improve bond detection between hydrogens, sulfurs, atoms with alt codes and prevent bonds between different models#2
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speleo3 wants to merge 2 commits intopekrau:masterfrom
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improve bond detection between hydrogens, sulfurs, atoms with alt codes and prevent bonds between different models#2speleo3 wants to merge 2 commits intopekrau:masterfrom
speleo3 wants to merge 2 commits intopekrau:masterfrom
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If the bonddistance parameter is 0.0, then: - prevent bonds between different alt locations - prevent bonds between different models - do radii overlap dependent bond detection, with special cutoffs for hydrogens and sulfurs (cutoffs borrowed from PyMOL)
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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.
The cutoffs are hard coded and borrowed from PyMOL.
I also suggest to make bonddistance=0.0 the default with molauto.