Example 1 with MSGroup
use of ffx.potential.bonded.MSGroup in project ffx by mjschnie.
the class MolecularAssembly method setColor.
/**
* {@inheritDoc}
*/
@Override
public void setColor(RendererCache.ColorModel newColorModel, Color3f color, Material mat) {
for (ListIterator<MSNode> li = getAtomNodeList().listIterator(); li.hasNext(); ) {
MSGroup group = (MSGroup) li.next();
group.setColor(newColorModel, color, mat);
}
for (MSNode m : molecules.getChildList()) {
m.setColor(newColorModel, color, mat);
}
for (MSNode m : water.getChildList()) {
m.setColor(newColorModel, color, mat);
}
for (MSNode m : ions.getChildList()) {
m.setColor(newColorModel, color, mat);
}
}Example 2 with MSGroup
use of ffx.potential.bonded.MSGroup in project ffx by mjschnie.
the class BiojavaFilter method numberAtoms.
/**
* <p>
* numberAtoms</p>
*/
public void numberAtoms() {
int index = 1;
for (Atom a : activeMolecularAssembly.getAtomArray()) {
a.setXyzIndex(index++);
}
index--;
if (logger.isLoggable(Level.INFO)) {
logger.info(String.format(" Total number of atoms: %d\n", index));
}
Polymer[] polymers = activeMolecularAssembly.getChains();
if (polymers != null) {
for (Polymer p : polymers) {
List<Residue> residues = p.getResidues();
for (Residue r : residues) {
r.reOrderAtoms();
}
}
}
List<Molecule> molecules = activeMolecularAssembly.getMolecules();
for (Molecule n : molecules) {
n.reOrderAtoms();
}
List<MSNode> waters = activeMolecularAssembly.getWaters();
for (MSNode n : waters) {
MSGroup m = (MSGroup) n;
m.reOrderAtoms();
}
List<MSNode> ions = activeMolecularAssembly.getIons();
for (MSNode n : ions) {
MSGroup m = (MSGroup) n;
m.reOrderAtoms();
}
}Example 3 with MSGroup
use of ffx.potential.bonded.MSGroup in project ffx by mjschnie.
the class MolecularAssembly method finalize.
/**
* {@inheritDoc}
*/
@Override
public void finalize(boolean finalizeGroups, ForceField forceField) {
setFinalized(false);
if (finalizeGroups) {
bondTime = 0;
angleTime = 0;
stretchBendTime = 0;
ureyBradleyTime = 0;
outOfPlaneBendTime = 0;
torsionTime = 0;
piOrbitalTorsionTime = 0;
torsionTorsionTime = 0;
ArrayList<MSNode> Polymers = getAtomNodeList();
for (ListIterator<MSNode> li = Polymers.listIterator(); li.hasNext(); ) {
MSGroup group = (MSGroup) li.next();
if (logger.isLoggable(Level.FINE)) {
logger.fine(" Finalizing bonded terms for polymer " + group.toString());
}
try {
group.finalize(true, forceField);
} catch (Exception e) {
String message = "Fatal exception finalizing " + group.toString();
logger.log(Level.SEVERE, message, e);
System.exit(-1);
}
if (logger.isLoggable(Level.FINE)) {
Runtime runtime = Runtime.getRuntime();
long occupiedMemory = runtime.totalMemory() - runtime.freeMemory();
long MB = 1024 * 1024;
logger.fine("\n In-Use Memory (Mb): " + occupiedMemory / MB + "\n Free Memory (Mb): " + runtime.freeMemory() / MB + "\n Total Memory (Mb): " + runtime.totalMemory() / MB);
}
}
for (MSNode m : molecules.getChildList()) {
Molecule molecule = (Molecule) m;
molecule.finalize(true, forceField);
}
for (MSNode m : water.getChildList()) {
Molecule molecule = (Molecule) m;
molecule.finalize(true, forceField);
}
for (MSNode m : ions.getChildList()) {
Molecule molecule = (Molecule) m;
molecule.finalize(true, forceField);
}
if (logger.isLoggable(Level.FINE)) {
StringBuilder sb = new StringBuilder("\n Time to create bonded energy terms\n\n");
sb.append(String.format(" Bond Streching %10.3f\n", bondTime * 1.0e-9));
sb.append(String.format(" Angle Bending %10.3f\n", angleTime * 1.0e-9));
sb.append(String.format(" Stretch-Bend %10.3f\n", stretchBendTime * 1.0e-9));
sb.append(String.format(" Urey-Bradley %10.3f\n", ureyBradleyTime * 1.0e-9));
sb.append(String.format(" Out-of-Plane Bend %10.3f\n", outOfPlaneBendTime * 1.0e-9));
sb.append(String.format(" Torsionanl Angle %10.3f\n", torsionTime * 1.0e-9));
sb.append(String.format(" Pi-Orbital Torsion %10.3f\n", piOrbitalTorsionTime * 1.0e-9));
sb.append(String.format(" Torsion-Torsion %10.3f\n", torsionTorsionTime * 1.0e-9));
logger.fine(sb.toString());
}
}
if (!java.awt.GraphicsEnvironment.isHeadless()) {
createScene(!finalizeGroups);
center();
}
removeLeaves();
setFinalized(true);
}Example 4 with MSGroup
use of ffx.potential.bonded.MSGroup in project ffx by mjschnie.
the class PDBFilter method numberAtoms.
/**
* <p>
* numberAtoms</p>
*/
private void numberAtoms() {
int index = 1;
for (Atom a : activeMolecularAssembly.getAtomArray()) {
a.setXyzIndex(index++);
}
index--;
if (logger.isLoggable(Level.INFO)) {
logger.info(String.format(" Total number of atoms: %d\n", index));
}
Polymer[] polymers = activeMolecularAssembly.getChains();
if (polymers != null) {
for (Polymer p : polymers) {
List<Residue> residues = p.getResidues();
for (Residue r : residues) {
r.reOrderAtoms();
}
}
}
List<Molecule> molecules = activeMolecularAssembly.getMolecules();
for (Molecule n : molecules) {
n.reOrderAtoms();
}
List<MSNode> waters = activeMolecularAssembly.getWaters();
for (MSNode n : waters) {
MSGroup m = (MSGroup) n;
m.reOrderAtoms();
}
List<MSNode> ions = activeMolecularAssembly.getIons();
for (MSNode n : ions) {
MSGroup m = (MSGroup) n;
m.reOrderAtoms();
}
}