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root/owl/trunk/src/owl/core/runners
r1647
File (rev) Last Change
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tinker/ 1392 (11 years ago) by jmduarteg: MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
gromacs/ 1009 (12 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
blast/ 1630 (9 years ago) by jmduarteg: New feature: now blast xml parser can read either raw xml or gzipped xml files. Also HomologList will use xml.gz files only as cache files
TcoffeeRunner.java 1489 (10 years ago) by jmduarteg: Fixed logging and error handling of tcoffee: now it will really log errors to log file, temp files won't be deleted when exit!=0, command line is logged
TcoffeeException.java 1334 (11 years ago) by jmduarteg: Refactoring xxxError to xxxException
SelectonRunner.java 1335 (11 years ago) by jmduarteg: Now throwing InterruptedException. Refactor BlastErro to BlastException
PymolRunner.java 1646 (9 years ago) by jmduarteg: Now interfaces pngs have transparent background. Also changed another instance of "select resi 0" to "select none"
PsipredRunner.java 1597 (9 years ago) by jmduarteg: Several changes related to blast: - now supporting blast+ blastp. - blast xml parser can now ignore the DTD url, avoiding unnecessary network access if desired - refactoring: legacy blast related stuff is now refactored to contain "legacy", runBlastp refers to blast+ Also updated uniprot jar.
PsipredException.java 1334 (11 years ago) by jmduarteg: Refactoring xxxError to xxxException
PolyposeRunner.java 1384 (11 years ago) by stehr: System.out.println(cmdline) is commented out.
NaccessRunner.java 1403 (11 years ago) by jmduarteg: Fixed a few bugs: - PdbChain: copy() was missing some important fields, PDB file writing method was printing SEQRES for nonpoly chains too - naccess BSA calculation had a few problems - PdbAsymUnit: a few important issues with PDB/CIF chain codes
MaxClusterRunner.java 1347 (11 years ago) by hstehr: moving project CCCP to this repository
DsspRunner.java 1392 (11 years ago) by jmduarteg: MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
DaliRunner.java 1435 (10 years ago) by jmduarteg: Fixed bugs in DaliRunner - it wouldn't run from cmview when the two chains had same pdb code and pdb chain code - it wouldn't work with newer versions of DaliLite as apparently the output file names and formats changed
ClustaloRunner.java 1593 (9 years ago) by jmduarteg: Now supporting clustalo as well as tcoffee for alignment of homologs
CalcSurfVolRunner.java 1399 (11 years ago) by jmduarteg: Improved PDB file writing: now writing SEQRES lines and fixed some formatting issues with long atom names (i.e. CL, NA,...)
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