Example 6 with Bond
use of ffx.potential.bonded.Bond in project ffx by mjschnie.
the class Utilities method assignResidue.
private static Residue assignResidue(List<Atom> backbone, int start, List<Atom> atoms, List<Atom> sidePolymer) {
Atom a;
int atomicnum;
// 0 = S, 1 = P, 2 = O, 3 = N, 4 = C
int[] bins = new int[5];
char[] chars = { 'S', 'P', 'O', 'N', 'C' };
for (ListIterator li = sidePolymer.listIterator(); li.hasNext(); ) {
a = (Atom) li.next();
atomicnum = a.getAtomicNumber();
switch(atomicnum) {
case 1:
// ignore hydrogens
break;
case 6:
// Carbon
bins[4]++;
break;
case 7:
// Nitrogen
bins[3]++;
break;
case 8:
// Oxygen
bins[2]++;
break;
case 15:
// Phosphorus
bins[1]++;
break;
case 16:
// Sulfur
bins[0]++;
break;
default:
return null;
}
}
StringBuilder key = new StringBuilder();
int atomCount = 0;
for (int i = 0; i < 5; i++) {
if (bins[i] != 0) {
atomCount += bins[i];
key.append(chars[i]);
key.append(Integer.toString(bins[i]));
}
}
if (atomCount == 0) {
// Glycine
key.append("H");
}
String resname = sidechainStoichiometry.get(key.toString());
if (resname == null) {
resname = "Unknown";
} else {
resname = resname.intern();
}
if (resname.equals("1") || resname.equals("2")) {
// Special case where atom string keys aren't unique
Atom alpha = backbone.get(start + 1);
Atom carbonyl = backbone.get(start + 2);
Atom beta = null;
List alphabonds = alpha.getBonds();
Bond abond;
for (ListIterator li = alphabonds.listIterator(); li.hasNext(); ) {
abond = (Bond) li.next();
beta = abond.get1_2(alpha);
// carbon
if (beta.getAtomicNumber() != 7 && beta.getAtomicNumber() != 1 && beta != carbonyl) {
break;
}
beta = null;
}
if (beta == null) {
return null;
}
List<Bond> betabonds = beta.getBonds();
Atom gamma;
int carboncount = 0;
for (ListIterator<Bond> li = betabonds.listIterator(); li.hasNext(); ) {
abond = li.next();
gamma = abond.get1_2(beta);
if (gamma.getAtomicNumber() == 6) {
carboncount++;
}
}
if (resname.equals("1")) {
if (carboncount == 2) {
resname = "PRO";
} else {
resname = "VAL";
}
} else {
if (carboncount == 2) {
resname = "LEU";
} else {
resname = "ILE";
}
}
} else if (resname.equals("3")) {
Atom c3 = backbone.get(start + 3);
int num = countCO(c3);
if (num == 2) {
resname = "A";
} else {
resname = "DG";
}
}
Residue residue = null;
try {
Residue.NA3.valueOf(resname.toUpperCase());
residue = new Residue(resname, Residue.ResidueType.NA);
} catch (Exception e) {
}
if (residue == null) {
try {
Residue.AA3.valueOf(resname.toUpperCase());
residue = new Residue(resname, Residue.ResidueType.AA);
} catch (Exception e) {
}
}
if (residue == null) {
residue = new Residue(resname, Residue.ResidueType.UNK);
}
// Create the Residue group
for (ListIterator li = atoms.listIterator(); li.hasNext(); ) {
a = (Atom) li.next();
residue.addMSNode(a);
}
return residue;
}Example 7 with Bond
use of ffx.potential.bonded.Bond in project ffx by mjschnie.
the class PhDiscount method crashDump.
/**
* Attempt to print sources of catastrophic system heating.
*/
private void crashDump(RuntimeException error) {
writeSnapshot(".meltdown-");
ffe.energy(false, true);
mola.getDescendants(BondedTerm.class).stream().filter(BondedTerm::isExtendedSystemMember).forEach(term -> {
try {
((Bond) term).log();
} catch (Exception ex) {
}
try {
((Angle) term).log();
} catch (Exception ex) {
}
try {
((Torsion) term).log();
} catch (Exception ex) {
}
});
if (ffe.getVanDerWaalsEnergy() > 1000) {
extendedAtoms = esvSystem.getExtendedAtoms();
nAtomsExt = esvSystem.getExtendedAtoms().length;
for (int i = 0; i < nAtomsExt; i++) {
Atom ai = extendedAtoms[i];
for (int j = 0; j < nAtomsExt; j++) {
Atom aj = extendedAtoms[j];
if (!esvSystem.isExtended(i) && !esvSystem.isExtended(j)) {
continue;
}
if (ai == aj || ai.getBond(aj) != null) {
continue;
}
double dist = FastMath.sqrt(FastMath.pow((aj.getX() - ai.getX()), 2) + FastMath.pow((aj.getY() - ai.getY()), 2) + FastMath.pow((aj.getZ() - ai.getZ()), 2));
if (dist < 0.8 * (aj.getVDWR() + ai.getVDWR())) {
logger.warning(String.format("Close vdW contact for atoms: \n %s\n %s", aj, ai));
}
}
}
}
throw error;
}
Also used :
BondedTerm(ffx.potential.bonded.BondedTerm)
Angle(ffx.potential.bonded.Angle)
Bond(ffx.potential.bonded.Bond)
Torsion(ffx.potential.bonded.Torsion)
SystemTemperatureException(ffx.potential.utils.SystemTemperatureException)
Atom(ffx.potential.bonded.Atom)
Example 8 with Bond
use of ffx.potential.bonded.Bond in project ffx by mjschnie.
the class ParticleMeshEwaldCart method assignMultipole.
private boolean assignMultipole(int i) {
Atom atom = atoms[i];
AtomType atomType = atoms[i].getAtomType();
if (atomType == null) {
String message = " Multipoles can only be assigned to atoms that have been typed.";
logger.severe(message);
return false;
}
PolarizeType polarizeType = forceField.getPolarizeType(atomType.getKey());
if (polarizeType != null) {
atom.setPolarizeType(polarizeType);
} else {
String message = " No polarization type was found for " + atom.toString();
logger.fine(message);
double polarizability = 0.0;
double thole = 0.0;
int[] polarizationGroup = null;
polarizeType = new PolarizeType(atomType.type, polarizability, thole, polarizationGroup);
forceField.addForceFieldType(polarizeType);
atom.setPolarizeType(polarizeType);
}
String key;
// No reference atoms.
key = atomType.getKey() + " 0 0";
MultipoleType multipoleType = forceField.getMultipoleType(key);
if (multipoleType != null) {
atom.setMultipoleType(multipoleType);
localMultipole[i][t000] = multipoleType.getCharge();
localMultipole[i][t100] = multipoleType.getDipole()[0];
localMultipole[i][t010] = multipoleType.getDipole()[1];
localMultipole[i][t001] = multipoleType.getDipole()[2];
localMultipole[i][t200] = multipoleType.getQuadrupole()[0][0];
localMultipole[i][t020] = multipoleType.getQuadrupole()[1][1];
localMultipole[i][t002] = multipoleType.getQuadrupole()[2][2];
localMultipole[i][t110] = multipoleType.getQuadrupole()[0][1];
localMultipole[i][t101] = multipoleType.getQuadrupole()[0][2];
localMultipole[i][t011] = multipoleType.getQuadrupole()[1][2];
axisAtom[i] = null;
frame[i] = multipoleType.frameDefinition;
return true;
}
// No bonds.
List<Bond> bonds = atom.getBonds();
if (bonds == null || bonds.size() < 1) {
String message = "Multipoles can only be assigned after bonded relationships are defined.\n";
logger.severe(message);
}
// 1 reference atom.
for (Bond b : bonds) {
Atom atom2 = b.get1_2(atom);
key = atomType.getKey() + " " + atom2.getAtomType().getKey() + " 0";
multipoleType = multipoleType = forceField.getMultipoleType(key);
if (multipoleType != null) {
int[] multipoleReferenceAtoms = new int[1];
multipoleReferenceAtoms[0] = atom2.getIndex() - 1;
atom.setMultipoleType(multipoleType);
localMultipole[i][t000] = multipoleType.getCharge();
localMultipole[i][t100] = multipoleType.getDipole()[0];
localMultipole[i][t010] = multipoleType.getDipole()[1];
localMultipole[i][t001] = multipoleType.getDipole()[2];
localMultipole[i][t200] = multipoleType.getQuadrupole()[0][0];
localMultipole[i][t020] = multipoleType.getQuadrupole()[1][1];
localMultipole[i][t002] = multipoleType.getQuadrupole()[2][2];
localMultipole[i][t110] = multipoleType.getQuadrupole()[0][1];
localMultipole[i][t101] = multipoleType.getQuadrupole()[0][2];
localMultipole[i][t011] = multipoleType.getQuadrupole()[1][2];
axisAtom[i] = multipoleReferenceAtoms;
frame[i] = multipoleType.frameDefinition;
return true;
}
}
// 2 reference atoms.
for (Bond b : bonds) {
Atom atom2 = b.get1_2(atom);
String key2 = atom2.getAtomType().getKey();
for (Bond b2 : bonds) {
if (b == b2) {
continue;
}
Atom atom3 = b2.get1_2(atom);
String key3 = atom3.getAtomType().getKey();
key = atomType.getKey() + " " + key2 + " " + key3;
multipoleType = forceField.getMultipoleType(key);
if (multipoleType != null) {
int[] multipoleReferenceAtoms = new int[2];
multipoleReferenceAtoms[0] = atom2.getIndex() - 1;
multipoleReferenceAtoms[1] = atom3.getIndex() - 1;
atom.setMultipoleType(multipoleType);
atom.setMultipoleType(multipoleType);
localMultipole[i][t000] = multipoleType.getCharge();
localMultipole[i][t100] = multipoleType.getDipole()[0];
localMultipole[i][t010] = multipoleType.getDipole()[1];
localMultipole[i][t001] = multipoleType.getDipole()[2];
localMultipole[i][t200] = multipoleType.getQuadrupole()[0][0];
localMultipole[i][t020] = multipoleType.getQuadrupole()[1][1];
localMultipole[i][t002] = multipoleType.getQuadrupole()[2][2];
localMultipole[i][t110] = multipoleType.getQuadrupole()[0][1];
localMultipole[i][t101] = multipoleType.getQuadrupole()[0][2];
localMultipole[i][t011] = multipoleType.getQuadrupole()[1][2];
axisAtom[i] = multipoleReferenceAtoms;
frame[i] = multipoleType.frameDefinition;
return true;
}
}
}
/**
* 3 reference atoms.
*/
for (Bond b : bonds) {
Atom atom2 = b.get1_2(atom);
String key2 = atom2.getAtomType().getKey();
for (Bond b2 : bonds) {
if (b == b2) {
continue;
}
Atom atom3 = b2.get1_2(atom);
String key3 = atom3.getAtomType().getKey();
for (Bond b3 : bonds) {
if (b == b3 || b2 == b3) {
continue;
}
Atom atom4 = b3.get1_2(atom);
String key4 = atom4.getAtomType().getKey();
key = atomType.getKey() + " " + key2 + " " + key3 + " " + key4;
multipoleType = forceField.getMultipoleType(key);
if (multipoleType != null) {
int[] multipoleReferenceAtoms = new int[3];
multipoleReferenceAtoms[0] = atom2.getIndex() - 1;
multipoleReferenceAtoms[1] = atom3.getIndex() - 1;
multipoleReferenceAtoms[2] = atom4.getIndex() - 1;
atom.setMultipoleType(multipoleType);
localMultipole[i][t000] = multipoleType.getCharge();
localMultipole[i][t100] = multipoleType.getDipole()[0];
localMultipole[i][t010] = multipoleType.getDipole()[1];
localMultipole[i][t001] = multipoleType.getDipole()[2];
localMultipole[i][t200] = multipoleType.getQuadrupole()[0][0];
localMultipole[i][t020] = multipoleType.getQuadrupole()[1][1];
localMultipole[i][t002] = multipoleType.getQuadrupole()[2][2];
localMultipole[i][t110] = multipoleType.getQuadrupole()[0][1];
localMultipole[i][t101] = multipoleType.getQuadrupole()[0][2];
localMultipole[i][t011] = multipoleType.getQuadrupole()[1][2];
axisAtom[i] = multipoleReferenceAtoms;
frame[i] = multipoleType.frameDefinition;
return true;
}
}
List<Angle> angles = atom.getAngles();
for (Angle angle : angles) {
Atom atom4 = angle.get1_3(atom);
if (atom4 != null) {
String key4 = atom4.getAtomType().getKey();
key = atomType.getKey() + " " + key2 + " " + key3 + " " + key4;
multipoleType = forceField.getMultipoleType(key);
if (multipoleType != null) {
int[] multipoleReferenceAtoms = new int[3];
multipoleReferenceAtoms[0] = atom2.getIndex() - 1;
multipoleReferenceAtoms[1] = atom3.getIndex() - 1;
multipoleReferenceAtoms[2] = atom4.getIndex() - 1;
atom.setMultipoleType(multipoleType);
localMultipole[i][t000] = multipoleType.getCharge();
localMultipole[i][t100] = multipoleType.getDipole()[0];
localMultipole[i][t010] = multipoleType.getDipole()[1];
localMultipole[i][t001] = multipoleType.getDipole()[2];
localMultipole[i][t200] = multipoleType.getQuadrupole()[0][0];
localMultipole[i][t020] = multipoleType.getQuadrupole()[1][1];
localMultipole[i][t002] = multipoleType.getQuadrupole()[2][2];
localMultipole[i][t110] = multipoleType.getQuadrupole()[0][1];
localMultipole[i][t101] = multipoleType.getQuadrupole()[0][2];
localMultipole[i][t011] = multipoleType.getQuadrupole()[1][2];
axisAtom[i] = multipoleReferenceAtoms;
frame[i] = multipoleType.frameDefinition;
return true;
}
}
}
}
}
/**
* Revert to a 2 reference atom definition that may include a 1-3 site.
* For example a hydrogen on water.
*/
for (Bond b : bonds) {
Atom atom2 = b.get1_2(atom);
String key2 = atom2.getAtomType().getKey();
List<Angle> angles = atom.getAngles();
for (Angle angle : angles) {
Atom atom3 = angle.get1_3(atom);
if (atom3 != null) {
String key3 = atom3.getAtomType().getKey();
key = atomType.getKey() + " " + key2 + " " + key3;
multipoleType = forceField.getMultipoleType(key);
if (multipoleType != null) {
int[] multipoleReferenceAtoms = new int[2];
multipoleReferenceAtoms[0] = atom2.getIndex() - 1;
multipoleReferenceAtoms[1] = atom3.getIndex() - 1;
atom.setMultipoleType(multipoleType);
localMultipole[i][t000] = multipoleType.getCharge();
localMultipole[i][t100] = multipoleType.getDipole()[0];
localMultipole[i][t010] = multipoleType.getDipole()[1];
localMultipole[i][t001] = multipoleType.getDipole()[2];
localMultipole[i][t200] = multipoleType.getQuadrupole()[0][0];
localMultipole[i][t020] = multipoleType.getQuadrupole()[1][1];
localMultipole[i][t002] = multipoleType.getQuadrupole()[2][2];
localMultipole[i][t110] = multipoleType.getQuadrupole()[0][1];
localMultipole[i][t101] = multipoleType.getQuadrupole()[0][2];
localMultipole[i][t011] = multipoleType.getQuadrupole()[1][2];
axisAtom[i] = multipoleReferenceAtoms;
frame[i] = multipoleType.frameDefinition;
return true;
}
for (Angle angle2 : angles) {
Atom atom4 = angle2.get1_3(atom);
if (atom4 != null && atom4 != atom3) {
String key4 = atom4.getAtomType().getKey();
key = atomType.getKey() + " " + key2 + " " + key3 + " " + key4;
multipoleType = forceField.getMultipoleType(key);
if (multipoleType != null) {
int[] multipoleReferenceAtoms = new int[3];
multipoleReferenceAtoms[0] = atom2.getIndex() - 1;
multipoleReferenceAtoms[1] = atom3.getIndex() - 1;
multipoleReferenceAtoms[2] = atom4.getIndex() - 1;
atom.setMultipoleType(multipoleType);
localMultipole[i][t000] = multipoleType.getCharge();
localMultipole[i][t100] = multipoleType.getDipole()[0];
localMultipole[i][t010] = multipoleType.getDipole()[1];
localMultipole[i][t001] = multipoleType.getDipole()[2];
localMultipole[i][t200] = multipoleType.getQuadrupole()[0][0];
localMultipole[i][t020] = multipoleType.getQuadrupole()[1][1];
localMultipole[i][t002] = multipoleType.getQuadrupole()[2][2];
localMultipole[i][t110] = multipoleType.getQuadrupole()[0][1];
localMultipole[i][t101] = multipoleType.getQuadrupole()[0][2];
localMultipole[i][t011] = multipoleType.getQuadrupole()[1][2];
axisAtom[i] = multipoleReferenceAtoms;
frame[i] = multipoleType.frameDefinition;
return true;
}
}
}
}
}
}
return false;
}
Also used :
PolarizeType(ffx.potential.parameters.PolarizeType)
Angle(ffx.potential.bonded.Angle)
AtomType(ffx.potential.parameters.AtomType)
ForceFieldString(ffx.potential.parameters.ForceField.ForceFieldString)
MultipoleType(ffx.potential.parameters.MultipoleType)
Bond(ffx.potential.bonded.Bond)
Atom(ffx.potential.bonded.Atom)
Example 9 with Bond
use of ffx.potential.bonded.Bond in project ffx by mjschnie.
the class MainPanel method merge.
/**
* Merge two or more selected FSystem Nodes into one FSystem node. There are
* a few gotchas that need to be fixed
*
* @param nodesToMerge a {@link java.util.ArrayList} object.
*/
public void merge(ArrayList<MSNode> nodesToMerge) {
ArrayList<MSNode> activeNodes = new ArrayList<MSNode>();
for (MSNode node : nodesToMerge) {
if (node != null && !(node instanceof MSRoot)) {
activeNodes.add(node);
}
}
if (activeNodes.size() <= 1) {
return;
}
// Set up a structure to hold the new system
FFXSystem active = hierarchy.getActive();
File file = SystemFilter.version(hierarchy.getActive().getFile());
FFXSystem system = new FFXSystem(file, "Merge Result", active.getProperties());
system.setKeyFile(active.getKeyFile());
system.setKeywords(KeyFilter.open(active.getKeyFile()));
// Fill arrays with the atoms and bonds from the systems to be combined
ArrayList<Atom> mergedAtoms = new ArrayList<Atom>();
ArrayList<Bond> mergedBonds = new ArrayList<Bond>();
ArrayList<FFXSystem> systems = new ArrayList<FFXSystem>();
TransformGroup parentTransformGroup = null;
FFXSystem parentSystem;
Transform3D parentTransform3D = new Transform3D();
Vector3d parentPosition = new Vector3d();
Vector3d atomPosition = new Vector3d();
// TINKER Atom Numbers start at 1
int atomNum = 1;
Vector3d zero = new Vector3d(0.0, 0.0, 0.0);
for (MSNode m : activeNodes) {
parentSystem = (FFXSystem) m.getMSNode(FFXSystem.class);
if (parentSystem == null) {
return;
}
if (!systems.contains(parentSystem)) {
graphicsCanvas.updateSceneWait(parentSystem, false, true, RendererCache.ViewModel.WIREFRAME, false, null);
systems.add(parentSystem);
}
// Move each atom into the global frame by applying the System
// Transform to
// relative atomic position
parentTransformGroup = parentSystem.getOriginToRot();
parentTransformGroup.getTransform(parentTransform3D);
parentTransform3D.get(parentPosition);
parentTransform3D.setTranslation(zero);
// parentTransform3D.setScale(1.0d);
ArrayList<Atom> atoms = m.getAtomList();
ArrayList<ROLS> bonds = m.getBondList();
for (Atom atom : atoms) {
atom.removeFromParent();
atom.setXyzIndex(atomNum++);
mergedAtoms.add(atom);
atom.getV3D(atomPosition);
parentTransform3D.transform(atomPosition);
atomPosition.add(parentPosition);
atom.moveTo(atomPosition);
}
for (ROLS msm : bonds) {
Bond bond = (Bond) msm;
bond.removeFromParent();
mergedBonds.add((Bond) msm);
}
}
for (FFXSystem sys : systems) {
close(sys);
}
MergeFilter mergeFilter = new MergeFilter(system, mergedAtoms, mergedBonds);
UIFileOpener fileOpener = new UIFileOpener(mergeFilter, this);
if (fileOpenerThreads > 0) {
fileOpener.setNThreads(fileOpenerThreads);
}
Thread thread = new Thread(fileOpener);
thread.start();
}
Also used :
ROLS(ffx.potential.bonded.ROLS)
Transform3D(javax.media.j3d.Transform3D)
ArrayList(java.util.ArrayList)
MergeFilter(ffx.potential.parsers.MergeFilter)
Atom(ffx.potential.bonded.Atom)
TransformGroup(javax.media.j3d.TransformGroup)
MSNode(ffx.potential.bonded.MSNode)
MSRoot(ffx.potential.bonded.MSRoot)
Vector3d(javax.vecmath.Vector3d)
Bond(ffx.potential.bonded.Bond)
File(java.io.File)
Example 10 with Bond
use of ffx.potential.bonded.Bond 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)
Aggregations
Bond (ffx.potential.bonded.Bond)38
Atom (ffx.potential.bonded.Atom)37
IOException (java.io.IOException)12
ArrayList (java.util.ArrayList)12
Polymer (ffx.potential.bonded.Polymer)10
Residue (ffx.potential.bonded.Residue)10
File (java.io.File)10
Angle (ffx.potential.bonded.Angle)9
Crystal (ffx.crystal.Crystal)8
MissingAtomTypeException (ffx.potential.bonded.BondedUtils.MissingAtomTypeException)8
MissingHeavyAtomException (ffx.potential.bonded.BondedUtils.MissingHeavyAtomException)8
MSNode (ffx.potential.bonded.MSNode)7
Molecule (ffx.potential.bonded.Molecule)7
AtomType (ffx.potential.parameters.AtomType)7
BufferedWriter (java.io.BufferedWriter)6
FileWriter (java.io.FileWriter)6
RestraintBond (ffx.potential.bonded.RestraintBond)5
Torsion (ffx.potential.bonded.Torsion)5
CoordRestraint (ffx.potential.nonbonded.CoordRestraint)5
MolecularAssembly (ffx.potential.MolecularAssembly)4
