scripps.vvm.manager
Class VVM_HighLevels

java.lang.Object
  |
  +--scripps.vvm.manager.VVM_HighLevels

public class VVM_HighLevels

extends java.lang.Object

A set of high level functions for controling nearly everything that can be controled from the GUI. This is intended for use with Java or Jython macros, but they can be used by extending ap-mods too.

Constructor Summary

VVM_HighLevels()
Ensures VincentVanMol module is loaded

Method Summary

void	addElements(VVM_RepShape rep, TreeNodeSet set) Add the elements to the rendition.
AtomSet	allAtoms(Molecule mol) All atoms in molecule
ChainSet	allChains(Molecule mol) All chains in molecule
ResidueSet	allResidues(Molecule mol) All residue in molecule
AtomSet	coerseToAtoms(TreeNodeSet defSet) Atoms from another set
BondSet	coerseToBonds(TreeNodeSet defSet) Bonds from another set
ChainSet	coerseToChains(TreeNodeSet defSet) Chains from another set
ResidueSet	coerseToResidues(TreeNodeSet defSet) Residues from another set
Molecule	findLoadedMol(java.lang.String name) Find molecule by name (this is its filename)
Molecule	getCurrentMol() Return the "current" molecule in the gui
TreeNodeSet	interpret(java.lang.String expression, Molecule mol) Return set of elements from expression.
AtomSet	interpretAtoms(java.lang.String expression, AtomSet superset) Atoms matching expression
AtomSet	interpretAtoms(java.lang.String expression, Molecule mol) Atoms matching expression
ChainSet	interpretChains(java.lang.String expression, ChainSet superset) Chains matching expression
ChainSet	interpretChains(java.lang.String expression, Molecule mol) Chains matching expression
ResidueSet	interpretResidues(java.lang.String expression, Molecule mol) Residues matching expression
ResidueSet	interpretResidues(java.lang.String expression, ResidueSet superset) Residues matching expression
Molecule	loadMol(java.lang.String filename) Load a protein or dna given a filename
AtomLabelShape	newAtomLabels(Molecule mol) Make a new AtomLabelShape visuization of the molecule, add it to database if set to
AtomLabelShape	newAtomLabels(Molecule mol, TreeNodeSet set)
BASShape	newBAS(Molecule mol) Make a new BASShape visuization of the molecule, add it to database if set to, and add all atoms and bonds of of the molecule if "showAllBAS" is true
BASShape	newBAS(Molecule mol, TreeNodeSet set)
CPKShape	newCPK(Molecule mol) Make a new CPKShape visuization of the molecule, add it to database if set to, and add all atoms of of the molecule if "showAllCPK" is true
CPKShape	newCPK(Molecule mol, TreeNodeSet set)
MolSurfaceShape	newMolSurface(Molecule mol) Make a new MolSurfaceShape visuization of the molecule, add it to database if set to, and add all atoms of of the molecule if "showAllMolSurface" is true
MolSurfaceShape	newMolSurface(Molecule mol, TreeNodeSet set)
ResidueLabelShape	newResidueLabels(Molecule mol) Make a new ResidueLabelShape visuization of the molecule, add it to database if set to
ResidueLabelShape	newResidueLabels(Molecule mol, TreeNodeSet set)
RibbonBackboneShape	newRibbons(Molecule mol) Make a new RibbonBackboneShape visuization of the molecule, add it to database if set to, and add all residues of of the molecule if "showAllRibbons" is true
RibbonBackboneShape	newRibbons(Molecule mol, TreeNodeSet set)
TubeBackboneShape	newTubes(Molecule mol) Make a new TubeBackboneShape visuization of the molecule, add it to database if set to, and add all residues of of the molecule if "showAllTubes" is true
TubeBackboneShape	newTubes(Molecule mol, TreeNodeSet set)
WireShape	newWire(Molecule mol) Make a new WireShape visuization of the molecule, add it to database if set to, and add all atoms and bonds of of the molecule if "showAllWire" is true
WireShape	newWire(Molecule mol, TreeNodeSet set)
void	removeElements(VVM_RepShape rep, TreeNodeSet set) Remove the elements from the rendition.
void	removeMol(Molecule mol) Remove the molecule and any visualizations of it
void	savePDB(Protein mol, java.lang.String filename) Save molecule as PDB file
void	setAutoAdd(boolean bAutoAdd)
void	setCurrentMol(Molecule mol) Make this the "current" molecule in the gui

Methods inherited from class java.lang.Object

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

Constructor Detail

VVM_HighLevels

public VVM_HighLevels()

Ensures VincentVanMol module is loaded

Method Detail

setAutoAdd

public void setAutoAdd(boolean bAutoAdd)

loadMol

public Molecule loadMol(java.lang.String filename)

Load a protein or dna given a filename

savePDB

public void savePDB(Protein mol,
                    java.lang.String filename)
             throws java.io.IOException

Save molecule as PDB file

java.io.IOException

removeMol

public void removeMol(Molecule mol)

Remove the molecule and any visualizations of it

findLoadedMol

public Molecule findLoadedMol(java.lang.String name)

Find molecule by name (this is its filename)

setCurrentMol

public void setCurrentMol(Molecule mol)

Make this the "current" molecule in the gui

getCurrentMol

public Molecule getCurrentMol()

Return the "current" molecule in the gui

newCPK

public CPKShape newCPK(Molecule mol)

Make a new CPKShape visuization of the molecule, add it to database if set to, and add all atoms of of the molecule if "showAllCPK" is true

newCPK

public CPKShape newCPK(Molecule mol,
                       TreeNodeSet set)

newMolSurface

public MolSurfaceShape newMolSurface(Molecule mol)

Make a new MolSurfaceShape visuization of the molecule, add it to database if set to, and add all atoms of of the molecule if "showAllMolSurface" is true

newMolSurface

public MolSurfaceShape newMolSurface(Molecule mol,
                                     TreeNodeSet set)

newAtomLabels

public AtomLabelShape newAtomLabels(Molecule mol)

Make a new AtomLabelShape visuization of the molecule, add it to database if set to

newAtomLabels

public AtomLabelShape newAtomLabels(Molecule mol,
                                    TreeNodeSet set)

newTubes

public TubeBackboneShape newTubes(Molecule mol)

Make a new TubeBackboneShape visuization of the molecule, add it to database if set to, and add all residues of of the molecule if "showAllTubes" is true

newTubes

public TubeBackboneShape newTubes(Molecule mol,
                                  TreeNodeSet set)

newRibbons

public RibbonBackboneShape newRibbons(Molecule mol)

Make a new RibbonBackboneShape visuization of the molecule, add it to database if set to, and add all residues of of the molecule if "showAllRibbons" is true

newRibbons

public RibbonBackboneShape newRibbons(Molecule mol,
                                      TreeNodeSet set)

newResidueLabels

public ResidueLabelShape newResidueLabels(Molecule mol)

Make a new ResidueLabelShape visuization of the molecule, add it to database if set to

newResidueLabels

public ResidueLabelShape newResidueLabels(Molecule mol,
                                          TreeNodeSet set)

newBAS

public BASShape newBAS(Molecule mol)

Make a new BASShape visuization of the molecule, add it to database if set to, and add all atoms and bonds of of the molecule if "showAllBAS" is true

newBAS

public BASShape newBAS(Molecule mol,
                       TreeNodeSet set)

newWire

public WireShape newWire(Molecule mol)

Make a new WireShape visuization of the molecule, add it to database if set to, and add all atoms and bonds of of the molecule if "showAllWire" is true

newWire

public WireShape newWire(Molecule mol,
                         TreeNodeSet set)

addElements

public void addElements(VVM_RepShape rep,
                        TreeNodeSet set)

Add the elements to the rendition. If the elements are in the wrong domain, the set is casted to a set of the right domain, for example if a residue set is passed into the CPK shape, the set is casted to an atom set first

removeElements

public void removeElements(VVM_RepShape rep,
                           TreeNodeSet set)

Remove the elements from the rendition. If the elements are in the wrong domain, the set is casted to a set of the right domain, for example if a residue set is passed into the CPK shape, the set is casted to an atom set first

interpret

public TreeNodeSet interpret(java.lang.String expression,
                             Molecule mol)

Return set of elements from expression. String is broken up in the traditional way like this: MOLSET:RESSET:ATOMSET. Each group after a colon is depenant on the context of the colon before it.

allChains

public ChainSet allChains(Molecule mol)

All chains in molecule

interpretChains

public ChainSet interpretChains(java.lang.String expression,
                                Molecule mol)

Chains matching expression

interpretChains

public ChainSet interpretChains(java.lang.String expression,
                                ChainSet superset)

Chains matching expression

coerseToChains

public ChainSet coerseToChains(TreeNodeSet defSet)

Chains from another set

allResidues

public ResidueSet allResidues(Molecule mol)

All residue in molecule

interpretResidues

public ResidueSet interpretResidues(java.lang.String expression,
                                    Molecule mol)

Residues matching expression

interpretResidues

public ResidueSet interpretResidues(java.lang.String expression,
                                    ResidueSet superset)

Residues matching expression

coerseToResidues

public ResidueSet coerseToResidues(TreeNodeSet defSet)

Residues from another set

allAtoms

public AtomSet allAtoms(Molecule mol)

All atoms in molecule

interpretAtoms

public AtomSet interpretAtoms(java.lang.String expression,
                              Molecule mol)

Atoms matching expression

interpretAtoms

public AtomSet interpretAtoms(java.lang.String expression,
                              AtomSet superset)

Atoms matching expression

coerseToAtoms

public AtomSet coerseToAtoms(TreeNodeSet defSet)

Atoms from another set

coerseToBonds

public BondSet coerseToBonds(TreeNodeSet defSet)

Bonds from another set