meshi.geometry
Class ResidueBuilder

java.lang.Object
  meshi.geometry.ResidueBuilder

public class ResidueBuilder
extends java.lang.Object

Field Summary

private static double[]

xyza

Constructor Summary

ResidueBuilder()

Method Summary

static void	build(Residue res, int typeIndex, double[] chi1to4)
static void	build(Residue res, ResidueType type, double[] chi1to4)
protected static void	buildALA(Residue originalRes)
protected static void	buildARG(Residue originalRes, double[] chi)
protected static void	buildASN(Residue originalRes, double[] chi)
protected static void	buildASP(Residue originalRes, double[] chi)
static void	buildBackbone(Residue originalRes, double phi, double psi)
protected static void	buildCYS(Residue originalRes, double[] chi)
protected static void	buildGLN(Residue originalRes, double[] chi)
protected static void	buildGLU(Residue originalRes, double[] chi)
protected static void	buildGLY(Residue originalRes)
protected static void	buildHIS(Residue originalRes, double[] chi)
protected static void	buildILE(Residue originalRes, double[] chi)
protected static void	buildLEU(Residue originalRes, double[] chi)
protected static void	buildLYS(Residue originalRes, double[] chi)
protected static void	buildMET(Residue originalRes, double[] chi)
protected static void	buildPHE(Residue originalRes, double[] chi)
protected static void	buildPRO(Residue originalRes, double[] chi)
protected static void	buildSER(Residue originalRes, double[] chi)
protected static void	buildTHR(Residue originalRes, double[] chi)
protected static void	buildTRP(Residue originalRes, double[] chi)
protected static void	buildTYR(Residue originalRes, double[] chi)
protected static void	buildVAL(Residue originalRes, double[] chi)
protected static void	getAtom_xyza(double[] xyza, double bond, double angle, double chi, Atom A1, Atom A2, Atom A3)
private static Atom	getAtom(AtomList al, java.lang.String atomName) Returns the specified atom from a residue.
private static ResidueType	getType(int index)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

xyza

private static double[] xyza

Constructor Detail

ResidueBuilder

public ResidueBuilder()

Method Detail

build

public static void build(Residue res,
                         int typeIndex,
                         double[] chi1to4)

getType

private static ResidueType getType(int index)

build

public static void build(Residue res,
                         ResidueType type,
                         double[] chi1to4)

getAtom_xyza

protected static void getAtom_xyza(double[] xyza,
                                   double bond,
                                   double angle,
                                   double chi,
                                   Atom A1,
                                   Atom A2,
                                   Atom A3)

buildBackbone

public static void buildBackbone(Residue originalRes,
                                 double phi,
                                 double psi)

buildALA

protected static void buildALA(Residue originalRes)

buildCYS

protected static void buildCYS(Residue originalRes,
                               double[] chi)

buildASP

protected static void buildASP(Residue originalRes,
                               double[] chi)

buildGLU

protected static void buildGLU(Residue originalRes,
                               double[] chi)

buildPHE

protected static void buildPHE(Residue originalRes,
                               double[] chi)

buildGLY

protected static void buildGLY(Residue originalRes)

buildHIS

protected static void buildHIS(Residue originalRes,
                               double[] chi)

buildILE

protected static void buildILE(Residue originalRes,
                               double[] chi)

buildLYS

protected static void buildLYS(Residue originalRes,
                               double[] chi)

buildLEU

protected static void buildLEU(Residue originalRes,
                               double[] chi)

buildMET

protected static void buildMET(Residue originalRes,
                               double[] chi)

buildASN

protected static void buildASN(Residue originalRes,
                               double[] chi)

buildPRO

protected static void buildPRO(Residue originalRes,
                               double[] chi)

buildGLN

protected static void buildGLN(Residue originalRes,
                               double[] chi)

buildARG

protected static void buildARG(Residue originalRes,
                               double[] chi)

buildSER

protected static void buildSER(Residue originalRes,
                               double[] chi)

buildTHR

protected static void buildTHR(Residue originalRes,
                               double[] chi)

buildVAL

protected static void buildVAL(Residue originalRes,
                               double[] chi)

buildTRP

protected static void buildTRP(Residue originalRes,
                               double[] chi)

buildTYR

protected static void buildTYR(Residue originalRes,
                               double[] chi)

getAtom

private static Atom getAtom(AtomList al,
                            java.lang.String atomName)

Returns the specified atom from a residue.