use of ffx.potential.bonded.Residue in project ffx by mjschnie.
the class PDBFilter method buildDisulfideBonds.
/**
* Assign parameters to disulfide bonds.
*
* @param ssBondList
*/
private void buildDisulfideBonds(List<Bond> ssBondList) {
StringBuilder sb = new StringBuilder(" Disulfide Bonds:");
for (Bond bond : ssBondList) {
Atom a1 = bond.getAtom(0);
Atom a2 = bond.getAtom(1);
int[] c = new int[2];
c[0] = a1.getAtomType().atomClass;
c[1] = a2.getAtomType().atomClass;
String key = BondType.sortKey(c);
BondType bondType = forceField.getBondType(key);
if (bondType == null) {
logger.severe(format("No BondType for key: %s\n %s\n %s", key, a1, a2));
} else {
bond.setBondType(bondType);
}
double d = VectorMath.dist(a1.getXYZ(null), a2.getXYZ(null));
Polymer c1 = activeMolecularAssembly.getChain(a1.getSegID());
Polymer c2 = activeMolecularAssembly.getChain(a2.getSegID());
Residue r1 = c1.getResidue(a1.getResidueNumber());
Residue r2 = c2.getResidue(a2.getResidueNumber());
sb.append(format("\n S-S distance of %6.2f for %s and %s.", d, r1.toString(), r2.toString()));
bondList.add(bond);
}
if (ssBondList.size() > 0) {
logger.info(sb.toString());
}
}
use of ffx.potential.bonded.Residue in project ffx by mjschnie.
the class PDBFilter method locateDisulfideBonds.
/**
* Locate disulfide bonds based on SSBOND records.
*
* @param ssbonds
*
* @return An ArrayList of Bond instances for SS-Bonds.
*/
private List<Bond> locateDisulfideBonds(List<String> ssbonds) {
List<Bond> ssBondList = new ArrayList<>();
for (String ssbond : ssbonds) {
// =============================================================================
try {
char c1ch = ssbond.charAt(15);
char c2ch = ssbond.charAt(29);
Polymer c1 = activeMolecularAssembly.getChain(String.format("%c", c1ch));
Polymer c2 = activeMolecularAssembly.getChain(String.format("%c", c2ch));
String origResNum1 = ssbond.substring(17, 21).trim();
char insChar1 = ssbond.charAt(21);
String origResNum2 = ssbond.substring(31, 35).trim();
char insChar2 = ssbond.charAt(35);
String pdbResNum1 = String.format("%c%s%c", c1ch, origResNum1, insChar1);
String pdbResNum2 = String.format("%c%s%c", c2ch, origResNum2, insChar2);
String resnum1 = pdbToNewResMap.get(pdbResNum1);
String resnum2 = pdbToNewResMap.get(pdbResNum2);
if (resnum1 == null) {
logger.warning(String.format(" Could not find residue %s for SS-bond %s", pdbResNum1, ssbond));
continue;
}
if (resnum2 == null) {
logger.warning(String.format(" Could not find residue %s for SS-bond %s", pdbResNum2, ssbond));
continue;
}
Residue r1 = c1.getResidue(Integer.parseInt(resnum1.substring(1)));
Residue r2 = c2.getResidue(Integer.parseInt(resnum2.substring(1)));
/*Residue r1 = c1.getResidue(Hybrid36.decode(4, ssbond.substring(17, 21)));
Residue r2 = c2.getResidue(Hybrid36.decode(4, ssbond.substring(31, 35)));*/
List<Atom> atoms1 = r1.getAtomList();
List<Atom> atoms2 = r2.getAtomList();
Atom SG1 = null;
Atom SG2 = null;
for (Atom atom : atoms1) {
if (atom.getName().equalsIgnoreCase("SG")) {
SG1 = atom;
break;
}
}
for (Atom atom : atoms2) {
if (atom.getName().equalsIgnoreCase("SG")) {
SG2 = atom;
break;
}
}
if (SG1 == null) {
logger.warning(String.format(" SG atom 1 of SS-bond %s is null", ssbond));
}
if (SG2 == null) {
logger.warning(String.format(" SG atom 2 of SS-bond %s is null", ssbond));
}
if (SG1 == null || SG2 == null) {
continue;
}
double d = VectorMath.dist(SG1.getXYZ(null), SG2.getXYZ(null));
if (d < 3.0) {
r1.setName("CYX");
r2.setName("CYX");
for (Atom atom : atoms1) {
atom.setResName("CYX");
}
for (Atom atom : atoms2) {
atom.setResName("CYX");
}
Bond bond = new Bond(SG1, SG2);
ssBondList.add(bond);
} else {
String message = format("Ignoring [%s]\n due to distance %8.3f A.", ssbond, d);
logger.log(Level.WARNING, message);
}
} catch (Exception e) {
String message = format("Ignoring [%s]", ssbond);
logger.log(Level.WARNING, message, e);
}
}
return ssBondList;
}
use of ffx.potential.bonded.Residue in project ffx by mjschnie.
the class BiojavaFilter method findChainBreaks.
private List<List<Residue>> findChainBreaks(List<Residue> residues, double cutoff) {
List<List<Residue>> subChains = new ArrayList<List<Residue>>();
List<Residue> subChain = null;
Residue previousResidue = null;
Atom pC = null;
StringBuilder sb = new StringBuilder(" Chain Breaks:");
for (Residue residue : residues) {
List<Atom> resAtoms = residue.getAtomList();
if (pC == null) {
/**
* Initialization.
*/
subChain = new ArrayList<Residue>();
subChain.add(residue);
subChains.add(subChain);
} else {
/**
* Find the Nitrogen of the current residue.
*/
Atom N = null;
for (Atom a : resAtoms) {
if (a.getName().equalsIgnoreCase("N")) {
N = a;
break;
}
}
/**
* Compute the distance between the previous carbonyl carbon and
* the current nitrogen.
*/
double r = VectorMath.dist(pC.getXYZ(null), N.getXYZ(null));
if (r > cutoff) {
/**
* Start a new chain.
*/
subChain = new ArrayList<Residue>();
subChain.add(residue);
subChains.add(subChain);
sb.append(format("\n C-N distance of %6.2f A for %s and %s.", r, previousResidue.toString(), residue.toString()));
} else {
/**
* Continue the current chain.
*/
subChain.add(residue);
}
}
/**
* Save the carbonyl carbon.
*/
for (Atom a : resAtoms) {
if (a.getName().equalsIgnoreCase("C")) {
pC = a;
break;
}
}
previousResidue = residue;
}
if (subChains.size() > 1) {
logger.info(sb.toString());
}
return subChains;
}
use of ffx.potential.bonded.Residue in project ffx by mjschnie.
the class BiojavaFilter method writeFile.
/**
* <p>
* writeFile</p>
*
* @param saveFile a {@link java.io.File} object.
* @param append a {@link java.lang.StringBuilder} object.
* @param printLinear Whether to print atoms linearly or by element
* @return Success of writing.
*/
public boolean writeFile(File saveFile, boolean append, boolean printLinear) {
if (saveFile == null) {
return false;
}
if (vdwH) {
logger.info(" Printing hydrogens to van der Waals centers instead of nuclear locations.");
}
/**
* Create StringBuilders for ATOM, ANISOU and TER records that can be
* reused.
*/
StringBuilder sb = new StringBuilder("ATOM ");
StringBuilder anisouSB = new StringBuilder("ANISOU");
StringBuilder terSB = new StringBuilder("TER ");
for (int i = 6; i < 80; i++) {
sb.append(' ');
anisouSB.append(' ');
terSB.append(' ');
}
FileWriter fw;
BufferedWriter bw;
try {
File newFile = saveFile;
if (!append) {
newFile = version(saveFile);
}
activeMolecularAssembly.setFile(newFile);
activeMolecularAssembly.setName(newFile.getName());
logger.log(Level.INFO, " Saving {0}", newFile.getName());
fw = new FileWriter(newFile, append);
bw = new BufferedWriter(fw);
// =============================================================================
// The CRYST1 record presents the unit cell parameters, space group, and Z
// value. If the structure was not determined by crystallographic means, CRYST1
// simply provides the unitary values, with an appropriate REMARK.
//
// 7 - 15 Real(9.3) a a (Angstroms).
// 16 - 24 Real(9.3) b b (Angstroms).
// 25 - 33 Real(9.3) c c (Angstroms).
// 34 - 40 Real(7.2) alpha alpha (degrees).
// 41 - 47 Real(7.2) beta beta (degrees).
// 48 - 54 Real(7.2) gamma gamma (degrees).
// 56 - 66 LString sGroup Space group.
// 67 - 70 Integer z Z value.
// =============================================================================
Crystal crystal = activeMolecularAssembly.getCrystal();
if (crystal != null && !crystal.aperiodic()) {
Crystal c = crystal.getUnitCell();
if (!listMode) {
bw.write(format("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %10s\n", c.a, c.b, c.c, c.alpha, c.beta, c.gamma, padRight(c.spaceGroup.pdbName, 10)));
} else {
listOutput.add(format("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %10s", c.a, c.b, c.c, c.alpha, c.beta, c.gamma, padRight(c.spaceGroup.pdbName, 10)));
}
}
// =============================================================================
// The SSBOND record identifies each disulfide bond in protein and polypeptide
// structures by identifying the two residues involved in the bond.
// The disulfide bond distance is included after the symmetry operations at
// the end of the SSBOND record.
//
// 8 - 10 Integer serNum Serial number.
// 12 - 14 LString(3) "CYS" Residue name.
// 16 Character chainID1 Chain identifier.
// 18 - 21 Integer seqNum1 Residue sequence number.
// 22 AChar icode1 Insertion code.
// 26 - 28 LString(3) "CYS" Residue name.
// 30 Character chainID2 Chain identifier.
// 32 - 35 Integer seqNum2 Residue sequence number.
// 36 AChar icode2 Insertion code.
// 60 - 65 SymOP sym1 Symmetry oper for 1st resid
// 67 - 72 SymOP sym2 Symmetry oper for 2nd resid
// 74 – 78 Real(5.2) Length Disulfide bond distance
//
// If SG of cysteine is disordered then there are possible alternate linkages.
// wwPDB practice is to put together all possible SSBOND records. This is
// problematic because the alternate location identifier is not specified in
// the SSBOND record.
// =============================================================================
int serNum = 1;
Polymer[] polymers = activeMolecularAssembly.getChains();
if (polymers != null) {
for (Polymer polymer : polymers) {
ArrayList<Residue> residues = polymer.getResidues();
for (Residue residue : residues) {
if (residue.getName().equalsIgnoreCase("CYS")) {
List<Atom> cysAtoms = residue.getAtomList();
Atom SG1 = null;
for (Atom atom : cysAtoms) {
if (atom.getName().equalsIgnoreCase("SG")) {
SG1 = atom;
break;
}
}
List<Bond> bonds = SG1.getBonds();
for (Bond bond : bonds) {
Atom SG2 = bond.get1_2(SG1);
if (SG2.getName().equalsIgnoreCase("SG")) {
if (SG1.getIndex() < SG2.getIndex()) {
bond.energy(false);
if (!listMode) {
bw.write(format("SSBOND %3d CYS %1s %4s CYS %1s %4s %36s %5.2f\n", serNum++, SG1.getChainID().toString(), Hybrid36.encode(4, SG1.getResidueNumber()), SG2.getChainID().toString(), Hybrid36.encode(4, SG2.getResidueNumber()), "", bond.getValue()));
} else {
listOutput.add(format("SSBOND %3d CYS %1s %4s CYS %1s %4s %36s %5.2f\n", serNum++, SG1.getChainID().toString(), Hybrid36.encode(4, SG1.getResidueNumber()), SG2.getChainID().toString(), Hybrid36.encode(4, SG2.getResidueNumber()), "", bond.getValue()));
}
}
}
}
}
}
}
}
// =============================================================================
//
// 7 - 11 Integer serial Atom serial number.
// 13 - 16 Atom name Atom name.
// 17 Character altLoc Alternate location indicator.
// 18 - 20 Residue name resName Residue name.
// 22 Character chainID Chain identifier.
// 23 - 26 Integer resSeq Residue sequence number.
// 27 AChar iCode Code for insertion of residues.
// 31 - 38 Real(8.3) x Orthogonal coordinates for X in Angstroms.
// 39 - 46 Real(8.3) y Orthogonal coordinates for Y in Angstroms.
// 47 - 54 Real(8.3) z Orthogonal coordinates for Z in Angstroms.
// 55 - 60 Real(6.2) occupancy Occupancy.
// 61 - 66 Real(6.2) tempFactor Temperature factor.
// 77 - 78 LString(2) element Element symbol, right-justified.
// 79 - 80 LString(2) charge Charge on the atom.
// =============================================================================
// 1 2 3 4 5 6 7
// 123456789012345678901234567890123456789012345678901234567890123456789012345678
// ATOM 1 N ILE A 16 60.614 71.140 -10.592 1.00 7.38 N
// ATOM 2 CA ILE A 16 60.793 72.149 -9.511 1.00 6.91 C
MolecularAssembly[] molecularAssemblies = this.getMolecularAssemblys();
int serial = 1;
// Loop over biomolecular chains
if (polymers != null) {
for (Polymer polymer : polymers) {
currentSegID = polymer.getName();
currentChainID = polymer.getChainID();
sb.setCharAt(21, currentChainID);
// Loop over residues
ArrayList<Residue> residues = polymer.getResidues();
for (Residue residue : residues) {
String resName = residue.getName();
if (resName.length() > 3) {
resName = resName.substring(0, 3);
}
int resID = residue.getResidueNumber();
sb.replace(17, 20, padLeft(resName.toUpperCase(), 3));
sb.replace(22, 26, String.format("%4s", Hybrid36.encode(4, resID)));
// Loop over atoms
ArrayList<Atom> residueAtoms = residue.getAtomList();
ArrayList<Atom> backboneAtoms = residue.getBackboneAtoms();
boolean altLocFound = false;
for (Atom atom : backboneAtoms) {
writeAtom(atom, serial++, sb, anisouSB, bw);
Character altLoc = atom.getAltLoc();
if (altLoc != null && !altLoc.equals(' ')) {
altLocFound = true;
}
residueAtoms.remove(atom);
}
for (Atom atom : residueAtoms) {
writeAtom(atom, serial++, sb, anisouSB, bw);
Character altLoc = atom.getAltLoc();
if (altLoc != null && !altLoc.equals(' ')) {
altLocFound = true;
}
}
// Write out alternate conformers
if (altLocFound) {
for (int ma = 1; ma < molecularAssemblies.length; ma++) {
MolecularAssembly altMolecularAssembly = molecularAssemblies[ma];
Polymer altPolymer = altMolecularAssembly.getPolymer(currentChainID, currentSegID, false);
Residue altResidue = altPolymer.getResidue(resName, resID, false);
backboneAtoms = altResidue.getBackboneAtoms();
residueAtoms = altResidue.getAtomList();
for (Atom atom : backboneAtoms) {
if (atom.getAltLoc() != null && !atom.getAltLoc().equals(' ') && !atom.getAltLoc().equals('A')) {
writeAtom(atom, serial++, sb, anisouSB, bw);
}
residueAtoms.remove(atom);
}
for (Atom atom : residueAtoms) {
if (atom.getAltLoc() != null && !atom.getAltLoc().equals(' ') && !atom.getAltLoc().equals('A')) {
writeAtom(atom, serial++, sb, anisouSB, bw);
}
}
}
}
}
terSB.replace(6, 11, String.format("%5s", Hybrid36.encode(5, serial++)));
terSB.replace(12, 16, " ");
terSB.replace(16, 26, sb.substring(16, 26));
if (!listMode) {
bw.write(terSB.toString());
bw.newLine();
} else {
listOutput.add(terSB.toString());
}
}
}
sb.replace(0, 6, "HETATM");
sb.setCharAt(21, 'A');
int resID = 1;
Polymer polymer = activeMolecularAssembly.getPolymer('A', "A", false);
if (polymer != null) {
ArrayList<Residue> residues = polymer.getResidues();
for (Residue residue : residues) {
int resID2 = residue.getResidueNumber();
if (resID2 >= resID) {
resID = resID2 + 1;
}
}
}
/**
* Loop over molecules, ions and then water.
*/
ArrayList<Molecule> molecules = activeMolecularAssembly.getMolecules();
for (int i = 0; i < molecules.size(); i++) {
Molecule molecule = (Molecule) molecules.get(i);
Character chainID = molecule.getChainID();
sb.setCharAt(21, chainID);
String resName = molecule.getResidueName();
if (resName.length() > 3) {
resName = resName.substring(0, 3);
}
sb.replace(17, 20, padLeft(resName.toUpperCase(), 3));
sb.replace(22, 26, String.format("%4s", Hybrid36.encode(4, resID)));
ArrayList<Atom> moleculeAtoms = molecule.getAtomList();
boolean altLocFound = false;
for (Atom atom : moleculeAtoms) {
writeAtom(atom, serial++, sb, anisouSB, bw);
Character altLoc = atom.getAltLoc();
if (altLoc != null && !altLoc.equals(' ')) {
altLocFound = true;
}
}
// Write out alternate conformers
if (altLocFound) {
for (int ma = 1; ma < molecularAssemblies.length; ma++) {
MolecularAssembly altMolecularAssembly = molecularAssemblies[ma];
MSNode altmolecule = altMolecularAssembly.getMolecules().get(i);
moleculeAtoms = altmolecule.getAtomList();
for (Atom atom : moleculeAtoms) {
if (atom.getAltLoc() != null && !atom.getAltLoc().equals(' ') && !atom.getAltLoc().equals('A')) {
writeAtom(atom, serial++, sb, anisouSB, bw);
}
}
}
}
resID++;
}
ArrayList<MSNode> ions = activeMolecularAssembly.getIons();
for (int i = 0; i < ions.size(); i++) {
Molecule ion = (Molecule) ions.get(i);
Character chainID = ion.getChainID();
sb.setCharAt(21, chainID);
String resName = ion.getResidueName();
if (resName.length() > 3) {
resName = resName.substring(0, 3);
}
sb.replace(17, 20, padLeft(resName.toUpperCase(), 3));
sb.replace(22, 26, String.format("%4s", Hybrid36.encode(4, resID)));
ArrayList<Atom> ionAtoms = ion.getAtomList();
boolean altLocFound = false;
for (Atom atom : ionAtoms) {
writeAtom(atom, serial++, sb, anisouSB, bw);
Character altLoc = atom.getAltLoc();
if (altLoc != null && !altLoc.equals(' ')) {
altLocFound = true;
}
}
// Write out alternate conformers
if (altLocFound) {
for (int ma = 1; ma < molecularAssemblies.length; ma++) {
MolecularAssembly altMolecularAssembly = molecularAssemblies[ma];
MSNode altion = altMolecularAssembly.getIons().get(i);
ionAtoms = altion.getAtomList();
for (Atom atom : ionAtoms) {
if (atom.getAltLoc() != null && !atom.getAltLoc().equals(' ') && !atom.getAltLoc().equals('A')) {
writeAtom(atom, serial++, sb, anisouSB, bw);
}
}
}
}
resID++;
}
ArrayList<MSNode> waters = activeMolecularAssembly.getWaters();
for (int i = 0; i < waters.size(); i++) {
Molecule water = (Molecule) waters.get(i);
Character chainID = water.getChainID();
sb.setCharAt(21, chainID);
String resName = water.getResidueName();
if (resName.length() > 3) {
resName = resName.substring(0, 3);
}
sb.replace(17, 20, padLeft(resName.toUpperCase(), 3));
sb.replace(22, 26, String.format("%4s", Hybrid36.encode(4, resID)));
ArrayList<Atom> waterAtoms = water.getAtomList();
boolean altLocFound = false;
for (Atom atom : waterAtoms) {
writeAtom(atom, serial++, sb, anisouSB, bw);
Character altLoc = atom.getAltLoc();
if (altLoc != null && !altLoc.equals(' ')) {
altLocFound = true;
}
}
// Write out alternate conformers
if (altLocFound) {
for (int ma = 1; ma < molecularAssemblies.length; ma++) {
MolecularAssembly altMolecularAssembly = molecularAssemblies[ma];
MSNode altwater = altMolecularAssembly.getWaters().get(i);
waterAtoms = altwater.getAtomList();
for (Atom atom : waterAtoms) {
if (atom.getAltLoc() != null && !atom.getAltLoc().equals(' ') && !atom.getAltLoc().equals('A')) {
writeAtom(atom, serial++, sb, anisouSB, bw);
}
}
}
}
resID++;
}
if (!listMode) {
bw.write("END");
bw.newLine();
} else {
listOutput.add("END");
}
bw.close();
} catch (Exception e) {
String message = "Exception writing to file: " + saveFile.toString();
logger.log(Level.WARNING, message, e);
return false;
}
return true;
}
use of ffx.potential.bonded.Residue in project ffx by mjschnie.
the class BiojavaFilter method writeSIFTFile.
/*public Structure writeToStructure(String header) {
return writeToStructure(activeMolecularAssembly, header);
}
public static Structure writeToStructure(MolecularAssembly assembly, String header) {
Structure structure = new StructureImpl();
for (Polymer polymer : assembly.getChains()) {
Chain chain = new ChainImpl();
for (Residue residue : polymer.getResidues()) {
Group group;
switch (residue.getResidueType()) {
case AA:
group = new AminoAcidImpl();
break;
case NA:
group = new NucleotideImpl();
break;
default:
group = new HetatomImpl();
break;
}
for (Atom atom : residue.getAtomList()) {
org.biojava.bio.structure.Atom bjAtom = new AtomImpl();
group.addAtom(bjAtom);
}
chain.addGroup(group);
}
structure.addChain(chain);
}
for (Molecule molecule : assembly.getMolecules()) {
for (Atom atom : molecule.getAtomList()) {
}
}
}*/
public boolean writeSIFTFile(File saveFile, boolean append, String[] resAndScore) {
if (saveFile == null) {
return false;
}
if (vdwH) {
logger.info(" Printing hydrogens to van der Waals centers instead of nuclear locations.");
}
/**
* Create StringBuilders for ATOM, ANISOU and TER records that can be
* reused.
*/
StringBuilder sb = new StringBuilder("ATOM ");
StringBuilder anisouSB = new StringBuilder("ANISOU");
StringBuilder terSB = new StringBuilder("TER ");
for (int i = 6; i < 80; i++) {
sb.append(' ');
anisouSB.append(' ');
terSB.append(' ');
}
FileWriter fw;
BufferedWriter bw;
try {
File newFile = saveFile;
if (!append) {
newFile = version(saveFile);
}
activeMolecularAssembly.setFile(newFile);
activeMolecularAssembly.setName(newFile.getName());
logger.log(Level.INFO, " Saving {0}", newFile.getName());
fw = new FileWriter(newFile, append);
bw = new BufferedWriter(fw);
// =============================================================================
// The CRYST1 record presents the unit cell parameters, space group, and Z
// value. If the structure was not determined by crystallographic means, CRYST1
// simply provides the unitary values, with an appropriate REMARK.
//
// 7 - 15 Real(9.3) a a (Angstroms).
// 16 - 24 Real(9.3) b b (Angstroms).
// 25 - 33 Real(9.3) c c (Angstroms).
// 34 - 40 Real(7.2) alpha alpha (degrees).
// 41 - 47 Real(7.2) beta beta (degrees).
// 48 - 54 Real(7.2) gamma gamma (degrees).
// 56 - 66 LString sGroup Space group.
// 67 - 70 Integer z Z value.
// =============================================================================
Crystal crystal = activeMolecularAssembly.getCrystal();
if (crystal != null && !crystal.aperiodic()) {
Crystal c = crystal.getUnitCell();
if (!listMode) {
bw.write(format("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %10s\n", c.a, c.b, c.c, c.alpha, c.beta, c.gamma, padRight(c.spaceGroup.pdbName, 10)));
} else {
listOutput.add(format("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %10s", c.a, c.b, c.c, c.alpha, c.beta, c.gamma, padRight(c.spaceGroup.pdbName, 10)));
}
}
// =============================================================================
// The SSBOND record identifies each disulfide bond in protein and polypeptide
// structures by identifying the two residues involved in the bond.
// The disulfide bond distance is included after the symmetry operations at
// the end of the SSBOND record.
//
// 8 - 10 Integer serNum Serial number.
// 12 - 14 LString(3) "CYS" Residue name.
// 16 Character chainID1 Chain identifier.
// 18 - 21 Integer seqNum1 Residue sequence number.
// 22 AChar icode1 Insertion code.
// 26 - 28 LString(3) "CYS" Residue name.
// 30 Character chainID2 Chain identifier.
// 32 - 35 Integer seqNum2 Residue sequence number.
// 36 AChar icode2 Insertion code.
// 60 - 65 SymOP sym1 Symmetry oper for 1st resid
// 67 - 72 SymOP sym2 Symmetry oper for 2nd resid
// 74 – 78 Real(5.2) Length Disulfide bond distance
//
// If SG of cysteine is disordered then there are possible alternate linkages.
// wwPDB practice is to put together all possible SSBOND records. This is
// problematic because the alternate location identifier is not specified in
// the SSBOND record.
// =============================================================================
int serNum = 1;
Polymer[] polymers = activeMolecularAssembly.getChains();
if (polymers != null) {
for (Polymer polymer : polymers) {
ArrayList<Residue> residues = polymer.getResidues();
for (Residue residue : residues) {
if (residue.getName().equalsIgnoreCase("CYS")) {
List<Atom> cysAtoms = residue.getAtomList();
Atom SG1 = null;
for (Atom atom : cysAtoms) {
if (atom.getName().equalsIgnoreCase("SG")) {
SG1 = atom;
break;
}
}
List<Bond> bonds = SG1.getBonds();
for (Bond bond : bonds) {
Atom SG2 = bond.get1_2(SG1);
if (SG2.getName().equalsIgnoreCase("SG")) {
if (SG1.getIndex() < SG2.getIndex()) {
bond.energy(false);
if (!listMode) {
bw.write(format("SSBOND %3d CYS %1s %4s CYS %1s %4s %36s %5.2f\n", serNum++, SG1.getChainID().toString(), Hybrid36.encode(4, SG1.getResidueNumber()), SG2.getChainID().toString(), Hybrid36.encode(4, SG2.getResidueNumber()), "", bond.getValue()));
} else {
listOutput.add(format("SSBOND %3d CYS %1s %4s CYS %1s %4s %36s %5.2f\n", serNum++, SG1.getChainID().toString(), Hybrid36.encode(4, SG1.getResidueNumber()), SG2.getChainID().toString(), Hybrid36.encode(4, SG2.getResidueNumber()), "", bond.getValue()));
}
}
}
}
}
}
}
}
// =============================================================================
//
// 7 - 11 Integer serial Atom serial number.
// 13 - 16 Atom name Atom name.
// 17 Character altLoc Alternate location indicator.
// 18 - 20 Residue name resName Residue name.
// 22 Character chainID Chain identifier.
// 23 - 26 Integer resSeq Residue sequence number.
// 27 AChar iCode Code for insertion of residues.
// 31 - 38 Real(8.3) x Orthogonal coordinates for X in Angstroms.
// 39 - 46 Real(8.3) y Orthogonal coordinates for Y in Angstroms.
// 47 - 54 Real(8.3) z Orthogonal coordinates for Z in Angstroms.
// 55 - 60 Real(6.2) occupancy Occupancy.
// 61 - 66 Real(6.2) tempFactor Temperature factor.
// 77 - 78 LString(2) element Element symbol, right-justified.
// 79 - 80 LString(2) charge Charge on the atom.
// =============================================================================
// 1 2 3 4 5 6 7
// 123456789012345678901234567890123456789012345678901234567890123456789012345678
// ATOM 1 N ILE A 16 60.614 71.140 -10.592 1.00 7.38 N
// ATOM 2 CA ILE A 16 60.793 72.149 -9.511 1.00 6.91 C
MolecularAssembly[] molecularAssemblies = this.getMolecularAssemblys();
int serial = 1;
// Loop over biomolecular chains
if (polymers != null) {
for (Polymer polymer : polymers) {
currentSegID = polymer.getName();
currentChainID = polymer.getChainID();
sb.setCharAt(21, currentChainID);
// Loop over residues
ArrayList<Residue> residues = polymer.getResidues();
for (Residue residue : residues) {
String resName = residue.getName();
if (resName.length() > 3) {
resName = resName.substring(0, 3);
}
int resID = residue.getResidueNumber();
int i = 0;
String[] entries = null;
for (; i < resAndScore.length; i++) {
entries = resAndScore[i].split("\\t");
if (!entries[0].equals(entries[0].replaceAll("\\D+", ""))) {
String[] subEntries = entries[0].split("[^0-9]");
entries[0] = subEntries[0];
}
if (entries[0].equals(String.valueOf(resID)) && !".".equals(entries[1])) {
break;
}
}
sb.replace(17, 20, padLeft(resName.toUpperCase(), 3));
sb.replace(22, 26, String.format("%4s", Hybrid36.encode(4, resID)));
// Loop over atoms
ArrayList<Atom> residueAtoms = residue.getAtomList();
boolean altLocFound = false;
for (Atom atom : residueAtoms) {
if (i != resAndScore.length) {
writeSIFTAtom(atom, serial++, sb, anisouSB, bw, entries[1]);
} else {
writeSIFTAtom(atom, serial++, sb, anisouSB, bw, null);
}
Character altLoc = atom.getAltLoc();
if (altLoc != null && !altLoc.equals(' ')) {
altLocFound = true;
}
}
// Write out alternate conformers
if (altLocFound) {
for (int ma = 1; ma < molecularAssemblies.length; ma++) {
MolecularAssembly altMolecularAssembly = molecularAssemblies[ma];
Polymer altPolymer = altMolecularAssembly.getPolymer(currentChainID, currentSegID, false);
Residue altResidue = altPolymer.getResidue(resName, resID, false);
residueAtoms = altResidue.getAtomList();
for (Atom atom : residueAtoms) {
if (atom.getAltLoc() != null && !atom.getAltLoc().equals(' ') && !atom.getAltLoc().equals('A')) {
if (i != resAndScore.length) {
writeSIFTAtom(atom, serial++, sb, anisouSB, bw, entries[1]);
} else {
writeSIFTAtom(atom, serial++, sb, anisouSB, bw, null);
}
}
}
}
}
}
terSB.replace(6, 11, String.format("%5s", Hybrid36.encode(5, serial++)));
terSB.replace(12, 16, " ");
terSB.replace(16, 26, sb.substring(16, 26));
if (!listMode) {
bw.write(terSB.toString());
bw.newLine();
} else {
listOutput.add(terSB.toString());
}
}
}
sb.replace(0, 6, "HETATM");
sb.setCharAt(21, 'A');
int resID = 1;
Polymer polymer = activeMolecularAssembly.getPolymer('A', "A", false);
if (polymer != null) {
ArrayList<Residue> residues = polymer.getResidues();
for (Residue residue : residues) {
int resID2 = residue.getResidueNumber();
if (resID2 >= resID) {
resID = resID2 + 1;
}
}
}
/**
* Loop over molecules, ions and then water.
*/
ArrayList<Molecule> molecules = activeMolecularAssembly.getMolecules();
for (int i = 0; i < molecules.size(); i++) {
Molecule molecule = (Molecule) molecules.get(i);
Character chainID = molecule.getChainID();
sb.setCharAt(21, chainID);
String resName = molecule.getResidueName();
if (resName.length() > 3) {
resName = resName.substring(0, 3);
}
sb.replace(17, 20, padLeft(resName.toUpperCase(), 3));
sb.replace(22, 26, String.format("%4s", Hybrid36.encode(4, resID)));
ArrayList<Atom> moleculeAtoms = molecule.getAtomList();
boolean altLocFound = false;
for (Atom atom : moleculeAtoms) {
writeSIFTAtom(atom, serial++, sb, anisouSB, bw, null);
Character altLoc = atom.getAltLoc();
if (altLoc != null && !altLoc.equals(' ')) {
altLocFound = true;
}
}
// Write out alternate conformers
if (altLocFound) {
for (int ma = 1; ma < molecularAssemblies.length; ma++) {
MolecularAssembly altMolecularAssembly = molecularAssemblies[ma];
MSNode altmolecule = altMolecularAssembly.getMolecules().get(i);
moleculeAtoms = altmolecule.getAtomList();
for (Atom atom : moleculeAtoms) {
if (atom.getAltLoc() != null && !atom.getAltLoc().equals(' ') && !atom.getAltLoc().equals('A')) {
writeSIFTAtom(atom, serial++, sb, anisouSB, bw, null);
}
}
}
}
resID++;
}
ArrayList<MSNode> ions = activeMolecularAssembly.getIons();
for (int i = 0; i < ions.size(); i++) {
Molecule ion = (Molecule) ions.get(i);
Character chainID = ion.getChainID();
sb.setCharAt(21, chainID);
String resName = ion.getResidueName();
if (resName.length() > 3) {
resName = resName.substring(0, 3);
}
sb.replace(17, 20, padLeft(resName.toUpperCase(), 3));
sb.replace(22, 26, String.format("%4s", Hybrid36.encode(4, resID)));
ArrayList<Atom> ionAtoms = ion.getAtomList();
boolean altLocFound = false;
for (Atom atom : ionAtoms) {
writeSIFTAtom(atom, serial++, sb, anisouSB, bw, null);
Character altLoc = atom.getAltLoc();
if (altLoc != null && !altLoc.equals(' ')) {
altLocFound = true;
}
}
// Write out alternate conformers
if (altLocFound) {
for (int ma = 1; ma < molecularAssemblies.length; ma++) {
MolecularAssembly altMolecularAssembly = molecularAssemblies[ma];
MSNode altion = altMolecularAssembly.getIons().get(i);
ionAtoms = altion.getAtomList();
for (Atom atom : ionAtoms) {
if (atom.getAltLoc() != null && !atom.getAltLoc().equals(' ') && !atom.getAltLoc().equals('A')) {
writeSIFTAtom(atom, serial++, sb, anisouSB, bw, null);
}
}
}
}
resID++;
}
ArrayList<MSNode> waters = activeMolecularAssembly.getWaters();
for (int i = 0; i < waters.size(); i++) {
Molecule water = (Molecule) waters.get(i);
Character chainID = water.getChainID();
sb.setCharAt(21, chainID);
String resName = water.getResidueName();
if (resName.length() > 3) {
resName = resName.substring(0, 3);
}
sb.replace(17, 20, padLeft(resName.toUpperCase(), 3));
sb.replace(22, 26, String.format("%4s", Hybrid36.encode(4, resID)));
ArrayList<Atom> waterAtoms = water.getAtomList();
boolean altLocFound = false;
for (Atom atom : waterAtoms) {
writeSIFTAtom(atom, serial++, sb, anisouSB, bw, null);
Character altLoc = atom.getAltLoc();
if (altLoc != null && !altLoc.equals(' ')) {
altLocFound = true;
}
}
// Write out alternate conformers
if (altLocFound) {
for (int ma = 1; ma < molecularAssemblies.length; ma++) {
MolecularAssembly altMolecularAssembly = molecularAssemblies[ma];
MSNode altwater = altMolecularAssembly.getWaters().get(i);
waterAtoms = altwater.getAtomList();
for (Atom atom : waterAtoms) {
if (atom.getAltLoc() != null && !atom.getAltLoc().equals(' ') && !atom.getAltLoc().equals('A')) {
writeSIFTAtom(atom, serial++, sb, anisouSB, bw, null);
}
}
}
}
resID++;
}
if (!listMode) {
bw.write("END");
bw.newLine();
} else {
listOutput.add("END");
}
bw.close();
} catch (Exception e) {
String message = "Exception writing to file: " + saveFile.toString();
logger.log(Level.WARNING, message, e);
return false;
}
return true;
}
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