org.strbio.mol
Class Monomer

java.lang.Object
  org.strbio.mol.Monomer

All Implemented Interfaces:

DLinkedList.Node

Direct Known Subclasses:

Nucleotide, Residue

public class Monomer
extends java.lang.Object
implements DLinkedList.Node

Class to represent a single monomer in a linear polymer. Having a monomer that's not part of a polymer doesn't make sense; use Molecule instead.

 Version 1.3, 12/15/04 - added molecularWeight
 Version 1.2, 1/11/00 - added stripAllBut
 Version 1.14, 12/13/99 - added stripAtomsByName
 Version 1.13, 2/16/99 - added YAPF support.  Changed readPDBAtom
   to readAtomRecord to avoid confusion with same function under
   Protein (which does something different), and to be more consistent
   with other readSomethingRecord functions under Residue.
 Version 1.12, 11/2/98 - added isGap, isValidType, isValidNonGap functions
 Version 1.11, 10/26/98 - can read lower case FASTA files
 Version 1.1, 10/16/98 - added centerOfMass()
 Version 1.01, 8/7/98 - changed PrintfStream to Printf
 Version 1.0, 4/16/98 - original version
 

Version:

1.2, 1/11/00

Author:

JMC

See Also:

Atom, AtomNode, Residue, Protein

Field Summary

DLinkedList	atoms pointer to the atoms, if there are any (if not, this is null).
int	n sequence number, which is the number in the file for files (like PDB) that contain this info; otherwise numbering starts at 0.
char	type type of monomer, in a one-letter code

Constructor Summary

Monomer()
Constructor makes everything null.

Monomer(char t)
Construct from a character with the monomer type.

Monomer(Monomer q)
copy another monomer, including the atoms.

Monomer(java.lang.String t)
Construct from a string with the monomer type.

Method Summary

Atom	atomSearch(java.lang.String name) Search the atoms of this monomer for the first atom with a given name.
DVector	centerOfMass() Return a new DVector(3) containing the center of mass for the monomer.
void	centerOfMass(DVector cm) Finds the center of mass for the monomer and puts in in the DVector(3) that you pass it.
void	copyAtoms(Monomer q) copy the atoms from another monomer.
void	copyDataFrom(Monomer q) copy another monomer, including the atoms.
DLinkedList.Node	copyNode() copy contents of a monomer.
boolean	isGap() does this monomer represent a gap?
boolean	isValidNonGap() Is this monomer something which is valid, but not a gap?
boolean	isValidType() is the character in 'type' valid for this monomer?
double	molecularWeight() molecular weight; default zero.
int	nAtoms() How many atoms are there?
int	nAtomsWithCoord() How many atoms are there with known coordinates?
DLinkedList.Node	next() return the next monomer in the polymer.
DLinkedList.Node	prev() return the previous monomer in the polymer.
void	readAtomRecord(java.lang.String buffer) Reads one PDB/YAPF atom record out of a buffer string, and inserts it into the list of atoms.
boolean	readFasta(java.io.BufferedReader infile) Read this monomer out of a Fasta format file.
void	readSeqRecord(java.lang.String buffer) Read this monomer out of a YAPF (sequence profile) format file (JMC's format).
void	rotate(DMatrix rot) rotate all atoms by multiplying by a 3x3 rotation matrix.
void	setNext(DLinkedList.Node x) set the next monomer in the polymer.
void	setPrev(DLinkedList.Node x) set the previous monomer in the polymer.
void	stripAllAtoms() Strip away all atoms from this monomer.
void	stripAllBut(java.lang.String[] names) Strip away all atoms except ones named in an array.
void	stripAllButFirstAtom() Strip all but first atom from this monomer.
void	stripAtomsByName(java.lang.String atomName) Strip away a named atom or atoms.
void	transform(DMatrix trans) transform the position of all atoms.
void	translate(DVector trans) translate all atoms by adding a DVector(3) to their coordinates.
java.lang.String	typeName() Return a long name for this monomer, based on the type.
void	writePDBAtom(Printf outfile, java.lang.String polyname, char chainid) Writes out PDB ATOM records for all atoms belonging to this monomer.
void	writePts(Printf outfile) Writes out this monomer in PTS (Jon Blake's) format.
void	writeSeqRecord(Printf outfile) Write this monomer in JMC's YAPF format.
void	writeYAPFAtom(Printf outfile, char chainid) Writes out YAPF ATOM records for all atoms belonging to this monomer.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

type

public char type

type of monomer, in a one-letter code

n

public int n

sequence number, which is the number in the file for files (like PDB) that contain this info; otherwise numbering starts at 0. This does not mean that it's the n'th monomer in a list, though!

atoms

public DLinkedList atoms

pointer to the atoms, if there are any (if not, this is null).

Constructor Detail

Monomer

public Monomer()

Constructor makes everything null.

Monomer

public Monomer(char t)

Construct from a character with the monomer type.

Monomer

public Monomer(java.lang.String t)

Construct from a string with the monomer type.

Monomer

public Monomer(Monomer q)

copy another monomer, including the atoms. This makes another copy of the data, but not the links.

Method Detail

copyAtoms

public void copyAtoms(Monomer q)

copy the atoms from another monomer. This makes another copy of the data.

centerOfMass

public DVector centerOfMass()

Return a new DVector(3) containing the center of mass for the monomer. Bug: Atoms don't have atomic weights, so all are treated as the same weight.

centerOfMass

public void centerOfMass(DVector cm)

Finds the center of mass for the monomer and puts in in the DVector(3) that you pass it. Bug: Atoms don't have atomic weights, so all are treated the same. No atoms will return 0,0,0.

nAtoms

public int nAtoms()

How many atoms are there?

nAtomsWithCoord

public int nAtomsWithCoord()

How many atoms are there with known coordinates?

copyDataFrom

public void copyDataFrom(Monomer q)

copy another monomer, including the atoms. This makes another copy of the data, but not the links.

next

public DLinkedList.Node next()

return the next monomer in the polymer.

Specified by:

next in interface DLinkedList.Node

prev

public DLinkedList.Node prev()

return the previous monomer in the polymer.

Specified by:

prev in interface DLinkedList.Node

setNext

public void setNext(DLinkedList.Node x)

set the next monomer in the polymer.

Specified by:

setNext in interface DLinkedList.Node

setPrev

public void setPrev(DLinkedList.Node x)

set the previous monomer in the polymer.

Specified by:

setPrev in interface DLinkedList.Node

copyNode

public DLinkedList.Node copyNode()

copy contents of a monomer.

Specified by:

copyNode in interface DLinkedList.Node

typeName

public java.lang.String typeName()

Return a long name for this monomer, based on the type. The default is to just return a string of whatever's in 'type', but that should be overridden for Residues, Bases, etc. (i.e. 'C' -> "CYS" for Residues).

atomSearch

public final Atom atomSearch(java.lang.String name)

Search the atoms of this monomer for the first atom with a given name. Returns null if there isn't one. Example... to search for the alpha carbon try atomSearch("CA").

stripAllAtoms

public final void stripAllAtoms()

Strip away all atoms from this monomer.

stripAllButFirstAtom

public final void stripAllButFirstAtom()

Strip all but first atom from this monomer.

stripAtomsByName

public final void stripAtomsByName(java.lang.String atomName)

Strip away a named atom or atoms.

stripAllBut

public final void stripAllBut(java.lang.String[] names)

Strip away all atoms except ones named in an array. This is a more general case of Residue.StripAllButCA, but is a bit less efficient due to having to set up the array with multiple names.

writePDBAtom

public void writePDBAtom(Printf outfile,
                         java.lang.String polyname,
                         char chainid)
                  throws java.io.IOException

Writes out PDB ATOM records for all atoms belonging to this monomer.

Parameters:

outfile - an open Printf

polyname - name of the polymer, or null for generic polymer.

chainid - the chain ID, or space if there isn't one.

Throws:

java.io.IOException

writeYAPFAtom

public void writeYAPFAtom(Printf outfile,
                          char chainid)
                   throws java.io.IOException

Writes out YAPF ATOM records for all atoms belonging to this monomer. This is the same as PDB, except without the redundant polymer name info on the right.

Parameters:

outfile - an open Printf

chainid - the chain ID, or space if there isn't one.

Throws:

java.io.IOException

readAtomRecord

public void readAtomRecord(java.lang.String buffer)

Reads one PDB/YAPF atom record out of a buffer string, and inserts it into the list of atoms. This does not set type or number from the record; it's quicker to do this only once, using the first record or a SEQRES entry.

Parameters:

buffer - a line from a PDB/YAPF file with an ATOM record belonging to this monomer.

See Also:

Atom.readPDB(java.lang.String)

writeSeqRecord

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

Write this monomer in JMC's YAPF format.

Throws:

java.io.IOException

readSeqRecord

public void readSeqRecord(java.lang.String buffer)
                   throws java.io.IOException

Read this monomer out of a YAPF (sequence profile) format file (JMC's format). The line must be a SEQ N X type line.

Throws:

java.io.IOException

writePts

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

Writes out this monomer in PTS (Jon Blake's) format. The coordinates of the first atom in the list are used. You normally want the coordinates of the CA atom, so call stripAllButCA before doing this. If there are no atoms, this function does nothing.

Throws:

java.io.IOException

See Also:

Protein.stripAllButCA(), Polymer.writePTS(org.strbio.io.Printf)

readFasta

public boolean readFasta(java.io.BufferedReader infile)
                  throws java.io.IOException

Read this monomer out of a Fasta format file. It looks through the file for the first character that looks like a residue (letters, '-', '!', and '.'). If it finds one, it upper-cases it, copies it into 'type' and returns true. If it finds a '>' (indicating a new Fasta sequence) it resets the input stream to before the character and returns false. If the end of file is reached without finding either of these things, it returns false.

Throws:

java.io.IOException

See Also:

Polymer.readFasta(java.io.BufferedReader, org.strbio.io.Printf)

translate

public final void translate(DVector trans)

translate all atoms by adding a DVector(3) to their coordinates.

See Also:

Atom.translate(org.strbio.math.DVector)

rotate

public final void rotate(DMatrix rot)

rotate all atoms by multiplying by a 3x3 rotation matrix.

See Also:

Atom.rotate(org.strbio.math.DMatrix)

transform

public final void transform(DMatrix trans)

transform the position of all atoms.

See Also:

Atom.transform(org.strbio.math.DMatrix)

isGap

public boolean isGap()

does this monomer represent a gap?

isValidType

public boolean isValidType()

is the character in 'type' valid for this monomer? Should be overridden for things like residues.

isValidNonGap

public boolean isValidNonGap()

Is this monomer something which is valid, but not a gap?

molecularWeight

public double molecularWeight()

molecular weight; default zero.