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r154
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AA.java 135 (12 years ago) by duarte: 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
Contact.java 123 (12 years ago) by duarte: Initial commit of the proteinstructure package. Contains classes to use pdb protein structures
ContactMap.java 143 (12 years ago) by duarte: 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
EdgeState.java 128 (12 years ago) by duarte: ContactMap and EdgeState classes moved here from CMPredict repository
Graph.java 152 (12 years ago) by duarte: 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
GraphIdNotFoundError.java 135 (12 years ago) by duarte: 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
MsdsdAcCodeNotFoundError.java 130 (12 years ago) by duarte: NEW FEATURE: reading pdb data from msdsd New classes MsdsdInfo and its exception classes FIXED BUG in dump2pdbfile in Pdb: was not sorting the atom lines
MsdsdInconsistentResidueNumbersError.java 130 (12 years ago) by duarte: NEW FEATURE: reading pdb data from msdsd New classes MsdsdInfo and its exception classes FIXED BUG in dump2pdbfile in Pdb: was not sorting the atom lines
MsdsdInfo.java 136 (12 years ago) by duarte: FIXED BUG: pdb data load from msdsd wasn't working for NULL chaincodes
Pdb.java 154 (12 years ago) by duarte: Recoded chain reading in read_pdb_data_from_file to make it clearer, no change in functionality
PdbaseAcCodeNotFoundError.java 124 (12 years ago) by duarte: Added error handling for PdbaseInfo: 2 new exception classes
PdbaseInconsistencyError.java 124 (12 years ago) by duarte: Added error handling for PdbaseInfo: 2 new exception classes
PdbaseInfo.java 135 (12 years ago) by duarte: 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
(Current path doesn't exist after revision 950)
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