biojava
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biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
See issue: https://github.com/rcsb/mmtf-python/issues/28 I looked at the entity information in the MMTF files and indeed for example in 1o2f the third entity is missing (3 non-polymer syn 'PHOSPHITE ION' )....
It is very usual that beta sheets form through symmetry partners in the crystal (be them biological contacts or not). It would be nice if our dssp-like secondary assignment implementation...
I've started building a test suite for the "toSdf" method. Need improved error handling and to deal with corner cases.
Now that the dssp algorithm for secondary structure assignment is implemented in biojava (see #336), it would be nice to also have the [promotif](http://www.img.bio.uni-goettingen.de/ms-www/internal/manuals/promotif/promotif.html) one that extends it slightly. Ideally...
Make use of the Protonation Variants Companion Dictionary (https://www.wwpdb.org/data/ccd) in addition to the Chemical Component Dictionary when assigning bonds. Would help with some of the entries in the issue https://github.com/rcsb/mmtf/issues/19
The idea is to fill in the missing fields of BioJava structures loaded from PDB files in order to be able to convert them to complete equivalent MMCIF and MMTF...
It is currently marked as work in progress.
this does not work: bash runCE.sh -file1 /tmp/data/structures/divided/mmCIF/cd/1cdg.cif.gz -file2 file:/tmp/data/structures/divided/mmCIF/ti/1tim.cif.gz -show3d it fails with the following, although the files do exist locally. 16:05:39 [main] WARN org.biojava.nbio.structure.align.util.UserConfiguration - Could not read...
PDB and mmCIF files use symmetry operators to reduce the number of atoms which need to be specified. This is used with NCS to reconstruct the asymmetric unit (e.g. in...
CATH releases [daily snapshots](http://cathdb.info/wiki/doku/?id=index#cath_daily_snapshot). It would be very nice to be able to access these in BioJava. Currently it's not easy to work with these in `CathInstallation`. We should add...