 ../
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blast/
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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
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gromacs/
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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
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tinker/
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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.
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CalcSurfVolRunner.java
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1399
(10 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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ClustaloRunner.java
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1593
(9 years ago)
by jmduarteg:
Now supporting clustalo as well as tcoffee for alignment of homologs
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DaliRunner.java
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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
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DsspRunner.java
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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.
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MaxClusterRunner.java
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1347
(11 years ago)
by hstehr:
moving project CCCP to this repository
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NaccessRunner.java
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1403
(10 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
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PolyposeRunner.java
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1384
(11 years ago)
by stehr:
System.out.println(cmdline) is commented out.
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PsipredException.java
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1334
(11 years ago)
by jmduarteg:
Refactoring xxxError to xxxException
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PsipredRunner.java
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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.
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PymolRunner.java
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1646
(8 years ago)
by jmduarteg:
Now interfaces pngs have transparent background. Also changed another instance of "select resi 0" to "select none"
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SelectonRunner.java
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1335
(11 years ago)
by jmduarteg:
Now throwing InterruptedException. Refactor BlastErro to BlastException
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TcoffeeException.java
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1334
(11 years ago)
by jmduarteg:
Refactoring xxxError to xxxException
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TcoffeeRunner.java
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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
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