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FIXED BUG: fixed restrictContactsToMax/MinRange. Couldn't delete contacts at the same time as looping in them NEW CLASSES NodeNbh and EdgeNbh, now used in getNodeNbh and getEdgeNbh New method getResidueType
FIXED BUG in initialisation of fullLength when reading from file. In case of no sequence and nodes provided, was not getting correctly the maximum value for contacts. Now using the method getMaxContact from new class ContactList NEW FUNCTIONALITY in Graph: -New member variable modified -New methods addEdge, delEdge, restrictContactsToMaxRange, restrictContactsToMinRange, getContacts, getNodes, copy -Improved slightly the implementation of getEdgeNbh FIXED BUG in initialisation of fullLenght when reading from file. In case of no sequence and nodes provided, was not getting correctly the maximum value for contacts. Now using the method getMaxContact from ContactList New class ContactList NEW FUNCTIONALITY in Graph: -New member variable modified -New methods addEdge, delEdge, restrictContactsToMaxRange, restrictContactsToMinRange, getContacts, getNodes, copy -Improved slightly the implementation of getEdgeNbh New method getRange in Contact
New functionality: added methods to get node/edge neighbours
made Graph.directed public
Moved ContactMap and EdgeState out of this repository. Extra functionality of ContactMap now in Graph: - new member variables fullLength, obsLength, numContacts. New method getIntMatrix - removed getCM method
FIXED BUG in get_db_graph_info, was not dealing well with the case of chaincode being NULL in the database
FIXED BUG: in getCM when directed was passing a reference to the contacts object and not deep copying it!
Now passing also chaincode from Pdb object to Graph object in get_graph
Fixed bug: wasn't initialising accode, chain and chaincode when reading to file. Now all set to "" when not present in file
FIXED 2 BUGS. NEW FEATURE reading graph from db given graph_id Bugs: - nodes TreeMap in read_graph_from_file contained one letter res codes, now three letter codes - in getCM was passing residues as a TreeMap of nums to three letter residue types, now passing one letter residue types New constructor for getting graph from db given graph_id, new method to go with that get_db_graph_info
Made cutoff and ct public
Made some fields public: sequence, accode, chaincode, model
NEW FEATURE: Read and write graphs from file fully implemented. Refactored read_contacts_from_file to read_graph_from_file. Now can read other fields as well as contacts. Also gets nodes if sequence present New method write_graph_to_file
FIXED BUG: last commit didn't fix bug correctly: Changed the ContactMap constructor to put into residueNums and residueTypes nums from 1 to maximum of residues.keySet() Made public accode and chain fields in Graph
FIXED BUG: getCM wasn't working well when reading from db and there were unobserved residues Now setting the sequence to blank when reading from db. Also when reading from file (still nodes reading is not implemented) In ContactMap constructor different handling when sequence is blank
Changed input in constructor for reading from db: chain->chaincode Now getgraphid initialises too the internal chain code (pchain_code from graph db)
NEW FUNCTIONALITY: reading of graph from db is fully implemented for all cases New chain member variable in the Info classes, read in get_asym_id (Pdbase) and in get_chain_id (Msdsd) Reading chain also in Pdb in read_pdb_data_from_file Not reading chain anymore in read_atomData of PdbaseInfo Added oneletter2threeletter and getoneletter2threeletter to AA class Changes in Graph: - added db static vars and getUserName method - new member variables graphid and sm_id - new method read_graph_from_db to read contacts, nodes (and sequence from nodes) from db - new method getgraphid New Exception class GraphIdNotFoundError
Implemented basic reading contacts from file
NEW FUNCTIONALITY: can retrieve now a ContactMap object from a Graph object New method getCM in Graph. New member variables: sequence, accode, chain, nodes, directed Passing more data from Pdb to Graph in get_graph New constructor in ContactMap
Initial commit of the proteinstructure package. Contains classes to use pdb protein structures
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