of indices that are True if the residue at that
         position is part of the binding pocket and false otherwise
     """
+    # Ensure that no '-' characters are present in the query sequence
+    query_seq = pocket_seq.replace('-', 'X')
     # Taken from tutorial https://biopython.org/docs/dev/Tutorial/chapter_pairwise.html
     aligner = Align.PairwiseAligner()
     # Pairwise alignment parameters as specified in paragraph 2
@@ -92,15 +101,165 @@ def mask_graph(data, mask: list[bool]):
     return data
 
 
+def _parse_json(json_path: str) -> str:
+    """
+    Parse a JSON file that holds binding pocket data downloaded from KLIFS.
+
+    Parameters
+    ----------
+    json_path : str 
+        The path to the JSON file
+
+    Returns
+    -------
+    str
+        The binding pocket sequence
+    """
+    with open(json_path, 'r') as json_file:
+        data = json.load(json_file)
+        return data[0]['pocket']
+
+
+def get_dataset_binding_pockets(
+        dataset_path: str = 'data/DavisKibaDataset/kiba/nomsa_binary_original_binary/full',
+        pockets_path: str = 'data/DavisKibaDataset/kiba_pocket'
+    ) -> tuple[dict[str, str], set[str]]:
+    """
+    Get all binding pocket sequences for a dataset
+
+    Parameters
+    ----------
+    dataset_path : str
+        The path to the directory containing the dataset (as of July 24, 2024,
+        only expecting Kiba dataset). Specify only the path to one of 'davis', 'kiba',
+        or 'PDBbind' (e.g., 'data/DavisKibaDataset/kiba')
+    pockets_path: str
+        The path to the new dataset directory after all the binding pockets have been found
+    
+    Returns
+    -------
+    tuple[dict[str, str], set[str]]
+        A tuple consisting of:
+            -A map of protein ID, binding pocket sequence pairs
+            -A set of protein IDs with no KLIFS binding pockets
+    """
+    csv_path = os.path.join(dataset_path, 'cleaned_XY.csv')
+    df = pd.read_csv(csv_path, usecols=['prot_id'])
+    prot_ids = list(set(df['prot_id']))
+    # Strip out mutations and '-(alpha, beta, gamma)' tags if they are present,
+    # the binding pocket sequence will be the same for mutated and non-mutated genes
+    prot_ids = [id.split('(')[0].split('-')[0] for id in prot_ids]
+    dl = Downloader()
+    seq_save_dir = os.path.join(pockets_path, 'pockets')
+    os.makedirs(seq_save_dir, exist_ok=True)
+    download_check = dl.download_pocket_seq(prot_ids, seq_save_dir)
+    download_errors = set()
+    for key, val in download_check.items():
+        if val == 400:
+            download_errors.add(key)
+    sequences = {}
+    for file in os.listdir(seq_save_dir):
+        pocket_seq = _parse_json(os.path.join(seq_save_dir, file))
+        if pocket_seq == 0 or len(pocket_seq) == 0:
+            download_errors.add(file.split('.')[0])
+        else:
+            sequences[file.split('.')[0]] = pocket_seq
+    return (sequences, download_errors)
+
+
+def create_binding_pocket_dataset(
+    dataset_path: str,
+    pocket_sequences: dict[str, str],
+    download_errors: set[str],
+    new_dataset_path: str
+) -> None:
+    """
+    Apply the graph mask based on binding pocket sequence for each
+    Data object in a PyTorch dataset.
+
+    dataset_path : str
+        The path to the PyTorch dataset object to be transformed
+    pocket_sequences : dict[str, str]
+        A map of protein ID, binding pocket sequence pairs
+    download_errors : set[str]
+        A set of protein IDs that have no binding pocket sequence
+        to be downloaded from KLIFS
+    new_dataset_path : str
+        A path to where the new dataset should be saved
+    """
+    dataset = torch.load(dataset_path)
+    new_dataset = {}
+    for id, data in dataset.items():
+        # If there are any mutations or (-alpha,beta,gamma) tags, strip them
+        stripped_id = id.split('(')[0].split('-')[0]
+        if stripped_id not in download_errors:
+            mask = create_pocket_mask(data.pro_seq, pocket_sequences[stripped_id])
+            new_data = mask_graph(data, mask)
+            new_dataset[id] = new_data
+    os.makedirs(os.path.dirname(new_dataset_path), exist_ok=True)
+    torch.save(dataset, new_dataset_path)
+
+
+def binding_pocket_filter(dataset_csv_path: str, download_errors: set[str], csv_save_path: str):
+    """
+    Filter out protein IDs that do not have a corresponding KLIFS
+    binding pocket sequence from the dataset.
+
+    Parameters
+    ----------
+    dataset_csv_path : str
+        The path to the original cleaned CSV. Will probably be a CSV named cleaned_XY.csv
+        or something like that.
+    download_errors : set[str]
+        A set of protein IDs with no KLIFS binding pocket sequences.
+    csv_save_path : str
+        The path to save the new CSV file to.
+    """
+    df = pd.read_csv(dataset_csv_path)
+    df = df[~df['prot_id'].isin(download_errors)]
+    os.makedirs(os.path.dirname(csv_save_path), exist_ok=True)
+    df.to_csv(csv_save_path)
+
+
+def pocket_dataset_full(
+    dataset_dir: str,
+    pocket_dir: str,
+    save_dir: str
+) -> None:
+    """
+    Create all elements of a dataset that includes binding pockets. This
+    function assumes the PyTorch object holding the dataset is named 'data_pro.pt'
+    and the CSV holding the cleaned data is named 'cleaned_XY.csv'.
+
+    Parameters
+    ----------
+    dataset_dir : str
+        The path to the dataset to be transformed
+    pocket_dir : str
+        The path to where the dataset raw pocket sequences are to be saved
+    save_dir : str
+        The path to where the new dataset is to be saved
+    """
+    pocket_map, download_errors = get_dataset_binding_pockets(dataset_dir, pocket_dir)
+    print(f'Binding pocket sequences were not found for the following {len(download_errors)} protein IDs:')
+    print(','.join(list(download_errors)))
+    create_binding_pocket_dataset(
+        os.path.join(dataset_dir, 'data_pro.pt'),
+        pocket_map,
+        download_errors,
+        os.path.join(save_dir, 'data_pro.pt')
+    )
+    binding_pocket_filter(
+        os.path.join(dataset_dir, 'cleaned_XY.csv'),
+        download_errors,
+        os.path.join(save_dir, 'cleaned_XY.csv')
+    )
+    shutil.copy2(os.path.join(dataset_dir, 'data_mol.pt'), os.path.join(save_dir, 'data_mol.pt'))
+
+
 if __name__ == '__main__':
-    graph_data = torch.load('sample_pro_data.torch')
-    seq = graph_data.pro_seq
-    seq = seq[:857] + 'R' + seq[858:]
-    graph_data.pro_seq = seq
-    torch.save(graph_data, 'sample_pro_data_unmutated.torch')
-    binding_pocket_sequence = 'KVLGSGAFGTVYKVAIKELEILDEAYVMASVDPHVCRLLGIQLITQLMPFGCLLDYVREYLEDRRLVHRDLAARNVLVITDFGLA'
-    mask = create_pocket_mask(
-        graph_data.pro_seq,
-        binding_pocket_sequence
+    pocket_dataset_full(
+        'data/DavisKibaDataset/kiba/nomsa_binary_original_binary/full/',
+        'data/DavisKibaDataset/kiba_pocket',
+        'data/DavisKibaDataset/kiba_pocket/nomsa_binary_original_binary/full/'
     )
-    masked_data = mask_graph(graph_data, mask)