Merge branch 'main' into autosolvate_merge_multicomponent

Conflicts:
	autosolvate/pubchem_api.py
	autosolvate/resp_classes/resptools/resp_gamess.py

autosolvate/pubchem_api.py

@@ -0,0 +1,257 @@
+import pubchempy as pcp
+from openbabel import pybel
+import os
+
+class PubChemAPI():
+    r"""
+    Solute molecule construction using PubChem API.
+    
+    Parameters
+    ----------
+        Name : str, Required
+            Given solute's IUPAC name, solute's information is obtained from PubChem API. 
+        
+            Simplified molecular-input line-entry system (SMILES) form and charge can
+            be retreived using get_info().
+
+        FilePath : str, Optional, default: local directory
+            Solute's XYZ file generated using openbabel is saved to given file path.
+
+    Returns
+    -------
+        Integer: 1 for sucessful completition; Otherwise problem occured while running.
+    
+    """
+
+    def __init__(self, name, filePath = os.getcwd()):
+        self.name = name
+        self.cID = ''
+        self.mol = None
+        self.sml = 'NONE'
+        self.charge = 0
+        self.ff = 'mmff94'
+        self.s = 50
+        self.filePath = filePath
+        self.export = os.path.join(self.filePath, 'tempFile')
+
+    def set_up_mol(self):
+        r"""
+        Set up molecule information using PubChem API.
+        
+        Parameters
+        ----------
+            NONE
+
+        Returns
+        -------
+            Integer: 1 for sucessful completition; Otherwise problem occured while running.
+        
+        """
+        try:
+            self.cID = pcp.get_cids(self.name)
+            try:
+                self.mol = pcp.Compound.from_cid(self.cID)
+                return 1
+            except:
+                print(f'Error, PubChem API could not access information about given compound ID {self.cID} \
+                      from the molecule database')
+                return 0
+        except:
+            print(f'Error, {self.name} corresponding compound ID cannot be obtained from PubChem API.')
+            return 0
+
+
+    def set_SMILES(self):
+        r"""
+        Update SMILES form of the solute molecule using PubChem API.
+
+        Parameters
+        ----------
+            NONE
+        
+        Returns
+        -------
+            Integer: 1 for sucessful completition; 0 for imcompletition.
+        
+        """
+        try:
+            self.sml = self.mol.canonical_smiles
+            return 1
+        except:
+            print(f'Error, solute molecule is not correctly set up, make sure set_up_mol() is called before.')
+            return 0
+
+    def set_charge(self):
+        r"""
+        Update charge of the molecule using PubChem API
+    
+        Parameters
+        ----------
+            NONE
+
+        Returns 
+        -------
+            Integer: 1 for sucessful completition; 0 for imcompletition.
+
+        """
+        try:
+            self.charge =  self.mol.charge
+            return 1  
+        except:
+            print(f'Error, solute molecule is not correctly set up, make sure set_up_mol() is called \
+                  before.')
+            return 0
+
+    def set_force_field(self, forcefield = 'mmff94'):
+        r"""
+        Set force field used in 3-D coordinates construction.
+        
+        Parameters
+        ----------
+            Force field: str, Optional, default: 'mmff94'
+
+            Available force field: 'mmff94', 'uff', 'ghemical'
+        
+        Returns
+        -------
+            NONE
+        
+        """
+        self.ff = forcefield
+
+    def get_force_field(self):
+        r"""
+        Return the force field used in 3D coordinate generation.
+        
+        Parameters
+        ----------
+            NONE
+
+        Returns
+        -------
+            Force field: str, force field used in the 3D coordinates 
+            construction
+        
+        """
+        return self.ff
+
+    def set_steps(self, steps = '50'):
+        r"""
+        Set steps used in 3-D coordinates construction.
+        
+        Parameters
+        ----------
+            steps: int, Optional, default: '50'
+        
+        Returns
+        -------
+            NONE
+        
+        """
+        self.s = steps
+
+    def get_steps(self):
+        r"""
+        Return steps used in 3-D coordinates construction. 
+        
+        Parameters
+        ----------
+            NONE
+        
+        Returns
+        -------
+            Steps: int, steps used in 3-D coordniates construction.
+        
+        """
+        return self.s
+
+    def set_path(self, path = os.getcwd()):
+        r"""
+        Set file path to save solute's xyz file.
+        
+        Parameters
+        ----------
+            path: str, Optional, default: local directory
+        
+        Returns
+        -------
+            NONE
+        
+        """
+        self.filePath = path
+
+    def get_path(self):
+        r"""
+        Return file path where solute's xyz file is saved.
+        
+        Parameters
+        ----------
+            NONE
+        
+        Returns
+        -------
+            File path: str
+        
+        """
+        return self.filePath
+
+    def get_XYZ(self):
+        r"""
+        Save XYZ file of the solute molecule.
+
+        Parameters
+        ----------
+            NONE
+        
+        Returns
+        -------
+            Integer: 1 for sucessful completition; Otherwise, it is for imcompletition.
+        
+        """
+        try:
+            compound_infos = pcp.get_compounds(self.name, 'name', record_type='3d')
+            try:
+                coord_info = compound_infos[0]
+                atoms = coord_info.atoms
+                num_atoms = str(len(atoms)) + '\n'
+                coordinates_3d = [(atom.element, atom.x, atom.y, atom.z) for atom in atoms]
+
+                with open(self.export, 'w') as file:
+                    file.write(num_atoms)
+                    for line in coordinates_3d:
+                        coord = '\n '
+                        for elem in line:
+                            if type(elem) == str:
+                                coord += ' '
+                                coord += elem
+                            else:
+                                coord += ' '
+                                coord += str(elem)
+                        file.write(coord)
+                print(f'XYZ file successfully saved as {self.export}')
+                return 1
+            except:
+                print('3D coordinate is unavailable from PubChem, try upload a xyz file')
+                return 0
+        except:
+            print(f'Error, invalid IUPAC name: {self.name}')
+            return 0
+
+    def get_info(self):
+        r"""
+        Provide information for given solute
+
+        Parameters
+        ----------
+            NONE
+        
+        Returns
+        -------
+            (IUPAC Name: str, SMILES: str, Charge: int, XYZ File Path: str) : Tuple
+        
+        """
+        if self.set_up_mol() and self.set_SMILES() and self.set_charge() and self.get_XYZ():
+            return (self.name, self.sml, self.charge, self.export)
+        else:
+            print('Unsuccessful running, please check the error messages above.')
+            return