Merge pull request #85 from hjkgrp/code_quality

Code quality

molSimplify/Classes/atom3D.py

@@ -143,7 +143,7 @@ def distancev(self, atom2):
         dz = xyz[2]-point[2]
         return [dx, dy, dz]
 
-    def ismetal(self, transition_metals_only=True):
+    def ismetal(self, transition_metals_only: bool = True) -> bool:
         """ Identify whether an atom is a metal.
 
         Parameters

molSimplify/Classes/mol3D.py

@@ -14,6 +14,7 @@
 from math import sqrt
 import numpy as np
 import openbabel
+from typing import List
 from scipy.spatial import ConvexHull
 
 from molSimplify.Classes.atom3D import atom3D
@@ -82,7 +83,7 @@ def __init__(self, name='ABC', loc='', use_atom_specific_cutoffs=False):
         # Holder for molecular group
         self.grps = False
         # Holder for metals
-        self.metals = False
+        self.metals = None
         # Conformation (empty string if irrelevant)
         self.loc = loc
         # Temporary list for storing conformations
@@ -213,7 +214,7 @@ def ACM_axis(self, idx1, idx2, axis, angle):
             xyz = submol_to_move.getAtomCoords(i)
             self.atoms[atidx].__init__(Sym=asym, xyz=xyz)
 
-    def addAtom(self, atom, index=None, auto_populate_BO_dict=True):
+    def addAtom(self, atom: atom3D, index: int = None, auto_populate_BO_dict: bool = True):
         """Adds an atom to the atoms attribute, which contains a list of
         atom3D class instances.
 
@@ -279,7 +280,7 @@ def addAtom(self, atom, index=None, auto_populate_BO_dict=True):
         self.natoms += 1
         self.mass += atom.mass
         self.size = self.molsize()
-        self.metal = False
+        self.metals = None
 
     def assign_graph_from_net(self, path_to_net, return_graph=False):
         """
@@ -610,7 +611,7 @@ def convert2mol3D(self):
             self.addAtom(atom3D(sym, pos))
         # self.atoms = atom3D_list
         # reset metal ID
-        self.metal = False
+        self.metals = None
 
     def convert2OBMol(self, force_clean=False, ignoreX=False):
         """Converts mol3D class instance to OBMol class instance.
@@ -785,7 +786,7 @@ def combine(self, mol, bond_to_add=[], dirty=False):
                         cmol.OBMol.AddBond(i + 1, j + 1, int(jointBOMat[i][j]))
         # reset graph
         cmol.graph = []
-        self.metal = False
+        self.metals = None
         return cmol
 
     def coords(self):
@@ -957,7 +958,7 @@ def deleteatom(self, atomIdx):
         if len(self.graph):
             self.graph = np.delete(
                 np.delete(self.graph, atomIdx, 0), atomIdx, 1)
-        self.metal = False
+        self.metals = None
         del (self.atoms[atomIdx])
 
     def deleteatoms(self, Alist):
@@ -995,7 +996,7 @@ def deleteatoms(self, Alist):
             del (self.atoms[h])
         if len(self.graph):
             self.graph = np.delete(np.delete(self.graph, Alist, 0), Alist, 1)
-        self.metal = False
+        self.metals = None
 
     def freezeatom(self, atomIdx):
         """Set the freeze attribute to be true for a given atom3D class.
@@ -1259,12 +1260,10 @@ def findcloseMetal(self, atom0):
                 index of the nearest metal, or heaviest atom if no metal found.
 
         """
-        if not self.metals:
-            self.findMetal()
 
         close_metal = False
         mindist = 1000
-        for i in enumerate(self.metals):
+        for i in enumerate(self.findMetal()):
             atom = self.getAtom(i)
             if distance(atom.coords(), atom0.coords()) < mindist:
                 mindist = distance(atom.coords(), atom0.coords())
@@ -1277,7 +1276,7 @@ def findcloseMetal(self, atom0):
                     close_metal = i
         return close_metal
 
-    def findMetal(self, transition_metals_only=True):
+    def findMetal(self, transition_metals_only: bool = True) -> List[int]:
         """Find metal(s) in a mol3D class.
 
         Parameters
@@ -1291,15 +1290,15 @@ def findMetal(self, transition_metals_only=True):
                 List of indices of metal atoms in mol3D.
 
         """
-        if not self.metals:
+        if self.metals is None:
             metal_list = []
             for i, atom in enumerate(self.atoms):
                 if atom.ismetal(transition_metals_only=transition_metals_only):
                     metal_list.append(i)
             self.metals = metal_list
-        return (self.metals)
+        return self.metals
 
-    def findAtomsbySymbol(self, sym):
+    def findAtomsbySymbol(self, sym: str) -> List[int]:
         """Find all elements with a given symbol in a mol3D class.
 
         Parameters

molSimplify/Informatics/decoration_manager.py

@@ -22,8 +22,7 @@
 ##########################################
 
 
-
-def decorate_ligand(args,ligand_to_decorate,decoration,decoration_index):
+def decorate_ligand(args, ligand_to_decorate, decoration, decoration_index):
     # structgen depends on decoration_manager, and decoration_manager depends on structgen.ffopt
     # Thus, this import needs to be placed here to avoid a circular dependence
     from molSimplify.Scripts.structgen import ffopt
@@ -40,30 +39,30 @@ def decorate_ligand(args,ligand_to_decorate,decoration,decoration_index):
     #if args.debug:
     #    print  'decorating ligand'
     lig = ligand_to_decorate
-    ## reorder to ensure highest atom index 
+    ## reorder to ensure highest atom index
     ## removed first
     sort_order = [i[0] for i in sorted(enumerate(decoration_index), key=lambda x:x[1])]
-    sort_order = sort_order[::-1] ## reverse
+    sort_order = sort_order[::-1]  # reverse
 
     decoration_index = [decoration_index[i] for i in sort_order]
-    decoration=[decoration[i] for i in sort_order]
+    decoration = [decoration[i] for i in sort_order]
     if args.debug:
         print(('decoration_index  is  ' + str(decoration_index)))
     licores = getlicores()
     if not isinstance(lig, mol3D):
-        lig,emsg = lig_load(lig,licores)
+        lig, emsg = lig_load(lig, licores)
     else:
         lig.convert2OBMol()
         lig.charge = lig.OBMol.GetTotalCharge()
-    lig.convert2mol3D() # convert to mol3D
-   
+    lig.convert2mol3D()  # convert to mol3D
+
     ## create new ligand
     merged_ligand = mol3D()
     merged_ligand.copymol3D(lig)
-    for i,dec in enumerate(decoration):
-        print(('** decoration number ' +str(i)+ ' attaching ' + dec + ' at site '+str(decoration_index[i]) 
-    + '**\n'))
-        dec,emsg = lig_load(dec,licores)
+    for i, dec in enumerate(decoration):
+        print(('** decoration number '  + str(i) + ' attaching ' + dec + ' at site '+str(decoration_index[i])
+               + '**\n'))
+        dec, emsg = lig_load(dec, licores)
         # dec.OBMol.AddHydrogens()
         dec.convert2mol3D() # convert to mol3D
         if args.debug:
@@ -123,16 +122,16 @@ def decorate_ligand(args,ligand_to_decorate,decoration,decoration_index):
                 theta,urot = rotation_params(r1,merged_ligand.getAtom(decoration_index[i]).coords(),r2)
                 theta = vecangle(vecdiff(r0,merged_ligand.getAtom(decoration_index[i]).coords()),urot)
                 dec = rotate_around_axis(dec,r0,urot,theta)
-                
-        ## get the default distance between atoms in question 
+
+        ## get the default distance between atoms in question
         connection_neighbours = merged_ligand.getAtom(merged_ligand.getBondedAtomsnotH(decoration_index[i])[0])
         new_atom = dec.getAtom(decind)
-        target_distance = connection_neighbours.rad + new_atom.rad 
+        target_distance = connection_neighbours.rad + new_atom.rad
         position_to_place = vecdiff(new_atom.coords(),connection_neighbours.coords())
         old_dist= norm(position_to_place)
         missing = (target_distance - old_dist)/2
         dec.translate([missing*position_to_place[j] for j in [0,1,2]])
-        
+
         r1 = dec.getAtom(decind).coords()
         u = vecdiff(r1,merged_ligand.getAtom(decoration_index[i]).coords())
         dtheta = 2
@@ -166,7 +165,7 @@ def decorate_ligand(args,ligand_to_decorate,decoration,decoration_index):
         BO_mat = merged_ligand.populateBOMatrix()
         row_deleted = BO_mat[decoration_index[i]]
         bonds_to_add = []
-        
+
         # find where to put the new bonds ->>> Issue here.
         for j,els in enumerate(row_deleted):
             if els > 0:
@@ -181,7 +180,7 @@ def decorate_ligand(args,ligand_to_decorate,decoration,decoration_index):
                     bonds_to_add.append((bond_partner,(merged_ligand.natoms-1)+dec.cat[0],els))
                 else:
                     bonds_to_add.append((bond_partner,merged_ligand.natoms-1,els))
-        
+
         ## perfrom delete
         merged_ligand.deleteatom(decoration_index[i])
 
@@ -196,11 +195,11 @@ def decorate_ligand(args,ligand_to_decorate,decoration,decoration_index):
             merged_ligand.writexyz('merged' + str(i) + '.xyz')
             merged_ligand.printxyz()
             print('************')
-    
+
     merged_ligand.convert2OBMol()
     merged_ligand,emsg = ffopt('MMFF94',merged_ligand,[],0,[],False,[],100)
     BO_mat = merged_ligand.populateBOMatrix()
     if args.debug:
         merged_ligand.writexyz('merged_relaxed.xyz')
-        print(BO_mat)    
+        print(BO_mat)
     return(merged_ligand)