-
Merge the relevant code from
https://github.com/ersilia-os/vsflow-ligand-based-3d-screening
https://github.com/ersilia-os/smiles-to-3d
into this repository if we prefer easiness of editing
-
Hi, thanks for the contribution on this library, especially the TorchProtein part.
One suggestion would be loadsequence optimization. In current implementation:
```python
for i, (sequence, smi…
-
Hi,
I am trying to get atoms' property (e.g bonds, atomic_mass), but the error shows 'Atom' object has no attribute 'bonds'
import skchem
import rdkit.Chem
mol = skchem.Mol.from_smiles('CC(…
-
In composer some of my users will change an atom to a lower case "o" thinking its an oxygen atom "O", and the smiles get screwed up. Is there some way to prevent lower case letters as input for atom …
-
Just pasting here a handy guide how to create new conda-forge packages.
https://www.pyopensci.org/python-package-guide/tutorials/publish-conda-forge.html
-
My current workaround in python:
```
# remap sequence encodings:
encoding_remapping = {
sbol3.IUPAC_DNA_ENCODING: sbol2.SBOL_ENCODING_IUPAC,
sbol3.IUPAC_PROTEIN_ENCODING: …
-
It has been observed that tetrahedral chirality setting at anomeric centers changes randomly in print via `Chemistry::OpenSMILES::Writer::write_SMILES()`. Failcase: `N[C@@]12NC(N[C@]2(NC(N1))N)`.
-
**Describe the bug**
I've come across a couple of cases where the library change handler SMARTS matching code hangs when attempting to match a full molecule SMILES.
This is likely because there …
-
您好,我现在希望使用您的软件进行分子批量对接。我在ZINC库中下载了smiles格式的配体,因为看到您的软件输入格式中没有这个选项,因此自己使用OPENBABEL进行小分子的文件转换,将.smi转换为.mol和.sdf。希望使用这个软件。但是我转换为这两个格式后,均不能成功完成软件中的准备配体部分。请问问题出在哪里呢?您的代码中要求的配体格式要求是什么呢?期望得到您的回复,万分感谢。
-
When the component is loaded with a smile variable that is asynchronously set:
``
A race condition between `componentDidUpdate` and `handleJsmeLoad` occurs:
![image](https://user-images.githu…