MNOVA spectra generation scripts?

[allcatsaregrey]

Do you have available the scripts you used to generate your spectra with MNOVA?

Thanks!

[FranklinHu1]

Hi,

Sorry for the delay in response! Will put something up by the end of the week either in response to this issue or on the repository itself.

Thanks!

[FranklinHu1]

Hello,

Here is the script we use for spectrum generation with Mnova. All it does is load the mol files at the specified directory into MestReNova and runs the 1H and 13C predictors to get the spectra.

function import_mol_get_peaks(){

	function getActiveMolecule(aDocWin, aMolPlugin) {
		molec = aMolPlugin.activeMolecule();

		if (molec.isValid()) {
			return molec;
		}
		if (aDocWin.itemCount("Molecule") === 1) {
			molec = new Molecule(aDocWin.item(0, "Molecule"));
			return molec;
		}
		return undefined;
	}		
	
	dirName = "<directory of mol files>";
	outdirName = "<directory to write output files to";	
	
	aDir = new Dir(dirName);	
		
	files = aDir.entryList("*.mol");				
	
	for (ifiles = 0; ifiles < files.length ; ifiles++) {
		fileName = files[ifiles];
		
		if (File.exists(outdirName + fileName.replace(".mol", "-1H.txt"))) {
			print("Skipping: " + outdirName+fileName);
			continue;
		}
		
		doc = new DocumentWindow(Application.mainWindow.newWindow());
	
		if (serialization.open(dirName+fileName)) {
			print("SUCCESS: opened " + dirName+fileName);
		} else {
			print("FAILED: could not open " + dirName+fileName);
			doc.close();
			continue;
		}
	
		mol = getActiveMolecule(doc, Application.molecule);
		
		// Get 1H NMR spectrum
		spcId1H = NMRPredictor.predict(mol, "1H");
				
		if (!spcId1H) {
			continue
		}
	
		spec1H = new NMRSpectrum(nmr.activeSpectrum());
	
		ppm1H = spec1H.hz() / spec1H.frequency();
		dPpm1H = spec1H.scaleWidth() / spec1H.count() / spec1H.frequency();				
	
		fout = new File(outdirName + fileName.replace(".mol", "-1H.txt"));
		fout.open(File.WriteOnly);
	
		sout = TextStream(fout);
		sout.precision = 10;
	
		for (si = spec1H.count() - 1; si >= 0 ; si--) {
			sout.write(ppm1H, "\t\t", spec1H.real(si), "\n");
			ppm1H += dPpm1H;
		}
		
		fout.close();		
		/*
		// Get 1H NMR peak shifts and splittings
		nmrPredTable1H = NMRPredictor.spinSimulationDataText(mol, "1H", 4);		
		
		fout = new File(outdirName + fileName.replace(".mol", "-1H.tbl"));
		fout.open(File.WriteOnly);
		
		sout = TextStream(fout);
		sout.precision = 4;	
		
		sout.write(nmrPredTable1H);
		*/
		// Get 13C NMR spectrum
		spcId13C = NMRPredictor.predict(mol, "13C");
				
		if (!spcId13C) {
			continue
		}
		/*
		spec13C = new NMRSpectrum(nmr.activeSpectrum());
		
		ppm13C = spec13C.hz() / spec13C.frequency();
		dPpm13C = spec13C.scaleWidth() / spec13C.count() / spec13C.frequency();				
	
		fout = new File(outdirName + fileName.replace(".mol", "-13C.txt"));
		fout.open(File.WriteOnly);
	
		sout = TextStream(fout);
		sout.precision = 10;
	
		for (si = spec13C.count() - 1; si >= 0 ; si--) {
			sout.write(ppm13C, "\t\t", spec13C.real(si), "\n");
			ppm13C += dPpm13C;
		}							
		*/
		// Get 13C NMR peak shifts and splittings
		nmrPredTable13C = NMRPredictor.spinSimulationDataText(mol, "13C", 4);		
		
		fout = new File(outdirName + fileName.replace(".mol", "-13C.tbl"));
		fout.open(File.WriteOnly);
		
		sout = TextStream(fout);
		sout.precision = 4;	
		
		sout.write(nmrPredTable13C);			
			
		fout.close();
		doc.close();

	}
}

Thanks!