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OpenChemistry / avogadrolibs

Avogadro libraries provide 3D rendering, visualization, analysis and data processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
https://two.avogadro.cc/
BSD 3-Clause "New" or "Revised" License
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Peptide builder command #910

Open ghutchis opened 2 years ago

ghutchis commented 2 years ago

We need to port the peptide builder tool from Avo1 for inserting simple peptide strands.

Screen Shot 2022-05-28 at 11 23 28 AM
ghutchis commented 2 years ago

It would be worth looking at the code in PeptideBuilder: https://github.com/clauswilke/PeptideBuilder/blob/master/PeptideBuilder/Geometry.py

ghutchis commented 2 years ago

Reference: M. Z. Tien, D. K. Sydykova, A. G. Meyer, C. O. Wilke (2013). PeptideBuilder: A simple Python library to generate model peptides. PeerJ 1:e80.

avo-bot commented 1 year ago

This issue has been mentioned on Avogadro Discussion. There might be relevant details there:

https://discuss.avogadro.cc/t/avogadro-2023-roadmap/4412/1

ghutchis commented 1 year ago

See also https://github.com/Boehringer-Ingelheim/pyPept

avo-bot commented 8 months ago

This issue has been mentioned on Avogadro Discussion. There might be relevant details there:

https://discuss.avogadro.cc/t/avogadro2-rev-1-98-1/5174/2

ghutchis commented 8 months ago

I generated the appropriate fragments: https://github.com/OpenChemistry/fragments/tree/main/amino

The script (https://github.com/OpenChemistry/fragments/blob/main/scripts/getamino.py) uses the PDB LigandExpo and Open Babel to generate z-matrix geometries from the ideal structures. This means we also have AIB PYL and SEC as well as NME and ACE caps.