org.strbio.app
Class ConvertProtein
java.lang.Object
org.strbio.app.ConvertProtein
public class ConvertProtein
- extends java.lang.Object
Convert proteins between file formats.
Run with no arguments to get syntax. To use most of the 'get'
flags, proteins have to be named something for which the PDB
file name can be figured out, i.e. '1abc' or '2xyzA'. You
also need the local PDB path set in a file in your home
directory called .pdb.properties; the file should contain the
word pdb.path followed by a
list of directories separated by colons or semicolons:
pdb.path /usr/mol/pdb:./morepdb:.
Details of how the path is searched are described in findPDBName.
Version 1.5, 3/29/04 - changed getseq to getpdbseq, added getentrezseq
Version 1.46, 2/12/02 - added more suffixes for fasta fmt
Version 1.45, 7/18/01 - added namelen, saf format
Version 1.44, 10/24/00 - added removeredundantseq, removeredundantsubseq
Version 1.43, 3/10/00 - added stripseqs
Version 1.42, 2/11/00 - added clustal format to help
Version 1.41, 1/14/00 - added makevirtualcb
Version 1.4, 1/11/00 - added -stripallbut
Version 1.39, 1/7/00 - added -fixdistancegaps
Version 1.38, 12/6/99 - added -reverse, kludgeChainID
Version 1.37, 11/10/99 - added stripnoatoms, rundssp
Version 1.36, 10/28/99 - added calcangles
Version 1.35, 9/2/99 - added findChain
Version 1.34, 7/22/99 - added getCATH, getPDB
Version 1.33, 6/9/99 - added splitProfiles, stripGaps
Version 1.32, 6/8/99 - added splitByName
Version 1.31, 4/14/99 - better error checking
Version 1.3, 3/31/99 - added multiple -fine support
Version 1.27, 2/10/99 - added YAPF support.
Version 1.26, 2/3/99 - added -combine option
Version 1.25, 2/2/99 - made profile the default
Version 1.24, 11/4/98 - made -find option fuzzy.
Version 1.23, 9/8/98 - added choose option
Version 1.22, 7/17/98 - added TDP support.
Version 1.21, 6/10/98 - added CASP support.
Version 1.2, 5/5/98 - added support for Profiles, writing Fasta
Version 1.1, 4/9/98 - added functionality from getatoms, getpdbinfo,
getpred, rotate. (all C++ programs). Added getenv.
Version 1.01, 4/2/98 - added more formats in Protein and ProteinSet
Version 1.0, 3/26/98 - based on (C++) convert 1.3.
- Version:
- 1.5, 3/29/04
- Author:
- JMC
- See Also:
ProteinSet
,
PDB.findPDBName(java.lang.String, org.strbio.io.Printf)
Field Summary |
static java.lang.String |
VERSION
|
Method Summary |
static void |
main(java.lang.String[] argv)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
VERSION
public static final java.lang.String VERSION
- See Also:
- Constant Field Values
ConvertProtein
public ConvertProtein()
main
public static final void main(java.lang.String[] argv)