recligmin

rdmin.py

@@ -0,0 +1,46 @@
+#!/usr/bin/env python3
+from rdkit.Chem import AllChem as Chem
+import numpy as np
+import sys, gzip, re
+
+rname = sys.argv[1]
+lname = sys.argv[2]
+rec = Chem.MolFromPDBFile(rname)  
+
+if lname.endswith('.gz'):
+    lig = next(Chem.ForwardSDMolSupplier(gzip.open(lname),sanitize=False))
+else:    
+    lig = next(Chem.SDMolSupplier(sys.argv[2],sanitize=False))
+
+complex = Chem.CombineMols(rec,lig)
+Chem.SanitizeMol(complex)
+
+ff = Chem.UFFGetMoleculeForceField(complex,ignoreInterfragInteractions=False)
+print("Before:",ff.CalcEnergy())
+
+for p in range(rec.GetNumAtoms()):
+    ff.AddFixedPoint(p)
+
+ff.Minimize()
+
+print("After:",ff.CalcEnergy())
+
+cpos = complex.GetConformer().GetPositions()
+conf = lig.GetConformer()
+for (i,xyz) in enumerate(cpos[-lig.GetNumAtoms():]):
+    conf.SetAtomPosition(i,xyz)
+
+m = m = re.search(r'(.*)_(\d+).sdf(.gz)?',lname)
+if m:
+    outname = '%s_rec_uff_%s.sdf.gz'%(m.group(1),m.group(2))
+else:
+    outname = lname.replace('.gz','').replace('.sdf','')+'_rec_uff.sdf.gz'
+outfile = gzip.open(outname,'wt')
+out = Chem.SDWriter(outfile)
+out.write(lig)
+out.close()
+outfile.close()
+
+
+
+