Package org.jmol.modelsetbio
Class Monomer
java.lang.Object
org.jmol.modelset.Group
org.jmol.modelsetbio.Monomer
- All Implemented Interfaces:
Structure
- Direct Known Subclasses:
AlphaMonomer
,CarbohydrateMonomer
,PhosphorusMonomer
A class to maintain information about biomolecule groups that are (potentially)
part of biopolymers -- peptides, nucleic acid strands, or complex carbohydrates.
Note that it is possible that a monomer is created but is not part of a BioPolymer.
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Field Summary
FieldsModifier and TypeFieldDescriptionboolean
protected byte[]
Fields inherited from class org.jmol.modelset.Group
chain, dssrNT, firstAtomIndex, group1, group3Names, groupID, groupIndex, lastAtomIndex, leadAtomIndex, selectedIndex, seqcode, shapeVisibilityFlags, specialAtomNames, standardGroupList
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected static final boolean
checkOptional
(byte[] offsets, byte atom, int firstAtomIndex, int index) protected final Atom
getAtomFromOffsetIndex
(int offsetIndex) int
getAtomIndex
(String name, int offset) int
int
protected boolean
getCrossLinkGroup
(int i, Lst<Integer> vReturn, Group group, boolean crosslinkCovalent, boolean crosslinkHBond, boolean isNotCheck) boolean
getCrossLinkVector
(Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond) char
protected char
float
getGroupParameter
(int tok) Monomers onlyprotected Object
getHelixData2
(int tokType, char qType, int mStep) final Atom
int
int
int
protected final Atom
getSpecialAtom
(byte[] interestingIDs, byte specialAtomID) protected final P3
getSpecialAtomPoint
(byte[] interestingIDs, byte specialAtomID) final Atom
protected static boolean
have
(byte[] offsets, byte n) boolean
boolean
boolean
isHelix()
boolean
isLeadAtom
(int atomIndex) boolean
isSheet()
protected static byte[]
scanForOffsets
(int firstAtomIndex, int[] specialAtomIndexes, byte[] interestingAtomIDs) protected Monomer
set2
(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] interestingAtomOffsets) void
setGroupID
(String group3) protected void
void
setStrucNo
(int id) toString()
Methods inherited from class org.jmol.modelset.Group
addAtoms, fixIndices, getBSSideChain, getCarbonylOxygenAtom, getGroup3, getGroupInfo, getHelixData, getInsCode, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, getNitrogenAtom, getProteinStructureSubType, getProteinStructureTag, getQuaternion, getQuaternionFrame, getResno, getSeqcodeFor, getSeqcodeString, getSeqcodeStringFor, getSeqNumberFor, getStrucNo, getStructure, haveSequenceNumber, isAdded, isCarbohydrate, isCursorOnTopOf, isDna, isDnaByID, isNucleic, isNucleicMonomer, isProtein, isPurine, isPurineByID, isPyrimidine, isPyrimidineByID, isRna, isRnaByID, isSelected, isWithinStructure, scaleToScreen, setAtomBits, setAtomBitsAndClear, setGroup, setProteinStructureType, setResno, setShapeVisibility
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Field Details
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bioPolymer
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offsets
protected byte[] offsets -
backboneBlockVis
public boolean backboneBlockVis
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Constructor Details
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Monomer
public Monomer()
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Method Details
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have
protected static boolean have(byte[] offsets, byte n) -
set2
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setLeadAtomIndex
protected void setLeadAtomIndex() -
getSelectedMonomerCount
public int getSelectedMonomerCount()- Overrides:
getSelectedMonomerCount
in classGroup
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getSelectedMonomerIndex
public int getSelectedMonomerIndex()- Overrides:
getSelectedMonomerIndex
in classGroup
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getBioPolymerLength
public int getBioPolymerLength()- Overrides:
getBioPolymerLength
in classGroup
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getMonomerIndex
public int getMonomerIndex()- Overrides:
getMonomerIndex
in classGroup
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getAtomIndex
- Overrides:
getAtomIndex
in classGroup
- Returns:
- index of atom based on offset
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getBioPolymerIndexInModel
public int getBioPolymerIndexInModel()- Overrides:
getBioPolymerIndexInModel
in classGroup
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scanForOffsets
protected static byte[] scanForOffsets(int firstAtomIndex, int[] specialAtomIndexes, byte[] interestingAtomIDs) -
getProteinStructureType
- Overrides:
getProteinStructureType
in classGroup
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isHelix
public boolean isHelix() -
isSheet
public boolean isSheet() -
setStrucNo
public void setStrucNo(int id) - Overrides:
setStrucNo
in classGroup
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getAtomFromOffsetIndex
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getSpecialAtom
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getSpecialAtomPoint
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isLeadAtom
public boolean isLeadAtom(int atomIndex) - Overrides:
isLeadAtom
in classGroup
- Returns:
- T/F
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getLeadAtom
- Overrides:
getLeadAtom
in classGroup
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getWingAtom
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getMyInfo
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getStructureId
- Overrides:
getStructureId
in classGroup
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checkOptional
protected static final boolean checkOptional(byte[] offsets, byte atom, int firstAtomIndex, int index) -
getHelixData2
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getUniqueID
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isCrossLinked
- Overrides:
isCrossLinked
in classGroup
- Returns:
- T/F
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getCrossLinkVector
public boolean getCrossLinkVector(Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond) - Overrides:
getCrossLinkVector
in classGroup
- Returns:
- T/F
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getCrossLinkGroup
protected boolean getCrossLinkGroup(int i, Lst<Integer> vReturn, Group group, boolean crosslinkCovalent, boolean crosslinkHBond, boolean isNotCheck) - Parameters:
i
-vReturn
- null implies just checking for a specific groupgroup
- specific group to check or null to indicate just PREVIOUS group (carbohydrates)crosslinkCovalent
- (S-S)crosslinkHBond
- (hbond)isNotCheck
- TODO- Returns:
- true if there is a cross-link of the allowed type
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isConnectedPrevious
public boolean isConnectedPrevious() -
getGroupParameter
public float getGroupParameter(int tok) Description copied from class:Group
Monomers only- Overrides:
getGroupParameter
in classGroup
- Returns:
- NaN
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getGroup1
public char getGroup1() -
getGroup1b
protected char getGroup1b() -
setGroupID
- Overrides:
setGroupID
in classGroup
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toString
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