Dear all,
I am producing rdkit conformers and writing them to pdb files but am finding
the atom indexing in rdkit is different from the written pdb. I would like this
because I want to do a substructure search (using rdkit) to give me a handle on
these atoms in the pdbfile.
Apologies if this has been discussed before.
Here is my code and output (the C=O looks like it's atoms 3,4 in rdkit but 4,5
in the pdb file):
Thanks,
Susan
*********************
In [1]: import rdkit
In [2]: from rdkit import Chem
...: from rdkit.Chem import AllChem
...: from rdkit.Chem.Draw import IPythonConsole
...:
In [3]: mol = Chem.MolFromSmiles("CC1=C(C(=O)C)C=CC=C1")
...: idx = AllChem.EmbedMultipleConfs(mol,numConfs=1,randomSeed=0xf00d,
...:
useExpTorsionAnglePrefs=True,useBasicKnowledge=True)
...:
In [4]: mol.GetSubstructMatch(Chem.MolFromSmiles('C(=O)'))
Out[4]: (3, 4)
In [5]: Chem.MolToPDBFile(mol,'./test.pdb')
In [6]: import biopandas
...: from biopandas.pdb import PandasPDB
...: ppdb = PandasPDB()
...: ppdb.read_pdb('./test.pdb')
...: ppdb.df['HETATM']
...:
Out[6]:
record_name atom_number blank_1 atom_name alt_loc residue_name blank_2 \
0 HETATM 1 C1 UNL
1 HETATM 2 C2 UNL
2 HETATM 3 C3 UNL
3 HETATM 4 C4 UNL
4 HETATM 5 O1 UNL
5 HETATM 6 C5 UNL
6 HETATM 7 C6 UNL
7 HETATM 8 C7 UNL
8 HETATM 9 C8 UNL
9 HETATM 10 C9 UNL
chain_id residue_number insertion ... x_coord y_coord z_coord \
0 1 ... 0.176 1.911 1.137
1 1 ... -0.513 0.759 0.511
2 1 ... 0.272 -0.184 -0.139
3 1 ... 1.717 -0.056 -0.210
4 1 ... 2.406 -0.917 -0.801
5 1 ... 2.344 1.118 0.435
6 1 ... -0.332 -1.286 -0.743
7 1 ... -1.696 -1.416 -0.682
8 1 ... -2.495 -0.504 -0.048
9 1 ... -1.879 0.575 0.540
occupancy b_factor blank_4 segment_id element_symbol charge line_idx
0 1.0 0.0 C NaN 0
1 1.0 0.0 C NaN 1
2 1.0 0.0 C NaN 2
3 1.0 0.0 C NaN 3
4 1.0 0.0 O NaN 4
5 1.0 0.0 C NaN 5
6 1.0 0.0 C NaN 6
7 1.0 0.0 C NaN 7
8 1.0 0.0 C NaN 8
9 1.0 0.0 C NaN 9
[10 rows x 21 columns]
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