charite.christo.protein
Class ProteinWriter1

java.lang.Object
  charite.christo.protein.ProteinWriter1

All Implemented Interfaces:

ProteinWriter

public class ProteinWriter1
extends java.lang.Object
implements ProteinWriter

Write a protein file

Field Summary

Fields inherited from interface charite.christo.protein.ProteinWriter

ATOM_LINES, CHAIN_A, CHAIN_B, CHAIN_SPACE, COMPLETE_PDB, FASTA, HELIX_SHEET, HETEROS, IDX_FOR_RESNUM, MET_INSTEAD_OF_MSE, NUCLEOTIDE_STRUCTURE, NUCLEOTIDES, PDB, SEQRES, SEQRES_IF_COORDINATES, SIDE_CHAIN_ATOMS

Constructor Summary

ProteinWriter1()

Method Summary

static java.lang.String	createPairfitTarget(Protein p, Matrix3D m, BA ba)
java.lang.String	getFileSuffix() Extension ".pdb" forPDB-files and ".fa" for fasta-files
static BA	mergePdbWithOriginal(Protein p)
void	selectResidues(boolean[] isSelected) do not write all residues but only a certain subset.
void	setResidueRange(int from, int to) index of first and last amino acid
boolean	toText(Protein p, Matrix3D[] mm3d, long options, BA sb) Writes the protein data e.g.

Methods inherited from class java.lang.Object

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

Constructor Detail

ProteinWriter1

public ProteinWriter1()

Method Detail

selectResidues

public void selectResidues(boolean[] isSelected)

do not write all residues but only a certain subset.

Specified by:

selectResidues in interface ProteinWriter

getFileSuffix

public java.lang.String getFileSuffix()

Description copied from interface: ProteinWriter

Extension ".pdb" forPDB-files and ".fa" for fasta-files

Specified by:

getFileSuffix in interface ProteinWriter

setResidueRange

public void setResidueRange(int from,
                            int to)

Description copied from interface: ProteinWriter

index of first and last amino acid

Specified by:

setResidueRange in interface ProteinWriter

toText

public boolean toText(Protein p,
                      Matrix3D[] mm3d,
                      long options,
                      BA sb)

Description copied from interface: ProteinWriter

Writes the protein data e.g. in fasta or PDB format

Specified by:

toText in interface ProteinWriter

Returns:

true: was able to produce the text, false: unable to produce the text because information is not set in the protein model. A ProteinWriter for protein structures returns false if the coordinate fields in the Protein instance are empty.

createPairfitTarget

public static final java.lang.String createPairfitTarget(Protein p,
                                                         Matrix3D m,
                                                         BA ba)

mergePdbWithOriginal

public static final BA mergePdbWithOriginal(Protein p)