Examples with HetAtoms ffx.potential.parsers.PDBFilter.HetAtoms used on opensource projects

Example 1 with HetAtoms

use of ffx.potential.parsers.PDBFilter.HetAtoms 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.");
        }
    }
}