 ../
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ContactMap.java
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142
(15 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
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Graph.java
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142
(15 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
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Pdb.java
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140
(15 years ago)
by stehr:
Made Pdb.acccode public
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MsdsdInfo.java
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136
(15 years ago)
by duarte:
FIXED BUG: pdb data load from msdsd wasn't working for NULL chaincodes
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PdbaseInfo.java
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135
(15 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
(15 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
(15 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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MsdsdAcCodeNotFoundError.java
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130
(15 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
(15 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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EdgeState.java
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128
(15 years ago)
by duarte:
ContactMap and EdgeState classes moved here from CMPredict repository
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PdbaseInconsistencyError.java
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124
(15 years ago)
by duarte:
Added error handling for PdbaseInfo: 2 new exception classes
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PdbaseAcCodeNotFoundError.java
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124
(15 years ago)
by duarte:
Added error handling for PdbaseInfo: 2 new exception classes
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Contact.java
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123
(15 years ago)
by duarte:
Initial commit of the proteinstructure package. Contains classes to use pdb protein structures
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