 ../
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contactTypes.dat
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326
(17 years ago)
by duarte:
Removed class AA and replace it by AAinfo, which reads contact types from separate file contactTypes.dat
New class ContactType which contains atoms for each contact type and residue. A static object for each contact type is loaded into AAinfo upon reading the contactTypes.dat file
Changed all references accordingly
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aapairsBounds.dat
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335
(17 years ago)
by duarte:
Now ConstraintsMaker works also for multi atom contact types (BB and SC) and crosses (either BB/SC or any cross to a single atom contact type)
New file aapairsBounds.dat with values for aminoacid side chains distance lower and upper bounds taken from statistics of a set of pdb representatives
New in AAinfo: aapairs2bounds and changed getUpperBoundDistance, getUpperBoundDistance to accomodate aapairs2bounds
PRMInfo: now for amber "OXT" gets transformed into "O"
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SimilarityGraph.java
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352
(17 years ago)
by stehr:
Major redesign of NodeSet, now contains objects of new class Node. Nodes are essentially integer which can have additional properties. Added equals methods to NodeSet, EdgeSet, NodesAndEdges. Moved some methods from SimilarityGraph to NodesAndEdges.
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SecondaryStructure.java
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276
(17 years ago)
by duarte:
Added secondary structure to write_graph_to_db
New method getNumSecStructureElements in SecondaryStructure
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SecStrucElement.java
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274
(17 years ago)
by stehr:
Added new SecondaryStructure object to Pdb and Graph
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PredEval.java
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362
(17 years ago)
by stehr:
renamed precision to accuracy (in accordance with Casp)
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PdbfilePdb.java
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360
(17 years ago)
by stehr:
Graph,PredEval: added fields coverage and title to predEval (and evalPrediction)
GraphAverager: added method to return average graph (with weighted edges)
PdbfilePdb: fixed bug when reading from Casp prediction files
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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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PdbasePdb.java
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336
(17 years ago)
by stehr:
extracted constant NULL_CHAIN_CODE from ...Pdb classes, added copy() methods to NodeSet and EdgeSet, added some functionality to NodesAndEdges, new class SimilarityGraph
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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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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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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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Pdb.java
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361
(17 years ago)
by duarte:
Now weights are kept in the Edge objects rather than separately in a member variable in Graph
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NodesAndEdges.java
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352
(17 years ago)
by stehr:
Major redesign of NodeSet, now contains objects of new class Node. Nodes are essentially integer which can have additional properties. Added equals methods to NodeSet, EdgeSet, NodesAndEdges. Moved some methods from SimilarityGraph to NodesAndEdges.
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NodeSet.java
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352
(17 years ago)
by stehr:
Major redesign of NodeSet, now contains objects of new class Node. Nodes are essentially integer which can have additional properties. Added equals methods to NodeSet, EdgeSet, NodesAndEdges. Moved some methods from SimilarityGraph to NodesAndEdges.
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NodeNbh.java
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326
(17 years ago)
by duarte:
Removed class AA and replace it by AAinfo, which reads contact types from separate file contactTypes.dat
New class ContactType which contains atoms for each contact type and residue. A static object for each contact type is loaded into AAinfo upon reading the contactTypes.dat file
Changed all references accordingly
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Node.java
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352
(17 years ago)
by stehr:
Major redesign of NodeSet, now contains objects of new class Node. Nodes are essentially integer which can have additional properties. Added equals methods to NodeSet, EdgeSet, NodesAndEdges. Moved some methods from SimilarityGraph to NodesAndEdges.
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NbhProbDistribution.java
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242
(17 years ago)
by duarte:
Got rid of doneRes ArrayList in getRanks, was redundant
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MsdsdPdb.java
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336
(17 years ago)
by stehr:
extracted constant NULL_CHAIN_CODE from ...Pdb classes, added copy() methods to NodeSet and EdgeSet, added some functionality to NodesAndEdges, new class SimilarityGraph
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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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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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GraphIdNotFoundError.java
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172
(17 years ago)
by duarte:
Got rid of some unnecessary warnings
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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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GraphAverager.java
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360
(17 years ago)
by stehr:
Graph,PredEval: added fields coverage and title to predEval (and evalPrediction)
GraphAverager: added method to return average graph (with weighted edges)
PdbfilePdb: fixed bug when reading from Casp prediction files
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Graph.java
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361
(17 years ago)
by duarte:
Now weights are kept in the Edge objects rather than separately in a member variable in Graph
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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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FileGraph.java
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361
(17 years ago)
by duarte:
Now weights are kept in the Edge objects rather than separately in a member variable in Graph
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EdgeSet.java
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352
(17 years ago)
by stehr:
Major redesign of NodeSet, now contains objects of new class Node. Nodes are essentially integer which can have additional properties. Added equals methods to NodeSet, EdgeSet, NodesAndEdges. Moved some methods from SimilarityGraph to NodesAndEdges.
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EdgeNbh.java
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326
(17 years ago)
by duarte:
Removed class AA and replace it by AAinfo, which reads contact types from separate file contactTypes.dat
New class ContactType which contains atoms for each contact type and residue. A static object for each contact type is loaded into AAinfo upon reading the contactTypes.dat file
Changed all references accordingly
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Edge.java
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352
(17 years ago)
by stehr:
Major redesign of NodeSet, now contains objects of new class Node. Nodes are essentially integer which can have additional properties. Added equals methods to NodeSet, EdgeSet, NodesAndEdges. Moved some methods from SimilarityGraph to NodesAndEdges.
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DbGraph.java
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361
(17 years ago)
by duarte:
Now weights are kept in the Edge objects rather than separately in a member variable in Graph
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ContactType.java
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326
(17 years ago)
by duarte:
Removed class AA and replace it by AAinfo, which reads contact types from separate file contactTypes.dat
New class ContactType which contains atoms for each contact type and residue. A static object for each contact type is loaded into AAinfo upon reading the contactTypes.dat file
Changed all references accordingly
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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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CiffilePdb.java
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357
(17 years ago)
by duarte:
Fixed bug: now does correctly quoting for any of the 3 cases: "", '' or ;;. Does also correctly multiline parsing of ;; quoted fields. Passed testing on cullpdb 90 (more than 9000 pdb entries)
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CiffileFormatError.java
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314
(17 years ago)
by duarte:
Checking number of fields per line in loop elements and throwing exception if count is not correect
Doing tokenisation of lines through new function that takes care of possible quoted string with spaces
New exception CiffileFormatError
Checking 1st line of cif file has correct format: data_1xxx, if not throwing exception
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Box.java
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282
(17 years ago)
by duarte:
Made get_graph a bit less memory hungry, by using a float[][] instead of double[][]
Not printing warnings about missing atoms anymore
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Alignment.java
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332
(17 years ago)
by stehr:
added constructor for trivial alignment, renamed getSequence to getAlignedSequence
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AAinfo.java
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336
(17 years ago)
by stehr:
extracted constant NULL_CHAIN_CODE from ...Pdb classes, added copy() methods to NodeSet and EdgeSet, added some functionality to NodesAndEdges, new class SimilarityGraph
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