segments can be present -- The
* first model is referred to as the "base" model -- The base model: -- will
* generally be of type MOL, but any known type is acceptable -- will be used to
* generate bonding for later models that have no bonding information -- will be
* the only model for NMR -- Additional models can represent vibrations (XYZ
* format) or MS fragmentation (MOL format, probably)
*
* ##$PEAKS= ...
*
* -- peak record must be a single line of information because Jmol will use
* line.trim() as a key to pass information to JSpecView.
*
*
*
*/
public class JcampdxReader extends MolReader implements JmolJDXMOLReader {
private int selectedModel;
private JmolJDXMOLParser mpr;
private String acdMolFile;
private int nPeaks;
private Lst acdAssignments; // JSV only
private String title;
private String nucleus = "";
private String type;
@Override
public void initializeReader() throws Exception {
// trajectories would be OK for IR, but just too complicated for others.
// tells Jmol to start talking with JSpecView
vwr.setBooleanProperty("_JSpecView".toLowerCase(), true);
// necessary to not use "jspecview" here, as buildtojs.xml will change that to "JSV"
if (isTrajectory) {
Logger.warn("TRAJECTORY keyword ignored");
isTrajectory = false;
}
// forget reversing models!
if (reverseModels) {
Logger.warn("REVERSE keyword ignored");
reverseModels = false;
}
selectedModel = desiredModelNumber;
desiredModelNumber = Integer.MIN_VALUE;
if (!checkFilterKey("NOSYNC"))
addJmolScript("sync on");
}
@Override
public boolean checkLine() throws Exception {
int i = line.indexOf("=");
if (i < 0 || !line.startsWith("##"))
return true;
String label = PT.replaceAllCharacters(line.substring(0, i).trim(), " ","").toUpperCase();
if (label.length() > 12)
label = label.substring(0, 12);
int pt = ("##$MODELS " + // 0
"##$PEAKS " + // 12
"##$SIGNALS " + // 24
"##$MOLFILE " + // 36
"##NPOINTS " + // 48
"##TITLE " + // 60
"##PEAKASSIGN" + // 72
"##$UVIR_ASSI" + // 84
"##$MS_FRAGME" + // 96
"##.OBSERVENU" + // 108
"##DATATYPE " // 120
).indexOf(label);
if (pt < 0)
return true;
if (mpr == null)
mpr = ((JmolJDXMOLParser) Interface
.getOption("jsv.JDXMOLParser", vwr, "file")).set(this, filePath,
htParams);
String value = line.substring(i + 1).trim();
mpr.setLine(value);
switch (pt) {
case 0:// $MODELS
mpr.readModels();
break;
case 12:// $PEAKS or $SIGNALS
case 24:
mpr.readPeaks(pt == 24, -1);
break;
case 36:// $MOLFILE
acdMolFile = mpr.readACDMolFile();
processModelData(acdMolFile, title + " (assigned)", "MOL", "mol", "", 0.01f, Float.NaN, true);
if (asc.errorMessage != null) {
continuing = false;
return false;
}
break;
case 48:// NPOINTS
nPeaks = PT.parseInt(value);
break;
case 60:// TITLE
title = PT.split(value, "$$")[0].trim();
break;
case 72:// PEAKASSIGNMENTS $UVIR_ASSIGNMENTS $MS_FRAGMENTS
case 84:
case 96:
acdAssignments = mpr.readACDAssignments(nPeaks, pt == 72);
break;
case 108:// .OBSERVENUCLEUS
nucleus = value.substring(1);
break;
case 120:// DATATYPE
type = value;
if ((pt = type.indexOf(" ")) >= 0)
type = type.substring(0, pt);
break;
}
return true;
}
@Override
public void finalizeSubclassReader() throws Exception {
if (mpr != null)
processPeakData();
finalizeReaderMR();
}
@Override
public void processModelData(String data, String id, String type,
String base, String last, float modelScale,
float vibScale, boolean isFirst) throws Exception {
int model0 = asc.iSet;
AtomSetCollection model = null;
while (true) {
Object ret = SmarterJmolAdapter.staticGetAtomSetCollectionReader(
filePath, type, Rdr.getBR(data), htParams);
if (ret instanceof String) {
Logger.warn("" + ret);
if (((String) ret).startsWith(JC.READER_NOT_FOUND))
asc.errorMessage = (String) ret;
break;
}
ret = SmarterJmolAdapter
.staticGetAtomSetCollection((AtomSetCollectionReader) ret);
if (ret instanceof String) {
Logger.warn("" + ret);
break;
}
model = (AtomSetCollection) ret;
String baseModel = base;
if (baseModel.length() == 0)
baseModel = last;
if (baseModel.length() != 0) {
int ibase = findModelById(baseModel);
if (ibase >= 0) {
asc.setModelInfoForSet("jdxModelID",
baseModel, ibase);
for (int i = model.atomSetCount; --i >= 0;)
model.setModelInfoForSet("jdxBaseModel", baseModel, i);
if (model.bondCount == 0)
setBonding(model, ibase);
}
}
if (!Float.isNaN(vibScale)) {
Logger.info("JcampdxReader applying vibration scaling of " + vibScale + " to "
+ model.ac + " atoms");
Atom[] atoms = model.atoms;
for (int i = model.ac; --i >= 0;) {
if (atoms[i].vib != null && !Float.isNaN(atoms[i].vib.z))
atoms[i].vib.scale(vibScale);
}
}
if (!Float.isNaN(modelScale)) {
Logger.info("JcampdxReader applying model scaling of " + modelScale + " to "
+ model.ac + " atoms");
Atom[] atoms = model.atoms;
for (int i = model.ac; --i >= 0;)
atoms[i].scale(modelScale);
}
Logger.info("jdx model=" + id + " type=" + model.fileTypeName);
asc.appendAtomSetCollection(-1, model);
break;
}
updateModelIDs(id, model0, isFirst);
}
/**
* add bonding to a set of ModelData based on a MOL file only if the this set
* has no bonding already
*
* @param a
* @param ibase
*/
private void setBonding(AtomSetCollection a, int ibase) {
int n0 = asc.getAtomSetAtomCount(ibase);
int n = a.ac;
if (n % n0 != 0) {
Logger.warn("atom count in secondary model (" + n
+ ") is not a multiple of " + n0 + " -- bonding ignored");
return;
}
Bond[] bonds = asc.bonds;
int b0 = 0;
for (int i = 0; i < ibase; i++)
b0 += asc.getAtomSetBondCount(i);
int b1 = b0 + asc.getAtomSetBondCount(ibase);
int ii0 = asc.getAtomSetAtomIndex(ibase);
int nModels = a.atomSetCount;
for (int j = 0; j < nModels; j++) {
int i0 = a.getAtomSetAtomIndex(j) - ii0;
if (a.getAtomSetAtomCount(j) != n0) {
Logger.warn("atom set atom count in secondary model ("
+ a.getAtomSetAtomCount(j) + ") is not equal to " + n0
+ " -- bonding ignored");
return;
}
for (int i = b0; i < b1; i++)
a.addNewBondWithOrder(bonds[i].atomIndex1 + i0, bonds[i].atomIndex2
+ i0, bonds[i].order);
}
}
/**
* The first model set is allowed to be a single model and given no extension.
* All other model sets are given .1 .2 .3 ... extensions to their IDs.
*
* @param id
* @param model0
* @param isFirst
*/
private void updateModelIDs(String id, int model0, boolean isFirst) {
int n = asc.atomSetCount;
if (isFirst && n == model0 + 2) {
asc.setCurrentModelInfo("modelID", id);
return;
}
for (int pt = 0, i = model0; ++i < n;)
asc.setModelInfoForSet("modelID", id + "."
+ (++pt), i);
}
private Lst peakData = new Lst();
@Override
public void addPeakData(String info) {
peakData.addLast(info);
}
/**
* integrate the records into the associated models, and
* delete unreferenced n.m models
*/
private void processPeakData() {
if (acdAssignments != null) {
try {
mpr.setACDAssignments(title, nucleus + type, 0, acdAssignments, acdMolFile);
} catch (Exception e) {
// ignore
}
}
int n = peakData.size();
if (n == 0)
return;
BS bsModels = new BS();
boolean havePeaks = (n > 0);
for (int p = 0; p < n; p++) {
line = peakData.get(p);
String type = mpr.getAttribute(line, "type");
String id = mpr.getAttribute(line, "model");
int i = findModelById(id);
if (i < 0) {
Logger.warn("cannot find model " + id + " required for " + line);
continue;
}
addType(i, type);
String title = type + ": " + mpr.getAttribute(line, "title");
String key = "jdxAtomSelect_" + mpr.getAttribute(line, "type");
bsModels.set(i);
String s;
if (mpr.getAttribute(line, "atoms").length() != 0) {
processPeakSelectAtom(i, key, line);
s = type + ": ";
} else if (processPeakSelectModel(i, title)) {
s = "model: ";
} else {
s = "ignored: ";
}
Logger.info(s + line);
}
n = asc.atomSetCount;
for (int i = n; --i >= 0;) {
String id = (String) asc.getAtomSetAuxiliaryInfoValue(i,
"modelID");
if (havePeaks && !bsModels.get(i) && id.indexOf(".") >= 0) {
asc.removeAtomSet(i);
n--;
}
}
if (selectedModel == Integer.MIN_VALUE) {
if (allTypes != null)
appendLoadNote(allTypes);
} else {
if (selectedModel == 0)
selectedModel = n - 1;
for (int i = asc.atomSetCount; --i >= 0;)
if (i + 1 != selectedModel)
asc.removeAtomSet(i);
if (n > 0)
appendLoadNote((String) asc.getAtomSetAuxiliaryInfoValue(
0, "name"));
}
for (int i = asc.atomSetCount; --i >= 0;)
asc.setAtomSetNumber(i, i + 1);
asc.centralize();
}
private int findModelById(String modelID) {
for (int i = asc.atomSetCount; --i >= 0;) {
String id = (String) asc.getAtomSetAuxiliaryInfoValue(i,
"modelID");
if (modelID.equals(id))
return i;
}
return -1;
}
private String allTypes;
/**
* sets an auxiliaryInfo string to "HNMR 13CNMR" or "IR" or "MS"
*
* @param imodel
* @param type
*/
private void addType(int imodel, String type) {
String types = addTypeStr(
(String) asc.getAtomSetAuxiliaryInfoValue(imodel,
"spectrumTypes"), type);
if (types == null)
return;
asc.setModelInfoForSet("spectrumTypes", types,
imodel);
String s = addTypeStr(allTypes, type);
if (s != null)
allTypes = s;
}
private String addTypeStr(String types, String type) {
if (types != null && types.contains(type))
return null;
if (types == null)
types = "";
else
types += ",";
return types + type;
}
@SuppressWarnings("unchecked")
private void processPeakSelectAtom(int i, String key, String data) {
Lst peaks = (Lst) asc
.getAtomSetAuxiliaryInfoValue(i, key);
if (peaks == null)
asc.setModelInfoForSet(key,
peaks = new Lst(), i);
peaks.addLast(data);
}
private boolean processPeakSelectModel(int i, String title) {
if (asc.getAtomSetAuxiliaryInfoValue(i, "jdxModelSelect") != null)
return false;
// assign name and jdxModelSelect ONLY if first found.
asc.setModelInfoForSet("name", title, i);
asc.setModelInfoForSet("jdxModelSelect", line, i);
return true;
}
@Override
public void setSpectrumPeaks(int nH, String piUnitsX, String piUnitsY) {
// JSpecView only
}
}