ViewVC Help
View Directory | Revision Log | Download Tarball | View Changeset | Root Listing
root/owl/trunk/src/owl/tests/core/structure/data
r1704
File Last Change
 ../
casp7/ 1030 (11 years ago) by jmduarteg: Extracted constants to owl_test_paths.dat and added CASP7 fasta files to resources dir. Now BlastParsersTest should be able to run anywhere.
2gpiA_SC_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
7odcA_Cb_8.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
2gpiA_Ca_8.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
2h6fB_Ca_8.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1d2sA_ALL_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1oewA_Cb_8.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1wb4A_SC_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1wvfA_ALL_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
2gpiA_Cb_8.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1od3A_Cb_8.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
2gpiA_BB_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
2h6fB_Cb_8.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
2gpiA_ALL_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1wb4A_Cb_8.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1wb4A_ALL_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
7odcA_ALL_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1oewA_SC_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
3nulA_Cb_8.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
3nulA_ALL_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1tdrB.pdb 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1oewA_BB_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
3nulA_SC_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1tdrA.rsa 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1wvfA_BB_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
2h6fB_ALL_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1d2sA_BB_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
testset10.list 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
3nulA_Ca_8.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1od3A_Ca_8.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1w0nA_Cb_8.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1wb4A_BB_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1oewA_Ca_8.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
7odcA_BB_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1d2sA_Ca_8.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1oewA_ALL_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1od3A_SC_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1w0nA_ALL_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1od3A_BB_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1w0nA_Ca_8.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1tdrA.pdb 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1wvfA_SC_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
2h6fB_SC_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1w0nA_BB_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1wvfA_Ca_8.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
2h6fB_BB_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1d2sA_Cb_8.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
7odcA_SC_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1d2sA_SC_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1wvfA_Cb_8.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1w0nA_SC_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1od3A_ALL_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1wb4A_Ca_8.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
7odcA_Ca_8.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
3nulA_BB_5.0.cm 1008 (11 years ago) by hstehr: refactoring: adapting test packages to match new package structure
1bxyA_tinker.pdb 1308 (10 years ago) by jmduarteg: Fixed important bug that broke the reconstruction programs. Tinker output files don't contain occupancy/bfactors. Thus we have to make their parsing optional. Added a test case for this.
T0515.tar.gz 1332 (10 years ago) by jmduarteg: Another fix to PdbfilePdb parser. Now it is more robust with bad formatting, tested on a whole tar ball of CASP predictions. Added the CASP predictions test set to tests.
1od3A_BB-SC_5.0.cm 1337 (10 years ago) by jmduarteg: Changing file names of contact map test files, windows didn't like the ':' in the file names
2gpiA_BB-SC_5.0.cm 1337 (10 years ago) by jmduarteg: Changing file names of contact map test files, windows didn't like the ':' in the file names
2h6fB_BB-SC_5.0.cm 1337 (10 years ago) by jmduarteg: Changing file names of contact map test files, windows didn't like the ':' in the file names
3nulA_BB-SC_5.0.cm 1337 (10 years ago) by jmduarteg: Changing file names of contact map test files, windows didn't like the ':' in the file names
1d2sA_BB-SC_5.0.cm 1337 (10 years ago) by jmduarteg: Changing file names of contact map test files, windows didn't like the ':' in the file names
1wvfA_BB-SC_5.0.cm 1337 (10 years ago) by jmduarteg: Changing file names of contact map test files, windows didn't like the ':' in the file names
1oewA_BB-SC_5.0.cm 1337 (10 years ago) by jmduarteg: Changing file names of contact map test files, windows didn't like the ':' in the file names
1wb4A_BB-SC_5.0.cm 1337 (10 years ago) by jmduarteg: Changing file names of contact map test files, windows didn't like the ':' in the file names
7odcA_BB-SC_5.0.cm 1337 (10 years ago) by jmduarteg: Changing file names of contact map test files, windows didn't like the ':' in the file names
1w0nA_BB-SC_5.0.cm 1337 (10 years ago) by jmduarteg: Changing file names of contact map test files, windows didn't like the ':' in the file names
1c52A.pdb 1455 (10 years ago) by jmduarteg: Committing test case file that was missing since a few revisions
testset_interfaces.txt 1573 (9 years ago) by jmduarteg: IMPORTANT changes and fixes in interface calculation: - very important bug fix: BoundingBox was not always telling properly whether 2 boxes overlap. This not only fixes the important bug but also boosts the speed of interface calculation - optimisation of PdbChain.getAICGraph not to return an empty graph whenever no overlap of boxes is found (instead of generating empty distance matrix and checking its emptiness): this alone gives the biggest performance boost to interface calculation, around 5x faster thanks to this alone - fine optimisation of max/min calculation in BoundingBox - made sure that bounds caching is done properly - introduced the right solution for symmetry redundancy elimination: operators multiplication is the identity. Before we had an ad-hoc solution that wasn't comprehensive at all - in any case the symmetry redundancy elimination is right now almost turned off because we introduced new conditions to re-check equivalent operators to fix cases like 2gsg, 3ka0, 1vzi, 1g3p and 1eaq, where some interfaces are missed due to an equivalent operator making the molecule fall in a cell where there's no contacts All in all this totally changes the interface calculation: 1) by a massive boost in performance 2) by making it more correct, surely there were cases with missing interfaces, we were just lucky not to find them in testing
testset_interfaces2.txt 1577 (9 years ago) by jmduarteg: Important change in interface calculation: - another massive gain in run-time and memory usage: we first use the bounding boxes translations to see if it is worth translating the whole unit cells - thanks to that we now go to 2nd neighbors! (still performance is better than before with only 1st neighbors!). With that we fixed the long-standing bug by which we miss interfaces beyond the 1st neighbor - included a few examples of 2nd neighbor problem in test - re-done the symmetry redundancy elimination, it is there but it has a very little effect on overall performance. Now we only don't use an operator when we are very sure its partner was in the right place. In effect we could get rid of it because it wouldn't really affect the performance, we rather keep it as it is good to remember that there is a lot of symmetry redundancy
testset_rmsd.list 1678 (8 years ago) by jmduarteg: Moved geometry related calculations to the GeometryTools class: rmsd, screw component, axis type, axis-angle etc. Like that the calculations can be used from anywhere. Introduced the OptSuperposition class as output of the rmsd calculation. Improved the rmsd calculation in PdbChain (and corrected some bugs). Also improved a lot the rmsd unit testing. All tests in PdbChainTest are now done with cif files and not anymore with pdbase. Implemented an optimal superposition method in ChainInterface and some output for that in enumerateInterfaces with the intention of finding the pseudo-symmetric relationship between NCS related chains in an interface. All tests passed.
cullpdb_20 1704 (7 years ago) by jmduarteg: Fixed bug in cif file parsing: was not tokenising correctly loop elements that had more multi-line quoting mixed with normal quoted fields and several records. Added one more test case for that.
         71 files shown