 ../
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AA.java
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320
(17 years ago)
by stehr:
added calculation of difference distance map
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Alignment.java
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248
(17 years ago)
by duarte:
Added method hasTag
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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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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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CiffilePdb.java
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319
(17 years ago)
by stehr:
added constructors for loading from online pdb
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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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DbGraph.java
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284
(17 years ago)
by duarte:
Introduced weights in Graph objects: we can read them from file or db and write them into file or db. On calling pdb.get_graph the weighs are taken as number of atom-edges per residue-edge (similar to Ioannis weights in chain_graph tables)
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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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EdgeNbh.java
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196
(17 years ago)
by duarte:
Added toString and getMotifFullGaps missing in EdgeNbh
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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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FileGraph.java
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284
(17 years ago)
by duarte:
Introduced weights in Graph objects: we can read them from file or db and write them into file or db. On calling pdb.get_graph the weighs are taken as number of atom-edges per residue-edge (similar to Ioannis weights in chain_graph tables)
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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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288
(17 years ago)
by spriya:
Better checks for sequence equality in compare
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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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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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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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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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278
(17 years ago)
by duarte:
Fixed bug with getFullLength when reading from pdb file
Now if SEQRES was missing then fullLength is maximum observed residue number instead of total number of observed residue numbers
New member variables obsLength and fullLength
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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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NodeNbh.java
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281
(17 years ago)
by stehr:
fixed little bug in NodeNbh
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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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Pdb.java
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324
(17 years ago)
by duarte:
2 new methods: getAllAtomSerials, getAtomCoord
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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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311
(17 years ago)
by duarte:
Fixed buf: sometimes struct_conf can be non-loop elements, now also taking care of that particular case
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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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PdbfilePdb.java
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301
(17 years ago)
by stehr:
changed constant for unknown pdb code from "Unknown" to XXXX
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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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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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