Hi Richard,
But... it still won't compile, but now for a different reason. It seems
that Andreas' check-in of his structure classes over the weekend was
missing the Matrix and SingularValueDecomposition classes. Andreas can
you fix this please?
They were all checked in at the same time yesterd
*doh!*
All working. Thanks, Andreas.
Richard Holland
Bioinformatics Specialist
GIS extension 8199
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I have some very plane pdb files (Coordinates only), and if I try to parsethem,
it throws:
java.lang.StringIndexOutOfBoundsException: String index out of range: 6at
java.lang.String.substring(String.java:1765)at
org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:7
Hi!
Regarding the question posted by Tamas for creating artificial
side-chains for amino acids last week:
To superimpose two (or more) residues/atoms, one needs to do a singular
value decomposition, which
gives the required rotation matrix and shift vector. The recent
biojava 1.4 release c
can you send me one of your files off list?
the parser could parse all of PDB about one year ago ...
And.
On 5 Dec 2005, at 14:13, Tamas Horvath wrote:
I have some very plane pdb files (Coordinates only), and if I try to
parsethem, it throws:
java.lang.StringIndexOutOfBoundsExce
Hi,
Can anyone tell me how I might get the value of the Hit_def tag from
blast xml output? I'm following the cookbook protocol for parsing and
extracting results
(http://www.biojava.org/docs/bj_in_anger/BlastParser.htm). I see a way to
get the subject (hit) id, but not the description.
t
You may need to customize your blast listeners. If you run the blast echo
example in biojava in anger you will find out what event type that
information is contained in. You can then listen for that event type.
http://www.biojava.org/docs/bj_in_anger/blastecho.htm
- Mark
"Michael E. Smoot"
