| Merge branch 'minor' |
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over 11 years ago
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| Merge pull request #270 from josemduarte/minor |
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over 11 years ago
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| Merge commit 'biojava/minor' into minor |
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over 11 years ago
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| Merge remote-tracking branch 'main/patch' into minor |
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over 11 years ago
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| Fixed issue in contact overlap calculation, when residues of chains in same entity are not numbered similarly, e.g. 3ddo. This was achieved by reimplementing ContactSet and ResidueIdentifier to use SEQRES residue indices. |
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over 11 years ago
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| Merge pull request #269 from lafita/patch |
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over 11 years ago
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| Fix #268: FatCat overwritten by Text |
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over 11 years ago
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| Renaming CrystalCell methods to clarify coordinate system |
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over 11 years ago
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| Fix #266 JmolPanel resize menu |
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over 11 years ago
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| Removing additional newly deprecated methods |
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over 11 years ago
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| Fix ligand handling following support for RNA alignments. |
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over 11 years ago
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| Merge pull request #265 from lafita/patch |
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over 11 years ago
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| Replacing deprecated CA methods with the new ones |
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over 11 years ago
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| Reducing assumptions that structures are protein |
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over 11 years ago
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| New feature: Compound.getAlignedResIndex() to map residue numbers to their corresponding indices in the seqres. This could be done already by checking the index in getSeqresGroups() but like this it is more convenient and faster since the mapping is cached in a map in Compound. |
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over 11 years ago
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| For CE-Symm only, the rotation axis is shown in the 3D jmol display and only the first model with the colored subunits is shown. |
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over 11 years ago
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| Changed back the StructureAlignmentJmol methods to static, passing the colors as an input. |
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over 11 years ago
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| Modified a test file for the AFPChain, because the blockScore variable is now calculated in the updateSuperposition method (before it was filled with 0.0). That was the only difference between the generated and the test files, so it has been updated. |
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over 11 years ago
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| Merge branch 'minor' |
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over 11 years ago
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| Merge branch 'patch' into minor |
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over 11 years ago
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| Fixed bug: CompoundFinder wasn't working for raw pdb files like 3ddo Now it does full alignments instead of simply trying to match residue numbers, it is the only way to be sure that all cases (like 3ddo) work |
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over 11 years ago
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| Changed CeStartupParams to static |
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over 11 years ago
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| Making contact overlap score cutoff a parameter |
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over 11 years ago
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| Merge pull request #263 from jgrzebyta/patch |
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over 11 years ago
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| GenbankProxySequenceReaderTest: add identifier alias GID test |
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over 11 years ago
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| add place for version and GenBank GI number in AccessionID class |
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over 11 years ago
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| Merge branch 'minor' into master |
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over 11 years ago
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| Merge pull request #262 from sbliven/minor |
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over 11 years ago
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| Add CrystalCell method to convert operators to function on the unit cell |
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over 11 years ago
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| Added new methods to the AlignmentTools class: a method to calculate the gaps in each block of an optimal alignment and a method to replace the optimal alignment of an AFPChain. |
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over 11 years ago
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