Example 41 with Residue
use of ffx.potential.bonded.Residue in project ffx by mjschnie.
the class TitrationUtils method chooseTitratables.
public static List<Residue> chooseTitratables(char chain, int resID, MolecularAssembly searchMe) {
List<Residue> chosen = new ArrayList<>();
Polymer[] polymers = searchMe.getChains();
for (Polymer polymer : polymers) {
if (polymer.getChainID() == chain) {
ArrayList<Residue> residues = polymer.getResidues();
for (Residue residue : residues) {
if (residue.getResidueNumber() == resID) {
chosen.add(residue);
logger.info(String.format(" Chosen: %s", residue));
}
}
}
}
return chosen;
}
Also used :
MultiResidue(ffx.potential.bonded.MultiResidue)
Residue(ffx.potential.bonded.Residue)
ArrayList(java.util.ArrayList)
Polymer(ffx.potential.bonded.Polymer)
Example 42 with Residue
use of ffx.potential.bonded.Residue in project ffx by mjschnie.
the class TitrationUtils method chooseTitratables.
/**
* Select titrating residues by amino acid.
*/
public static List<Residue> chooseTitratables(AminoAcid3 aa, MolecularAssembly searchMe) {
List<Residue> chosen = new ArrayList<>();
Polymer[] polymers = searchMe.getChains();
for (Polymer polymer : polymers) {
ArrayList<Residue> residues = polymer.getResidues();
for (Residue res : residues) {
if (res.getAminoAcid3() == aa) {
Titration[] avail = Titration.multiLookup(res);
if (avail != null) {
chosen.add(res);
}
}
}
}
return chosen;
}
Also used :
MultiResidue(ffx.potential.bonded.MultiResidue)
Residue(ffx.potential.bonded.Residue)
ArrayList(java.util.ArrayList)
Polymer(ffx.potential.bonded.Polymer)
Example 43 with Residue
use of ffx.potential.bonded.Residue in project ffx by mjschnie.
the class TitrationUtils method rebuildStrandedProtons.
/**
* Rebuild stranded titratable protons from ideal geometry. "Stranded
* protons" are titrating H+ atoms on inactive MultiRes members; when
* propagating new coordinates to inactive residues, no coords/velocity
* exist for them.
*/
private static void rebuildStrandedProtons(MultiResidue multiRes) {
// If inactive residue is a protonated form, move the stranded hydrogen to new coords (based on propagated heavies).
// Also give the stranded hydrogen a maxwell velocity and remove its accelerations.
List<Residue> inactives = multiRes.getInactive();
for (Residue inactive : inactives) {
List<Atom> resetMe = new ArrayList<>();
switch(inactive.getName()) {
case "LYS":
{
Atom HZ3 = (Atom) inactive.getAtomNode("HZ3");
Atom NZ = (Atom) inactive.getAtomNode("NZ");
Atom CE = (Atom) inactive.getAtomNode("CE");
Atom HZ1 = (Atom) inactive.getAtomNode("HZ1");
BondedUtils.intxyz(HZ3, NZ, 1.02, CE, 109.5, HZ1, 109.5, -1);
resetMe.add(HZ3);
break;
}
case "ASH":
{
Atom HD2 = (Atom) inactive.getAtomNode("HD2");
Atom OD2 = (Atom) inactive.getAtomNode("OD2");
Atom CG = (Atom) inactive.getAtomNode("CG");
Atom OD1 = (Atom) inactive.getAtomNode("OD1");
BondedUtils.intxyz(HD2, OD2, 0.98, CG, 108.7, OD1, 0.0, 0);
resetMe.add(HD2);
break;
}
case "GLH":
{
Atom HE2 = (Atom) inactive.getAtomNode("HE2");
Atom OE2 = (Atom) inactive.getAtomNode("OE2");
Atom CD = (Atom) inactive.getAtomNode("CD");
Atom OE1 = (Atom) inactive.getAtomNode("OE1");
BondedUtils.intxyz(HE2, OE2, 0.98, CD, 108.7, OE1, 0.0, 0);
resetMe.add(HE2);
break;
}
case "HIS":
{
Atom HE2 = (Atom) inactive.getAtomNode("HE2");
Atom NE2 = (Atom) inactive.getAtomNode("NE2");
Atom CD2 = (Atom) inactive.getAtomNode("CD2");
Atom CE1 = (Atom) inactive.getAtomNode("CE1");
Atom HD1 = (Atom) inactive.getAtomNode("HD1");
Atom ND1 = (Atom) inactive.getAtomNode("ND1");
Atom CG = (Atom) inactive.getAtomNode("CG");
Atom CB = (Atom) inactive.getAtomNode("CB");
BondedUtils.intxyz(HE2, NE2, 1.02, CD2, 126.0, CE1, 126.0, 1);
BondedUtils.intxyz(HD1, ND1, 1.02, CG, 126.0, CB, 0.0, 0);
resetMe.add(HE2);
resetMe.add(HD1);
break;
}
case "HID":
{
Atom HD1 = (Atom) inactive.getAtomNode("HD1");
Atom ND1 = (Atom) inactive.getAtomNode("ND1");
Atom CG = (Atom) inactive.getAtomNode("CG");
Atom CB = (Atom) inactive.getAtomNode("CB");
BondedUtils.intxyz(HD1, ND1, 1.02, CG, 126.0, CB, 0.0, 0);
resetMe.add(HD1);
break;
}
case "HIE":
{
Atom HE2 = (Atom) inactive.getAtomNode("HE2");
Atom NE2 = (Atom) inactive.getAtomNode("NE2");
Atom CD2 = (Atom) inactive.getAtomNode("CD2");
Atom CE1 = (Atom) inactive.getAtomNode("CE1");
BondedUtils.intxyz(HE2, NE2, 1.02, CD2, 126.0, CE1, 126.0, 1);
resetMe.add(HE2);
break;
}
case "CYS":
{
Atom HG = (Atom) inactive.getAtomNode("HG");
Atom SG = (Atom) inactive.getAtomNode("SG");
Atom CB = (Atom) inactive.getAtomNode("CB");
Atom CA = (Atom) inactive.getAtomNode("CA");
BondedUtils.intxyz(HG, SG, 1.34, CB, 96.0, CA, 180.0, 0);
resetMe.add(HG);
break;
}
case "TYR":
{
Atom HH = (Atom) inactive.getAtomNode("HH");
Atom OH = (Atom) inactive.getAtomNode("OH");
Atom CZ = (Atom) inactive.getAtomNode("CZ");
Atom CE2 = (Atom) inactive.getAtomNode("CE2");
BondedUtils.intxyz(HH, OH, 0.97, CZ, 108.0, CE2, 0.0, 0);
resetMe.add(HH);
break;
}
default:
}
for (Atom a : resetMe) {
if (heavyStrandedDynamics) {
// Use of heavy atom dynamics properties is in testing.
a.setXYZGradient(0, 0, 0);
double[] heavyVelocity = new double[3];
double[] heavyAccel = new double[3];
double[] heavyPrevAccel = new double[3];
Atom heavy = a.getBonds().get(0).get1_2(a);
heavy.getVelocity(heavyVelocity);
heavy.getAcceleration(heavyAccel);
heavy.getPreviousAcceleration(heavyPrevAccel);
a.setVelocity(heavyVelocity);
a.setAcceleration(heavyAccel);
a.setPreviousAcceleration(heavyPrevAccel);
} else {
// PREVIOUSLY: draw vel from maxwell and set accel to zero
a.setXYZGradient(0, 0, 0);
a.setVelocity(ExtUtils.maxwellVelocity(a.getMass(), ExtConstants.roomTemperature));
a.setAcceleration(new double[] { 0, 0, 0 });
a.setPreviousAcceleration(new double[] { 0, 0, 0 });
}
}
}
}
Also used :
MultiResidue(ffx.potential.bonded.MultiResidue)
Residue(ffx.potential.bonded.Residue)
ArrayList(java.util.ArrayList)
Atom(ffx.potential.bonded.Atom)
Example 44 with Residue
use of ffx.potential.bonded.Residue in project ffx by mjschnie.
the class PDBFilter 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 (Boolean.parseBoolean(System.getProperty("standardizeAtomNames", "false"))) {
renameAtomsToPDBStandard(activeMolecularAssembly);
}
if (saveFile == null) {
return false;
}
if (vdwH) {
logger.info(" Printing hydrogens to van der Waals centers instead of nuclear locations.");
}
if (nSymOp != 0) {
logger.info(String.format(" Printing atoms with symmetry operator %s\n", activeMolecularAssembly.getCrystal().spaceGroup.getSymOp(nSymOp).toString()));
}
/**
* 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 ");
StringBuilder model = null;
for (int i = 6; i < 80; i++) {
sb.append(' ');
anisouSB.append(' ');
terSB.append(' ');
}
FileWriter fw;
BufferedWriter bw;
try {
File newFile = saveFile;
if (!append) {
if (!noVersioning) {
newFile = version(saveFile);
}
} else if (modelsWritten >= 0) {
model = new StringBuilder(String.format("MODEL %-4d", ++modelsWritten));
for (int i = 15; i < 80; i++) {
model.append(' ');
}
}
activeMolecularAssembly.setFile(newFile);
activeMolecularAssembly.setName(newFile.getName());
if (logWrites) {
logger.log(Level.INFO, " Saving {0}", activeMolecularAssembly.getName());
}
fw = new FileWriter(newFile, append);
bw = new BufferedWriter(fw);
/**
* Will come before CRYST1 and ATOM records, but after anything
* written by writeFileWithHeader (particularly X-ray refinement
* statistics).
*/
String[] headerLines = activeMolecularAssembly.getHeaderLines();
for (String line : headerLines) {
bw.write(String.format("%s\n", line));
}
if (model != null) {
if (!listMode) {
bw.write(model.toString());
bw.newLine();
} else {
listOutput.add(model.toString());
}
}
// =============================================================================
// 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) {
String atName = atom.getName().toUpperCase();
if (atName.equals("SG") || atName.equals("SH")) {
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++;
}
String end = model != null ? "ENDMDL" : "END";
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;
}
Also used :
FileWriter(java.io.FileWriter)
BufferedWriter(java.io.BufferedWriter)
MSNode(ffx.potential.bonded.MSNode)
Polymer(ffx.potential.bonded.Polymer)
Atom(ffx.potential.bonded.Atom)
MissingHeavyAtomException(ffx.potential.bonded.BondedUtils.MissingHeavyAtomException)
IOException(java.io.IOException)
MissingAtomTypeException(ffx.potential.bonded.BondedUtils.MissingAtomTypeException)
Molecule(ffx.potential.bonded.Molecule)
MolecularAssembly(ffx.potential.MolecularAssembly)
Residue(ffx.potential.bonded.Residue)
Bond(ffx.potential.bonded.Bond)
File(java.io.File)
Crystal(ffx.crystal.Crystal)
Example 45 with Residue
use of ffx.potential.bonded.Residue in project ffx by mjschnie.
the class PDBFilter method writeSIFTFile.
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.");
}
if (nSymOp != 0) {
logger.info(String.format(" Printing atoms with symmetry operator %s", activeMolecularAssembly.getCrystal().spaceGroup.getSymOp(nSymOp).toString()));
}
/**
* 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 && !noVersioning) {
newFile = version(saveFile);
}
activeMolecularAssembly.setFile(newFile);
activeMolecularAssembly.setName(newFile.getName());
if (logWrites) {
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;
}
Also used :
FileWriter(java.io.FileWriter)
BufferedWriter(java.io.BufferedWriter)
MSNode(ffx.potential.bonded.MSNode)
Polymer(ffx.potential.bonded.Polymer)
Atom(ffx.potential.bonded.Atom)
MissingHeavyAtomException(ffx.potential.bonded.BondedUtils.MissingHeavyAtomException)
IOException(java.io.IOException)
MissingAtomTypeException(ffx.potential.bonded.BondedUtils.MissingAtomTypeException)
Molecule(ffx.potential.bonded.Molecule)
MolecularAssembly(ffx.potential.MolecularAssembly)
Residue(ffx.potential.bonded.Residue)
Bond(ffx.potential.bonded.Bond)
File(java.io.File)
Crystal(ffx.crystal.Crystal)
Aggregations
Residue (ffx.potential.bonded.Residue)102
MultiResidue (ffx.potential.bonded.MultiResidue)66
Rotamer (ffx.potential.bonded.Rotamer)44
Atom (ffx.potential.bonded.Atom)41
RotamerLibrary.applyRotamer (ffx.potential.bonded.RotamerLibrary.applyRotamer)39
ArrayList (java.util.ArrayList)30
Polymer (ffx.potential.bonded.Polymer)29
IOException (java.io.IOException)20
Molecule (ffx.potential.bonded.Molecule)13
NACorrectionException (ffx.potential.bonded.NACorrectionException)13
MSNode (ffx.potential.bonded.MSNode)12
ResidueState (ffx.potential.bonded.ResidueState)11
Bond (ffx.potential.bonded.Bond)10
Crystal (ffx.crystal.Crystal)8
MissingAtomTypeException (ffx.potential.bonded.BondedUtils.MissingAtomTypeException)8
MissingHeavyAtomException (ffx.potential.bonded.BondedUtils.MissingHeavyAtomException)8
File (java.io.File)8
AminoAcid3 (ffx.potential.bonded.ResidueEnumerations.AminoAcid3)7
TitrationUtils.inactivateResidue (ffx.potential.extended.TitrationUtils.inactivateResidue)6
BufferedWriter (java.io.BufferedWriter)6
