Merge pull request #27 from JacksonBurns/radii_dict_dev

Make Radii Table Modular via Argument
JacksonBurns · Jun 3, 2023 · 5030c88 · 5030c88
2 parents 9f54bd1 + e39cd74
commit 5030c88
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diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -51,3 +51,18 @@ jobs:
       - name: Show Coverage
         run: |
           coverage report -m
+
+  # This allows us to have a branch protection rule for tests and deploys with matrix
+  # 
+  # taken from https://github.com/orgs/community/discussions/4324#discussioncomment-3477871
+  ci-report-status:
+    runs-on: ubuntu-latest
+    needs: build
+    if: always()
+    steps:
+      - name: Successful CI
+        if: ${{ !(contains(needs.build.result, 'failure')) }}
+        run: exit 0
+      - name: Failing CI
+        if: ${{ contains(needs.build.result, 'failure') }}
+        run: exit 1 
diff --git a/README.md b/README.md
@@ -22,12 +22,12 @@
 pip install py2sambvca
 ```
 
-`py2sambvca` has __zero__ external depdencies.
+`py2sambvca` has __zero__ external dependencies.
 
-### Downloading and Compiling `Sambvca`
-`py2sambvca` can read and write input and output files for `Sambvca` without the actual program in place, but in order to run input files you must have an executable `sambvca21.exe` (or similar) somewhere on your machine.
+### Downloading and Compiling `SambVca`
+`py2sambvca` can read and write input and output files for `SambVca` without the actual program in place, but in order to run input files you must have an executable `sambvca21.exe` (or similar) somewhere on your machine.
 
-You can download the source code [on the `Sambvca` webserver](https://www.molnac.unisa.it/OMtools/sambvca2.1/download/download.html) and compile it using [`gfortran`](https://gcc.gnu.org/wiki/GFortranBinaries).
+You can download the source code [on the `SambVca` webserver](https://www.molnac.unisa.it/OMtools/sambvca2.1/download/download.html) and compile it using [`gfortran`](https://gcc.gnu.org/wiki/GFortranBinaries).
 
 By default, `py2sambvca` expects the executable to be present in the `cwd` and named `sambvca21.exe` on Windows or `sambvca21.x` on Unix-based systems. optionally, the filepath to your executable can be specified as shown below.
 
@@ -62,6 +62,7 @@ The following parameters are optional and will be filled with default values if
  - `path_to_sambvcax` (str): Path to the SambVca executable. Only needed to use py2sambvca.calc()(default "sambvca.exe")
  - `working_dir` (path): Path to the working directory where the output and input files are generated (default os.getcwd())
  - `verbose` (int): 0 for no output, 1 for some output, 2 for the most output (default 1)
+ - `radii_table` (dict or str): a dictionary of atomic symbols and their radii (angstroms), or "default" for the radii used in the original implementation
 
 
 From here, running can be done stepwise or with a single function:

diff --git a/py2sambvca/__init__.py b/py2sambvca/__init__.py
@@ -2,4 +2,4 @@
 
 __all__ = ["p2s"]
 
-__version__ = "1.3.4"
+__version__ = "1.4.0"
diff --git a/py2sambvca/py2sambvca.py b/py2sambvca/py2sambvca.py
@@ -2,9 +2,11 @@
 import re
 import glob
 import os
-from typing import List
+from typing import List, Union
 from warnings import warn
 
+from py2sambvca.radii_tables import table_lookup, format_radii_table
+
 
 class py2sambvca:
     """
@@ -28,6 +30,7 @@ class py2sambvca:
     path_to_sambvcax (str): Path to the SambVca executable. Only needed to use py2sambvca.calc()( default "/path/to/executable/sambvca.x")
     working_dir (path): Path to the working directory where the output and input files are generated (default os.getcwd())
     verbose (int): 0 for no output, 1 for some output, 2 for the most output
+    radii_table (dict or str): atomic symbols (ie. H, LI) and radii (Angstrom), "default" (bondii radii*1.17), or "vdw" for van Der Waals
     """
 
     def __init__(
@@ -46,6 +49,7 @@ def __init__(
         path_to_sambvcax: str = "sambvca.exe",
         working_dir: str = os.getcwd(),
         verbose: int = 1,
+        radii_table: Union[str, dict] = "default",
     ):
         """
         Wrapper class for py2sambvca functions.
@@ -68,6 +72,7 @@ def __init__(
         path_to_sambvcax (str): Path to the SambVca executable. Only needed to use py2sambvca.calc()( default "/path/to/executable/sambvca.x")
         working_dir (path): Path to the working directory where the output and input files are generated (default os.getcwd())
         verbose (int): 0 for no output, 1 for some output, 2 for the most output
+        radii_table (dict or str): atomic symbols (ie. H, LI) and radii (Angstrom), "default" (bondii radii*1.17), or "vdw" for van Der Waals
         """
         # if atoms are requested to be deleted, assign them and the number of them
         if atoms_to_delete_ids is not None:
@@ -114,6 +119,11 @@ def __init__(
         self.quadrant_results = None
         self.octant_results = None
 
+        # data table
+        self.__radii_table = format_radii_table(
+            table_lookup[radii_table] if type(radii_table) is str else radii_table
+        )
+
     def write_input(self):
         """
         Write input for the Sambvca buried-volume Fortran calculator based on the data entered
@@ -167,7 +177,7 @@ def write_input(self):
                 ]
             )
             # write radii
-            file.writelines(radii_table)
+            file.writelines(self.__radii_table)
             # write the atom coordinates
             file.writelines(self.xyz_data)
 
@@ -511,110 +521,3 @@ def run(self):
         self.parse_output()
         self.clean_files()
         return self.total_results, self.quadrant_results, self.octant_results
-
-
-radii_table = [
-    "H       1.28\n",
-    "HE      1.64\n",
-    "LI      2.13\n",
-    "BE      1.79\n",
-    "B       2.25\n",
-    "C       1.99\n",
-    "N       1.81\n",
-    "O       1.78\n",
-    "F       1.72\n",
-    "NE      1.80\n",
-    "NA      2.66\n",
-    "MG      2.02\n",
-    "AL      2.15\n",
-    "SI      2.46\n",
-    "P       2.11\n",
-    "S       2.11\n",
-    "CL      2.05\n",
-    "AR      2.20\n",
-    "K       3.22\n",
-    "CA      2.70\n",
-    "SC      2.52\n",
-    "TI      2.47\n",
-    "V       2.42\n",
-    "CR      2.41\n",
-    "MN      2.40\n",
-    "FE      2.39\n",
-    "CO      2.34\n",
-    "NI      1.91\n",
-    "CU      1.64\n",
-    "ZN      1.63\n",
-    "GA      2.19\n",
-    "GE      2.47\n",
-    "AS      2.16\n",
-    "SE      2.22\n",
-    "BR      2.16\n",
-    "KR      2.36\n",
-    "RB      3.55\n",
-    "SR      2.91\n",
-    "Y       2.71\n",
-    "ZR      2.61\n",
-    "NB      2.55\n",
-    "MO      2.54\n",
-    "TC      2.53\n",
-    "RU      2.49\n",
-    "RH      2.46\n",
-    "PD      1.91\n",
-    "AG      2.01\n",
-    "CD      1.85\n",
-    "IN      2.26\n",
-    "SN      2.54\n",
-    "SB      2.41\n",
-    "TE      2.41\n",
-    "I       2.32\n",
-    "XE      2.53\n",
-    "CS      4.01\n",
-    "BA      3.14\n",
-    "LA      2.84\n",
-    "CE      2.83\n",
-    "PR      2.81\n",
-    "ND      2.80\n",
-    "PM      2.78\n",
-    "SM      2.76\n",
-    "EU      2.75\n",
-    "GD      2.74\n",
-    "TB      2.73\n",
-    "DY      2.70\n",
-    "HO      2.69\n",
-    "ER      2.68\n",
-    "TM      2.66\n",
-    "YB      2.64\n",
-    "LU      2.62\n",
-    "HF      2.61\n",
-    "TA      2.60\n",
-    "W       2.55\n",
-    "RE      2.53\n",
-    "OS      2.53\n",
-    "IR      2.49\n",
-    "PT      2.01\n",
-    "AU      1.94\n",
-    "HG      1.81\n",
-    "TL      2.29\n",
-    "PB      2.36\n",
-    "BI      2.42\n",
-    "PO      2.30\n",
-    "AT      2.36\n",
-    "RN      2.57\n",
-    "FR      4.07\n",
-    "RA      3.31\n",
-    "AC      2.89\n",
-    "TH      2.87\n",
-    "PA      2.84\n",
-    "U       2.18\n",
-    "NP      2.80\n",
-    "PU      2.84\n",
-    "AM      2.85\n",
-    "CM      2.87\n",
-    "BK      2.85\n",
-    "CF      2.87\n",
-    "ES      2.87\n",
-    "FM      2.87\n",
-    "M       2.88\n",
-    "NO      2.88\n",
-    "LR      2.88\n",
-]
diff --git a/py2sambvca/radii_tables/__init__.py b/py2sambvca/radii_tables/__init__.py
@@ -0,0 +1,10 @@
+from py2sambvca.radii_tables.default import default_radii_table
+from py2sambvca.radii_tables.vanDerWaals import vdw_radii_table
+from py2sambvca.radii_tables.format_table import format_radii_table
+
+table_lookup = {
+    "default": default_radii_table,
+    "vdw": vdw_radii_table,
+}
+
+__all__ = ["format_radii_table", "table_lookup"]
diff --git a/py2sambvca/radii_tables/default.py b/py2sambvca/radii_tables/default.py
@@ -0,0 +1,107 @@
+# These are the radii used in the original Cavallo paper, which are just the vDW
+# radii multiplied by 1.17
+default_radii_table = {
+    "H": 1.28,
+    "HE": 1.64,
+    "LI": 2.13,
+    "BE": 1.79,
+    "B": 2.25,
+    "C": 1.99,
+    "N": 1.81,
+    "O": 1.78,
+    "F": 1.72,
+    "NE": 1.80,
+    "NA": 2.66,
+    "MG": 2.02,
+    "AL": 2.15,
+    "SI": 2.46,
+    "P": 2.11,
+    "S": 2.11,
+    "CL": 2.05,
+    "AR": 2.20,
+    "K": 3.22,
+    "CA": 2.70,
+    "SC": 2.52,
+    "TI": 2.47,
+    "V": 2.42,
+    "CR": 2.41,
+    "MN": 2.40,
+    "FE": 2.39,
+    "CO": 2.34,
+    "NI": 1.91,
+    "CU": 1.64,
+    "ZN": 1.63,
+    "GA": 2.19,
+    "GE": 2.47,
+    "AS": 2.16,
+    "SE": 2.22,
+    "BR": 2.16,
+    "KR": 2.36,
+    "RB": 3.55,
+    "SR": 2.91,
+    "Y": 2.71,
+    "ZR": 2.61,
+    "NB": 2.55,
+    "MO": 2.54,
+    "TC": 2.53,
+    "RU": 2.49,
+    "RH": 2.46,
+    "PD": 1.91,
+    "AG": 2.01,
+    "CD": 1.85,
+    "IN": 2.26,
+    "SN": 2.54,
+    "SB": 2.41,
+    "TE": 2.41,
+    "I": 2.32,
+    "XE": 2.53,
+    "CS": 4.01,
+    "BA": 3.14,
+    "LA": 2.84,
+    "CE": 2.83,
+    "PR": 2.81,
+    "ND": 2.80,
+    "PM": 2.78,
+    "SM": 2.76,
+    "EU": 2.75,
+    "GD": 2.74,
+    "TB": 2.73,
+    "DY": 2.70,
+    "HO": 2.69,
+    "ER": 2.68,
+    "TM": 2.66,
+    "YB": 2.64,
+    "LU": 2.62,
+    "HF": 2.61,
+    "TA": 2.60,
+    "W": 2.55,
+    "RE": 2.53,
+    "OS": 2.53,
+    "IR": 2.49,
+    "PT": 2.01,
+    "AU": 1.94,
+    "HG": 1.81,
+    "TL": 2.29,
+    "PB": 2.36,
+    "BI": 2.42,
+    "PO": 2.30,
+    "AT": 2.36,
+    "RN": 2.57,
+    "FR": 4.07,
+    "RA": 3.31,
+    "AC": 2.89,
+    "TH": 2.87,
+    "PA": 2.84,
+    "U": 2.18,
+    "NP": 2.80,
+    "PU": 2.84,
+    "AM": 2.85,
+    "CM": 2.87,
+    "BK": 2.85,
+    "CF": 2.87,
+    "ES": 2.87,
+    "FM": 2.87,
+    "M": 2.88,
+    "NO": 2.88,
+    "LR": 2.88,
+}
diff --git a/py2sambvca/radii_tables/format_table.py b/py2sambvca/radii_tables/format_table.py
@@ -0,0 +1,20 @@
+def format_radii_table(radii_table: dict):
+    """Formats a dictionary of atomic symbol: radii to a list of strings for sambvca
+
+    Args:
+        radii_table (dict): Mapping of atomic symbols to radii, i.e. {'H':1.0,'LI':1.1}
+    """
+    output_list = []
+    for element, radius in radii_table.items():
+        # sambvca expects each row in the radii table to look like this:
+        # "C       1.11" with _exactly_ six spaces for elements with two letter
+        # abbreviations and _exactly_ seven for elements with one letter
+        # abbreviations, and then three digits for the radius
+        output_list.append(
+            element
+            + (" " if len(element) == 1 else "")
+            + "      "
+            + str(round(radius, 2))
+            + "\n"
+        )
+    return output_list
diff --git a/py2sambvca/radii_tables/vanDerWaals.py b/py2sambvca/radii_tables/vanDerWaals.py
@@ -0,0 +1,8 @@
+# this radius table just returns to the plain old van Der Waals radii,
+# which are the radii reported in the original Cavallo paper divided by
+# 1.17
+from py2sambvca.radii_tables.default import default_radii_table
+
+vdw_radii_table = {
+    element: radius / 1.17 for element, radius in default_radii_table.items()
+}
diff --git a/test/test_py2sambvca.py b/test/test_py2sambvca.py
@@ -108,6 +108,7 @@ def test_full_init(self):
             self.orient_Z,
             self.write_surf_files,
             self.exe_path,
+            "default",
         )
         self.assertEqual(
             self.sphere_ids,