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r1304
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gromacs/ 1009 (11 years ago) by hstehr: refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
tinker/ 1127 (11 years ago) by matt4077: New Residuescoringfunctionimplementation
blast/ 1304 (10 years ago) by jmduarteg: Fixed important bug: we didn't model the blast data properly. A hit is composed of several hsps. Now our classes following that data model properly (before we treated a hit as an hsp).
PsipredError.java 1009 (11 years ago) by hstehr: refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
TcoffeeError.java 1009 (11 years ago) by hstehr: refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
DaliRunner.java 1009 (11 years ago) by hstehr: refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
PolyposeRunner.java 1009 (11 years ago) by hstehr: refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
CalcSurfVolRunner.java 1032 (11 years ago) by jmduarteg: Extracted the calc-vol and calc-surf runner code to its own Runner class.
DsspRunner.java 1046 (11 years ago) by hstehr: JPredConnection now returns a SecondaryStructure object; some updated javadocs
PsipredRunner.java 1046 (11 years ago) by hstehr: JPredConnection now returns a SecondaryStructure object; some updated javadocs
TcoffeeRunner.java 1097 (11 years ago) by jmduarteg: Now explicitely specifying output dnd file in tcoffee so it can be removed by the calling program.
SelectonRunner.java 1132 (11 years ago) by jmduarteg: New SelectonRunner class. More taxonomy information retrieved from uniprot.
MaxClusterRunner.java 1199 (11 years ago) by hstehr: added some debug output (commented out)
NaccessRunner.java 1242 (11 years ago) by jmduarteg: Fixed bug: NACCESS (weirdly) calculates slightly different ASA values for same molecule in different orientation (i.e. it depends on the choice of axes)!! That produces then some strange BSA values (including some negative) and slight discrepancies. Thus now we run NACCESS always for each of the 2 isolated molecules of the interface and then the complex (and so losing efficiency).
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