 ../
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Graph.java
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239
(17 years ago)
by duarte:
Fixed bug in addEdge method. In case of undirected we need to check that the contact is inserted in the right order j>i
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Edge.java
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238
(17 years ago)
by duarte:
Optimised slightly the compareTo method in Edge
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Pdb.java
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237
(17 years ago)
by duarte:
Now rmsd calculation works for 2 Pdb objects where there are missing residues (unobserved) or missing atoms
New Exception ConformationNotSameSizeError
Still not printing out individual distances between 2 conformations (altghough it is possible)
Can't specify yet a restricted range of residues to calculate rmsd only with them
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MsdsdPdb.java
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237
(17 years ago)
by duarte:
Now rmsd calculation works for 2 Pdb objects where there are missing residues (unobserved) or missing atoms
New Exception ConformationNotSameSizeError
Still not printing out individual distances between 2 conformations (altghough it is possible)
Can't specify yet a restricted range of residues to calculate rmsd only with them
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ConformationsNotSameSizeError.java
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237
(17 years ago)
by duarte:
Now rmsd calculation works for 2 Pdb objects where there are missing residues (unobserved) or missing atoms
New Exception ConformationNotSameSizeError
Still not printing out individual distances between 2 conformations (altghough it is possible)
Can't specify yet a restricted range of residues to calculate rmsd only with them
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PdbasePdb.java
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237
(17 years ago)
by duarte:
Now rmsd calculation works for 2 Pdb objects where there are missing residues (unobserved) or missing atoms
New Exception ConformationNotSameSizeError
Still not printing out individual distances between 2 conformations (altghough it is possible)
Can't specify yet a restricted range of residues to calculate rmsd only with them
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PdbfilePdb.java
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237
(17 years ago)
by duarte:
Now rmsd calculation works for 2 Pdb objects where there are missing residues (unobserved) or missing atoms
New Exception ConformationNotSameSizeError
Still not printing out individual distances between 2 conformations (altghough it is possible)
Can't specify yet a restricted range of residues to calculate rmsd only with them
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DbGraph.java
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234
(17 years ago)
by duarte:
Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear)
REFACTORING:
ContactList -> EdgeSet
Contact -> Edge
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FileGraph.java
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234
(17 years ago)
by duarte:
Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear)
REFACTORING:
ContactList -> EdgeSet
Contact -> Edge
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EdgeSet.java
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234
(17 years ago)
by duarte:
Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear)
REFACTORING:
ContactList -> EdgeSet
Contact -> Edge
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NodeNbh.java
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233
(17 years ago)
by duarte:
Added method getCopy
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NodeSet.java
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230
(17 years ago)
by stehr:
added class NodeSet
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AA.java
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229
(17 years ago)
by duarte:
Now calculate_dist_matrix returns the matrix with residue serials as indices (rather than atom serials)
Now AA.isValidSingleCT and AA.isValidMultiCT check also for crossed cases
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Box.java
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228
(17 years ago)
by duarte:
Now can do crossed contacts also with geometric hashing
Renamed getGraphGeometricHashing to get_graph (so interface remains as it was before we introduced the geometric hashing)
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Interval.java
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222
(17 years ago)
by duarte:
New secstruct2resinterval TreeMap to store secondary structure elements as a map of ss string ids to intervals
New class Interval
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PdbChainCodeNotFoundError.java
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215
(17 years ago)
by stehr:
some clean up of exceptions in Pdb and Graph classes:
merged PdbAcCodeNotFoundError and MsdAcCodeNotFoundError into PdbCodeNotFoundError,
created new PdbChainCodeNotFound, got rid of stderr output, throwing exceptions with informative messages instead
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PdbCodeNotFoundError.java
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215
(17 years ago)
by stehr:
some clean up of exceptions in Pdb and Graph classes:
merged PdbAcCodeNotFoundError and MsdAcCodeNotFoundError into PdbCodeNotFoundError,
created new PdbChainCodeNotFound, got rid of stderr output, throwing exceptions with informative messages instead
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GraphFileFormatError.java
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208
(17 years ago)
by duarte:
FIXED BUGS:
- directed was not set when reading from cm file
- pdbChainCode not set when reading from db given pdbCode
- filling pdbresser2resser and resser2pdbresser hashmaps also in reading from pdb file
- using "A" as chainCode when reading from pdb file
- some error handling for file formats: new exception classes GraphFileFormatError and PdbfileFormatError
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PdbfileFormatError.java
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208
(17 years ago)
by duarte:
FIXED BUGS:
- directed was not set when reading from cm file
- pdbChainCode not set when reading from db given pdbCode
- filling pdbresser2resser and resser2pdbresser hashmaps also in reading from pdb file
- using "A" as chainCode when reading from pdb file
- some error handling for file formats: new exception classes GraphFileFormatError and PdbfileFormatError
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NbhProbDistribution.java
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199
(17 years ago)
by duarte:
Implemented getRanks()
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EdgeNbh.java
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196
(17 years ago)
by duarte:
Added toString and getMotifFullGaps missing in EdgeNbh
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GenericContact.java
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185
(17 years ago)
by duarte:
Implemented hashCode method in Contact and GenericContact. Was necessary to use these classes as keys in Maps
Fixed bug in equals method in GenericContact
Changed middle character from "\t" to " " in toString
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MsdsdInconsistentResidueNumbersError.java
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172
(17 years ago)
by duarte:
Got rid of some unnecessary warnings
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GraphIdNotFoundError.java
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172
(17 years ago)
by duarte:
Got rid of some unnecessary warnings
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PdbaseInconsistencyError.java
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172
(17 years ago)
by duarte:
Got rid of some unnecessary warnings
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