private void initializeProcesses() throws Exception {
MolecularSystem system = null;
if (mainTopologyFile != null) {
List<MolecularSystem> systems = mainTopologyFile.getMolecularSystems();
if (systems != null && systems.size() > 0) {
system = systems.get(0);
List<Molecule> molecules = system.getSoluteMolecules();
// get list of molecules defined in ITP files
if (mainTopologyFile.getFormat().equals(LocalFile.FORMAT_GROMACS_TOP)) {
List<LocalFile> filesInclude = allFiles.get(LocalFile.FORMAT_GROMACS_ITP);
if (filesInclude != null && molecules != null) {
for (LocalFile fileItp : filesInclude) {
if (fileItp instanceof GROMACSIncludeTopologyFile) {
List<Molecule> localMoleculeDefs =
((GROMACSIncludeTopologyFile) fileItp).getMolecules();
if (localMoleculeDefs != null) {
// for each molecule in the ITP file, replace in the TOP file
for (Molecule molDef : localMoleculeDefs) {
for (int m = 0; m < molecules.size(); m++) {
Molecule mol = molecules.get(m);
if (molDef.getName() != null
&& mol.getName() != null
&& molDef.getName().toUpperCase().equals(mol.getName().toUpperCase())) {
molecules.set(m, molDef);
}
}
}
}
}
}
}
}
}
}
List<ExperimentProcess> processes = this.initializeProcesses(parameterFileFormats);
ExperimentProcessGroup processGroup =
new ExperimentProcessGroup(null, description, system, processes);
processGroup.organizeProcessesForMD();
this.processGroups = new ArrayList<ExperimentProcessGroup>();
this.processGroups.add(processGroup);
}
/**
* Get Gromacs collection metadata
*
* @throws Exception
*/
@Override
public MetadataAVUList getMetadata() throws Exception {
MetadataAVUList metadata = super.getMetadata();
// add aggregated metadata
SummaryExperimentTasks tasksSummary = this.getExperimentTasksSummary();
if (tasksSummary != null) {
metadata.addAll(tasksSummary.getMetadata());
}
// default to MD if no method found
if (!metadata.containsAttribute(MethodMetadata.COMPUTATIONAL_METHOD_NAME)) {
metadata.add(
new MetadataAVU(MethodMetadata.COMPUTATIONAL_METHOD_NAME, ParameterSet.METHOD_MD));
}
// if no task found, default software name to AMBER
if (!metadata.containsAttribute(PlatformMetadata.SOFTWARE_NAME))
metadata.add(new MetadataAVU(PlatformMetadata.SOFTWARE_NAME, Software.GROMACS));
// add topology info
if (mainTopologyFile != null
&& mainTopologyFile.getMolecularSystems() != null
&& mainTopologyFile.getMolecularSystems().size() > 0) {
MolecularSystem system = mainTopologyFile.getMolecularSystems().get(0);
metadata.addAll(system.getMetadata());
if (!metadata.containsAttribute(MethodMetadata.SOLVENT_TYPE)) {
// if water or ions are present, assume solvated system
if (system.getIonCount() > 0 || system.getSolventMoleculeCount() > 0)
metadata.updatePair(MethodMetadata.SOLVENT_TYPE, ParameterSet.SOLVENT_EXPLICIT);
else
metadata.add(new MetadataAVU(MethodMetadata.SOLVENT_TYPE, ParameterSet.SOLVENT_IN_VACUO));
}
}
return metadata;
}
