Hi Angelica,
if torsion_lists is the tuple of of (non_ring, ring) torsion lists in mol:
torsion_lists = TorsionFingerprints.CalculateTorsionLists(mol)
you can get the same list where the atom index is replaced by a
(PDB_atom_serial, PDB_atom_name) tuple as follows:
torsion_lists_sn = [[tuple([[tuple([(
mol.GetAtomWithIdx(i).GetMonomerInfo().GetSerialNumber(),
mol.GetAtomWithIdx(i).GetMonomerInfo().GetName().strip()
) for i in t]) for t in tt], v]) for tt, v in tl] for tl in torsion_lists]
which is a rather unreadable nested list comprehension equivalent to the
following series of nested loops:
torsion_lists_sn = []
for tl in torsion_lists:
tl2 = []
for tt, v in tl:
tv2 = []
for t in tt:
tt2 = []
for i in t:
pdb_res_info = mol.GetAtomWithIdx(i).GetMonomerInfo()
serial = pdb_res_info.GetSerialNumber()
name = pdb_res_info.GetName().strip()
tt2.append((serial, name))
tv2.append(tuple(tt2))
tl2.append((tv2, v))
torsion_lists_sn.append(tl2)
Cheers,
p.
On 03/27/19 21:43, Angelica Parente wrote:
I’m trying to use the module
|rdkit.Chem.TorsionFingerprints.||CalculateTorsionLists to print out a
list of torsions. I pass in a PDB file using Chem.MolFromPDBFile, and
would ideally like the torsion list to specify the atoms using the
atom names and/or numbers from the PDB file. Right now I get a list of
rdkit atom indices, and am not sure how to convert these back to the
original PDB naming/numbering schemes. |
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*Thanks,*
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*Angelica
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