_id stringlengths 2 7 | title stringlengths 3 140 | partition stringclasses 3
values | text stringlengths 73 34.1k | language stringclasses 1
value | meta_information dict |
|---|---|---|---|---|---|
q157400 | RingSetManipulator.getAllAtomContainers | train | public static List<IAtomContainer> getAllAtomContainers(IRingSet set) {
List<IAtomContainer> atomContainerList = new ArrayList<IAtomContainer>();
for (IAtomContainer atomContainer : set.atomContainers()) {
atomContainerList.add(atomContainer);
}
return atomContainerList;
... | java | {
"resource": ""
} |
q157401 | RingSetManipulator.sort | train | public static void sort(IRingSet ringSet) {
List<IRing> ringList = new ArrayList<IRing>();
for (IAtomContainer atomContainer : ringSet.atomContainers()) {
ringList.add((IRing) atomContainer);
}
Collections.sort(ringList, new RingSizeComparator(RingSizeComparator.SMALL_FIRST))... | java | {
"resource": ""
} |
q157402 | RingSetManipulator.getHeaviestRing | train | public static IRing getHeaviestRing(IRingSet ringSet, IBond bond) {
IRingSet rings = ringSet.getRings(bond);
IRing ring = null;
int maxOrderSum = 0;
for (Object ring1 : rings.atomContainers()) {
if (maxOrderSum < ((IRing) ring1).getBondOrderSum()) {
ring = (IR... | java | {
"resource": ""
} |
q157403 | RingSetManipulator.ringAlreadyInSet | train | public static boolean ringAlreadyInSet(IRing newRing, IRingSet ringSet) {
IRing ring;
// IBond[] bonds;
// IBond[] newBonds;
// IBond bond;
int equalCount;
boolean equals;
for (int f = 0; f < ringSet.getAtomContainerCount(); f++) {
equals = fa... | java | {
"resource": ""
} |
q157404 | RingSetManipulator.markAromaticRings | train | public static void markAromaticRings(IRingSet ringset) {
for (IAtomContainer atomContainer : ringset.atomContainers()) {
RingManipulator.markAromaticRings((IRing) atomContainer);
}
} | java | {
"resource": ""
} |
q157405 | SingleStructureRandomGenerator.generate | train | public IAtomContainer generate() throws CDKException {
boolean structureFound = false;
boolean bondFormed;
double order;
double max, cmax1, cmax2;
int iteration = 0;
IAtom partner;
IAtom atom;
do {
iteration++;
atomContainer.removeA... | java | {
"resource": ""
} |
q157406 | SingleStructureRandomGenerator.getAnotherUnsaturatedNode | train | private IAtom getAnotherUnsaturatedNode(IAtom exclusionAtom) throws CDKException {
IAtom atom;
int next = random.nextInt(atomContainer.getAtomCount());
for (int f = next; f < atomContainer.getAtomCount(); f++) {
atom = atomContainer.getAtom(f);
if (!satCheck.isSaturated(... | java | {
"resource": ""
} |
q157407 | DeduceBondSystemTool.isOK | train | public boolean isOK(IAtomContainer m) throws CDKException {
// OK, we take advantage here from the fact that this class does not take
// into account rings larger than 7 atoms. See fixAromaticBondOrders().
IRingSet rs = allRingsFinder.findAllRings(m, 7);
storeRingSystem(m, rs);
b... | java | {
"resource": ""
} |
q157408 | DeduceBondSystemTool.fixAromaticBondOrders | train | public IAtomContainer fixAromaticBondOrders(IAtomContainer atomContainer) throws CDKException {
// preset all bond orders to single
for (IBond bond : atomContainer.bonds()) {
if (bond.isAromatic() && bond.getOrder() == IBond.Order.UNSET)
bond.setOrder(IBond.Order.SINGLE);
... | java | {
"resource": ""
} |
q157409 | DeduceBondSystemTool.removeExtraRings | train | private IRingSet removeExtraRings(IAtomContainer m) {
try {
IRingSet rs = Cycles.sssr(m).toRingSet();
//remove rings which dont have all aromatic atoms (according to hybridization set by lower case symbols in smiles):
//logger.debug("numrings="+rs.size());
ilo... | java | {
"resource": ""
} |
q157410 | DeduceBondSystemTool.storeRingSystem | train | private void storeRingSystem(IAtomContainer mol, IRingSet ringSet) {
listOfRings = new ArrayList<Integer[]>(); // this is a list of int arrays
for (int r = 0; r < ringSet.getAtomContainerCount(); ++r) {
IRing ring = (IRing) ringSet.getAtomContainer(r);
Integer[] bondNumbers = new... | java | {
"resource": ""
} |
q157411 | ElementRule.setParameters | train | @Override
public void setParameters(Object[] params) throws CDKException {
if (params.length != 1) throw new CDKException("ElementRule expects one parameters");
if (!(params[0] == null || params[0] instanceof MolecularFormulaRange))
throw new CDKException("The parameter must be of type ... | java | {
"resource": ""
} |
q157412 | ElementRule.ensureDefaultOccurElements | train | private void ensureDefaultOccurElements(IChemObjectBuilder builder) {
if (mfRange == null) {
String[] elements = new String[]{"C", "H", "O", "N", "Si", "P", "S", "F", "Cl", "Br", "I", "Sn", "B", "Pb",
"Tl", "Ba", "In", "Pd", "Pt", "Os", "Ag", "Zr", "Se", "Zn", "Cu", "Ni", "Co", "... | java | {
"resource": ""
} |
q157413 | JumboCyclicVertexSearch.vertexColor | train | @Override
public int[] vertexColor() {
int[] result = colors;
if (result == null) {
synchronized (this) {
result = colors;
if (result == null) {
colors = result = buildVertexColor();
}
}
}
ret... | java | {
"resource": ""
} |
q157414 | JumboCyclicVertexSearch.xor | train | static BitSet xor(BitSet x, BitSet y) {
BitSet z = copy(x);
z.xor(y);
return z;
} | java | {
"resource": ""
} |
q157415 | JumboCyclicVertexSearch.and | train | static BitSet and(BitSet x, BitSet y) {
BitSet z = copy(x);
z.and(y);
return z;
} | java | {
"resource": ""
} |
q157416 | JumboCyclicVertexSearch.copy | train | static BitSet copy(BitSet org) {
BitSet cpy = (BitSet) org.clone();
return cpy;
} | java | {
"resource": ""
} |
q157417 | OWLAtomTypeMappingReader.readAtomTypeMappings | train | public Map<String, String> readAtomTypeMappings() {
Map<String, String> mappings = null;
try {
parser.setFeature("http://xml.org/sax/features/validation", false);
logger.info("Deactivated validation");
} catch (SAXException exception) {
logger.warn("Cannot dea... | java | {
"resource": ""
} |
q157418 | TemplateHandler3D.loadTemplates | train | private void loadTemplates() throws CDKException {
try (InputStream gin = getClass().getResourceAsStream(TEMPLATE_PATH);
InputStream in = new GZIPInputStream(gin);
IteratingSDFReader sdfr = new IteratingSDFReader(in, builder)) {
while (sdfr.hasNext()) {
fina... | java | {
"resource": ""
} |
q157419 | TemplateHandler3D.mapTemplates | train | public void mapTemplates(IAtomContainer mol, int numberOfRingAtoms)
throws CDKException, CloneNotSupportedException {
if (templates.isEmpty())
loadTemplates();
IAtomContainer best = null;
Map<IChemObject, IChemObject> bestMap = null;
IAt... | java | {
"resource": ""
} |
q157420 | SaturationChecker.isSaturated | train | @Override
public boolean isSaturated(IAtom atom, IAtomContainer ac) throws CDKException {
IAtomType[] atomTypes = getAtomTypeFactory(atom.getBuilder()).getAtomTypes(atom.getSymbol());
if (atomTypes.length == 0) return true;
double bondOrderSum = ac.getBondOrderSum(atom);
IBond.Order ... | java | {
"resource": ""
} |
q157421 | SaturationChecker.getCurrentMaxBondOrder | train | public double getCurrentMaxBondOrder(IAtom atom, IAtomContainer ac) throws CDKException {
IAtomType[] atomTypes = getAtomTypeFactory(atom.getBuilder()).getAtomTypes(atom.getSymbol());
if (atomTypes.length == 0) return 0;
double bondOrderSum = ac.getBondOrderSum(atom);
Integer hcount = at... | java | {
"resource": ""
} |
q157422 | SaturationChecker.unsaturate | train | public void unsaturate(IAtomContainer atomContainer) {
for (IBond bond : atomContainer.bonds())
bond.setOrder(Order.SINGLE);
} | java | {
"resource": ""
} |
q157423 | SaturationChecker.unsaturateBonds | train | public void unsaturateBonds(IAtomContainer container) {
for (IBond bond : container.bonds())
bond.setOrder(Order.SINGLE);
} | java | {
"resource": ""
} |
q157424 | SaturationChecker.newSaturate | train | public void newSaturate(IAtomContainer atomContainer) throws CDKException {
logger.info("Saturating atomContainer by adjusting bond orders...");
boolean allSaturated = allSaturated(atomContainer);
if (!allSaturated) {
IBond[] bonds = new IBond[atomContainer.getBondCount()];
... | java | {
"resource": ""
} |
q157425 | SaturationChecker.newSaturate | train | public boolean newSaturate(IBond[] bonds, IAtomContainer atomContainer) throws CDKException {
logger.debug("Saturating bond set of size: " + bonds.length);
boolean bondsAreFullySaturated = true;
if (bonds.length > 0) {
IBond bond = bonds[0];
// determine bonds left
... | java | {
"resource": ""
} |
q157426 | AtomContainerSet.setMultiplier | train | @Override
public boolean setMultiplier(IAtomContainer container, Double multiplier) {
for (int i = 0; i < atomContainers.length; i++) {
if (atomContainers[i] == container) {
multipliers[i] = multiplier;
return true;
}
}
return false;
... | java | {
"resource": ""
} |
q157427 | IDCreator.createIDs | train | public static void createIDs(IChemObject chemObject) {
if (chemObject == null) return;
resetCounters();
if (chemObject instanceof IAtomContainer) {
createIDsForAtomContainer((IAtomContainer) chemObject, null);
} else if (chemObject instanceof IAtomContainerSet) {
... | java | {
"resource": ""
} |
q157428 | IDCreator.resetCounters | train | private static void resetCounters() {
atomCount = 0;
bondCount = 0;
atomContainerCount = 0;
atomContainerSetCount = 0;
reactionCount = 0;
reactionSetCount = 0;
chemModelCount = 0;
chemSequenceCount = 0;
chemFileCount = 0;
} | java | {
"resource": ""
} |
q157429 | IDCreator.setID | train | private static int setID(String prefix, int identifier, IChemObject object, List<String> tabuList) {
identifier += 1;
while (tabuList.contains(prefix + identifier)) {
identifier += 1;
}
object.setID(prefix + identifier);
tabuList.add(prefix + identifier);
retu... | java | {
"resource": ""
} |
q157430 | IDCreator.createIDsForAtomContainer | train | private static void createIDsForAtomContainer(IAtomContainer container, List<String> tabuList) {
if (tabuList == null) tabuList = AtomContainerManipulator.getAllIDs(container);
if (null == container.getID()) {
// generate new ID and remember it
atomContainerCount = setID(ATOMCON... | java | {
"resource": ""
} |
q157431 | IDCreator.createIDsForAtomContainerSet | train | private static void createIDsForAtomContainerSet(IAtomContainerSet containerSet, List<String> tabuList) {
if (tabuList == null) tabuList = AtomContainerSetManipulator.getAllIDs(containerSet);
if (null == containerSet.getID()) {
atomContainerSetCount = setID(ATOMCONTAINERSET_PREFIX, atomCont... | java | {
"resource": ""
} |
q157432 | IDCreator.createIDsForReaction | train | private static void createIDsForReaction(IReaction reaction, List<String> tabuList) {
if (tabuList == null) tabuList = ReactionManipulator.getAllIDs(reaction);
if (null == reaction.getID()) {
// generate new ID
reactionCount = setID(REACTION_PREFIX, reactionCount , reaction, ta... | java | {
"resource": ""
} |
q157433 | ProtonTotalPartialChargeDescriptor.calculate | train | @Override
public DescriptorValue calculate(IAtom atom, IAtomContainer ac) {
neighboors = ac.getConnectedAtomsList(atom);
IAtomContainer clone;
try {
clone = (IAtomContainer) ac.clone();
} catch (CloneNotSupportedException e) {
return getDummyDescriptorValue(e... | java | {
"resource": ""
} |
q157434 | OptionIOSetting.setSetting | train | @Override
public void setSetting(String setting) throws CDKException {
if (settings.contains(setting)) {
this.setting = setting;
} else {
throw new CDKException("Setting " + setting + " is not allowed.");
}
} | java | {
"resource": ""
} |
q157435 | OptionIOSetting.setSetting | train | public void setSetting(int setting) throws CDKException {
if (setting < settings.size() + 1 && setting > 0) {
this.setting = (String) settings.get(setting - 1);
} else {
throw new CDKException("Setting " + setting + " does not exist.");
}
} | java | {
"resource": ""
} |
q157436 | SMILESWriter.write | train | @Override
public void write(IChemObject object) throws CDKException {
if (object instanceof IAtomContainerSet) {
writeAtomContainerSet((IAtomContainerSet) object);
} else if (object instanceof IAtomContainer) {
writeAtomContainer((IAtomContainer) object);
} else {
... | java | {
"resource": ""
} |
q157437 | SMILESWriter.writeAtomContainerSet | train | public void writeAtomContainerSet(IAtomContainerSet som) {
writeAtomContainer(som.getAtomContainer(0));
for (int i = 1; i <= som.getAtomContainerCount() - 1; i++) {
try {
writeAtomContainer(som.getAtomContainer(i));
} catch (Exception exc) {
}
... | java | {
"resource": ""
} |
q157438 | SMILESWriter.writeAtomContainer | train | public void writeAtomContainer(IAtomContainer molecule) {
SmilesGenerator sg = new SmilesGenerator();
if (useAromaticityFlag.isSet()) sg = sg.aromatic();
String smiles = "";
try {
smiles = sg.create(molecule);
logger.debug("Generated SMILES: " + smiles);
... | java | {
"resource": ""
} |
q157439 | BondsToAtomDescriptor.calculate | train | @Override
public DescriptorValue calculate(IAtom atom, IAtomContainer container) {
IAtom focus = container.getAtom(focusPosition);
// could be cached
int bondsToAtom = new ShortestPaths(container, atom).distanceTo(focus);
return new DescriptorValue(getSpecification(), getParameter... | java | {
"resource": ""
} |
q157440 | CDKHydrogenAdder.addImplicitHydrogens | train | public void addImplicitHydrogens(IAtomContainer container) throws CDKException {
for (IAtom atom : container.atoms()) {
if (!(atom instanceof IPseudoAtom)) {
addImplicitHydrogens(container, atom);
}
}
} | java | {
"resource": ""
} |
q157441 | CDKHydrogenAdder.addImplicitHydrogens | train | public void addImplicitHydrogens(IAtomContainer container, IAtom atom) throws CDKException {
if (atom.getAtomTypeName() == null) throw new CDKException("IAtom is not typed! " + atom.getSymbol());
if ("X".equals(atom.getAtomTypeName())) {
if (atom.getImplicitHydrogenCount() == null) atom.set... | java | {
"resource": ""
} |
q157442 | RangeMassDecomposer.init | train | private void init() {
if (ERTs != null) return;
synchronized (this) {
if (ERTs != null) return;
discretizeMasses();
divideByGCD();
computeLCMs();
calcERT();
computeErrors();
}
} | java | {
"resource": ""
} |
q157443 | RangeMassDecomposer.decomposeIterator | train | DecompIterator decomposeIterator(double from, double to, MolecularFormulaRange boundaries) {
init();
if (to < 0d || from < 0d)
throw new IllegalArgumentException("Expect positive mass for decomposition: [" + from + ", " + to + "]");
if (to < from) throw new IllegalArgumentException("... | java | {
"resource": ""
} |
q157444 | RangeMassDecomposer.calcERT | train | private void calcERT(int deviation) {
final int[][][] ERTs = this.ERTs;
final int currentLength = ERTs.length;
// we have to extend the ERT table
int[][] lastERT = ERTs[ERTs.length - 1];
int[][] nextERT = new int[lastERT.length][weights.size()];
if (currentLength == 1) ... | java | {
"resource": ""
} |
q157445 | ReactionSet.addReaction | train | @Override
public void addReaction(IReaction reaction) {
if (reactionCount + 1 >= reactions.length) growReactionArray();
reactions[reactionCount] = reaction;
reactionCount++;
} | java | {
"resource": ""
} |
q157446 | ReactionSet.removeAllReactions | train | @Override
public void removeAllReactions() {
for (int pos = this.reactionCount - 1; pos >= 0; pos--) {
this.reactions[pos] = null;
}
this.reactionCount = 0;
} | java | {
"resource": ""
} |
q157447 | PiBondingMovementReaction.setActiveCenters | train | private void setActiveCenters(IAtomContainer reactant) throws CDKException {
AllRingsFinder arf = new AllRingsFinder();
IRingSet ringSet = arf.findAllRings(reactant);
for (int ir = 0; ir < ringSet.getAtomContainerCount(); ir++) {
IRing ring = (IRing) ringSet.getAtomContainer(ir);
... | java | {
"resource": ""
} |
q157448 | RandomGenerator.proposeStructure | train | public IAtomContainer proposeStructure() {
logger.debug("RandomGenerator->proposeStructure() Start");
do {
try {
trial = molecule.clone();
} catch (CloneNotSupportedException e) {
throw new IllegalStateException("Could not clone IAtomContainer!" + ... | java | {
"resource": ""
} |
q157449 | HBondDonorCountDescriptor.calculate | train | @Override
public DescriptorValue calculate(IAtomContainer atomContainer) {
int hBondDonors = 0;
IAtomContainer ac;
try {
ac = (IAtomContainer) atomContainer.clone();
} catch (CloneNotSupportedException e) {
return getDummyDescriptorValue(e);
}
... | java | {
"resource": ""
} |
q157450 | RegularCyclicVertexSearch.buildVertexColor | train | private int[] buildVertexColor() {
int[] color = new int[g.length];
int n = 1;
Arrays.fill(color, -1);
for (long cycle : cycles) {
for (int i = 0; i < g.length; i++) {
if ((cycle & 0x1) == 0x1) color[i] = color[i] < 0 ? n : 0;
cycle >>= 1;
... | java | {
"resource": ""
} |
q157451 | IsotopeFactory.getSize | train | public int getSize() {
int count = 0;
for (List<IIsotope> isotope : isotopes)
if (isotope != null)
count += isotope.size();
return count;
} | java | {
"resource": ""
} |
q157452 | IsotopeFactory.add | train | protected void add(IIsotope isotope) {
Integer atomicNum = isotope.getAtomicNumber();
assert atomicNum != null;
List<IIsotope> isotopesForElement = isotopes[atomicNum];
if (isotopesForElement == null) {
isotopesForElement = new ArrayList<>();
isotopes[atomicNum] =... | java | {
"resource": ""
} |
q157453 | IsotopeFactory.getIsotopes | train | public IIsotope[] getIsotopes(int elem) {
if (isotopes[elem] == null)
return EMPTY_ISOTOPE_ARRAY;
List<IIsotope> list = new ArrayList<>();
for (IIsotope isotope : isotopes[elem]) {
list.add(clone(isotope));
}
return list.toArray(new IIsotope[0]);
} | java | {
"resource": ""
} |
q157454 | IsotopeFactory.getIsotopes | train | public IIsotope[] getIsotopes() {
List<IIsotope> list = new ArrayList<IIsotope>();
for (List<IIsotope> isotopes : this.isotopes) {
if (isotopes == null) continue;
for (IIsotope isotope : isotopes) {
list.add(clone(isotope));
}
}
return ... | java | {
"resource": ""
} |
q157455 | IsotopeFactory.getIsotopes | train | public IIsotope[] getIsotopes(double exactMass, double difference) {
List<IIsotope> list = new ArrayList<>();
for (List<IIsotope> isotopes : this.isotopes) {
if (isotopes == null) continue;
for (IIsotope isotope : isotopes) {
if (Math.abs(isotope.getExactMass() - ... | java | {
"resource": ""
} |
q157456 | IsotopeFactory.getIsotope | train | public IIsotope getIsotope(String symbol, int massNumber) {
int elem = Elements.ofString(symbol).number();
List<IIsotope> isotopes = this.isotopes[elem];
if (isotopes == null)
return null;
for (IIsotope isotope : isotopes) {
if (isotope.getSymbol().equals(symbol) ... | java | {
"resource": ""
} |
q157457 | IsotopeFactory.getIsotope | train | public IIsotope getIsotope(String symbol, double exactMass, double tolerance) {
IIsotope ret = null;
double minDiff = Double.MAX_VALUE;
int elem = Elements.ofString(symbol).number();
List<IIsotope> isotopes = this.isotopes[elem];
if (isotopes == null)
return null;
... | java | {
"resource": ""
} |
q157458 | IsotopeFactory.getExactMass | train | public double getExactMass(Integer atomicNumber, Integer massNumber) {
if (atomicNumber == null || massNumber == null)
return 0;
for (IIsotope isotope : this.isotopes[atomicNumber]) {
if (isotope.getMassNumber().equals(massNumber))
return isotope.getExactMass();
... | java | {
"resource": ""
} |
q157459 | IsotopeFactory.configure | train | public IAtom configure(IAtom atom, IIsotope isotope) {
atom.setMassNumber(isotope.getMassNumber());
atom.setSymbol(isotope.getSymbol());
atom.setExactMass(isotope.getExactMass());
atom.setAtomicNumber(isotope.getAtomicNumber());
atom.setNaturalAbundance(isotope.getNaturalAbundanc... | java | {
"resource": ""
} |
q157460 | IsotopeFactory.configureAtoms | train | public void configureAtoms(IAtomContainer container) {
for (int f = 0; f < container.getAtomCount(); f++) {
configure(container.getAtom(f));
}
} | java | {
"resource": ""
} |
q157461 | IsotopeFactory.getNaturalMass | train | public double getNaturalMass(int atomicNum) {
List<IIsotope> isotopes = this.isotopes[atomicNum];
if (isotopes == null)
return 0;
double summedAbundances = 0;
double summedWeightedAbundances = 0;
double getNaturalMass = 0;
for (IIsotope isotope : isotopes) {
... | java | {
"resource": ""
} |
q157462 | Congestion.initScore | train | private double initScore() {
double score = 0;
final int n = atoms.length;
for (int i = 0; i < n; i++) {
final Point2d p1 = atoms[i].getPoint2d();
for (int j = i + 1; j < n; j++) {
if (contribution[i][j] < 0) continue;
final Point2d p2 = at... | java | {
"resource": ""
} |
q157463 | Congestion.update | train | void update(boolean[] visit, int[] vs, int n) {
int len = atoms.length;
double subtract = 0;
for (int i = 0; i < n; i++) {
final int v = vs[i];
final Point2d p1 = atoms[v].getPoint2d();
for (int w = 0; w < len; w++) {
if (visit[w] || contributi... | java | {
"resource": ""
} |
q157464 | AllCycles.verticesInOrder | train | static int[] verticesInOrder(final int[] rank) {
int[] vs = new int[rank.length];
for (int v = 0; v < rank.length; v++)
vs[rank[v]] = v;
return vs;
} | java | {
"resource": ""
} |
q157465 | AllCycles.rank | train | static int[] rank(final int[][] g) {
final int ord = g.length;
final int[] count = new int[ord + 1];
final int[] rank = new int[ord];
// frequency of each degree
for (int v = 0; v < ord; v++)
count[g[v].length + 1]++;
// cumulated counts
for (int i =... | java | {
"resource": ""
} |
q157466 | AllCycles.paths | train | public int[][] paths() {
int[][] paths = new int[cycles.size()][];
for (int i = 0; i < cycles.size(); i++)
paths[i] = cycles.get(i).clone();
return paths;
} | java | {
"resource": ""
} |
q157467 | DepictionGenerator.depict | train | public Depiction depict(Iterable<IAtomContainer> mols, int nrow, int ncol) throws CDKException {
List<LayoutBackup> layoutBackups = new ArrayList<>();
int molId = 0;
for (IAtomContainer mol : mols) {
setIfMissing(mol, MarkedElement.ID_KEY, "mol" + ++molId);
layoutBackups... | java | {
"resource": ""
} |
q157468 | DepictionGenerator.makeHighlightAtomMap | train | private Map<IChemObject, Color> makeHighlightAtomMap(List<IAtomContainer> reactants,
List<IAtomContainer> products) {
Map<IChemObject, Color> colorMap = new HashMap<>();
Map<Integer, Color> mapToColor = new HashMap<>();
int colorIdx = -1;
... | java | {
"resource": ""
} |
q157469 | DepictionGenerator.generateTitle | train | private Bounds generateTitle(IChemObject chemObj, double scale) {
String title = chemObj.getProperty(CDKConstants.TITLE);
if (title == null || title.isEmpty())
return new Bounds();
scale = 1 / scale * getParameterValue(RendererModel.TitleFontScale.class);
return new Bounds(Ma... | java | {
"resource": ""
} |
q157470 | DepictionGenerator.ensure2dLayout | train | private boolean ensure2dLayout(IAtomContainer container) throws CDKException {
if (!GeometryUtil.has2DCoordinates(container)) {
StructureDiagramGenerator sdg = new StructureDiagramGenerator();
sdg.generateCoordinates(container);
return true;
}
return false;
... | java | {
"resource": ""
} |
q157471 | DepictionGenerator.ensure2dLayout | train | private void ensure2dLayout(IReaction rxn) throws CDKException {
if (!GeometryUtil.has2DCoordinates(rxn)) {
StructureDiagramGenerator sdg = new StructureDiagramGenerator();
sdg.setAlignMappedReaction(alignMappedReactions);
sdg.generateCoordinates(rxn);
}
} | java | {
"resource": ""
} |
q157472 | DepictionGenerator.withOuterGlowHighlight | train | public DepictionGenerator withOuterGlowHighlight(double width) {
return withParam(StandardGenerator.Highlighting.class,
StandardGenerator.HighlightStyle.OuterGlow)
.withParam(StandardGenerator.OuterGlowWidth.class,
width);
} | java | {
"resource": ""
} |
q157473 | DepictionGenerator.withAtomNumbers | train | public DepictionGenerator withAtomNumbers() {
if (annotateAtomMap || annotateAtomVal)
throw new IllegalArgumentException("Can not annotated atom numbers, atom values or maps are already annotated");
DepictionGenerator copy = new DepictionGenerator(this);
copy.annotateAtomNum = true;
... | java | {
"resource": ""
} |
q157474 | DepictionGenerator.withAtomValues | train | public DepictionGenerator withAtomValues() {
if (annotateAtomNum || annotateAtomMap)
throw new IllegalArgumentException("Can not annotated atom values, atom numbers or maps are already annotated");
DepictionGenerator copy = new DepictionGenerator(this);
copy.annotateAtomVal = true;
... | java | {
"resource": ""
} |
q157475 | DepictionGenerator.withAtomMapHighlight | train | public DepictionGenerator withAtomMapHighlight(Color[] colors) {
DepictionGenerator copy = new DepictionGenerator(this);
copy.highlightAtomMap = true;
copy.atomMapColors = Arrays.copyOf(colors, colors.length);
return copy;
} | java | {
"resource": ""
} |
q157476 | DepictionGenerator.withHighlight | train | public DepictionGenerator withHighlight(Iterable<? extends IChemObject> chemObjs, Color color) {
DepictionGenerator copy = new DepictionGenerator(this);
for (IChemObject chemObj : chemObjs)
copy.highlight.put(chemObj, color);
return copy;
} | java | {
"resource": ""
} |
q157477 | DepictionGenerator.withParam | train | public <T extends IGeneratorParameter<S>, S, U extends S> DepictionGenerator withParam(Class<T> key, U value) {
DepictionGenerator copy = new DepictionGenerator(this);
copy.setParam(key, value);
return copy;
} | java | {
"resource": ""
} |
q157478 | Orbitals.setCoefficients | train | public void setCoefficients(Matrix C) {
if (count_basis == C.rows) {
this.C = C;
count_orbitals = C.columns;
}
} | java | {
"resource": ""
} |
q157479 | Orbitals.getValues | train | public Vector getValues(int index, Matrix m) {
if (m.rows != 3) return null;
Vector result = basis.getValues(0, m).mul(C.matrix[0][index]);
for (int i = 1; i < count_basis; i++)
if (C.matrix[i][index] != 0d) result.add(basis.getValues(i, m).mul(C.matrix[0][index]));
return r... | java | {
"resource": ""
} |
q157480 | ConvexHull.ofShapes | train | public static ConvexHull ofShapes(final List<Shape> shapes) {
final Path2D combined = new Path2D.Double();
for (Shape shape : shapes)
combined.append(shape, false);
return new ConvexHull(shapeOf(grahamScan(pointsOf(combined))));
} | java | {
"resource": ""
} |
q157481 | ConvexHull.shapeOf | train | static Shape shapeOf(List<Point2D> points) {
Path2D path = new Path2D.Double();
if (!points.isEmpty()) {
path.moveTo(points.get(0).getX(), points.get(0).getY());
for (Point2D point : points)
path.lineTo(point.getX(), point.getY());
path.closePath();
... | java | {
"resource": ""
} |
q157482 | ConvexHull.pointsOf | train | static List<Point2D> pointsOf(final Shape shape) {
final List<Point2D> points = new ArrayList<Point2D>();
final double[] coordinates = new double[6];
for (PathIterator i = shape.getPathIterator(null); !i.isDone(); i.next()) {
switch (i.currentSegment(coordinates)) {
c... | java | {
"resource": ""
} |
q157483 | ConvexHull.lineLineIntersect | train | public static Point2D lineLineIntersect(final Line2D lineA, final Line2D lineB) {
return lineLineIntersect(lineA.getX1(), lineA.getY1(), lineA.getX2(), lineA.getY2(), lineB.getX1(),
lineB.getY1(), lineB.getX2(), lineB.getY2());
} | java | {
"resource": ""
} |
q157484 | ConvexHull.isLeftTurn | train | private static boolean isLeftTurn(Point2D a, Point2D b, Point2D c) {
return winding(a, b, c) > 0;
} | java | {
"resource": ""
} |
q157485 | ConvexHull.winding | train | private static int winding(Point2D a, Point2D b, Point2D c) {
return (int) Math.signum((b.getX() - a.getX()) * (c.getY() - a.getY()) - (b.getY() - a.getY())
* (c.getX() - a.getX()));
} | java | {
"resource": ""
} |
q157486 | AbstractFontManager.getFontSizeForZoom | train | protected Integer getFontSizeForZoom(double zoom) {
double lower = -1;
for (double upper : this.zoomToFontSizeMap.keySet()) {
if (lower == -1) {
lower = upper;
if (zoom <= lower) return this.zoomToFontSizeMap.get(upper);
continue;
}... | java | {
"resource": ""
} |
q157487 | AbstractFontManager.increaseFontSize | train | public void increaseFontSize() {
// move INTO range if we have just moved OUT of lower virtual
if (inRange() || (atMin() && atLowerBoundary())) {
currentFontIndex++;
} else if (atMax()) {
upperVirtualCount++;
} else if (atMin() && inLower()) {
lowerVir... | java | {
"resource": ""
} |
q157488 | AbstractFontManager.decreaseFontSize | train | public void decreaseFontSize() {
// move INTO range if we have just moved OUT of upper virtual
if (inRange() || (atMax() && atUpperBoundary())) {
currentFontIndex--;
} else if (atMin()) {
lowerVirtualCount--;
} else if (atMax() && inUpper()) {
upperVir... | java | {
"resource": ""
} |
q157489 | VdWRadiusDescriptor.calculate | train | @Override
public DescriptorValue calculate(IAtom atom, IAtomContainer container) {
String symbol = atom.getSymbol();
double vdwradius = PeriodicTable.getVdwRadius(symbol);
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new DoubleResult(vd... | java | {
"resource": ""
} |
q157490 | DynamicFactory.register | train | public <S extends ICDKObject, T extends S> boolean register(Class<S> intf, Constructor<T> constructor) {
return register(intf, constructor, null);
} | java | {
"resource": ""
} |
q157491 | DynamicFactory.register | train | public <S extends ICDKObject, T extends S> boolean register(Class<S> intf, Constructor<T> constructor,
CreationModifier<T> modifier) {
// do not register private constructors
if (Modifier.isPrivate(constructor.getModifiers()) ||
Modifier.isProtected(constructor.getModifiers())) ... | java | {
"resource": ""
} |
q157492 | DynamicFactory.register | train | private <T> Creator<T> register(ConstructorKey key, Constructor<T> constructor, CreationModifier<T> modifier) {
Creator<T> creator = new ReflectionCreator<T>(constructor);
if (modifier != null) creator = new ModifiedCreator<T>(creator, modifier);
return register(key, creator);
} | java | {
"resource": ""
} |
q157493 | DynamicFactory.ofClass | train | public <T extends ICDKObject> T ofClass(Class<T> intf, Object... objects) {
try {
if (!intf.isInterface()) throw new IllegalArgumentException("expected interface, got " + intf.getClass());
Creator<T> constructor = get(new ObjectBasedKey(intf, objects));
return constructor.... | java | {
"resource": ""
} |
q157494 | DynamicFactory.find | train | private <T> Creator<T> find(final ConstructorKey key) {
for (ConstructorKey candidate : lookup.getCandidates(key)) {
if (key.isAssignable(candidate)) {
return get(candidate);
}
}
// if the key has uniform parameter types
if (key.isUniform()) {
... | java | {
"resource": ""
} |
q157495 | DynamicFactory.implementorsOf | train | public <T extends ICDKObject> Set<Class<?>> implementorsOf(Class<T> intf) {
Set<Class<?>> implementations = new HashSet<Class<?>>(5);
for (ConstructorKey key : lookup.getConstructors(intf)) {
implementations.add(get(key).getDeclaringClass());
}
return implementations;
} | java | {
"resource": ""
} |
q157496 | SpanningTree.getSpanningTree | train | public IAtomContainer getSpanningTree() {
IAtomContainer container = molecule.getBuilder().newInstance(IAtomContainer.class);
for (int a = 0; a < totalVertexCount; a++)
container.addAtom(molecule.getAtom(a));
for (int b = 0; b < totalEdgeCount; b++)
if (bondsInTree[b]) co... | java | {
"resource": ""
} |
q157497 | SpanningTree.getBasicRings | train | public IRingSet getBasicRings() throws NoSuchAtomException {
IRingSet ringset = molecule.getBuilder().newInstance(IRingSet.class);
IAtomContainer spt = getSpanningTree();
for (int i = 0; i < totalEdgeCount; i++)
if (!bondsInTree[i]) ringset.addAtomContainer(getRing(spt, molecule.getB... | java | {
"resource": ""
} |
q157498 | SpanningTree.getCyclicFragmentsContainer | train | public IAtomContainer getCyclicFragmentsContainer() {
IAtomContainer fragContainer = this.molecule.getBuilder().newInstance(IAtomContainer.class);
IAtomContainer spt = getSpanningTree();
for (int i = 0; i < totalEdgeCount; i++)
if (!bondsInTree[i]) {
IRing ring = get... | java | {
"resource": ""
} |
q157499 | SpanningTree.identifyBonds | train | private void identifyBonds() {
IAtomContainer spt = getSpanningTree();
IRing ring;
int nBasicRings = 0;
for (int i = 0; i < totalEdgeCount; i++) {
if (!bondsInTree[i]) {
ring = getRing(spt, molecule.getBond(i));
for (int b = 0; b < ring.getBond... | java | {
"resource": ""
} |
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