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Use new SMARTS API in SmartsPattern. Tests are no longer needed as pa…
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…ckage-private method was removed.
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@johnmay
johnmay committed Oct 10, 2018
1 parent a6dfff8 commit 6e3562c
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Showing 2 changed files with 49 additions and 84 deletions.
92 changes: 49 additions & 43 deletions tool/smarts/src/main/java/org/openscience/cdk/smiles/smarts/SmartsPattern.java
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Original file line number Diff line number Diff line change
Expand Up @@ -23,18 +23,20 @@
*/
package org.openscience.cdk.smiles.smarts;

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.aromaticity.Aromaticity;
import org.openscience.cdk.aromaticity.ElectronDonation;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.Cycles;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.isomorphism.ComponentGrouping;
import org.openscience.cdk.isomorphism.Mappings;
import org.openscience.cdk.isomorphism.Pattern;
import org.openscience.cdk.isomorphism.Smarts;
import org.openscience.cdk.isomorphism.SmartsStereoMatch;
import org.openscience.cdk.isomorphism.matchers.smarts.SmartsMatchers;
import org.openscience.cdk.smiles.smarts.parser.SMARTSParser;
import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer;
import org.openscience.cdk.tools.LoggingToolFactory;

import java.io.IOException;
Expand Down Expand Up @@ -81,11 +83,17 @@ public final class SmartsPattern extends Pattern {
private final Pattern pattern;

/** Include invariants about ring size / number. */
private final boolean ringInfo, hasStereo, hasCompGrp, hasRxnMap;
private final boolean hasStereo, hasCompGrp, hasRxnMap;

/**
* Prepare the target molecule (i.e. detect rings, aromaticity) before
* matching the SMARTS.
*/
private boolean doPrep = true;

/** Aromaticity model. */
private final Aromaticity arom = new Aromaticity(ElectronDonation.daylight(), Cycles.or(Cycles.all(),
Cycles.relevant()));
private static final Aromaticity arom = new Aromaticity(ElectronDonation.daylight(),
Cycles.or(Cycles.all(), Cycles.relevant()));



Expand All @@ -97,22 +105,49 @@ public final class SmartsPattern extends Pattern {
* @throws IOException the pattern could not be parsed
*/
private SmartsPattern(final String smarts, IChemObjectBuilder builder) throws IOException {
try {
this.query = SMARTSParser.parse(smarts, builder);
} catch (Exception e) {
throw new IOException(e);
}
this.query = new QueryAtomContainer(null);
if (!Smarts.parse(query, smarts))
throw new IOException("Could not parse SMARTS: " + smarts);
this.pattern = Pattern.findSubstructure(query);

// X<num>, R and @ are cheap and done always but R<num>, r<num> are not
// we inspect the SMARTS pattern string to determine if ring
// size or number queries are needed
this.ringInfo = ringSizeOrNumber(smarts);
this.hasStereo = query.stereoElements().iterator().hasNext();
this.hasCompGrp = query.getProperty(ComponentGrouping.KEY) != null;
this.hasCompGrp = hasCompGrouping(query);
this.hasRxnMap = smarts.contains(":");
}

private boolean hasCompGrouping(IAtomContainer query) {
for (IAtom atom : query.atoms()) {
if (atom.getProperty(CDKConstants.REACTION_GROUP) != null)
return true;
}
return query.getProperty(ComponentGrouping.KEY) != null;
}

static void prepare(IAtomContainer target) {
// apply the daylight aromaticity model
try {
Cycles.markRingAtomsAndBonds(target);
arom.apply(target);
} catch (CDKException e) {
LoggingToolFactory.createLoggingTool(SmartsPattern.class).error(e);
}
}

/**
* Sets whether the molecule should be "prepared" for a SMARTS match,
* including set ring flags and perceiving aromaticity. The main reason
* to skip preparation (via {@link #prepare(IAtomContainer)}) is if it has
* already been done, for example when matching multiple SMARTS patterns.
*
* @param doPrep whether preparation should be done
*/
public void setPrepare(boolean doPrep) {
this.doPrep = doPrep;
}

/**
*{@inheritDoc}
*/
Expand Down Expand Up @@ -146,20 +181,8 @@ public int[] match(IAtomContainer container) {
@Override
public Mappings matchAll(final IAtomContainer target) {

// TODO: prescreen target for element frequency before intialising
// invariants and applying aromaticity, requires pattern enumeration -
// see http://www.daylight.com/meetings/emug00/Sayle/substruct.html.

// assign additional atom invariants for SMARTS queries, a CDK quirk
// as each atom knows not which molecule from wence it came
SmartsMatchers.prepare(target, ringInfo);

// apply the daylight aromaticity model
try {
arom.apply(target);
} catch (CDKException e) {
LoggingToolFactory.createLoggingTool(getClass()).error(e);
}
if (doPrep)
prepare(target);

Mappings mappings = pattern.matchAll(target);

Expand Down Expand Up @@ -199,21 +222,4 @@ public static SmartsPattern create(String smarts, IChemObjectBuilder builder) th
public static SmartsPattern create(String smarts) throws IOException {
return new SmartsPattern(smarts, null);
}

/**
* Checks a smarts string for !R, R<num> or r<num>. If found then the more
* expensive ring info needs to be initlised before querying.
*
* @param smarts pattern string
* @return the pattern has a ring size or number query
*/
static boolean ringSizeOrNumber(final String smarts) {
for (int i = 0, end = smarts.length() - 1; i <= end; i++) {
char c = smarts.charAt(i);
if ((c == 'r' || c == 'R') && i < end && Character.isDigit(smarts.charAt(i + 1))) return true;
// !R = R0
if (c == '!' && i < end && smarts.charAt(i + 1) == 'R') return true;
}
return false;
}
}
41 changes: 0 additions & 41 deletions tool/smarts/src/test/java/org/openscience/cdk/smiles/smarts/SmartsPatternTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -48,47 +48,6 @@ public class SmartsPatternTest {

IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();

@Test
public void ringSizeOrNumber_membership() throws Exception {
assertFalse(SmartsPattern.ringSizeOrNumber("[R]"));
}

@Test
public void ringSizeOrNumber_ringConnectivity() throws Exception {
assertFalse(SmartsPattern.ringSizeOrNumber("[X2]"));
}

@Test
public void ringSizeOrNumber_elements() throws Exception {
assertFalse(SmartsPattern.ringSizeOrNumber("[Br]"));
assertFalse(SmartsPattern.ringSizeOrNumber("[Cr]"));
assertFalse(SmartsPattern.ringSizeOrNumber("[Fr]"));
assertFalse(SmartsPattern.ringSizeOrNumber("[Sr]"));
assertFalse(SmartsPattern.ringSizeOrNumber("[Ra]"));
assertFalse(SmartsPattern.ringSizeOrNumber("[Re]"));
assertFalse(SmartsPattern.ringSizeOrNumber("[Rf]"));
}

@Test
public void ringSizeOrNumber_negatedMembership() throws Exception {
assertTrue(SmartsPattern.ringSizeOrNumber("[!R]"));
}

@Test
public void ringSizeOrNumber_membershipZero() throws Exception {
assertTrue(SmartsPattern.ringSizeOrNumber("[R0]"));
}

@Test
public void ringSizeOrNumber_membershipTwo() throws Exception {
assertTrue(SmartsPattern.ringSizeOrNumber("[R2]"));
}

@Test
public void ringSizeOrNumber_ringSize() throws Exception {
assertTrue(SmartsPattern.ringSizeOrNumber("[r5]"));
}

@Test
public void isotopes() throws Exception {
// FIXME SMARTS Grammar needs fixing/replacing [12] is not considered valid
Expand Down

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