/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testContains_IMolecularFormulaSet_IMolecularFormula() {
IMolecularFormula mf1 = new MolecularFormula();
mf1.addIsotope(builder.newIsotope("C"), 4);
mf1.addIsotope(builder.newIsotope("H"), 12);
mf1.addIsotope(builder.newIsotope("N"), 1);
mf1.addIsotope(builder.newIsotope("O"), 4);
IMolecularFormula mf3 = new MolecularFormula();
mf3.addIsotope(builder.newIsotope("C"), 9);
mf3.addIsotope(builder.newIsotope("H"), 5);
mf3.addIsotope(builder.newIsotope("O"), 7);
IMolecularFormulaSet formulaSet = new MolecularFormulaSet();
formulaSet.addMolecularFormula(mf1);
formulaSet.addMolecularFormula(mf3);
IMolecularFormula mf2 = new MolecularFormula();
mf2.addIsotope(builder.newIsotope("C"), 4);
mf2.addIsotope(builder.newIsotope("H"), 12);
mf2.addIsotope(builder.newIsotope("N"), 1);
mf2.addIsotope(builder.newIsotope("O"), 4);
IMolecularFormula mf4 = new MolecularFormula();
mf4.addIsotope(builder.newIsotope("C"), 4);
IIsotope hyd = builder.newIsotope("H");
hyd.setExactMass(2.0032342);
mf4.addIsotope(hyd, 12);
mf4.addIsotope(builder.newIsotope("N"), 1);
mf4.addIsotope(builder.newIsotope("O"), 4);
Assert.assertTrue(MolecularFormulaSetManipulator.contains(formulaSet, mf2));
Assert.assertFalse(MolecularFormulaSetManipulator.contains(formulaSet, mf4));
}
/**
* Get a list of IIsotope from a given IElement which is contained molecular. The search is based
* only on the IElement.
*
* @param formula The MolecularFormula to check
* @param element The IElement object
* @return The list with the IIsotopes in this molecular formula
*/
public static List<IIsotope> getIsotopes(IMolecularFormula formula, IElement element) {
List<IIsotope> isotopeList = new ArrayList<IIsotope>();
for (IIsotope isotope : formula.isotopes()) {
if (isotope.getSymbol().equals(element.getSymbol())) isotopeList.add(isotope);
}
return isotopeList;
}
/**
* True, if the MolecularFormula contains the given element as IIsotope object.
*
* @param formula IMolecularFormula molecularFormula
* @param element The element this MolecularFormula is searched for
* @return True, if the MolecularFormula contains the given element object
*/
public static boolean containsElement(IMolecularFormula formula, IElement element) {
for (IIsotope isotope : formula.isotopes()) {
if (element.getSymbol().equals(isotope.getSymbol())) return true;
}
return false;
}
/**
* Checks a set of Nodes for the occurrence of the isotopes in the molecular formula from a
* particular IElement. It returns 0 if the element does not exist. The search is based only on
* the IElement.
*
* @param formula The MolecularFormula to check
* @param element The IElement object
* @return The occurrence of this element in this molecular formula
*/
public static int getElementCount(IMolecularFormula formula, IElement element) {
int count = 0;
for (IIsotope isotope : formula.isotopes()) {
if (isotope.getSymbol().equals(element.getSymbol()))
count += formula.getIsotopeCount(isotope);
}
return count;
}
/**
* Get the summed natural abundance of all isotopes from an MolecularFormula. Assumes abundances
* to be preset, and will return 0.0 if not.
*
* @param formula The IMolecularFormula to calculate
* @return The summed natural abundance of all isotopes in this MolecularFormula
*/
public static double getTotalNaturalAbundance(IMolecularFormula formula) {
double abundance = 1.0;
for (IIsotope isotope : formula.isotopes()) {
if (isotope.getNaturalAbundance() == null) return 0.0;
abundance =
abundance * Math.pow(isotope.getNaturalAbundance(), formula.getIsotopeCount(isotope));
}
return abundance / Math.pow(100, getAtomCount(formula));
}
@Test
public void testDifference() {
IIsotope element1 = mock(IIsotope.class);
IIsotope element2 = mock(IIsotope.class);
when(element1.getSymbol()).thenReturn("H");
when(element2.getSymbol()).thenReturn("C");
IDifference difference = IsotopeDiff.difference(element1, element2);
Assert.assertNotNull(difference);
}
/**
* Get a list of all Elements which are contained molecular.
*
* @param formula The MolecularFormula to check
* @return The list with the IElements in this molecular formula
*/
public static List<IElement> elements(IMolecularFormula formula) {
List<IElement> elementList = new ArrayList<IElement>();
List<String> stringList = new ArrayList<String>();
for (IIsotope isotope : formula.isotopes()) {
if (!stringList.contains(isotope.getSymbol())) {
elementList.add(isotope);
stringList.add(isotope.getSymbol());
}
}
return elementList;
}
@Test
public void testDiff() {
IIsotope element1 = mock(IIsotope.class);
IIsotope element2 = mock(IIsotope.class);
when(element1.getSymbol()).thenReturn("H");
when(element2.getSymbol()).thenReturn("C");
String result = IsotopeDiff.diff(element1, element2);
Assert.assertNotNull(result);
Assert.assertNotSame(0, result.length());
assertContains(result, "IsotopeDiff");
assertContains(result, "H/C");
}
/**
* Get the summed mass number of all isotopes from an MolecularFormula. It assumes isotope masses
* to be preset, and returns 0.0 if not.
*
* @param formula The IMolecularFormula to calculate
* @return The summed nominal mass of all atoms in this MolecularFormula
*/
public static double getTotalMassNumber(IMolecularFormula formula) {
double mass = 0.0;
for (IIsotope isotope : formula.isotopes()) {
try {
IIsotope isotope2 = Isotopes.getInstance().getMajorIsotope(isotope.getSymbol());
if (isotope2 != null) {
mass += isotope2.getMassNumber() * formula.getIsotopeCount(isotope);
}
} catch (IOException e) {
e.printStackTrace();
}
}
return mass;
}
/**
* Get the summed major isotopic mass of all elements from an MolecularFormula.
*
* @param formula The IMolecularFormula to calculate
* @return The summed exact major isotope masses of all atoms in this MolecularFormula
*/
public static double getMajorIsotopeMass(IMolecularFormula formula) {
double mass = 0.0;
IsotopeFactory factory;
try {
factory = Isotopes.getInstance();
} catch (IOException e) {
throw new RuntimeException("Could not instantiate the IsotopeFactory.");
}
for (IIsotope isotope : formula.isotopes()) {
IIsotope major = factory.getMajorIsotope(isotope.getSymbol());
if (major != null) {
mass += major.getExactMass() * formula.getIsotopeCount(isotope);
}
}
return mass;
}
/**
* Returns the string representation of the molecule formula with numbers wrapped in
* <sub></sub> tags and the isotope of each Element in <sup></sup> tags
* and the total showCharge of IMolecularFormula in <sup></sup> tags. Useful for
* displaying formulae in Swing components or on the web.
*
* @param formula The IMolecularFormula object
* @param orderElements The order of Elements
* @param showCharge True, If it has to show the showCharge
* @param showIsotopes True, If it has to show the Isotope mass
* @return A HTML representation of the molecular formula
* @see #getHTML(IMolecularFormula)
*/
public static String getHTML(
IMolecularFormula formula, String[] orderElements, boolean showCharge, boolean showIsotopes) {
StringBuilder sb = new StringBuilder();
for (String orderElement : orderElements) {
IElement element = formula.getBuilder().newInstance(IElement.class, orderElement);
if (containsElement(formula, element)) {
if (!showIsotopes) {
sb.append(element.getSymbol());
int n = getElementCount(formula, element);
if (n > 1) {
sb.append("<sub>").append(n).append("</sub>");
}
} else {
for (IIsotope isotope : getIsotopes(formula, element)) {
Integer massNumber = isotope.getMassNumber();
if (massNumber != null) sb.append("<sup>").append(massNumber).append("</sup>");
sb.append(isotope.getSymbol());
int n = formula.getIsotopeCount(isotope);
if (n > 1) {
sb.append("<sub>").append(n).append("</sub>");
}
}
}
}
}
if (showCharge) {
Integer charge = formula.getCharge();
if (charge == CDKConstants.UNSET || charge == 0) {
return sb.toString();
} else {
sb.append("<sup>");
if (charge > 1 || charge < -1) sb.append(Math.abs(charge));
if (charge > 0) sb.append('+');
else sb.append(MINUS); // note, not a hyphen!
sb.append("</sup>");
}
}
return sb.toString();
}
/**
* Returns the string representation of the molecule formula.
*
* @param formula The IMolecularFormula Object
* @param orderElements The order of Elements
* @param setOne True, when must be set the value 1 for elements with one atom
* @return A String containing the molecular formula
* @see #getHTML(IMolecularFormula)
* @see #generateOrderEle()
* @see #generateOrderEle_Hill_NoCarbons()
* @see #generateOrderEle_Hill_WithCarbons()
*/
public static String getString(
IMolecularFormula formula, String[] orderElements, boolean setOne) {
StringBuffer stringMF = new StringBuffer();
List<IIsotope> isotopesList = putInOrder(orderElements, formula);
// collect elements in a map - since different isotopes of the
// same element will get repeated in the formula
List<String> elemSet = new ArrayList<String>();
for (IIsotope isotope : isotopesList) {
String symbol = isotope.getSymbol();
if (!elemSet.contains(symbol)) elemSet.add(symbol);
}
for (String elem : elemSet) {
int count = 0;
for (IIsotope isotope : formula.isotopes()) {
if (isotope.getSymbol().equals(elem)) count += formula.getIsotopeCount(isotope);
}
stringMF.append(elem);
if (!(count == 1 && !setOne)) stringMF.append(count);
}
return stringMF.toString();
}
private IAtomContainer makeAtomContainerFromFormula() {
IAtomContainer atomContainer = this.builder.newAtomContainer();
ArrayList<IAtom> atoms = new ArrayList<IAtom>();
for (IIsotope isotope : formula.isotopes()) {
for (int i = 0; i < formula.getIsotopeCount(isotope); i++) {
atoms.add(this.builder.newAtom(isotope));
System.out.println("added " + isotope.getSymbol());
}
}
// sort by symbol lexicographic order
Collections.sort(
atoms,
new Comparator<IAtom>() {
public int compare(IAtom o1, IAtom o2) {
return o1.getSymbol().compareTo(o2.getSymbol());
}
});
atomContainer.setAtoms(atoms.toArray(new IAtom[] {}));
return atomContainer;
}
/** @deprecated Use {@link #getString(org.openscience.cdk.interfaces.IMolecularFormula)} */
@Deprecated
public static String getHillString(IMolecularFormula formula) {
StringBuffer hillString = new StringBuffer();
Map<String, Integer> hillMap = new TreeMap<String, Integer>();
for (IIsotope isotope : formula.isotopes()) {
String symbol = isotope.getSymbol();
if (hillMap.containsKey(symbol))
hillMap.put(symbol, hillMap.get(symbol) + formula.getIsotopeCount(isotope));
else hillMap.put(symbol, formula.getIsotopeCount(isotope));
}
// if we have a C append it and also add in the H
// and then remove these elements
int count;
if (hillMap.containsKey("C")) {
hillString.append('C');
count = hillMap.get("C");
if (count > 1) hillString.append(count);
hillMap.remove("C");
if (hillMap.containsKey("H")) {
hillString.append('H');
count = hillMap.get("H");
if (count > 1) hillString.append(count);
hillMap.remove("H");
}
}
// now take all the rest in alphabetical order
for (String key : hillMap.keySet()) {
hillString.append(key);
count = hillMap.get(key);
if (count > 1) hillString.append(count);
}
return hillString.toString();
}
/**
* Adjust the protonation of a molecular formula. This utility method adjusts the hydrogen isotope
* count and charge at the same time.
*
* <pre>
* IMolecularFormula mf = MolecularFormulaManipulator.getMolecularFormula("[C6H5O]-", bldr);
* MolecularFormulaManipulator.adjustProtonation(mf, +1); // now "C6H6O"
* MolecularFormulaManipulator.adjustProtonation(mf, -1); // now "C6H5O-"
* </pre>
*
* The return value indicates whether the protonation could be adjusted:
*
* <pre>
* IMolecularFormula mf = MolecularFormulaManipulator.getMolecularFormula("[Cl]-", bldr);
* MolecularFormulaManipulator.adjustProtonation(mf, +0); // false still "[Cl]-"
* MolecularFormulaManipulator.adjustProtonation(mf, +1); // true now "HCl"
* MolecularFormulaManipulator.adjustProtonation(mf, -1); // true now "[Cl]-" (again)
* MolecularFormulaManipulator.adjustProtonation(mf, -1); // false still "[Cl]-" (no H to remove!)
* </pre>
*
* The method tries to select an existing hydrogen isotope to augment. If no hydrogen isotopes are
* found a new major isotope (<sup>1</sup>H) is created.
*
* @param mf molecular formula
* @param hcnt the number of hydrogens to add/remove, (>0 protonate:, <0: deprotonate)
* @return the protonation was be adjusted
*/
public static boolean adjustProtonation(IMolecularFormula mf, int hcnt) {
if (mf == null) throw new NullPointerException("No formula provided");
if (hcnt == 0) return false; // no protons to add
final IChemObjectBuilder bldr = mf.getBuilder();
final int chg = mf.getCharge() != null ? mf.getCharge() : 0;
IIsotope proton = null;
int pcount = 0;
for (IIsotope iso : mf.isotopes()) {
if ("H".equals(iso.getSymbol())) {
final int count = mf.getIsotopeCount(iso);
if (count < hcnt) continue;
// acceptable
if (proton == null && (iso.getMassNumber() == null || iso.getMassNumber() == 1)) {
proton = iso;
pcount = count;
}
// better
else if (proton != null
&& iso.getMassNumber() != null
&& iso.getMassNumber() == 1
&& proton.getMassNumber() == null) {
proton = iso;
pcount = count;
}
}
}
if (proton == null && hcnt < 0) {
return false;
} else if (proton == null && hcnt > 0) {
proton = bldr.newInstance(IIsotope.class, "H");
proton.setMassNumber(1);
}
mf.removeIsotope(proton);
if (pcount + hcnt > 0) mf.addIsotope(proton, pcount + hcnt);
mf.setCharge(chg + hcnt);
return true;
}
/**
* Get the summed exact mass of all isotopes from an MolecularFormula. It assumes isotope masses
* to be preset, and returns 0.0 if not.
*
* @param formula The IMolecularFormula to calculate
* @return The summed exact mass of all atoms in this MolecularFormula
*/
public static double getTotalExactMass(IMolecularFormula formula) {
Double mass = 0.0;
for (IIsotope isotope : formula.isotopes()) {
if (isotope.getExactMass() == CDKConstants.UNSET) {
try {
IIsotope majorIsotope = Isotopes.getInstance().getMajorIsotope(isotope.getSymbol());
if (majorIsotope != null) {
mass += majorIsotope.getExactMass() * formula.getIsotopeCount(isotope);
}
} catch (IOException e) {
throw new RuntimeException("Could not instantiate the IsotopeFactory.");
}
} else mass += isotope.getExactMass() * formula.getIsotopeCount(isotope);
}
if (formula.getCharge() != null) mass = correctMass(mass, formula.getCharge());
return mass;
}
/**
* Read an IAtomContainer from a file in MDL sd format
*
* @return The Molecule that was read from the MDL file.
*/
private IAtomContainer readAtomContainer(IAtomContainer molecule) throws CDKException {
logger.debug("Reading new molecule");
IAtomContainer outputContainer = null;
int linecount = 0;
int atoms = 0;
int bonds = 0;
int atom1 = 0;
int atom2 = 0;
int order = 0;
IBond.Stereo stereo = (IBond.Stereo) CDKConstants.UNSET;
int RGroupCounter = 1;
int Rnumber = 0;
String[] rGroup = null;
double x = 0.0;
double y = 0.0;
double z = 0.0;
double totalX = 0.0;
double totalY = 0.0;
double totalZ = 0.0;
String title = null;
String remark = null;
// int[][] conMat = new int[0][0];
// String help;
IAtom atom;
String line = "";
// A map to keep track of R# atoms so that RGP line can be parsed
Map<Integer, IPseudoAtom> rAtoms = new HashMap<Integer, IPseudoAtom>();
try {
IsotopeFactory isotopeFactory = Isotopes.getInstance();
logger.info("Reading header");
line = input.readLine();
linecount++;
if (line == null) {
return null;
}
logger.debug("Line " + linecount + ": " + line);
if (line.startsWith("$$$$")) {
logger.debug("File is empty, returning empty molecule");
return molecule;
}
if (line.length() > 0) {
title = line;
}
line = input.readLine();
linecount++;
logger.debug("Line " + linecount + ": " + line);
line = input.readLine();
linecount++;
logger.debug("Line " + linecount + ": " + line);
if (line.length() > 0) {
remark = line;
}
logger.info("Reading rest of file");
line = input.readLine();
linecount++;
logger.debug("Line " + linecount + ": " + line);
// if the line is empty we hav a problem - either a malformed
// molecule entry or just extra new lines at the end of the file
if (line.length() == 0) {
// read till the next $$$$ or EOF
while (true) {
line = input.readLine();
linecount++;
if (line == null) {
return null;
}
if (line.startsWith("$$$$")) {
return molecule; // an empty molecule
}
}
}
// check the CT block version
if (line.contains("V3000") || line.contains("v3000")) {
handleError("This file must be read with the MDLV3000Reader.");
} else if (!line.contains("V2000") && !line.contains("v2000")) {
handleError("This file must be read with the MDLReader.");
}
atoms = Integer.parseInt(line.substring(0, 3).trim());
List<IAtom> atomList = new ArrayList<IAtom>();
logger.debug("Atomcount: " + atoms);
bonds = Integer.parseInt(line.substring(3, 6).trim());
logger.debug("Bondcount: " + bonds);
List<IBond> bondList = new ArrayList<IBond>();
// used for applying the MDL valence model
int[] explicitValence = new int[atoms];
// read ATOM block
logger.info("Reading atom block");
atomsByLinePosition = new ArrayList<IAtom>();
atomsByLinePosition.add(null); // 0 is not a valid position
int atomBlockLineNumber = 0;
for (int f = 0; f < atoms; f++) {
line = input.readLine();
linecount++;
atomBlockLineNumber++;
Matcher trailingSpaceMatcher = TRAILING_SPACE.matcher(line);
if (trailingSpaceMatcher.find()) {
handleError(
"Trailing space found",
linecount,
trailingSpaceMatcher.start(),
trailingSpaceMatcher.end());
line = trailingSpaceMatcher.replaceAll("");
}
x = Double.parseDouble(line.substring(0, 10).trim());
y = Double.parseDouble(line.substring(10, 20).trim());
z = Double.parseDouble(line.substring(20, 30).trim());
// *all* values should be zero, not just the sum
totalX += Math.abs(x);
totalY += Math.abs(y);
totalZ += Math.abs(z);
logger.debug("Coordinates: " + x + "; " + y + "; " + z);
String element = line.substring(31, Math.min(line.length(), 34)).trim();
if (line.length() < 34) {
handleError(
"Element atom type does not follow V2000 format type should of length three"
+ " and padded with space if required",
linecount,
31,
34);
}
logger.debug("Atom type: ", element);
if (isotopeFactory.isElement(element)) {
atom = isotopeFactory.configure(molecule.getBuilder().newInstance(IAtom.class, element));
} else if ("A".equals(element)) {
atom = molecule.getBuilder().newInstance(IPseudoAtom.class, element);
} else if ("Q".equals(element)) {
atom = molecule.getBuilder().newInstance(IPseudoAtom.class, element);
} else if ("*".equals(element)) {
atom = molecule.getBuilder().newInstance(IPseudoAtom.class, element);
} else if ("LP".equals(element)) {
atom = molecule.getBuilder().newInstance(IPseudoAtom.class, element);
} else if ("L".equals(element)) {
atom = molecule.getBuilder().newInstance(IPseudoAtom.class, element);
} else if (element.equals("R") || (element.length() > 0 && element.charAt(0) == 'R')) {
logger.debug("Atom ", element, " is not an regular element. Creating a PseudoAtom.");
// check if the element is R
rGroup = element.split("^R");
atom = null;
if (rGroup.length > 1) {
try {
Rnumber = Integer.valueOf(rGroup[(rGroup.length - 1)]);
RGroupCounter = Rnumber;
element = "R" + Rnumber;
atom = molecule.getBuilder().newInstance(IPseudoAtom.class, element);
} catch (Exception ex) {
// This happens for atoms labeled "R#".
// The Rnumber may be set later on, using RGP line
atom = molecule.getBuilder().newInstance(IPseudoAtom.class, "R");
rAtoms.put(atomBlockLineNumber, (IPseudoAtom) atom);
}
} else {
atom = molecule.getBuilder().newInstance(IPseudoAtom.class, element);
}
} else {
handleError(
"Invalid element type. Must be an existing " + "element, or one in: A, Q, L, LP, *.",
linecount,
32,
35);
atom = molecule.getBuilder().newInstance(IPseudoAtom.class, element);
atom.setSymbol(element);
}
// store as 3D for now, convert to 2D (if totalZ == 0.0) later
atom.setPoint3d(new Point3d(x, y, z));
// parse further fields
if (line.length() >= 36) {
String massDiffString = line.substring(34, 36).trim();
logger.debug("Mass difference: ", massDiffString);
if (!(atom instanceof IPseudoAtom)) {
try {
int massDiff = Integer.parseInt(massDiffString);
if (massDiff != 0) {
IIsotope major = Isotopes.getInstance().getMajorIsotope(element);
atom.setMassNumber(major.getMassNumber() + massDiff);
}
} catch (Exception exception) {
handleError("Could not parse mass difference field.", linecount, 35, 37, exception);
}
} else {
logger.error("Cannot set mass difference for a non-element!");
}
} else {
handleError("Mass difference is missing", linecount, 34, 36);
}
// set the stereo partiy
Integer parity = line.length() > 41 ? Character.digit(line.charAt(41), 10) : 0;
atom.setStereoParity(parity);
if (line.length() >= 51) {
String valenceString = removeNonDigits(line.substring(48, 51));
logger.debug("Valence: ", valenceString);
if (!(atom instanceof IPseudoAtom)) {
try {
int valence = Integer.parseInt(valenceString);
if (valence != 0) {
// 15 is defined as 0 in mol files
if (valence == 15) atom.setValency(0);
else atom.setValency(valence);
}
} catch (Exception exception) {
handleError(
"Could not parse valence information field", linecount, 49, 52, exception);
}
} else {
logger.error("Cannot set valence information for a non-element!");
}
}
if (line.length() >= 39) {
String chargeCodeString = line.substring(36, 39).trim();
logger.debug("Atom charge code: ", chargeCodeString);
int chargeCode = Integer.parseInt(chargeCodeString);
if (chargeCode == 0) {
// uncharged species
} else if (chargeCode == 1) {
atom.setFormalCharge(+3);
} else if (chargeCode == 2) {
atom.setFormalCharge(+2);
} else if (chargeCode == 3) {
atom.setFormalCharge(+1);
} else if (chargeCode == 4) {
} else if (chargeCode == 5) {
atom.setFormalCharge(-1);
} else if (chargeCode == 6) {
atom.setFormalCharge(-2);
} else if (chargeCode == 7) {
atom.setFormalCharge(-3);
}
} else {
handleError("Atom charge is missing", linecount, 36, 39);
}
try {
// read the mmm field as position 61-63
String reactionAtomIDString = line.substring(60, 63).trim();
logger.debug("Parsing mapping id: ", reactionAtomIDString);
try {
int reactionAtomID = Integer.parseInt(reactionAtomIDString);
if (reactionAtomID != 0) {
atom.setProperty(CDKConstants.ATOM_ATOM_MAPPING, reactionAtomID);
}
} catch (Exception exception) {
logger.error("Mapping number ", reactionAtomIDString, " is not an integer.");
logger.debug(exception);
}
} catch (Exception exception) {
// older mol files don't have all these fields...
logger.warn("A few fields are missing. Older MDL MOL file?");
}
// shk3: This reads shifts from after the molecule. I don't think this is an official
// format, but I saw it frequently 80=>78 for alk
if (line.length() >= 78) {
double shift = Double.parseDouble(line.substring(69, 80).trim());
atom.setProperty("first shift", shift);
}
if (line.length() >= 87) {
double shift = Double.parseDouble(line.substring(79, 87).trim());
atom.setProperty("second shift", shift);
}
atomList.add(atom);
atomsByLinePosition.add(atom);
}
// convert to 2D, if totalZ == 0
if (totalX == 0.0 && totalY == 0.0 && totalZ == 0.0) {
logger.info("All coordinates are 0.0");
if (atomList.size() == 1) {
atomList.get(0).setPoint2d(new Point2d(x, y));
} else {
for (IAtom atomToUpdate : atomList) {
atomToUpdate.setPoint3d(null);
}
}
} else if (totalZ == 0.0 && !forceReadAs3DCoords.isSet()) {
logger.info("Total 3D Z is 0.0, interpreting it as a 2D structure");
for (IAtom atomToUpdate : atomList) {
Point3d p3d = atomToUpdate.getPoint3d();
if (p3d != null) {
atomToUpdate.setPoint2d(new Point2d(p3d.x, p3d.y));
atomToUpdate.setPoint3d(null);
}
}
}
// read BOND block
logger.info("Reading bond block");
int queryBondCount = 0;
for (int f = 0; f < bonds; f++) {
line = input.readLine();
linecount++;
atom1 = Integer.parseInt(line.substring(0, 3).trim());
atom2 = Integer.parseInt(line.substring(3, 6).trim());
order = Integer.parseInt(line.substring(6, 9).trim());
if (line.length() >= 12) {
int mdlStereo =
line.length() > 12
? Integer.parseInt(line.substring(9, 12).trim())
: Integer.parseInt(line.substring(9).trim());
if (mdlStereo == 1) {
// MDL up bond
stereo = IBond.Stereo.UP;
} else if (mdlStereo == 6) {
// MDL down bond
stereo = IBond.Stereo.DOWN;
} else if (mdlStereo == 0) {
if (order == 2) {
// double bond stereo defined by coordinates
stereo = IBond.Stereo.E_Z_BY_COORDINATES;
} else {
// bond has no stereochemistry
stereo = IBond.Stereo.NONE;
}
} else if (mdlStereo == 3 && order == 2) {
// unknown E/Z stereochemistry
stereo = IBond.Stereo.E_OR_Z;
} else if (mdlStereo == 4) {
// MDL bond undefined
stereo = IBond.Stereo.UP_OR_DOWN;
}
} else {
handleError("Missing expected stereo field at line: ", linecount, 10, 12);
}
if (logger.isDebugEnabled()) {
logger.debug("Bond: " + atom1 + " - " + atom2 + "; order " + order);
}
// interpret CTfile's special bond orders
IAtom a1 = atomList.get(atom1 - 1);
IAtom a2 = atomList.get(atom2 - 1);
IBond newBond = null;
if (order >= 1 && order <= 3) {
IBond.Order cdkOrder = IBond.Order.SINGLE;
if (order == 2) cdkOrder = IBond.Order.DOUBLE;
if (order == 3) cdkOrder = IBond.Order.TRIPLE;
if (stereo != null) {
newBond = molecule.getBuilder().newInstance(IBond.class, a1, a2, cdkOrder, stereo);
} else {
newBond = molecule.getBuilder().newInstance(IBond.class, a1, a2, cdkOrder);
}
} else if (order == 4) {
// aromatic bond
if (stereo != null) {
newBond =
molecule.getBuilder().newInstance(IBond.class, a1, a2, IBond.Order.UNSET, stereo);
} else {
newBond = molecule.getBuilder().newInstance(IBond.class, a1, a2, IBond.Order.UNSET);
}
// mark both atoms and the bond as aromatic and raise the SINGLE_OR_DOUBLE-flag
newBond.setFlag(CDKConstants.SINGLE_OR_DOUBLE, true);
newBond.setFlag(CDKConstants.ISAROMATIC, true);
a1.setFlag(CDKConstants.ISAROMATIC, true);
a2.setFlag(CDKConstants.ISAROMATIC, true);
} else {
queryBondCount++;
newBond = new CTFileQueryBond(molecule.getBuilder());
IAtom[] bondAtoms = {a1, a2};
newBond.setAtoms(bondAtoms);
newBond.setOrder(null);
CTFileQueryBond.Type queryBondType = null;
switch (order) {
case 5:
queryBondType = CTFileQueryBond.Type.SINGLE_OR_DOUBLE;
break;
case 6:
queryBondType = CTFileQueryBond.Type.SINGLE_OR_AROMATIC;
break;
case 7:
queryBondType = CTFileQueryBond.Type.DOUBLE_OR_AROMATIC;
break;
case 8:
queryBondType = CTFileQueryBond.Type.ANY;
break;
}
((CTFileQueryBond) newBond).setType(queryBondType);
newBond.setStereo(stereo);
}
bondList.add((newBond));
// add the bond order to the explicit valence for each atom
if (newBond.getOrder() != null && newBond.getOrder() != IBond.Order.UNSET) {
explicitValence[atom1 - 1] += newBond.getOrder().numeric();
explicitValence[atom2 - 1] += newBond.getOrder().numeric();
} else {
explicitValence[atom1 - 1] = Integer.MIN_VALUE;
explicitValence[atom2 - 1] = Integer.MIN_VALUE;
}
}
if (queryBondCount == 0) outputContainer = molecule;
else {
outputContainer = new QueryAtomContainer(molecule.getBuilder());
}
outputContainer.setProperty(CDKConstants.TITLE, title);
outputContainer.setProperty(CDKConstants.REMARK, remark);
for (IAtom at : atomList) {
outputContainer.addAtom(at);
}
for (IBond bnd : bondList) {
outputContainer.addBond(bnd);
}
// read PROPERTY block
logger.info("Reading property block");
while (true) {
line = input.readLine();
linecount++;
if (line == null) {
handleError("The expected property block is missing!", linecount, 0, 0);
}
if (line.startsWith("M END")) break;
boolean lineRead = false;
if (line.startsWith("M CHG")) {
// FIXME: if this is encountered for the first time, all
// atom charges should be set to zero first!
int infoCount = Integer.parseInt(line.substring(6, 9).trim());
StringTokenizer st = new StringTokenizer(line.substring(9));
for (int i = 1; i <= infoCount; i++) {
String token = st.nextToken();
int atomNumber = Integer.parseInt(token.trim());
token = st.nextToken();
int charge = Integer.parseInt(token.trim());
outputContainer.getAtom(atomNumber - 1).setFormalCharge(charge);
}
} else if (line.matches("A\\s{1,4}\\d+")) {
// Reads the pseudo atom property from the mol file
// The atom number of the to replaced atom
int aliasAtomNumber =
Integer.parseInt(line.replaceFirst("A\\s{1,4}", "")) - RGroupCounter;
line = input.readLine();
linecount++;
String[] aliasArray = line.split("\\\\");
// name of the alias atom like R1 or R2 etc.
String alias = "";
for (int i = 0; i < aliasArray.length; i++) {
alias += aliasArray[i];
}
IAtom aliasAtom = outputContainer.getAtom(aliasAtomNumber);
// skip if already a pseudoatom
if (aliasAtom instanceof IPseudoAtom) {
((IPseudoAtom) aliasAtom).setLabel(alias);
continue;
}
IAtom newPseudoAtom = molecule.getBuilder().newInstance(IPseudoAtom.class, alias);
if (aliasAtom.getPoint2d() != null) {
newPseudoAtom.setPoint2d(aliasAtom.getPoint2d());
}
if (aliasAtom.getPoint3d() != null) {
newPseudoAtom.setPoint3d(aliasAtom.getPoint3d());
}
outputContainer.addAtom(newPseudoAtom);
List<IBond> bondsOfAliasAtom = outputContainer.getConnectedBondsList(aliasAtom);
for (int i = 0; i < bondsOfAliasAtom.size(); i++) {
IBond bondOfAliasAtom = bondsOfAliasAtom.get(i);
IAtom connectedToAliasAtom = bondOfAliasAtom.getConnectedAtom(aliasAtom);
IBond newBond = bondOfAliasAtom.getBuilder().newInstance(IBond.class);
newBond.setAtoms(new IAtom[] {connectedToAliasAtom, newPseudoAtom});
newBond.setOrder(bondOfAliasAtom.getOrder());
outputContainer.addBond(newBond);
outputContainer.removeBond(aliasAtom, connectedToAliasAtom);
}
outputContainer.removeAtom(aliasAtom);
RGroupCounter++;
} else if (line.startsWith("M ISO")) {
try {
String countString = line.substring(6, 10).trim();
int infoCount = Integer.parseInt(countString);
StringTokenizer st = new StringTokenizer(line.substring(10));
for (int i = 1; i <= infoCount; i++) {
int atomNumber = Integer.parseInt(st.nextToken().trim());
int absMass = Integer.parseInt(st.nextToken().trim());
if (absMass != 0) {
IAtom isotope = outputContainer.getAtom(atomNumber - 1);
isotope.setMassNumber(absMass);
}
}
} catch (NumberFormatException exception) {
String error =
"Error ("
+ exception.getMessage()
+ ") while parsing line "
+ linecount
+ ": "
+ line
+ " in property block.";
logger.error(error);
handleError(
"NumberFormatException in isotope information.", linecount, 7, 11, exception);
}
} else if (line.startsWith("M RAD")) {
try {
String countString = line.substring(6, 9).trim();
int infoCount = Integer.parseInt(countString);
StringTokenizer st = new StringTokenizer(line.substring(9));
for (int i = 1; i <= infoCount; i++) {
int atomNumber = Integer.parseInt(st.nextToken().trim());
int spinMultiplicity = Integer.parseInt(st.nextToken().trim());
MDLV2000Writer.SPIN_MULTIPLICITY spin = MDLV2000Writer.SPIN_MULTIPLICITY.NONE;
if (spinMultiplicity > 0) {
IAtom radical = outputContainer.getAtom(atomNumber - 1);
switch (spinMultiplicity) {
case 1:
spin = MDLV2000Writer.SPIN_MULTIPLICITY.DOUBLET;
break;
case 2:
spin = MDLV2000Writer.SPIN_MULTIPLICITY.SINGLET;
break;
case 3:
spin = MDLV2000Writer.SPIN_MULTIPLICITY.TRIPLET;
break;
default:
logger.debug("Invalid spin multiplicity found: " + spinMultiplicity);
break;
}
for (int j = 0; j < spin.getSingleElectrons(); j++) {
outputContainer.addSingleElectron(
molecule.getBuilder().newInstance(ISingleElectron.class, radical));
}
}
}
} catch (NumberFormatException exception) {
String error =
"Error ("
+ exception.getMessage()
+ ") while parsing line "
+ linecount
+ ": "
+ line
+ " in property block.";
logger.error(error);
handleError(
"NumberFormatException in radical information", linecount, 7, 10, exception);
}
} else if (line.startsWith("G ")) {
try {
String atomNumberString = line.substring(3, 6).trim();
int atomNumber = Integer.parseInt(atomNumberString);
// String whatIsThisString = line.substring(6,9).trim();
String atomName = input.readLine();
// convert Atom into a PseudoAtom
IAtom prevAtom = outputContainer.getAtom(atomNumber - 1);
IPseudoAtom pseudoAtom = molecule.getBuilder().newInstance(IPseudoAtom.class, atomName);
if (prevAtom.getPoint2d() != null) {
pseudoAtom.setPoint2d(prevAtom.getPoint2d());
}
if (prevAtom.getPoint3d() != null) {
pseudoAtom.setPoint3d(prevAtom.getPoint3d());
}
AtomContainerManipulator.replaceAtomByAtom(molecule, prevAtom, pseudoAtom);
} catch (NumberFormatException exception) {
String error =
"Error ("
+ exception.toString()
+ ") while parsing line "
+ linecount
+ ": "
+ line
+ " in property block.";
logger.error(error);
handleError("NumberFormatException in group information", linecount, 4, 7, exception);
}
} else if (line.startsWith("M RGP")) {
StringTokenizer st = new StringTokenizer(line);
// Ignore first 3 tokens (overhead).
st.nextToken();
st.nextToken();
st.nextToken();
// Process the R group numbers as defined in RGP line.
while (st.hasMoreTokens()) {
Integer position = new Integer(st.nextToken());
Rnumber = new Integer(st.nextToken());
IPseudoAtom pseudoAtom = rAtoms.get(position);
if (pseudoAtom != null) {
pseudoAtom.setLabel("R" + Rnumber);
}
}
}
if (line.startsWith("V ")) {
Integer atomNumber = new Integer(line.substring(3, 6).trim());
IAtom atomWithComment = outputContainer.getAtom(atomNumber - 1);
atomWithComment.setProperty(CDKConstants.COMMENT, line.substring(7));
}
if (!lineRead) {
logger.warn("Skipping line in property block: ", line);
}
}
if (interpretHydrogenIsotopes.isSet()) {
fixHydrogenIsotopes(molecule, isotopeFactory);
}
// note: apply the valence model last so that all fixes (i.e. hydrogen
// isotopes) are in place
for (int i = 0; i < atoms; i++) {
applyMDLValenceModel(outputContainer.getAtom(i), explicitValence[i]);
}
} catch (CDKException exception) {
String error =
"Error while parsing line " + linecount + ": " + line + " -> " + exception.getMessage();
logger.error(error);
logger.debug(exception);
throw exception;
} catch (Exception exception) {
exception.printStackTrace();
String error =
"Error while parsing line " + linecount + ": " + line + " -> " + exception.getMessage();
logger.error(error);
logger.debug(exception);
handleError("Error while parsing line: " + line, linecount, 0, 0, exception);
}
return outputContainer;
}