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r142
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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
PdbaseInconsistencyError.java 124 (12 years ago) by duarte: Added error handling for PdbaseInfo: 2 new exception classes
PdbaseAcCodeNotFoundError.java 124 (12 years ago) by duarte: Added error handling for PdbaseInfo: 2 new exception classes
Pdb.java 140 (12 years ago) by stehr: Made Pdb.acccode public
MsdsdInfo.java 136 (12 years ago) by duarte: FIXED BUG: pdb data load from msdsd wasn't working for NULL chaincodes
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
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
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
Graph.java 142 (12 years ago) by duarte: 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
EdgeState.java 128 (12 years ago) by duarte: ContactMap and EdgeState classes moved here from CMPredict repository
ContactMap.java 142 (12 years ago) by duarte: 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
Contact.java 123 (12 years ago) by duarte: Initial commit of the proteinstructure package. Contains classes to use pdb protein structures
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
(Current path doesn't exist after revision 950)
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