use of ffx.realspace.RealSpaceFile in project ffx by mjschnie.
the class Rescore method rescoreSingle.
private File rescoreSingle(File modelFile, RescoreStrategy rscType, DoubleIndexPair[] energies, int i) {
Path filepath = generatePath(modelFile);
if (filepath == null) {
logger.warning(String.format(" Could not generate path to file %s", modelFile.toPath()));
return null;
}
String filename = pwdPath.relativize(filepath).toString();
File retFile = modelFile;
try {
MolecularAssembly assembly = utils.open(filename);
switch(rscType) {
case NO_RESCORE:
logger.warning(" Rescore is being called with rscType = NO_RESCORE");
break;
case ENERGY_EVAL:
break;
case MINIMIZE:
logger.info(String.format("\n Running minimize on %s", filename));
logger.info(String.format(" RMS gradient convergence criteria: %f", eps));
utils.energy(assembly);
utils.minimize(assembly, eps);
String ext = FilenameUtils.getExtension(filename);
ext = ".".concat(ext);
if (resultDir != null) {
filename = FilenameUtils.getBaseName(filename);
filename = FilenameUtils.concat(resultPath.toString(), filename);
} else {
filename = FilenameUtils.removeExtension(filename);
}
filename = filename.concat(fileSuffix).concat(ext);
retFile = new File(filename);
if (ext.toUpperCase().contains("XYZ")) {
utils.saveAsXYZ(assembly, retFile);
} else {
utils.saveAsPDB(assembly, retFile);
}
break;
case XRAY_MIN:
logger.info(String.format("\n Running x-ray minimize on %s", filename));
DiffractionFile diffractionFile = null;
if (diffractionFiles.isEmpty()) {
diffractionFile = new DiffractionFile(assembly, 1.0, false);
diffractionFiles.add(diffractionFile);
}
CompositeConfiguration properties = Keyword.loadProperties(modelFile);
DiffractionData diffractionData = new DiffractionData(assembly, properties, SolventModel.POLYNOMIAL, diffractionFiles.toArray(new DiffractionFile[diffractionFiles.size()]));
diffractionData.scaleBulkFit();
diffractionData.printStats();
utils.energy(assembly);
RefinementMinimize refinementMinimize = new RefinementMinimize(diffractionData, refinementMode);
if (eps < 0.0) {
eps = refinementMinimize.getEps();
}
logger.info(String.format("\n RMS gradient convergence criteria: %8.5f max number of iterations %d", eps, maxiter));
refinementMinimize.minimize(eps, maxiter);
diffractionData.scaleBulkFit();
diffractionData.printStats();
ext = FilenameUtils.getExtension(filename);
ext = ".".concat(ext);
if (resultDir != null) {
filename = FilenameUtils.getBaseName(filename);
filename = FilenameUtils.concat(resultPath.toString(), filename);
} else {
filename = FilenameUtils.removeExtension(filename);
}
filename = filename.concat(fileSuffix);
diffractionData.writeData(filename + ".mtz");
filename = filename.concat(ext);
diffractionData.writeModel(filename);
retFile = new File(filename);
if (diffractionFile != null) {
try {
diffractionFiles.remove(diffractionFile);
} catch (UnsupportedOperationException ex) {
// This should never occur, because diffractionFiles should be of a List type supporting remove(object).
diffractionFiles = new ArrayList<>();
}
}
break;
case RS_MIN:
logger.info(String.format("\n Running real-space minimize on %s", filename));
RealSpaceFile realspaceFile = null;
if (mapFiles.isEmpty()) {
realspaceFile = new RealSpaceFile(assembly);
mapFiles.add(realspaceFile);
}
properties = Keyword.loadProperties(modelFile);
RealSpaceData realspaceData = new RealSpaceData(assembly, properties, new ParallelTeam(), mapFiles.toArray(new RealSpaceFile[mapFiles.size()]));
utils.energy(assembly);
refinementMinimize = new RefinementMinimize(realspaceData, refinementMode);
if (eps < 0.0) {
eps = 1.0;
}
logger.info(String.format("\n RMS gradient convergence criteria: %8.5f max number of iterations %d", eps, maxiter));
refinementMinimize.minimize(eps, maxiter);
ext = FilenameUtils.getExtension(filename);
ext = ".".concat(ext);
if (resultDir != null) {
filename = FilenameUtils.getBaseName(filename);
filename = FilenameUtils.concat(resultPath.toString(), filename);
} else {
filename = FilenameUtils.removeExtension(filename);
}
filename = filename.concat(fileSuffix).concat(ext);
retFile = new File(filename);
if (ext.toUpperCase().contains("XYZ")) {
utils.saveAsXYZ(assembly, retFile);
} else {
utils.saveAsPDB(assembly, retFile);
}
if (realspaceFile != null) {
try {
mapFiles.remove(realspaceFile);
} catch (UnsupportedOperationException ex) {
// This should never occur, because diffractionFiles should be of a List type supporting remove(object).
mapFiles = new ArrayList<>();
}
}
break;
default:
logger.severe(" No valid rescore type: FFX will not continue.");
}
double e = utils.returnEnergy(assembly);
energies[i] = new DoubleIndexPair(i, e);
utils.close(assembly);
} catch (Exception ex) {
logger.warning(String.format(" Exception rescoring on file %s", filename));
logger.info(ex.toString());
}
return retFile;
}
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