| Simplified further and set AFPChain block values. |
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over 13 years ago
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| There's no longer any need to use AFPChainScorer. |
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over 13 years ago
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| Simplified FastaAFPChainConverter using new AlignmentTools.updateSuperposition. |
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over 13 years ago
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| Fixed AlignmentTools.updateSuperposition. The previous code was incorrectly using the square root of the RMSD, and was also getting 0 for the RMSD in some cases. |
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over 13 years ago
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| Wrote a simple test for AlignmentTools.updateSuperposition. |
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over 13 years ago
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| Merge branch 'master' of https://github.com/ulyssecarion/biojava into ulyssecarion-master |
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over 13 years ago
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| making water names publicly accessible |
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over 13 years ago
|
| adding new utility method to filter out polymeric and solvent groups |
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over 13 years ago
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| Find ligands by comparing seqResGroups and groups. |
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over 13 years ago
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| Fixed tests, though they're not (even close to) finished. |
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over 13 years ago
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| Fixed multiple bugs, including superposition bug. |
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over 13 years ago
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| Switched back to global alignment. |
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over 13 years ago
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| Fixed a couple bugs and disabled call to Spencer's new method in createAfpChain. |
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over 13 years ago
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| Merge branch 'replaceOptAln' of https://github.com/sbliven/biojava-sbliven |
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over 13 years ago
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| Merge branch 'master' of https://github.com/sbliven/biojava-sbliven |
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over 13 years ago
|
| Add additional methods to AlignmentTools |
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over 13 years ago
|
| Minor warnings & whitespace changes |
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over 13 years ago
|
| OptimalCECPMain: Added loop to display intermediate steps |
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over 13 years ago
|
| Minor formatting changes |
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over 13 years ago
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| Adding AlignmentTools#toConciseAlignmentString |
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over 13 years ago
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| cpFastaToAfpChain needs to use ungapped CP shift, not gapped. |
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over 13 years ago
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| Fixed a bug in CP code caused by a misused variable. There's still another bug somewhere. |
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over 13 years ago
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| Fixed a couple issues: 1. Can't use ProteinSequence.getSequenceAsString() to set aligned and unaligned userCollection. 2. In CP code, don't use cloneCAArray because it doesn't set the parent Structure. |
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over 13 years ago
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| Merge branch 'master' of https://github.com/biojava/biojava |
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over 13 years ago
|
| Committing unfinished changes for working with CP FASTAs. |
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over 13 years ago
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| Fixed negative permutations. |
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over 13 years ago
|
| Added methods for cyclic permutations. |
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over 13 years ago
|
| Modified FastaAFPChainConverter to allow filename parameters |
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over 13 years ago
|
| Adding flexible StructureTools.getStructure(String) method. |
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over 13 years ago
|
| UniprotFormat patch for handling newlines in OS (organism) field |
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over 13 years ago
|
