starfish.chemistry
Class Molecule

java.lang.Object
  starfish.chemistry.Molecule

All Implemented Interfaces:

java.io.Serializable

public class Molecule
extends java.lang.Object
implements java.io.Serializable

See Also:

Serialized Form

Nested Class Summary

static class

Molecule.SpatialSetIterator

Field Summary

static java.util.Vector	atomList
static java.util.Vector	bselected
float[]	color
java.lang.String	colorType
static java.util.LinkedHashSet	colorTypes
java.lang.String	comment
static java.util.Map	compoundMap
static java.util.Vector	conditions
java.util.TreeMap<java.lang.String,CoordSet>	coordSets
java.lang.String	crystal
static java.lang.String	defaultMol
boolean	deleted
java.lang.String	display
static java.util.LinkedHashSet	displayTypes
static int	ENERGY
java.lang.String	energyType
java.util.TreeMap<java.lang.String,Entity>	entities
java.util.LinkedHashMap	entityLabels
static java.util.Vector	globalSelected
static int	GRADIENT
static int	INTER_ENERGY
static int	INTRA_ENERGY
byte	label
static int	LABEL_BOND
static int	LABEL_CHARGE
static int	LABEL_CUSTOM
static int	LABEL_FC
static int	LABEL_FFC
static int	LABEL_HPPM
static int	LABEL_LABEL
static int	LABEL_MOLECULE_NAME
static int	LABEL_NAME
static int	LABEL_NONE
static int	LABEL_NUMBER
static int	LABEL_PPM
static int	LABEL_RESIDUE
static int	LABEL_SECONDARY_STRUCTURE
static int	LABEL_STRING
static int	LABEL_SYMBOL
static int	LABEL_SYMBOL_AND_NUMBER
static int	LABEL_TITLE
static int	LABEL_VALUE
boolean	labelsCurrent
static java.util.LinkedHashMap	labelTypes
float[][]	model
static java.util.Hashtable	molecules
java.lang.String	name
java.lang.String	negShapeType
int	nResidues
java.lang.String	originalName
java.lang.String	posShapeType
static int	R_FACTOR
static int	selCycleCount
static java.util.LinkedHashSet	shapeTypes
static java.util.Hashtable	sites
java.lang.String	source
static int	SQ_SCORE
java.util.Set	structures
java.lang.String	title
float[]	titlePosition
float[]	values
float[][]	view

Constructor Summary

Molecule(java.lang.String name)

Method Summary

void	addCoordSet(java.lang.String setName, Entity entity)
void	addEntity(Entity entity)
void	addEntity(Entity entity, java.lang.String coordSetName)
static void	addMoleculeModel(tcl.lang.Interp interp)
static void	avgCoords(tcl.lang.Interp interp, MolFilter molFilter1)
static int	buildTree(tcl.lang.Interp interp, Molecule molecule, Atom startAtom, java.util.Vector atomList, MTree mTree)
static void	calcAllBonds(tcl.lang.Interp interp)
static double	calcAngle(tcl.lang.Interp interp, MolFilter molFilter1, MolFilter molFilter2, MolFilter molFilter3)
void	calcBonds()
void	calcCenter(tcl.lang.Interp interp, int iStructure)
static double	calcDihedral(tcl.lang.Interp interp, MolFilter molFilter1, MolFilter molFilter2, MolFilter molFilter3, MolFilter molFilter4)
static double	calcDistance(tcl.lang.Interp interp, MolFilter molFilter1, MolFilter molFilter2)
void	calcRMSD()
void	center(int iStructure)
int	checkType()
static void	colorAtoms(tcl.lang.Interp interp, float red, float green, float blue)
static void	colorAtomsByType(tcl.lang.Interp interp)
static void	colorBonds(tcl.lang.Interp interp, float red, float green, float blue)
boolean	coordSetExists(java.lang.String setName)
int	createLabelArray(int iStructure, float[] coords, int i)
int	createLineArray(int iStructure, float[] coords, int i, float[] colors)
int	createSelectionArray(int iStructure, float[] coords, int[] levels)
int	createSphereArray(int iStructure, float[] coords, int i, float[] colors, float[] values)
static void	findEquivalentAtoms(Entity entity)
static void	findEquivalentAtoms(tcl.lang.Interp interp, java.lang.String atomName)
void	genCoords(tcl.lang.Interp interp, boolean fillCoords)
static Molecule	get(java.lang.String name)
int[]	getActiveStructures()
static Atom	getAtom(tcl.lang.Interp interp, MolFilter molFilter)
static Atom	getAtomByName(tcl.lang.Interp interp, java.lang.String name)
java.util.Vector	getAtoms()
int	getAtoms(int iStructure, Atom[] atoms)
java.util.Vector	getAtomsByProp(int property)
static void	getAtomTypes(Molecule molecule)
java.util.ArrayList<Atom>	getAttachedHydrogens(Atom atom)
void	getBonds()
static void	getColorTypes(tcl.lang.Interp interp)
java.lang.String[]	getCoordLoopStrings()
static void	getDisplayTypes(tcl.lang.Interp interp)
Entity	getEntity(java.lang.String name)
int	getLabelCount(int iStructure)
static void	getLabelTypes(tcl.lang.Interp interp)
int	getLineCount(int iStructure)
java.util.Vector	getMoleculeBonds()
static void	getShapeTypes(tcl.lang.Interp interp)
static SpatialSet	getSpatialSet(tcl.lang.Interp interp, MolFilter molFilter)
Molecule.SpatialSetIterator	getSpatialSetIterator()
int	getSphereCount(int iStructure)
static Atom	getStartAtom(Molecule molecule)
static void	listAtoms(tcl.lang.Interp interp)
void	listAtomsWithProperty(tcl.lang.Interp interp, int property)
void	listBonds(tcl.lang.Interp interp)
static void	makeAtomList(tcl.lang.Interp interp)
static void	makeSite(tcl.lang.Interp interp, java.lang.String siteName)
static java.util.Vector	matchAtoms(tcl.lang.Interp interp, MolFilter molFilter)
static java.util.Vector	matchAtoms(MolFilter molFilter)
static java.util.Vector	matchAtoms(MolFilter molFilter, Molecule molecule)
static java.util.Vector	matchBonds(tcl.lang.Interp interp)
void	nullCoords(tcl.lang.Interp interp)
static void	radiusAtoms(tcl.lang.Interp interp, float radius)
static void	radiusBonds(tcl.lang.Interp interp, float radius)
void	remove(tcl.lang.Interp interp)
static void	removeAll(tcl.lang.Interp interp)
void	reName(Molecule molecule, Compound compound, java.lang.String name1, java.lang.String name2)
void	resetActiveStructures()
static void	selectAtoms(tcl.lang.Interp interp, MolFilter molFilter, boolean append, boolean inverse)
static void	selectBonds(tcl.lang.Interp interp, java.lang.String mode)
static void	selectResidues(tcl.lang.Interp interp)
static void	selectSite(tcl.lang.Interp interp, java.lang.String siteName)
void	setActiveStructures(java.util.TreeSet selSet)
static void	setAtomProperty(int property, boolean state)
void	setBondProperty(int property, boolean state)
static int	setSelected(tcl.lang.Interp interp, java.util.Vector selected, boolean append, boolean inverse)
void	setupRotGroups()
static void	unSelectLastAtom(tcl.lang.Interp interp)
void	updateLabels()
void	updateNames()
void	updateSpatialSets()
static void	withinSite(tcl.lang.Interp interp, java.lang.String siteName, float tolerance)
void	writeAssignmentsSTAR3(tcl.lang.Interp interp, java.lang.String chanName)
void	writeMoleculeSTAR3(tcl.lang.Interp interp, java.lang.String chanName, int assemblyID)
static void	writePPM(tcl.lang.Interp interp, java.lang.String chanName, int whichStruct)
static void	writePPMToXML(tcl.lang.Interp interp, java.lang.String chanName, int whichStruct)
static void	writeXYZ(tcl.lang.Interp interp, java.lang.String chanName, int whichStruct)
static void	writeXYZToXML(tcl.lang.Interp interp, java.lang.String chanName, int whichStruct)

Methods inherited from class java.lang.Object

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

Field Detail

atomList

public static java.util.Vector atomList

conditions

public static java.util.Vector conditions

defaultMol

public static java.lang.String defaultMol

molecules

public static java.util.Hashtable molecules

sites

public static java.util.Hashtable sites

globalSelected

public static java.util.Vector globalSelected

bselected

public static java.util.Vector bselected

selCycleCount

public static int selCycleCount

ENERGY

public static final int ENERGY

See Also:

Constant Field Values

SQ_SCORE

public static final int SQ_SCORE

See Also:

Constant Field Values

GRADIENT

public static final int GRADIENT

See Also:

Constant Field Values

R_FACTOR

public static final int R_FACTOR

See Also:

Constant Field Values

INTRA_ENERGY

public static final int INTRA_ENERGY

See Also:

Constant Field Values

INTER_ENERGY

public static final int INTER_ENERGY

See Also:

Constant Field Values

LABEL_NONE

public static final int LABEL_NONE

See Also:

Constant Field Values

LABEL_LABEL

public static final int LABEL_LABEL

See Also:

Constant Field Values

LABEL_FC

public static final int LABEL_FC

See Also:

Constant Field Values

LABEL_SYMBOL

public static final int LABEL_SYMBOL

See Also:

Constant Field Values

LABEL_NUMBER

public static final int LABEL_NUMBER

See Also:

Constant Field Values

LABEL_SYMBOL_AND_NUMBER

public static final int LABEL_SYMBOL_AND_NUMBER

See Also:

Constant Field Values

LABEL_FFC

public static final int LABEL_FFC

See Also:

Constant Field Values

LABEL_SECONDARY_STRUCTURE

public static final int LABEL_SECONDARY_STRUCTURE

See Also:

Constant Field Values

LABEL_RESIDUE

public static final int LABEL_RESIDUE

See Also:

Constant Field Values

LABEL_CHARGE

public static final int LABEL_CHARGE

See Also:

Constant Field Values

LABEL_VALUE

public static final int LABEL_VALUE

See Also:

Constant Field Values

LABEL_TITLE

public static final int LABEL_TITLE

See Also:

Constant Field Values

LABEL_MOLECULE_NAME

public static final int LABEL_MOLECULE_NAME

See Also:

Constant Field Values

LABEL_STRING

public static final int LABEL_STRING

See Also:

Constant Field Values

LABEL_BOND

public static final int LABEL_BOND

See Also:

Constant Field Values

LABEL_CUSTOM

public static final int LABEL_CUSTOM

See Also:

Constant Field Values

LABEL_NAME

public static final int LABEL_NAME

See Also:

Constant Field Values

LABEL_HPPM

public static final int LABEL_HPPM

See Also:

Constant Field Values

LABEL_PPM

public static final int LABEL_PPM

See Also:

Constant Field Values

labelTypes

public static java.util.LinkedHashMap labelTypes

displayTypes

public static java.util.LinkedHashSet displayTypes

colorTypes

public static java.util.LinkedHashSet colorTypes

shapeTypes

public static java.util.LinkedHashSet shapeTypes

compoundMap

public static java.util.Map compoundMap

structures

public java.util.Set structures

labelsCurrent

public boolean labelsCurrent

nResidues

public int nResidues

name

public java.lang.String name

originalName

public java.lang.String originalName

source

public java.lang.String source

comment

public java.lang.String comment

display

public java.lang.String display

posShapeType

public java.lang.String posShapeType

negShapeType

public java.lang.String negShapeType

title

public java.lang.String title

label

public byte label

colorType

public java.lang.String colorType

model

public float[][] model

view

public float[][] view

values

public float[] values

color

public float[] color

titlePosition

public float[] titlePosition

energyType

public java.lang.String energyType

deleted

public boolean deleted

crystal

public java.lang.String crystal

entities

public java.util.TreeMap<java.lang.String,Entity> entities

entityLabels

public java.util.LinkedHashMap entityLabels

coordSets

public java.util.TreeMap<java.lang.String,CoordSet> coordSets

Constructor Detail

Molecule

public Molecule(java.lang.String name)

Method Detail

reName

public void reName(Molecule molecule,
                   Compound compound,
                   java.lang.String name1,
                   java.lang.String name2)

addMoleculeModel

public static void addMoleculeModel(tcl.lang.Interp interp)

removeAll

public static void removeAll(tcl.lang.Interp interp)

remove

public void remove(tcl.lang.Interp interp)

resetActiveStructures

public void resetActiveStructures()

setActiveStructures

public void setActiveStructures(java.util.TreeSet selSet)

getActiveStructures

public int[] getActiveStructures()

coordSetExists

public boolean coordSetExists(java.lang.String setName)

addCoordSet

public void addCoordSet(java.lang.String setName,
                        Entity entity)

addEntity

public void addEntity(Entity entity)

addEntity

public void addEntity(Entity entity,
                      java.lang.String coordSetName)

getEntity

public Entity getEntity(java.lang.String name)

get

public static Molecule get(java.lang.String name)

avgCoords

public static void avgCoords(tcl.lang.Interp interp,
                             MolFilter molFilter1)
                      throws tcl.lang.TclException

Throws:

tcl.lang.TclException

calcDistance

public static double calcDistance(tcl.lang.Interp interp,
                                  MolFilter molFilter1,
                                  MolFilter molFilter2)
                           throws tcl.lang.TclException

Throws:

tcl.lang.TclException

calcAngle

public static double calcAngle(tcl.lang.Interp interp,
                               MolFilter molFilter1,
                               MolFilter molFilter2,
                               MolFilter molFilter3)
                        throws tcl.lang.TclException

Throws:

tcl.lang.TclException

calcDihedral

public static double calcDihedral(tcl.lang.Interp interp,
                                  MolFilter molFilter1,
                                  MolFilter molFilter2,
                                  MolFilter molFilter3,
                                  MolFilter molFilter4)
                           throws tcl.lang.TclException

Throws:

tcl.lang.TclException

nullCoords

public void nullCoords(tcl.lang.Interp interp)
                throws tcl.lang.TclException

Throws:

tcl.lang.TclException

genCoords

public void genCoords(tcl.lang.Interp interp,
                      boolean fillCoords)
               throws tcl.lang.TclException

Throws:

tcl.lang.TclException

getAttachedHydrogens

public java.util.ArrayList<Atom> getAttachedHydrogens(Atom atom)

selectResidues

public static void selectResidues(tcl.lang.Interp interp)
                           throws tcl.lang.TclException

Throws:

tcl.lang.TclException

selectAtoms

public static void selectAtoms(tcl.lang.Interp interp,
                               MolFilter molFilter,
                               boolean append,
                               boolean inverse)
                        throws tcl.lang.TclException

Throws:

tcl.lang.TclException

setSelected

public static int setSelected(tcl.lang.Interp interp,
                              java.util.Vector selected,
                              boolean append,
                              boolean inverse)
                       throws tcl.lang.TclException

Throws:

tcl.lang.TclException

selectBonds

public static void selectBonds(tcl.lang.Interp interp,
                               java.lang.String mode)
                        throws tcl.lang.TclException

Throws:

tcl.lang.TclException

listAtoms

public static void listAtoms(tcl.lang.Interp interp)
                      throws tcl.lang.TclException

Throws:

tcl.lang.TclException

unSelectLastAtom

public static void unSelectLastAtom(tcl.lang.Interp interp)
                             throws tcl.lang.TclException

Throws:

tcl.lang.TclException

makeSite

public static void makeSite(tcl.lang.Interp interp,
                            java.lang.String siteName)
                     throws tcl.lang.TclException

Throws:

tcl.lang.TclException

selectSite

public static void selectSite(tcl.lang.Interp interp,
                              java.lang.String siteName)
                       throws tcl.lang.TclException

Throws:

tcl.lang.TclException

withinSite

public static void withinSite(tcl.lang.Interp interp,
                              java.lang.String siteName,
                              float tolerance)
                       throws tcl.lang.TclException

Throws:

tcl.lang.TclException

listBonds

public void listBonds(tcl.lang.Interp interp)
               throws tcl.lang.TclException

Throws:

tcl.lang.TclException

setAtomProperty

public static void setAtomProperty(int property,
                                   boolean state)
                            throws tcl.lang.TclException

Throws:

tcl.lang.TclException

setBondProperty

public void setBondProperty(int property,
                            boolean state)
                     throws tcl.lang.TclException

Throws:

tcl.lang.TclException

colorAtoms

public static void colorAtoms(tcl.lang.Interp interp,
                              float red,
                              float green,
                              float blue)
                       throws tcl.lang.TclException

Throws:

tcl.lang.TclException

colorAtomsByType

public static void colorAtomsByType(tcl.lang.Interp interp)
                             throws tcl.lang.TclException

Throws:

tcl.lang.TclException

colorBonds

public static void colorBonds(tcl.lang.Interp interp,
                              float red,
                              float green,
                              float blue)
                       throws tcl.lang.TclException

Throws:

tcl.lang.TclException

radiusAtoms

public static void radiusAtoms(tcl.lang.Interp interp,
                               float radius)
                        throws tcl.lang.TclException

Throws:

tcl.lang.TclException

radiusBonds

public static void radiusBonds(tcl.lang.Interp interp,
                               float radius)
                        throws tcl.lang.TclException

Throws:

tcl.lang.TclException

createLineArray

public int createLineArray(int iStructure,
                           float[] coords,
                           int i,
                           float[] colors)

getLineCount

public int getLineCount(int iStructure)

calcCenter

public void calcCenter(tcl.lang.Interp interp,
                       int iStructure)
                throws tcl.lang.TclException

Throws:

tcl.lang.TclException

center

public void center(int iStructure)

listAtomsWithProperty

public void listAtomsWithProperty(tcl.lang.Interp interp,
                                  int property)
                           throws tcl.lang.TclException

Throws:

tcl.lang.TclException

createSphereArray

public int createSphereArray(int iStructure,
                             float[] coords,
                             int i,
                             float[] colors,
                             float[] values)

createLabelArray

public int createLabelArray(int iStructure,
                            float[] coords,
                            int i)

createSelectionArray

public int createSelectionArray(int iStructure,
                                float[] coords,
                                int[] levels)

getSphereCount

public int getSphereCount(int iStructure)

getLabelCount

public int getLabelCount(int iStructure)

getAtoms

public int getAtoms(int iStructure,
                    Atom[] atoms)

matchBonds

public static java.util.Vector matchBonds(tcl.lang.Interp interp)
                                   throws tcl.lang.TclException

Throws:

tcl.lang.TclException

getMoleculeBonds

public java.util.Vector getMoleculeBonds()
                                  throws tcl.lang.TclException

Throws:

tcl.lang.TclException

updateSpatialSets

public void updateSpatialSets()

getAtoms

public java.util.Vector getAtoms()

getAtomsByProp

public java.util.Vector getAtomsByProp(int property)

calcRMSD

public void calcRMSD()

checkType

public int checkType()

getSpatialSetIterator

public Molecule.SpatialSetIterator getSpatialSetIterator()

matchAtoms

public static java.util.Vector matchAtoms(tcl.lang.Interp interp,
                                          MolFilter molFilter)
                                   throws tcl.lang.TclException

Throws:

tcl.lang.TclException

matchAtoms

public static java.util.Vector matchAtoms(MolFilter molFilter)

matchAtoms

public static java.util.Vector matchAtoms(MolFilter molFilter,
                                          Molecule molecule)

makeAtomList

public static void makeAtomList(tcl.lang.Interp interp)
                         throws tcl.lang.TclException

Throws:

tcl.lang.TclException

updateNames

public void updateNames()

getAtomByName

public static Atom getAtomByName(tcl.lang.Interp interp,
                                 java.lang.String name)
                          throws tcl.lang.TclException

Throws:

tcl.lang.TclException

getAtom

public static Atom getAtom(tcl.lang.Interp interp,
                           MolFilter molFilter)
                    throws tcl.lang.TclException

Throws:

tcl.lang.TclException

getSpatialSet

public static SpatialSet getSpatialSet(tcl.lang.Interp interp,
                                       MolFilter molFilter)
                                throws tcl.lang.TclException

Throws:

tcl.lang.TclException

setupRotGroups

public void setupRotGroups()

getBonds

public void getBonds()

calcAllBonds

public static void calcAllBonds(tcl.lang.Interp interp)
                         throws tcl.lang.TclException

Throws:

tcl.lang.TclException

calcBonds

public void calcBonds()

findEquivalentAtoms

public static void findEquivalentAtoms(tcl.lang.Interp interp,
                                       java.lang.String atomName)
                                throws tcl.lang.TclException

Throws:

tcl.lang.TclException

findEquivalentAtoms

public static void findEquivalentAtoms(Entity entity)
                                throws tcl.lang.TclException

Throws:

tcl.lang.TclException

getStartAtom

public static Atom getStartAtom(Molecule molecule)

buildTree

public static int buildTree(tcl.lang.Interp interp,
                            Molecule molecule,
                            Atom startAtom,
                            java.util.Vector atomList,
                            MTree mTree)
                     throws tcl.lang.TclException

Throws:

tcl.lang.TclException

writeXYZ

public static void writeXYZ(tcl.lang.Interp interp,
                            java.lang.String chanName,
                            int whichStruct)
                     throws tcl.lang.TclException

Throws:

tcl.lang.TclException

writePPM

public static void writePPM(tcl.lang.Interp interp,
                            java.lang.String chanName,
                            int whichStruct)
                     throws tcl.lang.TclException

Throws:

tcl.lang.TclException

writeXYZToXML

public static void writeXYZToXML(tcl.lang.Interp interp,
                                 java.lang.String chanName,
                                 int whichStruct)
                          throws tcl.lang.TclException

Throws:

tcl.lang.TclException

writePPMToXML

public static void writePPMToXML(tcl.lang.Interp interp,
                                 java.lang.String chanName,
                                 int whichStruct)
                          throws tcl.lang.TclException

Throws:

tcl.lang.TclException

getAtomTypes

public static void getAtomTypes(Molecule molecule)
                         throws tcl.lang.TclException

Throws:

tcl.lang.TclException

getLabelTypes

public static void getLabelTypes(tcl.lang.Interp interp)
                          throws tcl.lang.TclException

Throws:

tcl.lang.TclException

getDisplayTypes

public static void getDisplayTypes(tcl.lang.Interp interp)
                            throws tcl.lang.TclException

Throws:

tcl.lang.TclException

getShapeTypes

public static void getShapeTypes(tcl.lang.Interp interp)
                          throws tcl.lang.TclException

Throws:

tcl.lang.TclException

getColorTypes

public static void getColorTypes(tcl.lang.Interp interp)
                          throws tcl.lang.TclException

Throws:

tcl.lang.TclException

updateLabels

public void updateLabels()

writeMoleculeSTAR3

public void writeMoleculeSTAR3(tcl.lang.Interp interp,
                               java.lang.String chanName,
                               int assemblyID)
                        throws tcl.lang.TclException

Throws:

tcl.lang.TclException

writeAssignmentsSTAR3

public void writeAssignmentsSTAR3(tcl.lang.Interp interp,
                                  java.lang.String chanName)
                           throws tcl.lang.TclException

Throws:

tcl.lang.TclException

getCoordLoopStrings

public java.lang.String[] getCoordLoopStrings()