org.strbio.mol
Class ProteinSet

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.Vector
              org.strbio.mol.PolymerSet
                  org.strbio.mol.ProteinSet

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess

Direct Known Subclasses:

ProfileSet

public class ProteinSet
extends PolymerSet

Class to represent a set of proteins to be acted on in a group.

 Version 1.35, 7/22/99 - moved findPDBName to org.strbio.local.PDB
 Version 1.34, 7/9/99 - added thread
 Version 1.33, 6/4/99 - added predictSS
 Version 1.32, 11/23/98 - fixed findDSSP to handle compressed PDB files
 Version 1.31, 8/7/98 - added writeXXX(outfile)
 Version 1.3, 7/10/98 - can create a ProteinSet from a Profile
 Version 1.21, 6/10/98 - added writeCASP
 Version 1.2, 4/23/98 - now extends PolymerSet
 Version 1.1, 4/9/98 - added findPDB, findDSSP, readList
 Version 1.0, 4/2/98 - original version
 

Version:

1.35, 7/22/99

Author:

JMC

See Also:

Protein, ThreadSet, Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.strbio.mol.PolymerSet

PolymerSet.PolymerEnumeration

Field Summary

Fields inherited from class java.util.Vector

capacityIncrement, elementCount, elementData

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

ProteinSet()
Create an empty protein set.

ProteinSet(Profile q)
Make a protein set from a profile... the protein set will contain newly created Proteins, one per sequence in the profile.

ProteinSet(ProteinSet y)
Copy another protein set, but not the proteins (only the pointers to them).

Method Summary

static ProteinSet	findDSSP(java.lang.String name, Printf outfile) find and load proteins from a DSSP file (do DSSP on PDB file)
static ProteinSet	findPDB(java.lang.String name, Printf outfile) find and load proteins from a PDB file.
void	fixDistanceGaps() Fix distance gaps in this set; replace all proteins with gaps with a set of chains that has been split up at the gap boundaries.
Polymer	newPolymer() Make sure this set contains only Proteins.
void	predictSS(Printf outfile) Predict the secondary structure of these proteins, using the default method (Pred2ary, with large jury).
void	predictSS(Printf outfile, SSPredictor method) Predict the secondary structure of these proteins, using a specified prediction method.
Protein	protein(int i) Return the i'th protein in the array.
long	residues() total # of residues in the set
ThreadResults[]	thread(Printf outfile) Thread, using the default method.
ThreadResults[]	thread(Printf outfile, ThreadMethod method) Thread the proteins, using a specified threading method.
boolean	write(java.lang.String filename) Write set to a file, with name determined by the suffix.
void	writeCASP(Printf outfile) Write set to CASP file.
void	writeCASP(java.lang.String filename) Write set to CASP file.
void	writeConv(Printf outfile) Write set to Conv file.
void	writeConv(java.lang.String filename) Write set to Conv file.
void	writeEA(Printf outfile) Write set to EA file.
void	writeEA(java.lang.String filename) Write set to EA file.
void	writePDB(Printf outfile) Write set to PDB file, including all SEQRES, JMCSTR, and ATOM records.
void	writePDB(Printf outfile, boolean vanillaPDB) Write set to PDB file.
void	writePDB(java.lang.String filename) Write set to PDB file, including all SEQRES, JMCSTR, and ATOM records.
void	writePDB(java.lang.String filename, boolean vanillaPDB) Write set to PDB file.
void	writeVar2(Printf outfile) Write set to Var2 file.
void	writeVar2(java.lang.String filename) Write set to Var2 file.

Methods inherited from class org.strbio.mol.PolymerSet

add, add, add, addReversedCopies, clear, clearPolymers, clearProperties, clearProperty, ensureNames, findClosest, getNames, getPropertyAll, getPropertyOne, isEqual, keepOnlyChainID, keepOnlyNames, keepOnlyNamesFuzzy, load, n, nMonomers, noSpaceNames, nPolymersInFile, p, polymer, polymers, polymersInFile, polymersInFile, polymersInFile, polymersInFile, printNames, read, read, read, readList, remove, remove, removeRedundantSequences, save, searchByName, searchByNameFuzzy, searchByNameFuzzy, searchByNameFuzzyIndex, searchByNameFuzzyIndex, searchByNameIndex, setPolymerAt, setProperty, stripNoAtoms, writeFasta, writeFasta, writeList, writeList, writePTS, writePTS, writeYAPF, writeYAPF

Methods inherited from class java.util.Vector

add, add, addAll, addAll, addElement, capacity, clone, contains, containsAll, copyInto, elementAt, elements, ensureCapacity, equals, firstElement, get, hashCode, indexOf, indexOf, insertElementAt, isEmpty, lastElement, lastIndexOf, lastIndexOf, remove, removeAll, removeAllElements, removeElement, removeElementAt, removeRange, retainAll, set, setElementAt, setSize, size, subList, toArray, toArray, toString, trimToSize

Methods inherited from class java.util.AbstractList

iterator, listIterator, listIterator

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

iterator, listIterator, listIterator

Constructor Detail

ProteinSet

public ProteinSet()

Create an empty protein set.

ProteinSet

public ProteinSet(ProteinSet y)

Copy another protein set, but not the proteins (only the pointers to them).

ProteinSet

public ProteinSet(Profile q)

Make a protein set from a profile... the protein set will contain newly created Proteins, one per sequence in the profile. Information from each residue in the profile is copied into each residue of each protein. Gaps are also copied.

Method Detail

newPolymer

public Polymer newPolymer()

Make sure this set contains only Proteins.

Overrides:

newPolymer in class PolymerSet

protein

public Protein protein(int i)

Return the i'th protein in the array.

writePDB

public final void writePDB(java.lang.String filename,
                           boolean vanillaPDB)
                    throws java.io.IOException

Write set to PDB file.

Parameters:

filename - name of file to write to

vanillaPDB - if true, won't write JMCSTR records

Throws:

java.io.IOException

See Also:

Protein.writePDB(org.strbio.io.Printf, boolean)

writePDB

public final void writePDB(Printf outfile,
                           boolean vanillaPDB)
                    throws java.io.IOException

Write set to PDB file.

Parameters:

outfile - file to write to

vanillaPDB - if true, won't write JMCSTR records

Throws:

java.io.IOException

See Also:

Protein.writePDB(org.strbio.io.Printf, boolean)

writePDB

public final void writePDB(java.lang.String filename)
                    throws java.io.IOException

Write set to PDB file, including all SEQRES, JMCSTR, and ATOM records.

Overrides:

writePDB in class PolymerSet

Parameters:

filename - name of file to write to

Throws:

java.io.IOException

See Also:

Protein.writePDB(org.strbio.io.Printf, boolean)

writePDB

public final void writePDB(Printf outfile)
                    throws java.io.IOException

Write set to PDB file, including all SEQRES, JMCSTR, and ATOM records.

Overrides:

writePDB in class PolymerSet

Parameters:

outfile - open Printf to write to

Throws:

java.io.IOException

See Also:

Protein.writePDB(org.strbio.io.Printf, boolean)

writeEA

public final void writeEA(java.lang.String filename)
                   throws java.io.IOException

Write set to EA file.

Throws:

java.io.IOException

See Also:

Protein.writeEA(org.strbio.io.Printf)

writeEA

public final void writeEA(Printf outfile)
                   throws java.io.IOException

Write set to EA file.

Throws:

java.io.IOException

See Also:

Protein.writeEA(org.strbio.io.Printf)

writeCASP

public final void writeCASP(java.lang.String filename)
                     throws java.io.IOException

Write set to CASP file.

Throws:

java.io.IOException

See Also:

Protein.writeCASP(org.strbio.io.Printf)

writeCASP

public final void writeCASP(Printf outfile)
                     throws java.io.IOException

Write set to CASP file.

Throws:

java.io.IOException

See Also:

Protein.writeCASP(org.strbio.io.Printf)

writeConv

public final void writeConv(java.lang.String filename)
                     throws java.io.IOException

Write set to Conv file.

Throws:

java.io.IOException

See Also:

Protein.writeConv(org.strbio.io.Printf)

writeConv

public final void writeConv(Printf outfile)
                     throws java.io.IOException

Write set to Conv file.

Throws:

java.io.IOException

See Also:

Protein.writeConv(org.strbio.io.Printf)

writeVar2

public final void writeVar2(java.lang.String filename)
                     throws java.io.IOException

Write set to Var2 file.

Throws:

java.io.IOException

See Also:

Protein.writeVar2(org.strbio.io.Printf)

writeVar2

public final void writeVar2(Printf outfile)
                     throws java.io.IOException

Write set to Var2 file.

Throws:

java.io.IOException

See Also:

Protein.writeVar2(org.strbio.io.Printf)

write

public boolean write(java.lang.String filename)
              throws java.io.IOException

Write set to a file, with name determined by the suffix. Returns true if the name was understood, or false if a default (YAPF format) file was written.

Overrides:

write in class PolymerSet

Throws:

java.io.IOException

residues

public final long residues()

total # of residues in the set

findPDB

public static final ProteinSet findPDB(java.lang.String name,
                                       Printf outfile)
                                throws java.io.IOException

find and load proteins from a PDB file.

Throws:

java.io.IOException

findDSSP

public static final ProteinSet findDSSP(java.lang.String name,
                                        Printf outfile)
                                 throws java.io.IOException

find and load proteins from a DSSP file (do DSSP on PDB file)

Throws:

java.io.IOException

predictSS

public void predictSS(Printf outfile,
                      SSPredictor method)
               throws java.io.IOException

Predict the secondary structure of these proteins, using a specified prediction method.

Throws:

java.io.IOException

predictSS

public void predictSS(Printf outfile)
               throws java.io.IOException

Predict the secondary structure of these proteins, using the default method (Pred2ary, with large jury).

Throws:

java.io.IOException

thread

public ThreadResults[] thread(Printf outfile,
                              ThreadMethod method)
                       throws java.io.IOException

Thread the proteins, using a specified threading method.

Throws:

java.io.IOException

thread

public ThreadResults[] thread(Printf outfile)
                       throws java.io.IOException

Thread, using the default method.

Throws:

java.io.IOException

fixDistanceGaps

public void fixDistanceGaps()

Fix distance gaps in this set; replace all proteins with gaps with a set of chains that has been split up at the gap boundaries.