 ../
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tinker/
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1057
(11 years ago)
by matt4077:
add psi/phi constraints from secondary structure to tinker reconstructions
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blast/
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1045
(11 years ago)
by jmduarteg:
Uniprot and embl ws dbfetch connections can now do multiple entries per request. Update to parse also the hit_def tag in blast parser.
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gromacs/
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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
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TcoffeeRunner.java
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1070
(11 years ago)
by jmduarteg:
Fixed bug in TcoffeeRunner. The t_coffee process was hanging after spawning. This didn't happen before, it can be related to the version of t_coffee (I'm using 8.14). Basically t_coffee seems to be doing something weird with stderr and stdout, java doesn't like it and makes the process hang (as usual java has a lot of problems in this area, see StreamGobbler class). The way to solve it is use the -quiet switch of t_coffee that can be used to redirect output to a file or have a complete quiet terminal.
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DsspRunner.java
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1046
(11 years ago)
by hstehr:
JPredConnection now returns a SecondaryStructure object; some updated javadocs
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PsipredRunner.java
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1046
(11 years ago)
by hstehr:
JPredConnection now returns a SecondaryStructure object; some updated javadocs
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CalcSurfVolRunner.java
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1032
(11 years ago)
by jmduarteg:
Extracted the calc-vol and calc-surf runner code to its own Runner class.
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PsipredError.java
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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
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TcoffeeError.java
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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
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DaliRunner.java
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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
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MaxClusterRunner.java
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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
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PolyposeRunner.java
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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
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NaccessRunner.java
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1005
(11 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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