meshi.molecularElements
Class Protein

java.lang.Object
  meshi.molecularElements.Protein

Direct Known Subclasses:

ExtendedAtomsProtein, HydrogenTest.PolyAla, SymmetricComplex

public class Protein
extends java.lang.Object

A protein chain.

Nested Class Summary

static class

Protein.BackboneFilter Sets the chain of this protein, after asserting that it is comprised of residues belonging to a single polypeptide chain.

Field Summary

protected AngleList	angles
protected AtomList	atoms A list of the protein's atoms.
protected AtomPairList	bonds A list of the protein's bonds.
protected ChainList	chains
protected int	firstResidueIndex
protected java.lang.Integer	modelNumber Often many models of the same protein are generated.
protected java.lang.String	name The protein name.
protected ResidueList	residues A list of the protein's residues.
protected TorsionList	torsions
private boolean	verbose

Constructor Summary

Protein(AtomList atomList)
Builds a protein from a list of atoms.

Protein(AtomList atomList, ResidueCreator creator)
Builds a protein from a PDB formatted file and a line filter.

Protein(Residue residue)

Protein(Sequence sequence, java.lang.String name, ResidueCreator creator)
Builds a protein from AA sequence.

Protein(Sequence sequence, java.lang.String name, java.lang.String chainName, ResidueCreator creator)

Protein(java.lang.String name)

Protein(java.lang.String fileName, Filter filter, ResidueCreator creator)
Builds a protein from a PDB formatted file and a line filter.

Method Summary

void	addChain(Chain chain)
void	allYouWantToKnow()
AtomList	atoms() A list of the protein's atoms.
AtomPairList	bonds()
Chain	chain()
ChainList	chains()
void	defrost() Allow all atoms to move.
int	firstResidueIndex() For users who need this signature.
ResidueIdentifier[]	firstResidues() An array of the Residue Identifiers of the first residues in each chain In most cases it is residue 1 but in many other cases some n > 1 typicaly because the N-terminus is not present in the PDB file
void	freeze()
void	freeze(Filter filter)
Atom	getAtom(java.lang.String residueName, ResidueIdentifier residueID, java.lang.String atomName) Returns the specified atom.
private java.lang.Integer	getModelNumber(MeshiLineReader file) Extracts the model number from the filename.
static java.lang.String	getProteinName(MeshiLineReader file) Extract the protein name from the filename.
static java.lang.String	getProteinName(java.lang.String pathString)
java.lang.String	getSequence()
ResidueList	missingResidues()
int	modelNumber()
java.lang.String	name() The protein name.
AtomList	nowhereAtoms()
void	printAtomsToFile(java.lang.String fileName)
Residue	residue(int residueNumber) Returns the residue.
Residue	residue(ResidueIdentifier id) Returns the residue.
Residue	residueAt(int residueNumber)
ResidueList	residues() A list of the protein's residues.
Sequence	sequence()
void	setName(java.lang.String name)
void	setSS(SequenceAlignment alignment)
void	setSS(java.lang.String SS) A method to set the secondary structure of a protein.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

name

protected java.lang.String name

The protein name.

modelNumber

protected java.lang.Integer modelNumber

Often many models of the same protein are generated.

residues

protected ResidueList residues

A list of the protein's residues.

chains

protected ChainList chains

atoms

protected AtomList atoms

A list of the protein's atoms.

bonds

protected AtomPairList bonds

A list of the protein's bonds.

angles

protected AngleList angles

torsions

protected TorsionList torsions

firstResidueIndex

protected int firstResidueIndex

verbose

private boolean verbose

Constructor Detail

Protein

public Protein(java.lang.String name)

Protein

public Protein(Sequence sequence,
               java.lang.String name,
               ResidueCreator creator)

Builds a protein from AA sequence.

Protein

public Protein(Sequence sequence,
               java.lang.String name,
               java.lang.String chainName,
               ResidueCreator creator)

Protein

public Protein(AtomList atomList,
               ResidueCreator creator)

Builds a protein from a PDB formatted file and a line filter.

Protein

public Protein(java.lang.String fileName,
               Filter filter,
               ResidueCreator creator)

Builds a protein from a PDB formatted file and a line filter.

Protein

public Protein(Residue residue)

Protein

public Protein(AtomList atomList)

Builds a protein from a list of atoms. This constructor is used by HeliumClusterMinimization our work horse for development. It is not very useful in any other context.

Method Detail

chains

public ChainList chains()

addChain

public void addChain(Chain chain)

missingResidues

public ResidueList missingResidues()

nowhereAtoms

public AtomList nowhereAtoms()

bonds

public AtomPairList bonds()

getProteinName

public static java.lang.String getProteinName(MeshiLineReader file)

Extract the protein name from the filename. expects name.pdb or name.modelNumber.pdb or pdbname.ent

getProteinName

public static java.lang.String getProteinName(java.lang.String pathString)

getModelNumber

private java.lang.Integer getModelNumber(MeshiLineReader file)

Extracts the model number from the filename. Expects file name with the format name.modelNumber.pdb

name

public java.lang.String name()

The protein name.

modelNumber

public int modelNumber()

atoms

public AtomList atoms()

A list of the protein's atoms.

residues

public ResidueList residues()

A list of the protein's residues.

firstResidues

public ResidueIdentifier[] firstResidues()

An array of the Residue Identifiers of the first residues in each chain In most cases it is residue 1 but in many other cases some n > 1 typicaly because the N-terminus is not present in the PDB file

residue

public Residue residue(ResidueIdentifier id)

Returns the residue.

residue

public Residue residue(int residueNumber)

Returns the residue.

defrost

public void defrost()

Allow all atoms to move.

freeze

public void freeze()

freeze

public void freeze(Filter filter)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getAtom

public Atom getAtom(java.lang.String residueName,
                    ResidueIdentifier residueID,
                    java.lang.String atomName)

Returns the specified atom.

firstResidueIndex

public int firstResidueIndex()

For users who need this signature.

allYouWantToKnow

public void allYouWantToKnow()

setSS

public void setSS(java.lang.String SS)

A method to set the secondary structure of a protein. The input SS string currently support only C,E,H letters + A for the ALL type (= every SS is posible). This method works only if the number of letter in the SS string equals to the number of non-dummy residues. The assignment of SS is than sequential in the residue numbers.

setSS

public void setSS(SequenceAlignment alignment)

getSequence

public java.lang.String getSequence()

printAtomsToFile

public void printAtomsToFile(java.lang.String fileName)
                      throws java.lang.Exception

Throws:

java.lang.Exception

setName

public void setName(java.lang.String name)

residueAt

public Residue residueAt(int residueNumber)

sequence

public Sequence sequence()

chain

public Chain chain()