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After trying e3fp, I found that , for one molecule, many fingerprint can be generated. Which fingerprint should I use when performing machine learning tasks?
kexul updated
3 years ago
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Great project! I'm currently incorporating spyrmsd in my conformer generation code. Everything is fine except when there are fewer number of heavy atoms when I seem to run into some convergence proble…
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recog_wav shell:
wac@waccuda:/data/espnet/egs/aishell/asr1$ recog_wav.sh --cmvn /home/wac/PycharmProjects/espnet_tts/model.v2/data/train_sp/cmvn.ark --lang_model /home/wac/PycharmProjects/espnet_tts…
wac81 updated
3 years ago
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Some species cannot be embedded, e.g.: `COCO[O]`
If they happen to be radicals, generate conformers for the RH species, then remove the corresponding H atom from the coordinates
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There should be an option to submit conformer generation using FF as an ARC job to run these in parallel. Useful for large molecules.
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I built the 2020.03.1dev1 rdkit (current master branch) so I can set my own bound matrix during conformer generation.
However, what I found was when using `SetBoundsMat`, the time needed to generat…
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**Describe the bug**
Attempting to parameterize a molecule which has been created with the option `allow_undefined_stereo=True` will yield an exception when used with the OpenEye backend (I don't thi…
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#### Code Sample, a copy-pastable example if possible
```
#!/usr/bin/env python
import chemcoord as cc
import time
import sys
conformer=sys.argv[1]
try:
print (cc.Cartesian.read_xyz(con…
em819 updated
4 years ago
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Current ARC master errors when trying to generate conformers for `C1=CC2=CC=C1C2`.
![image](https://user-images.githubusercontent.com/10817103/66240575-09486600-e6cb-11e9-8431-65122f86efec.png)
…
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For some of the ring-cage host guest systems, the conformer generation step (possibly from charge assignment) fails:
``` python
from simtk.openmm.app import PDBFile
from openforcefield.topology i…