本文整理汇总了Java中org.openscience.cdk.smiles.SmilesParser.parseSmiles方法的典型用法代码示例。如果您正苦于以下问题:Java SmilesParser.parseSmiles方法的具体用法?Java SmilesParser.parseSmiles怎么用?Java SmilesParser.parseSmiles使用的例子?那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类org.openscience.cdk.smiles.SmilesParser
的用法示例。
在下文中一共展示了SmilesParser.parseSmiles方法的7个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: setUp
import org.openscience.cdk.smiles.SmilesParser; //导入方法依赖的package包/类
@Before
public void setUp() throws Exception {
this.testFile = new File("data_tests/pictureTest.png");
if (this.testFile.exists())
this.testFile.delete();
this.smiles = "c1ccccc1";
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
this.imol = null;
try {
this.imol = sp.parseSmiles(this.smiles);
} catch (InvalidSmilesException e) {
e.printStackTrace();
}
}
示例2: isIsomorph
import org.openscience.cdk.smiles.SmilesParser; //导入方法依赖的package包/类
/**
* Checks if the given structures are isomorph.
*
* @param candidate1 the candidate1
* @param candidate2 the candidate2
*
* @return true, if is isomorph
*
* @throws CDKException the CDK exception
*/
public boolean isIsomorph(String candidate1, String candidate2) throws CDKException
{
IAtomContainer cand1 = null;
IAtomContainer cand2 = null;
if(hasAtomContainer)
{
cand1 = this.candidateToStructure.get(candidate1);
cand2 = this.candidateToStructure.get(candidate2);
}
else
{
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
cand1 = sp.parseSmiles(candidatesToSmiles.get(candidate1));
cand2 = sp.parseSmiles(candidatesToSmiles.get(candidate2));
}
return UniversalIsomorphismTester.isIsomorph(cand1, cand2);
}
示例3: getMolFromSmiles
import org.openscience.cdk.smiles.SmilesParser; //导入方法依赖的package包/类
/**
* Gets the mol from smiles.
*
* @param smiles the smiles
*
* @return the mol from smiles
*/
public IAtomContainer getMolFromSmiles(String smiles) {
if (smiles == null || smiles.isEmpty())
return null;
IAtomContainer container = null;
try {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IMolecule m = sp.parseSmiles(smiles);
container = m;
// hydrogen handling
container = hydrogenHandling(container);
} catch (InvalidSmilesException ise) {
return null;
}
return container;
}
示例4: parseSmiles
import org.openscience.cdk.smiles.SmilesParser; //导入方法依赖的package包/类
public static IAtomContainer parseSmiles(String smiles) {
SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());
IAtomContainer precursorMolecule = null;
try {
precursorMolecule = sp.parseSmiles(smiles);
} catch (InvalidSmilesException e) {
e.printStackTrace();
}
prepareAtomContainer(precursorMolecule, true);
return precursorMolecule;
}
示例5: parseSmilesImplicitHydrogen
import org.openscience.cdk.smiles.SmilesParser; //导入方法依赖的package包/类
/**
*
* @param smiles
* @return
*/
public static IAtomContainer parseSmilesImplicitHydrogen(String smiles) {
SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());
IAtomContainer precursorMolecule = null;
try {
precursorMolecule = sp.parseSmiles(smiles);
} catch (InvalidSmilesException e) {
e.printStackTrace();
}
MoleculeFunctions.prepareAtomContainer(precursorMolecule, true);
MoleculeFunctions.convertExplicitToImplicitHydrogens(precursorMolecule);
return precursorMolecule;
}
示例6: createFromSmiles
import org.openscience.cdk.smiles.SmilesParser; //导入方法依赖的package包/类
public static ChemicalCompound createFromSmiles(String name, String smilesString)
throws CDKException
{
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IMolecule cdkMolecule = smilesParser.parseSmiles(smilesString);
return new ChemicalCompound(name, cdkMolecule);
}
示例7: main
import org.openscience.cdk.smiles.SmilesParser; //导入方法依赖的package包/类
public static void main(String[] args) throws IOException, InvalidSmilesException {
if (args.length < 1) {
System.err.println("Usage ./smi2fps {input.smi} [{output.smi}]");
return;
}
final String path = args[0];
final BufferedWriter bw = args.length > 1
? new BufferedWriter(new FileWriter(args[1])) :
new BufferedWriter(new OutputStreamWriter(System.out));
final BufferedReader rdr = new BufferedReader(new FileReader(path));
final SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
// TODO choose fingerprint
IFingerprinter fpr = new CircularFingerprinter(CircularFingerprinter.CLASS_ECFP4);
final int len = fpr.getSize();
int cnt = 0;
long t0 = System.nanoTime();
String line;
while ((line = rdr.readLine()) != null) {
try {
final IAtomContainer container = smipar.parseSmiles(line);
final String id = suffixedId(line);
final BitSet bitSet = fpr.getBitFingerprint(container).asBitSet();
StringBuilder sb = new StringBuilder();
FpsFmt.writeHex(sb, len, bitSet.toLongArray());
bw.write(sb.toString());
bw.write("\t");
bw.write(id);
bw.newLine();
if (++cnt % TIME_STAMP_INTERVAL == 0)
System.err.print("\r[RUN] processed " + cnt+ " compounds, elapsed time " + elapsedTime(t0, System.nanoTime()));
} catch (Exception e) {
System.err.println("[INFO] Skipping " + line + " " + e.getMessage());
}
}
long t1 = System.nanoTime();
System.err.println("\r[FINISHED] processed " + cnt+ " compounds, elapsed time " + elapsedTime(t0, t1));
rdr.close();
bw.close();
}