id stringlengths 25 27 | content stringlengths 190 15.4k | max_stars_repo_path stringlengths 31 217 |
|---|---|---|
robustness-copilot_data_201 | /**
* Calculate sp3/sp2 hybridization ratio in the supplied {@link IAtomContainer}.
*
* @param container The AtomContainer for which this descriptor is to be calculated.
* @return The ratio of sp3 to sp2 carbons
*/
public DescriptorValue calculate(IAtomContainer container){
try {
I... | /descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/HybridizationRatioDescriptor.java |
robustness-copilot_data_202 | /**
* Select the lowest ring number for use in SMARTS.
*
* @return ring number
* @throws IllegalStateException all ring numbers are used
*/
private int chooseRingNumber(){
for (int i = 1; i < rnums.length; i++) {
if (rnums[i] == 0) {
rnums[i] = 1;
return i;
... | /tool/smarts/src/main/java/org/openscience/cdk/smarts/SmartsFragmentExtractor.java |
robustness-copilot_data_203 | /**
* Check max time different seconds tolerable between job server and registry center.
*
* @throws JobExecutionEnvironmentException throe JobExecutionEnvironmentException if exceed max time different seconds
*/
public void checkMaxTimeDiffSecondsTolerable() throws JobExecutionEnvironmentExceptio... | /elasticjob-lite/elasticjob-lite-core/src/main/java/org/apache/shardingsphere/elasticjob/lite/internal/config/ConfigurationService.java |
robustness-copilot_data_204 | /**
* Find the 2nd terminus stop (1st terminus is at index 0 per definition).
*
* Returns stop index instead of the stop, in order to cater for stops which are
* served multiple times
*
* @param stops
* @return index of the stop which is half way on the r... | /contribs/minibus/src/main/java/org/matsim/contrib/minibus/genericUtils/TerminusStopFinder.java |
robustness-copilot_data_205 | /**
* Evaluates the simple chi index for a set of fragments.
*
* @param atomContainer The target <code>AtomContainer</code>
* @param fragLists A list of fragments
* @return The simple chi index
*/
public static double evalSimpleIndex(IAtomContainer atomContainer, List<List<Integer>> ... | /descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ChiIndexUtils.java |
robustness-copilot_data_206 | /**
* Returns whether the appender is valid is valid for use in a threshold definition.
*/
public synchronized boolean hasAppender(String appender){
return _appenders.contains(appender) || (_parent != null && _parent.hasAppender(appender));
} | /modules/cells/src/main/java/dmg/util/logback/FilterThresholdSet.java |
robustness-copilot_data_207 | /**
* Clones this bond object, including clones of the atoms between which the
* bond is defined.
*
* @return The cloned object
*/
public IBond clone() throws CloneNotSupportedException{
Bond clone = (Bond) super.clone();
if (atoms != null) {
clone.atoms = new IAtom[atoms.lengt... | /base/data/src/main/java/org/openscience/cdk/Bond.java |
robustness-copilot_data_208 | /**
* Method for registering {@link ValueInstantiator} to use when deserializing
* instances of type <code>beanType</code>.
*<p>
* Instantiator is
* registered when module is registered for <code>ObjectMapper</code>.
*/
public SimpleModule addValueInstantiator(Class<?> beanType, ValueInst... | /src/main/java/com/fasterxml/jackson/databind/module/SimpleModule.java |
robustness-copilot_data_209 | /**
* The method calculates the bond total Partial charge of a given bond
* It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
*
*@param ac AtomContainer
*@return return the sigma electronegativity
*/
public Descripto... | /descriptor/qsarbond/src/main/java/org/openscience/cdk/qsar/descriptors/bond/BondPartialTChargeDescriptor.java |
robustness-copilot_data_210 | /**
* Create a new checksum instance for an already computed digest of a particular type.
*
* @param digest the input must have the following format:
* <type>:<hexadecimal digest>
* @throws IllegalArgumentException if argument has wrong form
* @throws NullPointerException ... | /modules/common/src/main/java/org/dcache/util/Checksum.java |
robustness-copilot_data_211 | /**
* Test if the domain is deployed under Istio environment.
*
* @return istioEnabled
*/
boolean isIstioEnabled(){
return Optional.ofNullable(configuration).map(Configuration::getIstio).map(Istio::getEnabled).orElse(false);
} | /operator/src/main/java/oracle/kubernetes/weblogic/domain/model/DomainSpec.java |
robustness-copilot_data_212 | /**
* Returns true if one of the servers in the cluster has the specified name.
*
* @param serverName the name to look for
* @return true or false
*/
public boolean hasNamedServer(String serverName){
return getServerConfigs().stream().anyMatch(c -> serverName.equals(c.getName()));
} | /operator/src/main/java/oracle/kubernetes/operator/wlsconfig/WlsClusterConfig.java |
robustness-copilot_data_213 | /**
* Checks if the agent has a valid transport URI set.
*
* @param agent Agent to check
* @return true if the Agent's transport URI is in the proper form
*/
private boolean isDispatcherTransportURI(final Agent agent){
final String transportURI = agent.getConfiguration().getTransportURI();... | /bundle/src/main/java/com/adobe/acs/commons/replication/dispatcher/DispatcherFlushFilter.java |
robustness-copilot_data_214 | /**
* An iterator over {@code FileSegment} for the {@code DocumentCollection} iterable.
* A collection is comprised of one or more file segments.
*/
public final Iterator<FileSegment<T>> iterator(){
List<Path> paths = discover(this.path);
Iterator<Path> pathsIterator = paths.iterator();
return new... | /src/main/java/io/anserini/collection/DocumentCollection.java |
robustness-copilot_data_215 | /**
* Factory method used to create {@link MappingIterator} instances;
* either default, or custom subtype.
*
* @since 2.5
*/
protected MappingIterator<T> _newIterator(JsonParser p, DeserializationContext ctxt, JsonDeserializer<?> deser, boolean parserManaged){
return new MappingIterator<... | /src/main/java/com/fasterxml/jackson/databind/ObjectReader.java |
robustness-copilot_data_216 | /**
* Add extended tetrahedral stereo configuration to the Beam GraphBuilder.
*
* @param et stereo element specifying tetrahedral configuration
* @param gb the current graph builder
* @param indices atom indices
*/
private static void addExtendedTetrahedralConfiguration(Extended... | /storage/smiles/src/main/java/org/openscience/cdk/smiles/CDKToBeam.java |
robustness-copilot_data_217 | /**
* Expands the given Node in the routing algorithm; may be overridden in
* sub-classes.
*
* @param outNode
* The Node to be expanded.
* @param toNode
* The target Node of the route.
* @param pendingNodes
* ... | /matsim/src/main/java/org/matsim/core/router/Dijkstra.java |
robustness-copilot_data_218 | /** Build a reverse index for every join column in the table. */
private List<Index> buildIndexesForJoinColumns(List<Integer> joinColumnIndexes, Table table){
return joinColumnIndexes.stream().map(c -> indexFor(table, c)).collect(Collectors.toList());
} | /core/src/main/java/tech/tablesaw/joining/DataFrameJoiner.java |
robustness-copilot_data_219 | /**
* Randomly generates a single, connected, correctly bonded structure from
* a number of fragments. IMPORTANT: The AtomContainers in the set must be
* connected. If an AtomContainer is disconnected, no valid result will
* be formed
* @param atomContainers The fragments to generate for.
... | /tool/structgen/src/main/java/org/openscience/cdk/structgen/stochastic/PartialFilledStructureMerger.java |
robustness-copilot_data_220 | /**
* Gets structure from InChI, and converts InChI library data structure
* into an IAtomContainer.
*
* @throws CDKException
*/
protected void generateAtomContainerFromInchi(IChemObjectBuilder builder) throws CDKException{
InchiInput input = output.getInchiInput();
molecule = builder.... | /storage/inchi/src/main/java/org/openscience/cdk/inchi/InChIToStructure.java |
robustness-copilot_data_221 | /**
* Does a layout of all aliphatic parts connected to the parts of the molecule
* that have already been laid out. Starts at the first bond with unplaced
* neighbours and stops when a ring is encountered.
*
* @throws CDKException if an error occurs
*/
private void layoutAcyclicParts() t... | /tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java |
robustness-copilot_data_222 | /**
* Registers rendering parameters from {@link IGenerator}s
* with this model.
*
* @param generator
*/
public void registerParameters(IGenerator<? extends IChemObject> generator){
for (IGeneratorParameter<?> param : generator.getParameters()) {
try {
renderingParamete... | /display/render/src/main/java/org/openscience/cdk/renderer/RendererModel.java |
robustness-copilot_data_223 | /**
* Method to use for adding mix-in annotations to use for augmenting
* specified class or interface. All annotations from
* <code>mixinSource</code> are taken to override annotations
* that <code>target</code> (or its supertypes) has.
*
* @param target Class (or interface) whose annotat... | /src/main/java/com/fasterxml/jackson/databind/ObjectMapper.java |
robustness-copilot_data_224 | /**
* Decode coordinates that have been placed in a byte buffer.
*
* @param str the string to decode
* @return array of coordinates
*/
static Point2d[] decodeCoordinates(String str){
if (str.startsWith("|(")) {
int end = str.indexOf(')', 2);
if (end < 0)
return ... | /tool/sdg/src/main/java/org/openscience/cdk/layout/IdentityTemplateLibrary.java |
robustness-copilot_data_225 | /**
* Convenience function to resize the outline and maintain the existing
* center point.
*
* @param scaleX scale x-axis
* @param scaleY scale y-axis
* @return resized outline
*/
TextOutline resize(final double scaleX, final double scaleY){
final Point2D center = getCenter();
... | /display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/TextOutline.java |
robustness-copilot_data_226 | /**
* Mark all values in row i allowing it to be reset later.
*
* @param i row index
* @param marking the marking to store (should be negative)
*/
void markRow(int i, int marking){
for (int j = (i * mCols), end = j + mCols; j < end; j++) if (data[j] > 0)
data[j] = marking;
} | /base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/CompatibilityMatrix.java |
robustness-copilot_data_227 | /**
* Put the order the List of IIsotope according the probability occurrence.
*
* @param isotopes_TO The List of IIsotope
* @return The list of IIsotope ordered
*/
private List<IIsotope> orderList(List<IIsotope> isotopes_TO){
List<IIsotope> newOrderList = new ArrayList<IIsoto... | /legacy/src/main/java/org/openscience/cdk/formula/MassToFormulaTool.java |
robustness-copilot_data_228 | /**
* Sets the converter for reading attributes of the specified class.
*
* @param clazz
* @param converter
* @return the previously registered converter for this class, or <code>null</code> if none was set before.
*/
public AttributeConverter<?> putAttributeConverter(final Class<?> clazz, final AttributeC... | /matsim/src/main/java/org/matsim/utils/objectattributes/ObjectAttributesXmlReader.java |
robustness-copilot_data_229 | /**
* Query has sharding info in offline servers or not.
*
* @return has sharding info in offline servers or not
*/
public boolean hasShardingInfoInOfflineServers(){
List<String> onlineInstances = jobNodeStorage.getJobNodeChildrenKeys(InstanceNode.ROOT);
int shardingTotalCount = configServ... | /elasticjob-lite/elasticjob-lite-core/src/main/java/org/apache/shardingsphere/elasticjob/lite/internal/sharding/ShardingService.java |
robustness-copilot_data_230 | /**
* Applies the given function to each compound tag in a compound-list subtag, if that subtag
* exists.
*
* @param key the key to look up
* @param consumer the function to apply
* @return true if the tag exists and was iterated over (even if it was empty); false otherwise
*/
public... | /src/main/java/net/glowstone/util/nbt/CompoundTag.java |
robustness-copilot_data_231 | /**
* Melt implements the 'tidy' melt operation as described in these papers by Hadley Wickham.
*
* <p>Tidy concepts: {@see https://www.jstatsoft.org/article/view/v059i10}
*
* <p>Cast function details: {@see https://www.jstatsoft.org/article/view/v021i12}
*
* <p>In short, melt turns columns into ro... | /core/src/main/java/tech/tablesaw/api/Table.java |
robustness-copilot_data_232 | /**
* Returns a StringColumn with the year and week-of-year derived from this column concatenated
* into a String that will sort lexicographically in temporal order.
*
* <p>This simplifies the production of plots and tables that aggregate values into standard
* temporal units (e.g., you want monthly data... | /core/src/main/java/tech/tablesaw/columns/datetimes/DateTimeMapFunctions.java |
robustness-copilot_data_233 | /**
* Finds the cluster of links <pre>startLink</pre> is part of. The cluster
* contains all links which can be reached starting at <code>startLink</code>
* and from where it is also possible to return again to <code>startLink</code>.
*
* @param startLink the link to start building the cluster
* @param mode... | /matsim/src/main/java/org/matsim/core/network/algorithms/MultimodalNetworkCleaner.java |
robustness-copilot_data_234 | /**
* Generates the introspector job name based on the given domainUid.
*
* @param domainUid domainUid
* @param serverName WebLogic server name
* @return String introspector job name
*/
public static String toExternalServiceName(String domainUid, String serverName){
return toDns1123LegalName(Stri... | /operator/src/main/java/oracle/kubernetes/operator/helpers/LegalNames.java |
robustness-copilot_data_235 | /**
* Queues a 'picture' message to the socket (or actor), so it can be sent.
*
* @param picture The picture is a string that defines the type of each frame.
* This makes it easy to send a complex multiframe message in
* one call. The picture can contain any of the... | /src/main/java/org/zeromq/proto/ZPicture.java |
robustness-copilot_data_236 | /**
* Position the charge label on the top right of either the element or hydrogen label. Where the
* charge is placed depends on the number of hydrogens and their position relative to the
* element symbol.
*
* @param hydrogens number of hydrogen
* @param position position of hydrogen
... | /display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardAtomGenerator.java |
robustness-copilot_data_237 | /**
* Gererates the plain-text email sections for sets of Health Check Execution Results.
*
* @param title The section title
* @param results the Health Check Execution Results to render as plain text
* @return the String for this section to be embedded in the e-mail
*/
protected String ... | /bundle/src/main/java/com/adobe/acs/commons/hc/impl/HealthCheckStatusEmailer.java |
robustness-copilot_data_238 | /**
* Returns the Iterator to atoms making up this bond.
* Iterator.remove() is not implemented.
*
* @return An Iterator to atoms participating in this bond
* @see #setAtoms
*/
public Iterable<IAtom> atoms(){
return new Iterable<IAtom>() {
@Override
public Iterator<IA... | /base/data/src/main/java/org/openscience/cdk/Bond.java |
robustness-copilot_data_239 | /**
* Create the schema type entity, with the corresponding schema attributes and relationships if it doesn't exist or
* updates the existing one.
*
* @param userId the name of the calling user
* @param schemaType the schema type values
* @param externalSourceName the u... | /open-metadata-implementation/access-services/data-engine/data-engine-server/src/main/java/org/odpi/openmetadata/accessservices/dataengine/server/handlers/DataEngineSchemaTypeHandler.java |
robustness-copilot_data_240 | /**
* This method multiply all the element over a value.
*
* @param formula Formula to correct
* @param factor Factor to multiply
* @return Formula with the correction
*/
private static String muliplier(String formula, int factor){
String finalformula = "";
String recentEl... | /tool/formula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java |
robustness-copilot_data_241 | /**
* Removes a single instance of the specified element from this
* queue, if it is present.
*
* @return <tt>true</tt> if the queue contained the specified
* element.
*/
public boolean remove(E value){
if (value == null)
return false;
int index = indices[this.getIndex(value)];
... | /matsim/src/main/java/org/matsim/core/router/priorityqueue/BinaryMinHeap.java |
robustness-copilot_data_242 | /**
* Parse the input parameters into the form needed to call workflowInstanceRemover. The results are set into
* instance variables. Method is package scope for unit testing.
*
* @throws ParseException
* if the date is in an invalid format.
* @throws PatternSyntaxException
... | /bundle/src/main/java/com/adobe/acs/commons/mcp/impl/processes/WorkflowRemover.java |
robustness-copilot_data_243 | /**
* Method that can be used to serialize any Java value as
* a byte array. Functionally equivalent to calling
* {@link #writeValue(Writer,Object)} with {@link java.io.ByteArrayOutputStream}
* and getting bytes, but more efficient.
* Encoding used will be UTF-8.
*<p>
* Note: prior to... | /src/main/java/com/fasterxml/jackson/databind/ObjectMapper.java |
robustness-copilot_data_244 | /**
* Utility method for shifting a specified value in an index to the back
* (see {@link #permutation(int[])}).
*
* @param neighbors list of neighbors
* @param v the value to shift to the back
* @return <i>neighbors</i> array
*/
static int[] moveToBack(int[] neighbors, int v... | /tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometricDoubleBondEncoderFactory.java |
robustness-copilot_data_245 | /**
* Reads the property block from the {@code input} setting the values in the
* container.
*
* @param input input resource
* @param container the structure with atoms / bonds present
* @param nAtoms the number of atoms in the atoms block
* @throws IOException low-level IO err... | /storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java |
robustness-copilot_data_246 | /**
* Process the Web request and (optionally) delegate to the next
* {@code ShenyuPlugin} through the given {@link ShenyuPluginChain}.
*
* @param exchange the current server exchange
* @param chain provides a way to delegate to the next plugin
* @return {@code Mono<Void>} to indicate w... | /shenyu-plugin/shenyu-plugin-base/src/main/java/org/apache/shenyu/plugin/base/AbstractShenyuPlugin.java |
robustness-copilot_data_247 | /**
* Factory method for constructing {@link ObjectReader} that will
* read values of a type {@code List<type>}.
* Functionally same as:
*<pre>
* readerFor(type[].class);
*</pre>
*
* @since 2.11
*/
public ObjectReader readerForArrayOf(Class<?> type){
return _newReade... | /src/main/java/com/fasterxml/jackson/databind/ObjectMapper.java |
robustness-copilot_data_248 | /**
* Reads the introspector config map for the specified domain, populating the following packet entries.
* INTROSPECTION_STATE_LABEL the value of the domain's 'introspectVersion' when this map was created
*
* @param ns the namespace of the domain
* @param domainUid the unique domain ID
* ... | /operator/src/main/java/oracle/kubernetes/operator/helpers/ConfigMapHelper.java |
robustness-copilot_data_249 | /**
* writes a single frame in XYZ format to the Writer.
* @param mol the Molecule to write
*/
public void writeMolecule(IAtomContainer mol) throws IOException{
String st = "";
boolean writecharge = true;
try {
String s1 = "" + mol.getAtomCount();
writer.write(s1, 0, s1.length()... | /storage/io/src/main/java/org/openscience/cdk/io/XYZWriter.java |
robustness-copilot_data_250 | /** {@inheritDoc}
* Function is called by the main program and serves as a starting point for the comparison procedure.
*
* @param shouldMatchBonds
*/
public synchronized void searchMCS(boolean shouldMatchBonds){
List<List<Integer>> mappings = null;
try {
if (source.getAtomCount() >... | /legacy/src/main/java/org/openscience/cdk/smsd/algorithm/mcsplus/MCSPlusHandler.java |
robustness-copilot_data_251 | /**
* Save the inputstream to a binary property under the cache entry node.
* @throws RepositoryException
*/
private void populateBinaryContent() throws RepositoryException{
final Node contents = getOrCreateByPath(entryNode, JCRHttpCacheStoreConstants.PATH_CONTENTS, JcrConstants.NT_FILE, JcrConstant... | /bundle/src/main/java/com/adobe/acs/commons/httpcache/store/jcr/impl/writer/EntryNodeWriter.java |
robustness-copilot_data_252 | /**
* Find all the resources needed for the package definition.
*
* @param resourceResolver the resource resolver to find the resources
* @param language the Query language
* @param statement the Query statement
* @param relPath the relative path to resolve against ... | /bundle/src/main/java/com/adobe/acs/commons/util/impl/QueryHelperImpl.java |
robustness-copilot_data_253 | /**
* Creates asynchronous step to read WebLogic server state from a particular pod.
*
* @param info the domain presence
* @param pod The pod
* @param serverName Server name
* @param timeoutSeconds Timeout in seconds
* @return Created step
*/
private static Step createServerStatusReaderStep(Dom... | /operator/src/main/java/oracle/kubernetes/operator/ServerStatusReader.java |
robustness-copilot_data_254 | /**
* Find a a Location obove or below the specified Location, which is on ground.
*
* <p>The returned Location will be at the center of the block, X and Y wise.
*
* @param spawn The Location a safe spawn position should be found at.
* @return The location to spawn the player at.
*/
... | /src/main/java/net/glowstone/entity/GlowPlayer.java |
robustness-copilot_data_255 | /**
* Checks an atom to see if it should be drawn. There are three reasons
* not to draw an atom - a) no coordinates, b) an invisible hydrogen or
* c) an invisible carbon.
*
* @param atom the atom to check
* @param container the atom container the atom is part of
* @param model the re... | /display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java |
robustness-copilot_data_256 | /**
* Convert the serialized JSON data found in the node property to Resources.
*
* @return the list of children sorting using the comparator.
* @throws InvalidDataFormatException
*/
private List<SyntheticChildAsPropertyResource> deserialize() throws InvalidDataFormatException{
final long ... | /bundle/src/main/java/com/adobe/acs/commons/synth/children/ChildrenAsPropertyResource.java |
robustness-copilot_data_257 | /**
* Step through the record, character by character, extracting each column and enduring that escaped double quotes
* and other tricks found in CSV files are handled.
*
* @param fileRecord a single record from the CSV file store
* @return an array of column values extracted from the record
... | /open-metadata-implementation/adapters/open-connectors/data-store-connectors/file-connectors/csv-file-connector/src/main/java/org/odpi/openmetadata/adapters/connectors/datastore/csvfile/CSVFileStoreConnector.java |
robustness-copilot_data_258 | /**
* Construct the folder structure in which a data file is stored all the way to the SoftwareServerCapability. Care is
* taken to maintain uniqueness of the relationship NestedFile that is between the file and the first folder.
*
* @param fileGuid data file guid
* @param pathName ... | /open-metadata-implementation/access-services/data-engine/data-engine-server/src/main/java/org/odpi/openmetadata/accessservices/dataengine/server/handlers/DataEngineFolderHierarchyHandler.java |
robustness-copilot_data_259 | /**
* Flip the storage order of atoms in a bond.
* @param bond the bond
*/
private void flip(IBond bond){
bond.setAtoms(new IAtom[] { bond.getEnd(), bond.getBegin() });
} | /storage/inchi/src/main/java/org/openscience/cdk/inchi/InChIToStructure.java |
robustness-copilot_data_260 | /**
* Formats an integer to fit into the connection table and changes it
* to a String.
*
* @param x The int to be formated
* @param n Length of the String
* @return The String to be written into the connectiontable
*/
protected static String formatMDLInt(int x, int n){
char[] bu... | /storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java |
robustness-copilot_data_261 | /**
* Convert the a character (from an MDL V2000 input) to a charge value:
* 1 = +1, 2 = +2, 3 = +3, 4 = doublet radical, 5 = -1, 6 = -2, 7 = -3.
*
* @param c a character
* @return formal charge
*/
private static int toCharge(final char c){
switch(c) {
case '1':
re... | /storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java |
robustness-copilot_data_262 | /**
* Returns a selection for all records that don't match both of the given functions. In other
* words, if both sel1 and sel2 are true, the record as a whole is false, and if either (or both)
* of sel1 or sel2 is {@code false}, the record as a whole is {@code true}.
*/
public static Function<Table, Selec... | /core/src/main/java/tech/tablesaw/api/QuerySupport.java |
robustness-copilot_data_263 | /**
* Looking if the Atom belongs to the halogen family.
*
* @param atom The IAtom
* @return True, if it belongs
*/
private boolean familyHalogen(IAtom atom){
String symbol = atom.getSymbol();
return symbol.equals("F") || symbol.equals("Cl") || symbol.equals("Br") || symbol.equ... | /descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicHOSEDescriptor.java |
robustness-copilot_data_264 | /**
* Adds the specified module / config-group with the specified name to the
* configuration.
* <p></p>
* This is the typical way to "materialize" material that, so far, exists only as Map, into a specialized module.
* @param specializedConfigModule
*
* @throws IllegalArgumentException
* if... | /matsim/src/main/java/org/matsim/core/config/Config.java |
robustness-copilot_data_265 | /**
* Determine the length of the line excluding trailing whitespace.
*
* @param str a string
* @return the length when trailing white space is removed
*/
static int length(final String str){
int i = str.length() - 1;
while (i >= 0 && str.charAt(i) == ' ') {
i--;
}
retu... | /storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java |
robustness-copilot_data_266 | /**
* Run the {@link OnDeployScript}, if it has not previously been run successfully.
* @param resourceResolver the resource resolver to use when running
* @param script the script to run.
* @return true if the script is executed, false if it has previous been run successfully
*/
protected boo... | /bundle/src/main/java/com/adobe/acs/commons/ondeploy/impl/OnDeployExecutorImpl.java |
robustness-copilot_data_267 | /**
* Get all paths of lengths 0 to the specified length.
*
* This method will find all paths upto length N starting from each atom in the molecule and return the unique set
* of such paths.
*
* @param container The molecule to search
* @return A map of path strings, keyed on themselv... | /descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/ShortestPathFingerprinter.java |
robustness-copilot_data_268 | /**
* Method that can be used to find primitive type for given class if (but only if)
* it is either wrapper type or primitive type; returns {@code null} if type is neither.
*
* @since 2.7
*/
public static Class<?> primitiveType(Class<?> type){
if (type.isPrimitive()) {
return type... | /src/main/java/com/fasterxml/jackson/databind/util/ClassUtil.java |
robustness-copilot_data_269 | /**
* Checks if the hook has content meaning as it has at least attachment or result with error message.
*
* @return <code>true</code> if the hook has content otherwise <code>false</code>
*/
public boolean hasContent(){
if (embeddings.length > 0) {
// assuming that if the embedding exis... | /src/main/java/net/masterthought/cucumber/json/Hook.java |
robustness-copilot_data_270 | /**
* Obtain the InChI auxiliary info for the provided structure using
* using the specified InChI options.
*
* @param container the structure to obtain the numbers of
* @return auxiliary info
* @throws CDKException the inchi could not be generated
*/
static String auxInfo(IAtomCon... | /storage/inchi/src/main/java/org/openscience/cdk/graph/invariant/InChINumbersTools.java |
robustness-copilot_data_271 | /**
* Calculates the orbits of the atoms of the molecule.
*
* @return a list of orbits
*/
public List<Orbit> calculateOrbits(){
List<Orbit> orbits = new ArrayList<Orbit>();
List<SymmetryClass> symmetryClasses = super.getSymmetryClasses();
for (SymmetryClass symmetryClass : symmetryClass... | /descriptor/signature/src/main/java/org/openscience/cdk/signature/MoleculeSignature.java |
robustness-copilot_data_272 | /**
* Checks if the agent has valid CQ-Action-Scope: ResourceOnly header.
*
* @param agent Agent to check
* @return true if the Agent's headers contain the expected values
*/
private boolean isResourceOnly(final Agent agent){
final ValueMap properties = agent.getConfiguration().getProperti... | /bundle/src/main/java/com/adobe/acs/commons/replication/dispatcher/DispatcherFlushFilter.java |
robustness-copilot_data_273 | /**
* Format local date time from timestamp local date time.
*
* @param timestamp the timestamp
* @return the local date time
*/
public static LocalDateTime formatLocalDateTimeFromTimestamp(final Long timestamp){
return LocalDateTime.ofEpochSecond(timestamp / 1000, 0, ZoneOffset.ofHours(8)... | /shenyu-common/src/main/java/org/apache/shenyu/common/utils/DateUtils.java |
robustness-copilot_data_274 | /**
* Appends an empty row and returns a Row object indexed to the newly added row so values can be
* set.
*
* <p>Intended usage:
*
* <p>for (int i = 0; ...) { Row row = table.appendRow(); row.setString("name", "Bob");
* row.setFloat("IQ", 123.4f); ...etc. }
*/
public Row appendRow(){
for (... | /core/src/main/java/tech/tablesaw/api/Table.java |
robustness-copilot_data_275 | /**
* Computes the (expected or planned) activity end time, depending on the configured time interpretation.
*/
public static OptionalTime decideOnActivityEndTime(Activity act, double now, Config config){
return decideOnActivityEndTime(act, now, config.plans().getActivityDurationInterpretation())... | /matsim/src/main/java/org/matsim/core/population/PopulationUtils.java |
robustness-copilot_data_276 | /**
* Aggregates a set of checksum entries into a single checksum value.
* @param checksums the checksums
* @return the checksum value
*/
protected String aggregateChecksums(final Map<String, String> checksums){
if (checksums.isEmpty()) {
return null;
}
StringBuilder data = new ... | /bundle/src/main/java/com/adobe/acs/commons/analysis/jcrchecksum/impl/ChecksumGeneratorImpl.java |
robustness-copilot_data_277 | /**
* Adds an automatically calculated offset to the coordinates of all atoms
* such that all coordinates are positive and the smallest x or y coordinate
* is exactly zero.
* See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate... | /legacy/src/main/java/org/openscience/cdk/geometry/GeometryTools.java |
robustness-copilot_data_278 | /**
* Compute the permutation parity of the values {@code vs}. The parity is
* whether we need to do an odd or even number of swaps to put the values in
* sorted order.
*
* @param vs values
* @return parity of the permutation (odd = -1, even = +1)
*/
private int permutationParity(int... | /base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/StereoMatch.java |
robustness-copilot_data_279 | /**
* Test whether the subtag with the given key is of {@link List} type.
*
* @param key the key to look up
* @param type the {@link TagType} of the list's elements
* @return true if the subtag exists and is a {@link List}; false otherwise
*/
public boolean isList(@NonNls String key, TagT... | /src/main/java/net/glowstone/util/nbt/CompoundTag.java |
robustness-copilot_data_280 | /**
* Count and find first heavy atom(s) (non Hydrogens) in a chain.
*
* @param molecule the reference molecule for searching the chain
* @param chain chain to be searched
* @return the atom number of the first heavy atom the number of heavy atoms in the chain
*/
public int[] f... | /tool/builder3d/src/main/java/org/openscience/cdk/modeling/builder3d/AtomPlacer3D.java |
robustness-copilot_data_281 | /**
* Makes sure that the travel times "make sense".
* <p></p>
* Imagine short bin sizes (e.g. 5min), small links (e.g. 300 veh/hour)
* and small sample sizes (e.g. 2%). This would mean that effectively
* in the simulation only 6 vehicles can pass the link in one hour,
* one every 10min. So, the travel time... | /matsim/src/main/java/org/matsim/core/trafficmonitoring/TravelTimeCalculator.java |
robustness-copilot_data_282 | /**
* Attempts to discover classes that are assignable to the type provided. In the case
* that an interface is provided this method will collect implementations. In the case
* of a non-interface class, subclasses will be collected. Accumulated classes can be
* accessed by calling {@link #getClasses()}.
... | /src/main/java/org/apache/ibatis/io/ResolverUtil.java |
robustness-copilot_data_283 | /**
* Checks if one of the loaded templates is a substructure in the given
* Molecule. If so, it assigns the coordinates from the template to the
* respective atoms in the Molecule, and marks the atoms as ISPLACED.
*
* @param molecule The molecule to be check for potential templates
* @ret... | /tool/sdg/src/main/java/org/openscience/cdk/layout/TemplateHandler.java |
robustness-copilot_data_284 | /**
* Check whether the node is marked as count station. If that is the case, migrate its count data to outCounts and mark it as non modifiable
* @param node The node to be checked
*/
private void checkNodeIsMarkedAsCountStation(Node node){
Link linkToBlock = null;
if (this.shortName... | /contribs/vsp/src/main/java/playground/vsp/andreas/osmBB/PTCountsNetworkSimplifier.java |
robustness-copilot_data_285 | /**
* Tests if the electron count matches the Hückel 4n+2 rule.
*/
private static boolean isHueckelValid(IAtomContainer singleRing) throws CDKException{
int electronCount = 0;
for (IAtom ringAtom : singleRing.atoms()) {
if (ringAtom.getHybridization() != CDKConstants.UNSET && (ringAtom.g... | /legacy/src/main/java/org/openscience/cdk/aromaticity/DoubleBondAcceptingAromaticityDetector.java |
robustness-copilot_data_286 | /**
* Returns the largest ("top") n values in the column. Does not change the order in this column
*
* @param n The maximum number of records to return. The actual number will be smaller if n is
* greater than the number of observations in the column
* @return A list, possibly empty, of the largest o... | /core/src/main/java/tech/tablesaw/api/TimeColumn.java |
robustness-copilot_data_287 | /**
* Check whether the cloud job is disabled or not.
*
* @param jobName job name
* @return true is disabled, otherwise not
*/
public boolean isDisabled(@Param(name = "jobName", source = ParamSource.PATH) final String jobName){
return facadeService.isJobDisabled(jobName);
} | /elasticjob-cloud/elasticjob-cloud-scheduler/src/main/java/org/apache/shardingsphere/elasticjob/cloud/console/controller/CloudJobController.java |
robustness-copilot_data_288 | /**
* Pops and pushes its ways through the InChI connection table to build up a simple molecule.
* @param inputInchi user input InChI
* @param inputMolecule user input molecule
* @param inchiAtomsByPosition
* @return molecule with single bonds and no hydrogens.
*/
private IAtomContainer c... | /tool/tautomer/src/main/java/org/openscience/cdk/tautomers/InChITautomerGenerator.java |
robustness-copilot_data_289 | /**
* Calculates the FMF descriptor value for the given {@link IAtomContainer}.
*
* @param container An {@link org.openscience.cdk.interfaces.IAtomContainer} for which this descriptor
* should be calculated
* @return An object of {@link org.openscience.cdk.qsar.DescriptorValue}... | /descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/FMFDescriptor.java |
robustness-copilot_data_290 | /**
* Create job running context from job configuration and execution type.
*
* @param cloudJobConfig cloud job configuration
* @param type execution type
* @return Job running context
*/
public static JobContext from(final CloudJobConfiguration cloudJobConfig, final ExecutionType type){
... | /elasticjob-cloud/elasticjob-cloud-scheduler/src/main/java/org/apache/shardingsphere/elasticjob/cloud/scheduler/context/JobContext.java |
robustness-copilot_data_291 | /**
* Utility to determine if the specified mass is the major isotope for the given atomic number.
*
* @param number atomic number
* @param mass atomic mass
* @return the mass is the major mass for the atomic number
*/
private boolean isMajorIsotope(int number, int mass){
try {
... | /display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardAtomGenerator.java |
robustness-copilot_data_292 | /**
* Convenience method for generateChecksums(session, path, new DefaultChecksumGeneratorOptions()).
*
* @param session the session
* @param path tthe root path to generate checksums for
* @return the map of abs path ~> checksums
* @throws RepositoryException
* @throws IOExceptio... | /bundle/src/main/java/com/adobe/acs/commons/analysis/jcrchecksum/impl/ChecksumGeneratorImpl.java |
robustness-copilot_data_293 | /**
* Generate the next pseudorandom number for the provided <i>seed</i>.
*
* @param seed random number seed
* @return the next pseudorandom number
*/
long next(long seed){
seed = seed ^ seed << 21;
seed = seed ^ seed >>> 35;
return seed ^ seed << 4;
} | /tool/hash/src/main/java/org/openscience/cdk/hash/Xorshift.java |
robustness-copilot_data_294 | /**
* Return the variable name by removing invalid characters and proper escaping if
* it's a reserved word.
*
* @param name the variable name
* @return the sanitized variable name
*/
public String toVarName(final String name){
if (reservedWords.contains(name)) {
return escape... | /modules/openapi-generator/src/main/java/org/openapitools/codegen/DefaultCodegen.java |
robustness-copilot_data_295 | /**
* Check a permutation to see if it is better, equal, or worse than the
* current best.
*
* @param perm the permutation to check
* @return BETTER, EQUAL, or WORSE
*/
private Result compareRowwise(Permutation perm){
int m = perm.size();
for (int i = 0; i < m - 1; i++) {
... | /tool/group/src/main/java/org/openscience/cdk/group/AbstractDiscretePartitionRefiner.java |
robustness-copilot_data_296 | /**
* Returns the "contents" field of a document based on an internal Lucene docid.
* The method is named to be consistent with Lucene's {@link IndexReader#document(int)}, contra Java's standard
* method naming conventions.
*
* @param ldocid internal Lucene docid
* @return the "contents" f... | /src/main/java/io/anserini/search/SimpleImpactSearcher.java |
robustness-copilot_data_297 | /**
* Get sandbox of the cloud job by app name.
*
* @param appName application name
* @return sandbox info
* @throws JsonParseException parse json exception
*/
public Collection<Map<String, String>> sandbox(@Param(name = "appName", source = ParamSource.QUERY) final String appName) throws ... | /elasticjob-cloud/elasticjob-cloud-scheduler/src/main/java/org/apache/shardingsphere/elasticjob/cloud/console/controller/CloudOperationController.java |
robustness-copilot_data_298 | /**
* Push frame plus empty frame to front of message, before 1st frame.
* Message takes ownership of frame, will destroy it when message is sent.
* @param frame
*/
public ZMsg wrap(ZFrame frame){
if (frame != null) {
push(new ZFrame(""));
push(frame);
}
return this;
} | /src/main/java/org/zeromq/ZMsg.java |
robustness-copilot_data_299 | /**
* Find out if the PortAlias object is already stored in the repository. It uses the fully qualified name to retrieve the entity
*
* @param userId the name of the calling user
* @param qualifiedName the qualifiedName name of the process to be searched
*
* @return optional with en... | /open-metadata-implementation/access-services/data-engine/data-engine-server/src/main/java/org/odpi/openmetadata/accessservices/dataengine/server/handlers/DataEnginePortHandler.java |
robustness-copilot_data_300 | /**
* Determines if all this {@link IAtomContainer}'s atoms contain 3D coordinates. If any atom
* is null or has unset 3D coordinates this method will return false. If the provided
* container is null false is returned.
*
* @param container the atom container to examine
*
* @return in... | /legacy/src/main/java/org/openscience/cdk/geometry/GeometryTools.java |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.