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
(package private) int
private float
protected byte[]
private float
private float
private float
private float
private float
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) (package private) void
findNearestAtomIndex
(int x, int y, Atom[] closest, short madBegin, short madEnd) Selects LeadAtom when this Monomer is clicked iff it is closer to the user.protected final Atom
getAtomFromOffsetIndex
(int offsetIndex) int
getAtomIndex
(String name, int offset) int
int
protected boolean
getCrossLinkGroup
(int i, javajs.util.Lst<Integer> vReturn, Group group, boolean crosslinkCovalent, boolean crosslinkHBond, boolean isNotCheck) boolean
getCrossLinkVector
(javajs.util.Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond) char
protected char
float
getGroupParameter
(int tok) Monomers onlyprotected Object
getHelixData2
(int tokType, char qType, int mStep) (package private) Atom
final Atom
int
(package private) final void
getMonomerSequenceAtoms
(javajs.util.BS bsInclude, javajs.util.BS bsResult) getMyInfo
(javajs.util.P3 ptTemp) (package private) javajs.util.P3
getQuaternionFrameCenter
(char qtype) int
int
protected final Atom
getSpecialAtom
(byte[] interestingIDs, byte specialAtomID) protected final javajs.util.P3
getSpecialAtomPoint
(byte[] interestingIDs, byte specialAtomID) (package private) Atom
final Atom
protected static boolean
have
(byte[] offsets, byte n) (package private) abstract boolean
isConnectedAfter
(Monomer possiblyPreviousMonomer) 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) (package private) void
setBioPolymer
(BioPolymer polymer, int index) void
setGroupID
(String group3) (package private) void
setGroupParameter
(int tok, float f) protected void
void
setStrucNo
(int id) toString()
(package private) final void
updateOffsetsForAlternativeLocations
(Atom[] atoms, javajs.util.BS bsSelected) 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 -
monomerIndex
int monomerIndex -
phi
private float phi -
psi
private float psi -
omega
private float omega -
straightness
private float straightness -
mu
private float mu -
theta
private float theta -
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() -
setBioPolymer
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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
- Parameters:
name
-offset
-- 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
- Parameters:
id
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getAtomFromOffsetIndex
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getSpecialAtom
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getSpecialAtomPoint
protected final javajs.util.P3 getSpecialAtomPoint(byte[] interestingIDs, byte specialAtomID) -
isLeadAtom
public boolean isLeadAtom(int atomIndex) - Overrides:
isLeadAtom
in classGroup
- Parameters:
atomIndex
-- Returns:
- T/F
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getLeadAtom
- Overrides:
getLeadAtom
in classGroup
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getWingAtom
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getInitiatorAtom
Atom getInitiatorAtom() -
getTerminatorAtom
Atom getTerminatorAtom() -
isConnectedAfter
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findNearestAtomIndex
Selects LeadAtom when this Monomer is clicked iff it is closer to the user.- Parameters:
x
-y
-closest
-madBegin
-madEnd
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getMyInfo
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getStructureId
- Overrides:
getStructureId
in classGroup
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updateOffsetsForAlternativeLocations
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getMonomerSequenceAtoms
final void getMonomerSequenceAtoms(javajs.util.BS bsInclude, javajs.util.BS bsResult) -
checkOptional
protected static final boolean checkOptional(byte[] offsets, byte atom, int firstAtomIndex, int index) -
getQuaternionFrameCenter
javajs.util.P3 getQuaternionFrameCenter(char qtype) - Parameters:
qtype
-- Returns:
- center
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getHelixData2
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getUniqueID
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isCrossLinked
- Overrides:
isCrossLinked
in classGroup
- Parameters:
g
-- Returns:
- T/F
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getCrossLinkVector
public boolean getCrossLinkVector(javajs.util.Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond) - Overrides:
getCrossLinkVector
in classGroup
- Parameters:
vReturn
-crosslinkCovalent
-crosslinkHBond
-- Returns:
- T/F
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getCrossLinkGroup
protected boolean getCrossLinkGroup(int i, javajs.util.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()- Overrides:
isConnectedPrevious
in classGroup
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setGroupParameter
void setGroupParameter(int tok, float f) -
getGroupParameter
public float getGroupParameter(int tok) Description copied from class:Group
Monomers only- Overrides:
getGroupParameter
in classGroup
- Parameters:
tok
-- Returns:
- NaN
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getGroup1
public char getGroup1() -
getGroup1b
protected char getGroup1b() -
setGroupID
- Overrides:
setGroupID
in classGroup
- Parameters:
group3
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toString
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