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Merge pull request #237 from cdk/patch/improved-abbr-labels
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Patch/improved abbr labels
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@egonw
egonw committed Sep 17, 2016
2 parents da92110 + a3ddccb commit 0ce6a8a
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Showing 7 changed files with 336 additions and 15 deletions.
180 changes: 178 additions & 2 deletions app/depict/src/main/java/org/openscience/cdk/depict/Abbreviations.java
View file
Expand Up @@ -23,7 +23,10 @@

package org.openscience.cdk.depict;

import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.Multimap;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.config.Elements;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.exception.InvalidSmilesException;
import org.openscience.cdk.graph.ConnectedComponents;
Expand Down Expand Up @@ -61,6 +64,7 @@
import java.nio.charset.StandardCharsets;
import java.util.ArrayDeque;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.Deque;
Expand Down Expand Up @@ -127,6 +131,7 @@ public class Abbreviations implements Iterable<String> {
private final SmilesGenerator usmigen = SmilesGenerator.unique();

private final SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
private boolean contractOnHetero = true;

public Abbreviations() {
}
Expand Down Expand Up @@ -163,6 +168,17 @@ public boolean setEnabled(String label, boolean enabled) {
: labels.contains(label) && disabled.add(label);
}

/**
* Set whether abbreviations should be further contracted when they are connected
* to a heteroatom, for example -NH-Boc becomes -NHBoc. By default this option
* is enabled.
*
* @param val on/off
*/
public void setContractOnHetero(boolean val) {
this.contractOnHetero = val;
}

private static Set<IBond> findCutBonds(IAtomContainer mol, EdgeToBondMap bmap, int[][] adjlist) {
Set<IBond> cuts = new HashSet<>();
int numAtoms = mol.getAtomCount();
Expand Down Expand Up @@ -374,6 +390,7 @@ public List<Sgroup> generate(final IAtomContainer mol) {

final List<Sgroup> newSgroups = new ArrayList<>();
List<IAtomContainer> fragments = generateFragments(mol);
Multimap<IAtom, Sgroup> sgroupAdjs = ArrayListMultimap.create();

for (IAtomContainer frag : fragments) {
try {
Expand Down Expand Up @@ -403,21 +420,180 @@ public List<Sgroup> generate(final IAtomContainer mol) {
Sgroup sgroup = new Sgroup();
sgroup.setType(SgroupType.CtabAbbreviation);
sgroup.setSubscript(label);
sgroup.addBond(frag.getBond(0).getProperty(CUT_BOND, IBond.class));

IBond attachBond = frag.getBond(0).getProperty(CUT_BOND, IBond.class);
IAtom attachAtom = null;
sgroup.addBond(attachBond);
for (int i = 1; i < numAtoms; i++) {
IAtom atom = frag.getAtom(i);
usedAtoms.add(atom);
sgroup.addAtom(atom);
if (attachBond.getAtom(0) == atom)
attachAtom = attachBond.getAtom(1);
else if (attachBond.getAtom(1) == atom)
attachAtom = attachBond.getAtom(0);
}

if (attachAtom != null)
sgroupAdjs.put(attachAtom, sgroup);
newSgroups.add(sgroup);
} catch (CDKException e) {

} catch (CDKException e) {
// ignore
}
}

// now collapse
for (IAtom attach : mol.atoms()) {
if (usedAtoms.contains(attach))
continue;

// skip charged or isotopic labelled, C or R/*, H, He
if ((attach.getFormalCharge() != null && attach.getFormalCharge() != 0)
|| attach.getMassNumber() != null
|| attach.getAtomicNumber() == 6
|| attach.getAtomicNumber() < 2)
continue;

int hcount = attach.getImplicitHydrogenCount();
Set<IAtom> xatoms = new HashSet<>();
Set<IBond> xbonds = new HashSet<>();
Set<IBond> newbonds = new HashSet<>();
xatoms.add(attach);

List<String> nbrSymbols = new ArrayList<>();
Set<Sgroup> todelete = new HashSet<>();
for (Sgroup sgroup : sgroupAdjs.get(attach)) {
if (containsChargeChar(sgroup.getSubscript()))
continue;
xbonds.addAll(sgroup.getBonds());
xatoms.addAll(sgroup.getAtoms());
nbrSymbols.add(sgroup.getSubscript());
todelete.add(sgroup);
}
for (IBond bond : mol.getConnectedBondsList(attach)) {
if (!xbonds.contains(bond)) {
IAtom nbr = bond.getConnectedAtom(attach);
// contract terminal bonds
if (mol.getConnectedBondsCount(nbr) == 1) {
if (nbr.getMassNumber() != null ||
(nbr.getFormalCharge() != null && nbr.getFormalCharge() != 0)) {
newbonds.add(bond);
} else if (nbr.getAtomicNumber() == 1) {
hcount++;
xatoms.add(nbr);
} else if (nbr.getAtomicNumber() > 0){
nbrSymbols.add(newSymbol(nbr.getAtomicNumber(), nbr.getImplicitHydrogenCount()));
xatoms.add(nbr);
}
} else {
newbonds.add(bond);
}
}
}

if (newbonds.size() < 1 || newbonds.size() > 3 || nbrSymbols.isEmpty())
continue;

// create the symbol
StringBuilder sb = new StringBuilder();
sb.append(newSymbol(attach.getAtomicNumber(), hcount));
String prev = null;
int count = 0;
Collections.sort(nbrSymbols, new Comparator<String>() {
@Override
public int compare(String o1, String o2) {
int cmp = Integer.compare(o1.length(), o2.length());
if (cmp != 0) return cmp;
return o1.compareTo(o2);
}
});
for (String nbrSymbol : nbrSymbols) {
if (nbrSymbol.equals(prev)) {
count++;
} else {
appendGroup(sb, prev, count, count == 0 || countUpper(prev) > 1);
prev = nbrSymbol;
count = 1;
}
}
appendGroup(sb, prev, count, false);

// remove existing
newSgroups.removeAll(todelete);

// create new
Sgroup newSgroup = new Sgroup();
newSgroup.setType(SgroupType.CtabAbbreviation);
newSgroup.setSubscript(sb.toString());
for (IBond bond : newbonds)
newSgroup.addBond(bond);
for (IAtom atom : xatoms)
newSgroup.addAtom(atom);

newSgroups.add(newSgroup);
usedAtoms.addAll(xatoms);
}

return newSgroups;
}

/**
* Count number of upper case chars.
*/
private int countUpper(String str) {
if (str == null)
return 0;
int num = 0;
for (int i = 0; i < str.length(); i++)
if (Character.isUpperCase(str.charAt(i)))
num++;
return num;
}

private boolean containsChargeChar(String str) {
for (int i = 0; i < str.length(); i++) {
final char c = str.charAt(i);
if (c == '-' || c == '+')
return true;
}
return false;
}

/**
* Check if last char is a digit.
*/
private boolean digitAtEnd(String str) {
return Character.isDigit(str.charAt(str.length()-1));
}

private String newSymbol(int atomnum, int hcount) {
StringBuilder sb = new StringBuilder();
Elements elem = Elements.ofNumber(atomnum);
if (elem == Elements.Carbon && hcount == 3)
return "Me";
sb.append(elem.symbol());
if (hcount > 0) {
sb.append('H');
if (hcount > 1)
sb.append(hcount);
}
return sb.toString();
}

private void appendGroup(StringBuilder sb, String group, int coef, boolean useParen) {
if (coef <= 0 || group == null || group.isEmpty()) return;
if (!useParen)
useParen = coef > 1 && (countUpper(group) > 1 || digitAtEnd(group));
if (useParen)
sb.append('(');
sb.append(group);
if (useParen)
sb.append(')');
if (coef > 1)
sb.append(coef);
}

/**
* Generates and assigns abbreviations to a molecule. Abbrevations are first
* generated with {@link #generate} and the filtered based on
Expand Down
78 changes: 78 additions & 0 deletions app/depict/src/test/java/org/openscience/cdk/depict/AbbreviationsTest.java
View file
Expand Up @@ -23,8 +23,10 @@

package org.openscience.cdk.depict;

import org.junit.Ignore;
import org.junit.Test;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.exception.InvalidSmilesException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.sgroup.Sgroup;
import org.openscience.cdk.sgroup.SgroupType;
Expand Down Expand Up @@ -169,6 +171,82 @@ public void dontOverwriteExistingSgroups() throws Exception {
assertThat(sgroups.size(), is(0));
}

@Test public void NHBocFromHeteroCollapse() throws Exception {
Abbreviations factory = new Abbreviations();
factory.add("*C(=O)OC(C)(C)C Boc");
IAtomContainer mol = smi("c1ccccc1NC(=O)OC(C)(C)C");
List<Sgroup> sgroups = factory.generate(mol);
assertThat(sgroups.size(), is(1));
assertThat(sgroups.get(0).getSubscript(), is("NHBoc"));
assertThat(sgroups.get(0).getBonds().size(), is(1));
assertThat(sgroups.get(0).getAtoms().size(), is(8));
}

@Test public void NHBocFromHeteroCollapseExplicitH() throws Exception {
Abbreviations factory = new Abbreviations();
factory.add("*C(=O)OC(C)(C)C Boc");
IAtomContainer mol = smi("c1ccccc1N([H])C(=O)OC(C)(C)C");
List<Sgroup> sgroups = factory.generate(mol);
assertThat(sgroups.size(), is(1));
assertThat(sgroups.get(0).getSubscript(), is("NHBoc"));
assertThat(sgroups.get(0).getBonds().size(), is(1));
assertThat(sgroups.get(0).getAtoms().size(), is(9));
}

@Test public void NBocClFromHeteroCollapseExplicit() throws Exception {
Abbreviations factory = new Abbreviations();
factory.add("*C(=O)OC(C)(C)C Boc");
IAtomContainer mol = smi("c1ccccc1N(Cl)C(=O)OC(C)(C)C");
List<Sgroup> sgroups = factory.generate(mol);
assertThat(sgroups.size(), is(1));
assertThat(sgroups.get(0).getSubscript(), is("N(Cl)Boc"));
assertThat(sgroups.get(0).getBonds().size(), is(1));
assertThat(sgroups.get(0).getAtoms().size(), is(9));
}

@Test public void NBoc2FromHeteroCollapse() throws Exception {
Abbreviations factory = new Abbreviations();
factory.add("*C(=O)OC(C)(C)C Boc");
IAtomContainer mol = smi("c1cc2ccccc2cc1N(C(=O)OC(C)(C)C)C(=O)OC(C)(C)C");
List<Sgroup> sgroups = factory.generate(mol);
assertThat(sgroups.size(), is(1));
assertThat(sgroups.get(0).getSubscript(), is("NBoc2"));
assertThat(sgroups.get(0).getBonds().size(), is(1));
assertThat(sgroups.get(0).getAtoms().size(), is(15));
}

@Test public void iPrFromHeteroCollapse() throws Exception {
Abbreviations factory = new Abbreviations();
factory.add("*C(C)C iPr");
IAtomContainer mol = smi("[CH3:27][CH:19]([CH3:28])[C:20]1=[N:26][C:23](=[CH:22][S:21]1)[C:24](=[O:25])O");
List<Sgroup> sgroups = factory.generate(mol);
assertThat(sgroups.size(), is(1));
assertThat(sgroups.get(0).getSubscript(), is("iPr"));
assertThat(sgroups.get(0).getBonds().size(), is(1));
assertThat(sgroups.get(0).getAtoms().size(), is(3));
}

@Test public void NBocFromHeteroCollapseExplicitH() throws Exception {
Abbreviations factory = new Abbreviations();
factory.add("*C(=O)OC(C)(C)C Boc");
IAtomContainer mol = smi("c1cc2ccccc2ccn1C(=O)OC(C)(C)C");
List<Sgroup> sgroups = factory.generate(mol);
assertThat(sgroups.size(), is(1));
assertThat(sgroups.get(0).getSubscript(), is("NBoc"));
assertThat(sgroups.get(0).getBonds().size(), is(2));
assertThat(sgroups.get(0).getAtoms().size(), is(8));
}

@Test public void SO3minusFromHeteroCollapseNone() throws Exception {
Abbreviations factory = new Abbreviations();
factory.add("*S(=O)(=O)[O-] SO3-");
IAtomContainer mol = smi("c1ccccc1N(S(=O)(=O)[O-])S(=O)(=O)[O-]");
List<Sgroup> sgroups = factory.generate(mol);
assertThat(sgroups.size(), is(2));
assertThat(sgroups.get(0).getSubscript(), is("SO3-"));
assertThat(sgroups.get(1).getSubscript(), is("SO3-"));
}

@Test
public void loadFromFile() throws Exception {
Abbreviations factory = new Abbreviations();
Expand Down

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