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Bad SMILES are marked with an empty molecule and property. This mirro…
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…rs behaviour of the IteratingSMILESReader.
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@johnmay
johnmay committed Aug 2, 2015
1 parent 8afd272 commit 6ded684
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Showing 2 changed files with 68 additions and 24 deletions.
60 changes: 38 additions & 22 deletions storage/smiles/src/main/java/org/openscience/cdk/io/SMILESReader.java
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Expand Up @@ -23,13 +23,7 @@
*/
package org.openscience.cdk.io;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
Expand All @@ -39,18 +33,30 @@
import org.openscience.cdk.interfaces.IChemSequence;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.SMILESFormat;
import org.openscience.cdk.io.iterator.IteratingSMILESReader;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;

/**
* This Reader reads files which has one SMILES string on each
* line, where the format is given as below:
* <pre>
* COC ethoxy ethane
* </pre>
* Thus first the SMILES, and then after the first space (or tab) on the line a title
* that is stored as "SMIdbNAME" property in the Molecule.
* that is stored as {@link CDKConstants#TITLE}. For legacy comparability the
* title is also placed in a "SMIdbNAME" property. If a line is invalid an empty
* molecule is inserted into the container set. The molecule with have the prop
* {@link IteratingSMILESReader#BAD_SMILES_INPUT} set to the input line that
* could not be read.
*
* <p>For each line a molecule is generated, and multiple Molecules are
* read as MoleculeSet.
Expand Down Expand Up @@ -160,25 +166,20 @@ private IAtomContainerSet readAtomContainerSet(IAtomContainerSet som) {
while (line != null) {
logger.debug("Line: ", line);

String[] tokens = line.split("[\\s\\t]+", 2);
if (tokens.length > 2) throw new Exception("Malformed line");

String SMILES = tokens[0];
String name = null;
if (tokens.length == 2) name = tokens[1];

logger.debug("Line contains SMILES and name: ", SMILES, " + ", name);
final String name = suffix(line);

try {
IAtomContainer molecule = sp.parseSmiles(SMILES);
IAtomContainer molecule = sp.parseSmiles(line);
molecule.setProperty("SMIdbNAME", name);
molecule.setProperty(CDKConstants.TITLE, name);
som.addAtomContainer(molecule);
if (name != null) {
molecule.setProperty("SMIdbNAME", name);
}
} catch (Exception exception) {
logger.warn("This SMILES could not be parsed: ", SMILES);
} catch (CDKException exception) {
logger.warn("This SMILES could not be parsed: ", line);
logger.warn("Because of: ", exception.getMessage());
logger.debug(exception);
IAtomContainer empty = som.getBuilder().newInstance(IAtomContainer.class, 0, 0, 0, 0);
empty.setProperty(IteratingSMILESReader.BAD_SMILES_INPUT, line);
som.addAtomContainer(empty);
}
if (input.ready()) {
line = input.readLine();
Expand All @@ -197,4 +198,19 @@ private IAtomContainerSet readAtomContainerSet(IAtomContainerSet som) {
public void close() throws IOException {
input.close();
}

/**
* Obtain the suffix after a line containing SMILES. The suffix follows
* any ' ' or '\t' termination characters.
*
* @param line input line
* @return the suffix - or an empty line
*/
private String suffix(final String line) {
for (int i = 0; i < line.length(); i++) {
char c = line.charAt(i);
if (c == ' ' || c == '\t') return line.substring(i + 1);
}
return "";
}
}
32 changes: 30 additions & 2 deletions storage/smiles/src/test/java/org/openscience/cdk/io/SMILESReaderTest.java
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Expand Up @@ -22,18 +22,28 @@
* */
package org.openscience.cdk.io;

import java.io.InputStream;

import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
import org.openscience.cdk.AtomContainerSet;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.io.iterator.IteratingSMILESReader;
import org.openscience.cdk.silent.SilentChemObjectBuilder;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;

import java.io.InputStream;
import java.io.StringReader;

import static org.hamcrest.CoreMatchers.is;
import static org.hamcrest.CoreMatchers.notNullValue;
import static org.hamcrest.CoreMatchers.nullValue;
import static org.hamcrest.MatcherAssert.assertThat;

/**
* TestCase for the reading MDL mol files using one test file.
*
Expand Down Expand Up @@ -100,5 +110,23 @@ public void testReadingSmiFile_3() throws Exception {
IAtomContainerSet som = reader.read(new AtomContainerSet());
Assert.assertEquals(5, som.getAtomContainerCount());
}

@Test
public void badSmilesLine() throws CDKException {
IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
String input = "C\nn1cccc1\nc1ccccc1\n";
DefaultChemObjectReader cor = new SMILESReader(new StringReader(input));
IAtomContainerSet mols = cor.read(bldr.newInstance(IAtomContainerSet.class));
assertThat(mols.getAtomContainerCount(), is(3));
assertThat(mols.getAtomContainer(0).getAtomCount(), is(1));
assertThat(mols.getAtomContainer(0).getProperty(IteratingSMILESReader.BAD_SMILES_INPUT),
nullValue());
assertThat(mols.getAtomContainer(1).getAtomCount(), is(0));
assertThat(mols.getAtomContainer(1).getProperty(IteratingSMILESReader.BAD_SMILES_INPUT),
notNullValue());
assertThat(mols.getAtomContainer(2).getAtomCount(), is(6));
assertThat(mols.getAtomContainer(2).getProperty(IteratingSMILESReader.BAD_SMILES_INPUT),
nullValue());
}

}

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