Hi,
I'm having a few problems in creating molecules from scratch in Python (see
attached code)
My code creates a molecule by creating atoms from coordinates, elements and
bonds.
The main issue is that I get different atom types than I would get by parsing a simple PDB
created with same coordinates and elements (but no bonds).
Is there any other step to do other than BeginModify()/EndModify() to be applied to the
molecule to achieve the same results I would get by reading a file?
Thanks!
S
--
Stefano Forli, PhD
Staff Scientist
Molecular Graphics Laboratory
Dept. of Integrative Structural
and Computational Biology, MB-112F
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.
tel: +1 (858)784-2055
fax: +1 (858)784-2860
email: [email protected]
http://www.scripps.edu/~forli/
obmol = ob.OBMol()
obmol.BeginModify()
for chain in chainList:
cId = chain.getChid()
for res in chain
obres = obmol.NewResidue()
obres.SetName(res.name )
obres.SetNum( res.num )
obres.SetChain(cId)
for atom in res.atoms:
obatom = obmol.NewAtom()
obatom.SetAtomicNum( atom.atomicNum )
obres.AddAtom(obatom)
obatom.SetResidue(obres)
obres.SetAtomID(obatom, atom.name )
coords = atom.coords
vec = ob.vector3()
vec.SetX(coords[0])
vec.SetY(coords[1])
vec.SetZ(coords[2])
obatom.SetVector(vec)
for i,j in bonds[1]:
bondOrder = bondOrderList['%d,%d'%(i,j)]
obmol.AddBond(i, j, bondOrder)
obmol.SetTitle(title)
obmol.EndModify(True)
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