Hi;
I am using RDKit_2014_03_1, on a red-hat desktop. In particular, I am
using the python bindings (python 2.4) and following the examples here:
http://nbviewer.ipython.org/github/rdkit/UGM_2013/blob/master/Notebooks/Whats_new.ipynb
Specifically I tried doing the following:
import rdkit
from rdkit import Chem
mol=Chem.MolFromPDBFile("PHE_93.1")
for i in range(0, mol.GetNumAtoms(), 1):
mi = mol.GetAtomWithIdx(i).GetMonomerInfo()
print i, mi.GetName(), mi.GetResidueName()
and obtained the following error:
Traceback (most recent call last):
File "./test.py", line 16, in ?
print i, mi.GetName(), mi.GetResidueName()
Boost.Python.ArgumentError: Python argument types in
AtomPDBResidueInfo.GetResidueName(AtomPDBResidueInfo)
did not match C++ signature:
GetResidueName(RDKit::AtomPDBResidueInfo {lvalue})
The pdb file only includes one residue and looks like this:
ATOM 1436 N PHE 93 196.314 9.904 38.012 0.00 0.00
ATOM 1437 H PHE 93 195.347 9.975 38.305 0.00 0.00
ATOM 1438 CA PHE 93 196.781 8.564 37.635 0.00 0.00
ATOM 1439 HA PHE 93 197.578 8.262 38.314 0.00 0.00
ATOM 1440 CB PHE 93 195.593 7.589 37.796 0.00 0.00
ATOM 1441 HB2 PHE 93 195.307 7.554 38.849 0.00 0.00
ATOM 1442 HB3 PHE 93 194.735 7.992 37.267 0.00 0.00
ATOM 1443 CG PHE 93 195.779 6.161 37.314 0.00 0.00
ATOM 1444 CD1 PHE 93 195.346 5.781 36.026 0.00 0.00
ATOM 1445 HD1 PHE 93 194.917 6.516 35.357 0.00 0.00
ATOM 1446 CE1 PHE 93 195.458 4.442 35.608 0.00 0.00
ATOM 1447 HE1 PHE 93 195.127 4.154 34.619 0.00 0.00
ATOM 1448 CZ PHE 93 195.991 3.474 36.479 0.00 0.00
ATOM 1449 HZ PHE 93 196.073 2.443 36.161 0.00 0.00
ATOM 1450 CE2 PHE 93 196.416 3.849 37.766 0.00 0.00
ATOM 1451 HE2 PHE 93 196.826 3.108 38.437 0.00 0.00
ATOM 1452 CD2 PHE 93 196.315 5.190 38.180 0.00 0.00
ATOM 1453 HD2 PHE 93 196.641 5.475 39.169 0.00 0.00
ATOM 1454 C PHE 93 197.350 8.560 36.207 0.00 0.00
ATOM 1455 O PHE 93 198.419 8.002 35.973 0.00 0.00
Did I mess up the installation??
Thanks!
-Sergio
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