 ../
|
AA.java
|
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
|
|
Contact.java
|
123
(17 years ago)
by duarte:
Initial commit of the proteinstructure package. Contains classes to use pdb protein structures
|
|
ContactMap.java
|
143
(17 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
(17 years ago)
by duarte:
ContactMap and EdgeState classes moved here from CMPredict repository
|
|
Graph.java
|
157
(17 years ago)
by duarte:
FIXED BUG: in getCM when directed was passing a reference to the contacts object and not deep copying it!
|
|
GraphIdNotFoundError.java
|
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
|
|
MsdsdAcCodeNotFoundError.java
|
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
|
|
MsdsdInconsistentResidueNumbersError.java
|
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
|
|
MsdsdInfo.java
|
136
(17 years ago)
by duarte:
FIXED BUG: pdb data load from msdsd wasn't working for NULL chaincodes
|
|
Pdb.java
|
156
(17 years ago)
by duarte:
Now passing also chaincode from Pdb object to Graph object in get_graph
|
|
PdbaseAcCodeNotFoundError.java
|
124
(17 years ago)
by duarte:
Added error handling for PdbaseInfo: 2 new exception classes
|
|
PdbaseInconsistencyError.java
|
124
(17 years ago)
by duarte:
Added error handling for PdbaseInfo: 2 new exception classes
|
|
PdbaseInfo.java
|
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
|
