use of ffx.potential.bonded.BondedUtils.findAtomType in project ffx by mjschnie.
the class AminoAcidUtils method assignAminoAcidAtomTypes.
public static void assignAminoAcidAtomTypes(Residue residue, Residue previousResidue, Residue nextResidue, ForceField forceField, ArrayList<Bond> bondList) throws MissingHeavyAtomException, MissingAtomTypeException {
String residueName = residue.getName().toUpperCase();
int j = 1;
ResiduePosition position = MIDDLE_RESIDUE;
if (previousResidue == null) {
j = 0;
position = FIRST_RESIDUE;
} else if (nextResidue == null) {
j = 2;
position = LAST_RESIDUE;
/**
* If the last residue only contains a nitrogen turn it into an NH2
* group.
*/
Atom N = (Atom) residue.getAtomNode("N");
if (residue.getAtomNodeList().size() == 1 && N != null) {
residueName = "NH2".intern();
residue.setName(residueName);
}
}
AminoAcid3 aminoAcid = getAminoAcid(residueName);
int aminoAcidNumber = getAminoAcidNumber(residueName);
/**
* Non-standard Amino Acid; use ALA backbone types.
*/
boolean nonStandard = false;
if (aminoAcid == AminoAcid3.UNK) {
aminoAcidNumber = getAminoAcidNumber("ALA");
nonStandard = true;
}
/**
* Only the last residue in a chain should have an OXT/OT2 atom.
*/
if (nextResidue != null) {
removeOXT_OT2(residue);
}
/**
* Only the first nitrogen should have H1, H2 and H3 atoms, unless it's
* an NME cap.
*/
if (previousResidue != null) {
removeH1_H2_H3(aminoAcid, residue);
}
/**
* Check for missing heavy atoms. This check ignores special terminating
* groups like FOR, NH2, etc.
*/
if (!nonStandard) {
try {
checkForMissingHeavyAtoms(aminoAcidNumber, aminoAcid, position, residue);
} catch (BondedUtils.MissingHeavyAtomException e) {
logger.log(Level.INFO, " {0} could not be parsed.", residue.toString());
logger.warning("MissingHeavyAtomException incoming from 194.");
throw e;
}
}
Atom pC = null;
Atom pCA = null;
if (previousResidue != null) {
pC = (Atom) previousResidue.getAtomNode("C");
pCA = (Atom) previousResidue.getAtomNode("CA");
}
/**
* Backbone heavy atoms.
*/
Atom N = (Atom) residue.getAtomNode("N");
if (N != null) {
N.setAtomType(BondedUtils.findAtomType(AA_N[j][aminoAcidNumber], forceField));
if (position != FIRST_RESIDUE) {
buildBond(pC, N, forceField, bondList);
}
}
Atom CA = null;
Atom C = null;
Atom O = null;
if (!(position == LAST_RESIDUE && aminoAcid == AminoAcid3.NH2)) {
if (aminoAcid == AminoAcid3.ACE || aminoAcid == AminoAcid3.NME) {
CA = buildHeavy(residue, "CH3", N, AA_CA[j][aminoAcidNumber], forceField, bondList);
} else {
CA = buildHeavy(residue, "CA", N, AA_CA[j][aminoAcidNumber], forceField, bondList);
}
if (!(position == LAST_RESIDUE && aminoAcid == AminoAcid3.NME)) {
C = buildHeavy(residue, "C", CA, AA_C[j][aminoAcidNumber], forceField, bondList);
O = (Atom) residue.getAtomNode("O");
if (O == null) {
O = (Atom) residue.getAtomNode("OT1");
}
AtomType atomType = findAtomType(AA_O[j][aminoAcidNumber], forceField);
if (O == null) {
MissingHeavyAtomException missingHeavyAtom = new MissingHeavyAtomException("O", atomType, C);
logger.warning(" MissingHeavyAtomException incoming from 234.");
throw missingHeavyAtom;
}
O.setAtomType(atomType);
buildBond(C, O, forceField, bondList);
}
}
/**
* Nitrogen hydrogen atoms.
*/
AtomType atomType = findAtomType(AA_HN[j][aminoAcidNumber], forceField);
switch(position) {
case FIRST_RESIDUE:
switch(aminoAcid) {
case PRO:
buildHydrogenAtom(residue, "H2", N, 1.02, CA, 109.5, C, 0.0, 0, atomType, forceField, bondList);
buildHydrogenAtom(residue, "H3", N, 1.02, CA, 109.5, C, -120.0, 0, atomType, forceField, bondList);
break;
case PCA:
buildHydrogenAtom(residue, "H", N, 1.02, CA, 109.5, C, -60.0, 0, atomType, forceField, bondList);
break;
case ACE:
break;
default:
buildHydrogenAtom(residue, "H1", N, 1.02, CA, 109.5, C, 180.0, 0, atomType, forceField, bondList);
buildHydrogenAtom(residue, "H2", N, 1.02, CA, 109.5, C, 60.0, 0, atomType, forceField, bondList);
buildHydrogenAtom(residue, "H3", N, 1.02, CA, 109.5, C, -60.0, 0, atomType, forceField, bondList);
}
break;
case LAST_RESIDUE:
switch(aminoAcid) {
case NH2:
buildHydrogenAtom(residue, "H1", N, 1.02, pC, 119.0, pCA, 0.0, 0, atomType, forceField, bondList);
buildHydrogenAtom(residue, "H2", N, 1.02, pC, 119.0, pCA, 180.0, 0, atomType, forceField, bondList);
break;
case NME:
buildHydrogenAtom(residue, "H", N, 1.02, pC, 118.0, CA, 121.0, 1, atomType, forceField, bondList);
break;
default:
buildHydrogenAtom(residue, "H", N, 1.02, pC, 119.0, CA, 119.0, 1, atomType, forceField, bondList);
}
break;
default:
// Mid-chain nitrogen hydrogen.
buildHydrogenAtom(residue, "H", N, 1.02, pC, 119.0, CA, 119.0, 1, atomType, forceField, bondList);
}
/**
* C-alpha hydrogen atoms.
*/
String haName = "HA";
if (aminoAcid == AminoAcid3.GLY) {
haName = "HA2";
}
atomType = findAtomType(AA_HA[j][aminoAcidNumber], forceField);
switch(position) {
case FIRST_RESIDUE:
switch(aminoAcid) {
case FOR:
buildHydrogenAtom(residue, "H", C, 1.12, O, 0.0, null, 0.0, 0, atomType, forceField, bondList);
break;
case ACE:
buildHydrogenAtom(residue, "H1", CA, 1.10, C, 109.5, O, 180.0, 0, atomType, forceField, bondList);
buildHydrogenAtom(residue, "H2", CA, 1.10, C, 109.5, O, 60.0, 0, atomType, forceField, bondList);
buildHydrogenAtom(residue, "H3", CA, 1.10, C, 109.5, O, -60.0, 0, atomType, forceField, bondList);
break;
default:
buildHydrogenAtom(residue, haName, CA, 1.10, N, 109.5, C, 109.5, -1, atomType, forceField, bondList);
break;
}
break;
case LAST_RESIDUE:
switch(aminoAcid) {
case NME:
buildHydrogenAtom(residue, "H1", CA, 1.10, N, 109.5, pC, 180.0, 0, atomType, forceField, bondList);
buildHydrogenAtom(residue, "H2", CA, 1.10, N, 109.5, pC, 60.0, 0, atomType, forceField, bondList);
buildHydrogenAtom(residue, "H3", CA, 1.10, N, 109.5, pC, -60.0, 0, atomType, forceField, bondList);
break;
default:
buildHydrogenAtom(residue, haName, CA, 1.10, N, 109.5, C, 109.5, -1, atomType, forceField, bondList);
}
break;
default:
buildHydrogenAtom(residue, haName, CA, 1.10, N, 109.5, C, 109.0, -1, atomType, forceField, bondList);
}
/**
* Build the amino acid side chain.
*/
assignAminoAcidSideChain(position, aminoAcid, residue, CA, N, C, forceField, bondList);
/**
* Build the terminal oxygen if the residue is not NH2 or NME.
*/
if (position == LAST_RESIDUE && !(aminoAcid == AminoAcid3.NH2 || aminoAcid == AminoAcid3.NME)) {
atomType = findAtomType(AA_O[2][aminoAcidNumber], forceField);
Atom OXT = (Atom) residue.getAtomNode("OXT");
if (OXT == null) {
OXT = (Atom) residue.getAtomNode("OT2");
if (OXT != null) {
OXT.setName("OXT");
}
}
if (OXT == null) {
String resName = C.getResidueName();
int resSeq = C.getResidueNumber();
Character chainID = C.getChainID();
Character altLoc = C.getAltLoc();
String segID = C.getSegID();
double occupancy = C.getOccupancy();
double tempFactor = C.getTempFactor();
OXT = new Atom(0, "OXT", altLoc, new double[3], resName, resSeq, chainID, occupancy, tempFactor, segID);
OXT.setAtomType(atomType);
residue.addMSNode(OXT);
intxyz(OXT, C, 1.25, CA, 117.0, O, 126.0, 1);
} else {
OXT.setAtomType(atomType);
}
buildBond(C, OXT, forceField, bondList);
}
/**
* Do some checks on the current residue to make sure all atoms have
* been assigned an atom type.
*/
List<Atom> resAtoms = residue.getAtomList();
for (Atom atom : resAtoms) {
atomType = atom.getAtomType();
if (atomType == null) {
/**
* Sometimes, with deuterons, a proton has been constructed in
* its place, so we have a "dummy" deuteron still hanging
* around.
*/
String protonEq = atom.getName().replaceFirst("D", "H");
Atom correspH = (Atom) residue.getAtomNode(protonEq);
if (correspH == null || correspH.getAtomType() == null) {
MissingAtomTypeException missingAtomTypeException = new MissingAtomTypeException(residue, atom);
logger.warning("MissingAtomTypeException incoming from 393.");
throw missingAtomTypeException;
} else {
correspH.setName(atom.getName());
atom.removeFromParent();
atom = correspH;
atomType = atom.getAtomType();
}
}
int numberOfBonds = atom.getNumBonds();
if (numberOfBonds != atomType.valence) {
if (atom == C && numberOfBonds == atomType.valence - 1 && position != LAST_RESIDUE) {
continue;
}
logger.warning(format(" An atom for residue %s has the wrong number of bonds:\n %s", residueName, atom.toString()));
logger.warning(format(" Expected: %d Actual: %d.", atomType.valence, numberOfBonds));
}
}
}
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