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On my version of OpenBabel (v. 2.0.2, Windows), if I read in the attached mol2 file and convert to xyz format, the carbonyl O in the mol2 file is changed to a H atom in the xyz file. The mol2 file wa…
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Caches for prior knowledge about subClassOf relationships for any nodes like diseases in a hierarchy, protein families, components of protein complexes
- [ ] Data model in `sqlalchemy` that connect…
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`readline` is a dependency of `pybel`'s ontology/rdf parser, `ontospy`. It is backed by a C library that currently fails to build on the readthedocs.org server.
Possible solutions:
1. RTFD are b…
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When the SMILES C=CCc1ccccc1OCC(O)CNC(C)C is converted to mol2 format, the first two atoms are assigned type C.cat - carbocation. If openbabel 2.1.1 is used, they are assigned the correct type of C.…
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There are serious problems with the Java bindings. It took me quite a while to get them working in both Linux and Mac OS. In Windows 7 x64 I had no problems. I just needed openbabel_java.dll from the …
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Yuan Zhao has sent me example.pdb after recently reporting problems converting from PDB to MOL2 using OB 2.0.0 (http://dx.doi.org/10.1021/ci7000028w).
On Windows, using OB 2.0.0a and 2.1.0, I've tr…
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Do this so graph manager knows what namespaces actually refer to, and this data can be traced
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[dbSNP](https://www.ncbi.nlm.nih.gov/projects/SNP/) is a website of single nucleotide polymorphisms. There might be around 100 million of these, but that's no match for modern computers!
- [x] Find…
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This database should be importable to python as a dictionary of `{namespace: {name: (canonical_namesapce, canonical_name)}}`
To Do:
- Write script to import and populate data from scratch (HGNC websi…
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When attempting to re-install RStudio from my Mac terminal using 'conda install rstudio', I get the following error message:
```
The following specifications were found to be in conflict:
- csd-p…