Read MOL strings instead of PDB strings (#117)

Reading and writing to PDB strings can alter the structure of output molecules due to poor information on bonding in PDB strings. Reading and writing to MOL strings maintains structural information of output molecules.

Changes:
Line 250 -> mol_string = cmd.get_str('mol',selection)
253 -> obconversion.SetInAndOutFormats('mol', 'mol')
255 -> obconversion.ReadString(mol, mol_string)
256 -> removed
269 -> mol_string = obconversion.WriteString(mol)
273 -> cmd.read_molstr(mol_string, name,state=0,finish=1,discrete=1)
280 -> mol_string = cmd.get_str('mol',selection)
283 -> obconversion.SetInAndOutFormats('mol', 'mol')
285 -> obconversion.ReadString(mol, mol_string)
286 -> removed
320 -> mol_string = obconversion.WriteString(mol)
321 -> cmd.read_molstr(mol_string, name_n,state=0,finish=1,discrete=1)
329 -> mol_string = obconversion.WriteString(mol)
331 -> cmd.read_molstr(mol_string, name,state=0,finish=1,discrete=1)

Author: Polo-Zecc

plugins/optimize.py

@@ -247,13 +247,12 @@ def enable_disable_entry(var):
 
 
 def minimize(selection='all', forcefield='MMFF94s', method='Conjugate Gradients', nsteps0= 500, conv=0.0001, cutoff=False, cut_vdw=6.0, cut_elec=8.0):
-    pdb_string = cmd.get_pdbstr(selection)
+    mol_string = cmd.get_str('mol',selection)
     name = cmd.get_legal_name(selection)
     obconversion = ob.OBConversion()
-    obconversion.SetInAndOutFormats('pdb', 'pdb')
+    obconversion.SetInAndOutFormats('mol', 'mol')
     mol = ob.OBMol()
-    obconversion.ReadString(mol, pdb_string)
-    mol.AddHydrogens()
+    obconversion.ReadString(mol, mol_string)
     ff = ob.OBForceField.FindForceField(forcefield) ## GAFF, MMFF94s, MMFF94, UFF, Ghemical
     ff.Setup(mol)
     if cutoff == True:
@@ -266,24 +265,23 @@ def minimize(selection='all', forcefield='MMFF94s', method='Conjugate Gradients'
         ff.SteepestDescent(nsteps0, conv)
     ff.GetCoordinates(mol)
     nrg = ff.Energy()
-    pdb_string = obconversion.WriteString(mol)
+    mol_string = obconversion.WriteString(mol)
     cmd.delete(name)
     if name == 'all':
         name = 'all_'
-    cmd.read_pdbstr(pdb_string, name)
+    cmd.read_molstr(mol_string, name,state=0,finish=1,discrete=1)
     print('#########################################')
     print('The Energy of %s is %8.2f %s       '  % (name, nrg, ff.GetUnit()))
     print('#########################################')
 
 
 def conf_search(selection='all', forcefield='MMFF94s', method='Weighted', nsteps1= 500, conformers=25, lowest_conf=5):
-    pdb_string = cmd.get_pdbstr(selection)
+    mol_string = cmd.get_str('mol',selection)
     name = cmd.get_legal_name(selection)
     obconversion = ob.OBConversion()
-    obconversion.SetInAndOutFormats('pdb', 'pdb')
+    obconversion.SetInAndOutFormats('mol', 'mol')
     mol = ob.OBMol()
-    obconversion.ReadString(mol, pdb_string)
-    mol.AddHydrogens()
+    obconversion.ReadString(mol, mol_string)
     ff = ob.OBForceField.FindForceField(forcefield) ## GAFF, MMFF94s, MMFF94, UFF, Ghemical
     ff.Setup(mol)
     if method == 'Weighted':
@@ -317,21 +315,22 @@ def conf_search(selection='all', forcefield='MMFF94s', method='Weighted', nsteps
             name_n = '%s%02d' % (name, i)
             cmd.delete(name_n)
             mol.SetConformer(orden) 
-            pdb_string = obconversion.WriteString(mol)
-            cmd.read_pdbstr(pdb_string, name_n)
+            mol_string = obconversion.WriteString(mol)
+            cmd.read_molstr(mol_string, name_n,state=0,finish=1,discrete=1)
             if i != 0:
                 rmsd = cmd.fit(name_n, '%s00' % name, quiet=1)
             print('%15s | %10.2f%9s |%6.1f'    % (name_n, nrg, nrg_unit, rmsd))
         print('##############################################')
     else:
         ff.GetCoordinates(mol)
         nrg = ff.Energy()
-        pdb_string = obconversion.WriteString(mol)
+        mol_string = obconversion.WriteString(mol)
         cmd.delete(name)
-        cmd.read_pdbstr(pdb_string, name)
+        cmd.read_molstr(mol_string, name,state=0,finish=1,discrete=1)
         print('#########################################')
         print('The Energy of %s is %8.2f %s       '  % (name, nrg, ff.GetUnit()))
         print('#########################################')
 
 cmd.extend('minimize', minimize)
 cmd.extend('conf_search', conf_search)
+