I'm trying to use RDKit to calculate the radial distribution function of selected atom types (e.g. oxygen atoms in water clusters).
Simple application of RDF implementation as available through rdkit.Chem.rdMolDescriptors (https://www.rdkit.org/docs/source/rdkit.Chem.rdMolDescriptors.html#rdkit.Chem.rdMolDescriptors.CalcRDF) applied to a molecule/conformer instance gives me a list of values, but i find it difficult to understand what this list represents and whether i can use it for my specific purpose (e.g. the plot of RDF between two atom types). Do you know where could I find more information on how this function is implemented, ideally with examples?
The minimal example could be:
from rdkit import Chem
from rdkit.Chem import rdMolDescriptors
with open("water3.sdf") as f:
data = f.read()
mol=Chem.MolFromMolBlock(data)
rdf=rdMolDescriptors.CalcRDF(mol)
rdf
which gives:
[0.0,
0.0,
0.0,
0.0,
1.56,
0.0,
0.0,
0.0,
0.015,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
2.768,
0.0,
0.0,
0.0,
0.027,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.797,
0.0,
0.0,
0.0,
0.008,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
2.747,
0.0,
0.0,
0.0,
0.026,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.322,
0.0,
0.0,
0.0,
0.003,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
2.281,
0.0,
0.0,
0.0,
0.022,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
1.56,
0.0,
0.0,
0.0,
0.015,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0]
The geometry on "water3.sdf" is (from https://bpb-us-e1.wpmucdn.com/sites.uw.edu/dist/1/2323/files/2019/01/W3_mp2_avtz_opt_geoms_1KJ-yuxycx.txt):
$ cat water3.sdf
-229.001716383436
OpenBabel11232314423D
9 6 0 0 0 0 0 0 0 0999 V2000
-2.5974 -0.1622 0.5184 O 0 0 0 0 0 0 0 0 0 0 0 0
-3.1124 0.5916 0.2141 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9915 -0.9170 0.0699 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 -0.8710 O 0 0 0 0 0 0 0 0 0 0 0 0
0.7671 0.0252 -0.2838 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.7671 -0.0252 -0.2838 H 0 0 0 0 0 0 0 0 0 0 0 0
2.5974 0.1622 0.5184 O 0 0 0 0 0 0 0 0 0 0 0 0
3.1124 -0.5916 0.2141 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9915 0.9170 0.0699 H 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
3 1 1 0 0 0 0
4 5 1 0 0 0 0
4 6 1 0 0 0 0
8 7 1 0 0 0 0
9 7 1 0 0 0 0
M END
$$$$