org.strbio.app
Class ConvertProtein

java.lang.Object
  extended by 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
           
 
Constructor Summary
ConvertProtein()
           
 
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
 

Field Detail

VERSION

public static final java.lang.String VERSION
See Also:
Constant Field Values
Constructor Detail

ConvertProtein

public ConvertProtein()
Method Detail

main

public static final void main(java.lang.String[] argv)