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build/lib/mispr/__init__.py

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+__version__ = "0.0.4"

build/lib/mispr/common/pubchem.py

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+"""Implement a core class PubChemRunner for retrieving molecules from the PubChem
+database using a molecule name as a query criteria."""
+
+import os
+
+import pubchempy as pcp
+
+from pymatgen.core.structure import Molecule
+
+__author__ = "Rasha Atwi"
+__maintainer__ = "Rasha Atwi"
+__email__ = "[email protected]"
+__status__ = "Development"
+__date__ = "Aug 2022"
+__version__ = "0.0.4"
+
+
+class PubChemRunner:
+    """
+    Wrapper for retrieving molecules from PubChem database.
+    """
+
+    def __init__(self, abbreviation, working_dir=None):
+        """
+        Args:
+            abbreviation (str): Abbreviation to be used when saving molecule file.
+            working_dir (str, optional): Working directory for saving the molecule file
+                in; will use the current working directory if not specified.
+        """
+        self.abbreviation = abbreviation
+        self.working_dir = working_dir or os.getcwd()
+        self.cid = None
+
+    def get_mol(self, name, save_to_file=True, fmt="pdb", cleanup=True):
+        """
+        Wrapper function that searches for a molecule in the PubChem database, downloads
+        it in the form of an SDF file, and converts the file to a pymatgen ``Molecule``
+        object.
+
+        Args:
+            name (str): Name of the molecule to use for searching PubChem.
+            save_to_file (bool, optional): Whether to save the ``Molecule`` object to a
+                file. Defaults to ``True``.
+            fmt (str, optional): Molecule file format if ``save_to_file`` is ``True``;
+                defaults to "pdb".
+            cleanup (bool, optional): Whether to remove the intermediate sdf file.
+
+        Returns:
+            Molecule: pymatgen ``Molecule`` object.
+        """
+        self.download_sdf(name)
+        molecule = self.convert_sdf_to_mol(save_to_file, fmt)
+        if cleanup:
+            self.cleanup()
+        return molecule
+
+    def download_sdf(self, name):
+        """
+        Download an SDF file from PubChem using a common name for the molecule as an
+        identifier.
+
+        Args:
+            name (str): Name of the molecule to use for searching PubChem.
+        """
+        cids = pcp.get_cids(name, record_type="3d")
+        if cids:
+            self.cid = cids[0]
+            pcp.download(
+                outformat="SDF",
+                path=f"{self.working_dir}/{self.abbreviation}_{self.cid}.sdf",
+                identifier=self.cid,
+                record_type="3d",
+                overwrite=True,
+            )
+        else:
+            raise ValueError("No matching molecule found in the PubChem database")
+
+    def convert_sdf_to_mol(self, save_to_file, fmt):
+        """
+        Convert an SDF file to a pymatgen ``Molecule`` object.
+
+        Args:
+            save_to_file (bool): Whether to save the ``Molecule`` object to a file.
+            fmt (str): Molecule file format if ``save_to_file`` is ``True``.
+
+        Returns:
+            Molecule: pymatgen ``Molecule`` object.
+        """
+        mol = Molecule.from_file(
+            f"{self.working_dir}/{self.abbreviation}_{self.cid}.sdf"
+        )
+        if save_to_file:
+            mol.to(fmt, f"{self.working_dir}/{self.abbreviation}_{self.cid}.{fmt}")
+        return mol
+
+    def cleanup(self):
+        """
+        Delete the sdf file downloaded from PubChem.
+        """
+        os.remove(f"{self.working_dir}/{self.abbreviation}_{self.cid}.sdf")