T , 2012-05-23 16:06 +0200, Hitesh Patel rakstīja:
> How can I join two molecules at specified atoms. These joining atoms might
> have same Index numbers, because two joining atoms are in different
> molecules.
It goes along these lines:
builder = ob.OBBuilder()
# Use ring conformations from existing 3D coordinates
builder.SetKeepRings()
# Copy molecule if necessary
mol = ob.OBMol(parent)
# Disable charge perception if desired
mol.SetAutomaticPartialCharge(False)
# Remember the size of molecule
n = mol.NumAtoms()
# Add second molecule
mol += mol2
# Copy over any extra residue info from mol2 if necessary, since +=
# doesn't do it for you.
# Figure out the numbers for atoms in connection
a = n
b = n + 5 # 5th atom in mol2
# There are alternatives to this, e.g., finding atom by name.
# Atom names are stored in residues, so first get the residue
res = mol.GetResidue(mol.NumResidues()-2)
for i in ob.OBResidueAtomIter(res):
if res.GetAtomID(i) == aname:
a = i.GetIdx()
break
# The same for the second atom
res = mol.GetResidue(mol.NumResidues()-1)
for i in ob.OBResidueAtomIter(res):
if res.GetAtomID(i) == bname:
b = i.GetIdx()
break
# Connect the fragments
builder.Connect(mol, a, b)
Reinis
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