use of ffx.potential.bonded.ResidueEnumerations.AminoAcid3 in project ffx by mjschnie.
the class RosenbluthOBMC method getChiZeroTorsion.
private Torsion getChiZeroTorsion(Residue residue) {
AminoAcid3 name = AminoAcid3.valueOf(residue.getName());
ArrayList<ROLS> torsions = residue.getTorsionList();
switch(name) {
case VAL:
{
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)) {
return torsion;
}
}
break;
}
case ILE:
{
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)) {
return torsion;
}
}
break;
}
case SER:
{
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)) {
return torsion;
}
}
break;
}
case THR:
{
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)) {
return torsion;
}
}
break;
}
case CYX:
{
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)) {
return torsion;
}
}
break;
}
case CYD:
{
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)) {
return torsion;
}
}
break;
}
default:
{
// All other residues' chi[0] are defined by N,CA,CB,CG.
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)) {
return torsion;
}
}
logger.info("Couldn't find chi[0] for residue " + residue.toString());
return null;
}
}
logger.info("Couldn't find chi[0] for residue " + residue.toString());
return null;
}
use of ffx.potential.bonded.ResidueEnumerations.AminoAcid3 in project ffx by mjschnie.
the class MultiResidue method addResiduesByName.
public void addResiduesByName(List<String> resNames) {
boolean resAdded = false;
Residue currentRes = activeResidue;
for (String resName : resNames) {
try {
AminoAcid3 aa3 = AminoAcid3.valueOf(resName.toUpperCase());
logger.info(String.format(" Adding residue %s to multi-residue " + "%s", aa3.toString(), this.toString()));
addResidue(new Residue(aa3.toString(), getResidueNumber(), getResidueType()));
resAdded = true;
} catch (IllegalArgumentException e) {
logger.warning(String.format(" Could not parse %s as an amino " + "acid; not adding to multi-residue %s", resName, this.toString()));
}
}
if (resAdded) {
setActiveResidue(currentRes);
if (automaticReinitialization) {
forceFieldEnergy.reInit();
}
}
}
use of ffx.potential.bonded.ResidueEnumerations.AminoAcid3 in project ffx by mjschnie.
the class PDBFilter method assignAtomTypes.
/**
* Assign force field atoms types to common chemistries using "biotype"
* records.
*/
private void assignAtomTypes() {
/**
* Create a list to store bonds defined by PDB atom names.
*/
bondList = new ArrayList<>();
/**
* To Do: Look for cyclic peptides and disulfides.
*/
Polymer[] polymers = activeMolecularAssembly.getChains();
/**
* Loop over chains.
*/
if (polymers != null) {
logger.info(format("\n Assigning atom types for %d chains.", polymers.length));
for (Polymer polymer : polymers) {
List<Residue> residues = polymer.getResidues();
int numberOfResidues = residues.size();
/**
* Check if all residues are known amino acids.
*/
boolean isProtein = true;
for (int residueNumber = 0; residueNumber < numberOfResidues; residueNumber++) {
Residue residue = residues.get(residueNumber);
String name = residue.getName().toUpperCase();
boolean aa = false;
for (AminoAcid3 amino : aminoAcidList) {
if (amino.toString().equalsIgnoreCase(name)) {
aa = true;
checkHydrogenAtomNames(residue);
break;
}
}
// Check for a patch.
if (!aa) {
logger.info(" Checking for non-standard amino acid patch " + name);
HashMap<String, AtomType> types = forceField.getAtomTypes(name);
if (types.isEmpty()) {
isProtein = false;
break;
} else {
logger.info(" Patch found for non-standard amino acid " + name);
}
}
}
/**
* If all the residues in this chain have known amino acids
* names, then attempt to assign atom types.
*/
if (isProtein) {
try {
logger.info(format(" Amino acid chain %s", polymer.getName()));
double dist = properties.getDouble("chainbreak", 3.0);
// Detect main chain breaks!
List<List<Residue>> subChains = findChainBreaks(residues, dist);
for (List<Residue> subChain : subChains) {
assignAminoAcidAtomTypes(subChain);
}
} catch (MissingHeavyAtomException missingHeavyAtomException) {
logger.severe(missingHeavyAtomException.toString());
} catch (MissingAtomTypeException missingAtomTypeException) {
logger.severe(missingAtomTypeException.toString());
}
continue;
}
/**
* Check if all residues have known nucleic acids names.
*/
boolean isNucleicAcid = true;
for (int residueNumber = 0; residueNumber < numberOfResidues; residueNumber++) {
Residue residue = residues.get(residueNumber);
String name = residue.getName().toUpperCase();
/**
* Convert 1 and 2-character nucleic acid names to
* 3-character names.
*/
if (name.length() == 1) {
if (name.equals("A")) {
name = NucleicAcid3.ADE.toString();
} else if (name.equals("C")) {
name = NucleicAcid3.CYT.toString();
} else if (name.equals("G")) {
name = NucleicAcid3.GUA.toString();
} else if (name.equals("T")) {
name = NucleicAcid3.THY.toString();
} else if (name.equals("U")) {
name = NucleicAcid3.URI.toString();
}
} else if (name.length() == 2) {
if (name.equals("YG")) {
name = NucleicAcid3.YYG.toString();
}
}
residue.setName(name);
NucleicAcid3 nucleicAcid = null;
for (NucleicAcid3 nucleic : nucleicAcidList) {
String nuc3 = nucleic.toString();
nuc3 = nuc3.substring(nuc3.length() - 3);
if (nuc3.equalsIgnoreCase(name)) {
nucleicAcid = nucleic;
break;
}
}
if (nucleicAcid == null) {
logger.info(format("Nucleic acid was not recognized %s.", name));
isNucleicAcid = false;
break;
}
}
/**
* If all the residues in this chain have known nucleic acids
* names, then attempt to assign atom types.
*/
if (isNucleicAcid) {
try {
logger.info(format(" Nucleic acid chain %s", polymer.getName()));
assignNucleicAcidAtomTypes(residues, forceField, bondList);
} catch (MissingHeavyAtomException | MissingAtomTypeException e) {
logger.severe(e.toString());
}
}
}
}
// Assign ion atom types.
ArrayList<MSNode> ions = activeMolecularAssembly.getIons();
if (ions != null && ions.size() > 0) {
logger.info(format(" Assigning atom types for %d ions.", ions.size()));
for (MSNode m : ions) {
Molecule ion = (Molecule) m;
String name = ion.getResidueName().toUpperCase();
HetAtoms hetatm = HetAtoms.valueOf(name);
Atom atom = ion.getAtomList().get(0);
if (ion.getAtomList().size() != 1) {
logger.severe(format(" Check residue %s of chain %s.", ion.toString(), ion.getChainID()));
}
try {
switch(hetatm) {
case NA:
atom.setAtomType(findAtomType(2003));
break;
case K:
atom.setAtomType(findAtomType(2004));
break;
case MG:
case MG2:
atom.setAtomType(findAtomType(2005));
break;
case CA:
case CA2:
atom.setAtomType(findAtomType(2006));
break;
case CL:
atom.setAtomType(findAtomType(2007));
break;
case ZN:
case ZN2:
atom.setAtomType(findAtomType(2008));
break;
case BR:
atom.setAtomType(findAtomType(2009));
break;
default:
logger.severe(format(" Check residue %s of chain %s.", ion.toString(), ion.getChainID()));
}
} catch (Exception e) {
String message = "Error assigning atom types.";
logger.log(Level.SEVERE, message, e);
}
}
}
// Assign water atom types.
ArrayList<MSNode> water = activeMolecularAssembly.getWaters();
if (water != null && water.size() > 0) {
logger.info(format(" Assigning atom types for %d waters.", water.size()));
for (MSNode m : water) {
Molecule wat = (Molecule) m;
try {
Atom O = buildHeavy(wat, "O", null, 2001);
Atom H1 = buildHydrogen(wat, "H1", O, 0.96e0, null, 109.5e0, null, 120.0e0, 0, 2002);
H1.setHetero(true);
Atom H2 = buildHydrogen(wat, "H2", O, 0.96e0, H1, 109.5e0, null, 120.0e0, 0, 2002);
H2.setHetero(true);
} catch (Exception e) {
String message = "Error assigning atom types to a water.";
logger.log(Level.SEVERE, message, e);
}
}
}
// Assign small molecule atom types.
ArrayList<Molecule> molecules = activeMolecularAssembly.getMolecules();
for (MSNode m : molecules) {
Molecule molecule = (Molecule) m;
String moleculeName = molecule.getResidueName();
logger.info(" Attempting to patch " + moleculeName);
ArrayList<Atom> moleculeAtoms = molecule.getAtomList();
boolean patched = true;
HashMap<String, AtomType> types = forceField.getAtomTypes(moleculeName);
/**
* Assign atom types for all known atoms.
*/
for (Atom atom : moleculeAtoms) {
String atomName = atom.getName().toUpperCase();
AtomType atomType = types.get(atomName);
if (atomType == null) {
logger.info(" No atom type was found for " + atomName + " of " + moleculeName + ".");
patched = false;
break;
} else {
logger.fine(" " + atom.toString() + " -> " + atomType.toString());
atom.setAtomType(atomType);
types.remove(atomName);
}
}
/**
* Create missing hydrogen atoms. Check for missing heavy atoms.
*/
if (patched && !types.isEmpty()) {
for (AtomType type : types.values()) {
if (type.atomicNumber != 1) {
logger.info(" Missing heavy atom " + type.name);
patched = false;
break;
}
}
}
// Create bonds between known atoms.
if (patched) {
for (Atom atom : moleculeAtoms) {
String atomName = atom.getName();
String[] bonds = forceField.getBonds(moleculeName, atomName);
if (bonds != null) {
for (String name : bonds) {
Atom atom2 = molecule.getAtom(name);
if (atom2 != null && !atom.isBonded(atom2)) {
buildBond(atom, atom2);
}
}
}
}
}
// Create missing hydrogen atoms.
if (patched && !types.isEmpty()) {
// Create a hashmap of the molecule's atoms
HashMap<String, Atom> atomMap = new HashMap<String, Atom>();
for (Atom atom : moleculeAtoms) {
atomMap.put(atom.getName().toUpperCase(), atom);
}
for (String atomName : types.keySet()) {
AtomType type = types.get(atomName);
String[] bonds = forceField.getBonds(moleculeName, atomName.toUpperCase());
if (bonds == null || bonds.length != 1) {
patched = false;
logger.info(" Check biotype for hydrogen " + type.name + ".");
break;
}
// Get the heavy atom the hydrogen is bonded to.
Atom ia = atomMap.get(bonds[0].toUpperCase());
Atom hydrogen = new Atom(0, atomName, ia.getAltLoc(), new double[3], ia.getResidueName(), ia.getResidueNumber(), ia.getChainID(), ia.getOccupancy(), ia.getTempFactor(), ia.getSegID());
logger.fine(" Created hydrogen " + atomName + ".");
hydrogen.setAtomType(type);
hydrogen.setHetero(true);
molecule.addMSNode(hydrogen);
int valence = ia.getAtomType().valence;
List<Bond> aBonds = ia.getBonds();
int numBonds = aBonds.size();
/**
* Try to find the following configuration: ib-ia-ic
*/
Atom ib = null;
Atom ic = null;
Atom id = null;
if (numBonds > 0) {
Bond bond = aBonds.get(0);
ib = bond.get1_2(ia);
}
if (numBonds > 1) {
Bond bond = aBonds.get(1);
ic = bond.get1_2(ia);
}
if (numBonds > 2) {
Bond bond = aBonds.get(2);
id = bond.get1_2(ia);
}
/**
* Building the hydrogens depends on hybridization and the
* locations of other bonded atoms.
*/
logger.fine(" Bonding " + atomName + " to " + ia.getName() + " (" + numBonds + " of " + valence + ").");
switch(valence) {
case 4:
switch(numBonds) {
case 3:
// Find the average coordinates of atoms ib, ic and id.
double[] b = ib.getXYZ(null);
double[] c = ib.getXYZ(null);
double[] d = ib.getXYZ(null);
double[] a = new double[3];
a[0] = (b[0] + c[0] + d[0]) / 3.0;
a[1] = (b[1] + c[1] + d[1]) / 3.0;
a[2] = (b[2] + c[2] + d[2]) / 3.0;
// Place the hydrogen at chiral position #1.
intxyz(hydrogen, ia, 1.0, ib, 109.5, ic, 109.5, 1);
double[] e1 = new double[3];
hydrogen.getXYZ(e1);
double[] ret = new double[3];
diff(a, e1, ret);
double l1 = r(ret);
// Place the hydrogen at chiral position #2.
intxyz(hydrogen, ia, 1.0, ib, 109.5, ic, 109.5, -1);
double[] e2 = new double[3];
hydrogen.getXYZ(e2);
diff(a, e2, ret);
double l2 = r(ret);
// Revert to #1 if it is farther from the average.
if (l1 > l2) {
hydrogen.setXYZ(e1);
}
break;
case 2:
intxyz(hydrogen, ia, 1.0, ib, 109.5, ic, 109.5, 0);
break;
case 1:
intxyz(hydrogen, ia, 1.0, ib, 109.5, null, 0.0, 0);
break;
case 0:
intxyz(hydrogen, ia, 1.0, null, 0.0, null, 0.0, 0);
break;
default:
logger.info(" Check biotype for hydrogen " + atomName + ".");
patched = false;
}
break;
case 3:
switch(numBonds) {
case 2:
intxyz(hydrogen, ia, 1.0, ib, 120.0, ic, 0.0, 0);
break;
case 1:
intxyz(hydrogen, ia, 1.0, ib, 120.0, null, 0.0, 0);
break;
case 0:
intxyz(hydrogen, ia, 1.0, null, 0.0, null, 0.0, 0);
break;
default:
logger.info(" Check biotype for hydrogen " + atomName + ".");
patched = false;
}
break;
case 2:
switch(numBonds) {
case 1:
intxyz(hydrogen, ia, 1.0, ib, 120.0, null, 0.0, 0);
break;
case 0:
intxyz(hydrogen, ia, 1.0, null, 0.0, null, 0.0, 0);
break;
default:
logger.info(" Check biotype for hydrogen " + atomName + ".");
patched = false;
}
break;
case 1:
switch(numBonds) {
case 0:
intxyz(hydrogen, ia, 1.0, null, 0.0, null, 0.0, 0);
break;
default:
logger.info(" Check biotype for hydrogen " + atomName + ".");
patched = false;
}
break;
default:
logger.info(" Check biotype for hydrogen " + atomName + ".");
patched = false;
}
if (!patched) {
break;
} else {
buildBond(ia, hydrogen);
}
}
}
if (!patched) {
logger.log(Level.WARNING, format(" Deleting unrecognized molecule %s.", m.toString()));
activeMolecularAssembly.deleteMolecule((Molecule) m);
} else {
logger.info(" Patch for " + moleculeName + " succeeded.");
}
}
resolvePolymerLinks(molecules);
}
use of ffx.potential.bonded.ResidueEnumerations.AminoAcid3 in project ffx by mjschnie.
the class BiojavaFilter method assignAminoAcidAtomTypes.
private void assignAminoAcidAtomTypes(Residue residue, Residue previousResidue, Residue nextResidue) 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 (MissingHeavyAtomException e) {
logger.log(Level.INFO, " {0} could not be parsed.", residue.toString());
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(findAtomType(AA_N[j][aminoAcidNumber]));
if (position != FIRST_RESIDUE) {
buildBond(pC, N);
}
}
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]);
} else {
CA = buildHeavy(residue, "CA", N, AA_CA[j][aminoAcidNumber]);
}
if (!(position == LAST_RESIDUE && aminoAcid == AminoAcid3.NME)) {
C = buildHeavy(residue, "C", CA, AA_C[j][aminoAcidNumber]);
O = (Atom) residue.getAtomNode("O");
if (O == null) {
O = (Atom) residue.getAtomNode("OT1");
}
AtomType atomType = findAtomType(AA_O[j][aminoAcidNumber]);
if (O == null) {
MissingHeavyAtomException missingHeavyAtom = new MissingHeavyAtomException("O", atomType, C);
throw missingHeavyAtom;
}
O.setAtomType(atomType);
buildBond(C, O);
}
}
/**
* Nitrogen hydrogen atoms.
*/
AtomType atomType = findAtomType(AA_HN[j][aminoAcidNumber]);
switch(position) {
case FIRST_RESIDUE:
switch(aminoAcid) {
case PRO:
buildHydrogenAtom(residue, "H2", N, 1.02, CA, 109.5, C, 0.0, 0, atomType);
buildHydrogenAtom(residue, "H3", N, 1.02, CA, 109.5, C, -120.0, 0, atomType);
break;
case PCA:
buildHydrogenAtom(residue, "H", N, 1.02, CA, 109.5, C, -60.0, 0, atomType);
break;
case ACE:
break;
default:
buildHydrogenAtom(residue, "H1", N, 1.02, CA, 109.5, C, 180.0, 0, atomType);
buildHydrogenAtom(residue, "H2", N, 1.02, CA, 109.5, C, 60.0, 0, atomType);
buildHydrogenAtom(residue, "H3", N, 1.02, CA, 109.5, C, -60.0, 0, atomType);
}
break;
case LAST_RESIDUE:
switch(aminoAcid) {
case NH2:
buildHydrogenAtom(residue, "H1", N, 1.02, pC, 119.0, pCA, 0.0, 0, atomType);
buildHydrogenAtom(residue, "H2", N, 1.02, pC, 119.0, pCA, 180.0, 0, atomType);
break;
case NME:
buildHydrogenAtom(residue, "H", N, 1.02, pC, 118.0, CA, 121.0, 1, atomType);
break;
default:
buildHydrogenAtom(residue, "H", N, 1.02, pC, 119.0, CA, 119.0, 1, atomType);
}
break;
default:
// Mid-chain nitrogen hydrogen.
buildHydrogenAtom(residue, "H", N, 1.02, pC, 119.0, CA, 119.0, 1, atomType);
}
/**
* C-alpha hydrogen atoms.
*/
String haName = "HA";
if (aminoAcid == AminoAcid3.GLY) {
haName = "HA2";
}
atomType = findAtomType(AA_HA[j][aminoAcidNumber]);
switch(position) {
case FIRST_RESIDUE:
switch(aminoAcid) {
case FOR:
buildHydrogenAtom(residue, "H", C, 1.12, O, 0.0, null, 0.0, 0, atomType);
break;
case ACE:
buildHydrogenAtom(residue, "H1", CA, 1.10, C, 109.5, O, 180.0, 0, atomType);
buildHydrogenAtom(residue, "H2", CA, 1.10, C, 109.5, O, 60.0, 0, atomType);
buildHydrogenAtom(residue, "H3", CA, 1.10, C, 109.5, O, -60.0, 0, atomType);
break;
default:
buildHydrogenAtom(residue, haName, CA, 1.10, N, 109.5, C, 109.5, -1, atomType);
break;
}
break;
case LAST_RESIDUE:
switch(aminoAcid) {
case NME:
buildHydrogenAtom(residue, "H1", CA, 1.10, N, 109.5, pC, 180.0, 0, atomType);
buildHydrogenAtom(residue, "H2", CA, 1.10, N, 109.5, pC, 60.0, 0, atomType);
buildHydrogenAtom(residue, "H3", CA, 1.10, N, 109.5, pC, -60.0, 0, atomType);
break;
default:
buildHydrogenAtom(residue, haName, CA, 1.10, N, 109.5, C, 109.5, -1, atomType);
}
break;
default:
buildHydrogenAtom(residue, haName, CA, 1.10, N, 109.5, C, 109.0, -1, atomType);
}
/**
* Build the amino acid side chain.
*/
assignAminoAcidSideChain(position, aminoAcid, residue, CA, N, C);
/**
* 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]);
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);
}
/**
* 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) {
MissingAtomTypeException missingAtomTypeException = new MissingAtomTypeException(residue, atom);
throw missingAtomTypeException;
}
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));
}
}
}
use of ffx.potential.bonded.ResidueEnumerations.AminoAcid3 in project ffx by mjschnie.
the class BiojavaFilter method assignAtomTypes.
/**
* Assign force field atoms types to common chemistries using "biotype"
* records.
*/
public void assignAtomTypes() {
/**
* Create a new List to store bonds determined based on PDB atom names.
*/
bondList = new ArrayList<>();
/**
* To Do: Look for cyclic peptides and disulfides.
*/
Polymer[] polymers = activeMolecularAssembly.getChains();
/**
* Loop over chains.
*/
if (polymers != null) {
logger.info(format("\n Assigning atom types for %d chains.", polymers.length));
for (Polymer polymer : polymers) {
List<Residue> residues = polymer.getResidues();
int numberOfResidues = residues.size();
/**
* Check if all residues are known amino acids.
*/
boolean isProtein = true;
if (!residues.isEmpty()) {
// renameNTerminusHydrogens(residues.get(0)); Not safe to use until it distinguishes between true N-termini and N-terminal residues in general.
}
for (int residueNumber = 0; residueNumber < numberOfResidues; residueNumber++) {
Residue residue = residues.get(residueNumber);
String name = residue.getName().toUpperCase();
boolean aa = false;
for (AminoAcid3 amino : aminoAcidList) {
if (amino.toString().equalsIgnoreCase(name)) {
aa = true;
renameNonstandardHydrogens(residue);
break;
}
}
// Check for a patch.
if (!aa) {
HashMap<String, AtomType> types = forceField.getAtomTypes(name);
if (types.isEmpty()) {
isProtein = false;
break;
} else {
logger.info(" Patch found for non-standard amino acid " + name);
}
}
}
/**
* If all the residues in this chain have known amino acids
* names, then attempt to assign atom types.
*/
if (isProtein) {
try {
logger.info(format(" Amino acid chain %s", polymer.getName()));
double dist = properties.getDouble("chainbreak", 3.0);
// Detect main chain breaks!
List<List<Residue>> subChains = findChainBreaks(residues, dist);
for (List<Residue> subChain : subChains) {
assignAminoAcidAtomTypes(subChain);
}
} catch (MissingHeavyAtomException missingHeavyAtomException) {
logger.severe(missingHeavyAtomException.toString());
} catch (MissingAtomTypeException missingAtomTypeException) {
logger.severe(missingAtomTypeException.toString());
}
continue;
}
/**
* Check if all residues have known nucleic acids names.
*/
boolean isNucleicAcid = true;
for (int residueNumber = 0; residueNumber < numberOfResidues; residueNumber++) {
Residue residue = residues.get(residueNumber);
String name = residue.getName().toUpperCase();
/**
* Convert 1 and 2-character nucleic acid names to
* 3-character names.
*/
if (name.length() == 1) {
if (name.equals("A")) {
name = NucleicAcid3.ADE.toString();
} else if (name.equals("C")) {
name = NucleicAcid3.CYT.toString();
} else if (name.equals("G")) {
name = NucleicAcid3.GUA.toString();
} else if (name.equals("T")) {
name = NucleicAcid3.THY.toString();
} else if (name.equals("U")) {
name = NucleicAcid3.URI.toString();
}
} else if (name.length() == 2) {
if (name.equals("YG")) {
name = NucleicAcid3.YYG.toString();
}
}
residue.setName(name);
NucleicAcid3 nucleicAcid = null;
for (NucleicAcid3 nucleic : nucleicAcidList) {
String nuc3 = nucleic.toString();
nuc3 = nuc3.substring(nuc3.length() - 3);
if (nuc3.equalsIgnoreCase(name)) {
nucleicAcid = nucleic;
break;
}
}
if (nucleicAcid == null) {
logger.info(format("Nucleic acid was not recognized %s.", name));
isNucleicAcid = false;
break;
}
}
/**
* If all the residues in this chain have known nucleic acids
* names, then attempt to assign atom types.
*/
if (isNucleicAcid) {
try {
logger.info(format(" Nucleic acid chain %s", polymer.getName()));
assignNucleicAcidAtomTypes(residues);
} catch (MissingHeavyAtomException missingHeavyAtomException) {
logger.severe(missingHeavyAtomException.toString());
} catch (MissingAtomTypeException missingAtomTypeException) {
logger.severe(missingAtomTypeException.toString());
}
}
}
}
// Assign ion atom types.
ArrayList<MSNode> ions = activeMolecularAssembly.getIons();
if (ions != null && ions.size() > 0) {
logger.info(format(" Assigning atom types for %d ions.", ions.size()));
for (MSNode m : ions) {
Molecule ion = (Molecule) m;
String name = ion.getResidueName().toUpperCase();
HetAtoms hetatm = HetAtoms.valueOf(name);
Atom atom = ion.getAtomList().get(0);
if (ion.getAtomList().size() != 1) {
logger.severe(format(" Check residue %s of chain %s.", ion.toString(), ion.getChainID()));
}
try {
switch(hetatm) {
case NA:
atom.setAtomType(findAtomType(2003));
break;
case K:
atom.setAtomType(findAtomType(2004));
break;
case MG:
case MG2:
atom.setAtomType(findAtomType(2005));
break;
case CA:
case CA2:
atom.setAtomType(findAtomType(2006));
break;
case CL:
atom.setAtomType(findAtomType(2007));
break;
case ZN:
case ZN2:
atom.setAtomType(findAtomType(2008));
break;
case BR:
atom.setAtomType(findAtomType(2009));
break;
default:
logger.severe(format(" Check residue %s of chain %s.", ion.toString(), ion.getChainID()));
}
} catch (Exception e) {
String message = "Error assigning atom types.";
logger.log(Level.SEVERE, message, e);
}
}
}
// Assign water atom types.
ArrayList<MSNode> water = activeMolecularAssembly.getWaters();
if (water != null && water.size() > 0) {
logger.info(format(" Assigning atom types for %d waters.", water.size()));
for (MSNode m : water) {
Molecule wat = (Molecule) m;
try {
Atom O = buildHeavy(wat, "O", null, 2001);
Atom H1 = buildHydrogen(wat, "H1", O, 0.96e0, null, 109.5e0, null, 120.0e0, 0, 2002);
H1.setHetero(true);
Atom H2 = buildHydrogen(wat, "H2", O, 0.96e0, H1, 109.5e0, null, 120.0e0, 0, 2002);
H2.setHetero(true);
} catch (Exception e) {
String message = "Error assigning atom types to a water.";
logger.log(Level.SEVERE, message, e);
}
}
}
// Assign small molecule atom types.
ArrayList<Molecule> molecules = activeMolecularAssembly.getMolecules();
for (MSNode m : molecules) {
Molecule molecule = (Molecule) m;
String moleculeName = molecule.getResidueName();
logger.info(" Attempting to patch " + moleculeName);
ArrayList<Atom> moleculeAtoms = molecule.getAtomList();
boolean patched = true;
HashMap<String, AtomType> types = forceField.getAtomTypes(moleculeName);
/**
* Assign atom types for all known atoms.
*/
for (Atom atom : moleculeAtoms) {
String atomName = atom.getName().toUpperCase();
AtomType atomType = types.get(atomName);
if (atomType == null) {
logger.info(" No atom type was found for " + atomName + " of " + moleculeName + ".");
patched = false;
break;
} else {
atom.setAtomType(atomType);
types.remove(atomName);
}
}
/**
* Create missing hydrogen atoms. Check for missing heavy atoms.
*/
if (patched && !types.isEmpty()) {
for (AtomType type : types.values()) {
if (type.atomicNumber != 1) {
logger.info(" Missing heavy atom " + type.name);
patched = false;
break;
}
}
}
// Create bonds between known atoms.
if (patched) {
for (Atom atom : moleculeAtoms) {
String atomName = atom.getName();
String[] bonds = forceField.getBonds(moleculeName, atomName);
if (bonds != null) {
for (String name : bonds) {
Atom atom2 = molecule.getAtom(name);
if (atom2 != null && !atom.isBonded(atom2)) {
buildBond(atom, atom2);
}
}
}
}
}
// Create missing hydrogen atoms.
if (patched && !types.isEmpty()) {
// Create a hashmap of the molecule's atoms
HashMap<String, Atom> atomMap = new HashMap<String, Atom>();
for (Atom atom : moleculeAtoms) {
atomMap.put(atom.getName().toUpperCase(), atom);
}
for (String atomName : types.keySet()) {
AtomType type = types.get(atomName);
String[] bonds = forceField.getBonds(moleculeName, atomName.toUpperCase());
if (bonds == null || bonds.length != 1) {
patched = false;
logger.info(" Check biotype for hydrogen " + type.name + ".");
break;
}
// Get the heavy atom the hydrogen is bonded to.
Atom ia = atomMap.get(bonds[0].toUpperCase());
Atom hydrogen = new Atom(0, atomName, ia.getAltLoc(), new double[3], ia.getResidueName(), ia.getResidueNumber(), ia.getChainID(), ia.getOccupancy(), ia.getTempFactor(), ia.getSegID());
logger.fine(" Created hydrogen " + atomName + ".");
hydrogen.setAtomType(type);
hydrogen.setHetero(true);
molecule.addMSNode(hydrogen);
int valence = ia.getAtomType().valence;
List<Bond> aBonds = ia.getBonds();
int numBonds = aBonds.size();
/**
* Try to find the following configuration: ib-ia-ic
*/
Atom ib = null;
Atom ic = null;
Atom id = null;
if (numBonds > 0) {
Bond bond = aBonds.get(0);
ib = bond.get1_2(ia);
}
if (numBonds > 1) {
Bond bond = aBonds.get(1);
ic = bond.get1_2(ia);
}
if (numBonds > 2) {
Bond bond = aBonds.get(2);
id = bond.get1_2(ia);
}
/**
* Building the hydrogens depends on hybridization and the
* locations of other bonded atoms.
*/
logger.fine(" Bonding " + atomName + " to " + ia.getName() + " (" + numBonds + " of " + valence + ").");
switch(valence) {
case 4:
switch(numBonds) {
case 3:
// Find the average coordinates of atoms ib, ic and id.
double[] b = ib.getXYZ(null);
double[] c = ib.getXYZ(null);
double[] d = ib.getXYZ(null);
double[] a = new double[3];
a[0] = (b[0] + c[0] + d[0]) / 3.0;
a[1] = (b[1] + c[1] + d[1]) / 3.0;
a[2] = (b[2] + c[2] + d[2]) / 3.0;
// Place the hydrogen at chiral position #1.
intxyz(hydrogen, ia, 1.0, ib, 109.5, ic, 109.5, 1);
double[] e1 = new double[3];
hydrogen.getXYZ(e1);
double[] ret = new double[3];
diff(a, e1, ret);
double l1 = r(ret);
// Place the hydrogen at chiral position #2.
intxyz(hydrogen, ia, 1.0, ib, 109.5, ic, 109.5, -1);
double[] e2 = new double[3];
hydrogen.getXYZ(e2);
diff(a, e2, ret);
double l2 = r(ret);
// Revert to #1 if it is farther from the average.
if (l1 > l2) {
hydrogen.setXYZ(e1);
}
break;
case 2:
intxyz(hydrogen, ia, 1.0, ib, 109.5, ic, 109.5, 0);
break;
case 1:
intxyz(hydrogen, ia, 1.0, ib, 109.5, null, 0.0, 0);
break;
case 0:
intxyz(hydrogen, ia, 1.0, null, 0.0, null, 0.0, 0);
break;
default:
logger.info(" Check biotype for hydrogen " + atomName + ".");
patched = false;
}
break;
case 3:
switch(numBonds) {
case 2:
intxyz(hydrogen, ia, 1.0, ib, 120.0, ic, 0.0, 0);
break;
case 1:
intxyz(hydrogen, ia, 1.0, ib, 120.0, null, 0.0, 0);
break;
case 0:
intxyz(hydrogen, ia, 1.0, null, 0.0, null, 0.0, 0);
break;
default:
logger.info(" Check biotype for hydrogen " + atomName + ".");
patched = false;
}
break;
case 2:
switch(numBonds) {
case 1:
intxyz(hydrogen, ia, 1.0, ib, 120.0, null, 0.0, 0);
break;
case 0:
intxyz(hydrogen, ia, 1.0, null, 0.0, null, 0.0, 0);
break;
default:
logger.info(" Check biotype for hydrogen " + atomName + ".");
patched = false;
}
break;
case 1:
switch(numBonds) {
case 0:
intxyz(hydrogen, ia, 1.0, null, 0.0, null, 0.0, 0);
break;
default:
logger.info(" Check biotype for hydrogen " + atomName + ".");
patched = false;
}
break;
default:
logger.info(" Check biotype for hydrogen " + atomName + ".");
patched = false;
}
if (!patched) {
break;
} else {
buildBond(ia, hydrogen);
}
}
}
if (!patched) {
logger.log(Level.WARNING, format(" Deleting unrecognized molecule %s.", m.toString()));
activeMolecularAssembly.deleteMolecule((Molecule) m);
} else {
logger.info(" Patch for " + moleculeName + " succeeded.");
}
}
}
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