Adapt Fit3D and the data model to be able to locate intermolecular matches

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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Adapt Fit3D and the data model to be able to locate intermolecular matches #36

Closed fkaiserbio closed 7 years ago

fkaiserbio commented 7 years ago

to adapt Fit3D to be able to locate intermolecular matches (across multiple chains) we have to implement Structure#getCopy
subsequently constructors of Fit3DAlignment should be modified in such a way: (StructuralMotif,Structure)
currently this is not possible because identifiers are unique only on chain level (see BranchSubstructure#removeSubstructure)
we should discuss how we can achieve this

fkaiserbio commented 7 years ago

this was solved by allowing Fit3D to search motifs in StructuralModels
however, implementation of substructure removing is not ideal