improve bond detection between hydrogens, sulfurs, atoms with alt codes and prevent bonds between different models

pekrau / MolScript

The MolScript program produces publication-quality images of macromolecular 3D structures.

https://pekrau.github.io/MolScript/

MIT License

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improve bond detection between hydrogens, sulfurs, atoms with alt codes and prevent bonds between different models #2

Open speleo3 opened 8 years ago

speleo3 commented 8 years ago

This patch doesn't change the default behavior of MolScript, but it activates some fine tuned bonding rules if the bonddistance parameter is set to 0.0.

prevent bonds between different alt locations
prevent bonds between different models
do radii overlap dependent bond detection, with special cutoffs for hydrogens and sulfurs

The cutoffs are hard coded and borrowed from PyMOL.

I also suggest to make bonddistance=0.0 the default with molauto.