_id stringlengths 2 7 | title stringlengths 3 140 | partition stringclasses 3
values | text stringlengths 73 34.1k | language stringclasses 1
value | meta_information dict |
|---|---|---|---|---|---|
q156200 | NotificationsActor.onBusEvent | train | @Override
public void onBusEvent(Event event) {
if (event instanceof AppVisibleChanged) {
AppVisibleChanged visibleChanged = (AppVisibleChanged) event;
if (visibleChanged.isVisible()) {
onAppVisible();
} else {
onAppHidden();
}
... | java | {
"resource": ""
} |
q156201 | KuznechikCipher.encryptBlock | train | public void encryptBlock(byte[] data, int offset, byte[] dest, int destOffset) {
// w128_t x;
// x.q[0] = ((uint64_t *) blk)[0];
// x.q[1] = ((uint64_t *) blk)[1];
Kuz128 x = new Kuz128();
x.setQ(0, ByteStrings.bytesToLong(data, offset));
x.setQ(1, ByteStrings.bytesToLong... | java | {
"resource": ""
} |
q156202 | KuznechikCipher.decryptBlock | train | @Override
public void decryptBlock(byte[] data, int offset, byte[] dest, int destOffset) {
// w128_t x;
// x.q[0] = ((uint64_t *) blk)[0] ^ key->k[9].q[0];
// x.q[1] = ((uint64_t *) blk)[1] ^ key->k[9].q[1];
Kuz128 x = new Kuz128();
x.setQ(0, ByteStrings.bytesToLong(data, off... | java | {
"resource": ""
} |
q156203 | KuznechikCipher.convertKey | train | static KuzIntKey convertKey(byte[] key) {
if (key.length != 32) {
throw new RuntimeException("Key might be 32 bytes length");
}
KuzIntKey kuz = new KuzIntKey();
// w128_t c, x, y, z;
Kuz128 c = new Kuz128(), x = new Kuz128(), y = new Kuz128(), z = new Kuz128();
... | java | {
"resource": ""
} |
q156204 | ActorSDK.waitForReady | train | public void waitForReady() {
if (!isLoaded) {
synchronized (LOAD_LOCK) {
if (!isLoaded) {
try {
long start = Runtime.getActorTime();
LOAD_LOCK.wait();
Log.d(TAG, "Waited for startup in " + (Ru... | java | {
"resource": ""
} |
q156205 | ActorSDK.getDelegatedFragment | train | public <T> T getDelegatedFragment(ActorIntent delegatedIntent, android.support.v4.app.Fragment baseFragment, Class<T> type) {
if (delegatedIntent != null &&
delegatedIntent instanceof ActorIntentFragmentActivity &&
((ActorIntentFragmentActivity) delegatedIntent).getFragment() !=... | java | {
"resource": ""
} |
q156206 | Promises.tuple | train | @ObjectiveCName("tupleWithT1:withT2:")
public static <T1, T2> Promise<Tuple2<T1, T2>> tuple(Promise<T1> t1, Promise<T2> t2) {
return PromisesArray.ofPromises((Promise<Object>) t1, (Promise<Object>) t2)
.zip()
.map(src -> new Tuple2<>((T1) src.get(0), (T2) src.get(1)));
} | java | {
"resource": ""
} |
q156207 | Promises.tuple | train | @ObjectiveCName("tupleWithT1:withT2:withT3:")
public static <T1, T2, T3> Promise<Tuple3<T1, T2, T3>> tuple(Promise<T1> t1, Promise<T2> t2, Promise<T3> t3) {
return PromisesArray.ofPromises((Promise<Object>) t1, (Promise<Object>) t2, (Promise<Object>) t3)
.zip()
.map(src -> ne... | java | {
"resource": ""
} |
q156208 | Promises.traverse | train | public static <T> Promise traverse(List<Supplier<Promise<T>>> queue) {
if (queue.size() == 0) {
return Promise.success(null);
}
return queue.remove(0).get()
.flatMap(v -> traverse(queue));
} | java | {
"resource": ""
} |
q156209 | Patterns.concatGroups | train | public static final String concatGroups(MatcherCompat matcher) {
StringBuilder b = new StringBuilder();
final int numGroups = matcher.groupCount();
for (int i = 1; i <= numGroups; i++) {
String s = matcher.group(i);
if (s != null) {
b.append(s);
... | java | {
"resource": ""
} |
q156210 | Patterns.digitsAndPlusOnly | train | public static final String digitsAndPlusOnly(MatcherCompat matcher) {
StringBuilder buffer = new StringBuilder();
String matchingRegion = matcher.group();
for (int i = 0, size = matchingRegion.length(); i < size; i++) {
char character = matchingRegion.charAt(i);
if (chara... | java | {
"resource": ""
} |
q156211 | BitmapUtil.writeInt | train | private static byte[] writeInt(int value) throws IOException {
byte[] b = new byte[4];
b[0] = (byte) (value & 0x000000FF);
b[1] = (byte) ((value & 0x0000FF00) >> 8);
b[2] = (byte) ((value & 0x00FF0000) >> 16);
b[3] = (byte) ((value & 0xFF000000) >> 24);
return b;
} | java | {
"resource": ""
} |
q156212 | Actor.reply | train | public void reply(Object message) {
if (context.sender() != null) {
context.sender().send(message, self());
}
} | java | {
"resource": ""
} |
q156213 | Actor.drop | train | public void drop(Object message) {
if (system().getTraceInterface() != null) {
system().getTraceInterface().onDrop(sender(), message, this);
}
reply(new DeadLetter(message));
} | java | {
"resource": ""
} |
q156214 | ExponentialBackoff.exponentialWait | train | public synchronized long exponentialWait() {
long maxDelayRet = minDelay + ((maxDelay - minDelay) / maxFailureCount) * currentFailureCount;
return (long) (random.nextFloat() * maxDelayRet);
} | java | {
"resource": ""
} |
q156215 | Promise.then | train | @ObjectiveCName("then:")
public synchronized Promise<T> then(final Consumer<T> then) {
if (isFinished) {
if (exception == null) {
dispatcher.dispatch(() -> then.apply(result));
}
} else {
callbacks.add(new PromiseCallback<T>() {
@Ov... | java | {
"resource": ""
} |
q156216 | Promise.map | train | @ObjectiveCName("map:")
public <R> Promise<R> map(final Function<T, R> res) {
final Promise<T> self = this;
return new Promise<>((PromiseFunc<R>) resolver -> {
self.then(t -> {
R r;
try {
r = res.apply(t);
} catch (Excep... | java | {
"resource": ""
} |
q156217 | Promise.flatMap | train | @ObjectiveCName("flatMap:")
public <R> Promise<R> flatMap(final Function<T, Promise<R>> res) {
final Promise<T> self = this;
return new Promise<>((PromiseFunc<R>) resolver -> {
self.then(t -> {
Promise<R> promise;
try {
promise = res.ap... | java | {
"resource": ""
} |
q156218 | Promise.chain | train | public <R> Promise<T> chain(final Function<T, Promise<R>> res) {
final Promise<T> self = this;
return new Promise<>(resolver -> {
self.then(t -> {
Promise<R> chained = res.apply(t);
chained.then(t2 -> resolver.result(t));
chained.failure(e -> r... | java | {
"resource": ""
} |
q156219 | Promise.after | train | public Promise<T> after(final ConsumerDouble<T, Exception> afterHandler) {
then(t -> afterHandler.apply(t, null));
failure(e -> afterHandler.apply(null, e));
return this;
} | java | {
"resource": ""
} |
q156220 | Promise.pipeTo | train | @ObjectiveCName("pipeTo:")
public Promise<T> pipeTo(PromiseResolver<T> resolver) {
then(t -> resolver.result(t));
failure(e -> resolver.error(e));
return this;
} | java | {
"resource": ""
} |
q156221 | Hex.hex | train | public static String hex(byte[] bytes) {
char[] hexChars = new char[bytes.length * 2];
for (int j = 0; j < bytes.length; j++) {
int v = bytes[j] & 0xFF;
hexChars[j * 2] = HEXES_SMALL[v >>> 4];
hexChars[j * 2 + 1] = HEXES_SMALL[v & 0x0F];
}
return new S... | java | {
"resource": ""
} |
q156222 | BubbleContainer.onMeasure | train | @Override
protected void onMeasure(int widthMeasureSpec, int heightMeasureSpec) {
int topOffset = 0;
View messageView = findMessageView();
int padding = Screen.dp(8);
if (showAvatar) {
padding += Screen.dp(48);
}
measureChildWithMargins(messageView, widt... | java | {
"resource": ""
} |
q156223 | ActorApi.request | train | public synchronized <T extends Response> long request(Request<T> request, RpcCallback<T> callback, long timeout) {
if (request == null) {
throw new RuntimeException("Request can't be null");
}
long rid = NEXT_RPC_ID.incrementAndGet();
this.apiBroker.send(new ApiBroker.Perform... | java | {
"resource": ""
} |
q156224 | ActorBox.openBox | train | public static byte[] openBox(byte[] header, byte[] cipherText, ActorBoxKey key) throws IntegrityException {
CBCHmacBox aesCipher =
new CBCHmacBox(Crypto.createAES128(key.getKeyAES()), Crypto.createSHA256(), key.getMacAES());
CBCHmacBox kuzCipher =
new CBCHmacBox(new Kuzne... | java | {
"resource": ""
} |
q156225 | ActorBox.closeBox | train | public static byte[] closeBox(byte[] header, byte[] plainText, byte[] random32, ActorBoxKey key) throws IntegrityException {
CBCHmacBox aesCipher = new CBCHmacBox(Crypto.createAES128(key.getKeyAES()), Crypto.createSHA256(), key.getMacAES());
CBCHmacBox kuzCipher = new CBCHmacBox(new KuznechikFastEngine(... | java | {
"resource": ""
} |
q156226 | JavaUtil.contains | train | public static boolean contains(String[] vals, String value) {
for (int i = 0; i < vals.length; i++) {
if (vals[i].equals(value)) {
return true;
}
}
return false;
} | java | {
"resource": ""
} |
q156227 | JavaUtil.equalsE | train | public static <T> boolean equalsE(T a, T b) {
if (a == null && b == null) {
return true;
}
if (a != null && b == null) {
return false;
}
if (a == null) {
return false;
}
return a.equals(b);
} | java | {
"resource": ""
} |
q156228 | JavaUtil.last | train | public static <T> List<T> last(List<T> elements, int limit) {
ArrayList<T> res = new ArrayList<T>();
for (int i = 0; i < elements.size(); i++) {
if (res.size() >= limit) {
break;
}
res.add(elements.get(elements.size() - 1 - i));
}
retur... | java | {
"resource": ""
} |
q156229 | JavaUtil.unbox | train | public static long[] unbox(List<Long> list) {
long[] res = new long[list.size()];
for (int i = 0; i < res.length; i++) {
res[i] = list.get(i);
}
return res;
} | java | {
"resource": ""
} |
q156230 | GlobalStateVM.onGlobalCounterChanged | train | public synchronized void onGlobalCounterChanged(int value) {
globalCounter.change(value);
if (!isAppVisible.get()) {
globalTempCounter.change(value);
}
} | java | {
"resource": ""
} |
q156231 | AsyncListEngine.addOrUpdateItem | train | @Override
public void addOrUpdateItem(T item) {
synchronized (LOCK) {
// Update memory cache
cache.onObjectUpdated(item.getEngineId(), item);
List<T> items = new ArrayList<T>();
items.add(item);
asyncStorageInt.addOrUpdateItems(items);
... | java | {
"resource": ""
} |
q156232 | KeyManagerActor.fetchOwnIdentity | train | private Promise<OwnIdentity> fetchOwnIdentity() {
return Promise.success(new OwnIdentity(ownKeys.getKeyGroupId(), ownKeys.getIdentityKey()));
} | java | {
"resource": ""
} |
q156233 | KeyManagerActor.fetchPreKey | train | private Promise<PrivateKey> fetchPreKey(byte[] publicKey) {
try {
return Promise.success(ManagedList.of(ownKeys.getPreKeys())
.filter(PrivateKey.PRE_KEY_EQUALS(publicKey))
.first());
} catch (Exception e) {
Log.d(TAG, "Unable to find own pr... | java | {
"resource": ""
} |
q156234 | KeyManagerActor.fetchPreKey | train | private Promise<PrivateKey> fetchPreKey(long keyId) {
try {
return Promise.success(ManagedList.of(ownKeys.getPreKeys())
.filter(PrivateKey.PRE_KEY_EQUALS_ID(keyId))
.first());
} catch (Exception e) {
Log.d(TAG, "Unable to find own pre key #... | java | {
"resource": ""
} |
q156235 | KeyManagerActor.fetchUserGroups | train | private Promise<UserKeys> fetchUserGroups(final int uid) {
User user = users().getValue(uid);
if (user == null) {
throw new RuntimeException("Unable to find user #" + uid);
}
final UserKeys userKeys = getCachedUserKeys(uid);
if (userKeys != null) {
retur... | java | {
"resource": ""
} |
q156236 | KeyManagerActor.fetchUserPreKey | train | private Promise<PublicKey> fetchUserPreKey(final int uid, final int keyGroupId, final long keyId) {
User user = users().getValue(uid);
if (user == null) {
throw new RuntimeException("Unable to find user #" + uid);
}
return pickUserGroup(uid, keyGroupId)
.fla... | java | {
"resource": ""
} |
q156237 | KeyManagerActor.fetchUserPreKey | train | private Promise<PublicKey> fetchUserPreKey(final int uid, final int keyGroupId) {
return pickUserGroup(uid, keyGroupId)
.flatMap(new Function<Tuple2<UserKeysGroup, UserKeys>, Promise<PublicKey>>() {
@Override
public Promise<PublicKey> apply(final Tuple2<Us... | java | {
"resource": ""
} |
q156238 | KeyManagerActor.onPublicKeysGroupAdded | train | private void onPublicKeysGroupAdded(int uid, ApiEncryptionKeyGroup keyGroup) {
UserKeys userKeys = getCachedUserKeys(uid);
if (userKeys == null) {
return;
}
UserKeysGroup validatedKeysGroup = validateUserKeysGroup(uid, keyGroup);
if (validatedKeysGroup != null) {
... | java | {
"resource": ""
} |
q156239 | KeyManagerActor.onPublicKeysGroupRemoved | train | private void onPublicKeysGroupRemoved(int uid, int keyGroupId) {
UserKeys userKeys = getCachedUserKeys(uid);
if (userKeys == null) {
return;
}
UserKeys updatedUserKeys = userKeys.removeUserKeyGroup(keyGroupId);
cacheUserKeys(updatedUserKeys);
context().getEnc... | java | {
"resource": ""
} |
q156240 | ClcMessenger.clearPref | train | public void clearPref() {
try {
((ClcJavaPreferenceStorage) modules.getPreferences()).getPref().clear();
} catch (BackingStoreException e) {
logger.error("Cannot clear preferences", e);
}
} | java | {
"resource": ""
} |
q156241 | ImageLoading.loadBitmap | train | public static Bitmap loadBitmap(Uri uri, Context context) throws ImageLoadException {
return loadBitmap(new UriSource(uri, context));
} | java | {
"resource": ""
} |
q156242 | ImageLoading.loadBitmapOptimized | train | public static Bitmap loadBitmapOptimized(Uri uri, Context context) throws ImageLoadException {
return loadBitmapOptimized(uri, context, MAX_PIXELS);
} | java | {
"resource": ""
} |
q156243 | ImageLoading.save | train | public static byte[] save(Bitmap src) throws ImageSaveException {
return save(src, Bitmap.CompressFormat.JPEG, JPEG_QUALITY);
} | java | {
"resource": ""
} |
q156244 | ImageLoading.saveHq | train | public static byte[] saveHq(Bitmap src) throws ImageSaveException {
return save(src, Bitmap.CompressFormat.JPEG, JPEG_QUALITY_HQ);
} | java | {
"resource": ""
} |
q156245 | ImageLoading.save | train | public static void save(Bitmap src, String fileName) throws ImageSaveException {
saveJpeg(src, fileName, JPEG_QUALITY);
} | java | {
"resource": ""
} |
q156246 | ImageLoading.saveLq | train | public static void saveLq(Bitmap src, String fileName) throws ImageSaveException {
saveJpeg(src, fileName, JPEG_QUALITY_LOW);
} | java | {
"resource": ""
} |
q156247 | ImageLoading.savePng | train | public static void savePng(Bitmap src, String fileName) throws ImageSaveException {
save(src, fileName, Bitmap.CompressFormat.PNG, 100);
} | java | {
"resource": ""
} |
q156248 | ImageLoading.saveBmp | train | public static void saveBmp(Bitmap src, String fileName) throws ImageSaveException {
try {
BitmapUtil.save(src, fileName);
} catch (IOException e) {
throw new ImageSaveException(e);
}
} | java | {
"resource": ""
} |
q156249 | ImageLoading.bitmapSize | train | public static int bitmapSize(Bitmap bitmap) {
if (Build.VERSION.SDK_INT >= Build.VERSION_CODES.KITKAT) {
return bitmap.getByteCount();
} else {
return bitmap.getRowBytes() * bitmap.getHeight();
}
} | java | {
"resource": ""
} |
q156250 | ImageLoading.loadBitmapReuseExact | train | private static ReuseResult loadBitmapReuseExact(ImageSource source, Bitmap dest) throws ImageLoadException {
ImageMetadata metadata = source.getImageMetadata();
boolean tryReuse = false;
if (dest.isMutable()
&& dest.getWidth() == metadata.getW()
&& dest.getHeight(... | java | {
"resource": ""
} |
q156251 | ImageLoading.save | train | private static void save(Bitmap src, String fileName, Bitmap.CompressFormat format, int quality) throws ImageSaveException {
FileOutputStream outputStream = null;
try {
outputStream = new FileOutputStream(fileName);
src.compress(format, quality, outputStream);
outputS... | java | {
"resource": ""
} |
q156252 | CIPTool.getLigands | train | private static ILigand[] getLigands(IAtom atom, IAtomContainer container, IAtom exclude) {
List<IAtom> neighbors = container.getConnectedAtomsList(atom);
ILigand[] ligands = new ILigand[neighbors.size() - 1];
int i = 0;
for (IAtom neighbor : neighbors) {
if (!neighbor.equa... | java | {
"resource": ""
} |
q156253 | CIPTool.getLigandLigands | train | public static ILigand[] getLigandLigands(ILigand ligand) {
if (ligand instanceof TerminalLigand) return new ILigand[0];
IAtomContainer container = ligand.getAtomContainer();
IAtom ligandAtom = ligand.getLigandAtom();
IAtom centralAtom = ligand.getCentralAtom();
VisitedAtoms visi... | java | {
"resource": ""
} |
q156254 | Gaussian03Reader.readCoordinates | train | private void readCoordinates(IChemModel model) throws CDKException, IOException {
IAtomContainer container = model.getBuilder().newInstance(IAtomContainer.class);
String line = input.readLine();
line = input.readLine();
line = input.readLine();
line = input.readLine();
wh... | java | {
"resource": ""
} |
q156255 | Gaussian03Reader.readPartialCharges | train | private void readPartialCharges(IChemModel model) throws CDKException, IOException {
logger.info("Reading partial atomic charges");
IAtomContainerSet moleculeSet = model.getMoleculeSet();
IAtomContainer molecule = moleculeSet.getAtomContainer(0);
String line = input.readLine(); // skip f... | java | {
"resource": ""
} |
q156256 | PeriodicTablePositionDescriptor.calculate | train | @Override
public DescriptorValue calculate(IAtom atom, IAtomContainer container) {
int period;
String symbol = atom.getSymbol();
period = periodicTable.get(symbol);
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(period),
... | java | {
"resource": ""
} |
q156257 | FormatStringBuffer.skipDigits | train | private int skipDigits() {
char ch;
int i = 0;
while (index < format.length()) {
if (Character.isDigit(ch = format.charAt(index))) {
index++;
i = i * 10 + Character.digit(ch, 10);
} else {
break;
}
}
... | java | {
"resource": ""
} |
q156258 | AbstractDiscretePartitionRefiner.getAutomorphismPartition | train | public Partition getAutomorphismPartition() {
final int n = group.getSize();
final DisjointSetForest forest = new DisjointSetForest(n);
group.apply(new PermutationGroup.Backtracker() {
boolean[] inOrbit = new boolean[n];
private int inOrbitCount = 0;
... | java | {
"resource": ""
} |
q156259 | AbstractDiscretePartitionRefiner.getHalfMatrixString | train | private String getHalfMatrixString(Permutation permutation) {
StringBuilder builder = new StringBuilder(permutation.size());
int size = permutation.size();
for (int indexI = 0; indexI < size - 1; indexI++) {
for (int indexJ = indexI + 1; indexJ < size; indexJ++) {
bui... | java | {
"resource": ""
} |
q156260 | AbstractDiscretePartitionRefiner.refine | train | private void refine(PermutationGroup group, Partition coarser) {
int vertexCount = getVertexCount();
Partition finer = equitableRefiner.refine(coarser);
int firstNonDiscreteCell = finer.getIndexOfFirstNonDiscreteCell();
if (firstNonDiscreteCell == -1) {
firstNonDiscreteCell... | java | {
"resource": ""
} |
q156261 | AbstractDiscretePartitionRefiner.compareRowwise | train | private Result compareRowwise(Permutation perm) {
int m = perm.size();
for (int i = 0; i < m - 1; i++) {
for (int j = i + 1; j < m; j++) {
int x = getConnectivity(best.get(i), best.get(j));
int y = getConnectivity(perm.get(i), perm.get(j));
if ... | java | {
"resource": ""
} |
q156262 | PermutationGroup.order | train | public long order() {
// A group may have a size larger than Integer.MAX_INTEGER
// (2 ** 32 - 1) - for example sym(13) is larger.
long total = 1;
for (int i = 0; i < size; i++) {
int sum = 0;
for (int j = 0; j < size; j++) {
if (this.permutations[... | java | {
"resource": ""
} |
q156263 | PermutationGroup.transversal | train | public List<Permutation> transversal(final PermutationGroup subgroup) {
final long m = this.order() / subgroup.order();
final List<Permutation> results = new ArrayList<Permutation>();
Backtracker transversalBacktracker = new Backtracker() {
private boolean finished = false;
... | java | {
"resource": ""
} |
q156264 | PermutationGroup.all | train | public List<Permutation> all() {
final List<Permutation> permutations = new ArrayList<Permutation>();
Backtracker counter = new Backtracker() {
@Override
public void applyTo(Permutation p) {
permutations.add(p);
}
@Override
pu... | java | {
"resource": ""
} |
q156265 | PermutationGroup.enter | train | public void enter(Permutation g) {
int deg = size;
int i = test(g);
if (i == deg) {
return;
} else {
permutations[i][g.get(base.get(i))] = new Permutation(g);
}
for (int j = 0; j <= i; j++) {
for (int a = 0; a < deg; a++) {
... | java | {
"resource": ""
} |
q156266 | DictionaryDatabase.readDictionary | train | public void readDictionary(Reader reader, String name) {
name = name.toLowerCase();
logger.debug("Reading dictionary: ", name);
if (!dictionaries.containsKey(name)) {
try {
Dictionary dictionary = Dictionary.unmarshal(reader);
dictionaries.put(name, di... | java | {
"resource": ""
} |
q156267 | DictionaryDatabase.hasEntry | train | public boolean hasEntry(String dictName, String entryID) {
if (hasDictionary(dictName)) {
Dictionary dictionary = (Dictionary) dictionaries.get(dictName);
return dictionary.hasEntry(entryID.toLowerCase());
} else {
return false;
}
} | java | {
"resource": ""
} |
q156268 | Strand.removeMonomer | train | @Override
public void removeMonomer(String name) {
if (monomers.containsKey(name)) {
Monomer monomer = (Monomer) monomers.get(name);
this.remove(monomer);
monomers.remove(name);
}
} | java | {
"resource": ""
} |
q156269 | IsProtonInConjugatedPiSystemDescriptor.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": ""
} |
q156270 | PharmacophoreMatcher.matches | train | public boolean matches(IAtomContainer atomContainer, boolean initializeTarget) throws CDKException {
if (!GeometryUtil.has3DCoordinates(atomContainer)) throw new CDKException("Molecule must have 3D coordinates");
if (pharmacophoreQuery == null) throw new CDKException("Must set the query pharmacophore be... | java | {
"resource": ""
} |
q156271 | PharmacophoreMatcher.getMatchingPharmacophoreBonds | train | public List<List<IBond>> getMatchingPharmacophoreBonds() {
if (mappings == null) return null;
// XXX: re-subsearching the query
List<List<IBond>> bonds = new ArrayList<>();
for (Map<IBond,IBond> map : mappings.toBondMap()) {
bonds.add(new ArrayList<>(map.values()));
... | java | {
"resource": ""
} |
q156272 | PharmacophoreMatcher.getTargetQueryBondMappings | train | public List<HashMap<IBond, IBond>> getTargetQueryBondMappings() {
if (mappings == null) return null;
List<HashMap<IBond,IBond>> bondMap = new ArrayList<>();
// query -> target so need to inverse the mapping
// XXX: re-subsearching the query
for (Map<IBond,IBond>... | java | {
"resource": ""
} |
q156273 | PharmacophoreMatcher.getMatchingPharmacophoreAtoms | train | public List<List<PharmacophoreAtom>> getMatchingPharmacophoreAtoms() {
if (pharmacophoreMolecule == null || mappings == null) return null;
return getPCoreAtoms(mappings);
} | java | {
"resource": ""
} |
q156274 | PharmacophoreMatcher.getUniqueMatchingPharmacophoreAtoms | train | public List<List<PharmacophoreAtom>> getUniqueMatchingPharmacophoreAtoms() {
if (pharmacophoreMolecule == null || mappings == null) return null;
return getPCoreAtoms(mappings.uniqueAtoms());
} | java | {
"resource": ""
} |
q156275 | DeAromatizationTool.deAromatize | train | public static boolean deAromatize(IRing ring) {
boolean allaromatic = true;
for (int i = 0; i < ring.getBondCount(); i++) {
if (!ring.getBond(i).getFlag(CDKConstants.ISAROMATIC)) allaromatic = false;
}
if (!allaromatic) return false;
for (int i = 0; i < ring.getBondCo... | java | {
"resource": ""
} |
q156276 | RDFProtonDescriptor_GSR.calculateAngleBetweenTwoLines | train | private double calculateAngleBetweenTwoLines(Vector3d a, Vector3d b, Vector3d c, Vector3d d) {
Vector3d firstLine = new Vector3d();
firstLine.sub(a, b);
Vector3d secondLine = new Vector3d();
secondLine.sub(c, d);
Vector3d firstVec = new Vector3d(firstLine);
Vector3d secon... | java | {
"resource": ""
} |
q156277 | RDFProtonDescriptor_GSR.calculateDistanceBetweenTwoAtoms | train | private double calculateDistanceBetweenTwoAtoms(IAtom atom1, IAtom atom2) {
double distance;
Point3d firstPoint = atom1.getPoint3d();
Point3d secondPoint = atom2.getPoint3d();
distance = firstPoint.distance(secondPoint);
return distance;
} | java | {
"resource": ""
} |
q156278 | RDFProtonDescriptor_GSR.calculateDistanceBetweenAtomAndBond | train | private double[] calculateDistanceBetweenAtomAndBond(IAtom proton, IBond theBond) {
Point3d middlePoint = theBond.get3DCenter();
Point3d protonPoint = proton.getPoint3d();
double[] values = new double[4];
values[0] = middlePoint.distance(protonPoint);
values[1] = middlePoint.x;
... | java | {
"resource": ""
} |
q156279 | RDFProtonDescriptor_GSR.getParameterType | train | @Override
public Object getParameterType(String name) {
if (name.equals("checkAromaticity")) return Boolean.TRUE;
return null;
} | java | {
"resource": ""
} |
q156280 | AdductFormula.add | train | @Override
public void add(IMolecularFormulaSet formulaSet) {
for (IMolecularFormula mf : formulaSet.molecularFormulas()) {
addMolecularFormula(mf);
}
} | java | {
"resource": ""
} |
q156281 | AdductFormula.contains | train | @Override
public boolean contains(IIsotope isotope) {
for (Iterator<IIsotope> it = isotopes().iterator(); it.hasNext();) {
IIsotope thisIsotope = it.next();
if (isTheSame(thisIsotope, isotope)) {
return true;
}
}
return false;
} | java | {
"resource": ""
} |
q156282 | AdductFormula.getCharge | train | @Override
public Integer getCharge() {
Integer charge = 0;
Iterator<IMolecularFormula> componentIterator = components.iterator();
while (componentIterator.hasNext()) {
charge += componentIterator.next().getCharge();
}
return charge;
} | java | {
"resource": ""
} |
q156283 | AdductFormula.getIsotopeCount | train | @Override
public int getIsotopeCount(IIsotope isotope) {
int count = 0;
Iterator<IMolecularFormula> componentIterator = components.iterator();
while (componentIterator.hasNext()) {
count += componentIterator.next().getIsotopeCount(isotope);
}
return count;
} | java | {
"resource": ""
} |
q156284 | AdductFormula.isotopes | train | @Override
public Iterable<IIsotope> isotopes() {
return new Iterable<IIsotope>() {
@Override
public Iterator<IIsotope> iterator() {
return isotopesList().iterator();
}
};
} | java | {
"resource": ""
} |
q156285 | AdductFormula.isotopesList | train | private List<IIsotope> isotopesList() {
List<IIsotope> isotopes = new ArrayList<IIsotope>();
Iterator<IMolecularFormula> componentIterator = components.iterator();
while (componentIterator.hasNext()) {
Iterator<IIsotope> compIsotopes = componentIterator.next().isotopes().iterator();
... | java | {
"resource": ""
} |
q156286 | ChargeRule.setParameters | train | @Override
public void setParameters(Object[] params) throws CDKException {
if (params.length != 1) throw new CDKException("ChargeRule expects only one parameter");
if (!(params[0] instanceof Double)) throw new CDKException("The parameter must be of type Double");
charge = (Double) params[0... | java | {
"resource": ""
} |
q156287 | ChargeRule.validate | train | @Override
public double validate(IMolecularFormula formula) throws CDKException {
logger.info("Start validation of ", formula);
if (formula.getCharge() == null) {
return 0.0;
} else if (formula.getCharge() == charge) {
return 1.0;
} else {
return ... | java | {
"resource": ""
} |
q156288 | BeamToCDK.findDirectionalEdge | train | private Edge findDirectionalEdge(Graph g, int u) {
List<Edge> edges = g.edges(u);
if (edges.size() == 1)
return null;
Edge first = null;
for (Edge e : edges) {
Bond b = e.bond();
if (b == Bond.UP || b == Bond.DOWN) {
if (first == null)
... | java | {
"resource": ""
} |
q156289 | BeamToCDK.newTetrahedral | train | private IStereoElement newTetrahedral(int u, int[] vs, IAtom[] atoms, Configuration c) {
// no way to handle tetrahedral configurations with implicit
// hydrogen or lone pair at the moment
if (vs.length != 4) {
// sanity check
if (vs.length != 3) return null;
... | java | {
"resource": ""
} |
q156290 | BeamToCDK.insert | train | private static int[] insert(int v, int[] vs) {
final int n = vs.length;
final int[] ws = Arrays.copyOf(vs, n + 1);
ws[n] = v;
// insert 'u' in to sorted position
for (int i = n; i > 0 && ws[i] < ws[i - 1]; i--) {
int tmp = ws[i];
ws[i] = ws[i - 1];
... | java | {
"resource": ""
} |
q156291 | BeamToCDK.createAtom | train | private IAtom createAtom(Element element) {
IAtom atom = builder.newAtom();
atom.setSymbol(element.symbol());
atom.setAtomicNumber(element.atomicNumber());
return atom;
} | java | {
"resource": ""
} |
q156292 | SmilesValencyChecker.saturate | train | @Override
public void saturate(IAtomContainer atomContainer) throws CDKException {
logger.info("Saturating atomContainer by adjusting bond orders...");
boolean allSaturated = allSaturated(atomContainer);
if (!allSaturated) {
logger.info("Saturating bond orders is needed...");
... | java | {
"resource": ""
} |
q156293 | SmilesValencyChecker.saturate | train | public boolean saturate(IBond[] bonds, IAtomContainer atomContainer) throws CDKException {
logger.debug("Saturating bond set of size: ", bonds.length);
boolean bondsAreFullySaturated = false;
if (bonds.length > 0) {
IBond bond = bonds[0];
// determine bonds left
... | java | {
"resource": ""
} |
q156294 | SmilesValencyChecker.saturateByIncreasingBondOrder | train | public boolean saturateByIncreasingBondOrder(IBond bond, IAtomContainer atomContainer) throws CDKException {
IAtom[] atoms = BondManipulator.getAtomArray(bond);
IAtom atom = atoms[0];
IAtom partner = atoms[1];
logger.debug(" saturating bond: ", atom.getSymbol(), "-", partner.getSymbol()... | java | {
"resource": ""
} |
q156295 | SmilesValencyChecker.couldMatchAtomType | train | public boolean couldMatchAtomType(IAtom atom, double bondOrderSum, IBond.Order maxBondOrder, IAtomType type) {
logger.debug("couldMatchAtomType: ... matching atom ", atom, " vs ", type);
int hcount = atom.getImplicitHydrogenCount();
int charge = atom.getFormalCharge();
if (charge == ty... | java | {
"resource": ""
} |
q156296 | SmilesValencyChecker.calculateNumberOfImplicitHydrogens | train | public int calculateNumberOfImplicitHydrogens(IAtom atom, double bondOrderSum, IBond.Order maxBondOrder,
int neighbourCount) throws CDKException {
int missingHydrogens = 0;
if (atom instanceof IPseudoAtom) {
logger.debug("don't figure it out... it simply does not lack H's");
... | java | {
"resource": ""
} |
q156297 | SmilesValencyChecker.isSaturated | train | @Override
public boolean isSaturated(IAtom atom, IAtomContainer container) throws CDKException {
if (atom instanceof IPseudoAtom) {
logger.debug("don't figure it out... it simply does not lack H's");
return true;
}
IAtomType[] atomTypes = getAtomTypeFactory(atom.getB... | java | {
"resource": ""
} |
q156298 | IonizationPotentialTool.familyHalogen | train | private static boolean familyHalogen(IAtom atom) {
String symbol = atom.getSymbol();
if (symbol.equals("F") || symbol.equals("Cl") || symbol.equals("Br") || symbol.equals("I"))
return true;
else
return false;
} | java | {
"resource": ""
} |
q156299 | IonizationPotentialTool.familyBond | train | private static boolean familyBond(IAtomContainer container, IBond bond) {
List<String> normalAt = new ArrayList<String>();
normalAt.add("C");
normalAt.add("H");
if (getDoubleBondNumber(container) > 30) // taking to long
return false;
StructureResonanceGenerator gRN ... | java | {
"resource": ""
} |
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