Aleix Lafita
Aleix Lafita
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.
Since we are releasing a new version of biojava that introduces a number of **API** changes, I would like to suggest a review of some of the command line (**CLI**)...
It would be great to be able to create sequence aligner objects without specifying target and query sequences, so that the parameters (or options), like gap penalty, alignment type and...
When trying to display a structure in **Jmol**, for example from the `MultipleAlignmentGUI`, the following error gets thrown and the JmolPanel remains empty: java.lang.ArithmeticException: / by zero at org.jmol.adapter.readers.cif.MessagePackReader.getInts(MessagePackReader.java:406) at...
When an alignment is performed in the `AlignmentGUI`, the resulting Jmol panel does show the first structure and the ligand of the second structure, but it does not show any...
Most methods to convert `MultipleAlignment` objects into String formats (FASTA, FatCat, XML) need structure identifiers for each `Atom `array to be printed. At the moment, only the Atom arrays are...
The secondary structure assigned by the authors can only be parsed with the PDBFileParser.
Related to #393. The idea is to extract _selectors_ from the alignment data structures in BioJava (**AFPChain** and **MultipleAlignment**) so that any molecular viewer can represent structure alignments. A good...
I encountered an Exception when trying to parse some structures, with something that seems related to insertion codes. The two I looked at are obsoleted, so it may be a...