PIP.IO.CreatePeripheralData
Class PDBFileDomainBased

java.lang.Object
  PIP.IO.CreatePeripheralData.PDBFile
      PIP.IO.CreatePeripheralData.PDBFileDomainBased

public class PDBFileDomainBased
extends PDBFile

Field Summary

Fields inherited from class PIP.IO.CreatePeripheralData.PDBFile

FORMAT_STRING_old, FORMAT_STRING_rightJustifiedAtomName

Constructor Summary

PDBFileDomainBased(java.io.PrintStream out)

Method Summary

int	write(java.util.Collection<Residue> residues, int count, java.lang.String chain, Domain d) Core getiRMSD of this class which takes in a list of residues and writes them out in PDB file format to the PrintStream ps using residue position numbering which starts at count.
int	writeInteractingResiduesPlusNeighbours(Domain wholeDomain, int count, java.util.Collection<Residue> interacting, java.lang.String chain) This function was written to create templates of interaction sites, initally for the program Multiprot which needs the interacting residue (residue interacting with a residue in another domain) in addition to the residues at a distance of one residue upstream and one residue downstream of the interacting residue.
void	writeOutAtom(Atom a, Residue res, int count, java.lang.String chain, Domain d, java.lang.String[] coordinates)
int	writeResidues(Domain d)
int	writeResidues(Domain d, java.lang.String chain)
int	writeResidues(java.util.List<Residue> residues, Domain d, java.lang.String chain) This is just a helper getiRMSD which essentially just calls the write(Collection residues, int count) getiRMSD using the default value of 0 for the count parameter.
int	writeResidues(java.util.List<Residue> residues, Domain d, java.lang.String chain, int count)
int	writeTransformedCoordinates(java.util.Collection<Residue> residues, java.lang.String chain, Domain d, double[][] matrix, int count)

Methods inherited from class PIP.IO.CreatePeripheralData.PDBFile

writeOutRepresentativeCoordinates

Methods inherited from class java.lang.Object

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

Constructor Detail

PDBFileDomainBased

public PDBFileDomainBased(java.io.PrintStream out)

Parameters:

out - - a PrintStream to which to write the PDB file info

Method Detail

writeResidues

public int writeResidues(java.util.List<Residue> residues,
                         Domain d,
                         java.lang.String chain)

This is just a helper getiRMSD which essentially just calls the write(Collection residues, int count) getiRMSD using the default value of 0 for the count parameter.

Parameters:

residues - - This is a list of residues to write to the PDB file

Returns:

int of the position of the residue last printed +1. Therefore the next series of residues which need to be written to this PDB file can begin using the int returned.

writeResidues

public int writeResidues(Domain d,
                         java.lang.String chain)

writeResidues

public int writeResidues(Domain d)

writeResidues

public int writeResidues(java.util.List<Residue> residues,
                         Domain d,
                         java.lang.String chain,
                         int count)

writeInteractingResiduesPlusNeighbours

public int writeInteractingResiduesPlusNeighbours(Domain wholeDomain,
                                                  int count,
                                                  java.util.Collection<Residue> interacting,
                                                  java.lang.String chain)

This function was written to create templates of interaction sites, initally for the program Multiprot which needs the interacting residue (residue interacting with a residue in another domain) in addition to the residues at a distance of one residue upstream and one residue downstream of the interacting residue.

Parameters:

wholeDomain - - This is a list of residues which make up the whole domain of the template site. The whole domain is need to determine the residues at +1 and -1 of the interacting residues

count - - This is required to determine the position of the residue to start printing at

interacting - - These are the residues which are interacting with another domain at the interaction site

Returns:

int of the position of the residue last printed + 1. Therefore the next series of residues which need to be written to this PDB file can begin using the int returned.

writeTransformedCoordinates

public int writeTransformedCoordinates(java.util.Collection<Residue> residues,
                                       java.lang.String chain,
                                       Domain d,
                                       double[][] matrix,
                                       int count)

write

public int write(java.util.Collection<Residue> residues,
                 int count,
                 java.lang.String chain,
                 Domain d)

Core getiRMSD of this class which takes in a list of residues and writes them out in PDB file format to the PrintStream ps using residue position numbering which starts at count.

Parameters:

residues - - This is a list of residues to write to the PDB file

count - - int of the position to start the residue numbering

Returns:

int of the position of the residue last printed + 1. Therefore the next series of residues which need to be written to this PDB file can begin using the int returned.

writeOutAtom

public void writeOutAtom(Atom a,
                         Residue res,
                         int count,
                         java.lang.String chain,
                         Domain d,
                         java.lang.String[] coordinates)