 ../
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AAinfo.java
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372
(16 years ago)
by lpetzo:
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Alignment.java
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405
(16 years ago)
by duarte:
Alignment and PairwiseAlignmentConverter now using Interval, IntervalSet and TreeSet<Integer> to replace Edge, EdgeSet and NodeSet
New class IntervalSet
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AlignmentConstructionError.java
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385
(16 years ago)
by lpetzo:
NEW TYPES
---------
- FileFormatError
- FastaFileFormatError
- PirFileFormatError
- AlignmentConstructionError
MODIFICATIONS
-------------
class Alignment:
- introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur
- changed accession rules of function getGapCharacter from "public" to "public static"
- new functions:
* writeFasta
class CiffileFormatError:
- changed super class from Exception to the new FileFormatError class
class GraphFileFormatError:
- s. class CiffileFormatError
class PairwiseAlignmentConverter:
- added exception handling features due to class Alignment
class PairwiseAlignmentGraphConverter:
- s. class PairwiseAlignmentConverter
class PdbFileFormatError:
- s. class CifffileFormatError
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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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CatalSiteSet.java
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382
(16 years ago)
by filippis:
Methods added for:
-parsing CSA
-parsing EC
-parsing CONSURF-HSSP
-running & parsing Naccess
-parsing SCOP
-writing residues' info in a db table
Modifications have been also made in DSSP parsing:
-sheet serial is taken into account
-flexibility in reduced state preferred
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CatalyticSite.java
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382
(16 years ago)
by filippis:
Methods added for:
-parsing CSA
-parsing EC
-parsing CONSURF-HSSP
-running & parsing Naccess
-parsing SCOP
-writing residues' info in a db table
Modifications have been also made in DSSP parsing:
-sheet serial is taken into account
-flexibility in reduced state preferred
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CiffileFormatError.java
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385
(16 years ago)
by lpetzo:
NEW TYPES
---------
- FileFormatError
- FastaFileFormatError
- PirFileFormatError
- AlignmentConstructionError
MODIFICATIONS
-------------
class Alignment:
- introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur
- changed accession rules of function getGapCharacter from "public" to "public static"
- new functions:
* writeFasta
class CiffileFormatError:
- changed super class from Exception to the new FileFormatError class
class GraphFileFormatError:
- s. class CiffileFormatError
class PairwiseAlignmentConverter:
- added exception handling features due to class Alignment
class PairwiseAlignmentGraphConverter:
- s. class PairwiseAlignmentConverter
class PdbFileFormatError:
- s. class CifffileFormatError
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CiffilePdb.java
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402
(16 years ago)
by duarte:
Forgot CiffilePdb!: not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!
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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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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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DbGraph.java
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361
(16 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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EC.java
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382
(16 years ago)
by filippis:
Methods added for:
-parsing CSA
-parsing EC
-parsing CONSURF-HSSP
-running & parsing Naccess
-parsing SCOP
-writing residues' info in a db table
Modifications have been also made in DSSP parsing:
-sheet serial is taken into account
-flexibility in reduced state preferred
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ECRegion.java
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382
(16 years ago)
by filippis:
Methods added for:
-parsing CSA
-parsing EC
-parsing CONSURF-HSSP
-running & parsing Naccess
-parsing SCOP
-writing residues' info in a db table
Modifications have been also made in DSSP parsing:
-sheet serial is taken into account
-flexibility in reduced state preferred
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Edge.java
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352
(16 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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EdgeSet.java
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372
(16 years ago)
by lpetzo:
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FastaFileFormatError.java
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385
(16 years ago)
by lpetzo:
NEW TYPES
---------
- FileFormatError
- FastaFileFormatError
- PirFileFormatError
- AlignmentConstructionError
MODIFICATIONS
-------------
class Alignment:
- introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur
- changed accession rules of function getGapCharacter from "public" to "public static"
- new functions:
* writeFasta
class CiffileFormatError:
- changed super class from Exception to the new FileFormatError class
class GraphFileFormatError:
- s. class CiffileFormatError
class PairwiseAlignmentConverter:
- added exception handling features due to class Alignment
class PairwiseAlignmentGraphConverter:
- s. class PairwiseAlignmentConverter
class PdbFileFormatError:
- s. class CifffileFormatError
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FileFormatError.java
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385
(16 years ago)
by lpetzo:
NEW TYPES
---------
- FileFormatError
- FastaFileFormatError
- PirFileFormatError
- AlignmentConstructionError
MODIFICATIONS
-------------
class Alignment:
- introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur
- changed accession rules of function getGapCharacter from "public" to "public static"
- new functions:
* writeFasta
class CiffileFormatError:
- changed super class from Exception to the new FileFormatError class
class GraphFileFormatError:
- s. class CiffileFormatError
class PairwiseAlignmentConverter:
- added exception handling features due to class Alignment
class PairwiseAlignmentGraphConverter:
- s. class PairwiseAlignmentConverter
class PdbFileFormatError:
- s. class CifffileFormatError
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FileGraph.java
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361
(16 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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Graph.java
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404
(16 years ago)
by duarte:
Not asserting anymore pdbChainCode to be uppercase. pdb chain codes are case sensitive!
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GraphAverager.java
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379
(16 years ago)
by stehr:
redesign of TinkerRunner: added 2 reconstruct methods, one which generates normal tinker output for a given number of models, and one fully automatic one which simply returns one pdb object;
updated reconstruct.java to make use of the new TinkerRunner method;
updated GraphAverager: now assigning edgetype and cutoff to consensus graph
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GraphFileFormatError.java
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385
(16 years ago)
by lpetzo:
NEW TYPES
---------
- FileFormatError
- FastaFileFormatError
- PirFileFormatError
- AlignmentConstructionError
MODIFICATIONS
-------------
class Alignment:
- introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur
- changed accession rules of function getGapCharacter from "public" to "public static"
- new functions:
* writeFasta
class CiffileFormatError:
- changed super class from Exception to the new FileFormatError class
class GraphFileFormatError:
- s. class CiffileFormatError
class PairwiseAlignmentConverter:
- added exception handling features due to class Alignment
class PairwiseAlignmentGraphConverter:
- s. class PairwiseAlignmentConverter
class PdbFileFormatError:
- s. class CifffileFormatError
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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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Interval.java
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405
(16 years ago)
by duarte:
Alignment and PairwiseAlignmentConverter now using Interval, IntervalSet and TreeSet<Integer> to replace Edge, EdgeSet and NodeSet
New class IntervalSet
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IntervalSet.java
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405
(16 years ago)
by duarte:
Alignment and PairwiseAlignmentConverter now using Interval, IntervalSet and TreeSet<Integer> to replace Edge, EdgeSet and NodeSet
New class IntervalSet
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MaxClusterRunner.java
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391
(16 years ago)
by stehr:
started implementing a wrapper for the Maxcluster application (some related code is now in SimilarityGraph but should be moved to MaxClusterRunner in the future)
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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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MsdsdPdb.java
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401
(16 years ago)
by duarte:
Not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!
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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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Node.java
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352
(16 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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394
(16 years ago)
by duarte:
New method getMotifReducedAlphabet to get neighbourhood strings in Michael's reduced style (must pass a Graph with weights which indicate BB or SC domination)
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NodeSet.java
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352
(16 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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NodesAndEdges.java
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352
(16 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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PairwiseAlignmentConverter.java
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406
(16 years ago)
by duarte:
Reverting to last revision, changes made in 405 were wrong
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PairwiseAlignmentGraphConverter.java
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385
(16 years ago)
by lpetzo:
NEW TYPES
---------
- FileFormatError
- FastaFileFormatError
- PirFileFormatError
- AlignmentConstructionError
MODIFICATIONS
-------------
class Alignment:
- introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur
- changed accession rules of function getGapCharacter from "public" to "public static"
- new functions:
* writeFasta
class CiffileFormatError:
- changed super class from Exception to the new FileFormatError class
class GraphFileFormatError:
- s. class CiffileFormatError
class PairwiseAlignmentConverter:
- added exception handling features due to class Alignment
class PairwiseAlignmentGraphConverter:
- s. class PairwiseAlignmentConverter
class PdbFileFormatError:
- s. class CifffileFormatError
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PairwiseSequenceAlignment.java
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399
(16 years ago)
by stehr:
added class PairwiseSequenceAlignment
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Pdb.java
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403
(16 years ago)
by filippis:
OXT is taken into account now also for BB contact type
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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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PdbaseInconsistencyError.java
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172
(17 years ago)
by duarte:
Got rid of some unnecessary warnings
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PdbasePdb.java
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401
(16 years ago)
by duarte:
Not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!
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PdbfileFormatError.java
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385
(16 years ago)
by lpetzo:
NEW TYPES
---------
- FileFormatError
- FastaFileFormatError
- PirFileFormatError
- AlignmentConstructionError
MODIFICATIONS
-------------
class Alignment:
- introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur
- changed accession rules of function getGapCharacter from "public" to "public static"
- new functions:
* writeFasta
class CiffileFormatError:
- changed super class from Exception to the new FileFormatError class
class GraphFileFormatError:
- s. class CiffileFormatError
class PairwiseAlignmentConverter:
- added exception handling features due to class Alignment
class PairwiseAlignmentGraphConverter:
- s. class PairwiseAlignmentConverter
class PdbFileFormatError:
- s. class CifffileFormatError
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PdbfilePdb.java
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401
(16 years ago)
by duarte:
Not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!
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PirFileFormatError.java
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385
(16 years ago)
by lpetzo:
NEW TYPES
---------
- FileFormatError
- FastaFileFormatError
- PirFileFormatError
- AlignmentConstructionError
MODIFICATIONS
-------------
class Alignment:
- introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur
- changed accession rules of function getGapCharacter from "public" to "public static"
- new functions:
* writeFasta
class CiffileFormatError:
- changed super class from Exception to the new FileFormatError class
class GraphFileFormatError:
- s. class CiffileFormatError
class PairwiseAlignmentConverter:
- added exception handling features due to class Alignment
class PairwiseAlignmentGraphConverter:
- s. class PairwiseAlignmentConverter
class PdbFileFormatError:
- s. class CifffileFormatError
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PredEval.java
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362
(16 years ago)
by stehr:
renamed precision to accuracy (in accordance with Casp)
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Scop.java
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382
(16 years ago)
by filippis:
Methods added for:
-parsing CSA
-parsing EC
-parsing CONSURF-HSSP
-running & parsing Naccess
-parsing SCOP
-writing residues' info in a db table
Modifications have been also made in DSSP parsing:
-sheet serial is taken into account
-flexibility in reduced state preferred
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ScopRegion.java
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382
(16 years ago)
by filippis:
Methods added for:
-parsing CSA
-parsing EC
-parsing CONSURF-HSSP
-running & parsing Naccess
-parsing SCOP
-writing residues' info in a db table
Modifications have been also made in DSSP parsing:
-sheet serial is taken into account
-flexibility in reduced state preferred
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SecStrucElement.java
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383
(16 years ago)
by filippis:
inSameSheet, isOther and getSheetSerial methods added in SecStrucElement
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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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SimilarityGraph.java
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352
(16 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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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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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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