ViewVC Help
| View Changeset | Root Listing
root/owl
Jump to revision: Previous Next
Author: duarte
Date: Tue Aug 11 16:01:00 2009 UTC (10 years, 1 month ago)
Log Message:
Major commit: 
- change of the implementation of Pdb (interface remains backwards compatible). Now data stored in a proper object-oriented way. Pdb not abstract anymore, a protein model can be created by using one of the constructors
- added many tests and test files for Pdb (and merged some already existing tests from the default package)
- removed obsolete classes related to msd
- bug fix: PdbfilePdb now properly reads files with alt codes
- all tests passed

Changed paths

Path Details
Directorytrunk/embed/Embedder.java modified , text changed
Directorytrunk/embed/Reconstructer.java modified , text changed
Directorytrunk/proteinstructure/AminoAcid.java modified , text changed
Directorytrunk/proteinstructure/Atom.java modified , text changed
Directorytrunk/proteinstructure/AtomType.java added
Directorytrunk/proteinstructure/CiffilePdb.java modified , text changed
Directorytrunk/proteinstructure/FileRIGraph.java modified , text changed
Directorytrunk/proteinstructure/ModelPdb.java deleted
Directorytrunk/proteinstructure/MsdsdInconsistentResidueNumbersError.java deleted
Directorytrunk/proteinstructure/MsdsdPdb.java deleted
Directorytrunk/proteinstructure/Pdb.java modified , text changed
Directorytrunk/proteinstructure/PdbasePdb.java modified , text changed
Directorytrunk/proteinstructure/PdbfilePdb.java modified , text changed
Directorytrunk/proteinstructure/Residue.java modified , text changed
Directorytrunk/testDeltaDistanceMap.java deleted
Directorytrunk/testGetChains.java deleted
Directorytrunk/testResidueSelectionString.java deleted
Directorytrunk/tests/proteinstructure/IntervalTest.java added
Directorytrunk/tests/proteinstructure/PdbParsersTest.java modified , text changed
Directorytrunk/tests/proteinstructure/PdbTest.java modified , text changed
Directorytrunk/tests/proteinstructure/data/1d2sA_ALL_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1d2sA_BB:SC_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1d2sA_BB_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1d2sA_Ca_8.0.cm added
Directorytrunk/tests/proteinstructure/data/1d2sA_Cb_8.0.cm added
Directorytrunk/tests/proteinstructure/data/1d2sA_SC_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1od3A_ALL_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1od3A_BB:SC_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1od3A_BB_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1od3A_Ca_8.0.cm added
Directorytrunk/tests/proteinstructure/data/1od3A_Cb_8.0.cm added
Directorytrunk/tests/proteinstructure/data/1od3A_SC_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1oewA_ALL_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1oewA_BB:SC_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1oewA_BB_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1oewA_Ca_8.0.cm added
Directorytrunk/tests/proteinstructure/data/1oewA_Cb_8.0.cm added
Directorytrunk/tests/proteinstructure/data/1oewA_SC_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1tdrB.pdb added
Directorytrunk/tests/proteinstructure/data/1w0nA_ALL_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1w0nA_BB:SC_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1w0nA_BB_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1w0nA_Ca_8.0.cm added
Directorytrunk/tests/proteinstructure/data/1w0nA_Cb_8.0.cm added
Directorytrunk/tests/proteinstructure/data/1w0nA_SC_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1wb4A_ALL_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1wb4A_BB:SC_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1wb4A_BB_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1wb4A_Ca_8.0.cm added
Directorytrunk/tests/proteinstructure/data/1wb4A_Cb_8.0.cm added
Directorytrunk/tests/proteinstructure/data/1wb4A_SC_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1wvfA_ALL_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1wvfA_BB:SC_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1wvfA_BB_5.0.cm added
Directorytrunk/tests/proteinstructure/data/1wvfA_Ca_8.0.cm added
Directorytrunk/tests/proteinstructure/data/1wvfA_Cb_8.0.cm added
Directorytrunk/tests/proteinstructure/data/1wvfA_SC_5.0.cm added
Directorytrunk/tests/proteinstructure/data/2gpiA_ALL_5.0.cm added
Directorytrunk/tests/proteinstructure/data/2gpiA_BB:SC_5.0.cm added
Directorytrunk/tests/proteinstructure/data/2gpiA_BB_5.0.cm added
Directorytrunk/tests/proteinstructure/data/2gpiA_Ca_8.0.cm added
Directorytrunk/tests/proteinstructure/data/2gpiA_Cb_8.0.cm added
Directorytrunk/tests/proteinstructure/data/2gpiA_SC_5.0.cm added
Directorytrunk/tests/proteinstructure/data/2h6fB_ALL_5.0.cm added
Directorytrunk/tests/proteinstructure/data/2h6fB_BB:SC_5.0.cm added
Directorytrunk/tests/proteinstructure/data/2h6fB_BB_5.0.cm added
Directorytrunk/tests/proteinstructure/data/2h6fB_Ca_8.0.cm added
Directorytrunk/tests/proteinstructure/data/2h6fB_Cb_8.0.cm added
Directorytrunk/tests/proteinstructure/data/2h6fB_SC_5.0.cm added
Directorytrunk/tests/proteinstructure/data/3nulA_ALL_5.0.cm added
Directorytrunk/tests/proteinstructure/data/3nulA_BB:SC_5.0.cm added
Directorytrunk/tests/proteinstructure/data/3nulA_BB_5.0.cm added
Directorytrunk/tests/proteinstructure/data/3nulA_Ca_8.0.cm added
Directorytrunk/tests/proteinstructure/data/3nulA_Cb_8.0.cm added
Directorytrunk/tests/proteinstructure/data/3nulA_SC_5.0.cm added
Directorytrunk/tests/proteinstructure/data/7odcA_ALL_5.0.cm added
Directorytrunk/tests/proteinstructure/data/7odcA_BB:SC_5.0.cm added
Directorytrunk/tests/proteinstructure/data/7odcA_BB_5.0.cm added
Directorytrunk/tests/proteinstructure/data/7odcA_Ca_8.0.cm added
Directorytrunk/tests/proteinstructure/data/7odcA_Cb_8.0.cm added
Directorytrunk/tests/proteinstructure/data/7odcA_SC_5.0.cm added
Directorytrunk/tests/proteinstructure/data/cullpdb_20 added
Directorytrunk/tests/proteinstructure/data/testset10.list added