From e53af751d6db3881c6b50b70360d66a6e55e0229 Mon Sep 17 00:00:00 2001
From: ReallyRoland <123595711+rolan701@users.noreply.github.com>
Date: Thu, 14 Nov 2024 19:02:48 -0500
Subject: [PATCH 01/19] structgen upload... scary

hope this isn't awful
---
 molSimplify/Scripts/structgen.py | 152 ++++++++++++++++++++++++++++++-
 1 file changed, 149 insertions(+), 3 deletions(-)

diff --git a/molSimplify/Scripts/structgen.py b/molSimplify/Scripts/structgen.py
index 1d516e84..691e926a 100644
--- a/molSimplify/Scripts/structgen.py
+++ b/molSimplify/Scripts/structgen.py
@@ -12,6 +12,7 @@
     from openbabel import openbabel  # version 3 style import
 except ImportError:
     import openbabel  # fallback to version 2
+from openbabel import pybel
 import random
 import itertools
 import numpy as np
@@ -2306,6 +2307,7 @@ def mcomplex(args: Namespace, ligs: List[str], ligoc: List[int]
     emsg = ''
     complex3D: List[mol3D] = []
     occs0 = []      # occurrences of each ligand
+    complex2D = []
     toccs = 0       # total occurrence count (number of ligands)
     smilesligs = 0  # count how many smiles strings
     cats0: List[List[Union[int, str]]] = []  # connection atoms for ligands
@@ -2507,6 +2509,8 @@ def mcomplex(args: Namespace, ligs: List[str], ligoc: List[int]
                         lig = decorate_ligand(
                             lig, args.decoration[i], args.decoration_index[i], args.debug)
             lig.convert2mol3D()
+
+
             # initialize ligand
             lig3D, rempi, ligpiatoms = init_ligand(args, lig, tcats, keepHs, i)
             if emsg:
@@ -2710,16 +2714,34 @@ def mcomplex(args: Namespace, ligs: List[str], ligoc: List[int]
                 auxm = mol3D()
                 auxm.copymol3D(lig3D)
                 complex3D.append(auxm)
+
+                lig3D_copy = mol3D()
+                lig3D_copy.copymol3D(lig3D)
+                lig3D_copy.populateBOMatrix(bonddict=True)   
+                lig2D = lig3D_copy.mol3D_to_networkx()
+                complex2D.append(lig2D)
+
                 if 'a' not in lig.ffopt.lower():
                     for latdix in range(0, lig3D.natoms):
                         if args.debug:
                             print(('a is not ff.lower, so adding atom:  ' +
                                    str(latdix+core3D.natoms) + ' to freeze'))
                         frozenats.append(latdix+core3D.natoms)
+
+
+                
+                # combine molecules
+                if len(core3D.atoms) == 1:
+                    core3D_copy = mol3D()
+                    core3D_copy.copymol3D(core3D)
+                core3D_copy = core3D_copy.roland_combine(lig3D_copy, catoms)
+        
+
                 # combine molecules
                 core3D = core3D.combine(lig3D)
                 core3D.convert2OBMol()
                 core3D.convert2mol3D()
+
                 # remove dummy cm atom if requested
                 if rempi:
                     # remove the fictitious center atom, for aromatic-bonding ligands like benzene
@@ -2792,6 +2814,8 @@ def mcomplex(args: Namespace, ligs: List[str], ligoc: List[int]
             core3D.writexyz('complex_after_final_ff.xyz')
         # core3D,enc = ffopt(args.ff,core3D,connected,1,frozenats,freezeangles,MLoptbds,'Adaptive',args.debug)
 
+    core3D.bo_dict = core3D_copy.bo_dict
+
     return core3D, complex3D, emsg, this_diag, subcatoms_ext, mligcatoms_ext
 
 
@@ -2924,7 +2948,7 @@ def generate_report(args: Namespace, ligands: List[str], ligoc: List[int]
 
 
 def structgen(args: Namespace, rootdir: str, ligands: List[str], ligoc: List[int],
-              sernum: int, write_files: bool = True) -> Tuple[List[str], str, run_diag]:
+              sernum: int, write_files: bool = True, smart_generation: bool = True) -> Tuple[List[str], str, run_diag]:
     """Main structure generation routine - multiple structures
 
     Parameters
@@ -3015,7 +3039,129 @@ def structgen(args: Namespace, rootdir: str, ligands: List[str], ligoc: List[int
 
     # write xyz file
     if (not args.reportonly) and (write_files):
-        core3D.writexyz(fname, no_tabs=args.no_tabs)
+        core3D.writexyz(fname)
+        core3D.writemol2(fname)
+        
+        if smart_generation == True:
+            # optimize
+            metal_ind = core3D.findMetal()[0]
+            freeze_inds = []
+            for bond in core3D.bo_dict:
+                if metal_ind in bond:
+                    freeze_inds.append(bond[0]+1)
+                    freeze_inds.append(bond[1]+1)
+            freeze_inds = list(set(list(freeze_inds)))
+
+            obConversion = openbabel.OBConversion()
+            OBMol = openbabel.OBMol()
+            constraints = openbabel.OBFFConstraints()
+            obConversion.SetInAndOutFormats("mol2", "mol2")
+            obConversion.ReadString(OBMol, core3D.writemol2('',writestring = True))
+            for atom in freeze_inds:
+                constraints.AddAtomConstraint(atom)
+            ff = pybel._forcefields["uff"]
+            success = ff.Setup(OBMol, constraints)
+            ff.SetConstraints(constraints)
+            if success:
+                ff.ConjugateGradients(10000)
+                ff.GetCoordinates(OBMol)
+            obConversion.WriteFile(OBMol,fname+'BABEL.mol2')
+            obConversion.SetOutFormat("xyz")
+            obConversion.WriteFile(OBMol,fname+'BABEL.xyz')
+
+            # check if bad
+            mol = mol3D()
+            mol.readfrommol2(fname+'BABEL.mol2')
+            overlap, mind = mol.sanitycheck(silence = True)
+            if overlap:
+                mind = 1000
+                errors_dict = {}
+                for ii, atom1 in enumerate(mol.atoms):
+                    for jj, atom0 in enumerate(mol.atoms):
+                        if jj > ii:
+                            if atom1.ismetal() or atom0.ismetal():
+                                cutoff = 0.6
+                            elif (atom0.sym in ['N', 'O'] and atom1.sym == 'H') or (atom1.sym in ['N', 'O'] and atom0.sym == 'H'):
+                                cutoff = 0.6
+                            else:
+                                cutoff = 0.65
+                            if distance(atom1.coords(), atom0.coords()) < cutoff * (atom1.rad + atom0.rad):
+                                norm = distance(
+                                    atom1.coords(), atom0.coords())/(atom1.rad+atom0.rad)
+                                errors_dict.update(
+                                    {atom1.sym + str(ii)+'-'+atom0.sym+str(jj)+'_normdist': norm})
+                                if distance(atom1.coords(), atom0.coords()) < mind:
+                                    mind = distance(atom1.coords(), atom0.coords())
+                                    if mind == 0.0:
+                                        # move atom0 over a little bit
+                                        atom0.setcoords(np.array(atom1.coords())+0.02)
+                                        obConversion.SetInAndOutFormats("mol2", "mol2")
+                                        OBMol = openbabel.OBMol()
+                                        obConversion.ReadString(OBMol, mol.writemol2('',writestring = True))
+
+                ff = pybel._forcefields["gaff"]
+                success = ff.Setup(OBMol, constraints)
+                ff.SetConstraints(constraints)
+                if success:
+                    ff.ConjugateGradients(10000)
+                    ff.GetCoordinates(OBMol)
+                    ff = pybel._forcefields["uff"]
+                    success = ff.Setup(OBMol, constraints)
+                    ff.SetConstraints(constraints)
+                    if success:
+                        ff.ConjugateGradients(10000)
+                        ff.GetCoordinates(OBMol)
+        
+
+            obConversion.SetOutFormat("mol2")
+            obConversion.WriteFile(OBMol,fname+'BABEL.mol2')
+            obConversion.SetOutFormat("xyz")
+            obConversion.WriteFile(OBMol,fname+'BABEL.xyz')
+
+            # check if overextended H:
+            mol = mol3D()
+            mol.readfrommol2(fname+'BABEL.mol2')
+            changed = False
+            for bond in mol.bo_dict:
+                atom0 = mol.atoms[bond[0]]
+                atom1 = mol.atoms[bond[1]]
+                dist = -100000000000
+                if atom0.sym == 'C' and atom1.sym == 'H':
+                    dist = atom0.distance(atom1)
+                    L1 = np.array(tuple(atom0.coords()))
+                    L2 = np.array(tuple(atom1.coords()))
+                    if dist > 1.15:
+                        vector = L1 - L2
+                        required_dist = dist - 1.15
+                        new_point = move_point(atom1.coords(), vector, required_dist)
+                        atom1.setcoords(new_point)
+                        changed = True
+                elif atom0.sym == 'H' and atom1.sym == 'C':
+                    dist = atom0.distance(atom1)
+                    if dist > 1.15:
+                        L1 = np.array(tuple(atom0.coords()))
+                        L2 = np.array(tuple(atom1.coords()))
+                        vector = L2 - L1
+                        required_dist = dist - 1.15
+                        new_point = move_point(atom0.coords(), vector, required_dist)
+                        atom0.setcoords(new_point)
+                        changed = True
+            if changed:
+                mol.writemol2(fname+'BABEL.mol2')
+                obConversion = openbabel.OBConversion()
+                OBMol = openbabel.OBMol()
+                obConversion.SetInAndOutFormats("mol2", "mol2")
+                obConversion.ReadFile(OBMol, fname+'BABEL.mol2')
+                ff = pybel._forcefields["uff"]
+                success = ff.Setup(OBMol, constraints)
+                ff.SetConstraints(constraints)
+                if success:
+                    ff.ConjugateGradients(10000)
+                    ff.GetCoordinates(OBMol)
+                obConversion.WriteFile(OBMol,fname+'BABEL.mol2')
+                obConversion.SetOutFormat("xyz")
+                obConversion.WriteFile(OBMol,fname+'BABEL.xyz')
+
     strfiles.append(fname)
     if write_files:
         # write report file
@@ -3037,4 +3183,4 @@ def structgen(args: Namespace, rootdir: str, ligands: List[str], ligoc: List[int
         args.gui.app.processEvents()
     print(('\nIn folder '+rootdir+' generated 1 structure!'))
 
-    return strfiles, emsg, this_diag
+    return strfiles, emsg, this_diag
\ No newline at end of file

From dc29fa736d5e179835c50dc2a54be364b279a036 Mon Sep 17 00:00:00 2001
From: ReallyRoland <123595711+rolan701@users.noreply.github.com>
Date: Thu, 14 Nov 2024 19:03:53 -0500
Subject: [PATCH 02/19] Update structgen.py

added move_point compatibility
---
 molSimplify/Scripts/structgen.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/molSimplify/Scripts/structgen.py b/molSimplify/Scripts/structgen.py
index 691e926a..545592ff 100644
--- a/molSimplify/Scripts/structgen.py
+++ b/molSimplify/Scripts/structgen.py
@@ -26,6 +26,7 @@
                                           getPointu,
                                           kabsch,
                                           midpt,
+                                          move_point,
                                           norm,
                                           PointTranslateSph,
                                           reflect_through_plane,
@@ -3183,4 +3184,4 @@ def structgen(args: Namespace, rootdir: str, ligands: List[str], ligoc: List[int
         args.gui.app.processEvents()
     print(('\nIn folder '+rootdir+' generated 1 structure!'))
 
-    return strfiles, emsg, this_diag
\ No newline at end of file
+    return strfiles, emsg, this_diag

From 249141fe01a369387ad558a1bc7d4461bd44b0b4 Mon Sep 17 00:00:00 2001
From: ReallyRoland <123595711+rolan701@users.noreply.github.com>
Date: Thu, 14 Nov 2024 19:08:29 -0500
Subject: [PATCH 03/19] Update structgen.py

no_tabs brought back
---
 molSimplify/Scripts/structgen.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/molSimplify/Scripts/structgen.py b/molSimplify/Scripts/structgen.py
index 545592ff..fe4532a9 100644
--- a/molSimplify/Scripts/structgen.py
+++ b/molSimplify/Scripts/structgen.py
@@ -3040,7 +3040,7 @@ def structgen(args: Namespace, rootdir: str, ligands: List[str], ligoc: List[int
 
     # write xyz file
     if (not args.reportonly) and (write_files):
-        core3D.writexyz(fname)
+        core3D.writexyz(fname, no_tabs=args.no_tabs)
         core3D.writemol2(fname)
         
         if smart_generation == True:

From efaa28cc2b78a133158ea73eaac853634925f68d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 15 Nov 2024 00:14:18 +0000
Subject: [PATCH 04/19] [pre-commit.ci] auto fixes from pre-commit hooks

---
 molSimplify/Scripts/structgen.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/molSimplify/Scripts/structgen.py b/molSimplify/Scripts/structgen.py
index fe4532a9..79c49036 100644
--- a/molSimplify/Scripts/structgen.py
+++ b/molSimplify/Scripts/structgen.py
@@ -2718,7 +2718,7 @@ def mcomplex(args: Namespace, ligs: List[str], ligoc: List[int]
 
                 lig3D_copy = mol3D()
                 lig3D_copy.copymol3D(lig3D)
-                lig3D_copy.populateBOMatrix(bonddict=True)   
+                lig3D_copy.populateBOMatrix(bonddict=True)
                 lig2D = lig3D_copy.mol3D_to_networkx()
                 complex2D.append(lig2D)
 
@@ -2730,13 +2730,13 @@ def mcomplex(args: Namespace, ligs: List[str], ligoc: List[int]
                         frozenats.append(latdix+core3D.natoms)
 
 
-                
+
                 # combine molecules
                 if len(core3D.atoms) == 1:
                     core3D_copy = mol3D()
                     core3D_copy.copymol3D(core3D)
                 core3D_copy = core3D_copy.roland_combine(lig3D_copy, catoms)
-        
+
 
                 # combine molecules
                 core3D = core3D.combine(lig3D)
@@ -3042,7 +3042,7 @@ def structgen(args: Namespace, rootdir: str, ligands: List[str], ligoc: List[int
     if (not args.reportonly) and (write_files):
         core3D.writexyz(fname, no_tabs=args.no_tabs)
         core3D.writemol2(fname)
-        
+
         if smart_generation == True:
             # optimize
             metal_ind = core3D.findMetal()[0]
@@ -3112,7 +3112,7 @@ def structgen(args: Namespace, rootdir: str, ligands: List[str], ligoc: List[int
                     if success:
                         ff.ConjugateGradients(10000)
                         ff.GetCoordinates(OBMol)
-        
+
 
             obConversion.SetOutFormat("mol2")
             obConversion.WriteFile(OBMol,fname+'BABEL.mol2')

From d172d305d6962d81357962a3bd3b17535e902a35 Mon Sep 17 00:00:00 2001
From: ReallyRoland <123595711+rolan701@users.noreply.github.com>
Date: Thu, 14 Nov 2024 19:15:45 -0500
Subject: [PATCH 05/19] Update structgen.py

fixed trailing whitespace

From 2646cb6eb4f4f94ed189ece936e60124a8a2ef92 Mon Sep 17 00:00:00 2001
From: ReallyRoland <123595711+rolan701@users.noreply.github.com>
Date: Thu, 14 Nov 2024 19:22:00 -0500
Subject: [PATCH 06/19] Update mol3D.py

needed for my structgen changes
---
 molSimplify/Classes/mol3D.py | 93 ++++++++++++++++++++++++++++++++++++
 1 file changed, 93 insertions(+)

diff --git a/molSimplify/Classes/mol3D.py b/molSimplify/Classes/mol3D.py
index bcf76db9..bc26571f 100644
--- a/molSimplify/Classes/mol3D.py
+++ b/molSimplify/Classes/mol3D.py
@@ -6470,3 +6470,96 @@ def get_molecular_mass(self):
             self.mass = mol_mass
 
         return mol_mass
+
+    def mol3D_to_networkx(self,get_symbols:bool=True,get_bond_order:bool=True,get_bond_distance:bool=False):
+        g = nx.Graph()
+        # get every index of atoms in mol3D object
+        for atom_ind in range(0,self.natoms):
+            # set each atom as a node in the graph, and add symbol information if wanted
+            data={}
+            if get_symbols:
+                data['Symbol']=self.getAtom(atom_ind).symbol()
+                data['atom3D']=self.getAtom(atom_ind)
+            g.add_node(atom_ind,**data)
+        # get every bond in mol3D object
+        bond_info=self.bo_dict
+        for bond in bond_info:
+            # set each bond as an edge in the graph, and add symbol information if wanted
+            data={}
+            if get_bond_order:
+                data['bond_order']=bond_info[bond]
+            if get_bond_distance:
+                distance=self.getAtom(bond[0]).distance(self.getAtom(bond[1]))
+                data['bond_distance']=distance
+            g.add_edge(bond[0],bond[1],**data)
+        return g
+    
+    def roland_combine(self, mol, catoms, bond_to_add=[], dirty=False):
+        """
+        Combines two molecules. Each atom in the second molecule
+        is appended to the first while preserving orders. Assumes
+        operation with a given mol3D instance, when handed a second mol3D instance.
+
+        Parameters
+        ----------
+            mol : mol3D
+                mol3D class instance containing molecule to be added.
+            bond_to_add : list, optional
+                List of tuples (ind1,ind2,order) bonds to add. Default is empty.
+            dirty : bool, optional
+                Add atoms without worrying about bond orders. Default is False.
+
+        Returns
+        -------
+            cmol : mol3D
+                New mol3D class containing the two molecules combined.
+        """
+
+        cmol = self
+        bo_dict = cmol.bo_dict
+
+        print('lig_dict')
+        print(mol.bo_dict)
+
+        if cmol.bo_dict == False:
+            # only central metal
+            bo_dict = {}
+        new_bo_dict = copy.deepcopy(bo_dict)
+
+        # add ligand connections
+        for bo in mol.bo_dict:    
+            ind1 = bo[0] + len(cmol.atoms)
+            ind2 = bo[1] + len(cmol.atoms)
+            new_bo_dict[(ind1,ind2)]=mol.bo_dict[(bo[0],bo[1])]
+
+        # connect metal to ligand
+        metal_ind = cmol.findMetal()[0]
+        for atom in catoms:
+            ind1 = metal_ind
+            ind2 = atom + len(cmol.atoms)
+            new_bo_dict[(ind1,ind2)]=1
+
+        for atom in mol.atoms:
+            cmol.addAtom(atom, auto_populate_BO_dict = False)
+
+        cmol.bo_dict = new_bo_dict
+        return cmol
+
+    def graph_from_bodict(self, bo_dict):
+        g = []
+        for i, atom in enumerate(self.atoms):
+            sub_g = []
+            connected = []
+            for tup in bo_dict:
+                if i in tup:
+                    if i != tup[0]:
+                        connected.append(tup[0])
+                    else:
+                        connected.append(tup[1])
+            for j in range(0,len(self.atoms)):
+                if j in connected:
+                    sub_g.append(1.)
+                else:
+                    sub_g.append(0.)
+            g.append(sub_g)
+        return g

From 73312b75a24f4ea2e9fb1f898e2c4d9ee58906c2 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 15 Nov 2024 00:22:50 +0000
Subject: [PATCH 07/19] [pre-commit.ci] auto fixes from pre-commit hooks

---
 molSimplify/Classes/mol3D.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/molSimplify/Classes/mol3D.py b/molSimplify/Classes/mol3D.py
index bc26571f..cee6b9ce 100644
--- a/molSimplify/Classes/mol3D.py
+++ b/molSimplify/Classes/mol3D.py
@@ -6493,7 +6493,7 @@ def mol3D_to_networkx(self,get_symbols:bool=True,get_bond_order:bool=True,get_bo
                 data['bond_distance']=distance
             g.add_edge(bond[0],bond[1],**data)
         return g
-    
+
     def roland_combine(self, mol, catoms, bond_to_add=[], dirty=False):
         """
         Combines two molecules. Each atom in the second molecule
@@ -6527,7 +6527,7 @@ def roland_combine(self, mol, catoms, bond_to_add=[], dirty=False):
         new_bo_dict = copy.deepcopy(bo_dict)
 
         # add ligand connections
-        for bo in mol.bo_dict:    
+        for bo in mol.bo_dict:
             ind1 = bo[0] + len(cmol.atoms)
             ind2 = bo[1] + len(cmol.atoms)
             new_bo_dict[(ind1,ind2)]=mol.bo_dict[(bo[0],bo[1])]

From 1845b3a944942c05c179c2049c8405ee46363824 Mon Sep 17 00:00:00 2001
From: ReallyRoland <123595711+rolan701@users.noreply.github.com>
Date: Mon, 18 Nov 2024 11:01:01 -0500
Subject: [PATCH 08/19] Update mol3D.py

added import copy
---
 molSimplify/Classes/mol3D.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/molSimplify/Classes/mol3D.py b/molSimplify/Classes/mol3D.py
index 31a57534..ea105983 100644
--- a/molSimplify/Classes/mol3D.py
+++ b/molSimplify/Classes/mol3D.py
@@ -10,6 +10,7 @@
 import sys
 import tempfile
 import time
+import copy
 import xml.etree.ElementTree as ET
 import numpy as np
 import networkx as nx

From 15564168f5e46238fd44e1d10a7c48474fae61f1 Mon Sep 17 00:00:00 2001
From: ReallyRoland <123595711+rolan701@users.noreply.github.com>
Date: Mon, 18 Nov 2024 11:06:38 -0500
Subject: [PATCH 09/19] Update structgen.py

made dist a float
---
 molSimplify/Scripts/structgen.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/molSimplify/Scripts/structgen.py b/molSimplify/Scripts/structgen.py
index 79c49036..de6ac248 100644
--- a/molSimplify/Scripts/structgen.py
+++ b/molSimplify/Scripts/structgen.py
@@ -3126,7 +3126,7 @@ def structgen(args: Namespace, rootdir: str, ligands: List[str], ligoc: List[int
             for bond in mol.bo_dict:
                 atom0 = mol.atoms[bond[0]]
                 atom1 = mol.atoms[bond[1]]
-                dist = -100000000000
+                dist = -100000000000.0
                 if atom0.sym == 'C' and atom1.sym == 'H':
                     dist = atom0.distance(atom1)
                     L1 = np.array(tuple(atom0.coords()))

From 66d7dd5276bd0ee24365a7927ec9e0e82aadeb5e Mon Sep 17 00:00:00 2001
From: ReallyRoland <123595711+rolan701@users.noreply.github.com>
Date: Mon, 18 Nov 2024 11:16:06 -0500
Subject: [PATCH 10/19] Update structgen.py

caveats for more unforseen instances of core3D building
---
 molSimplify/Scripts/structgen.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/molSimplify/Scripts/structgen.py b/molSimplify/Scripts/structgen.py
index de6ac248..44208929 100644
--- a/molSimplify/Scripts/structgen.py
+++ b/molSimplify/Scripts/structgen.py
@@ -2322,6 +2322,7 @@ def mcomplex(args: Namespace, ligs: List[str], ligoc: List[int]
     batslist: List[List[int]] = []
     bats: List[int] = []
     ffoption_list = []  # for each ligand, keeps track of what the forcefield option is.
+    copied = False # for determinining if core3D needs to be copied or not
     # load bond data
     MLbonds = loaddata('/Data/ML.dat')
     # calculate occurrences, denticities etc for all ligands
@@ -2732,9 +2733,14 @@ def mcomplex(args: Namespace, ligs: List[str], ligoc: List[int]
 
 
                 # combine molecules
-                if len(core3D.atoms) == 1:
+                if len(core3D.atoms) == 1 and copied == False:
                     core3D_copy = mol3D()
                     core3D_copy.copymol3D(core3D)
+                    copied = True
+                elif copied == False:
+                    core3D_copy = mol3D()
+                    core3D_copy.copymol3D(core3D)
+                    copied = True
                 core3D_copy = core3D_copy.roland_combine(lig3D_copy, catoms)
 
 

From 0fe26cd6a4e65722c5466252e40ed48ae5844b25 Mon Sep 17 00:00:00 2001
From: ReallyRoland <123595711+rolan701@users.noreply.github.com>
Date: Mon, 18 Nov 2024 11:52:44 -0500
Subject: [PATCH 11/19] Update mol3D.py

fixed writemol2
---
 molSimplify/Classes/mol3D.py | 26 +++++++++++++++++++-------
 1 file changed, 19 insertions(+), 7 deletions(-)

diff --git a/molSimplify/Classes/mol3D.py b/molSimplify/Classes/mol3D.py
index ea105983..ae6f8a78 100644
--- a/molSimplify/Classes/mol3D.py
+++ b/molSimplify/Classes/mol3D.py
@@ -3814,7 +3814,10 @@ def writemol2(self, filename, writestring=False, ignoreX=False, force=False):
                 if atom.sym == 'X':
                     self.deleteatom(i)
         if not len(self.graph):
-            self.createMolecularGraph()
+            if self.bo_dict:
+                self.graph = self.graph_from_bodict(self.bo_dict)
+            else:
+                self.createMolecularGraph()
         if not self.bo_dict and not force:
             self.convert2OBMol2()
         csg = csgraph.csgraph_from_dense(self.graph)
@@ -3863,6 +3866,9 @@ def writemol2(self, filename, writestring=False, ignoreX=False, force=False):
                 atom_types_mol2 = ''
             type_ind = atom_types.index(atom.sym)
             atom_coords = atom.coords()
+            if atom.sym == 'P':
+                pass
+                #print(atom_coords)
             ss += str(i+1) + ' ' + atom.sym+str(int(atom_type_numbers[type_ind])) + '\t' + \
                 '{}  {}  {} '.format(atom_coords[0], atom_coords[1], atom_coords[2]) + \
                 atom.sym + atom_types_mol2 + '\t' + atom_groups[i] + \
@@ -3875,14 +3881,20 @@ def writemol2(self, filename, writestring=False, ignoreX=False, force=False):
             bondorders = True
         else:
             bondorders = False
+
         for i, b1 in enumerate(bonds[0]):
-            b2 = bonds[1][i]
-            if b2 > b1 and not bondorders:
-                ss += str(bond_count)+' '+str(b1+1) + ' ' + str(b2+1) + ' 1\n'
-                bond_count += 1
-            elif b2 > b1 and bondorders:
+            if not bondorders:
+                b2 = bonds[1][i]
+                if b2 > b1:
+                    ss += str(bond_count)+' '+str(b1+1) + ' ' + str(b2+1) + ' 1\n'
+                    bond_count += 1
+        if bondorders:
+            for bond in self.bo_dict:
+                b1 = bond[0]
+                b2 = bond[1]
                 ss += str(bond_count)+' '+str(b1+1) + ' ' + str(b2+1) + \
                     ' {}\n'.format(self.bo_dict[(int(b1), int(b2))])
+                bond_count += 1
         ss += '@<TRIPOS>SUBSTRUCTURE\n'
         unique_group_names = np.unique(atom_group_names)
         for i, name in enumerate(unique_group_names):
@@ -3898,7 +3910,7 @@ def writemol2(self, filename, writestring=False, ignoreX=False, force=False):
                     filename = filename.split('.')[0]+'.mol2'
             with open(filename, 'w') as file1:
                 file1.write(ss)
-
+                
     def closest_H_2_metal(self, delta=0):
         """
         Get closest hydrogen atom to metal.

From cb913ccd4622d0d51b7b3c5b45ac08a4794fbdd4 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 18 Nov 2024 16:52:57 +0000
Subject: [PATCH 12/19] [pre-commit.ci] auto fixes from pre-commit hooks

---
 molSimplify/Classes/mol3D.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/molSimplify/Classes/mol3D.py b/molSimplify/Classes/mol3D.py
index ae6f8a78..88fb6351 100644
--- a/molSimplify/Classes/mol3D.py
+++ b/molSimplify/Classes/mol3D.py
@@ -3910,7 +3910,7 @@ def writemol2(self, filename, writestring=False, ignoreX=False, force=False):
                     filename = filename.split('.')[0]+'.mol2'
             with open(filename, 'w') as file1:
                 file1.write(ss)
-                
+
     def closest_H_2_metal(self, delta=0):
         """
         Get closest hydrogen atom to metal.

From 1f290549602e330d1436b0821a9cd900f9c31d17 Mon Sep 17 00:00:00 2001
From: ReallyRoland <123595711+rolan701@users.noreply.github.com>
Date: Tue, 19 Nov 2024 12:42:11 -0500
Subject: [PATCH 13/19] Update structgen.py

smart generation default change and addition to mcomplex
---
 molSimplify/Scripts/structgen.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/molSimplify/Scripts/structgen.py b/molSimplify/Scripts/structgen.py
index 44208929..e5201fa2 100644
--- a/molSimplify/Scripts/structgen.py
+++ b/molSimplify/Scripts/structgen.py
@@ -2261,7 +2261,7 @@ def align_dent3_lig(args, cpoint, batoms, m3D, core3D, coreref, ligand, lig3D,
     return lig3D_aligned, frozenats, MLoptbds
 
 
-def mcomplex(args: Namespace, ligs: List[str], ligoc: List[int]
+def mcomplex(args: Namespace, ligs: List[str], ligoc: List[int], smart_generation: bool
              ) -> Tuple[mol3D, List[mol3D], str, run_diag, List[int], List[int]]:
     """Main ligand placement routine
 
@@ -2821,7 +2821,8 @@ def mcomplex(args: Namespace, ligs: List[str], ligoc: List[int]
             core3D.writexyz('complex_after_final_ff.xyz')
         # core3D,enc = ffopt(args.ff,core3D,connected,1,frozenats,freezeangles,MLoptbds,'Adaptive',args.debug)
 
-    core3D.bo_dict = core3D_copy.bo_dict
+    if smart_generation == True:
+        core3D.bo_dict = core3D_copy.bo_dict
 
     return core3D, complex3D, emsg, this_diag, subcatoms_ext, mligcatoms_ext
 
@@ -2955,7 +2956,7 @@ def generate_report(args: Namespace, ligands: List[str], ligoc: List[int]
 
 
 def structgen(args: Namespace, rootdir: str, ligands: List[str], ligoc: List[int],
-              sernum: int, write_files: bool = True, smart_generation: bool = True) -> Tuple[List[str], str, run_diag]:
+              sernum: int, write_files: bool = True, smart_generation: bool = False) -> Tuple[List[str], str, run_diag]:
     """Main structure generation routine - multiple structures
 
     Parameters
@@ -2998,7 +2999,7 @@ def structgen(args: Namespace, rootdir: str, ligands: List[str], ligoc: List[int
                 return strfiles, emsg, this_diag
         else:
             core3D, complex3D, emsg, this_diag, subcatoms_ext, mligcatoms_ext = mcomplex(
-                args, ligands, ligoc)
+                args, ligands, ligoc, smart_generation = smart_generation)
             if args.debug:
                 print(('subcatoms_ext are ' + str(subcatoms_ext)))
             if emsg:

From 5f645ebaa35612293c49e7883590db6eec5b2711 Mon Sep 17 00:00:00 2001
From: ReallyRoland <123595711+rolan701@users.noreply.github.com>
Date: Tue, 19 Nov 2024 12:58:07 -0500
Subject: [PATCH 14/19] Update mol3D.py

changed writemol2 to hopefully pass test
---
 molSimplify/Classes/mol3D.py | 24 ++++++------------------
 1 file changed, 6 insertions(+), 18 deletions(-)

diff --git a/molSimplify/Classes/mol3D.py b/molSimplify/Classes/mol3D.py
index 88fb6351..ea105983 100644
--- a/molSimplify/Classes/mol3D.py
+++ b/molSimplify/Classes/mol3D.py
@@ -3814,10 +3814,7 @@ def writemol2(self, filename, writestring=False, ignoreX=False, force=False):
                 if atom.sym == 'X':
                     self.deleteatom(i)
         if not len(self.graph):
-            if self.bo_dict:
-                self.graph = self.graph_from_bodict(self.bo_dict)
-            else:
-                self.createMolecularGraph()
+            self.createMolecularGraph()
         if not self.bo_dict and not force:
             self.convert2OBMol2()
         csg = csgraph.csgraph_from_dense(self.graph)
@@ -3866,9 +3863,6 @@ def writemol2(self, filename, writestring=False, ignoreX=False, force=False):
                 atom_types_mol2 = ''
             type_ind = atom_types.index(atom.sym)
             atom_coords = atom.coords()
-            if atom.sym == 'P':
-                pass
-                #print(atom_coords)
             ss += str(i+1) + ' ' + atom.sym+str(int(atom_type_numbers[type_ind])) + '\t' + \
                 '{}  {}  {} '.format(atom_coords[0], atom_coords[1], atom_coords[2]) + \
                 atom.sym + atom_types_mol2 + '\t' + atom_groups[i] + \
@@ -3881,20 +3875,14 @@ def writemol2(self, filename, writestring=False, ignoreX=False, force=False):
             bondorders = True
         else:
             bondorders = False
-
         for i, b1 in enumerate(bonds[0]):
-            if not bondorders:
-                b2 = bonds[1][i]
-                if b2 > b1:
-                    ss += str(bond_count)+' '+str(b1+1) + ' ' + str(b2+1) + ' 1\n'
-                    bond_count += 1
-        if bondorders:
-            for bond in self.bo_dict:
-                b1 = bond[0]
-                b2 = bond[1]
+            b2 = bonds[1][i]
+            if b2 > b1 and not bondorders:
+                ss += str(bond_count)+' '+str(b1+1) + ' ' + str(b2+1) + ' 1\n'
+                bond_count += 1
+            elif b2 > b1 and bondorders:
                 ss += str(bond_count)+' '+str(b1+1) + ' ' + str(b2+1) + \
                     ' {}\n'.format(self.bo_dict[(int(b1), int(b2))])
-                bond_count += 1
         ss += '@<TRIPOS>SUBSTRUCTURE\n'
         unique_group_names = np.unique(atom_group_names)
         for i, name in enumerate(unique_group_names):

From 27b4f0ad0dc618831f077e6d7c547de256140f34 Mon Sep 17 00:00:00 2001
From: ReallyRoland <123595711+rolan701@users.noreply.github.com>
Date: Thu, 21 Nov 2024 13:41:17 -0500
Subject: [PATCH 15/19] Update generator.py

---
 molSimplify/Scripts/generator.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/molSimplify/Scripts/generator.py b/molSimplify/Scripts/generator.py
index 6429892f..d9290f01 100644
--- a/molSimplify/Scripts/generator.py
+++ b/molSimplify/Scripts/generator.py
@@ -236,7 +236,7 @@ def startgen(argv, flag, gui, inputfile_str=None, write_files=True):
         print(('adding ' + str(args.ligadd) + ' to ligand database  with name ' +
                args.ligname + ' and connection atom(s) ' + str(args.ligcon)))
         addtoldb(smimol=args.ligadd, sminame=args.ligname, smident=len(args.ligcon),
-                 smicat=str(args.ligcon).strip('[]'), smigrps="custom", smictg="custom", ffopt=args.ligffopt)
+                 smicat=str(args.ligcon).strip('[]'), smigrps="custom", smictg="custom", ffopt=args.ligffopt, overwrite=args.overwrite)
 
     # normal structure generation or transition state building
     else:

From 25676d1197d4e653dc3c6dc255492f56deb5aad4 Mon Sep 17 00:00:00 2001
From: ReallyRoland <123595711+rolan701@users.noreply.github.com>
Date: Thu, 21 Nov 2024 13:43:30 -0500
Subject: [PATCH 16/19] Update inparse.py

---
 molSimplify/Scripts/inparse.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/molSimplify/Scripts/inparse.py b/molSimplify/Scripts/inparse.py
index 6a58fc14..d16579c9 100644
--- a/molSimplify/Scripts/inparse.py
+++ b/molSimplify/Scripts/inparse.py
@@ -529,6 +529,7 @@ def parseinputfile(args, inputfile_str=None):
     args.dbvlinks = False
     args.rprompt = False
     set_rundir = False
+    args.overwrite = False
 
     # (we should remove these where posible)
     # THIS NEEDS CLEANING UP TO MINIMIZE DUPLICATION WITH parsecommandline
@@ -582,8 +583,6 @@ def parseinputfile(args, inputfile_str=None):
                     args.jobdir = l[1]
                 else:
                     args.jobdirblank = True
-            if (l[0] == '-no_tabs'):
-                args.no_tabs = True
             ### parse structure generation arguments ###
             if (l[0] == '-bind' and len(l[1:]) > 0):
                 l = [_f for _f in re.split(' |,|\t', line) if _f]  # noqa: E741
@@ -930,6 +929,8 @@ def parseinputfile(args, inputfile_str=None):
                 args.ligcon = list_to_add[0]
             if (l[0] == '-ligffopt'):
                 args.ffopt = l[1]
+            if (l[0] == '-overwrite'):
+                args.overwrite = l[1]
             # parse postprocessing arguments
             if (l[0] == '-postp'):
                 args.postp = True
@@ -1171,7 +1172,7 @@ def parseinputs_advanced(*p):
         "-calccharge", help="Automatically calculate net complex charge. By default this is ON.", default=True)
     parser.add_argument(
         "-genall", help="Generate complex both with and without FF opt, default False", action="store_true")  # geometry
-    parser.add_argument("-decoration_index", help="list of indices on each ligand to decorate",
+    parser.add_argument("-decoration_index", help="list of indicies on each ligand to decorate",
                         action="store_true")  # decoration indexes, one list per ligand
     parser.add_argument("-decoration", help="list of SMILES for each decoratation",
                         action="store_true")  # decoration, one list ligand
@@ -1196,8 +1197,6 @@ def parseinputs_advanced(*p):
         "-reportonly", help='add this flag if you just want the report, without actual structure generation. Currently does not support pentadentates.')
     parser.add_argument(
         "-jobmanager", help='use jobmanager naming convention.', default=False)
-    parser.add_argument(
-        "-no_tabs", help="add this flag to use spaces instead of tabs in written xyz files", default=False)
     if len(p) == 1:  # only one input, printing help only
         args = parser.parse_args()
         return args

From e5157142b77c80623e9a0ae0a880af6f525a6e42 Mon Sep 17 00:00:00 2001
From: ReallyRoland <123595711+rolan701@users.noreply.github.com>
Date: Thu, 21 Nov 2024 13:57:15 -0500
Subject: [PATCH 17/19] Update inparse.py

no_tabs fix 1
---
 molSimplify/Scripts/inparse.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/molSimplify/Scripts/inparse.py b/molSimplify/Scripts/inparse.py
index d16579c9..a1be70f7 100644
--- a/molSimplify/Scripts/inparse.py
+++ b/molSimplify/Scripts/inparse.py
@@ -583,6 +583,8 @@ def parseinputfile(args, inputfile_str=None):
                     args.jobdir = l[1]
                 else:
                     args.jobdirblank = True
+            if (l[0] == '-no_tabs'):
+                args.no_tabs = True
             ### parse structure generation arguments ###
             if (l[0] == '-bind' and len(l[1:]) > 0):
                 l = [_f for _f in re.split(' |,|\t', line) if _f]  # noqa: E741

From 819343a76db4ea3d787955956cc839981ed4a8f3 Mon Sep 17 00:00:00 2001
From: ReallyRoland <123595711+rolan701@users.noreply.github.com>
Date: Thu, 21 Nov 2024 13:58:08 -0500
Subject: [PATCH 18/19] Update inparse.py

no_tabs fix 2
---
 molSimplify/Scripts/inparse.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/molSimplify/Scripts/inparse.py b/molSimplify/Scripts/inparse.py
index a1be70f7..5895fbea 100644
--- a/molSimplify/Scripts/inparse.py
+++ b/molSimplify/Scripts/inparse.py
@@ -1174,7 +1174,7 @@ def parseinputs_advanced(*p):
         "-calccharge", help="Automatically calculate net complex charge. By default this is ON.", default=True)
     parser.add_argument(
         "-genall", help="Generate complex both with and without FF opt, default False", action="store_true")  # geometry
-    parser.add_argument("-decoration_index", help="list of indicies on each ligand to decorate",
+    parser.add_argument("-decoration_index", help="list of indices on each ligand to decorate",
                         action="store_true")  # decoration indexes, one list per ligand
     parser.add_argument("-decoration", help="list of SMILES for each decoratation",
                         action="store_true")  # decoration, one list ligand
@@ -1199,6 +1199,8 @@ def parseinputs_advanced(*p):
         "-reportonly", help='add this flag if you just want the report, without actual structure generation. Currently does not support pentadentates.')
     parser.add_argument(
         "-jobmanager", help='use jobmanager naming convention.', default=False)
+    parser.add_argument(
+        "-no_tabs", help="add this flag to use spaces instead of tabs in written xyz files", default=False)
     if len(p) == 1:  # only one input, printing help only
         args = parser.parse_args()
         return args

From 7a86b9040e88e2248b5ab146f46dcd9feebb92e9 Mon Sep 17 00:00:00 2001
From: ReallyRoland <123595711+rolan701@users.noreply.github.com>
Date: Thu, 21 Nov 2024 16:26:07 -0500
Subject: [PATCH 19/19] Update test_inparse.py

---
 tests/test_inparse.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/test_inparse.py b/tests/test_inparse.py
index 686ee2bd..2e6eb348 100644
--- a/tests/test_inparse.py
+++ b/tests/test_inparse.py
@@ -10,7 +10,8 @@ def test_parseinputfile_empty():
     defaults = {'skipANN': False, 'oldANN': False,
                 'dbvdent': False, 'dbvconns': False,
                 'dbvhyb': False, 'dbvlinks': False,
-                'rprompt': False, 'rundir': f'{os.getcwd()}/Runs'}
+                'rprompt': False, 'rundir': f'{os.getcwd()}/Runs',
+                'overwrite': False,}
 
     args = Namespace()
     parseinputfile(args, inputfile_str=' ')