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r328
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contactTypes.dat 326 (12 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
SecondaryStructure.java 276 (12 years ago) by duarte: Added secondary structure to write_graph_to_db New method getNumSecStructureElements in SecondaryStructure
SecStrucElement.java 274 (12 years ago) by stehr: Added new SecondaryStructure object to Pdb and Graph
PdbfilePdb.java 326 (12 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
PdbfileFormatError.java 208 (12 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
PdbasePdb.java 326 (12 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
PdbaseInconsistencyError.java 172 (12 years ago) by duarte: Got rid of some unnecessary warnings
PdbCodeNotFoundError.java 215 (12 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
PdbChainCodeNotFoundError.java 215 (12 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
Pdb.java 328 (12 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
NodeSet.java 325 (12 years ago) by stehr: added parsing of residue selection strings
NodeNbh.java 326 (12 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
NbhProbDistribution.java 242 (12 years ago) by duarte: Got rid of doneRes ArrayList in getRanks, was redundant
MsdsdPdb.java 326 (12 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
MsdsdInconsistentResidueNumbersError.java 172 (12 years ago) by duarte: Got rid of some unnecessary warnings
Interval.java 222 (12 years ago) by duarte: New secstruct2resinterval TreeMap to store secondary structure elements as a map of ss string ids to intervals New class Interval
GraphIdNotFoundError.java 172 (12 years ago) by duarte: Got rid of some unnecessary warnings
GraphFileFormatError.java 208 (12 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
Graph.java 326 (12 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
GenericContact.java 185 (12 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
FileGraph.java 326 (12 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
EdgeSet.java 234 (12 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
EdgeNbh.java 326 (12 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
Edge.java 238 (12 years ago) by duarte: Optimised slightly the compareTo method in Edge
DbGraph.java 326 (12 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
ContactType.java 326 (12 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
ConformationsNotSameSizeError.java 237 (12 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
CiffilePdb.java 326 (12 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
CiffileFormatError.java 314 (12 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
Box.java 282 (12 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
Alignment.java 248 (12 years ago) by duarte: Added method hasTag
AAinfo.java 328 (12 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
(Current path doesn't exist after revision 950)
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