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When I try to run scan with either an xyz and key file generated with sdf2tinkerxyz for toluene or benzene (sdf files obtained from pubchem) I get the following error:
```bash
$ scan toluene.xyz …
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Trying to use:
```
openforcefield.topology.Molecule.from_rdkit( rdmol, allow_undefined_stereo=False)
```
where the molecule in question is `c1c[cH:1][c:2](cc1)[CH2:3][c:4]2ccccc2`:
![image](https…
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- [x ] I believe this to be a bug with Open Babel
## Environment Information
Open Babel version: 2.4.1
Operating system and version: Fedora 27 Linux
## Expected Behavior
% obabel -iinchi …
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In slide 4 of https://www.slideshare.net/NextMoveSoftware/building-on-sand-standard-inchis-on-nonstandard-molfiles, @johnmay shows that Open Babel is not reading the "atomic mass delta" in Mol files c…
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Using the connection table provided below, OpenBabel and the InChI code directly from IUPAC generates different parity:
OpenBabel :
InChI=1/C10H13N5O4/c1-5-3-15(10(18)12-9(5)17)8-2-6(13-14-11)7(4-…
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Hello,
Can the following nuclei be added to ChEBI?
name: tin-119
is_a: CHEBI:27007 ! tin
InChI=1/Sn/i1-1
name: boron-11
is_a: CHEBI:27560 ! boron
InChI=1/B/i1+0
name: tellurium-125
is_a: CHEBI:30…
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We need some extra fields in the compounds table. I underestimated a bit of complexity. The following fields are needed in addition to what we currently have:
permanent_charge: signed integer
inchi…
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InChI generation seems to be failing for phenylic radicals. I end up with gaps like this in inchiDictionary.txt:
CH2CO(38) CH2CO InChI=1/C2H2O/c1-2-3/h1H2 CCGKOQOJPYTBIH-UHFFFAOYAO
PHE…