Package org.jmol.modelsetbio
Class BioPolymer
java.lang.Object
org.jmol.modelsetbio.BioPolymer
- All Implemented Interfaces:
Structure
- Direct Known Subclasses:
AlphaPolymer
,CarbohydratePolymer
,PhosphorusPolymer
A "BioPolymer" is a constructed set of contiguous (probably connected) "Monomers",
which may be one of Alpha (Calpha atoms), Amino (Calpha + backbone),
Phosphorus (P atoms), Nucleic (DNA/RNA), or Carbohydrate.
BioPolymers are constructed after file loading and after various changes that might
affect secondary structure.
BioPolymers are not Chains. Chains are set at load time and just constitute
collections of unique chain identifiers in the file.
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Field Summary
FieldsModifier and TypeFieldDescriptionint
protected P3[]
int
protected boolean
protected boolean
boolean
protected boolean
protected int[]
protected P3[]
protected P3[]
int
Monomer[]
protected float
boolean
protected int
protected static final int
protected static final int
protected static final int
protected static final int
protected V3[]
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected boolean
boolean
protected boolean
void
calcRasmolHydrogenBonds
(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vHBonds, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens) void
calcSelectedMonomersCount
(BS bsSelected) protected float
calculateRamachandranHelixAngle
(int m, char qtype) void
void
findNearestAtomIndex
(int xMouse, int yMouse, Atom[] closest, short[] mads, int myVisibilityFlag, BS bsNot) protected P3
getControlPoint
(int i, V3 v) P3[]
getControlPoints
(boolean isTraceAlpha, float sheetSmoothing, boolean invalidate) protected int
getIndex
(int chainID, int seqcode, int istart, int iend) int[]
P3[]
int
getPolymerPointsAndVectors
(int last, BS bs, Lst<P3[]> vList, boolean isTraceAlpha, float sheetSmoothing) void
getPolymerSequenceAtoms
(int group1, int nGroups, BS bsInclude, BS bsResult) getProteinStructure
(int monomerIndex) void
void
getRangeGroups
(int nResidues, BS bsAtoms, BS bsResult) int
getType()
final V3[]
boolean
isCyclic()
boolean
void
protected void
void
setAtomBits
(BS bs) void
setAtomBitsAndClear
(BS bs, BS bsOut) void
setConformation
(BS bsSelected) toString()
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Field Details
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model
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monomers
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hasStructure
protected boolean hasStructure -
leadMidpoints
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leadPoints
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controlPoints
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wingVectors
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leadAtomIndices
protected int[] leadAtomIndices -
type
protected int type -
bioPolymerIndexInModel
public int bioPolymerIndexInModel -
monomerCount
public int monomerCount -
TYPE_NOBONDING
protected static final int TYPE_NOBONDING- See Also:
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TYPE_AMINO
protected static final int TYPE_AMINO- See Also:
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TYPE_NUCLEIC
protected static final int TYPE_NUCLEIC- See Also:
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TYPE_CARBOHYDRATE
protected static final int TYPE_CARBOHYDRATE- See Also:
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cyclicFlag
public int cyclicFlag -
invalidControl
protected boolean invalidControl -
sheetSmoothing
protected float sheetSmoothing -
hasWingPoints
protected boolean hasWingPoints -
reversed
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twistedSheets
public boolean twistedSheets -
haveParameters
public boolean haveParameters
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Constructor Details
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BioPolymer
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Method Details
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setAtomBits
- Specified by:
setAtomBits
in interfaceStructure
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setAtomBitsAndClear
- Specified by:
setAtomBitsAndClear
in interfaceStructure
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getRange
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clearStructures
public void clearStructures() -
getLeadAtomIndices
public int[] getLeadAtomIndices() -
getIndex
protected int getIndex(int chainID, int seqcode, int istart, int iend) -
setConformation
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recalculateLeadMidpointsAndWingVectors
public void recalculateLeadMidpointsAndWingVectors() -
resetHydrogenPoints
protected void resetHydrogenPoints() -
getLeadMidpoints
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getControlPoints
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getControlPoint
- Parameters:
i
-v
-- Returns:
- the leadPoint unless a protein sheet residue (see AlphaPolymer)
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getWingVectors
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findNearestAtomIndex
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calcSelectedMonomersCount
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getPolymerPointsAndVectors
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getSequence
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getPolymerSequenceAtoms
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getProteinStructure
- Parameters:
monomerIndex
-- Returns:
- "HELIX" "TURN" etc
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calcParameters
public boolean calcParameters() -
calcEtaThetaAngles
protected boolean calcEtaThetaAngles() -
calcPhiPsiAngles
protected boolean calcPhiPsiAngles() -
calculateRamachandranHelixAngle
protected float calculateRamachandranHelixAngle(int m, char qtype) - Parameters:
m
-qtype
-- Returns:
- calculated value
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isNucleic
public boolean isNucleic() -
getRangeGroups
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calcRasmolHydrogenBonds
public void calcRasmolHydrogenBonds(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vHBonds, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens) - Parameters:
polymer
-bsA
-bsB
-vHBonds
-nMaxPerResidue
-min
-checkDistances
-dsspIgnoreHydrogens
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getType
public int getType() -
isCyclic
public boolean isCyclic() -
toString
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