Using the new checks for polymer type in Group, ... - #555
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* 'master' of github.com:biojava/biojava: (36 commits) Add some tests for negative residue ranges Minor javadoc & warnings fixes Fix compilation errors from merge Fix MultipleAlignmentJmol resizing bug Fixed bug where bonds from struct conn records were not made for multiple models. Latest ECOD now contains string quotes around some data fields. Need to remove them for junit tests to parse. update test for type of group based on comments from @josemduarte Fixing cath urls according to their final layout [maven-release-plugin]prepare for next development iteration [maven-release-plugin]prepare release biojava-4.2.4 new utility class for chromosome mappings. adding new dependency on guava new utility class for chromosome mappings. new utility class for chromosome mappings. Adding test for genome mapping Complete new CATH file names biojava#546 and biojava#544 Fixing biojava#544 and improving logging Some work towards fixing biojava#544 Back-porting cloning fix (see biojava#541) into bugfixes-4.2 biojava#542 changing default SCOP download location to Berkeley- SCOP. ...
* 'master' of github.com:biojava/biojava: [maven-release-plugin]prepare for next development iteration [maven-release-plugin]prepare release biojava-5.0.0-alpha6 Fixed the logic of working out which type of group a group is. Fixed a typo Immutability test fails with Cobertura instrumented classes Fixed the formatting and added some javadocs Upgrade to v1.0.0 Fixed handling of entities with no chains Fixed a null pointer exception from getAtomFromRecord Added handling of different residue types. Fixed a bug in generation of disulphide bonds - including a test case. Added support for D-GAMMA-PEPTIDE being a heatatm (as with mmCIF) not an amino. # Conflicts: # biojava-sequencing/src/test/java/org/biojava/nbio/sequencing/io/fastq/FastqTest.java
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Were the pom changes intended to belong to this PR? |
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| ChemComp cc = g.getChemComp(); | ||
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| if (ResidueType.lPeptideLinking.equals(cc.getResidueType()) |
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This check is not included in g.isPolymeric(). Do we need to add it too? I really can't remember why this is important or not. Ideas anyone?
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What would be lPeptideLinking but not PROTEIN_ONLY? Non-ribosomal peptides?
* 'master' of github.com:biojava/biojava: Making recent MmtfActions.writeToOutputStream static Fix the doc Update the outputstream to be created outside the function Update readme.md Add Gitter badge Write MMTF to an OutputStream
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To comment on the status of this: During the wednesday skype call we agreed that the checks for polymer type should get added also on the |
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| if ( info == null || info.getType() == null) { | ||
| logger.warn("No entity info could be found while adding chain with asym id {} (author id {}). Will consider it a polymer chain.", c.getId(), c.getName()); | ||
| logger.debug("No entity info could be found while adding chain with asym id {} (author id {}). Will consider it a polymer chain.", c.getId(), c.getName()); |
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I'd keep this at least on INFO level, this is quite a strong indication that there's something wrong in reading the structure.
* 'master' of github.com:biojava/biojava: Updating to latest version in readme
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... instead of repeating similar checks in StructureTools.