[Open Babel] split multi-molecule structure into single-molecules

2021-08-27 Thread Jan Hummel via OpenBabel-discuss
Dear OpenBabel team! Please consider PubChem Comound with ID 74935604 https://pubchem.ncbi.nlm.nih.gov/compound/74935604 The InChI reads as InChI=1S/C21H30O2.C11H16O2/c1-5-6-7-8-15-12-18(22)20-16-11-14(2)9-10-17(16)2 1(3,4)23-19(20)13-15;1-2-3-4-5-9-6-10(12)8-11(13)7-9/h11-13,16-17,22H,5-10H2

[Open Babel] Random seeds in --gen3d? (followup)

2021-08-27 Thread theokindb
Dear developers, I want to generate 3d coordinates reproducibly. This issue came up in the past, https://github.com/openbabel/openbabel/issues/1934 with the suggested solution to provide an enviroment variable like so: export OB_RANDOM_SEED=42 My question: The page mentioned says #2241 is

Re: [Open Babel] Validating a SMILES string

2021-08-27 Thread Noel O'Boyle
Hi Anonymous, There is a one-line change source change that governs this behaviour, and it's one that I've changed in the past, and maybe it should be an option. If you have compiled Open Babel yourself, all you need to do is change "return true" to "return false" in the right place. The thing

[Open Babel] Validating a SMILES string

2021-08-27 Thread theokindb
Hi, I want to use openbabel to validate a SMILES string. I tried this: #!/usr/bin/env python3 from openbabel import openbabel mol = openbabel.OBMol() obConversion = openbabel.OBConversion() obConversion.SetInFormat('smi') # case_1: success is True success = obConversion.ReadString(mol,