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I am preparing a Debian package for openchemlib. Each package on Debian requires a description of at least ~200 characters. What would be the best description for openchemlib? It could as well go to R…
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I see in the examples (and the code) that the first column of the output csv file should contain the input SMILES, but when I run the program I just get id numbers and there is no way that I see to ma…
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Some tests at Travis are failing due to:
AttributeError: 'module' object has no attribute 'OBConformerSearch'
It seems that the OpenBabel version provided by Travis (`libopenbabel4 amd64 2.3…
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**Description:**
- RDKit Version: 2018.03.1
- Platform: Windows / Ubuntu
Depending on the contents of line 2 of a molfile, bonds at stereocenters are drawn in correctly (wedges) or wrong(fl…
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Hello,
I' m trying to run a conformer generation starting from a Smile string.
Some atoms in the input file have got a specific stereochemistry but this is not retain in all the output structure.
…
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**Description:**
Running conformer searches with RDKit and for some molecules takes extremely long (citronellal). The 2nd filter step (after optimization) takes hours even for relatively small number…
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None of the existing examples explain the useful fingerprint algebra that can be done. This should be added as an example or to the README.
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Before release, no SEA code should be present in this repo. Not certain the best place to put this, but it shouldn't be in the version history here either. A few ways to handle this off the top of my …
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Since several other feature requests suggest conformer evaluation, coordinate generation, etc. it makes sense to have a framework for molecular mechanics evaluations.
For example, loadable force fi…
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When generating structures from SMILES (or INCHI, when supported) - by default we only generate a single conformer, but should an an option to build a trajectory with multiple conformers.
Will also n…