org.jmol.modelsetbio

Class PhosphorusMonomer

java.lang.Object

org.jmol.modelset.Group

org.jmol.modelsetbio.Monomer

org.jmol.modelsetbio.PhosphorusMonomer

Direct Known Subclasses:

NucleicMonomer

public class PhosphorusMonomer
extends Monomer

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	isPurine
protected boolean	isPyrimidine
private static float	MAX_ADJACENT_PHOSPHORUS_DISTANCE
protected static byte	P
private static byte[]	phosphorusOffsets

Fields inherited from class org.jmol.modelsetbio.Monomer

bioPolymer, monomerIndex, offsets

Fields inherited from class org.jmol.modelset.Group

chain, firstAtomIndex, group1, group3Names, groupID, groupIndex, htGroup, lastAtomIndex, leadAtomIndex, seqcode, shapeVisibilityFlags, specialAtomNames, standardGroupList

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	PhosphorusMonomer()

Method Summary

Modifier and Type	Method and Description
java.lang.Object	getHelixData(int tokType, char qType, int mStep)
(package private) Atom	getP()
STR	getProteinStructureType()
javajs.util.Quat	getQuaternion(char qType)
(package private) javajs.util.P3	getQuaternionFrameCenter(char qType)
protected javajs.util.Quat	getQuaternionP()
java.lang.Object	getStructure()
protected boolean	isCA2(Monomer possiblyPreviousMonomer)
(package private) boolean	isConnectedAfter(Monomer possiblyPreviousMonomer)
boolean	isDna()
boolean	isNucleic()
(package private) boolean	isPhosphorusMonomer()
boolean	isPurine()
boolean	isPyrimidine()
boolean	isRna()
protected PhosphorusMonomer	set3(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)
(package private) static Monomer	validateAndAllocateP(Chain chain, java.lang.String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes)

Methods inherited from class org.jmol.modelsetbio.Monomer

calcBioParameters, checkOptional, findNearestAtomIndex, getAtomFromOffsetIndex, getAtomIndex, getBioPolymerIndexInModel, getBioPolymerLength, getConformation, getCrossLinkGroup, getCrossLinkLead, getGroup1, getGroup1b, getGroupParameter, getGroups, getHelixData2, getInitiatorAtom, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureId, getTerminatorAtom, getUniqueID, getWingAtom, have, haveParameters, isConnectedPrevious, isCrossLinked, isHelix, isLeadAtom, isSheet, scanForOffsets, set2, setBioPolymer, setGroupID, setGroupParameter, setStrucNo, updateOffsetsForAlternativeLocations

Methods inherited from class org.jmol.modelset.Group

addAtoms, fixIndices, getBSSideChain, getCarbonylOxygenAtom, getGroup3, getGroupInfo, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, getModelIndex, getNitrogenAtom, getProteinStructureSubType, getProteinStructureTag, getQuaternionFrame, getResno, getSelectedGroupIndex, getSeqcodeFor, getSeqcodeString, getSeqcodeStringFor, getSeqNumberFor, getStrucNo, haveSequenceNumber, isAdded, isCarbohydrate, isCursorOnTopOf, isProtein, isSelected, isWithinStructure, scaleToScreen, selectAtoms, setGroup, setProteinStructureType, setShapeVisibility, toString

Methods inherited from class java.lang.Object

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

Field Detail

P

protected static final byte P

See Also:

Constant Field Values

phosphorusOffsets

private static final byte[] phosphorusOffsets

MAX_ADJACENT_PHOSPHORUS_DISTANCE

private static float MAX_ADJACENT_PHOSPHORUS_DISTANCE

isPurine

protected boolean isPurine

isPyrimidine

protected boolean isPyrimidine

Constructor Detail

PhosphorusMonomer

protected PhosphorusMonomer()

Method Detail

isNucleic

public final boolean isNucleic()

Overrides:

isNucleic in class Group

validateAndAllocateP

static Monomer validateAndAllocateP(Chain chain,
                                    java.lang.String group3,
                                    int seqcode,
                                    int firstIndex,
                                    int lastIndex,
                                    int[] specialAtomIndexes)

set3

protected PhosphorusMonomer set3(Chain chain,
                                 java.lang.String group3,
                                 int seqcode,
                                 int firstAtomIndex,
                                 int lastAtomIndex,
                                 byte[] offsets)

getP

Atom getP()

isPhosphorusMonomer

boolean isPhosphorusMonomer()

isDna

public boolean isDna()

Overrides:

isDna in class Group

isRna

public boolean isRna()

Overrides:

isRna in class Group

isPurine

public boolean isPurine()

Overrides:

isPurine in class Group

isPyrimidine

public boolean isPyrimidine()

Overrides:

isPyrimidine in class Group

getStructure

public java.lang.Object getStructure()

Overrides:

getStructure in class Group

getProteinStructureType

public STR getProteinStructureType()

Overrides:

getProteinStructureType in class Monomer

isConnectedAfter

boolean isConnectedAfter(Monomer possiblyPreviousMonomer)

Specified by:

isConnectedAfter in class Monomer

isCA2

protected boolean isCA2(Monomer possiblyPreviousMonomer)

getQuaternion

public javajs.util.Quat getQuaternion(char qType)

Overrides:

getQuaternion in class Group

Returns:

quaternion

getQuaternionP

protected javajs.util.Quat getQuaternionP()

getQuaternionFrameCenter

javajs.util.P3 getQuaternionFrameCenter(char qType)

Overrides:

getQuaternionFrameCenter in class Monomer

Returns:

center

getHelixData

public java.lang.Object getHelixData(int tokType,
                                     char qType,
                                     int mStep)

Overrides:

getHelixData in class Group

Returns:

helix data of some sort