_id stringlengths 2 7 | title stringlengths 3 140 | partition stringclasses 3
values | text stringlengths 73 34.1k | language stringclasses 1
value | meta_information dict |
|---|---|---|---|---|---|
q157200 | MolecularFormulaManipulator.correctMass | train | private static double correctMass(double mass, Integer charge) {
if (charge == null)
return mass;
double massE = 0.00054857990927;
if (charge > 0)
mass -= massE * charge;
else if (charge < 0) mass += massE * Math.abs(charge);
return mass;
} | java | {
"resource": ""
} |
q157201 | MolecularFormulaManipulator.getTotalMassNumber | train | 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) {
... | java | {
"resource": ""
} |
q157202 | MolecularFormulaManipulator.getTotalNaturalAbundance | train | 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.getIsoto... | java | {
"resource": ""
} |
q157203 | MolecularFormulaManipulator.getDBE | train | public static double getDBE(IMolecularFormula formula) throws CDKException {
int valencies[] = new int[5];
IAtomContainer ac = getAtomContainer(formula);
AtomTypeFactory factory = AtomTypeFactory.getInstance(
"org/openscience/cdk/config/data/structgen_atomtypes.xml", ac.getBuilde... | java | {
"resource": ""
} |
q157204 | MolecularFormulaManipulator.compare | train | public static boolean compare(IMolecularFormula formula1, IMolecularFormula formula2) {
if (!Objects.equals(formula1.getCharge(), formula2.getCharge())) return false;
if (formula1.getIsotopeCount() != formula2.getIsotopeCount()) return false;
for (IIsotope isotope : formula1.isotopes()) {
... | java | {
"resource": ""
} |
q157205 | MolecularFormulaManipulator.muliplier | train | private static String muliplier(String formula, int factor) {
String finalformula = "";
String recentElementSymbol = "";
String recentElementCountString = "0";
for (int f = 0; f < formula.length(); f++) {
char thisChar = formula.charAt(f);
if (f < formula.length()... | java | {
"resource": ""
} |
q157206 | MolecularFormulaManipulator.adjustProtonation | train | 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.getCharg... | java | {
"resource": ""
} |
q157207 | DoubleBondElementEncoderFactory.findOther | train | private static int findOther(int[] vs, int u, int x) {
for (int v : vs) {
if (v != u && v != x) return v;
}
throw new IllegalArgumentException("vs[] did not contain another vertex");
} | java | {
"resource": ""
} |
q157208 | DoubleBondElementEncoderFactory.indexMap | train | private static Map<IAtom, Integer> indexMap(Map<IAtom, Integer> map, IAtomContainer container) {
if (map != null) return map;
map = new HashMap<IAtom, Integer>();
for (IAtom a : container.atoms()) {
map.put(a, map.size());
}
return map;
} | java | {
"resource": ""
} |
q157209 | IsotopePatternGenerator.getIsotopes | train | public IsotopePattern getIsotopes(IMolecularFormula molFor) {
if (builder == null) {
try {
isoFactory = Isotopes.getInstance();
builder = molFor.getBuilder();
} catch (Exception e) {
e.printStackTrace();
}
}
Str... | java | {
"resource": ""
} |
q157210 | BasicAtomGenerator.canDraw | train | protected boolean canDraw(IAtom atom, IAtomContainer container, RendererModel model) {
// don't draw atoms without coordinates
if (!hasCoordinates(atom)) {
return false;
}
// don't draw invisible hydrogens
if (invisibleHydrogen(atom, model)) {
return fals... | java | {
"resource": ""
} |
q157211 | BasicAtomGenerator.generateCompactElement | train | public IRenderingElement generateCompactElement(IAtom atom, RendererModel model) {
Point2d point = atom.getPoint2d();
double radius = (Double) model.get(AtomRadius.class) / model.getParameter(Scale.class).getValue();
double distance = 2 * radius;
if (model.get(CompactShape.class) == Shap... | java | {
"resource": ""
} |
q157212 | BasicAtomGenerator.generateElement | train | public AtomSymbolElement generateElement(IAtom atom, int alignment, RendererModel model) {
String text;
if (atom instanceof IPseudoAtom) {
text = ((IPseudoAtom) atom).getLabel();
} else {
text = atom.getSymbol();
}
return new AtomSymbolElement(atom.getPoin... | java | {
"resource": ""
} |
q157213 | BasicAtomGenerator.showCarbon | train | protected boolean showCarbon(IAtom carbonAtom, IAtomContainer container, RendererModel model) {
if ((Boolean) model.get(KekuleStructure.class)) return true;
if (carbonAtom.getFormalCharge() != 0) return true;
int connectedBondCount = container.getConnectedBondsList(carbonAtom).size();
... | java | {
"resource": ""
} |
q157214 | AminoAcidManipulator.removeAcidicOxygen | train | public static void removeAcidicOxygen(IAminoAcid acid) throws CDKException {
if (acid.getCTerminus() == null) throw new CDKException("Cannot remove oxygen: C-terminus is not defined!");
java.util.List<IBond> bonds = acid.getConnectedBondsList(acid.getCTerminus());
// ok, look for the oxygen whi... | java | {
"resource": ""
} |
q157215 | AminoAcidManipulator.addAcidicOxygen | train | public static void addAcidicOxygen(IAminoAcid acid) throws CDKException {
if (acid.getCTerminus() == null) throw new CDKException("Cannot add oxygen: C-terminus is not defined!");
IAtom acidicOxygen = acid.getBuilder().newInstance(IAtom.class, "O");
acid.addAtom(acidicOxygen);
acid.addB... | java | {
"resource": ""
} |
q157216 | MassToFormulaTool.setRestrictions | train | public void setRestrictions(List<IRule> rulesNew) throws CDKException {
Iterator<IRule> itRules = rulesNew.iterator();
while (itRules.hasNext()) {
IRule rule = itRules.next();
if (rule instanceof ElementRule) {
mfRange = (MolecularFormulaRange) ((Object[]) rule.g... | java | {
"resource": ""
} |
q157217 | MassToFormulaTool.setDefaultRestrictions | train | public void setDefaultRestrictions() {
try {
callDefaultRestrictions();
} catch (CDKException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
}
} | java | {
"resource": ""
} |
q157218 | MassToFormulaTool.orderList | train | private List<IIsotope> orderList(List<IIsotope> isotopes_TO) {
List<IIsotope> newOrderList = new ArrayList<IIsotope>();
for (int i = 0; i < orderElements.length; i++) {
String symbol = orderElements[i];
Iterator<IIsotope> itIso = isotopes_TO.iterator();
while (itIso.h... | java | {
"resource": ""
} |
q157219 | MassToFormulaTool.getMaxOccurence | train | private int getMaxOccurence(double massTo, int element_pos, int[] matrix, List<IIsotope> isoToCond_new) {
double massIn = isoToCond_new.get(element_pos).getExactMass();
double massToM = massTo;
for (int i = 0; i < matrix.length; i++)
if (i != element_pos) if (matrix[i] != 0) massToM ... | java | {
"resource": ""
} |
q157220 | MassToFormulaTool.getFormula | train | private IMolecularFormula getFormula(List<IIsotope> isoToCond_new, int[] value_In) {
IMolecularFormula mf = builder.newInstance(IMolecularFormula.class);
for (int i = 0; i < isoToCond_new.size(); i++) {
if (value_In[i] != 0) {
for (int j = 0; j < value_In[i]; j++)
... | java | {
"resource": ""
} |
q157221 | MassToFormulaTool.putInOrder | train | private IMolecularFormula putInOrder(IMolecularFormula formula) {
IMolecularFormula new_formula = formula.getBuilder().newInstance(IMolecularFormula.class);
for (int i = 0; i < orderElements.length; i++) {
IElement element = builder.newInstance(IElement.class, orderElements[i]);
... | java | {
"resource": ""
} |
q157222 | MassToFormulaTool.calculateMassT | train | private double calculateMassT(List<IIsotope> isoToCond_new, int[] value_In) {
double result = 0;
for (int i = 0; i < isoToCond_new.size(); i++) {
if (value_In[i] != 0) {
result += isoToCond_new.get(i).getExactMass() * value_In[i];
}
}
return result... | java | {
"resource": ""
} |
q157223 | MassToFormulaTool.returnOrdered | train | private IMolecularFormulaSet returnOrdered(double mass, IMolecularFormulaSet formulaSet) {
IMolecularFormulaSet solutions_new = null;
if (formulaSet.size() != 0) {
double valueMin = 100;
int i_final = 0;
solutions_new = formulaSet.getBuilder().newInstance(IMolecular... | java | {
"resource": ""
} |
q157224 | MassToFormulaTool.getMatrix | train | private int[][] getMatrix(int size) {
logger.info("Creating matrix for isotopes combination");
int lengthM = (int) Math.pow(2, size);
lengthM--;// less 1 because the matrix 00000 we don't need
int[][] matrix = new int[lengthM][size];
int[] combi = new int[size];
for (in... | java | {
"resource": ""
} |
q157225 | ChemFileManipulator.getAtomCount | train | public static int getAtomCount(IChemFile file) {
int count = 0;
for (int i = 0; i < file.getChemSequenceCount(); i++) {
count += ChemSequenceManipulator.getAtomCount(file.getChemSequence(i));
}
return count;
} | java | {
"resource": ""
} |
q157226 | ChemFileManipulator.getBondCount | train | public static int getBondCount(IChemFile file) {
int count = 0;
for (int i = 0; i < file.getChemSequenceCount(); i++) {
count += ChemSequenceManipulator.getBondCount(file.getChemSequence(i));
}
return count;
} | java | {
"resource": ""
} |
q157227 | ChemFileManipulator.getAllChemObjects | train | public static List<IChemObject> getAllChemObjects(IChemFile file) {
List<IChemObject> list = new ArrayList<IChemObject>();
//list.add(file); // should not add the original file
for (int i = 0; i < file.getChemSequenceCount(); i++) {
list.add(file.getChemSequence(i));
list... | java | {
"resource": ""
} |
q157228 | ChemFileManipulator.getAllAtomContainers | train | public static List<IAtomContainer> getAllAtomContainers(IChemFile file) {
List<IAtomContainer> acList = new ArrayList<IAtomContainer>();
for (IChemSequence sequence : file.chemSequences()) {
acList.addAll(ChemSequenceManipulator.getAllAtomContainers(sequence));
}
return acLis... | java | {
"resource": ""
} |
q157229 | ChemFileManipulator.getAllChemModels | train | public static List<IChemModel> getAllChemModels(IChemFile file) {
List<IChemModel> modelsList = new ArrayList<IChemModel>();
for (int f = 0; f < file.getChemSequenceCount(); f++) {
for (IChemModel model : file.getChemSequence(f).chemModels()) {
modelsList.add(model);
... | java | {
"resource": ""
} |
q157230 | ChemFileManipulator.getAllReactions | train | public static List<IReaction> getAllReactions(IChemFile file) {
List<IReaction> reactonList = new ArrayList<IReaction>();
List<IChemModel> chemModel = getAllChemModels(file);
for (int f = 0; f < chemModel.size(); f++) {
for (IReaction reaction : chemModel.get(f).getReactionSet().reac... | java | {
"resource": ""
} |
q157231 | AtomPlacer3D.getHybridisationState | train | private int getHybridisationState(IAtom atom1) {
IBond.Order maxBondOrder = atom1.getMaxBondOrder();
// if (atom1.getFormalNeighbourCount() == 1 || maxBondOrder > 4) {
if (atom1.getFormalNeighbourCount() == 1) {
// WTF??
} else if (atom1.getFormalNeighbourCount() == ... | java | {
"resource": ""
} |
q157232 | AtomPlacer3D.getDoubleBondConfiguration2D | train | private int getDoubleBondConfiguration2D(IBond bond, Point2d a, Point2d b, Point2d c, Point2d d)
throws CDKException {
if (bond.getOrder() != IBond.Order.DOUBLE) {
return 0;
}
// no 2D coordinates or existing configuration
if (a == null || b == null || c == null |... | java | {
"resource": ""
} |
q157233 | AtomPlacer3D.getBondLengthValue | train | public double getBondLengthValue(String id1, String id2) {
String dkey = "";
if (pSet.containsKey(("bond" + id1 + ";" + id2))) {
dkey = "bond" + id1 + ";" + id2;
} else if (pSet.containsKey(("bond" + id2 + ";" + id1))) {
dkey = "bond" + id2 + ";" + id1;
} else {
... | java | {
"resource": ""
} |
q157234 | AtomPlacer3D.getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour | train | public IAtom getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(IAtomContainer molecule) {
Iterator<IBond> bonds = molecule.bonds().iterator();
while (bonds.hasNext()) {
IBond bond = bonds.next();
if (bond.getBegin().getFlag(CDKConstants.ISPLACED) && !(bond.getEnd().getFlag(CDK... | java | {
"resource": ""
} |
q157235 | AtomPlacer3D.getUnplacedHeavyAtom | train | IAtom getUnplacedHeavyAtom(IAtomContainer molecule) {
for (IAtom atom : molecule.atoms()) {
if (isUnplacedHeavyAtom(atom))
return atom;
}
return null;
} | java | {
"resource": ""
} |
q157236 | AtomPlacer3D.getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour | train | public IAtom getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(IAtomContainer molecule) {
Iterator<IBond> bonds = molecule.bonds().iterator();
while (bonds.hasNext()) {
IBond bond = bonds.next();
IAtom atom0 = bond.getBegin();
IAtom atom1 = bond.getEnd();
... | java | {
"resource": ""
} |
q157237 | AtomPlacer3D.getFarthestAtom | train | public IAtom getFarthestAtom(Point3d refAtomPoint, IAtomContainer ac) {
double distance = 0;
IAtom atom = null;
for (int i = 0; i < ac.getAtomCount(); i++) {
if (ac.getAtom(i).getPoint3d() != null) {
if (Math.abs(refAtomPoint.distance(ac.getAtom(i).getPoint3d())) > di... | java | {
"resource": ""
} |
q157238 | AtomPlacer3D.getUnplacedRingHeavyAtom | train | public IAtom getUnplacedRingHeavyAtom(IAtomContainer molecule, IAtom atom) {
List<IBond> bonds = molecule.getConnectedBondsList(atom);
IAtom connectedAtom = null;
for (IBond bond : bonds) {
connectedAtom = bond.getOther(atom);
if (isUnplacedHeavyAtom(connectedAtom) && con... | java | {
"resource": ""
} |
q157239 | AtomPlacer3D.geometricCenterAllPlacedAtoms | train | public Point3d geometricCenterAllPlacedAtoms(IAtomContainer molecule) {
IAtomContainer allPlacedAtoms = getAllPlacedAtoms(molecule);
return GeometryUtil.get3DCenter(allPlacedAtoms);
} | java | {
"resource": ""
} |
q157240 | AtomPlacer3D.getPlacedHeavyAtom | train | public IAtom getPlacedHeavyAtom(IAtomContainer molecule, IAtom atom) {
List<IBond> bonds = molecule.getConnectedBondsList(atom);
for (IBond bond : bonds) {
IAtom connectedAtom = bond.getOther(atom);
if (isPlacedHeavyAtom(connectedAtom)) {
return connectedAtom;
... | java | {
"resource": ""
} |
q157241 | AtomPlacer3D.getPlacedHeavyAtom | train | public IAtom getPlacedHeavyAtom(IAtomContainer molecule, IAtom atomA, IAtom atomB) {
List<IBond> bonds = molecule.getConnectedBondsList(atomA);
for (IBond bond : bonds) {
IAtom connectedAtom = bond.getOther(atomA);
if (isPlacedHeavyAtom(connectedAtom) && !connectedAtom.equals(ato... | java | {
"resource": ""
} |
q157242 | AtomPlacer3D.getPlacedHeavyAtoms | train | public IAtomContainer getPlacedHeavyAtoms(IAtomContainer molecule, IAtom atom) {
List<IBond> bonds = molecule.getConnectedBondsList(atom);
IAtomContainer connectedAtoms = molecule.getBuilder().newInstance(IAtomContainer.class);
IAtom connectedAtom = null;
for (IBond bond : bonds) {
... | java | {
"resource": ""
} |
q157243 | AtomPlacer3D.getAllPlacedAtoms | train | private IAtomContainer getAllPlacedAtoms(IAtomContainer molecule) {
IAtomContainer placedAtoms = new AtomContainer();
for (int i = 0; i < molecule.getAtomCount(); i++) {
if (molecule.getAtom(i).getFlag(CDKConstants.ISPLACED)) {
placedAtoms.addAtom(molecule.getAtom(i));
... | java | {
"resource": ""
} |
q157244 | AtomPlacer3D.allHeavyAtomsPlaced | train | public boolean allHeavyAtomsPlaced(IAtomContainer ac) {
for (int i = 0; i < ac.getAtomCount(); i++) {
if (isUnplacedHeavyAtom(ac.getAtom(i))) {
return false;
}
}
return true;
} | java | {
"resource": ""
} |
q157245 | MannholdLogPDescriptor.calculate | train | @Override
public DescriptorValue calculate(IAtomContainer atomContainer) {
IAtomContainer ac = null;
try {
ac = (IAtomContainer) atomContainer.clone();
} catch (CloneNotSupportedException e) {
return getDummyDescriptorValue(e);
}
int carbonCount = 0;
... | java | {
"resource": ""
} |
q157246 | Geometry3DValidator.validateBond | train | @Override
public ValidationReport validateBond(IBond subject) {
ValidationReport report = new ValidationReport();
// only consider two atom bonds
if (subject.getAtomCount() == 2) {
double distance = subject.getBegin().getPoint3d().distance(subject.getEnd().getPoint3d());
... | java | {
"resource": ""
} |
q157247 | AbstractStereo.invapply | train | protected static <T> T[] invapply(T[] src, int[] perm) {
T[] res = src.clone();
for (int i = 0; i < src.length; i++)
res[i] = src[perm[i]];
return res;
} | java | {
"resource": ""
} |
q157248 | HighlightGenerator.createAtomHighlight | train | private static Shape createAtomHighlight(IAtom atom, double radius) {
double x = atom.getPoint2d().x;
double y = atom.getPoint2d().y;
return new RoundRectangle2D.Double(x - radius, y - radius, 2 * radius, 2 * radius, 2 * radius, 2 * radius);
} | java | {
"resource": ""
} |
q157249 | HighlightGenerator.createBondHighlight | train | private static Shape createBondHighlight(IBond bond, double radius) {
double x1 = bond.getBegin().getPoint2d().x;
double x2 = bond.getEnd().getPoint2d().x;
double y1 = bond.getBegin().getPoint2d().y;
double y2 = bond.getEnd().getPoint2d().y;
double dx = x2 - x1;
double ... | java | {
"resource": ""
} |
q157250 | HighlightGenerator.createPalette | train | public static Palette createPalette(final Color color, final Color... colors) {
Color[] cs = new Color[colors.length + 1];
cs[0] = color;
System.arraycopy(colors, 0, cs, 1, colors.length);
return new FixedPalette(cs);
} | java | {
"resource": ""
} |
q157251 | IVector.sub | train | public IVector sub(IVector b) {
IVector result = new IVector(size);
sub(b, result);
return result;
} | java | {
"resource": ""
} |
q157252 | IVector.dot | train | public Complex dot(IVector b) {
if ((b == null) || (size != b.size)) return new Complex(Double.NaN, Double.NaN);
Complex result = new Complex(0d, 0d);
int i;
for (i = 0; i < size; i++) {
result.real += realvector[i] * b.realvector[i] - imagvector[i] * b.imagvector[i];
... | java | {
"resource": ""
} |
q157253 | IVector.duplicate | train | public void duplicate(IVector result) {
if (result.size != size) result.reshape(size);
int i;
for (i = 0; i < size; i++) {
result.realvector[i] = realvector[i];
result.imagvector[i] = imagvector[i];
}
} | java | {
"resource": ""
} |
q157254 | IVector.reshape | train | public void reshape(int newsize) {
if ((newsize == size) || (newsize <= 0)) return;
double[] newrealvector = new double[newsize];
double[] newimagvector = new double[newsize];
int min = Math.min(size, newsize);
int i;
for (i = 0; i < min; i++) {
newrealvector... | java | {
"resource": ""
} |
q157255 | InChIGenerator.getInchiKey | train | public String getInchiKey() throws CDKException {
JniInchiOutputKey key;
try {
key = JniInchiWrapper.getInchiKey(output.getInchi());
if (key.getReturnStatus() == INCHI_KEY.OK) {
return key.getKey();
} else {
throw new CDKException("Erro... | java | {
"resource": ""
} |
q157256 | CMLModuleStack.push | train | public void push(ICMLModule item) {
if (sp == stack.length) {
ICMLModule[] temp = new ICMLModule[2 * sp];
System.arraycopy(stack, 0, temp, 0, sp);
stack = temp;
}
stack[sp++] = item;
} | java | {
"resource": ""
} |
q157257 | AtomContainerDiscretePartitionRefinerImpl.getAutomorphismGroup | train | public PermutationGroup getAutomorphismGroup(IAtomContainer atomContainer, Partition initialPartition) {
setup(atomContainer);
super.refine(initialPartition);
return super.getAutomorphismGroup();
} | java | {
"resource": ""
} |
q157258 | InductivePartialCharges.assignInductivePartialCharges | train | public IAtomContainer assignInductivePartialCharges(IAtomContainer ac) throws Exception {
if (factory == null) {
factory = AtomTypeFactory
.getInstance("org/openscience/cdk/config/data/jmol_atomtypes.txt", ac.getBuilder());
}
int stepsLimit = 9;
IAtom[] a... | java | {
"resource": ""
} |
q157259 | InductivePartialCharges.getPaulingElectronegativities | train | public double[] getPaulingElectronegativities(IAtomContainer ac, boolean modified) throws CDKException {
double[] paulingElectronegativities = new double[ac.getAtomCount()];
IElement element = null;
String symbol = null;
int atomicNumber = 0;
try {
ifac = Isotopes.get... | java | {
"resource": ""
} |
q157260 | InductivePartialCharges.getAtomicSoftnessCore | train | public double getAtomicSoftnessCore(IAtomContainer ac, int atomPosition) throws CDKException {
if (factory == null) {
factory = AtomTypeFactory
.getInstance("org/openscience/cdk/config/data/jmol_atomtypes.txt", ac.getBuilder());
}
IAtom target = null;
doub... | java | {
"resource": ""
} |
q157261 | InductivePartialCharges.getAtomicChargeIncrement | train | private double getAtomicChargeIncrement(IAtomContainer ac, int atomPosition, double[] ElEn, int as)
throws CDKException {
IAtom[] allAtoms = null;
IAtom target = null;
double incrementedCharge = 0;
double radiusTarget = 0;
target = ac.getAtom(atomPosition);
//... | java | {
"resource": ""
} |
q157262 | InductivePartialCharges.getCovalentRadius | train | private double getCovalentRadius(String symbol, IBond.Order maxBondOrder) {
double radiusTarget = 0;
if (symbol.equals("F")) {
radiusTarget = 0.64;
} else if (symbol.equals("Cl")) {
radiusTarget = 0.99;
} else if (symbol.equals("Br")) {
radiusTarget = ... | java | {
"resource": ""
} |
q157263 | IsProtonInAromaticSystemDescriptor.calculate | train | @Override
public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer) {
IAtomContainer clonedAtomContainer;
try {
clonedAtomContainer = (IAtomContainer) atomContainer.clone();
} catch (CloneNotSupportedException e) {
return new DescriptorValue(getSpecif... | java | {
"resource": ""
} |
q157264 | MACCSFingerprinter.keys | train | private MaccsKey[] keys(final IChemObjectBuilder builder) throws CDKException {
MaccsKey[] result = keys;
if (result == null) {
synchronized (lock) {
result = keys;
if (result == null) {
try {
keys = result = readKey... | java | {
"resource": ""
} |
q157265 | MACCSFingerprinter.createPattern | train | private Pattern createPattern(String smarts, IChemObjectBuilder builder) throws IOException {
SmartsPattern ptrn = SmartsPattern.create(smarts, builder);
ptrn.setPrepare(false); // avoid redoing aromaticity etc
return ptrn;
} | java | {
"resource": ""
} |
q157266 | EventCMLReader.process | train | public void process() throws CDKException {
logger.debug("Started parsing from input...");
try {
parser.setFeature("http://xml.org/sax/features/validation", false);
logger.info("Deactivated validation");
} catch (SAXException e) {
logger.warn("Cannot deactivat... | java | {
"resource": ""
} |
q157267 | Reaction.addReactant | train | @Override
public void addReactant(IAtomContainer reactant, Double coefficient) {
reactants.addAtomContainer(reactant, coefficient);
notifyChanged();
} | java | {
"resource": ""
} |
q157268 | Reaction.setReactantCoefficients | train | @Override
public boolean setReactantCoefficients(Double[] coefficients) {
boolean result = reactants.setMultipliers(coefficients);
notifyChanged();
return result;
} | java | {
"resource": ""
} |
q157269 | Reaction.setProductCoefficients | train | @Override
public boolean setProductCoefficients(Double[] coefficients) {
boolean result = products.setMultipliers(coefficients);
notifyChanged();
return result;
} | java | {
"resource": ""
} |
q157270 | Reaction.addMapping | train | @Override
public void addMapping(IMapping mapping) {
if (mappingCount + 1 >= map.length) growMappingArray();
map[mappingCount] = mapping;
mappingCount++;
notifyChanged();
} | java | {
"resource": ""
} |
q157271 | Reaction.removeMapping | train | @Override
public void removeMapping(int pos) {
for (int i = pos; i < mappingCount - 1; i++) {
map[i] = map[i + 1];
}
map[mappingCount - 1] = null;
mappingCount--;
notifyChanged();
} | java | {
"resource": ""
} |
q157272 | MolecularFormulaRangeManipulator.getRange | train | public static MolecularFormulaRange getRange(IMolecularFormulaSet mfSet) {
MolecularFormulaRange mfRange = new MolecularFormulaRange();
for (IMolecularFormula mf : mfSet.molecularFormulas()) {
for (IIsotope isotope : mf.isotopes()) {
int occur_new = mf.getIsotopeCount(isotop... | java | {
"resource": ""
} |
q157273 | MolecularFormulaRangeManipulator.getMaximalFormula | train | public static IMolecularFormula getMaximalFormula(MolecularFormulaRange mfRange, IChemObjectBuilder builder) {
IMolecularFormula formula = builder.newInstance(IMolecularFormula.class);
for (IIsotope isotope : mfRange.isotopes()) {
formula.addIsotope(isotope, mfRange.getIsotopeCountMax(isoto... | java | {
"resource": ""
} |
q157274 | MolecularFormulaRangeManipulator.getMinimalFormula | train | public static IMolecularFormula getMinimalFormula(MolecularFormulaRange mfRange, IChemObjectBuilder builder) {
IMolecularFormula formula = builder.newInstance(IMolecularFormula.class);
for (IIsotope isotope : mfRange.isotopes()) {
formula.addIsotope(isotope, mfRange.getIsotopeCountMin(isoto... | java | {
"resource": ""
} |
q157275 | AbstractAWTDrawVisitor.transformPoint | train | public int[] transformPoint(double xCoord, double yCoord) {
double[] src = new double[]{xCoord, yCoord};
double[] dest = new double[2];
this.transform.transform(src, 0, dest, 0, 1);
return new int[]{(int) dest[0], (int) dest[1]};
} | java | {
"resource": ""
} |
q157276 | AbstractAWTDrawVisitor.getTextBounds | train | protected Rectangle2D getTextBounds(String text, double xCoord, double yCoord, Graphics2D graphics) {
FontMetrics fontMetrics = graphics.getFontMetrics();
Rectangle2D bounds = fontMetrics.getStringBounds(text, graphics);
double widthPad = 3;
double heightPad = 1;
double width =... | java | {
"resource": ""
} |
q157277 | LargestChainDescriptor.getParameters | train | @Override
public Object[] getParameters() {
// return the parameters as used for the descriptor calculation
Object[] params = new Object[2];
params[0] = checkAromaticity;
params[1] = checkRingSystem;
return params;
} | java | {
"resource": ""
} |
q157278 | SmartsFragmentExtractor.setMode | train | public void setMode(int mode) {
// check arg
switch (mode) {
case MODE_EXACT:
case MODE_JCOMPOUNDMAPPER:
break;
default:
throw new IllegalArgumentException("Invalid mode specified!");
}
this.mode = mode;
// re-g... | java | {
"resource": ""
} |
q157279 | SmartsFragmentExtractor.generate | train | public String generate(int[] atomIdxs) {
if (atomIdxs == null)
throw new NullPointerException("No atom indexes provided");
if (atomIdxs.length == 0)
return null; // makes sense?
// special case
if (atomIdxs.length == 1 && mode == MODE_EXACT)
return a... | java | {
"resource": ""
} |
q157280 | SmartsFragmentExtractor.encodeExpr | train | private void encodeExpr(int idx, int bprev, StringBuilder sb) {
avisit[idx] = numVisit++;
sb.append(aexpr[idx]);
final int d = deg[idx];
int remain = d;
for (int j = 0; j < d; j++) {
int nbr = atomAdj[idx][j];
int bidx = bondAdj[idx][j];
// r... | java | {
"resource": ""
} |
q157281 | SmartsFragmentExtractor.chooseRingNumber | train | private int chooseRingNumber() {
for (int i = 1; i < rnums.length; i++) {
if (rnums[i] == 0) {
rnums[i] = 1;
return i;
}
}
throw new IllegalStateException("No more ring numbers available!");
} | java | {
"resource": ""
} |
q157282 | MoleculeGraphs.getMoleculeGraph | train | static public SimpleGraph getMoleculeGraph(IAtomContainer molecule) {
SimpleGraph graph = new SimpleGraph();
for (int i = 0; i < molecule.getAtomCount(); i++) {
IAtom atom = molecule.getAtom(i);
graph.addVertex(atom);
}
for (int i = 0; i < molecule.getBondCount()... | java | {
"resource": ""
} |
q157283 | TaeAminoAcidDescriptor.calculate | train | @Override
public DescriptorValue calculate(IAtomContainer container) {
if (taeParams == null) return getDummyDescriptorValue(new CDKException("TAE parameters were not initialized"));
if (!(container instanceof IBioPolymer))
return getDummyDescriptorValue(new CDKException("The molecule sh... | java | {
"resource": ""
} |
q157284 | MacroCycleLayout.getAttachedInOrder | train | private List<Integer> getAttachedInOrder(IRing macrocycle, IAtomContainer shared) {
List<Integer> ringAttach = new ArrayList<>();
Set<IAtom> visit = new HashSet<>();
IAtom atom = shared.getAtom(0);
while (atom != null) {
visit.add(atom);
ringAttach.add(macrocycle.... | java | {
"resource": ""
} |
q157285 | MacroCycleLayout.selectCoords | train | private int selectCoords(Collection<Point2d[]> ps, Point2d[] coords, IRing macrocycle, IRingSet ringset) {
assert ps.size() != 0;
final int[] winding = new int[coords.length];
MacroScore best = null;
for (Point2d[] p : ps) {
final int wind = winding(p, winding);
... | java | {
"resource": ""
} |
q157286 | MacroCycleLayout.winding | train | private static int winding(final Point2d[] coords, final int[] winding) {
int cw = 0, ccw = 0;
Point2d prev = coords[coords.length - 1];
for (int i = 0; i < coords.length; i++) {
Point2d curr = coords[i];
Point2d next = coords[(i + 1) % coords.length];
windin... | java | {
"resource": ""
} |
q157287 | MacroCycleLayout.winding | train | private static int winding(Point2d a, Point2d b, Point2d c) {
return (int) Math.signum((b.x - a.x) * (c.y - a.y) - (b.y - a.y) * (c.x - a.x));
} | java | {
"resource": ""
} |
q157288 | MacroCycleLayout.roundUpIfNeeded | train | private static IAtomContainer roundUpIfNeeded(IAtomContainer anon) {
IChemObjectBuilder bldr = anon.getBuilder();
if ((anon.getAtomCount() & 0x1) != 0) {
IBond bond = anon.removeBond(anon.getBondCount() - 1);
IAtom dummy = bldr.newInstance(IAtom.class, "C");
anon.addA... | java | {
"resource": ""
} |
q157289 | StructGenMatcher.findMatchingAtomType | train | @Override
public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atom) throws CDKException {
if (factory == null) {
try {
factory = AtomTypeFactory.getInstance("org/openscience/cdk/config/data/structgen_atomtypes.xml",
atom.getBuilder())... | java | {
"resource": ""
} |
q157290 | IPBondLearningDescriptor.calculate | train | @Override
public DescriptorValue calculate(IBond bond, IAtomContainer atomContainer) {
double value = 0;
// FIXME: for now I'll cache a few modified atomic properties, and restore them at the end of this method
String originalAtomtypeName1 = bond.getBegin().getAtomTypeName();
Integer... | java | {
"resource": ""
} |
q157291 | BondRefinable.getInitialPartition | train | public Partition getInitialPartition() {
int bondCount = atomContainer.getBondCount();
Map<String, SortedSet<Integer>> cellMap = new HashMap<String, SortedSet<Integer>>();
// make mini-'descriptors' for bonds like "C=O" or "C#N" etc
for (int bondIndex = 0; bondIndex < bondCount; bondInd... | java | {
"resource": ""
} |
q157292 | AtomTypeTools.ringSystemClassifier | train | private int ringSystemClassifier(IRing ring, String smile) throws CDKException {
/* System.out.println("IN AtomTypeTools Smile:"+smile); */
logger.debug("Comparing ring systems: SMILES=", smile);
if (PYRROLE_SMI == null) {
final SmilesParser smipar = new SmilesParser(ring.ge... | java | {
"resource": ""
} |
q157293 | QueryAtomContainer.setAtoms | train | @Override
public void setAtoms(IAtom[] atoms) {
this.atoms = atoms;
for (IAtom atom : atoms) {
atom.addListener(this);
}
this.atomCount = atoms.length;
notifyChanged();
} | java | {
"resource": ""
} |
q157294 | QueryAtomContainer.setBonds | train | @Override
public void setBonds(IBond[] bonds) {
this.bonds = bonds;
for (IBond bond : bonds) {
bond.addListener(this);
}
this.bondCount = bonds.length;
} | java | {
"resource": ""
} |
q157295 | QueryAtomContainer.getConnectedAtomsList | train | @Override
public List<IAtom> getConnectedAtomsList(IAtom atom) {
List<IAtom> atomsList = new ArrayList<IAtom>();
for (int i = 0; i < bondCount; i++) {
if (bonds[i].contains(atom)) atomsList.add(bonds[i].getOther(atom));
}
return atomsList;
} | java | {
"resource": ""
} |
q157296 | QueryAtomContainer.getConnectedBondsList | train | @Override
public List<IBond> getConnectedBondsList(IAtom atom) {
List<IBond> bondsList = new ArrayList<IBond>();
for (int i = 0; i < bondCount; i++) {
if (bonds[i].contains(atom)) bondsList.add(bonds[i]);
}
return bondsList;
} | java | {
"resource": ""
} |
q157297 | QueryAtomContainer.getConnectedSingleElectronsList | train | @Override
public List<ISingleElectron> getConnectedSingleElectronsList(IAtom atom) {
List<ISingleElectron> lps = new ArrayList<ISingleElectron>();
for (int i = 0; i < singleElectronCount; i++) {
if (singleElectrons[i].contains(atom)) lps.add(singleElectrons[i]);
}
return ... | java | {
"resource": ""
} |
q157298 | QueryAtomContainer.getConnectedAtomsCount | train | @Override
public int getConnectedAtomsCount(IAtom atom) {
int count = 0;
for (int i = 0; i < bondCount; i++) {
if (bonds[i].contains(atom)) ++count;
}
return count;
} | java | {
"resource": ""
} |
q157299 | QueryAtomContainer.getConnectedLonePairsCount | train | @Override
public int getConnectedLonePairsCount(IAtom atom) {
int count = 0;
for (int i = 0; i < lonePairCount; i++) {
if (lonePairs[i].contains(atom)) ++count;
}
return count;
} | java | {
"resource": ""
} |
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