Example 11 with AminoAcid3
use of ffx.potential.bonded.ResidueEnumerations.AminoAcid3 in project ffx by mjschnie.
the class Loop method getSolutionCoordinates.
private double[] getSolutionCoordinates(int k, double[][][] r_soln_n, double[][][] r_soln_a, double[][][] r_soln_c, int stt_res, int end_res) {
for (int i = 0; i < 3; i++) {
for (int j = 0; j < 3; j++) {
r_n[i][j] = r_soln_n[k][i][j];
r_a[i][j] = r_soln_a[k][i][j];
r_c[i][j] = r_soln_c[k][i][j];
}
}
// double sum = 0.0;
/* For RMSD?
for (int i = 0; i < 3; i++) {
for (int j = 0; j < 3; j++) {
dr[j] = r_soln_n[k][i][j] - r_n[i + 1][j];
}
sum += dot(dr, dr);
for (int j = 0; j < 3; j++) {
dr[j] = r_soln_a[k][i][j] - r_a[i + 1][j];
}
sum += dot(dr, dr);
for (int j = 0; j < 3; j++) {
dr[j] = r_soln_c[k][i][j] - r_c[i + 1][j];
}
sum += dot(dr, dr);
}
*/
Polymer[] newChain = molAss.getChains();
ArrayList<Atom> backBoneAtoms;
Atom[] atomArray = molAss.getAtomArray();
double[][] coordsArray = new double[atomArray.length][3];
if (useAltCoords) {
System.arraycopy(this.altCoords, 0, coordsArray, 0, coordsArray.length);
} else {
for (int i = 0; i < atomArray.length; i++) {
Atom a = atomArray[i];
coordsArray[i][0] = a.getX();
coordsArray[i][1] = a.getY();
coordsArray[i][2] = a.getZ();
}
}
// Loop through residues to build backbone C,N,CA
for (int i = stt_res; i <= end_res; i++) {
Residue newResidue = newChain[0].getResidue(i);
Residue backResidue = newChain[0].getResidue(i - 1);
backBoneAtoms = newResidue.getBackboneAtoms();
Atom C = null;
Atom N = null;
Atom CA = null;
double[] c = new double[3];
double[] ca = new double[3];
double[] n = new double[3];
double[] bc = new double[3];
double[] determinedXYZ = new double[3];
for (Atom backBoneAtom : backBoneAtoms) {
// backBoneAtom.setBuilt(true);
int backBoneIndex = backBoneAtom.getIndex() - 1;
switch(backBoneAtom.getAtomType().name) {
case "C":
C = backBoneAtom;
coordsArray[backBoneIndex][0] = r_c[i - stt_res][0];
coordsArray[backBoneIndex][1] = r_c[i - stt_res][1];
coordsArray[backBoneIndex][2] = r_c[i - stt_res][2];
break;
case "N":
N = backBoneAtom;
coordsArray[backBoneIndex][0] = r_n[i - stt_res][0];
coordsArray[backBoneIndex][1] = r_n[i - stt_res][1];
coordsArray[backBoneIndex][2] = r_n[i - stt_res][2];
break;
case "CA":
CA = backBoneAtom;
coordsArray[backBoneIndex][0] = r_a[i - stt_res][0];
coordsArray[backBoneIndex][1] = r_a[i - stt_res][1];
coordsArray[backBoneIndex][2] = r_a[i - stt_res][2];
break;
default:
break;
}
}
}
// Loop through again to build Hydrogens and side-chains with current C,N,CA coordinates
for (int i = stt_res + 1; i < end_res - 1; i++) {
Residue newResidue = newChain[0].getResidue(i);
Residue backResidue = newChain[0].getResidue(i - 1);
Residue forwardResidue = newChain[0].getResidue(i + 1);
backBoneAtoms = newResidue.getBackboneAtoms();
double[] c = new double[3];
double[] ca = new double[3];
double[] n = new double[3];
double[] bc = new double[3];
double[] fn = new double[3];
double[] determinedXYZ = new double[3];
// Obtaining coordinates for sidechains
Atom C = (Atom) newResidue.getAtomNode("C");
System.arraycopy(coordsArray[C.getIndex() - 1], 0, c, 0, 3);
Atom CA = (Atom) newResidue.getAtomNode("CA");
System.arraycopy(coordsArray[CA.getIndex() - 1], 0, ca, 0, 3);
Atom N = (Atom) newResidue.getAtomNode("N");
System.arraycopy(coordsArray[N.getIndex() - 1], 0, n, 0, 3);
Atom BC = (Atom) backResidue.getAtomNode("C");
System.arraycopy(coordsArray[BC.getIndex() - 1], 0, bc, 0, 3);
Atom FN = (Atom) forwardResidue.getAtomNode("N");
System.arraycopy(coordsArray[FN.getIndex() - 1], 0, fn, 0, 3);
/*
for (Atom backBoneAtom : backBoneAtoms) {
// backBoneAtom.setBuilt(true);
logger.info(String.format("getAtomType().name "+backBoneAtom.getAtomType().name));
switch (backBoneAtom.getAtomType().name) {
case "H":
logger.info(String.format("H getAtomType().name "+backBoneAtom.getAtomType().name));
determinedXYZ = BondedUtils.determineIntxyz(ca, 1.0, n, 109.5, c, 109.5, -1);
coordsArray = fillCoordsArray(backBoneAtom,coordsArray, determinedXYZ);
break;
case "HA":
logger.info(String.format("HA getAtomType().name "+backBoneAtom.getAtomType().name));
determinedXYZ = BondedUtils.determineIntxyz(n, 1.0, bc, 119.0, ca, 119.0, 1);
coordsArray = fillCoordsArray(backBoneAtom,coordsArray, determinedXYZ);
break;
case "O":
logger.info(String.format("O getAtomType().name "+backBoneAtom.getAtomType().name));
determinedXYZ = BondedUtils.determineIntxyz(c, 1.2255, ca, 122.4, n, 180, 0);
coordsArray = fillCoordsArray(backBoneAtom,coordsArray, determinedXYZ);
break;
default:
break;
}
}
*/
Atom H = (Atom) newResidue.getAtomNode("H");
double[] h = coordsArray[H.getIndex() - 1];
// H
System.arraycopy(BondedUtils.determineIntxyz(n, 1.0, bc, 119.0, ca, 119.0, 1), 0, h, 0, 3);
coordsArray = fillCoordsArray(H, coordsArray, h);
Atom O = (Atom) newResidue.getAtomNode("O");
double[] o = coordsArray[O.getIndex() - 1];
// O
System.arraycopy(BondedUtils.determineIntxyz(c, 1.2255, ca, 122.4, fn, 180, 0), 0, o, 0, 3);
coordsArray = fillCoordsArray(O, coordsArray, o);
AminoAcid3 name = AminoAcid3.valueOf(newResidue.getName());
if (name != AminoAcid3.GLY) {
Atom HA = (Atom) newResidue.getAtomNode("HA");
double[] ha = coordsArray[HA.getIndex() - 1];
// HA
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.0, n, 109.5, c, 109.5, -1), 0, ha, 0, 3);
coordsArray = fillCoordsArray(HA, coordsArray, ha);
}
double rotScale = rng.nextDouble();
switch(name) {
case GLY:
{
Atom HA2 = (Atom) newResidue.getAtomNode("HA2");
double[] ha2 = coordsArray[HA2.getIndex() - 1];
Atom HA3 = (Atom) newResidue.getAtomNode("HA3");
double[] ha3 = coordsArray[HA3.getIndex() - 1];
// HA2
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.00, n, 109.5, c, 109.5, 0), 0, ha2, 0, 3);
coordsArray = fillCoordsArray(HA2, coordsArray, ha2);
// HA3
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.00, n, 109.5, ha2, 109.5, -1), 0, ha3, 0, 3);
coordsArray = fillCoordsArray(HA3, coordsArray, ha3);
break;
}
case ALA:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom HB1 = (Atom) newResidue.getAtomNode("HB1");
double[] hb1 = coordsArray[HB1.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
// CB
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// HB1
System.arraycopy(BondedUtils.determineIntxyz(cb, 1.11, ca, 109.5, n, 180.0, 0), 0, hb1, 0, 3);
coordsArray = fillCoordsArray(HB1, coordsArray, hb1);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, 1.11, ca, 109.5, hb1, 109.4, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, 1.11, ca, 109.5, hb1, 109.4, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
break;
}
case VAL:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom CG1 = (Atom) newResidue.getAtomNode("CG1");
double[] cg1 = coordsArray[CG1.getIndex() - 1];
Atom CG2 = (Atom) newResidue.getAtomNode("CG2");
double[] cg2 = coordsArray[CG2.getIndex() - 1];
Atom HB = (Atom) newResidue.getAtomNode("HB");
double[] hb = coordsArray[HB.getIndex() - 1];
Atom HG11 = (Atom) newResidue.getAtomNode("HG11");
double[] hg11 = coordsArray[HG11.getIndex() - 1];
Atom HG12 = (Atom) newResidue.getAtomNode("HG12");
double[] hg12 = coordsArray[HG12.getIndex() - 1];
Atom HG13 = (Atom) newResidue.getAtomNode("HG13");
double[] hg13 = coordsArray[HG13.getIndex() - 1];
Atom HG21 = (Atom) newResidue.getAtomNode("HG21");
double[] hg21 = coordsArray[HG21.getIndex() - 1];
Atom HG22 = (Atom) newResidue.getAtomNode("HG22");
double[] hg22 = coordsArray[HG22.getIndex() - 1];
Atom HG23 = (Atom) newResidue.getAtomNode("HG23");
double[] hg23 = coordsArray[HG23.getIndex() - 1];
Bond CG_CB = CB.getBond(CG1);
Bond HB_CB = CB.getBond(HB);
Bond HG_CG = HG11.getBond(CG1);
double dCG_CB = CG_CB.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHG_CG = HG_CG.bondType.distance;
Angle CG_CB_CA = CG1.getAngle(CB, CA);
Angle HB_CB_CA = HB.getAngle(CB, CA);
Angle HG_CG_CB = HG11.getAngle(CG1, CB);
double dCG_CB_CA = CG_CB_CA.angleType.angle[CG_CB_CA.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHG_CG_CB = HG_CG_CB.angleType.angle[HG_CG_CB.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// CG1
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG_CB, ca, dCG_CB_CA, n, rotScale * 180.0, 0), 0, cg1, 0, 3);
coordsArray = fillCoordsArray(CG1, coordsArray, cg1);
// CG2
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG_CB, ca, dCG_CB_CA, cg1, 109.5, -1), 0, cg2, 0, 3);
coordsArray = fillCoordsArray(CG2, coordsArray, cg2);
// HB
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg1, 109.4, 1), 0, hb, 0, 3);
coordsArray = fillCoordsArray(HB, coordsArray, hb);
// HG11
System.arraycopy(BondedUtils.determineIntxyz(cg1, dHG_CG, cb, dHG_CG_CB, ca, 180.0, 0), 0, hg11, 0, 3);
coordsArray = fillCoordsArray(HG11, coordsArray, hg11);
// HG12
System.arraycopy(BondedUtils.determineIntxyz(cg1, dHG_CG, cb, dHG_CG_CB, hg11, 109.4, 1), 0, hg12, 0, 3);
coordsArray = fillCoordsArray(HG12, coordsArray, hg12);
// HG13
System.arraycopy(BondedUtils.determineIntxyz(cg1, dHG_CG, cb, dHG_CG_CB, hg11, 109.4, -1), 0, hg13, 0, 3);
coordsArray = fillCoordsArray(HG13, coordsArray, hg13);
// HG21
System.arraycopy(BondedUtils.determineIntxyz(cg2, dHG_CG, cb, dHG_CG_CB, ca, 180.0, 0), 0, hg21, 0, 3);
coordsArray = fillCoordsArray(HG21, coordsArray, hg21);
// HG22
System.arraycopy(BondedUtils.determineIntxyz(cg2, dHG_CG, cb, dHG_CG_CB, hg21, 109.4, 1), 0, hg22, 0, 3);
coordsArray = fillCoordsArray(HG22, coordsArray, hg22);
// HG23
System.arraycopy(BondedUtils.determineIntxyz(cg2, dHG_CG, cb, dHG_CG_CB, hg21, 109.4, -1), 0, hg23, 0, 3);
coordsArray = fillCoordsArray(HG23, coordsArray, hg23);
break;
}
case LEU:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom CG = (Atom) newResidue.getAtomNode("CG");
double[] cg = coordsArray[CG.getIndex() - 1];
Atom CD1 = (Atom) newResidue.getAtomNode("CD1");
double[] cd1 = coordsArray[CD1.getIndex() - 1];
Atom CD2 = (Atom) newResidue.getAtomNode("CD2");
double[] cd2 = coordsArray[CD2.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Atom HG = (Atom) newResidue.getAtomNode("HG");
double[] hg = coordsArray[HG.getIndex() - 1];
Atom HD11 = (Atom) newResidue.getAtomNode("HD11");
double[] hd11 = coordsArray[HD11.getIndex() - 1];
Atom HD12 = (Atom) newResidue.getAtomNode("HD12");
double[] hd12 = coordsArray[HD12.getIndex() - 1];
Atom HD13 = (Atom) newResidue.getAtomNode("HD13");
double[] hd13 = coordsArray[HD13.getIndex() - 1];
Atom HD21 = (Atom) newResidue.getAtomNode("HD21");
double[] hd21 = coordsArray[HD21.getIndex() - 1];
Atom HD22 = (Atom) newResidue.getAtomNode("HD22");
double[] hd22 = coordsArray[HD22.getIndex() - 1];
Atom HD23 = (Atom) newResidue.getAtomNode("HD23");
double[] hd23 = coordsArray[HD23.getIndex() - 1];
Bond CG_CB = CG.getBond(CB);
Bond CD_CG = CD1.getBond(CG);
Bond HB_CB = HB2.getBond(CB);
Bond HG_CG = HG.getBond(CG);
Bond HD_CD = HD11.getBond(CD1);
double dCG_CB = CG_CB.bondType.distance;
double dCD_CG = CD_CG.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHG_CG = HG_CG.bondType.distance;
double dHD_CD = HD_CD.bondType.distance;
Angle CG_CB_CA = CG.getAngle(CB, CA);
Angle CD_CG_CB = CD1.getAngle(CG, CB);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
Angle HG_CG_CB = HG.getAngle(CG, CB);
Angle HD_CD_CG = HD11.getAngle(CD1, CG);
double dCG_CB_CA = CG_CB_CA.angleType.angle[CG_CB_CA.nh];
double dCD_CG_CB = CD_CG_CB.angleType.angle[CD_CG_CB.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHG_CG_CB = HG_CG_CB.angleType.angle[HG_CG_CB.nh];
double dHD_CD_CG = HD_CD_CG.angleType.angle[HD_CD_CG.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// CG
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG_CB, ca, dCG_CB_CA, n, rotScale * 180.0, 0), 0, cg, 0, 3);
coordsArray = fillCoordsArray(CG, coordsArray, cg);
// CD1
System.arraycopy(BondedUtils.determineIntxyz(cg, dCD_CG, cb, dCD_CG_CB, ca, 180.0, 0), 0, cd1, 0, 3);
coordsArray = fillCoordsArray(CD1, coordsArray, cd1);
// CD2
System.arraycopy(BondedUtils.determineIntxyz(cg, dCD_CG, cb, dCD_CG_CB, cd1, 109.5, -1), 0, cd2, 0, 3);
coordsArray = fillCoordsArray(CD2, coordsArray, cd2);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
// HG
System.arraycopy(BondedUtils.determineIntxyz(cg, dHG_CG, cb, dHG_CG_CB, cd1, 109.4, 1), 0, hg, 0, 3);
coordsArray = fillCoordsArray(HG, coordsArray, hg);
// HD11
System.arraycopy(BondedUtils.determineIntxyz(cd1, dHD_CD, cg, dHD_CD_CG, cb, 180.0, 0), 0, hd11, 0, 3);
coordsArray = fillCoordsArray(HD11, coordsArray, hd11);
// HD12
System.arraycopy(BondedUtils.determineIntxyz(cd1, dHD_CD, cg, dHD_CD_CG, hd11, 109.4, 1), 0, hd12, 0, 3);
coordsArray = fillCoordsArray(HD12, coordsArray, hd12);
// HD13
System.arraycopy(BondedUtils.determineIntxyz(cd1, dHD_CD, cg, dHD_CD_CG, hd11, 109.4, -1), 0, hd13, 0, 3);
coordsArray = fillCoordsArray(HD13, coordsArray, hd13);
// HD21
System.arraycopy(BondedUtils.determineIntxyz(cd2, dHD_CD, cg, dHD_CD_CG, cb, 180.0, 0), 0, hd21, 0, 3);
coordsArray = fillCoordsArray(HD21, coordsArray, hd21);
// HD22
System.arraycopy(BondedUtils.determineIntxyz(cd2, dHD_CD, cg, dHD_CD_CG, hd21, 109.4, 1), 0, hd22, 0, 3);
coordsArray = fillCoordsArray(HD22, coordsArray, hd22);
// HD23
System.arraycopy(BondedUtils.determineIntxyz(cd2, dHD_CD, cg, dHD_CD_CG, hd21, 109.4, -1), 0, hd23, 0, 3);
coordsArray = fillCoordsArray(HD23, coordsArray, hd23);
break;
}
case ILE:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom CG1 = (Atom) newResidue.getAtomNode("CG1");
double[] cg1 = coordsArray[CG1.getIndex() - 1];
Atom CG2 = (Atom) newResidue.getAtomNode("CG2");
double[] cg2 = coordsArray[CG2.getIndex() - 1];
Atom CD1 = (Atom) newResidue.getAtomNode("CD1");
double[] cd1 = coordsArray[CD1.getIndex() - 1];
Atom HB = (Atom) newResidue.getAtomNode("HB");
double[] hb = coordsArray[HB.getIndex() - 1];
Atom HG12 = (Atom) newResidue.getAtomNode("HG12");
double[] hg12 = coordsArray[HG12.getIndex() - 1];
Atom HG13 = (Atom) newResidue.getAtomNode("HG13");
double[] hg13 = coordsArray[HG13.getIndex() - 1];
Atom HG21 = (Atom) newResidue.getAtomNode("HG21");
double[] hg21 = coordsArray[HG21.getIndex() - 1];
Atom HG22 = (Atom) newResidue.getAtomNode("HG22");
double[] hg22 = coordsArray[HG22.getIndex() - 1];
Atom HG23 = (Atom) newResidue.getAtomNode("HG23");
double[] hg23 = coordsArray[HG23.getIndex() - 1];
Atom HD11 = (Atom) newResidue.getAtomNode("HD11");
double[] hd11 = coordsArray[HD11.getIndex() - 1];
Atom HD12 = (Atom) newResidue.getAtomNode("HD12");
double[] hd12 = coordsArray[HD12.getIndex() - 1];
Atom HD13 = (Atom) newResidue.getAtomNode("HD13");
double[] hd13 = coordsArray[HD13.getIndex() - 1];
Bond CG1_CB = CG1.getBond(CB);
Bond CG2_CB = CG2.getBond(CB);
Bond CD1_CG1 = CD1.getBond(CG1);
Bond HB_CB = HB.getBond(CB);
Bond HG1_CG = HG12.getBond(CG1);
Bond HG2_CG = HG22.getBond(CG2);
Bond HD_CD = HD12.getBond(CD1);
double dCG1_CB = CG1_CB.bondType.distance;
double dCG2_CB = CG2_CB.bondType.distance;
double dCD1_CG1 = CD1_CG1.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHG1_CG = HG1_CG.bondType.distance;
double dHG2_CG = HG2_CG.bondType.distance;
double dHD_CD = HD_CD.bondType.distance;
Angle CG1_CB_CA = CG1.getAngle(CB, CA);
Angle CG2_CB_CA = CG2.getAngle(CB, CA);
Angle CD1_CG1_CB = CD1.getAngle(CG1, CB);
Angle HB_CB_CA = HB.getAngle(CB, CA);
Angle HG1_CG_CB = HG12.getAngle(CG1, CB);
Angle HG2_CG_CB = HG21.getAngle(CG2, CB);
Angle HD_CD1_CG1 = HD11.getAngle(CD1, CG1);
double dCG1_CB_CA = CG1_CB_CA.angleType.angle[CG1_CB_CA.nh];
double dCG2_CB_CA = CG2_CB_CA.angleType.angle[CG2_CB_CA.nh];
double dCD1_CG1_CB = CD1_CG1_CB.angleType.angle[CD1_CG1_CB.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHG1_CG_CB = HG1_CG_CB.angleType.angle[HG1_CG_CB.nh];
double dHG2_CG_CB = HG2_CG_CB.angleType.angle[HG2_CG_CB.nh];
double dHD_CD1_CG1 = HD_CD1_CG1.angleType.angle[HD_CD1_CG1.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// CG1
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG1_CB, ca, dCG1_CB_CA, n, rotScale * 180.0, 0), 0, cg1, 0, 3);
coordsArray = fillCoordsArray(CG1, coordsArray, cg1);
// CG2
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG2_CB, ca, dCG2_CB_CA, cg1, 109.5, 1), 0, cg2, 0, 3);
coordsArray = fillCoordsArray(CG2, coordsArray, cg2);
// CD1
System.arraycopy(BondedUtils.determineIntxyz(cg1, dCD1_CG1, cb, dCD1_CG1_CB, ca, 180, 0), 0, cd1, 0, 3);
coordsArray = fillCoordsArray(CD1, coordsArray, cd1);
// HB
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg2, 109.4, 1), 0, hb, 0, 3);
coordsArray = fillCoordsArray(HB, coordsArray, hb);
// HG12
System.arraycopy(BondedUtils.determineIntxyz(cg1, dHG1_CG, cb, dHG1_CG_CB, cd1, 109.4, 1), 0, hg12, 0, 3);
coordsArray = fillCoordsArray(HG12, coordsArray, hg12);
// HG13
System.arraycopy(BondedUtils.determineIntxyz(cg1, dHG1_CG, cb, dHG1_CG_CB, cd1, 109.4, -1), 0, hg13, 0, 3);
coordsArray = fillCoordsArray(HG13, coordsArray, hg13);
// HG21
System.arraycopy(BondedUtils.determineIntxyz(cg2, dHG2_CG, cb, dHG2_CG_CB, cg1, 180.0, 0), 0, hg21, 0, 3);
coordsArray = fillCoordsArray(HG21, coordsArray, hg21);
// HG22
System.arraycopy(BondedUtils.determineIntxyz(cg2, dHG2_CG, cb, dHG2_CG_CB, hg21, 109.0, 1), 0, hg22, 0, 3);
coordsArray = fillCoordsArray(HG22, coordsArray, hg22);
// HG23
System.arraycopy(BondedUtils.determineIntxyz(cg2, dHG2_CG, cb, dHG2_CG_CB, hg21, 109.0, -1), 0, hg23, 0, 3);
coordsArray = fillCoordsArray(HG23, coordsArray, hg23);
// HD11
System.arraycopy(BondedUtils.determineIntxyz(cd1, dHD_CD, cg1, dHD_CD1_CG1, cb, 180.0, 0), 0, hd11, 0, 3);
coordsArray = fillCoordsArray(HD11, coordsArray, hd11);
// HD12
System.arraycopy(BondedUtils.determineIntxyz(cd1, dHD_CD, cg1, dHD_CD1_CG1, hd11, 109.0, 1), 0, hd12, 0, 3);
coordsArray = fillCoordsArray(HD12, coordsArray, hd12);
// HD13
System.arraycopy(BondedUtils.determineIntxyz(cd1, dHD_CD, cg1, dHD_CD1_CG1, hd11, 109.0, -1), 0, hd13, 0, 3);
coordsArray = fillCoordsArray(HD13, coordsArray, hd13);
break;
}
case SER:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom OG = (Atom) newResidue.getAtomNode("OG");
double[] og = coordsArray[OG.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Atom HG = (Atom) newResidue.getAtomNode("HG");
double[] hg = coordsArray[HG.getIndex() - 1];
Bond OG_CB = OG.getBond(CB);
Bond HB_CB = HB2.getBond(CB);
Bond HG_OG = HG.getBond(OG);
double dOG_CB = OG_CB.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHG_OG = HG_OG.bondType.distance;
Angle OG_CB_CA = OG.getAngle(CB, CA);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
Angle HG_OG_CB = HG.getAngle(OG, CB);
double dOG_CB_CA = OG_CB_CA.angleType.angle[OG_CB_CA.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHG_OG_CB = HG_OG_CB.angleType.angle[HG_OG_CB.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// OG
System.arraycopy(BondedUtils.determineIntxyz(cb, dOG_CB, ca, dOG_CB_CA, n, rotScale * 180.0, 0), 0, og, 0, 3);
coordsArray = fillCoordsArray(OG, coordsArray, og);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, og, 106.7, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, og, 106.7, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
// HG
System.arraycopy(BondedUtils.determineIntxyz(og, dHG_OG, cb, dHG_OG_CB, ca, 180.0, 0), 0, hg, 0, 3);
coordsArray = fillCoordsArray(HG, coordsArray, hg);
break;
}
case THR:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom OG1 = (Atom) newResidue.getAtomNode("OG1");
double[] og1 = coordsArray[OG1.getIndex() - 1];
Atom CG2 = (Atom) newResidue.getAtomNode("CG2");
double[] cg2 = coordsArray[CG2.getIndex() - 1];
Atom HB = (Atom) newResidue.getAtomNode("HB");
double[] hb = coordsArray[HB.getIndex() - 1];
Atom HG1 = (Atom) newResidue.getAtomNode("HG1");
double[] hg1 = coordsArray[HG1.getIndex() - 1];
Atom HG21 = (Atom) newResidue.getAtomNode("HG21");
double[] hg21 = coordsArray[HG21.getIndex() - 1];
Atom HG22 = (Atom) newResidue.getAtomNode("HG22");
double[] hg22 = coordsArray[HG22.getIndex() - 1];
Atom HG23 = (Atom) newResidue.getAtomNode("HG23");
double[] hg23 = coordsArray[HG23.getIndex() - 1];
Bond OG1_CB = OG1.getBond(CB);
Bond CG2_CB = CG2.getBond(CB);
Bond HB_CB = HB.getBond(CB);
Bond HG1_OG1 = HG1.getBond(OG1);
Bond HG2_CG2 = HG21.getBond(CG2);
double dOG1_CB = OG1_CB.bondType.distance;
double dCG2_CB = CG2_CB.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHG1_OG1 = HG1_OG1.bondType.distance;
double dHG2_CG2 = HG2_CG2.bondType.distance;
Angle OG1_CB_CA = OG1.getAngle(CB, CA);
Angle CG2_CB_CA = CG2.getAngle(CB, CA);
Angle HB_CB_CA = HB.getAngle(CB, CA);
Angle HG1_OG1_CB = HG1.getAngle(OG1, CB);
Angle HG2_CG2_CB = HG21.getAngle(CG2, CB);
double dOG1_CB_CA = OG1_CB_CA.angleType.angle[OG1_CB_CA.nh];
double dCG2_CB_CA = CG2_CB_CA.angleType.angle[CG2_CB_CA.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHG1_OG1_CB = HG1_OG1_CB.angleType.angle[HG1_OG1_CB.nh];
double dHG2_CG2_CB = HG2_CG2_CB.angleType.angle[HG2_CG2_CB.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// OG1
System.arraycopy(BondedUtils.determineIntxyz(cb, dOG1_CB, ca, dOG1_CB_CA, n, rotScale * 180.0, 0), 0, og1, 0, 3);
coordsArray = fillCoordsArray(OG1, coordsArray, og1);
// CG2
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG2_CB, ca, dCG2_CB_CA, og1, 107.7, 1), 0, cg2, 0, 3);
coordsArray = fillCoordsArray(CG2, coordsArray, cg2);
// HB
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, og1, 106.7, -1), 0, hb, 0, 3);
coordsArray = fillCoordsArray(HB, coordsArray, hb);
// HG1
System.arraycopy(BondedUtils.determineIntxyz(og1, dHG1_OG1, cb, dHG1_OG1_CB, ca, 180.0, 0), 0, hg1, 0, 3);
coordsArray = fillCoordsArray(HG1, coordsArray, hg1);
// HG21
System.arraycopy(BondedUtils.determineIntxyz(cg2, dHG2_CG2, cb, dHG2_CG2_CB, ca, 180.0, 0), 0, hg21, 0, 3);
coordsArray = fillCoordsArray(HG21, coordsArray, hg21);
// HG22
System.arraycopy(BondedUtils.determineIntxyz(cg2, dHG2_CG2, cb, dHG2_CG2_CB, hg21, 109.0, 1), 0, hg22, 0, 3);
coordsArray = fillCoordsArray(HG22, coordsArray, hg22);
// HG23
System.arraycopy(BondedUtils.determineIntxyz(cg2, dHG2_CG2, cb, dHG2_CG2_CB, hg21, 109.0, -1), 0, hg23, 0, 3);
coordsArray = fillCoordsArray(HG23, coordsArray, hg23);
break;
}
case CYS:
case CYX:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom SG = (Atom) newResidue.getAtomNode("SG");
double[] sg = coordsArray[SG.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Atom HG = (Atom) newResidue.getAtomNode("HG");
double[] hg = coordsArray[HG.getIndex() - 1];
Bond SG_CB = SG.getBond(CB);
Bond HB_CB = HB2.getBond(CB);
Bond HG_SG = HG.getBond(SG);
double dSG_CB = SG_CB.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHG_SG = HG_SG.bondType.distance;
Angle SG_CB_CA = SG.getAngle(CB, CA);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
Angle HG_SG_CB = HG.getAngle(SG, CB);
double dSG_CB_CA = SG_CB_CA.angleType.angle[SG_CB_CA.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHG_SG_CB = HG_SG_CB.angleType.angle[HG_SG_CB.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// SG
System.arraycopy(BondedUtils.determineIntxyz(cb, dSG_CB, ca, dSG_CB_CA, n, rotScale * 180.0, 0), 0, sg, 0, 3);
coordsArray = fillCoordsArray(SG, coordsArray, sg);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, sg, 112.0, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, sg, 112.0, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
// HG
System.arraycopy(BondedUtils.determineIntxyz(sg, dHG_SG, cb, dHG_SG_CB, ca, 180.0, 0), 0, hg, 0, 3);
coordsArray = fillCoordsArray(HG, coordsArray, hg);
break;
}
case CYD:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom SG = (Atom) newResidue.getAtomNode("SG");
double[] sg = coordsArray[SG.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Bond SG_CB = SG.getBond(CB);
Bond HB_CB = HB2.getBond(CB);
double dSG_CB = SG_CB.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
Angle SG_CB_CA = SG.getAngle(CB, CA);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
double dSG_CB_CA = SG_CB_CA.angleType.angle[SG_CB_CA.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// SG
System.arraycopy(BondedUtils.determineIntxyz(cb, dSG_CB, ca, dSG_CB_CA, n, rotScale * 180.0, 0), 0, sg, 0, 3);
coordsArray = fillCoordsArray(SG, coordsArray, sg);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, sg, 112.0, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, sg, 112.0, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
break;
}
case PHE:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom CG = (Atom) newResidue.getAtomNode("CG");
double[] cg = coordsArray[CG.getIndex() - 1];
Atom CD1 = (Atom) newResidue.getAtomNode("CD1");
double[] cd1 = coordsArray[CD1.getIndex() - 1];
Atom CD2 = (Atom) newResidue.getAtomNode("CD2");
double[] cd2 = coordsArray[CD2.getIndex() - 1];
Atom CE1 = (Atom) newResidue.getAtomNode("CE1");
double[] ce1 = coordsArray[CE1.getIndex() - 1];
Atom CE2 = (Atom) newResidue.getAtomNode("CE2");
double[] ce2 = coordsArray[CE2.getIndex() - 1];
Atom CZ = (Atom) newResidue.getAtomNode("CZ");
double[] cz = coordsArray[CZ.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Atom HD1 = (Atom) newResidue.getAtomNode("HD1");
double[] hd1 = coordsArray[HD1.getIndex() - 1];
Atom HD2 = (Atom) newResidue.getAtomNode("HD2");
double[] hd2 = coordsArray[HD2.getIndex() - 1];
Atom HE1 = (Atom) newResidue.getAtomNode("HE1");
double[] he1 = coordsArray[HE1.getIndex() - 1];
Atom HE2 = (Atom) newResidue.getAtomNode("HE2");
double[] he2 = coordsArray[HE2.getIndex() - 1];
Atom HZ = (Atom) newResidue.getAtomNode("HZ");
double[] hz = coordsArray[HZ.getIndex() - 1];
Bond CG_CB = CG.getBond(CB);
Bond CD_CG = CD1.getBond(CG);
Bond CE_CD = CE1.getBond(CD1);
Bond CZ_CE1 = CZ.getBond(CE1);
Bond HB_CB = HB2.getBond(CB);
Bond HD_CD = HD1.getBond(CD1);
Bond HE_CE = HE1.getBond(CE1);
Bond HZ_CZ = HZ.getBond(CZ);
double dCG_CB = CG_CB.bondType.distance;
double dCD_CG = CD_CG.bondType.distance;
double dCE_CD = CE_CD.bondType.distance;
double dCZ_CE1 = CZ_CE1.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHD_CD = HD_CD.bondType.distance;
double dHE_CE = HE_CE.bondType.distance;
double dHZ_CZ = HZ_CZ.bondType.distance;
Angle CG_CB_CA = CG.getAngle(CB, CA);
Angle CD_CG_CB = CD1.getAngle(CG, CB);
Angle CE_CD_CG = CE1.getAngle(CD1, CG);
Angle CZ_CE1_CD1 = CZ.getAngle(CE1, CD1);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
Angle HD_CD1_CG = HD1.getAngle(CD1, CG);
Angle HE_CE_CD = HE1.getAngle(CE1, CD1);
Angle HZ_CZ_CE1 = HZ.getAngle(CZ, CE1);
double dCG_CB_CA = CG_CB_CA.angleType.angle[CG_CB_CA.nh];
double dCD_CG_CB = CD_CG_CB.angleType.angle[CD_CG_CB.nh];
double dCE_CD_CG = CE_CD_CG.angleType.angle[CE_CD_CG.nh];
double dCZ_CE1_CD1 = CZ_CE1_CD1.angleType.angle[CZ_CE1_CD1.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHD_CD1_CG = HD_CD1_CG.angleType.angle[HD_CD1_CG.nh];
double dHE_CE_CD = HE_CE_CD.angleType.angle[HE_CE_CD.nh];
double dHZ_CZ_CE1 = HZ_CZ_CE1.angleType.angle[HZ_CZ_CE1.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// CG
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG_CB, ca, dCG_CB_CA, n, rotScale * 180.0, 0), 0, cg, 0, 3);
coordsArray = fillCoordsArray(CG, coordsArray, cg);
// CD1
System.arraycopy(BondedUtils.determineIntxyz(cg, dCD_CG, cb, dCD_CG_CB, ca, 180.0, 0), 0, cd1, 0, 3);
coordsArray = fillCoordsArray(CD1, coordsArray, cd1);
// CD2
System.arraycopy(BondedUtils.determineIntxyz(cg, dCD_CG, cb, dCD_CG_CB, cd1, 120.0, 1), 0, cd2, 0, 3);
coordsArray = fillCoordsArray(CD2, coordsArray, cd2);
// CE1
System.arraycopy(BondedUtils.determineIntxyz(cd1, dCE_CD, cg, dCE_CD_CG, cb, 180, 0), 0, ce1, 0, 3);
coordsArray = fillCoordsArray(CE1, coordsArray, ce1);
// CE2
System.arraycopy(BondedUtils.determineIntxyz(cd2, dCE_CD, cg, dCE_CD_CG, cb, 180, 0), 0, ce2, 0, 3);
coordsArray = fillCoordsArray(CE2, coordsArray, ce2);
// CZ
System.arraycopy(BondedUtils.determineIntxyz(ce1, dCZ_CE1, cd1, dCZ_CE1_CD1, cg, 0.0, 0), 0, cz, 0, 3);
coordsArray = fillCoordsArray(CZ, coordsArray, cz);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
// HD1
System.arraycopy(BondedUtils.determineIntxyz(cd1, dHD_CD, cg, dHD_CD1_CG, ce1, 120.0, 1), 0, hd1, 0, 3);
coordsArray = fillCoordsArray(HD1, coordsArray, hd1);
// HD2
System.arraycopy(BondedUtils.determineIntxyz(cd2, dHD_CD, cg, dHD_CD1_CG, ce2, 120.0, 1), 0, hd2, 0, 3);
coordsArray = fillCoordsArray(HD2, coordsArray, hd2);
// HE1
System.arraycopy(BondedUtils.determineIntxyz(ce1, dHE_CE, cd1, dHE_CE_CD, cz, 120.0, 1), 0, he1, 0, 3);
coordsArray = fillCoordsArray(HE1, coordsArray, he1);
// HE2
System.arraycopy(BondedUtils.determineIntxyz(ce2, dHE_CE, cd2, dHE_CE_CD, cz, 120.0, 1), 0, he2, 0, 3);
coordsArray = fillCoordsArray(HE2, coordsArray, he2);
// HZ
System.arraycopy(BondedUtils.determineIntxyz(cz, dHZ_CZ, ce1, dHZ_CZ_CE1, ce2, 120.0, 1), 0, hz, 0, 3);
coordsArray = fillCoordsArray(HZ, coordsArray, hz);
break;
}
case PRO:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom CG = (Atom) newResidue.getAtomNode("CG");
double[] cg = coordsArray[CG.getIndex() - 1];
Atom CD = (Atom) newResidue.getAtomNode("CD");
double[] cd = coordsArray[CD.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Atom HG2 = (Atom) newResidue.getAtomNode("HG2");
double[] hg2 = coordsArray[HG2.getIndex() - 1];
Atom HG3 = (Atom) newResidue.getAtomNode("HG3");
double[] hg3 = coordsArray[HG3.getIndex() - 1];
Atom HD2 = (Atom) newResidue.getAtomNode("HD2");
double[] hd2 = coordsArray[HD2.getIndex() - 1];
Atom HD3 = (Atom) newResidue.getAtomNode("HD3");
double[] hd3 = coordsArray[HD3.getIndex() - 1];
Bond CG_CB = CG.getBond(CB);
Bond CD_CG = CD.getBond(CG);
Bond HB_CB = HB2.getBond(CB);
Bond HG_CG = HG2.getBond(CG);
Bond HD_CD = HD2.getBond(CD);
double dCG_CB = CG_CB.bondType.distance;
double dCD_CG = CD_CG.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHG_CG = HG_CG.bondType.distance;
double dHD_CD = HD_CD.bondType.distance;
Angle CG_CB_CA = CG.getAngle(CB, CA);
Angle CD_CG_CB = CD.getAngle(CG, CB);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
Angle HG_CG_CB = HG2.getAngle(CG, CB);
Angle HD_CD_CG = HD2.getAngle(CD, CG);
double dCG_CB_CA = CG_CB_CA.angleType.angle[CG_CB_CA.nh];
double dCD_CG_CB = CD_CG_CB.angleType.angle[CD_CG_CB.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHG_CG_CB = HG_CG_CB.angleType.angle[HG_CG_CB.nh];
double dHD_CD_CG = HD_CD_CG.angleType.angle[HD_CD_CG.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// CG
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG_CB, ca, dCG_CB_CA, n, rotScale * 180.0, 0), 0, cg, 0, 3);
coordsArray = fillCoordsArray(CG, coordsArray, cg);
// CD
System.arraycopy(BondedUtils.determineIntxyz(cg, dCD_CG, cb, dCD_CG_CB, ca, 30.0, 0), 0, cd, 0, 3);
coordsArray = fillCoordsArray(CD, coordsArray, cd);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
// HG2
System.arraycopy(BondedUtils.determineIntxyz(cg, dHG_CG, cb, dHG_CG_CB, cd, 109.4, 1), 0, hg2, 0, 3);
coordsArray = fillCoordsArray(HG2, coordsArray, hg2);
// HG3
System.arraycopy(BondedUtils.determineIntxyz(cg, dHG_CG, cb, dHG_CG_CB, cd, 109.4, -1), 0, hg3, 0, 3);
coordsArray = fillCoordsArray(HG3, coordsArray, hg3);
// HD2
System.arraycopy(BondedUtils.determineIntxyz(cd, dHD_CD, cg, dHD_CD_CG, n, 109.4, 1), 0, hd2, 0, 3);
coordsArray = fillCoordsArray(HD2, coordsArray, hd2);
// HD3
System.arraycopy(BondedUtils.determineIntxyz(cd, dHD_CD, cg, dHD_CD_CG, n, 109.4, -1), 0, hd3, 0, 3);
coordsArray = fillCoordsArray(HD3, coordsArray, hd3);
break;
}
case TYR:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom CG = (Atom) newResidue.getAtomNode("CG");
double[] cg = coordsArray[CG.getIndex() - 1];
Atom CD1 = (Atom) newResidue.getAtomNode("CD1");
double[] cd1 = coordsArray[CD1.getIndex() - 1];
Atom CD2 = (Atom) newResidue.getAtomNode("CD2");
double[] cd2 = coordsArray[CD2.getIndex() - 1];
Atom CE1 = (Atom) newResidue.getAtomNode("CE1");
double[] ce1 = coordsArray[CE1.getIndex() - 1];
Atom CE2 = (Atom) newResidue.getAtomNode("CE2");
double[] ce2 = coordsArray[CE2.getIndex() - 1];
Atom CZ = (Atom) newResidue.getAtomNode("CZ");
double[] cz = coordsArray[CZ.getIndex() - 1];
Atom OH = (Atom) newResidue.getAtomNode("OH");
double[] oh = coordsArray[OH.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Atom HD1 = (Atom) newResidue.getAtomNode("HD1");
double[] hd1 = coordsArray[HD1.getIndex() - 1];
Atom HD2 = (Atom) newResidue.getAtomNode("HD2");
double[] hd2 = coordsArray[HD2.getIndex() - 1];
Atom HE1 = (Atom) newResidue.getAtomNode("HE1");
double[] he1 = coordsArray[HE1.getIndex() - 1];
Atom HE2 = (Atom) newResidue.getAtomNode("HE2");
double[] he2 = coordsArray[HE2.getIndex() - 1];
Atom HH = (Atom) newResidue.getAtomNode("HH");
double[] hh = coordsArray[HH.getIndex() - 1];
Bond CB_CA = CB.getBond(CA);
Bond CG_CB = CG.getBond(CB);
Bond CD_CG = CD1.getBond(CG);
Bond CE_CD = CE1.getBond(CD1);
Bond CZ_CE1 = CZ.getBond(CE1);
Bond OH_CZ = OH.getBond(CZ);
Bond HB_CB = HB2.getBond(CB);
Bond HD_CD = HD1.getBond(CD1);
Bond HE_CE = HE1.getBond(CE1);
Bond HH_OH = HH.getBond(OH);
double dCB_CA = CB_CA.bondType.distance;
double dCG_CB = CG_CB.bondType.distance;
double dCD_CG = CD_CG.bondType.distance;
double dCE_CD = CE_CD.bondType.distance;
double dCZ_CE1 = CZ_CE1.bondType.distance;
double dOH_CZ = OH_CZ.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHD_CD = HD_CD.bondType.distance;
double dHE_CE = HE_CE.bondType.distance;
double dHH_OH = HH_OH.bondType.distance;
Angle CG_CB_CA = CG.getAngle(CB, CA);
Angle CD_CG_CB = CD1.getAngle(CG, CB);
Angle CE_CD_CG = CE1.getAngle(CD1, CG);
Angle CZ_CE1_CD1 = CZ.getAngle(CE1, CD1);
Angle OH_CZ_CE2 = OH.getAngle(CZ, CE2);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
Angle HD_CD_CG = HD1.getAngle(CD1, CG);
Angle HE_CE_CD = HE1.getAngle(CE1, CD1);
Angle HH_OH_CZ = HH.getAngle(OH, CZ);
double dCG_CB_CA = CG_CB_CA.angleType.angle[CG_CB_CA.nh];
double dCD_CG_CB = CD_CG_CB.angleType.angle[CD_CG_CB.nh];
double dCE_CD_CG = CE_CD_CG.angleType.angle[CE_CD_CG.nh];
double dCZ_CE1_CD1 = CZ_CE1_CD1.angleType.angle[CZ_CE1_CD1.nh];
double dOH_CZ_CE2 = OH_CZ_CE2.angleType.angle[OH_CZ_CE2.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHD_CD_CG = HD_CD_CG.angleType.angle[HD_CD_CG.nh];
double dHE_CE_CD = HE_CE_CD.angleType.angle[HE_CE_CD.nh];
double dHH_OH_CZ = HH_OH_CZ.angleType.angle[HH_OH_CZ.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, dCB_CA, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// CG
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG_CB, ca, dCG_CB_CA, n, rotScale * 180.0, 0), 0, cg, 0, 3);
coordsArray = fillCoordsArray(CG, coordsArray, cg);
// CD1
System.arraycopy(BondedUtils.determineIntxyz(cg, dCD_CG, cb, dCD_CG_CB, ca, 90.0, 0), 0, cd1, 0, 3);
coordsArray = fillCoordsArray(CD1, coordsArray, cd1);
// CD2
System.arraycopy(BondedUtils.determineIntxyz(cg, dCD_CG, cb, dCD_CG_CB, cd1, 120.0, 1), 0, cd2, 0, 3);
coordsArray = fillCoordsArray(CD2, coordsArray, cd2);
// CE1
System.arraycopy(BondedUtils.determineIntxyz(cd1, dCE_CD, cg, dCE_CD_CG, cb, 180, 0), 0, ce1, 0, 3);
coordsArray = fillCoordsArray(CE1, coordsArray, ce1);
// CE2
System.arraycopy(BondedUtils.determineIntxyz(cd2, dCE_CD, cg, dCE_CD_CG, cb, 180, 0), 0, ce2, 0, 3);
coordsArray = fillCoordsArray(CE2, coordsArray, ce2);
// CZ
System.arraycopy(BondedUtils.determineIntxyz(ce1, dCZ_CE1, cd1, dCZ_CE1_CD1, cg, 0.0, 0), 0, cz, 0, 3);
coordsArray = fillCoordsArray(CZ, coordsArray, cz);
// OH
System.arraycopy(BondedUtils.determineIntxyz(cz, dOH_CZ, ce2, dOH_CZ_CE2, ce1, 120.0, 1), 0, oh, 0, 3);
coordsArray = fillCoordsArray(OH, coordsArray, oh);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
// HD1
System.arraycopy(BondedUtils.determineIntxyz(cd1, dHD_CD, cg, dHD_CD_CG, ce1, 120.0, 1), 0, hd1, 0, 3);
coordsArray = fillCoordsArray(HD1, coordsArray, hd1);
// HD2
System.arraycopy(BondedUtils.determineIntxyz(cd2, dHD_CD, cg, dHD_CD_CG, ce2, 120.0, 1), 0, hd2, 0, 3);
coordsArray = fillCoordsArray(HD2, coordsArray, hd2);
// HE1
System.arraycopy(BondedUtils.determineIntxyz(ce1, dHE_CE, cd1, dHE_CE_CD, cz, 120.0, 1), 0, he1, 0, 3);
coordsArray = fillCoordsArray(HE1, coordsArray, he1);
// HE2
System.arraycopy(BondedUtils.determineIntxyz(ce2, dHE_CE, cd2, dHE_CE_CD, cz, 120.0, 1), 0, he2, 0, 3);
coordsArray = fillCoordsArray(HE2, coordsArray, he2);
// HH
System.arraycopy(BondedUtils.determineIntxyz(oh, dHH_OH, cz, dHH_OH_CZ, ce2, 0.0, 0), 0, hh, 0, 3);
coordsArray = fillCoordsArray(HH, coordsArray, hh);
break;
}
case TYD:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom CG = (Atom) newResidue.getAtomNode("CG");
double[] cg = coordsArray[CG.getIndex() - 1];
Atom CD1 = (Atom) newResidue.getAtomNode("CD1");
double[] cd1 = coordsArray[CD1.getIndex() - 1];
Atom CD2 = (Atom) newResidue.getAtomNode("CD2");
double[] cd2 = coordsArray[CD2.getIndex() - 1];
Atom CE1 = (Atom) newResidue.getAtomNode("CE1");
double[] ce1 = coordsArray[CE1.getIndex() - 1];
Atom CE2 = (Atom) newResidue.getAtomNode("CE2");
double[] ce2 = coordsArray[CE2.getIndex() - 1];
Atom CZ = (Atom) newResidue.getAtomNode("CZ");
double[] cz = coordsArray[CZ.getIndex() - 1];
Atom OH = (Atom) newResidue.getAtomNode("OH");
double[] oh = coordsArray[OH.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Atom HD1 = (Atom) newResidue.getAtomNode("HD1");
double[] hd1 = coordsArray[HD1.getIndex() - 1];
Atom HD2 = (Atom) newResidue.getAtomNode("HD2");
double[] hd2 = coordsArray[HD2.getIndex() - 1];
Atom HE1 = (Atom) newResidue.getAtomNode("HE1");
double[] he1 = coordsArray[HE1.getIndex() - 1];
Atom HE2 = (Atom) newResidue.getAtomNode("HE2");
double[] he2 = coordsArray[HE2.getIndex() - 1];
Bond CG_CB = CG.getBond(CB);
Bond CD_CG = CD1.getBond(CG);
Bond CE_CD = CE1.getBond(CD1);
Bond CZ_CE1 = CZ.getBond(CE1);
Bond OH_CZ = OH.getBond(CZ);
Bond HB_CB = HB2.getBond(CB);
Bond HD_CD = HD1.getBond(CD1);
Bond HE_CE = HE1.getBond(CE1);
double dCG_CB = CG_CB.bondType.distance;
double dCD_CG = CD_CG.bondType.distance;
double dCE_CD = CE_CD.bondType.distance;
double dCZ_CE1 = CZ_CE1.bondType.distance;
double dOH_CZ = OH_CZ.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHD_CD = HD_CD.bondType.distance;
double dHE_CE = HE_CE.bondType.distance;
Angle CG_CB_CA = CG.getAngle(CB, CA);
Angle CD_CG_CB = CD1.getAngle(CG, CB);
Angle CE_CD_CG = CE1.getAngle(CD1, CG);
Angle CZ_CE1_CD1 = CZ.getAngle(CE1, CD1);
Angle OH_CZ_CE2 = OH.getAngle(CZ, CE2);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
Angle HD_CD_CG = HD1.getAngle(CD1, CG);
Angle HE_CE_CD = HE1.getAngle(CE1, CD1);
double dCG_CB_CA = CG_CB_CA.angleType.angle[CG_CB_CA.nh];
double dCD_CG_CB = CD_CG_CB.angleType.angle[CD_CG_CB.nh];
double dCE_CD_CG = CE_CD_CG.angleType.angle[CE_CD_CG.nh];
double dCZ_CE1_CD1 = CZ_CE1_CD1.angleType.angle[CZ_CE1_CD1.nh];
double dOH_CZ_CE2 = OH_CZ_CE2.angleType.angle[OH_CZ_CE2.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHD_CD_CG = HD_CD_CG.angleType.angle[HD_CD_CG.nh];
double dHE_CE_CD = HE_CE_CD.angleType.angle[HE_CE_CD.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// CG
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG_CB, ca, dCG_CB_CA, n, rotScale * 180.0, 0), 0, cg, 0, 3);
coordsArray = fillCoordsArray(CG, coordsArray, cg);
// CD1
System.arraycopy(BondedUtils.determineIntxyz(cg, dCD_CG, cb, dCD_CG_CB, ca, 90.0, 0), 0, cd1, 0, 3);
coordsArray = fillCoordsArray(CD1, coordsArray, cd1);
// CD2
System.arraycopy(BondedUtils.determineIntxyz(cg, dCD_CG, cb, dCD_CG_CB, cd1, 120.0, 1), 0, cd2, 0, 3);
coordsArray = fillCoordsArray(CD2, coordsArray, cd2);
// CE1
System.arraycopy(BondedUtils.determineIntxyz(cd1, dCE_CD, cg, dCE_CD_CG, cb, 180, 0), 0, ce1, 0, 3);
coordsArray = fillCoordsArray(CE1, coordsArray, ce1);
// CE2
System.arraycopy(BondedUtils.determineIntxyz(cd2, dCE_CD, cg, dCE_CD_CG, cb, 180, 0), 0, ce2, 0, 3);
coordsArray = fillCoordsArray(CE2, coordsArray, ce2);
// CZ
System.arraycopy(BondedUtils.determineIntxyz(ce1, dCZ_CE1, cd1, dCZ_CE1_CD1, cg, 0.0, 0), 0, cz, 0, 3);
coordsArray = fillCoordsArray(CZ, coordsArray, cz);
// OH
System.arraycopy(BondedUtils.determineIntxyz(cz, dOH_CZ, ce2, dOH_CZ_CE2, ce1, 120.0, 1), 0, oh, 0, 3);
coordsArray = fillCoordsArray(OH, coordsArray, oh);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
// HD1
System.arraycopy(BondedUtils.determineIntxyz(cd1, dHD_CD, cg, dHD_CD_CG, ce1, 120.0, 1), 0, hd1, 0, 3);
coordsArray = fillCoordsArray(HD1, coordsArray, hd1);
// HD2
System.arraycopy(BondedUtils.determineIntxyz(cd2, dHD_CD, cg, dHD_CD_CG, ce2, 120.0, 1), 0, hd2, 0, 3);
coordsArray = fillCoordsArray(HD2, coordsArray, hd2);
// HE1
System.arraycopy(BondedUtils.determineIntxyz(ce1, dHE_CE, cd1, dHE_CE_CD, cz, 120.0, 1), 0, he1, 0, 3);
coordsArray = fillCoordsArray(HE1, coordsArray, he1);
// HE2
System.arraycopy(BondedUtils.determineIntxyz(ce2, dHE_CE, cd2, dHE_CE_CD, cz, 120.0, 1), 0, he2, 0, 3);
coordsArray = fillCoordsArray(HE2, coordsArray, he2);
break;
}
case TRP:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom CG = (Atom) newResidue.getAtomNode("CG");
double[] cg = coordsArray[CG.getIndex() - 1];
Atom CD1 = (Atom) newResidue.getAtomNode("CD1");
double[] cd1 = coordsArray[CD1.getIndex() - 1];
Atom CD2 = (Atom) newResidue.getAtomNode("CD2");
double[] cd2 = coordsArray[CD2.getIndex() - 1];
Atom NE1 = (Atom) newResidue.getAtomNode("NE1");
double[] ne1 = coordsArray[NE1.getIndex() - 1];
Atom CE2 = (Atom) newResidue.getAtomNode("CE2");
double[] ce2 = coordsArray[CE2.getIndex() - 1];
Atom CE3 = (Atom) newResidue.getAtomNode("CE3");
double[] ce3 = coordsArray[CE3.getIndex() - 1];
Atom CZ2 = (Atom) newResidue.getAtomNode("CZ2");
double[] cz2 = coordsArray[CZ2.getIndex() - 1];
Atom CZ3 = (Atom) newResidue.getAtomNode("CZ3");
double[] cz3 = coordsArray[CZ3.getIndex() - 1];
Atom CH2 = (Atom) newResidue.getAtomNode("CH2");
double[] ch2 = coordsArray[CH2.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Atom HD1 = (Atom) newResidue.getAtomNode("HD1");
double[] hd1 = coordsArray[HD1.getIndex() - 1];
Atom HE1 = (Atom) newResidue.getAtomNode("HE1");
double[] he1 = coordsArray[HE1.getIndex() - 1];
Atom HE3 = (Atom) newResidue.getAtomNode("HE3");
double[] he3 = coordsArray[HE3.getIndex() - 1];
Atom HZ2 = (Atom) newResidue.getAtomNode("HZ2");
double[] hz2 = coordsArray[HZ2.getIndex() - 1];
Atom HZ3 = (Atom) newResidue.getAtomNode("HZ3");
double[] hz3 = coordsArray[HZ3.getIndex() - 1];
Atom HH2 = (Atom) newResidue.getAtomNode("HH2");
double[] hh2 = coordsArray[HH2.getIndex() - 1];
Bond CG_CB = CG.getBond(CB);
Bond CD1_CG = CD1.getBond(CG);
Bond CD2_CG = CD2.getBond(CG);
Bond NE1_CD1 = NE1.getBond(CD1);
Bond CE2_NE1 = CE2.getBond(NE1);
Bond CE3_CD2 = CE3.getBond(CD2);
Bond CZ2_CE2 = CZ2.getBond(CE2);
Bond CZ3_CE3 = CZ3.getBond(CE3);
Bond CH2_CZ2 = CH2.getBond(CZ2);
Bond HB_CB = HB2.getBond(CB);
Bond HD1_CD1 = HD1.getBond(CD1);
Bond HE1_NE1 = HE1.getBond(NE1);
Bond HE3_CE3 = HE3.getBond(CE3);
Bond HZ2_CZ2 = HZ2.getBond(CZ2);
Bond HZ3_CZ3 = HZ3.getBond(CZ3);
Bond HH2_CH2 = HH2.getBond(CH2);
double dCG_CB = CG_CB.bondType.distance;
double dCD1_CG = CD1_CG.bondType.distance;
double dCD2_CG = CD2_CG.bondType.distance;
double dNE1_CD1 = NE1_CD1.bondType.distance;
double dCE2_NE1 = CE2_NE1.bondType.distance;
double dCE3_CD2 = CE3_CD2.bondType.distance;
double dCZ2_CE2 = CZ2_CE2.bondType.distance;
double dCZ3_CE3 = CZ3_CE3.bondType.distance;
double dCH2_CZ2 = CH2_CZ2.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHD1_CD1 = HD1_CD1.bondType.distance;
double dHE1_NE1 = HE1_NE1.bondType.distance;
double dHE3_CE3 = HE3_CE3.bondType.distance;
double dHZ2_CZ2 = HZ2_CZ2.bondType.distance;
double dHZ3_CZ3 = HZ3_CZ3.bondType.distance;
double dHH2_CH2 = HH2_CH2.bondType.distance;
Angle CG_CB_CA = CG.getAngle(CB, CA);
Angle CD1_CG_CB = CD1.getAngle(CG, CB);
Angle CD2_CG_CB = CD2.getAngle(CG, CB);
Angle NE1_CD1_CG = NE1.getAngle(CD1, CG);
Angle CE2_NE1_CD1 = CE2.getAngle(NE1, CD1);
Angle CE3_CD2_CE2 = CE3.getAngle(CD2, CE2);
Angle CZ2_CE2_CD2 = CZ2.getAngle(CE2, CD2);
Angle CZ3_CE3_CD2 = CZ3.getAngle(CE3, CD2);
Angle CH2_CZ2_CE2 = CH2.getAngle(CZ2, CE2);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
Angle HD1_CD1_CG = HD1.getAngle(CD1, CG);
Angle HE1_NE1_CD1 = HE1.getAngle(NE1, CD1);
Angle HE3_CE3_CD2 = HE3.getAngle(CE3, CD2);
Angle HZ2_CZ2_CE2 = HZ2.getAngle(CZ2, CE2);
Angle HZ3_CZ3_CE3 = HZ3.getAngle(CZ3, CH2);
Angle HH2_CH2_CZ2 = HH2.getAngle(CH2, CZ3);
double dCG_CB_CA = CG_CB_CA.angleType.angle[CG_CB_CA.nh];
double dCD1_CG_CB = CD1_CG_CB.angleType.angle[CD1_CG_CB.nh];
double dCD2_CG_CB = CD2_CG_CB.angleType.angle[CD2_CG_CB.nh];
double dNE1_CD1_CG = NE1_CD1_CG.angleType.angle[NE1_CD1_CG.nh];
double dCE2_NE1_CD1 = CE2_NE1_CD1.angleType.angle[CE2_NE1_CD1.nh];
double dCE3_CD2_CE2 = CE3_CD2_CE2.angleType.angle[CE3_CD2_CE2.nh];
double dCZ2_CE2_CD2 = CZ2_CE2_CD2.angleType.angle[CZ2_CE2_CD2.nh];
double dCZ3_CE3_CD2 = CZ3_CE3_CD2.angleType.angle[CZ3_CE3_CD2.nh];
double dCH2_CZ2_CE2 = CH2_CZ2_CE2.angleType.angle[CH2_CZ2_CE2.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHD1_CD1_CG = HD1_CD1_CG.angleType.angle[HD1_CD1_CG.nh];
double dHE1_NE1_CD1 = HE1_NE1_CD1.angleType.angle[HE1_NE1_CD1.nh];
double dHE3_CE3_CD2 = HE3_CE3_CD2.angleType.angle[HE3_CE3_CD2.nh];
double dHZ2_CZ2_CE2 = HZ2_CZ2_CE2.angleType.angle[HZ2_CZ2_CE2.nh];
double dHZ3_CZ3_CE3 = HZ3_CZ3_CE3.angleType.angle[HZ3_CZ3_CE3.nh];
double dHH2_CH2_CZ2 = HH2_CH2_CZ2.angleType.angle[HH2_CH2_CZ2.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// CG
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG_CB, ca, dCG_CB_CA, n, rotScale * 180.0, 0), 0, cg, 0, 3);
coordsArray = fillCoordsArray(CG, coordsArray, cg);
// CD1
System.arraycopy(BondedUtils.determineIntxyz(cg, dCD1_CG, cb, dCD1_CG_CB, ca, -90.0, 0), 0, cd1, 0, 3);
coordsArray = fillCoordsArray(CD1, coordsArray, cd1);
// CD2
System.arraycopy(BondedUtils.determineIntxyz(cg, dCD2_CG, cb, dCD2_CG_CB, cd1, 108.0, 1), 0, cd2, 0, 3);
coordsArray = fillCoordsArray(CD2, coordsArray, cd2);
// NE1
System.arraycopy(BondedUtils.determineIntxyz(cd1, dNE1_CD1, cg, dNE1_CD1_CG, cd2, 0.0, 0), 0, ne1, 0, 3);
coordsArray = fillCoordsArray(NE1, coordsArray, ne1);
// CE2
System.arraycopy(BondedUtils.determineIntxyz(ne1, dCE2_NE1, cd1, dCE2_NE1_CD1, cg, 0.0, 0), 0, ce2, 0, 3);
coordsArray = fillCoordsArray(CE2, coordsArray, ce2);
// CE3
System.arraycopy(BondedUtils.determineIntxyz(cd2, dCE3_CD2, ce2, dCE3_CD2_CE2, ne1, 180.0, 0), 0, ce3, 0, 3);
coordsArray = fillCoordsArray(CE3, coordsArray, ce3);
// CZ2
System.arraycopy(BondedUtils.determineIntxyz(ce2, dCZ2_CE2, cd2, dCZ2_CE2_CD2, ce3, 0.0, 0), 0, cz2, 0, 3);
coordsArray = fillCoordsArray(CZ2, coordsArray, cz2);
// CZ3
System.arraycopy(BondedUtils.determineIntxyz(ce3, dCZ3_CE3, cd2, dCZ3_CE3_CD2, ce2, 0.0, 0), 0, cz3, 0, 3);
coordsArray = fillCoordsArray(CZ3, coordsArray, cz3);
// CH2
System.arraycopy(BondedUtils.determineIntxyz(cz2, dCH2_CZ2, ce2, dCH2_CZ2_CE2, cd2, 0.0, 0), 0, ch2, 0, 3);
coordsArray = fillCoordsArray(CH2, coordsArray, ch2);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
// HD1
System.arraycopy(BondedUtils.determineIntxyz(cd1, dHD1_CD1, cg, dHD1_CD1_CG, ne1, 126.0, 1), 0, hd1, 0, 3);
coordsArray = fillCoordsArray(HD1, coordsArray, hd1);
// HE1
System.arraycopy(BondedUtils.determineIntxyz(ne1, dHE1_NE1, cd1, dHE1_NE1_CD1, ce2, 126.0, 1), 0, he1, 0, 3);
coordsArray = fillCoordsArray(HE1, coordsArray, he1);
// HE3
System.arraycopy(BondedUtils.determineIntxyz(ce3, dHE3_CE3, cd2, dHE3_CE3_CD2, cz3, 120.0, 1), 0, he3, 0, 3);
coordsArray = fillCoordsArray(HE3, coordsArray, he3);
// HZ2
System.arraycopy(BondedUtils.determineIntxyz(cz2, dHZ2_CZ2, ce2, dHZ2_CZ2_CE2, ch2, 120.0, 1), 0, hz2, 0, 3);
coordsArray = fillCoordsArray(HZ2, coordsArray, hz2);
// HZ3
System.arraycopy(BondedUtils.determineIntxyz(cz3, dHZ3_CZ3, ce3, dHZ3_CZ3_CE3, ch2, 120.0, 1), 0, hz3, 0, 3);
coordsArray = fillCoordsArray(HZ3, coordsArray, hz3);
// HH2
System.arraycopy(BondedUtils.determineIntxyz(ch2, dHH2_CH2, cz2, dHH2_CH2_CZ2, cz3, 120.0, 1), 0, hh2, 0, 3);
coordsArray = fillCoordsArray(HH2, coordsArray, hh2);
break;
}
case HIS:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom CG = (Atom) newResidue.getAtomNode("CG");
double[] cg = coordsArray[CG.getIndex() - 1];
Atom ND1 = (Atom) newResidue.getAtomNode("ND1");
double[] nd1 = coordsArray[ND1.getIndex() - 1];
Atom CD2 = (Atom) newResidue.getAtomNode("CD2");
double[] cd2 = coordsArray[CD2.getIndex() - 1];
Atom CE1 = (Atom) newResidue.getAtomNode("CE1");
double[] ce1 = coordsArray[CE1.getIndex() - 1];
Atom NE2 = (Atom) newResidue.getAtomNode("NE2");
double[] ne2 = coordsArray[NE2.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Atom HD1 = (Atom) newResidue.getAtomNode("HD1");
double[] hd1 = coordsArray[HD1.getIndex() - 1];
Atom HD2 = (Atom) newResidue.getAtomNode("HD2");
double[] hd2 = coordsArray[HD2.getIndex() - 1];
Atom HE1 = (Atom) newResidue.getAtomNode("HE1");
double[] he1 = coordsArray[HE1.getIndex() - 1];
Atom HE2 = (Atom) newResidue.getAtomNode("HE2");
double[] he2 = coordsArray[HE2.getIndex() - 1];
Bond CG_CB = CG.getBond(CB);
Bond ND1_CG = ND1.getBond(CG);
Bond CD2_CG = CD2.getBond(CG);
Bond CE1_ND1 = CE1.getBond(ND1);
Bond NE2_CD2 = NE2.getBond(CD2);
Bond HB_CB = HB2.getBond(CB);
Bond HD1_ND1 = HD1.getBond(ND1);
Bond HD2_CD2 = HD2.getBond(CD2);
Bond HE1_CE1 = HE1.getBond(CE1);
Bond HE2_NE2 = HE2.getBond(NE2);
double dCG_CB = CG_CB.bondType.distance;
double dND1_CG = ND1_CG.bondType.distance;
double dCD2_CG = CD2_CG.bondType.distance;
double dCE1_ND1 = CE1_ND1.bondType.distance;
double dNE2_CD2 = NE2_CD2.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHD1_ND1 = HD1_ND1.bondType.distance;
double dHD2_CD2 = HD2_CD2.bondType.distance;
double dHE1_CE1 = HE1_CE1.bondType.distance;
double dHE2_NE2 = HE2_NE2.bondType.distance;
Angle CG_CB_CA = CG.getAngle(CB, CA);
Angle ND1_CG_CB = ND1.getAngle(CG, CB);
Angle CD2_CG_CB = CD2.getAngle(CG, CB);
Angle CE1_ND1_CG = CE1.getAngle(ND1, CG);
Angle NE2_CD2_CG = NE2.getAngle(CD2, CG);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
Angle HD1_ND1_CG = HD1.getAngle(ND1, CG);
Angle HD2_CD2_CG = HD2.getAngle(CD2, CG);
Angle HE1_CE1_ND1 = HE1.getAngle(CE1, ND1);
Angle HE2_NE2_CD2 = HE2.getAngle(NE2, CD2);
double dCG_CB_CA = CG_CB_CA.angleType.angle[CG_CB_CA.nh];
double dND1_CG_CB = ND1_CG_CB.angleType.angle[ND1_CG_CB.nh];
double dCD2_CG_CB = CD2_CG_CB.angleType.angle[CD2_CG_CB.nh];
double dCE1_ND1_CG = CE1_ND1_CG.angleType.angle[CE1_ND1_CG.nh];
double dNE2_CD2_CG = NE2_CD2_CG.angleType.angle[NE2_CD2_CG.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHD1_ND1_CG = HD1_ND1_CG.angleType.angle[HD1_ND1_CG.nh];
double dHD2_CD2_CG = HD2_CD2_CG.angleType.angle[HD2_CD2_CG.nh];
double dHE1_CE1_ND1 = HE1_CE1_ND1.angleType.angle[HE1_CE1_ND1.nh];
double dHE2_NE2_CD2 = HE2_NE2_CD2.angleType.angle[HE2_NE2_CD2.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// CG
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG_CB, ca, dCG_CB_CA, n, rotScale * 180.0, 0), 0, cg, 0, 3);
coordsArray = fillCoordsArray(CG, coordsArray, cg);
// ND1
System.arraycopy(BondedUtils.determineIntxyz(cg, dND1_CG, cb, dND1_CG_CB, ca, 180.0, 0), 0, nd1, 0, 3);
coordsArray = fillCoordsArray(ND1, coordsArray, nd1);
// CD2
System.arraycopy(BondedUtils.determineIntxyz(cg, dCD2_CG, cb, dCD2_CG_CB, nd1, 108.0, 1), 0, cd2, 0, 3);
coordsArray = fillCoordsArray(CD2, coordsArray, cd2);
// CE1
System.arraycopy(BondedUtils.determineIntxyz(nd1, dCE1_ND1, cg, dCE1_ND1_CG, cd2, 0.0, 0), 0, ce1, 0, 3);
coordsArray = fillCoordsArray(CE1, coordsArray, ce1);
// NE2
System.arraycopy(BondedUtils.determineIntxyz(cd2, dNE2_CD2, cg, dNE2_CD2_CG, nd1, 0.0, 0), 0, ne2, 0, 3);
coordsArray = fillCoordsArray(NE2, coordsArray, ne2);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
// HD1
System.arraycopy(BondedUtils.determineIntxyz(nd1, dHD1_ND1, cg, dHD1_ND1_CG, cb, 0.0, 0), 0, hd1, 0, 3);
coordsArray = fillCoordsArray(HD1, coordsArray, hd1);
// HD2
System.arraycopy(BondedUtils.determineIntxyz(cd2, dHD2_CD2, cg, dHD2_CD2_CG, ne2, 126.0, 1), 0, hd2, 0, 3);
coordsArray = fillCoordsArray(HD2, coordsArray, hd2);
// HE1
System.arraycopy(BondedUtils.determineIntxyz(ce1, dHE1_CE1, nd1, dHE1_CE1_ND1, ne2, 126.0, 1), 0, he1, 0, 3);
coordsArray = fillCoordsArray(HE1, coordsArray, he1);
// HE2
System.arraycopy(BondedUtils.determineIntxyz(ne2, dHE2_NE2, cd2, dHE2_NE2_CD2, ce1, 126.0, 1), 0, he2, 0, 3);
coordsArray = fillCoordsArray(HE2, coordsArray, he2);
break;
}
case HID:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom CG = (Atom) newResidue.getAtomNode("CG");
double[] cg = coordsArray[CG.getIndex() - 1];
Atom ND1 = (Atom) newResidue.getAtomNode("ND1");
double[] nd1 = coordsArray[ND1.getIndex() - 1];
Atom CD2 = (Atom) newResidue.getAtomNode("CD2");
double[] cd2 = coordsArray[CD2.getIndex() - 1];
Atom CE1 = (Atom) newResidue.getAtomNode("CE1");
double[] ce1 = coordsArray[CE1.getIndex() - 1];
Atom NE2 = (Atom) newResidue.getAtomNode("NE2");
double[] ne2 = coordsArray[NE2.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Atom HD1 = (Atom) newResidue.getAtomNode("HD1");
double[] hd1 = coordsArray[HD1.getIndex() - 1];
Atom HD2 = (Atom) newResidue.getAtomNode("HD2");
double[] hd2 = coordsArray[HD2.getIndex() - 1];
Atom HE1 = (Atom) newResidue.getAtomNode("HE1");
double[] he1 = coordsArray[HE1.getIndex() - 1];
Bond CG_CB = CG.getBond(CB);
Bond ND1_CG = ND1.getBond(CG);
Bond CD2_CG = CD2.getBond(CG);
Bond CE1_ND1 = CE1.getBond(ND1);
Bond NE2_CD2 = NE2.getBond(CD2);
Bond HB_CB = HB2.getBond(CB);
Bond HD1_ND1 = HD1.getBond(ND1);
Bond HD2_CD2 = HD2.getBond(CD2);
Bond HE1_CE1 = HE1.getBond(CE1);
double dCG_CB = CG_CB.bondType.distance;
double dND1_CG = ND1_CG.bondType.distance;
double dCD2_CG = CD2_CG.bondType.distance;
double dCE1_ND1 = CE1_ND1.bondType.distance;
double dNE2_CD2 = NE2_CD2.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHD1_ND1 = HD1_ND1.bondType.distance;
double dHD2_CD2 = HD2_CD2.bondType.distance;
double dHE1_CE1 = HE1_CE1.bondType.distance;
Angle CG_CB_CA = CG.getAngle(CB, CA);
Angle ND1_CG_CB = ND1.getAngle(CG, CB);
Angle CD2_CG_CB = CD2.getAngle(CG, CB);
Angle CE1_ND1_CG = CE1.getAngle(ND1, CG);
Angle NE2_CD2_CG = NE2.getAngle(CD2, CG);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
Angle HD1_ND1_CG = HD1.getAngle(ND1, CG);
Angle HD2_CD2_CG = HD2.getAngle(CD2, CG);
Angle HE1_CE1_ND1 = HE1.getAngle(CE1, ND1);
double dCG_CB_CA = CG_CB_CA.angleType.angle[CG_CB_CA.nh];
double dND1_CG_CB = ND1_CG_CB.angleType.angle[ND1_CG_CB.nh];
double dCD2_CG_CB = CD2_CG_CB.angleType.angle[CD2_CG_CB.nh];
double dCE1_ND1_CG = CE1_ND1_CG.angleType.angle[CE1_ND1_CG.nh];
double dNE2_CD2_CG = NE2_CD2_CG.angleType.angle[NE2_CD2_CG.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHD1_ND1_CG = HD1_ND1_CG.angleType.angle[HD1_ND1_CG.nh];
double dHD2_CD2_CG = HD2_CD2_CG.angleType.angle[HD2_CD2_CG.nh];
double dHE1_CE1_ND1 = HE1_CE1_ND1.angleType.angle[HE1_CE1_ND1.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// CG
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG_CB, ca, dCG_CB_CA, n, rotScale * 180.0, 0), 0, cg, 0, 3);
coordsArray = fillCoordsArray(CG, coordsArray, cg);
// ND1
System.arraycopy(BondedUtils.determineIntxyz(cg, dND1_CG, cb, dND1_CG_CB, ca, 180.0, 0), 0, nd1, 0, 3);
coordsArray = fillCoordsArray(ND1, coordsArray, nd1);
// CD2
System.arraycopy(BondedUtils.determineIntxyz(cg, dCD2_CG, cb, dCD2_CG_CB, nd1, 108.0, 1), 0, cd2, 0, 3);
coordsArray = fillCoordsArray(CD2, coordsArray, cd2);
// CE1
System.arraycopy(BondedUtils.determineIntxyz(nd1, dCE1_ND1, cg, dCE1_ND1_CG, cd2, 0.0, 0), 0, ce1, 0, 3);
coordsArray = fillCoordsArray(CE1, coordsArray, ce1);
// NE2
System.arraycopy(BondedUtils.determineIntxyz(cd2, dNE2_CD2, cg, dNE2_CD2_CG, nd1, 0.0, 0), 0, ne2, 0, 3);
coordsArray = fillCoordsArray(NE2, coordsArray, ne2);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
// HD1
System.arraycopy(BondedUtils.determineIntxyz(nd1, dHD1_ND1, cg, dHD1_ND1_CG, cb, 0.0, 0), 0, hd1, 0, 3);
coordsArray = fillCoordsArray(HD1, coordsArray, hd1);
// HD2
System.arraycopy(BondedUtils.determineIntxyz(cd2, dHD2_CD2, cg, dHD2_CD2_CG, ne2, 126.0, 1), 0, hd2, 0, 3);
coordsArray = fillCoordsArray(HD2, coordsArray, hd2);
// HE1
System.arraycopy(BondedUtils.determineIntxyz(ce1, dHE1_CE1, nd1, dHE1_CE1_ND1, ne2, 126.0, 1), 0, he1, 0, 3);
coordsArray = fillCoordsArray(HE1, coordsArray, he1);
break;
}
case HIE:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom CG = (Atom) newResidue.getAtomNode("CG");
double[] cg = coordsArray[CG.getIndex() - 1];
Atom ND1 = (Atom) newResidue.getAtomNode("ND1");
double[] nd1 = coordsArray[ND1.getIndex() - 1];
Atom CD2 = (Atom) newResidue.getAtomNode("CD2");
double[] cd2 = coordsArray[CD2.getIndex() - 1];
Atom CE1 = (Atom) newResidue.getAtomNode("CE1");
double[] ce1 = coordsArray[CE1.getIndex() - 1];
Atom NE2 = (Atom) newResidue.getAtomNode("NE2");
double[] ne2 = coordsArray[NE2.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Atom HD2 = (Atom) newResidue.getAtomNode("HD2");
double[] hd2 = coordsArray[HD2.getIndex() - 1];
Atom HE1 = (Atom) newResidue.getAtomNode("HE1");
double[] he1 = coordsArray[HE1.getIndex() - 1];
Atom HE2 = (Atom) newResidue.getAtomNode("HE2");
double[] he2 = coordsArray[HE2.getIndex() - 1];
Bond CG_CB = CG.getBond(CB);
Bond ND1_CG = ND1.getBond(CG);
Bond CD2_CG = CD2.getBond(CG);
Bond CE1_ND1 = CE1.getBond(ND1);
Bond NE2_CD2 = NE2.getBond(CD2);
Bond HB_CB = HB2.getBond(CB);
Bond HD2_CD2 = HD2.getBond(CD2);
Bond HE1_CE1 = HE1.getBond(CE1);
Bond HE2_NE2 = HE2.getBond(NE2);
double dCG_CB = CG_CB.bondType.distance;
double dND1_CG = ND1_CG.bondType.distance;
double dCD2_CG = CD2_CG.bondType.distance;
double dCE1_ND1 = CE1_ND1.bondType.distance;
double dNE2_CD2 = NE2_CD2.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHD2_CD2 = HD2_CD2.bondType.distance;
double dHE1_CE1 = HE1_CE1.bondType.distance;
double dHE2_NE2 = HE2_NE2.bondType.distance;
Angle CG_CB_CA = CG.getAngle(CB, CA);
Angle ND1_CG_CB = ND1.getAngle(CG, CB);
Angle CD2_CG_CB = CD2.getAngle(CG, CB);
Angle CE1_ND1_CG = CE1.getAngle(ND1, CG);
Angle NE2_CD2_CG = NE2.getAngle(CD2, CG);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
Angle HD2_CD2_CG = HD2.getAngle(CD2, CG);
Angle HE1_CE1_ND1 = HE1.getAngle(CE1, ND1);
Angle HE2_NE2_CD2 = HE2.getAngle(NE2, CD2);
double dCG_CB_CA = CG_CB_CA.angleType.angle[CG_CB_CA.nh];
double dND1_CG_CB = ND1_CG_CB.angleType.angle[ND1_CG_CB.nh];
double dCD2_CG_CB = CD2_CG_CB.angleType.angle[CD2_CG_CB.nh];
double dCE1_ND1_CG = CE1_ND1_CG.angleType.angle[CE1_ND1_CG.nh];
double dNE2_CD2_CG = NE2_CD2_CG.angleType.angle[NE2_CD2_CG.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHD2_CD2_CG = HD2_CD2_CG.angleType.angle[HD2_CD2_CG.nh];
double dHE1_CE1_ND1 = HE1_CE1_ND1.angleType.angle[HE1_CE1_ND1.nh];
double dHE2_NE2_CD2 = HE2_NE2_CD2.angleType.angle[HE2_NE2_CD2.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// CG
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG_CB, ca, dCG_CB_CA, n, rotScale * 180.0, 0), 0, cg, 0, 3);
coordsArray = fillCoordsArray(CG, coordsArray, cg);
// ND1
System.arraycopy(BondedUtils.determineIntxyz(cg, dND1_CG, cb, dND1_CG_CB, ca, 180.0, 0), 0, nd1, 0, 3);
coordsArray = fillCoordsArray(ND1, coordsArray, nd1);
// CD2
System.arraycopy(BondedUtils.determineIntxyz(cg, dCD2_CG, cb, dCD2_CG_CB, nd1, 108.0, 1), 0, cd2, 0, 3);
coordsArray = fillCoordsArray(CD2, coordsArray, cd2);
// CE1
System.arraycopy(BondedUtils.determineIntxyz(nd1, dCE1_ND1, cg, dCE1_ND1_CG, cd2, 0.0, 0), 0, ce1, 0, 3);
coordsArray = fillCoordsArray(CE1, coordsArray, ce1);
// NE2
System.arraycopy(BondedUtils.determineIntxyz(cd2, dNE2_CD2, cg, dNE2_CD2_CG, nd1, 0.0, 0), 0, ne2, 0, 3);
coordsArray = fillCoordsArray(NE2, coordsArray, ne2);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
// HD2
System.arraycopy(BondedUtils.determineIntxyz(cd2, dHD2_CD2, cg, dHD2_CD2_CG, ne2, 126.0, 1), 0, hd2, 0, 3);
coordsArray = fillCoordsArray(HD2, coordsArray, hd2);
// HE1
System.arraycopy(BondedUtils.determineIntxyz(ce1, dHE1_CE1, nd1, dHE1_CE1_ND1, ne2, 126.0, 1), 0, he1, 0, 3);
coordsArray = fillCoordsArray(HE1, coordsArray, he1);
// HE2
System.arraycopy(BondedUtils.determineIntxyz(ne2, dHE2_NE2, cd2, dHE2_NE2_CD2, ce1, 126.0, 1), 0, he2, 0, 3);
coordsArray = fillCoordsArray(HE2, coordsArray, he2);
break;
}
case ASP:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom CG = (Atom) newResidue.getAtomNode("CG");
double[] cg = coordsArray[CG.getIndex() - 1];
Atom OD1 = (Atom) newResidue.getAtomNode("OD1");
double[] od1 = coordsArray[OD1.getIndex() - 1];
Atom OD2 = (Atom) newResidue.getAtomNode("OD2");
double[] od2 = coordsArray[OD2.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Bond CG_CB = CG.getBond(CB);
Bond OD1_CG = OD1.getBond(CG);
Bond OD2_CG = OD2.getBond(CG);
Bond HB_CB = HB2.getBond(CB);
double dCG_CB = CG_CB.bondType.distance;
double dOD1_CG = OD1_CG.bondType.distance;
double dOD2_CG = OD2_CG.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
Angle CG_CB_CA = CG.getAngle(CB, CA);
Angle OD1_CG_CB = OD1.getAngle(CG, CB);
Angle OD2_CG_CB = OD2.getAngle(CG, CB);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
double dCG_CB_CA = CG_CB_CA.angleType.angle[CG_CB_CA.nh];
double dOD1_CG_CB = OD1_CG_CB.angleType.angle[OD1_CG_CB.nh];
double dOD2_CG_CB = OD2_CG_CB.angleType.angle[OD2_CG_CB.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// CG
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG_CB, ca, dCG_CB_CA, n, rotScale * 180.0, 0), 0, cg, 0, 3);
coordsArray = fillCoordsArray(CG, coordsArray, cg);
// OD1
System.arraycopy(BondedUtils.determineIntxyz(cg, dOD1_CG, cb, dOD1_CG_CB, ca, 0.0, 0), 0, od1, 0, 3);
coordsArray = fillCoordsArray(OD1, coordsArray, od1);
// OD2
System.arraycopy(BondedUtils.determineIntxyz(cg, dOD2_CG, cb, dOD2_CG_CB, od1, 126.0, 1), 0, od2, 0, 3);
coordsArray = fillCoordsArray(OD2, coordsArray, od2);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 107.9, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 107.9, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
break;
}
case ASH:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom CG = (Atom) newResidue.getAtomNode("CG");
double[] cg = coordsArray[CG.getIndex() - 1];
Atom OD1 = (Atom) newResidue.getAtomNode("OD1");
double[] od1 = coordsArray[OD1.getIndex() - 1];
Atom OD2 = (Atom) newResidue.getAtomNode("OD2");
double[] od2 = coordsArray[OD2.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Atom HD2 = (Atom) newResidue.getAtomNode("HD2");
double[] hd2 = coordsArray[HD2.getIndex() - 1];
Bond CG_CB = CG.getBond(CB);
Bond OD1_CG = OD1.getBond(CG);
Bond OD2_CG = OD2.getBond(CG);
Bond HB_CB = HB2.getBond(CB);
Bond HD2_OD2 = HD2.getBond(OD2);
double dCG_CB = CG_CB.bondType.distance;
double dOD1_CG = OD1_CG.bondType.distance;
double dOD2_CG = OD2_CG.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHD2_OD2 = HD2_OD2.bondType.distance;
Angle CG_CB_CA = CG.getAngle(CB, CA);
Angle OD1_CG_CB = OD1.getAngle(CG, CB);
Angle OD2_CG_CB = OD2.getAngle(CG, CB);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
Angle HD2_OD2_CG = HD2.getAngle(OD2, CG);
double dCG_CB_CA = CG_CB_CA.angleType.angle[CG_CB_CA.nh];
double dOD1_CG_CB = OD1_CG_CB.angleType.angle[OD1_CG_CB.nh];
double dOD2_CG_CB = OD2_CG_CB.angleType.angle[OD2_CG_CB.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHD2_OD2_CG = HD2_OD2_CG.angleType.angle[HD2_OD2_CG.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// CG
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG_CB, ca, dCG_CB_CA, n, rotScale * 180.0, 0), 0, cg, 0, 3);
coordsArray = fillCoordsArray(CG, coordsArray, cg);
// OD1
System.arraycopy(BondedUtils.determineIntxyz(cg, dOD1_CG, cb, dOD1_CG_CB, ca, 0.0, 0), 0, od1, 0, 3);
coordsArray = fillCoordsArray(OD1, coordsArray, od1);
// OD2
System.arraycopy(BondedUtils.determineIntxyz(cg, dOD2_CG, cb, dOD2_CG_CB, od1, 126.0, 1), 0, od2, 0, 3);
coordsArray = fillCoordsArray(OD2, coordsArray, od2);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 107.9, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 107.9, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
// HD2
System.arraycopy(BondedUtils.determineIntxyz(od2, dHD2_OD2, cg, dHD2_OD2_CG, od1, 0.0, 0), 0, hd2, 0, 3);
coordsArray = fillCoordsArray(HD2, coordsArray, hd2);
break;
}
case ASN:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom CG = (Atom) newResidue.getAtomNode("CG");
double[] cg = coordsArray[CG.getIndex() - 1];
Atom OD1 = (Atom) newResidue.getAtomNode("OD1");
double[] od1 = coordsArray[OD1.getIndex() - 1];
Atom ND2 = (Atom) newResidue.getAtomNode("ND2");
double[] nd2 = coordsArray[ND2.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Atom HD21 = (Atom) newResidue.getAtomNode("HD21");
double[] hd21 = coordsArray[HD21.getIndex() - 1];
Atom HD22 = (Atom) newResidue.getAtomNode("HD22");
double[] hd22 = coordsArray[HD22.getIndex() - 1];
Bond CG_CB = CG.getBond(CB);
Bond OD1_CG = OD1.getBond(CG);
Bond ND2_CG = ND2.getBond(CG);
Bond HB_CB = HB2.getBond(CB);
Bond HD2_ND2 = HD21.getBond(ND2);
double dCG_CB = CG_CB.bondType.distance;
double dOD1_CG = OD1_CG.bondType.distance;
double dND2_CG = ND2_CG.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHD2_ND2 = HD2_ND2.bondType.distance;
Angle CG_CB_CA = CG.getAngle(CB, CA);
Angle OD1_CG_CB = OD1.getAngle(CG, CB);
Angle ND2_CG_CB = ND2.getAngle(CG, CB);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
Angle HD2_ND2_CG = HD21.getAngle(ND2, CG);
double dCG_CB_CA = CG_CB_CA.angleType.angle[CG_CB_CA.nh];
double dOD1_CG_CB = OD1_CG_CB.angleType.angle[OD1_CG_CB.nh];
double dND2_CG_CB = ND2_CG_CB.angleType.angle[ND2_CG_CB.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHD2_ND2_CG = HD2_ND2_CG.angleType.angle[HD2_ND2_CG.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// CG
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG_CB, ca, dCG_CB_CA, n, rotScale * 180.0, 0), 0, cg, 0, 3);
coordsArray = fillCoordsArray(CG, coordsArray, cg);
// OD1
System.arraycopy(BondedUtils.determineIntxyz(cg, dOD1_CG, cb, dOD1_CG_CB, ca, 0.0, 0), 0, od1, 0, 3);
coordsArray = fillCoordsArray(OD1, coordsArray, od1);
// ND2
System.arraycopy(BondedUtils.determineIntxyz(cg, dND2_CG, cb, dND2_CG_CB, od1, 124.0, 1), 0, nd2, 0, 3);
coordsArray = fillCoordsArray(ND2, coordsArray, nd2);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 107.9, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 107.9, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
// HD21
System.arraycopy(BondedUtils.determineIntxyz(nd2, dHD2_ND2, cg, dHD2_ND2_CG, cb, 0.0, 0), 0, hd21, 0, 3);
coordsArray = fillCoordsArray(HD21, coordsArray, hd21);
// HD22
System.arraycopy(BondedUtils.determineIntxyz(nd2, dHD2_ND2, cg, dHD2_ND2_CG, hd21, 120.0, 1), 0, hd22, 0, 3);
coordsArray = fillCoordsArray(HD22, coordsArray, hd22);
break;
}
case GLU:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom CG = (Atom) newResidue.getAtomNode("CG");
double[] cg = coordsArray[CG.getIndex() - 1];
Atom CD = (Atom) newResidue.getAtomNode("CD");
double[] cd = coordsArray[CD.getIndex() - 1];
Atom OE1 = (Atom) newResidue.getAtomNode("OE1");
double[] oe1 = coordsArray[OE1.getIndex() - 1];
Atom OE2 = (Atom) newResidue.getAtomNode("OE2");
double[] oe2 = coordsArray[OE2.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Atom HG2 = (Atom) newResidue.getAtomNode("HG2");
double[] hg2 = coordsArray[HG2.getIndex() - 1];
Atom HG3 = (Atom) newResidue.getAtomNode("HG3");
double[] hg3 = coordsArray[HG3.getIndex() - 1];
Bond CG_CB = CG.getBond(CB);
Bond CD_CG = CD.getBond(CG);
Bond OE1_CD = OE1.getBond(CD);
Bond OE2_CD = OE2.getBond(CD);
Bond HB_CB = HB2.getBond(CB);
Bond HG_CG = HG2.getBond(CG);
double dCG_CB = CG_CB.bondType.distance;
double dCD_CG = CD_CG.bondType.distance;
double dOE1_CD = OE1_CD.bondType.distance;
double dOE2_CD = OE2_CD.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHG_CG = HG_CG.bondType.distance;
Angle CG_CB_CA = CG.getAngle(CB, CA);
Angle CD_CG_CB = CD.getAngle(CG, CB);
Angle OE1_CD_CG = OE1.getAngle(CD, CG);
Angle OE2_CD_CG = OE2.getAngle(CD, CG);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
Angle HG_CG_CB = HG2.getAngle(CG, CB);
double dCG_CB_CA = CG_CB_CA.angleType.angle[CG_CB_CA.nh];
double dCD_CG_CB = CD_CG_CB.angleType.angle[CD_CG_CB.nh];
double dOE1_CD_CG = OE1_CD_CG.angleType.angle[OE1_CD_CG.nh];
double dOE2_CD_CG = OE2_CD_CG.angleType.angle[OE2_CD_CG.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHG_CG_CB = HG_CG_CB.angleType.angle[HG_CG_CB.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// CG
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG_CB, ca, dCG_CB_CA, n, rotScale * 180.0, 0), 0, cg, 0, 3);
coordsArray = fillCoordsArray(CG, coordsArray, cg);
// CD
System.arraycopy(BondedUtils.determineIntxyz(cg, dCD_CG, cb, dCD_CG_CB, ca, 180.0, 0), 0, cd, 0, 3);
coordsArray = fillCoordsArray(CD, coordsArray, cd);
// OE1
System.arraycopy(BondedUtils.determineIntxyz(cd, dOE1_CD, cg, dOE1_CD_CG, cb, 180.0, 0), 0, oe1, 0, 3);
coordsArray = fillCoordsArray(OE1, coordsArray, oe1);
// OE2
System.arraycopy(BondedUtils.determineIntxyz(cd, dOE2_CD, cg, dOE2_CD_CG, oe1, 126.0, 1), 0, oe2, 0, 3);
coordsArray = fillCoordsArray(OE2, coordsArray, oe2);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
// HG2
System.arraycopy(BondedUtils.determineIntxyz(cg, dHG_CG, cb, dHG_CG_CB, cd, 107.9, 1), 0, hg2, 0, 3);
coordsArray = fillCoordsArray(HG2, coordsArray, hg2);
// HG3
System.arraycopy(BondedUtils.determineIntxyz(cg, dHG_CG, cb, dHG_CG_CB, cd, 107.9, -1), 0, hg3, 0, 3);
coordsArray = fillCoordsArray(HG3, coordsArray, hg3);
break;
}
case GLH:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom CG = (Atom) newResidue.getAtomNode("CG");
double[] cg = coordsArray[CG.getIndex() - 1];
Atom CD = (Atom) newResidue.getAtomNode("CD");
double[] cd = coordsArray[CD.getIndex() - 1];
Atom OE1 = (Atom) newResidue.getAtomNode("OE1");
double[] oe1 = coordsArray[OE1.getIndex() - 1];
Atom OE2 = (Atom) newResidue.getAtomNode("OE2");
double[] oe2 = coordsArray[OE2.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Atom HG2 = (Atom) newResidue.getAtomNode("HG2");
double[] hg2 = coordsArray[HG2.getIndex() - 1];
Atom HG3 = (Atom) newResidue.getAtomNode("HG3");
double[] hg3 = coordsArray[HG3.getIndex() - 1];
Atom HE2 = (Atom) newResidue.getAtomNode("HE2");
double[] he2 = coordsArray[HE2.getIndex() - 1];
Bond CG_CB = CG.getBond(CB);
Bond CD_CG = CD.getBond(CG);
Bond OE1_CD = OE1.getBond(CD);
Bond OE2_CD = OE2.getBond(CD);
Bond HB_CB = HB2.getBond(CB);
Bond HG_CG = HG2.getBond(CG);
Bond HE2_OE2 = HE2.getBond(OE2);
double dCG_CB = CG_CB.bondType.distance;
double dCD_CG = CD_CG.bondType.distance;
double dOE1_CD = OE1_CD.bondType.distance;
double dOE2_CD = OE2_CD.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHG_CG = HG_CG.bondType.distance;
double dHE2_OE2 = HE2_OE2.bondType.distance;
Angle CG_CB_CA = CG.getAngle(CB, CA);
Angle CD_CG_CB = CD.getAngle(CG, CB);
Angle OE1_CD_CG = OE1.getAngle(CD, CG);
Angle OE2_CD_CG = OE2.getAngle(CD, CG);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
Angle HG_CG_CB = HG2.getAngle(CG, CB);
Angle HE2_OE2_CD = HE2.getAngle(OE2, CD);
double dCG_CB_CA = CG_CB_CA.angleType.angle[CG_CB_CA.nh];
double dCD_CG_CB = CD_CG_CB.angleType.angle[CD_CG_CB.nh];
double dOE1_CD_CG = OE1_CD_CG.angleType.angle[OE1_CD_CG.nh];
double dOE2_CD_CG = OE2_CD_CG.angleType.angle[OE2_CD_CG.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHG_CG_CB = HG_CG_CB.angleType.angle[HG_CG_CB.nh];
double dHE2_OE2_CD = HE2_OE2_CD.angleType.angle[HE2_OE2_CD.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// CG
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG_CB, ca, dCG_CB_CA, n, rotScale * 180.0, 0), 0, cg, 0, 3);
coordsArray = fillCoordsArray(CG, coordsArray, cg);
// CD
System.arraycopy(BondedUtils.determineIntxyz(cg, dCD_CG, cb, dCD_CG_CB, ca, 180.0, 0), 0, cd, 0, 3);
coordsArray = fillCoordsArray(CD, coordsArray, cd);
// OE1
System.arraycopy(BondedUtils.determineIntxyz(cd, dOE1_CD, cg, dOE1_CD_CG, cb, 180.0, 0), 0, oe1, 0, 3);
coordsArray = fillCoordsArray(OE1, coordsArray, oe1);
// OE2
System.arraycopy(BondedUtils.determineIntxyz(cd, dOE2_CD, cg, dOE2_CD_CG, oe1, 126.0, 1), 0, oe2, 0, 3);
coordsArray = fillCoordsArray(OE2, coordsArray, oe2);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
// HG2
System.arraycopy(BondedUtils.determineIntxyz(cg, dHG_CG, cb, dHG_CG_CB, cd, 107.9, 1), 0, hg2, 0, 3);
coordsArray = fillCoordsArray(HG2, coordsArray, hg2);
// HG3
System.arraycopy(BondedUtils.determineIntxyz(cg, dHG_CG, cb, dHG_CG_CB, cd, 107.9, -1), 0, hg3, 0, 3);
coordsArray = fillCoordsArray(HG3, coordsArray, hg3);
// HE2
System.arraycopy(BondedUtils.determineIntxyz(oe2, dHE2_OE2, cd, dHE2_OE2_CD, oe1, 0.0, 0), 0, he2, 0, 3);
coordsArray = fillCoordsArray(HE2, coordsArray, he2);
break;
}
case GLN:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom CG = (Atom) newResidue.getAtomNode("CG");
double[] cg = coordsArray[CG.getIndex() - 1];
Atom CD = (Atom) newResidue.getAtomNode("CD");
double[] cd = coordsArray[CD.getIndex() - 1];
Atom OE1 = (Atom) newResidue.getAtomNode("OE1");
double[] oe1 = coordsArray[OE1.getIndex() - 1];
Atom NE2 = (Atom) newResidue.getAtomNode("NE2");
double[] ne2 = coordsArray[NE2.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Atom HG2 = (Atom) newResidue.getAtomNode("HG2");
double[] hg2 = coordsArray[HG2.getIndex() - 1];
Atom HG3 = (Atom) newResidue.getAtomNode("HG3");
double[] hg3 = coordsArray[HG3.getIndex() - 1];
Atom HE21 = (Atom) newResidue.getAtomNode("HE21");
double[] he21 = coordsArray[HE21.getIndex() - 1];
Atom HE22 = (Atom) newResidue.getAtomNode("HE22");
double[] he22 = coordsArray[HE22.getIndex() - 1];
Bond CG_CB = CG.getBond(CB);
Bond CD_CG = CD.getBond(CG);
Bond OE1_CD = OE1.getBond(CD);
Bond NE2_CD = NE2.getBond(CD);
Bond HB_CB = HB2.getBond(CB);
Bond HG_CG = HG2.getBond(CG);
Bond HE2_NE2 = HE21.getBond(NE2);
double dCG_CB = CG_CB.bondType.distance;
double dCD_CG = CD_CG.bondType.distance;
double dOE1_CD = OE1_CD.bondType.distance;
double dNE2_CD = NE2_CD.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHG_CG = HG_CG.bondType.distance;
double dHE2_NE2 = HE2_NE2.bondType.distance;
Angle CG_CB_CA = CG.getAngle(CB, CA);
Angle CD_CG_CB = CD.getAngle(CG, CB);
Angle OE1_CD_CG = OE1.getAngle(CD, CG);
Angle NE2_CD_CG = NE2.getAngle(CD, CG);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
Angle HG_CG_CB = HG2.getAngle(CG, CB);
Angle HE2_NE2_CD = HE21.getAngle(NE2, CD);
double dCG_CB_CA = CG_CB_CA.angleType.angle[CG_CB_CA.nh];
double dCD_CG_CB = CD_CG_CB.angleType.angle[CD_CG_CB.nh];
double dOE1_CD_CG = OE1_CD_CG.angleType.angle[OE1_CD_CG.nh];
double dNE2_CD_CG = NE2_CD_CG.angleType.angle[NE2_CD_CG.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHG_CG_CB = HG_CG_CB.angleType.angle[HG_CG_CB.nh];
double dHE2_NE2_CD = HE2_NE2_CD.angleType.angle[HE2_NE2_CD.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// CG
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG_CB, ca, dCG_CB_CA, n, rotScale * 180.0, 0), 0, cg, 0, 3);
coordsArray = fillCoordsArray(CG, coordsArray, cg);
// CD
System.arraycopy(BondedUtils.determineIntxyz(cg, dCD_CG, cb, dCD_CG_CB, ca, 180.0, 0), 0, cd, 0, 3);
coordsArray = fillCoordsArray(CD, coordsArray, cd);
// OE1
System.arraycopy(BondedUtils.determineIntxyz(cd, dOE1_CD, cg, dOE1_CD_CG, cb, 180.0, 0), 0, oe1, 0, 3);
coordsArray = fillCoordsArray(OE1, coordsArray, oe1);
// NE2
System.arraycopy(BondedUtils.determineIntxyz(cd, dNE2_CD, cg, dNE2_CD_CG, oe1, 124.0, 1), 0, ne2, 0, 3);
coordsArray = fillCoordsArray(NE2, coordsArray, ne2);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
// HG2
System.arraycopy(BondedUtils.determineIntxyz(cg, dHG_CG, cb, dHG_CG_CB, cd, 107.9, 1), 0, hg2, 0, 3);
coordsArray = fillCoordsArray(HG2, coordsArray, hg2);
// HG3
System.arraycopy(BondedUtils.determineIntxyz(cg, dHG_CG, cb, dHG_CG_CB, cd, 107.9, -1), 0, hg3, 0, 3);
coordsArray = fillCoordsArray(HG3, coordsArray, hg3);
// HE21
System.arraycopy(BondedUtils.determineIntxyz(ne2, dHE2_NE2, cd, dHE2_NE2_CD, cg, 0.0, 0), 0, he21, 0, 3);
coordsArray = fillCoordsArray(HE21, coordsArray, he21);
// HE22
System.arraycopy(BondedUtils.determineIntxyz(ne2, dHE2_NE2, cd, dHE2_NE2_CD, he21, 120.0, 1), 0, he22, 0, 3);
coordsArray = fillCoordsArray(HE22, coordsArray, he22);
break;
}
case MET:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom CG = (Atom) newResidue.getAtomNode("CG");
double[] cg = coordsArray[CG.getIndex() - 1];
Atom SD = (Atom) newResidue.getAtomNode("SD");
double[] sd = coordsArray[SD.getIndex() - 1];
Atom CE = (Atom) newResidue.getAtomNode("CE");
double[] ce = coordsArray[CE.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Atom HG2 = (Atom) newResidue.getAtomNode("HG2");
double[] hg2 = coordsArray[HG2.getIndex() - 1];
Atom HG3 = (Atom) newResidue.getAtomNode("HG3");
double[] hg3 = coordsArray[HG3.getIndex() - 1];
Atom HE1 = (Atom) newResidue.getAtomNode("HE1");
double[] he1 = coordsArray[HE1.getIndex() - 1];
Atom HE2 = (Atom) newResidue.getAtomNode("HE2");
double[] he2 = coordsArray[HE2.getIndex() - 1];
Atom HE3 = (Atom) newResidue.getAtomNode("HE3");
double[] he3 = coordsArray[HE3.getIndex() - 1];
Bond CG_CB = CG.getBond(CB);
Bond SD_CG = SD.getBond(CG);
Bond CE_SD = CE.getBond(SD);
Bond HB_CB = HB2.getBond(CB);
Bond HG_CG = HG2.getBond(CG);
Bond HE_CE = HE1.getBond(CE);
double dCG_CB = CG_CB.bondType.distance;
double dSD_CG = SD_CG.bondType.distance;
double dCE_SD = CE_SD.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHG_CG = HG_CG.bondType.distance;
double dHE_CE = HE_CE.bondType.distance;
Angle CG_CB_CA = CG.getAngle(CB, CA);
Angle SD_CG_CB = SD.getAngle(CG, CB);
Angle CE_SD_CG = CE.getAngle(SD, CG);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
Angle HG_CG_CB = HG2.getAngle(CG, CB);
Angle HE_CE_SD = HE1.getAngle(CE, SD);
double dCG_CB_CA = CG_CB_CA.angleType.angle[CG_CB_CA.nh];
double dSD_CG_CB = SD_CG_CB.angleType.angle[SD_CG_CB.nh];
double dCE_SD_CG = CE_SD_CG.angleType.angle[CE_SD_CG.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHG_CG_CB = HG_CG_CB.angleType.angle[HG_CG_CB.nh];
double dHE_CE_SD = HE_CE_SD.angleType.angle[HE_CE_SD.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// CG
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG_CB, ca, dCG_CB_CA, n, rotScale * 180.0, 0), 0, cg, 0, 3);
coordsArray = fillCoordsArray(CG, coordsArray, cg);
// SD
System.arraycopy(BondedUtils.determineIntxyz(cg, dSD_CG, cb, dSD_CG_CB, ca, 180.0, 0), 0, sd, 0, 3);
coordsArray = fillCoordsArray(SD, coordsArray, sd);
// CE
System.arraycopy(BondedUtils.determineIntxyz(sd, dCE_SD, cg, dCE_SD_CG, cb, 180.0, 0), 0, ce, 0, 3);
coordsArray = fillCoordsArray(CE, coordsArray, ce);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
// HG2
System.arraycopy(BondedUtils.determineIntxyz(cg, dHG_CG, cb, dHG_CG_CB, sd, 112.0, 1), 0, hg2, 0, 3);
coordsArray = fillCoordsArray(HG2, coordsArray, hg2);
// HG3
System.arraycopy(BondedUtils.determineIntxyz(cg, dHG_CG, cb, dHG_CG_CB, sd, 112.0, -1), 0, hg3, 0, 3);
coordsArray = fillCoordsArray(HG3, coordsArray, hg3);
// HE1
System.arraycopy(BondedUtils.determineIntxyz(ce, dHE_CE, sd, dHE_CE_SD, cg, 180.0, 0), 0, he1, 0, 3);
coordsArray = fillCoordsArray(HE1, coordsArray, he1);
// HE2
System.arraycopy(BondedUtils.determineIntxyz(ce, dHE_CE, sd, dHE_CE_SD, he1, 109.4, 1), 0, he2, 0, 3);
coordsArray = fillCoordsArray(HE2, coordsArray, he2);
// HE3
System.arraycopy(BondedUtils.determineIntxyz(ce, dHE_CE, sd, dHE_CE_SD, he1, 109.4, -1), 0, he3, 0, 3);
coordsArray = fillCoordsArray(HE3, coordsArray, he3);
break;
}
case LYS:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom CG = (Atom) newResidue.getAtomNode("CG");
double[] cg = coordsArray[CG.getIndex() - 1];
Atom CD = (Atom) newResidue.getAtomNode("CD");
double[] cd = coordsArray[CD.getIndex() - 1];
Atom CE = (Atom) newResidue.getAtomNode("CE");
double[] ce = coordsArray[CE.getIndex() - 1];
Atom NZ = (Atom) newResidue.getAtomNode("NZ");
double[] nz = coordsArray[NZ.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Atom HG2 = (Atom) newResidue.getAtomNode("HG2");
double[] hg2 = coordsArray[HG2.getIndex() - 1];
Atom HG3 = (Atom) newResidue.getAtomNode("HG3");
double[] hg3 = coordsArray[HG3.getIndex() - 1];
Atom HD2 = (Atom) newResidue.getAtomNode("HD2");
double[] hd2 = coordsArray[HD2.getIndex() - 1];
Atom HD3 = (Atom) newResidue.getAtomNode("HD3");
double[] hd3 = coordsArray[HD3.getIndex() - 1];
Atom HE2 = (Atom) newResidue.getAtomNode("HE2");
double[] he2 = coordsArray[HE2.getIndex() - 1];
Atom HE3 = (Atom) newResidue.getAtomNode("HE3");
double[] he3 = coordsArray[HE3.getIndex() - 1];
Atom HZ1 = (Atom) newResidue.getAtomNode("HZ1");
double[] hz1 = coordsArray[HZ1.getIndex() - 1];
Atom HZ2 = (Atom) newResidue.getAtomNode("HZ2");
double[] hz2 = coordsArray[HZ2.getIndex() - 1];
Atom HZ3 = (Atom) newResidue.getAtomNode("HZ3");
double[] hz3 = coordsArray[HZ3.getIndex() - 1];
Bond CG_CB = CG.getBond(CB);
Bond CD_CG = CD.getBond(CG);
Bond CE_CD = CE.getBond(CD);
Bond NZ_CE = NZ.getBond(CE);
Bond HB_CB = HB2.getBond(CB);
Bond HG_CG = HG2.getBond(CG);
Bond HD_CD = HD2.getBond(CD);
Bond HE_CE = HE2.getBond(CE);
Bond HZ_NZ = HZ1.getBond(NZ);
double dCG_CB = CG_CB.bondType.distance;
double dCD_CG = CD_CG.bondType.distance;
double dCE_CD = CE_CD.bondType.distance;
double dNZ_CE = NZ_CE.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHG_CG = HG_CG.bondType.distance;
double dHD_CD = HD_CD.bondType.distance;
double dHE_CE = HE_CE.bondType.distance;
double dHZ_NZ = HZ_NZ.bondType.distance;
Angle CG_CB_CA = CG.getAngle(CB, CA);
Angle CD_CG_CB = CD.getAngle(CG, CB);
Angle CE_CD_CG = CE.getAngle(CD, CG);
Angle NZ_CE_CD = NZ.getAngle(CE, CD);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
Angle HG_CG_CB = HG2.getAngle(CG, CB);
Angle HD_CD_CG = HD2.getAngle(CD, CG);
Angle HE_CE_CD = HE2.getAngle(CE, CD);
Angle HZ_NZ_CE = HZ1.getAngle(NZ, CE);
double dCG_CB_CA = CG_CB_CA.angleType.angle[CG_CB_CA.nh];
double dCD_CG_CB = CD_CG_CB.angleType.angle[CD_CG_CB.nh];
double dCE_CD_CG = CE_CD_CG.angleType.angle[CE_CD_CG.nh];
double dNZ_CE_CD = NZ_CE_CD.angleType.angle[NZ_CE_CD.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHG_CG_CB = HG_CG_CB.angleType.angle[HG_CG_CB.nh];
double dHD_CD_CG = HD_CD_CG.angleType.angle[HD_CD_CG.nh];
double dHE_CE_CD = HE_CE_CD.angleType.angle[HE_CE_CD.nh];
double dHZ_NZ_CE = HZ_NZ_CE.angleType.angle[HZ_NZ_CE.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// CG
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG_CB, ca, dCG_CB_CA, n, rotScale * 180.0, 0), 0, cg, 0, 3);
coordsArray = fillCoordsArray(CG, coordsArray, cg);
// CD
System.arraycopy(BondedUtils.determineIntxyz(cg, dCD_CG, cb, dCD_CG_CB, ca, 180.0, 0), 0, cd, 0, 3);
coordsArray = fillCoordsArray(CD, coordsArray, cd);
// CE
System.arraycopy(BondedUtils.determineIntxyz(cd, dCE_CD, cg, dCE_CD_CG, cb, 180.0, 0), 0, ce, 0, 3);
coordsArray = fillCoordsArray(CE, coordsArray, ce);
// NZ
System.arraycopy(BondedUtils.determineIntxyz(ce, dNZ_CE, cd, dNZ_CE_CD, cg, 180.0, 0), 0, nz, 0, 3);
coordsArray = fillCoordsArray(NZ, coordsArray, nz);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
// HG2
System.arraycopy(BondedUtils.determineIntxyz(cg, dHG_CG, cb, dHG_CG_CB, cd, 109.4, 1), 0, hg2, 0, 3);
coordsArray = fillCoordsArray(HG2, coordsArray, hg2);
// HG3
System.arraycopy(BondedUtils.determineIntxyz(cg, dHG_CG, cb, dHG_CG_CB, cd, 109.4, -1), 0, hg3, 0, 3);
coordsArray = fillCoordsArray(HG3, coordsArray, hg3);
// HD2
System.arraycopy(BondedUtils.determineIntxyz(cd, dHD_CD, cg, dHD_CD_CG, ce, 109.4, 1), 0, hd2, 0, 3);
coordsArray = fillCoordsArray(HD2, coordsArray, hd2);
// HD3
System.arraycopy(BondedUtils.determineIntxyz(cd, dHD_CD, cg, dHD_CD_CG, ce, 109.4, -1), 0, hd3, 0, 3);
coordsArray = fillCoordsArray(HD3, coordsArray, hd3);
// HE2
System.arraycopy(BondedUtils.determineIntxyz(ce, dHE_CE, cd, dHE_CE_CD, nz, 108.8, 1), 0, he2, 0, 3);
coordsArray = fillCoordsArray(HE2, coordsArray, he2);
// HE3
System.arraycopy(BondedUtils.determineIntxyz(ce, dHE_CE, cd, dHE_CE_CD, nz, 108.8, -1), 0, he3, 0, 3);
coordsArray = fillCoordsArray(HE3, coordsArray, he3);
// HZ1
System.arraycopy(BondedUtils.determineIntxyz(nz, dHZ_NZ, ce, dHZ_NZ_CE, cd, 180.0, 0), 0, hz1, 0, 3);
coordsArray = fillCoordsArray(HZ1, coordsArray, hz1);
// HZ2
System.arraycopy(BondedUtils.determineIntxyz(nz, dHZ_NZ, ce, dHZ_NZ_CE, hz1, 109.5, 1), 0, hz2, 0, 3);
coordsArray = fillCoordsArray(HZ2, coordsArray, hz2);
// HZ3
System.arraycopy(BondedUtils.determineIntxyz(nz, dHZ_NZ, ce, dHZ_NZ_CE, hz1, 109.5, -1), 0, hz3, 0, 3);
coordsArray = fillCoordsArray(HZ3, coordsArray, hz3);
break;
}
case LYD:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom CG = (Atom) newResidue.getAtomNode("CG");
double[] cg = coordsArray[CG.getIndex() - 1];
Atom CD = (Atom) newResidue.getAtomNode("CD");
double[] cd = coordsArray[CD.getIndex() - 1];
Atom CE = (Atom) newResidue.getAtomNode("CE");
double[] ce = coordsArray[CE.getIndex() - 1];
Atom NZ = (Atom) newResidue.getAtomNode("NZ");
double[] nz = coordsArray[NZ.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Atom HG2 = (Atom) newResidue.getAtomNode("HG2");
double[] hg2 = coordsArray[HG2.getIndex() - 1];
Atom HG3 = (Atom) newResidue.getAtomNode("HG3");
double[] hg3 = coordsArray[HG3.getIndex() - 1];
Atom HD2 = (Atom) newResidue.getAtomNode("HD2");
double[] hd2 = coordsArray[HD2.getIndex() - 1];
Atom HD3 = (Atom) newResidue.getAtomNode("HD3");
double[] hd3 = coordsArray[HD3.getIndex() - 1];
Atom HE2 = (Atom) newResidue.getAtomNode("HE2");
double[] he2 = coordsArray[HE2.getIndex() - 1];
Atom HE3 = (Atom) newResidue.getAtomNode("HE3");
double[] he3 = coordsArray[HE3.getIndex() - 1];
Atom HZ1 = (Atom) newResidue.getAtomNode("HZ1");
double[] hz1 = coordsArray[HZ1.getIndex() - 1];
Atom HZ2 = (Atom) newResidue.getAtomNode("HZ2");
double[] hz2 = coordsArray[HZ2.getIndex() - 1];
Bond CG_CB = CG.getBond(CB);
Bond CD_CG = CD.getBond(CG);
Bond CE_CD = CE.getBond(CD);
Bond NZ_CE = NZ.getBond(CE);
Bond HB_CB = HB2.getBond(CB);
Bond HG_CG = HG2.getBond(CG);
Bond HD_CD = HD2.getBond(CD);
Bond HE_CE = HE2.getBond(CE);
Bond HZ_NZ = HZ1.getBond(NZ);
double dCG_CB = CG_CB.bondType.distance;
double dCD_CG = CD_CG.bondType.distance;
double dCE_CD = CE_CD.bondType.distance;
double dNZ_CE = NZ_CE.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHG_CG = HG_CG.bondType.distance;
double dHD_CD = HD_CD.bondType.distance;
double dHE_CE = HE_CE.bondType.distance;
double dHZ_NZ = HZ_NZ.bondType.distance;
Angle CG_CB_CA = CG.getAngle(CB, CA);
Angle CD_CG_CB = CD.getAngle(CG, CB);
Angle CE_CD_CG = CE.getAngle(CD, CG);
Angle NZ_CE_CD = NZ.getAngle(CE, CD);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
Angle HG_CG_CB = HG2.getAngle(CG, CB);
Angle HD_CD_CG = HD2.getAngle(CD, CG);
Angle HE_CE_CD = HE2.getAngle(CE, CD);
Angle HZ_NZ_CE = HZ1.getAngle(NZ, CE);
double dCG_CB_CA = CG_CB_CA.angleType.angle[CG_CB_CA.nh];
double dCD_CG_CB = CD_CG_CB.angleType.angle[CD_CG_CB.nh];
double dCE_CD_CG = CE_CD_CG.angleType.angle[CE_CD_CG.nh];
double dNZ_CE_CD = NZ_CE_CD.angleType.angle[NZ_CE_CD.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHG_CG_CB = HG_CG_CB.angleType.angle[HG_CG_CB.nh];
double dHD_CD_CG = HD_CD_CG.angleType.angle[HD_CD_CG.nh];
double dHE_CE_CD = HE_CE_CD.angleType.angle[HE_CE_CD.nh];
double dHZ_NZ_CE = HZ_NZ_CE.angleType.angle[HZ_NZ_CE.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// CG
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG_CB, ca, dCG_CB_CA, n, rotScale * 180.0, 0), 0, cg, 0, 3);
coordsArray = fillCoordsArray(CG, coordsArray, cg);
// CD
System.arraycopy(BondedUtils.determineIntxyz(cg, dCD_CG, cb, dCD_CG_CB, ca, 180.0, 0), 0, cd, 0, 3);
coordsArray = fillCoordsArray(CD, coordsArray, cd);
// CE
System.arraycopy(BondedUtils.determineIntxyz(cd, dCE_CD, cg, dCE_CD_CG, cb, 180.0, 0), 0, ce, 0, 3);
coordsArray = fillCoordsArray(CE, coordsArray, ce);
// NZ
System.arraycopy(BondedUtils.determineIntxyz(ce, dNZ_CE, cd, dNZ_CE_CD, cg, 180.0, 0), 0, nz, 0, 3);
coordsArray = fillCoordsArray(NZ, coordsArray, nz);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
// HG2
System.arraycopy(BondedUtils.determineIntxyz(cg, dHG_CG, cb, dHG_CG_CB, cd, 109.4, 1), 0, hg2, 0, 3);
coordsArray = fillCoordsArray(HG2, coordsArray, hg2);
// HG3
System.arraycopy(BondedUtils.determineIntxyz(cg, dHG_CG, cb, dHG_CG_CB, cd, 109.4, -1), 0, hg3, 0, 3);
coordsArray = fillCoordsArray(HG3, coordsArray, hg3);
// HD2
System.arraycopy(BondedUtils.determineIntxyz(cd, dHD_CD, cg, dHD_CD_CG, ce, 109.4, 1), 0, hd2, 0, 3);
coordsArray = fillCoordsArray(HD2, coordsArray, hd2);
// HD3
System.arraycopy(BondedUtils.determineIntxyz(cd, dHD_CD, cg, dHD_CD_CG, ce, 109.4, -1), 0, hd3, 0, 3);
coordsArray = fillCoordsArray(HD3, coordsArray, hd3);
// HE2
System.arraycopy(BondedUtils.determineIntxyz(ce, dHE_CE, cd, dHE_CE_CD, nz, 108.8, 1), 0, he2, 0, 3);
coordsArray = fillCoordsArray(HE2, coordsArray, he2);
// HE3
System.arraycopy(BondedUtils.determineIntxyz(ce, dHE_CE, cd, dHE_CE_CD, nz, 108.8, -1), 0, he3, 0, 3);
coordsArray = fillCoordsArray(HE3, coordsArray, he3);
// HZ1
System.arraycopy(BondedUtils.determineIntxyz(nz, dHZ_NZ, ce, dHZ_NZ_CE, cd, 180.0, 0), 0, hz1, 0, 3);
coordsArray = fillCoordsArray(HZ1, coordsArray, hz1);
// HZ2
System.arraycopy(BondedUtils.determineIntxyz(nz, dHZ_NZ, ce, dHZ_NZ_CE, hz1, 109.5, 1), 0, hz2, 0, 3);
coordsArray = fillCoordsArray(HZ2, coordsArray, hz2);
break;
}
case ARG:
{
Atom CB = (Atom) newResidue.getAtomNode("CB");
double[] cb = coordsArray[CB.getIndex() - 1];
Atom CG = (Atom) newResidue.getAtomNode("CG");
double[] cg = coordsArray[CG.getIndex() - 1];
Atom CD = (Atom) newResidue.getAtomNode("CD");
double[] cd = coordsArray[CD.getIndex() - 1];
Atom NE = (Atom) newResidue.getAtomNode("NE");
double[] ne = coordsArray[NE.getIndex() - 1];
Atom CZ = (Atom) newResidue.getAtomNode("CZ");
double[] cz = coordsArray[CZ.getIndex() - 1];
Atom NH1 = (Atom) newResidue.getAtomNode("NH1");
double[] nh1 = coordsArray[NH1.getIndex() - 1];
Atom NH2 = (Atom) newResidue.getAtomNode("NH2");
double[] nh2 = coordsArray[NH2.getIndex() - 1];
Atom HB2 = (Atom) newResidue.getAtomNode("HB2");
double[] hb2 = coordsArray[HB2.getIndex() - 1];
Atom HB3 = (Atom) newResidue.getAtomNode("HB3");
double[] hb3 = coordsArray[HB3.getIndex() - 1];
Atom HG2 = (Atom) newResidue.getAtomNode("HG2");
double[] hg2 = coordsArray[HG2.getIndex() - 1];
Atom HG3 = (Atom) newResidue.getAtomNode("HG3");
double[] hg3 = coordsArray[HG3.getIndex() - 1];
Atom HD2 = (Atom) newResidue.getAtomNode("HD2");
double[] hd2 = coordsArray[HG2.getIndex() - 1];
Atom HD3 = (Atom) newResidue.getAtomNode("HD3");
double[] hd3 = coordsArray[HD3.getIndex() - 1];
Atom HE = (Atom) newResidue.getAtomNode("HE");
double[] he = coordsArray[HE.getIndex() - 1];
Atom HH11 = (Atom) newResidue.getAtomNode("HH11");
double[] hh11 = coordsArray[HH11.getIndex() - 1];
Atom HH12 = (Atom) newResidue.getAtomNode("HH12");
double[] hh12 = coordsArray[HH12.getIndex() - 1];
Atom HH21 = (Atom) newResidue.getAtomNode("HH21");
double[] hh21 = coordsArray[HH21.getIndex() - 1];
Atom HH22 = (Atom) newResidue.getAtomNode("HH22");
double[] hh22 = coordsArray[HH22.getIndex() - 1];
Bond CG_CB = CG.getBond(CB);
Bond CD_CG = CD.getBond(CG);
Bond NE_CD = NE.getBond(CD);
Bond CZ_NE = CZ.getBond(NE);
Bond NH_CZ = NH1.getBond(CZ);
Bond HB_CB = HB2.getBond(CB);
Bond HG_CG = HG2.getBond(CG);
Bond HD_CD = HD2.getBond(CD);
Bond HE_NE = HE.getBond(NE);
Bond HH_NH = HH11.getBond(NH1);
double dCG_CB = CG_CB.bondType.distance;
double dCD_CG = CD_CG.bondType.distance;
double dNE_CD = NE_CD.bondType.distance;
double dCZ_NE = CZ_NE.bondType.distance;
double dNH_CZ = NH_CZ.bondType.distance;
double dHB_CB = HB_CB.bondType.distance;
double dHG_CG = HG_CG.bondType.distance;
double dHD_CD = HD_CD.bondType.distance;
double dHE_NE = HE_NE.bondType.distance;
double dHH_NH = HH_NH.bondType.distance;
Angle CG_CB_CA = CG.getAngle(CB, CA);
Angle CD_CG_CB = CD.getAngle(CG, CB);
Angle NE_CD_CG = NE.getAngle(CD, CG);
Angle CZ_NE_CD = CZ.getAngle(NE, CD);
Angle NH_CZ_NE = NH1.getAngle(CZ, NE);
Angle HB_CB_CA = HB2.getAngle(CB, CA);
Angle HG_CG_CB = HG2.getAngle(CG, CB);
Angle HD_CD_CG = HD2.getAngle(CD, CG);
Angle HE_NE_CD = HE.getAngle(NE, CD);
Angle HH_NH_CZ = HH11.getAngle(NH1, CZ);
double dCG_CB_CA = CG_CB_CA.angleType.angle[CG_CB_CA.nh];
double dCD_CG_CB = CD_CG_CB.angleType.angle[CD_CG_CB.nh];
double dNE_CD_CG = NE_CD_CG.angleType.angle[NE_CD_CG.nh];
double dCZ_NE_CD = CZ_NE_CD.angleType.angle[CZ_NE_CD.nh];
double dNH_CZ_NE = NH_CZ_NE.angleType.angle[NH_CZ_NE.nh];
double dHB_CB_CA = HB_CB_CA.angleType.angle[HB_CB_CA.nh];
double dHG_CG_CB = HG_CG_CB.angleType.angle[HG_CG_CB.nh];
double dHD_CD_CG = HD_CD_CG.angleType.angle[HD_CD_CG.nh];
double dHE_NE_CD = HE_NE_CD.angleType.angle[HE_NE_CD.nh];
double dHH_NH_CZ = HH_NH_CZ.angleType.angle[HH_NH_CZ.nh];
System.arraycopy(BondedUtils.determineIntxyz(ca, 1.54, n, 109.5, c, 107.8, 1), 0, cb, 0, 3);
coordsArray = fillCoordsArray(CB, coordsArray, cb);
// CG
System.arraycopy(BondedUtils.determineIntxyz(cb, dCG_CB, ca, dCG_CB_CA, n, rotScale * 180.0, 0), 0, cg, 0, 3);
coordsArray = fillCoordsArray(CG, coordsArray, cg);
// CD
System.arraycopy(BondedUtils.determineIntxyz(cg, dCD_CG, cb, dCD_CG_CB, ca, 180.0, 0), 0, cd, 0, 3);
coordsArray = fillCoordsArray(CD, coordsArray, cd);
// NE
System.arraycopy(BondedUtils.determineIntxyz(cd, dNE_CD, cg, dNE_CD_CG, cb, 180.0, 0), 0, ne, 0, 3);
coordsArray = fillCoordsArray(NE, coordsArray, ne);
// CZ
System.arraycopy(BondedUtils.determineIntxyz(ne, dCZ_NE, cd, dCZ_NE_CD, cg, 180.0, 0), 0, cz, 0, 3);
coordsArray = fillCoordsArray(CZ, coordsArray, cz);
// NH1
System.arraycopy(BondedUtils.determineIntxyz(cz, dNH_CZ, ne, dNH_CZ_NE, cd, 180, 0), 0, nh1, 0, 3);
coordsArray = fillCoordsArray(NH1, coordsArray, nh1);
// NH2
System.arraycopy(BondedUtils.determineIntxyz(cz, dNH_CZ, ne, dNH_CZ_NE, nh1, 120.0, 1), 0, nh2, 0, 3);
coordsArray = fillCoordsArray(NH2, coordsArray, nh2);
// HB2
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, 1), 0, hb2, 0, 3);
coordsArray = fillCoordsArray(HB2, coordsArray, hb2);
// HB3
System.arraycopy(BondedUtils.determineIntxyz(cb, dHB_CB, ca, dHB_CB_CA, cg, 109.4, -1), 0, hb3, 0, 3);
coordsArray = fillCoordsArray(HB3, coordsArray, hb3);
// HG2
System.arraycopy(BondedUtils.determineIntxyz(cg, dHG_CG, cb, dHG_CG_CB, cd, 109.4, 1), 0, hg2, 0, 3);
coordsArray = fillCoordsArray(HG2, coordsArray, hg2);
// HG3
System.arraycopy(BondedUtils.determineIntxyz(cg, dHG_CG, cb, dHG_CG_CB, cd, 109.4, -1), 0, hg3, 0, 3);
coordsArray = fillCoordsArray(HG3, coordsArray, hg3);
// HD2
System.arraycopy(BondedUtils.determineIntxyz(cd, dHD_CD, cg, dHD_CD_CG, ne, 109.4, 1), 0, hd2, 0, 3);
coordsArray = fillCoordsArray(HD2, coordsArray, hd2);
// HD3
System.arraycopy(BondedUtils.determineIntxyz(cd, dHD_CD, cg, dHD_CD_CG, ne, 109.4, -1), 0, hd3, 0, 3);
coordsArray = fillCoordsArray(HD3, coordsArray, hd3);
// HE
System.arraycopy(BondedUtils.determineIntxyz(ne, dHE_NE, cd, dHE_NE_CD, cz, 120.0, 1), 0, he, 0, 3);
coordsArray = fillCoordsArray(HE, coordsArray, he);
// HH11
System.arraycopy(BondedUtils.determineIntxyz(nh1, dHH_NH, cz, dHH_NH_CZ, ne, 180.0, 0), 0, hh11, 0, 3);
coordsArray = fillCoordsArray(HH11, coordsArray, hh11);
// HH12
System.arraycopy(BondedUtils.determineIntxyz(nh1, dHH_NH, cz, dHH_NH_CZ, hh11, 120.0, 1), 0, hh12, 0, 3);
coordsArray = fillCoordsArray(HH12, coordsArray, hh12);
// HH21
System.arraycopy(BondedUtils.determineIntxyz(nh2, dHH_NH, cz, dHH_NH_CZ, ne, 180.0, 0), 0, hh21, 0, 3);
coordsArray = fillCoordsArray(HH21, coordsArray, hh21);
// HH22
System.arraycopy(BondedUtils.determineIntxyz(nh2, dHH_NH, cz, dHH_NH_CZ, hh21, 120.0, 1), 0, hh22, 0, 3);
coordsArray = fillCoordsArray(HH22, coordsArray, hh22);
break;
}
default:
break;
}
}
double[] coordsArray1D = new double[atomArray.length * 3];
for (int i = 0; i < atomArray.length; i++) {
for (int j = 0; j < 3; j++) {
coordsArray1D[i * 3 + j] = coordsArray[i][j];
}
}
return coordsArray1D;
}
Also used :
AminoAcid3(ffx.potential.bonded.ResidueEnumerations.AminoAcid3)
Example 12 with AminoAcid3
use of ffx.potential.bonded.ResidueEnumerations.AminoAcid3 in project ffx by mjschnie.
the class Residue method getRotamers.
/**
* Gets the Rotamers for this residue, potentially incorporating the
* original coordinates if RotamerLibrary's original coordinates rotamer
* flag has been set.
*
* @param library Rotamer library to use
* @return An array of Rotamer.
*/
public Rotamer[] getRotamers(RotamerLibrary library) {
/**
* If the rotamers for this residue have been cached, return them.
*/
if (rotamers != null) {
return rotamers;
}
/**
* Return rotamers for this residue from the RotamerLibrary.
*/
Rotamer[] libRotamers = library.getRotamers(this);
/**
* If there are no rotamers, and addOrigRot is true, return an array with
* only an original-coordinates rotamer. Else if there are no rotamers,
* return (null) library rotamers. If there are rotamers, and original
* coordinates are turned off, return (filled) library rotamers. Else,
* continue generating the rotamers array.
*/
if (libRotamers == null) {
if (addOrigRot) {
rotamers = new Rotamer[1];
ResidueState origState = this.storeState();
double[] chi = RotamerLibrary.measureRotamer(this, false);
switch(residueType) {
case AA:
AminoAcid3 aa3 = AminoAcid3.UNK;
try {
aa3 = AminoAcid3.valueOf(getName());
} catch (Exception e) {
}
originalRotamer = new Rotamer(aa3, origState, chi[0], 0, chi[1], 0, chi[2], 0, chi[3], 0);
rotamers[0] = originalRotamer;
break;
case NA:
NucleicAcid3 na3 = NucleicAcid3.UNK;
try {
na3 = NucleicAcid3.valueOf(getName());
} catch (Exception e) {
}
originalRotamer = new Rotamer(na3, origState, chi[0], 0, chi[1], 0, chi[2], 0, chi[3], 0, chi[4], 0, chi[5], 0);
rotamers[0] = originalRotamer;
break;
default:
originalRotamer = null;
// Resets to null.
rotamers = libRotamers;
}
return rotamers;
} else {
return libRotamers;
}
} else if (!library.getUsingOrigCoordsRotamer()) {
return libRotamers;
}
/**
* Define the current coordinates as a new rotamer.
*/
ResidueState origState = storeState();
double[] chi = RotamerLibrary.measureRotamer(this, false);
switch(residueType) {
case AA:
AminoAcid3 aa3 = this.getAminoAcid3();
originalRotamer = new Rotamer(aa3, origState, chi[0], 0, chi[1], 0, chi[2], 0, chi[3], 0);
break;
case NA:
NucleicAcid3 na3 = this.getNucleicAcid3();
originalRotamer = new Rotamer(na3, origState, chi[0], 0, chi[1], 0, chi[2], 0, chi[3], 0, chi[4], 0, chi[5], 0);
break;
default:
double[] rotaValues = new double[chi.length * 2];
for (int i = 0; i < chi.length; i++) {
int ii = i * 2;
rotaValues[ii] = chi[i];
rotaValues[ii + 1] = 0.0;
}
originalRotamer = new Rotamer(origState, rotaValues);
break;
}
/**
* Add the new rotamer to those from the library and cache the result.
*/
int nRots = libRotamers.length;
rotamers = new Rotamer[nRots + 1];
if (origAtEnd) {
System.arraycopy(libRotamers, 0, rotamers, 0, nRots);
rotamers[rotamers.length - 1] = originalRotamer;
} else {
System.arraycopy(libRotamers, 0, rotamers, 1, nRots);
rotamers[0] = originalRotamer;
}
/**
* Return the rotamer array.
*/
return rotamers;
}
Also used :
NucleicAcid3(ffx.potential.bonded.ResidueEnumerations.NucleicAcid3)
AminoAcid3(ffx.potential.bonded.ResidueEnumerations.AminoAcid3)
Example 13 with AminoAcid3
use of ffx.potential.bonded.ResidueEnumerations.AminoAcid3 in project ffx by mjschnie.
the class TitrationUtils method performTitration.
/**
* Perform the requested titration on the given MultiResidue. Remember to
* call reInit() on affected ForceFieldEnergy and MolecularDynamics objects!
*
* @param multiRes
* @param titration
*/
public static TitrationType performTitration(MultiResidue multiRes, Titration titration, boolean inactivateBackground) {
AminoAcid3 current = multiRes.getActive().getAminoAcid3();
final TitrationType type;
final AminoAcid3 target;
if (current == titration.protForm) {
type = TitrationType.DEPROT;
target = titration.deprotForm;
} else if (current == titration.deprotForm) {
type = TitrationType.PROT;
target = titration.protForm;
} else {
throw new IllegalStateException();
}
boolean success = multiRes.requestSetActiveResidue(target);
if (!success) {
logger.severe(String.format("Couldn't perform requested titration for MultiRes: %s", multiRes.toString()));
}
List<Atom> oldAtoms = multiRes.getActive().getAtomList();
List<Atom> newAtoms = multiRes.getActive().getAtomList();
// identify which atoms were actually inserted/removed
List<Atom> removedAtoms = new ArrayList<>();
List<Atom> insertedAtoms = new ArrayList<>();
for (Atom oldAtom : oldAtoms) {
boolean found = false;
for (Atom newAtom : newAtoms) {
if (newAtom == oldAtom || (newAtom.getResidueNumber() == oldAtom.getResidueNumber() && newAtom.getName().equals(oldAtom.getName()))) {
found = true;
break;
}
}
if (!found) {
removedAtoms.add(oldAtom);
}
}
for (Atom newAtom : newAtoms) {
boolean found = false;
for (Atom oldAtom : oldAtoms) {
if (newAtom == oldAtom || (newAtom.getResidueNumber() == oldAtom.getResidueNumber() && newAtom.getName().equals(oldAtom.getName()))) {
found = true;
break;
}
}
if (!found) {
insertedAtoms.add(newAtom);
}
}
if (insertedAtoms.size() + removedAtoms.size() > 1) {
logger.warning("Protonate: removed + inserted atom count > 1.");
}
if (inactivateBackground) {
activateResidue(multiRes.getActive());
for (Residue res : multiRes.getInactive()) {
inactivateResidue(res);
}
}
return type;
}
Also used :
MultiResidue(ffx.potential.bonded.MultiResidue)
Residue(ffx.potential.bonded.Residue)
AminoAcid3(ffx.potential.bonded.ResidueEnumerations.AminoAcid3)
ArrayList(java.util.ArrayList)
Atom(ffx.potential.bonded.Atom)
Example 14 with AminoAcid3
use of ffx.potential.bonded.ResidueEnumerations.AminoAcid3 in project ffx by mjschnie.
the class RotamerLibrary method measureAARotamer.
/**
* Measures the torsions of an amino acid Residue's current configuration.
*
* @param residue To be measured.
* @param chi Array to be filled with torsion values.
* @param print Verbosity flag.
*/
public static void measureAARotamer(Residue residue, double[] chi, boolean print) {
if (residue instanceof MultiResidue) {
residue = ((MultiResidue) residue).getActive();
}
AminoAcid3 name = residue.getAminoAcid3();
/*try {
name = AminoAcid3.valueOf(residue.getName());
} catch (IllegalArgumentException ex) {
logger.info(String.format("(IAE) valueOf(%s)", residue.getName()));
throw ex;
}*/
switch(name) {
case VAL:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom CG1 = (Atom) residue.getAtomNode("CG1");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, CG1)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
break;
}
}
break;
}
case LEU:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom CG = (Atom) residue.getAtomNode("CG");
Atom CD1 = (Atom) residue.getAtomNode("CD1");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, CG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CA, CB, CG, CD1)) {
chi[1] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
}
break;
}
case ILE:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom CD1 = (Atom) residue.getAtomNode("CD1");
Atom CG1 = (Atom) residue.getAtomNode("CG1");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, CG1)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CA, CB, CG1, CD1)) {
chi[1] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
}
break;
}
case SER:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom OG = (Atom) residue.getAtomNode("OG");
Atom HG = (Atom) residue.getAtomNode("HG");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, OG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CA, CB, OG, HG)) {
chi[1] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
}
break;
}
case THR:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom OG1 = (Atom) residue.getAtomNode("OG1");
Atom HG1 = (Atom) residue.getAtomNode("HG1");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, OG1)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CA, CB, OG1, HG1)) {
chi[1] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
}
break;
}
case CYX:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom SG = (Atom) residue.getAtomNode("SG");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, SG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
break;
}
}
break;
}
case CYD:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom SG = (Atom) residue.getAtomNode("SG");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, SG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
break;
}
}
break;
}
case PHE:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom CD1 = (Atom) residue.getAtomNode("CD1");
Atom CG = (Atom) residue.getAtomNode("CG");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, CG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
break;
}
}
break;
}
case PRO:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom CD = (Atom) residue.getAtomNode("CD");
Atom CG = (Atom) residue.getAtomNode("CG");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, CG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CA, CB, CG, CD)) {
chi[1] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
}
break;
}
case TYR:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom CD1 = (Atom) residue.getAtomNode("CD1");
Atom CE2 = (Atom) residue.getAtomNode("CE2");
Atom CG = (Atom) residue.getAtomNode("CG");
Atom CZ = (Atom) residue.getAtomNode("CZ");
Atom OH = (Atom) residue.getAtomNode("OH");
Atom HH = (Atom) residue.getAtomNode("HH");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, CG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CA, CB, CG, CD1)) {
chi[1] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CE2, CZ, OH, HH)) {
chi[2] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
}
break;
}
case TYD:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom CD1 = (Atom) residue.getAtomNode("CD1");
Atom CG = (Atom) residue.getAtomNode("CG");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, CG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CA, CB, CG, CD1)) {
chi[1] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
}
break;
}
case TRP:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom CD1 = (Atom) residue.getAtomNode("CD1");
Atom CG = (Atom) residue.getAtomNode("CG");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, CG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CA, CB, CG, CD1)) {
chi[1] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
}
break;
}
case HIS:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom CG = (Atom) residue.getAtomNode("CG");
Atom ND1 = (Atom) residue.getAtomNode("ND1");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, CG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CA, CB, CG, ND1)) {
chi[1] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
}
break;
}
case HID:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom CG = (Atom) residue.getAtomNode("CG");
Atom ND1 = (Atom) residue.getAtomNode("ND1");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, CG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CA, CB, CG, ND1)) {
chi[1] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
}
break;
}
case HIE:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom CG = (Atom) residue.getAtomNode("CG");
Atom ND1 = (Atom) residue.getAtomNode("ND1");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, CG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CA, CB, CG, ND1)) {
chi[1] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
}
break;
}
case ASP:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom CG = (Atom) residue.getAtomNode("CG");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, CG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
break;
}
}
break;
}
case ASH:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom CG = (Atom) residue.getAtomNode("CG");
Atom OD1 = (Atom) residue.getAtomNode("OD1");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, CG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CA, CB, CG, OD1)) {
chi[1] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
}
break;
}
case ASN:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom CG = (Atom) residue.getAtomNode("CG");
Atom OD1 = (Atom) residue.getAtomNode("OD1");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, CG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CA, CB, CG, OD1)) {
chi[1] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
}
break;
}
case GLU:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom CG = (Atom) residue.getAtomNode("CG");
Atom CD = (Atom) residue.getAtomNode("CD");
Atom OE1 = (Atom) residue.getAtomNode("OE1");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, CG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CA, CB, CG, CD)) {
chi[1] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CB, CG, CD, OE1)) {
chi[2] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
}
break;
}
case GLH:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom CG = (Atom) residue.getAtomNode("CG");
Atom CD = (Atom) residue.getAtomNode("CD");
Atom OE1 = (Atom) residue.getAtomNode("OE1");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, CG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CA, CB, CG, CD)) {
chi[1] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CB, CG, CD, OE1)) {
chi[2] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
}
break;
}
case GLN:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom CG = (Atom) residue.getAtomNode("CG");
Atom CD = (Atom) residue.getAtomNode("CD");
Atom OE1 = (Atom) residue.getAtomNode("OE1");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, CG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CA, CB, CG, CD)) {
chi[1] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CB, CG, CD, OE1)) {
chi[2] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
}
break;
}
case MET:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom CG = (Atom) residue.getAtomNode("CG");
Atom CE = (Atom) residue.getAtomNode("CE");
Atom SD = (Atom) residue.getAtomNode("SD");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, CG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CA, CB, CG, SD)) {
chi[1] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CB, CG, SD, CE)) {
chi[2] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
}
break;
}
case LYS:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom CD = (Atom) residue.getAtomNode("CD");
Atom CE = (Atom) residue.getAtomNode("CE");
Atom CG = (Atom) residue.getAtomNode("CG");
Atom NZ = (Atom) residue.getAtomNode("NZ");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, CG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CA, CB, CG, CD)) {
chi[1] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CB, CG, CD, CE)) {
chi[2] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CG, CD, CE, NZ)) {
chi[3] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
}
break;
}
case LYD:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom CD = (Atom) residue.getAtomNode("CD");
Atom CE = (Atom) residue.getAtomNode("CE");
Atom CG = (Atom) residue.getAtomNode("CG");
Atom NZ = (Atom) residue.getAtomNode("NZ");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, CG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CA, CB, CG, CD)) {
chi[1] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CB, CG, CD, CE)) {
chi[2] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CG, CD, CE, NZ)) {
chi[3] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
}
break;
}
case ARG:
{
ArrayList<ROLS> torsions = residue.getTorsionList();
Atom N = (Atom) residue.getAtomNode("N");
Atom CA = (Atom) residue.getAtomNode("CA");
Atom CB = (Atom) residue.getAtomNode("CB");
Atom CD = (Atom) residue.getAtomNode("CD");
Atom CG = (Atom) residue.getAtomNode("CG");
Atom CZ = (Atom) residue.getAtomNode("CZ");
Atom NE = (Atom) residue.getAtomNode("NE");
for (ROLS rols : torsions) {
Torsion torsion = (Torsion) rols;
if (torsion.compare(N, CA, CB, CG)) {
chi[0] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CA, CB, CG, CD)) {
chi[1] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CB, CG, CD, NE)) {
chi[2] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
if (torsion.compare(CG, CD, NE, CZ)) {
chi[3] = torsion.getValue();
if (print) {
logger.info(torsion.toString());
}
}
}
break;
}
case UNK:
chi = new double[7];
String resName = residue.getName().toUpperCase();
if (nonstdRotCache.containsKey(resName)) {
nonstdRotCache.get(resName).measureNonstdRot(residue, chi, print);
// nonstdRotCache.get(resName).applyNonstdRotamer(residue, rotamer);
} else {
throw new IllegalArgumentException(String.format("(IAE) valueOf(%s)", residue.getName()));
}
break;
default:
{
}
}
}
Also used :
AminoAcid3(ffx.potential.bonded.ResidueEnumerations.AminoAcid3)
ArrayList(java.util.ArrayList)
Example 15 with AminoAcid3
use of ffx.potential.bonded.ResidueEnumerations.AminoAcid3 in project ffx by mjschnie.
the class MultiResidue method getRotamers.
@Override
public Rotamer[] getRotamers(RotamerLibrary library) {
if (rotamers != null) {
return rotamers;
}
List<Rotamer[]> usual = new ArrayList<>();
int nRots = 0;
for (Residue residue : consideredResidues) {
Rotamer[] rotamers = library.getRotamers(residue);
if (rotamers != null && rotamers.length > 0) {
usual.add(rotamers);
nRots += rotamers.length;
}
}
if (library.getUsingOrigCoordsRotamer()) {
if (originalRotamer == null && (residueType == ResidueType.AA || residueType == ResidueType.NA)) {
ResidueState origState = storeState();
double[] chi = RotamerLibrary.measureRotamer(activeResidue, false);
if (residueType == ResidueType.AA) {
AminoAcid3 aa3 = this.getAminoAcid3();
originalRotamer = new Rotamer(aa3, origState, chi);
} else if (residueType == ResidueType.NA) {
NucleicAcid3 na3 = this.getNucleicAcid3();
originalRotamer = new Rotamer(na3, origState, chi);
}
}
Rotamer[] allRotamers;
if (originalRotamer != null) {
allRotamers = new Rotamer[nRots + 1];
int index;
if (origAtEnd) {
index = 0;
allRotamers[allRotamers.length - 1] = originalRotamer;
} else {
index = 1;
allRotamers[0] = originalRotamer;
}
for (Rotamer[] rotamersI : usual) {
int nrotamers = rotamersI.length;
System.arraycopy(rotamersI, 0, allRotamers, index, nrotamers);
index += nrotamers;
}
} else {
allRotamers = addAllDefaultRotamers(usual, nRots);
}
return allRotamers;
} else {
return addAllDefaultRotamers(usual, nRots);
}
}
Also used :
NucleicAcid3(ffx.potential.bonded.ResidueEnumerations.NucleicAcid3)
AminoAcid3(ffx.potential.bonded.ResidueEnumerations.AminoAcid3)
ArrayList(java.util.ArrayList)
Aggregations
AminoAcid3 (ffx.potential.bonded.ResidueEnumerations.AminoAcid3)19
Atom (ffx.potential.bonded.Atom)9
ArrayList (java.util.ArrayList)9
Residue (ffx.potential.bonded.Residue)7
MissingAtomTypeException (ffx.potential.bonded.BondedUtils.MissingAtomTypeException)4
MissingHeavyAtomException (ffx.potential.bonded.BondedUtils.MissingHeavyAtomException)4
MultiResidue (ffx.potential.bonded.MultiResidue)4
NucleicAcid3 (ffx.potential.bonded.ResidueEnumerations.NucleicAcid3)4
AtomType (ffx.potential.parameters.AtomType)4
Bond (ffx.potential.bonded.Bond)3
Polymer (ffx.potential.bonded.Polymer)3
ResidueEnumerations.aminoAcidList (ffx.potential.bonded.ResidueEnumerations.aminoAcidList)3
ResidueEnumerations.nucleicAcidList (ffx.potential.bonded.ResidueEnumerations.nucleicAcidList)3
Torsion (ffx.potential.bonded.Torsion)3
TitrationUtils.inactivateResidue (ffx.potential.extended.TitrationUtils.inactivateResidue)3
List (java.util.List)3
MSNode (ffx.potential.bonded.MSNode)2
Molecule (ffx.potential.bonded.Molecule)2
ResiduePosition (ffx.potential.bonded.Residue.ResiduePosition)2
ResidueState (ffx.potential.bonded.ResidueState)2
