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**Is your feature request related to a problem? Please describe.**
Currently `RDKitToolkitWrapper._elf_compute_electrostatic_energy` computes the energy for one conformer at a time. Perhaps it wo…
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Dear developers,
I attempted to calculate coarse-grained partial charges for graphene-like molecules using a Python script.
Initially, my atomistic model comprises ~ 40 atoms and, after coarse…
yel21 updated
2 years ago
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## Expected behavior ##
The contents of `charges` is always expected to contain partial charges.
## Actual behavior ##
For mmtf, formal charges are fed into `charges`, which a) leads to confu…
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I believe this to be a bug with LigParGen
## Issue Information
Software name & Version : LigParGen server from website
Method: I am a first time user of this server, so tested alanine to check i…
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The fastest (but not necessarily least accurate!) method to treat the interaction of a peptide with the cell membrane is via electrostatics. One of the simplest models here is to consider the material…
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## Flow 1
### On Search
- default_selection and lower.range is not correctly calculated for the item_id : ‘7a1eb7d6-c522-5a69-936d-b9ebbaf88869’. Kindly check for others as well or please explain th…
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I am using a new protein dataset and using pafnucy predict the score. As the Pafnucy README said, I need to specify the --charge_scaler if I am using a dataset different from PDBbindv2016. BUT how ca…
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**Describe the bug**
The newer version of `openeye-toolkits` fails to assign partial charges where the previous version did so successfully. The core of the attached Python script is
```python
fr…
ntBre updated
1 month ago
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### Describe the bug
For some inputs, xtb-python produces impossible outputs which are not handled as errors.
### To Reproduce
This is a script to demonstrate unhandled xTB errors for simple cube…
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I am generate charges using espaloma via the OpenFF toolkitwrapper interface in the following manner: https://github.com/IAlibay/partial_charge_experiments/blob/main/scripts/run-espaloma.py
Calling…