org.jmol.modelsetbio
Class AminoPolymer
java.lang.Object
org.jmol.modelset.Polymer
org.jmol.modelsetbio.BioPolymer
org.jmol.modelsetbio.AlphaPolymer
org.jmol.modelsetbio.AminoPolymer
public class AminoPolymer
- extends AlphaPolymer
Method Summary |
private void |
bondAminoHydrogen(AminoMonomer source,
int indexDonor,
javax.vecmath.Point3f hydrogenPoint,
java.util.BitSet bsA,
java.util.BitSet bsB)
|
private int |
calcHbondEnergy(Atom nitrogen,
javax.vecmath.Point3f nitrogenPoint,
javax.vecmath.Point3f hydrogenPoint,
AminoMonomer target)
|
void |
calcHydrogenBonds(Polymer polymer,
java.util.BitSet bsA,
java.util.BitSet bsB)
|
protected boolean |
calcPhiPsiAngles()
|
private void |
calcPhiPsiAngles(AminoMonomer leadingResidue,
AminoMonomer trailingResidue)
|
private void |
calcProteinMainchainHydrogenBonds(AminoPolymer polymer,
java.util.BitSet bsA,
java.util.BitSet bsB)
|
void |
calculateStructures()
Uses Levitt & Greer algorithm to calculate protien secondary
structures using only alpha-carbon atoms. |
private boolean |
checkWingAtoms()
|
private void |
createResidueHydrogenBond(AminoMonomer donor,
int indexAminoGroup,
int indexCarbonylGroup,
java.util.BitSet bsA,
java.util.BitSet bsB)
|
void |
freeze()
|
void |
getPdbData(char ctype,
char qtype,
int derivType,
boolean isDraw,
java.util.BitSet bsAtoms,
java.lang.StringBuffer pdbATOM,
java.lang.StringBuffer pdbCONECT,
java.util.BitSet bsSelected,
boolean addHeader,
java.util.BitSet bsWritten)
|
(package private) boolean |
hasWingPoints()
|
private static boolean |
isHelix(float psi,
float phi)
|
private static boolean |
isSheet(float psi,
float phi)
|
private static boolean |
isTurn(float psi,
float phi)
|
Methods inherited from class org.jmol.modelsetbio.BioPolymer |
allocateBioPolymer, calcSelectedMonomersCount, clearStructures, findNearestAtomIndex, getControlPoints, getIndex, getInitiatorPoint, getLeadAtomIndices, getLeadMidPoint, getLeadMidpoints, getLeadPoint, getLeadPoint, getLeadPoints, getMonomerCount, getMonomers, getPdbData, getPointPoint, getPolymerInfo, getPolymerPointsAndVectors, getPolymerSequenceAtoms, getProteinStructure, getSelectedMonomerCount, getSequence, getTerminatorPoint, getWingPoint, getWingVectors, isMonomerSelected, recalculateLeadMidpointsAndWingVectors, removeProteinStructure, setConformation |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
hasOAtoms
private boolean hasOAtoms
maxHbondAlphaDistance
private static final float maxHbondAlphaDistance
- See Also:
- Constant Field Values
maxHbondAlphaDistance2
private static final float maxHbondAlphaDistance2
- See Also:
- Constant Field Values
minimumHbondDistance2
private static final float minimumHbondDistance2
- See Also:
- Constant Field Values
QConst
private static final double QConst
- See Also:
- Constant Field Values
AminoPolymer
AminoPolymer(Monomer[] monomers)
hasWingPoints
boolean hasWingPoints()
- Overrides:
hasWingPoints
in class BioPolymer
calcHydrogenBonds
public void calcHydrogenBonds(Polymer polymer,
java.util.BitSet bsA,
java.util.BitSet bsB)
- Overrides:
calcHydrogenBonds
in class Polymer
calcProteinMainchainHydrogenBonds
private void calcProteinMainchainHydrogenBonds(AminoPolymer polymer,
java.util.BitSet bsA,
java.util.BitSet bsB)
bondAminoHydrogen
private void bondAminoHydrogen(AminoMonomer source,
int indexDonor,
javax.vecmath.Point3f hydrogenPoint,
java.util.BitSet bsA,
java.util.BitSet bsB)
calcHbondEnergy
private int calcHbondEnergy(Atom nitrogen,
javax.vecmath.Point3f nitrogenPoint,
javax.vecmath.Point3f hydrogenPoint,
AminoMonomer target)
createResidueHydrogenBond
private void createResidueHydrogenBond(AminoMonomer donor,
int indexAminoGroup,
int indexCarbonylGroup,
java.util.BitSet bsA,
java.util.BitSet bsB)
calculateStructures
public void calculateStructures()
- Description copied from class:
AlphaPolymer
- Uses Levitt & Greer algorithm to calculate protien secondary
structures using only alpha-carbon atoms.
Levitt and Greer
Automatic Identification of Secondary Structure in Globular Proteins
J.Mol.Biol.(1977) 114, 181-293
http://csb.stanford.edu/levitt/Levitt_JMB77_Secondary_structure.pdf
- Overrides:
calculateStructures
in class AlphaPolymer
checkWingAtoms
private boolean checkWingAtoms()
freeze
public void freeze()
- Overrides:
freeze
in class Polymer
calcPhiPsiAngles
protected boolean calcPhiPsiAngles()
- Overrides:
calcPhiPsiAngles
in class BioPolymer
calcPhiPsiAngles
private void calcPhiPsiAngles(AminoMonomer leadingResidue,
AminoMonomer trailingResidue)
isHelix
private static boolean isHelix(float psi,
float phi)
- Parameters:
psi
- N-C-CA-N torsion for NEXT groupphi
- C-CA-N-C torsion for THIS group
- Returns:
- whether this corresponds to a helix
isSheet
private static boolean isSheet(float psi,
float phi)
isTurn
private static boolean isTurn(float psi,
float phi)
getPdbData
public void getPdbData(char ctype,
char qtype,
int derivType,
boolean isDraw,
java.util.BitSet bsAtoms,
java.lang.StringBuffer pdbATOM,
java.lang.StringBuffer pdbCONECT,
java.util.BitSet bsSelected,
boolean addHeader,
java.util.BitSet bsWritten)
- Overrides:
getPdbData
in class Polymer