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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…
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Hi,
I read your recent [post](http://rdkit.blogspot.co.uk/2017/05/looking-at-platinum-dataset.html) about conformer generation and decided to install rdkit to give it a go in my machine.
It look…
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```
File "/home/yutong/Code/deepchem/deepchem/models/tests/test_api.py", line 101, in test_singletask_sklearn_rf_RDKIT_descriptor_regression_API
dataset = loader.featurize(input_file)
File …
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It's very easy to add support for forcefield-defined bond charge corrections, so I'm going to do that now, since it will enable dielectric corrections (timely with @cfennell's visit).
### API Proposal…
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Using the following script:
```
#!/usr/bin/env python2
# output the MACCS bitstring of each molecule found in a MOL2 file
import rdkit.Chem
import sys
def RetrieveMol2Block(fileLikeObject, delimit…
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Just a quick question. I was trying to understand the output files, its bit challenging for me. How does the numbers tells the connectivity of atoms(how to know which atom connects to which atom) for …
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when running `native_tuples_from_sdf` I get a warning with certain sdf files.
Here's the debug log (with our added print statements) when generating fingerprints for
/srv/home/ecaceres/chembl20_mini…
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Given `CC(=O)[C@@]1(O)CC[C@H]2[C@@H]3CCC4=CC(=O)CC[C@]4(C)[C@H]3CC[C@]12C`, the babel-generated 3d molecules differ at two stereocenters from the Schrodinger Ligprep-generated molecule.
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Currently, the `openeye.get_charges` function has an undocumented "feature" in that it generates entirely new conformations for the provided molecule and returns those along with the new charges (http…