public static double getGenChi1(Residue res) {
// Get the generalized chi1 of a residue
if (res.template.name.equalsIgnoreCase("GLY")) return 0;
else {
String lastAtom = getGenChi1LastAtom(res.template.name);
double lastCoords[] = res.getCoordsByAtomName(lastAtom);
double[][] keyCoords = HardCodedResidueInfo.getKeyCoords(res);
double[] NCoords = keyCoords[0];
double[] CACoords = keyCoords[1];
double[] CBCoords = keyCoords[2];
if (lastCoords == null || NCoords == null || CACoords == null | CBCoords == null) {
// not a protein residue. Doesn't have gen chi1
return Double.NaN;
}
if (lastCoords == null || NCoords == null || CACoords == null | CBCoords == null) {
// not a protein residue. Doesn't have gen chi1
return Double.NaN;
}
// coordinates defining dihedral
double dihCoords[][] = new double[][] {NCoords, CACoords, CBCoords, lastCoords};
return Protractor.measureDihedral(dihCoords);
}
}
public static void setGenChi1(Residue res, double ang) {
// set the residue to have the specified gen chi1 (in degrees)
if ((!HardCodedResidueInfo.hasAminoAcidBB(res))
|| res.template.name.equalsIgnoreCase("GLY")
|| res.template.name.equalsIgnoreCase("PRO")) {
// Glycine doesn't have a generalized chi1,
// and we cannot freely change proline's (sidechain idealization sets
// a chi1 for proline that should remain in place)
return;
}
double curGenChi1 = getGenChi1(res);
double genChi1Change = ang - curGenChi1;
DihedralRotation dihRot =
new DihedralRotation(
res.getCoordsByAtomName("CA"), res.getCoordsByAtomName("CB"), genChi1Change);
// now carry out the rotation on all the sidechain atoms
// (expect CB, since it's part of the bond begin rotated around)
int numAtoms = res.atoms.size();
for (int atomNum = 0; atomNum < numAtoms; atomNum++) {
String atomName = res.atoms.get(atomNum).name;
if (SidechainIdealizer.isSidechainAtom(atomName, res)) {
if (!(atomName.equalsIgnoreCase("CB"))) dihRot.transform(res.coords, atomNum);
}
}
}
public static void setGenChi1(Residue res, double ang) {
// set the residue to have the specified gen chi1 (in degrees)
if ((!HardCodedResidueInfo.hasAminoAcidBB(res))
|| !(HardCodedResidueInfo.hasNucleicAcidBB(res)) // DZ: NA BBs are fine now
|| res.template.name.equalsIgnoreCase("GLY")
|| res.template.name.equalsIgnoreCase("PRO")) {
// Glycine doesn't have a generalized chi1,
// and we cannot freely change proline's (sidechain idealization sets
// a chi1 for proline that should remain in place)
return;
}
double curGenChi1 = getGenChi1(res);
double genChi1Change = ang - curGenChi1;
double[][] keyCoords = HardCodedResidueInfo.getKeyCoords(res);
double[] CACoords = keyCoords[1];
double[] CBCoords = keyCoords[2];
// pivotAtom will be CB for amino acids, N9 or N1 for nucleic acids.
String pivotAtom =
HardCodedResidueInfo.hasNucleicAcidBB(res)
? HardCodedResidueInfo.isPyrimidine(res.template.name) ? "N9" : "N1"
: "CB";
DihedralRotation dihRot = new DihedralRotation(CACoords, CBCoords, genChi1Change);
// now carry out the rotation on all the sidechain atoms
// (expect CB, since it's part of the bond begin rotated around)
int numAtoms = res.atoms.size();
for (int atomNum = 0; atomNum < numAtoms; atomNum++) {
String atomName = res.atoms.get(atomNum).name;
if (SidechainIdealizer.isSidechainAtom(atomName, res)) {
if (!(atomName.equalsIgnoreCase(pivotAtom))) {
dihRot.transform(res.coords, atomNum);
}
}
}
}
public static String getGenChi1LastAtom(String resName) {
// Get atom name X where generalized chi1 is N-CA-CB-X
if (resName.equalsIgnoreCase("val") || resName.equalsIgnoreCase("ile")) {
return "CG1";
} else if (resName.equalsIgnoreCase("ser")) {
return "OG";
} else if (resName.equalsIgnoreCase("thr")) {
return "OG1";
} else if (resName.equalsIgnoreCase("cys") || resName.equalsIgnoreCase("cyx")) {
return "SG";
} else if (resName.equalsIgnoreCase("ala")) {
return "HB1";
} else if (HardCodedResidueInfo.isPyrimidine(resName)) {
return "C2";
} else if (HardCodedResidueInfo.isPurine(resName)) {
return "C4";
} else {
return "CG";
}
}