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singa-bio / singa

:leaves: SiNGA (Simulation of Natural Systems using Graph Automata) is an open-source library containing tools especially for structural bioinformatics and systems biology.
MIT License
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bonds are not assigned correctly #41

Closed cleberecht closed 6 years ago

cleberecht commented 7 years ago

If leafs of the same kind have identifiers that are successive, they are considered connected. Hoever, this is not always true.

We should try to parse the SEQRES lines if they are there to determine the correct assignment of bonds. If no SEQRES lines are provided maybe we could determine the distance of the atoms that are to be connected and assign the bond on that basis.

cleberecht commented 6 years ago

Should be fixed with the new implementation of structures in version 3.0.1.