 ../
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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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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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329
(17 years ago)
by duarte:
Added GraphAverager class and PredEval class. GraphAverager copied from HomologyPredictor (in CMPredict): doing the averaging correctly now
Added method evaluatePrediction to Graph
Some refactoring in Alignment and better javadocs
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PdbfilePdb.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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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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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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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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328
(17 years ago)
by duarte:
First commit of ConstraintsMaker (and PRMInfo needed for it)
Does correct atom serial mapping when using amber prm files, except for some atoms of ASP, ARG, GLU, PHE, TYR (where there are some nomenclature differences between amber and pdb)
Does not work yet with multi atom contact types, should work fine for all single atom contact types and for crossed single atom contact types
The pdb/xyz atom mapping using coordinates (as in python) is commented out because it doesn't work due to rounding differences between java and fortran
Thus the PRMInfo class was needed, at the moment can read only amber prm files
Some new methods and better javadoc in Pdb.
Some new methods in AAinfo
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NodeSet.java
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325
(17 years ago)
by stehr:
added parsing of residue selection strings
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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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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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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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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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331
(17 years ago)
by duarte:
Better handling of graph averaging for different thresholds
Refactored predict to doAveraging, not returning anymore a Grap but rather modifying the reference
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Graph.java
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329
(17 years ago)
by duarte:
Added GraphAverager class and PredEval class. GraphAverager copied from HomologyPredictor (in CMPredict): doing the averaging correctly now
Added method evaluatePrediction to Graph
Some refactoring in Alignment and better javadocs
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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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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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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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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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330
(17 years ago)
by stehr:
added a weight field to Edge class (set using alternative constructor, maintaining backwards compatibility)
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DbGraph.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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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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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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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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329
(17 years ago)
by duarte:
Added GraphAverager class and PredEval class. GraphAverager copied from HomologyPredictor (in CMPredict): doing the averaging correctly now
Added method evaluatePrediction to Graph
Some refactoring in Alignment and better javadocs
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AAinfo.java
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328
(17 years ago)
by duarte:
First commit of ConstraintsMaker (and PRMInfo needed for it)
Does correct atom serial mapping when using amber prm files, except for some atoms of ASP, ARG, GLU, PHE, TYR (where there are some nomenclature differences between amber and pdb)
Does not work yet with multi atom contact types, should work fine for all single atom contact types and for crossed single atom contact types
The pdb/xyz atom mapping using coordinates (as in python) is commented out because it doesn't work due to rounding differences between java and fortran
Thus the PRMInfo class was needed, at the moment can read only amber prm files
Some new methods and better javadoc in Pdb.
Some new methods in AAinfo
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