 ../
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pisa/
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1217
(10 years ago)
by jmduarteg:
First fully working version (this time hopefully for real...) of interface enumeration. Works for many examples, still there are problems in many others due to area discrepancies with pisa, but those are minor things. The elimination of duplicates is based on chain codes and number of contacting atoms, it is of course possible that 2 different interfaces happen to have the same chain codes and same number of contacting atoms (but unlikely). Would need a more fine grained comparison.
New test class to compare automatically to PISA output.
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package-info.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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UniProtConnection.java
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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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SiftsConnection.java
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1226
(10 years ago)
by hstehr:
Refactoring of SiftsConnection and SiftsFeature, now implementing Uniprot2Pdb
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ScopConnection.java
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1034
(11 years ago)
by jmduarteg:
Extracted Scop parsing code to its own connection class.
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PrositeScanner.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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PrositeHit.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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PhosphoSitePlusConnection.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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PDomainsConnection.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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NoMatchFoundException.java
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1040
(11 years ago)
by jmduarteg:
New UniprotConnection taken from Henning's structural impact project (lots of new jar dependencies with that). New EmblWSDBFetchConnection class to get sequences from EMBL web services.
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JPredStopNotifier.java
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1060
(10 years ago)
by hstehr:
New helper classes JPredProgressRetriever and JPredNotifier which can be used to run JPredConnection in a thread and notify some GUI component of the progress.
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JPredProgressRetriever.java
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1060
(10 years ago)
by hstehr:
New helper classes JPredProgressRetriever and JPredNotifier which can be used to run JPredConnection in a thread and notify some GUI component of the progress.
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JPredConnection.java
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1062
(10 years ago)
by stehr:
fixed a minor bug in JPredConnection; new method SecondaryStructure.getConsensusSecondaryStructure(); changed visibility of RIGEnsemble.addFile() to public
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GTGParser.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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GTGHitList.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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GTGHit.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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EmblWSDBfetchConnection.java
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1172
(10 years ago)
by jmduarteg:
Now using apache commons logging
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ECConnection.java
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1035
(11 years ago)
by jmduarteg:
Extracted the EC data parsing code to its own connection class.
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ConsurfConnection.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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CSAConnection.java
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1034
(11 years ago)
by jmduarteg:
Extracted Scop parsing code to its own connection class.
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