scripps.mol_data
Class Protein

java.lang.Object
  |
  +--harmonic.mz.data.ModelNode
        |
        +--harmonic.mz.data.ShapeGroup
              |
              +--scripps.mol_data.Molecule
                    |
                    +--scripps.mol_data.Protein

All Implemented Interfaces:

java.awt.event.ActionListener, harmonic.mz.data.DataNode, harmonic.mz.gui.Documentable, java.util.EventListener, harmonic.mz.data.Interpolater, harmonic.meshGeom.math.MarkableObject, harmonic.mz.event.NodeListener, harmonic.mz.data.Transformable

public class Protein

extends Molecule

Field Summary

AtomSet	allAtomsCache
BondSet	allBondsCache
ChainSet	allChainsCache
ResidueSet	allResiduesCache
boolean	bFromPDB
harmonic.mz.data.fields.NodeSetField	bonds
boolean	bSavePDB
harmonic.mz.data.fields.NodeSetField	chains
harmonic.mz.data.fields.FileField	source_file

Fields inherited from class scripps.mol_data.Molecule

filename

Fields inherited from class harmonic.mz.data.ShapeGroup

coordSystem, localKludge

Fields inherited from class harmonic.mz.data.ModelNode

_fileRoot_, _thread_, ATTRIB_CONTROL_WIDGET, ATTRIB_LISTABLE, ATTRIB_PRESENTABLE, ATTRIB_PRIVATE, ATTRIB_REMOVEABLE, ATTRIB_RENAMEABLE, ATTRIB_SHOW_CONTEXT_MENU, ATTRIB_TYPE_FILTER, ATTRIB_USERGROUP, ATTRIB_VALUE_GROUP, ATTRIB_VE_LISTENER, bCustomCS, bDebug, bValid, name

Constructor Summary

Protein()

Method Summary

void	applyDataTransfer(harmonic.mz.data.DataTransfer transfer)
ChainSet	getChains()
harmonic.mz.data.DataTransfer[]	getDataTransfer(java.lang.String type)
java.lang.String[]	getDataTransferTypes()
harmonic.mz.data.DataNode[]	getSavedChildren()
void	makeBonds()
void	purgeFinal()
void	readMol(java.lang.String filename)
void	validate()

Methods inherited from class scripps.mol_data.Molecule

addAtomListener, expectedValidationTime, findAtom, getAtoms, getBonds, removeAtomListener

Methods inherited from class harmonic.mz.data.ShapeGroup

beginTransform, endTransform, getCoordSystem, getMoveableCoordSystem, getTransformable, hasFixedCS, scaleCoordSystem, translateCoordSystem

Methods inherited from class harmonic.mz.data.ModelNode

actionPerformed, addAll, addAlphaed, addField, addField, addField, addFields, addNetworkInput, addNetworkOutput, addNode, addNodeListener, addNodeListener, addNodes, addNodes, addToCurrent, addToGlobals, addToNetworkEditor, addToTemps, addWithUndo, allFieldsAreFinal, areFieldsValid, assignFromMetaFields, assignFromXMLAttributes, assignFromXMLString, assignToMetaFields, assignToXMLAttributes, assignToXMLString, at, bind, canSelect, castSelection, checkFileRead, checkNetworkInput, childCount, clean, clearAttrib, clearNotified, compare, copyFrom, createControlWidget, createCopy, createXMLElement, deepCopy, defeatNodeEvents, disableEvents, enableEvents, fileRoot, finalize, findFieldElement, findNode, fromXMLNodes, getAttrib, getBound, getCatagory, getControlWidget, getCurrentNames, getDeleted, getDirectInputs, getDirectOutputs, getEffectors, getEntryListener, getErrorState, getFilterType, getFullName, getHandles, getInstanceURL, getInterpolater, getIsLeaf, getListable, getMark, getMetaFields, getName, getNodeChildren_V, getNodeChildren, getNodeID, getNodeParent, getObjectRep, getPresentable, getPrivate, getReferencePoolName, getRemoteOwner, getRemoveable, getRenameable, getSaveable, getSelect, getSeparateDirectInputs, getSeparateDirectOutputs, getSequenced, getSerialNo, getTags, getTentativeSelect, getTransformableParent, getTransient, getTreeName, getTypeImage, getTypeURL, getUnfoldedChildren, getUpdateTime, getUserGroup, getValidates, getValue, getXMLNodes, hasDependants, hasExternalRef, hashKey, hasValidationLock, hideControlWidget, indexOf, initControlWidget, insertNode, interpolate_Linear, interpolate_Quadratic, invalidate, isField, isFinal, isInSubtree, isInTree, isLinked, isNotified, isPurged, isSet, isTemporary, isValid, linkedTo, linksChildren, makeContextMenu, makeFixed, makePrototype, makeReferenced, makeUnreferenced, makeVisibleInGUI, markNotified, mayValidate, nodeChanged, notifyListeners, postAssignFromXMLElement, preAssignToXMLElement, printChildren, printTags, printTree, printTree, purge, pythonString, remove, removeAll, removeAll, removeHandles, removeNetworkInput, removeNetworkOutput, removeNode, removeNode, removeNode, removeNodeListener, replace, selfNodeChanged, set, setActualName, setAttrib, setBound, setCatagory, setChildrenExcept, setCoordSystem, setCurrentControlWidget, setCurrentNames, setDeleted, setEntryListener, setErrorState, setFromPrototype, setIsField, setIsLeaf, setIsSet, setListable, setMark, setMetaFields, setName, setNodeParent, setPresentable, setPrivate, setRemoteOwner, setRemoveable, setRenameable, setSaveable, setSelect, setSelect, setSequenced, setSerialNo, setTentativeSelect, setTentativeSelect, setToLink, setTransient, setTransientChildren, setUpdateTime, setUserGroup, setValidates, setValidationLock, setValue, setValueGroup, showControlWidget, showControlWidget, showControlWidget, showHandles, startRename, tag, toString, unlinkListeners, unmarkNotified, untag, updateBindable, valChanged, valChanged, valueString

Methods inherited from class java.lang.Object

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

Field Detail

source_file

public harmonic.mz.data.fields.FileField source_file

bonds

public harmonic.mz.data.fields.NodeSetField bonds

chains

public harmonic.mz.data.fields.NodeSetField chains

bSavePDB

public boolean bSavePDB

bFromPDB

public boolean bFromPDB

allAtomsCache

public AtomSet allAtomsCache

allResiduesCache

public ResidueSet allResiduesCache

allChainsCache

public ChainSet allChainsCache

allBondsCache

public BondSet allBondsCache

Constructor Detail

Protein

public Protein()

Method Detail

purgeFinal

public void purgeFinal()

Specified by:

purgeFinal in interface harmonic.mz.data.DataNode

Overrides:

purgeFinal in class Molecule

getDataTransferTypes

public java.lang.String[] getDataTransferTypes()

Overrides:

getDataTransferTypes in class harmonic.mz.data.ModelNode

getDataTransfer

public harmonic.mz.data.DataTransfer[] getDataTransfer(java.lang.String type)

Overrides:

getDataTransfer in class harmonic.mz.data.ModelNode

applyDataTransfer

public void applyDataTransfer(harmonic.mz.data.DataTransfer transfer)

Overrides:

applyDataTransfer in class harmonic.mz.data.ModelNode

getChains

public ChainSet getChains()

getSavedChildren

public harmonic.mz.data.DataNode[] getSavedChildren()

Overrides:

getSavedChildren in class harmonic.mz.data.ModelNode

validate

public void validate()

Overrides:

validate in class harmonic.mz.data.ModelNode

readMol

public void readMol(java.lang.String filename)

makeBonds

public void makeBonds()