PIP.IO
Class PymolScript

java.lang.Object
  PIP.IO.PymolScript

public class PymolScript
extends java.lang.Object

Constructor Summary

PymolScript(DomainInteraction di, Domain d, FamilyType ft)

PymolScript(DomainInteraction di, java.lang.String s, FamilyType ft)

PymolScript(DomainInteraction di, java.lang.String s, java.lang.String dir, FamilyType ft)

PymolScript(Domain d, java.lang.String domainColour, java.util.Collection<Residue> residues, java.lang.String resColour, java.lang.String type, java.lang.String extension)

PymolScript(java.lang.String pdbFileDir, Assembly ass, DomainInteraction di, Domain domInEntry, java.lang.String namePDBFile)

PymolScript(java.lang.String pdbFileDir, DomainInteraction di, FamilyType ft)

PymolScript(java.lang.String pdbFileDir, Entry entry, Domain d, java.lang.String namePDBFile)

Method Summary

static void	colourAtoms(java.util.Collection<Atom> atoms, java.io.PrintStream ps, java.lang.String colour)
static void	colourChain(Chain c, java.io.PrintStream ps, java.lang.String colour)
static void	colourResidues(java.util.Collection<Residue> residues, java.io.PrintStream ps, java.lang.String colour)
static void	colourResidues(Domain d, java.io.PrintStream ps, java.lang.String colour)
static void	colourResiduesToRename(DomainInteraction di, Domain domInEntry, java.io.PrintStream ps)
void	run()
static void	showType(java.util.Collection<Residue> d, java.io.PrintStream ps, java.lang.String type)
static void	stickifyResidues(Domain d, java.io.PrintStream ps)

Methods inherited from class java.lang.Object

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

Constructor Detail

PymolScript

public PymolScript(DomainInteraction di,
                   java.lang.String s,
                   FamilyType ft)
            throws java.lang.Exception

Throws:

java.lang.Exception

PymolScript

public PymolScript(java.lang.String pdbFileDir,
                   DomainInteraction di,
                   FamilyType ft)
            throws java.lang.Exception

Throws:

java.lang.Exception

PymolScript

public PymolScript(Domain d,
                   java.lang.String domainColour,
                   java.util.Collection<Residue> residues,
                   java.lang.String resColour,
                   java.lang.String type,
                   java.lang.String extension)
            throws java.lang.Exception

Throws:

java.lang.Exception

PymolScript

public PymolScript(DomainInteraction di,
                   Domain d,
                   FamilyType ft)
            throws java.lang.Exception

Throws:

java.lang.Exception

PymolScript

public PymolScript(java.lang.String pdbFileDir,
                   Entry entry,
                   Domain d,
                   java.lang.String namePDBFile)
            throws java.io.FileNotFoundException

Throws:

java.io.FileNotFoundException

PymolScript

public PymolScript(java.lang.String pdbFileDir,
                   Assembly ass,
                   DomainInteraction di,
                   Domain domInEntry,
                   java.lang.String namePDBFile)
            throws java.io.FileNotFoundException

Throws:

java.io.FileNotFoundException

PymolScript

public PymolScript(DomainInteraction di,
                   java.lang.String s,
                   java.lang.String dir,
                   FamilyType ft)
            throws java.lang.Exception

Throws:

java.lang.Exception

Method Detail

showType

public static void showType(java.util.Collection<Residue> d,
                            java.io.PrintStream ps,
                            java.lang.String type)

colourResiduesToRename

public static void colourResiduesToRename(DomainInteraction di,
                                          Domain domInEntry,
                                          java.io.PrintStream ps)

stickifyResidues

public static void stickifyResidues(Domain d,
                                    java.io.PrintStream ps)

colourAtoms

public static void colourAtoms(java.util.Collection<Atom> atoms,
                               java.io.PrintStream ps,
                               java.lang.String colour)

colourResidues

public static void colourResidues(Domain d,
                                  java.io.PrintStream ps,
                                  java.lang.String colour)

colourChain

public static void colourChain(Chain c,
                               java.io.PrintStream ps,
                               java.lang.String colour)

colourResidues

public static void colourResidues(java.util.Collection<Residue> residues,
                                  java.io.PrintStream ps,
                                  java.lang.String colour)

run

public void run()
         throws java.io.IOException

Throws:

java.io.IOException