Hello, Sometimes, as a computer scientist, I am quite worried by chemical software libraries:
$ cat data/ethanol.pqr COMPND ethanol AUTHOR GENERATED BY OPEN BABEL 2.3.2 HETATM 1 C LIG 1 -0.017 -0.601 0.000 0.04138432 1.700 C HETATM 2 C LIG 1 1.247 0.248 -0.000 -0.04182526 1.700 C HETATM 3 H LIG 1 1.285 0.894 -0.888 0.02516417 1.100 H HETATM 4 H LIG 1 1.270 0.916 0.872 0.02516417 1.100 H HETATM 5 H LIG 1 2.150 -0.369 0.015 0.02516417 1.100 H HETATM 6 H LIG 1 -0.096 -1.231 -0.903 0.05542120 1.100 H HETATM 7 H LIG 1 -0.096 -1.231 0.903 0.05542120 1.100 H HETATM 8 O LIG 1 -1.086 0.337 0.000 -0.39527743 1.520 O HETATM 9 H LIG 1 -1.944 -0.125 -0.003 0.20938346 1.100 H CONECT 1 8 7 2 6 CONECT 1 CONECT 2 1 5 4 3 CONECT 2 CONECT 3 2 CONECT 4 2 CONECT 5 2 CONECT 6 1 CONECT 7 1 CONECT 8 1 9 CONECT 9 8 MASTER 0 0 0 0 0 0 0 0 9 0 9 0 END # cat data/ethanol.plr COMPND ethanol -0.016600 -0.601400 0.000000 -0.203500 1.950000 1.247400 0.248500 -0.000100 0.144100 1.950000 1.285200 0.894300 -0.887700 0.123000 1.200000 1.270100 0.915700 0.872200 0.123000 1.200000 2.149700 -0.369300 0.015500 0.123000 1.200000 -0.095800 -1.230700 -0.903200 0.123000 1.200000 -0.095700 -1.230800 0.903400 0.123000 1.200000 -1.085800 0.337100 0.000300 -0.289300 1.700000 -1.944300 -0.124700 -0.003200 -0.267700 1.200000 END The .plr file was generated with rdkit. The .pqr file with obabel. Maybe I'm out of luck, or I don't understand something, but the two files don't agree on any single VdW radius (5th column in the .plr file; 10th column in the .pqr file for HETATM lines). Here is the code I used for rdkit: --- periodic_table = Chem.GetPeriodicTable() def get_radius(atom): return periodic_table.GetRvdw(atom.GetAtomicNum()) [...] atoms = mol.GetAtoms() [...] radius = get_radius(atom) [...] --- Am I doing something wrong? Isn't there a more direct way to access the VdW radius of an atom when iterating over the atoms of a molecule? Who should I trust? obabel? rdkit? the nearest real-world chemist? Thanks, F. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss