parse from local pdb - Githubissues

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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parse from local pdb #45

Closed cleberecht closed 7 years ago

cleberecht commented 7 years ago

To speed up the parsing for time critical applications we should provide a possibility to parse structures from local distributions.

fkaiserbio commented 7 years ago

added first stub for parsing of structures from local PDB
introduced LocalPDB object to configure a local PDB installation: this should be extended further to allow configuration of spitted directories, zipped files or not, etc.
if a local file cannot be found, online fetching is tried as fallback