 ../
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Contact.java
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123
(17 years ago)
by duarte:
Initial commit of the proteinstructure package. Contains classes to use pdb protein structures
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PdbaseInconsistencyError.java
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124
(17 years ago)
by duarte:
Added error handling for PdbaseInfo: 2 new exception classes
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PdbaseAcCodeNotFoundError.java
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124
(17 years ago)
by duarte:
Added error handling for PdbaseInfo: 2 new exception classes
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MsdsdAcCodeNotFoundError.java
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130
(17 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
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MsdsdInconsistentResidueNumbersError.java
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130
(17 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
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PdbaseInfo.java
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135
(17 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
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GraphIdNotFoundError.java
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135
(17 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
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AA.java
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135
(17 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
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MsdsdInfo.java
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136
(17 years ago)
by duarte:
FIXED BUG: pdb data load from msdsd wasn't working for NULL chaincodes
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Graph.java
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159
(17 years ago)
by duarte:
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
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Pdb.java
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159
(17 years ago)
by duarte:
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
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