Help With A Biojava Method "Getproteinsequenceforstructure"

Question

[potassiumiodide0990]

I am still a newbie to biojava. I wanted a sample example to learn how to use getProteinSequenceForStructure(Structure struct, Map<Integer,Group> groupIndexPosition) of class StructureSequenceMatcher to obtain a the protein sequence. I have the pdb file of a protein and i know how to get the structure based on the pdbid. I need to get the protein sequence from the structure now.. Please help me..

[Michael]

Another case of RTFM

Answer 1

[Michael]

Read the documentation, there is an example how to read a pdb file: http://www.biojava.org/docs/api/org/biojava/bio/structure/Structure.html

[potassiumiodide0990]

Hi Michael! The example does show how to read a PDB file but now how to use the method in question.

[Michael]

Then read the documentation of the method http://www.biojava.org/docs/api/org/biojava/bio/structure/io/StructureSequenceMatcher.html and combine them, the only objects you need is a Structure from reading the PDB file and an empty Map.

[Ram]

OP has not been active for >6 months so I'm toggling the Accepted Status on this now.