public class AminoPolymer extends AlphaPolymer
Modifier and Type | Field and Description |
---|---|
private static float |
maxHbondAlphaDistance |
private static float |
maxHbondAlphaDistance2 |
private static float |
minimumHbondDistance2 |
private java.util.Map<STR,float[]> |
structureList |
bioPolymerIndexInModel, bsSelectedMonomers, controlPoints, hasStructure, hasWingPoints, haveParameters, invalidControl, leadAtomIndices, leadMidpoints, leadPoints, model, monomerCount, monomers, reversed, sheetSmoothing, twistedSheets, type, TYPE_AMINO, TYPE_CARBOHYDRATE, TYPE_NOBONDING, TYPE_NUCLEIC, wingVectors
Constructor and Description |
---|
AminoPolymer(Monomer[] monomers) |
Modifier and Type | Method and Description |
---|---|
private void |
addResidueHydrogenBond(Atom nitrogen,
Atom oxygen,
int indexAminoGroup,
int indexCarbonylGroup,
float energy,
javajs.util.Lst<Bond> vHBonds) |
private int |
calcHbondEnergy(javajs.util.P3 nitrogenPoint,
javajs.util.P3 hydrogenPoint,
AminoMonomer target,
boolean checkDistances)
based on RasMol 2.7.2.1.1 model
checkDistances:
When we are seriously looking for H bonds, we want to
also check that distCN > distCH and that the OH distance
is less than 3 Angstroms.
|
protected boolean |
calcPhiPsiAngles() |
private void |
calcPhiPsiAngles2(AminoMonomer residue1,
AminoMonomer residue2) |
void |
calcRasmolHydrogenBonds(BioPolymer polymer,
BS bsA,
BS bsB,
javajs.util.Lst<Bond> vHBonds,
int nMaxPerResidue,
int[][][] min,
boolean checkDistances,
boolean dsspIgnoreHydrogens) |
protected float |
calculateRamachandranHelixAngle(int m,
char qtype) |
void |
calculateStructures(boolean alphaOnly)
Uses Levitt & Greer algorithm to calculate protein secondary
structures using only alpha-carbon atoms.
|
private static boolean |
checkPhiPsi(float[] list,
float psi,
float phi) |
private void |
checkRasmolHydrogenBond(AminoMonomer source,
BioPolymer polymer,
int indexDonor,
javajs.util.P3 hydrogenPoint,
BS bsB,
javajs.util.Lst<Bond> vHBonds,
int[][] min,
boolean checkDistances) |
private boolean |
isHelix(float psi,
float phi) |
private boolean |
isSheet(float psi,
float phi) |
private boolean |
isTurn(float psi,
float phi) |
protected void |
resetHydrogenPoints() |
void |
setStructureList(java.util.Map<STR,float[]> structureList) |
addStructure, addStructureProtected, calculateStruts, clearStructures, getControlPoint, getProteinStructure
calcEtaThetaAngles, calcParameters, calcSelectedMonomersCount, drawQuat, findNearestAtomIndex, getConformation, getControlPoints, getIndex, getLeadAtomIndices, getLeadMidPoint, getLeadMidpoints, getLeadPoint, getLeadPoints, getPdbData, getPolymerInfo, getPolymerPointsAndVectors, getPolymerSequenceAtoms, getRange, getRangeGroups, getSelectedMonomerCount, getSequence, getType, getWingPoint, getWingVectors, isMonomerSelected, isNucleic, isRna, recalculateLeadMidpointsAndWingVectors, set, setConformation
private static final float maxHbondAlphaDistance
private static final float maxHbondAlphaDistance2
private static final float minimumHbondDistance2
private java.util.Map<STR,float[]> structureList
AminoPolymer(Monomer[] monomers)
protected void resetHydrogenPoints()
resetHydrogenPoints
in class BioPolymer
protected boolean calcPhiPsiAngles()
calcPhiPsiAngles
in class BioPolymer
private void calcPhiPsiAngles2(AminoMonomer residue1, AminoMonomer residue2)
protected float calculateRamachandranHelixAngle(int m, char qtype)
calculateRamachandranHelixAngle
in class BioPolymer
public void calcRasmolHydrogenBonds(BioPolymer polymer, BS bsA, BS bsB, javajs.util.Lst<Bond> vHBonds, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens)
calcRasmolHydrogenBonds
in class BioPolymer
private void checkRasmolHydrogenBond(AminoMonomer source, BioPolymer polymer, int indexDonor, javajs.util.P3 hydrogenPoint, BS bsB, javajs.util.Lst<Bond> vHBonds, int[][] min, boolean checkDistances)
private int calcHbondEnergy(javajs.util.P3 nitrogenPoint, javajs.util.P3 hydrogenPoint, AminoMonomer target, boolean checkDistances)
nitrogenPoint
- hydrogenPoint
- target
- checkDistances
- private void addResidueHydrogenBond(Atom nitrogen, Atom oxygen, int indexAminoGroup, int indexCarbonylGroup, float energy, javajs.util.Lst<Bond> vHBonds)
public void calculateStructures(boolean alphaOnly)
AlphaPolymer
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
calculateStructures
in class AlphaPolymer
alphaOnly
- caught by AminoPolymer and discarded if desiredprivate boolean isTurn(float psi, float phi)
psi
- N-C-CA-N torsion for NEXT groupphi
- C-CA-N-C torsion for THIS groupprivate boolean isSheet(float psi, float phi)
private boolean isHelix(float psi, float phi)
private static boolean checkPhiPsi(float[] list, float psi, float phi)
public void setStructureList(java.util.Map<STR,float[]> structureList)
setStructureList
in class BioPolymer
structureList
- protein only -- helix, sheet, turn definitions