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Improved the abbreviation handling over atom sets, this is useful for… #996

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Aug 24, 2023
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Improved the abbreviation handling over atom sets, this is useful for… #996

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139 changes: 68 additions & 71 deletions app/depict/src/main/java/org/openscience/cdk/depict/Abbreviations.java
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Original file line number Diff line number Diff line change
Expand Up @@ -147,11 +147,11 @@ public enum Option {
*/
private static final String INTERPUNCT = "·";

private final Map<String, String> connectedAbbreviations = new LinkedHashMap<>();
private final Map<String, String> connectedAbbreviations = new LinkedHashMap<>();
private final Map<String, String> disconnectedAbbreviations = new LinkedHashMap<>();
private final Set<String> labels = new LinkedHashSet<>();
private final Set<String> disabled = new HashSet<>();
private final SmilesGenerator usmigen = SmilesGenerator.unique();
private final Set<String> labels = new LinkedHashSet<>();
private final Set<String> disabled = new HashSet<>();
private final SmilesGenerator usmigen = SmilesGenerator.unique();

private final SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
private final Set<Option> options = EnumSet.of(Option.AUTO_CONTRACT_HETERO);
Expand All @@ -162,7 +162,9 @@ private static final class AdjacentGroup implements Comparable<AdjacentGroup> {

private final String symbol;

/** The abbreviation is only composed of carbons */
/**
* The abbreviation is only composed of carbons
*/
private final boolean allCarbon;

/**
Expand All @@ -172,7 +174,9 @@ private static final class AdjacentGroup implements Comparable<AdjacentGroup> {
*/
private final boolean isTrivial;

/** Number of times the group occurs. */
/**
* Number of times the group occurs.
*/
private int count = 0;

private AdjacentGroup(Sgroup sgroup) {
Expand All @@ -184,7 +188,7 @@ private AdjacentGroup(Sgroup sgroup) {
}

private AdjacentGroup(String symbol, IAtom nbr) {
this.symbol = symbol;
this.symbol = symbol;
this.allCarbon = !isNonCarbon(nbr);
this.isTrivial = isTrivial(symbol);
}
Expand Down Expand Up @@ -284,7 +288,7 @@ public boolean isEnabled(final String label) {
*/
public boolean setEnabled(String label, boolean enabled) {
return enabled ? labels.contains(label) && disabled.remove(label)
: labels.contains(label) && disabled.add(label);
: labels.contains(label) && disabled.add(label);
}

/**
Expand Down Expand Up @@ -335,7 +339,7 @@ private static Set<IBond> findCutBonds(IAtomContainer mol, EdgeToBondMap bmap, i
int numAtoms = mol.getAtomCount();
for (int i = 0; i < numAtoms; i++) {
final IAtom atom = mol.getAtom(i);
int deg = adjlist[i].length;
int deg = adjlist[i].length;
int elem = atom.getAtomicNumber();

if (elem == 6 && deg <= 2)
Expand Down Expand Up @@ -462,16 +466,16 @@ private static List<IAtomContainer> generateFragments(IAtomContainer mol) {
return frags;
}

private Map<IAtom,List<Sgroup>> getSgroupAdjacency(List<Sgroup> sgroups) {
Map<IAtom,List<Sgroup>> sgroupAdjs = new HashMap<>();
private Map<IAtom, List<Sgroup>> getSgroupAdjacency(List<Sgroup> sgroups) {
Map<IAtom, List<Sgroup>> sgroupAdjs = new HashMap<>();
for (Sgroup sgroup : sgroups) {
if (nonTerminal(sgroup))
continue;
IBond attachBond = sgroup.getBonds().iterator().next();
Set<IAtom> atoms = sgroup.getAtoms();
final IAtom attachAtom;
if (!atoms.contains(attachBond.getBegin()) &&
atoms.contains(attachBond.getEnd()))
atoms.contains(attachBond.getEnd()))
attachAtom = attachBond.getBegin();
else if (atoms.contains(attachBond.getBegin()) &&
!atoms.contains(attachBond.getEnd()))
Expand Down Expand Up @@ -509,13 +513,13 @@ public List<Sgroup> generate(final IAtomContainer mol) {
* Find all enabled abbreviations in the provided molecule. They are not
* added to the existing Sgroups and may need filtering.
*
* @param mol molecule
* @param mol molecule
* @param atomSets mark atoms are belong to a set, sets can not be split in
* an abbreviation
* @return list of new abbreviation Sgroups
*/
public List<Sgroup> generate(final IAtomContainer mol,
final Map<IAtom,Integer> atomSets) {
final Map<IAtom, Integer> atomSets) {

// mark which atoms have already been abbreviated or are
// part of an existing Sgroup
Expand Down Expand Up @@ -543,7 +547,7 @@ public List<Sgroup> generate(final IAtomContainer mol,
for (IAtom atom : mol.atoms())
sgroup.addAtom(atom);

if (splitsAtomSet(atomSets, sgroup))
if (!isAcceptableSet(atomSets, sgroup))
return Collections.emptyList();

return Collections.singletonList(sgroup);
Expand All @@ -561,9 +565,9 @@ public List<Sgroup> generate(final IAtomContainer mol,
Sgroup sgroup1 = getAbbr(a);
Sgroup sgroup2 = getAbbr(b);

if (splitsAtomSet(atomSets, sgroup1))
if (!isAcceptableSet(atomSets, sgroup1))
sgroup1 = null;
if (splitsAtomSet(atomSets, sgroup2))
if (!isAcceptableSet(atomSets, sgroup2))
sgroup2 = null;

if (sgroup1 != null && sgroup2 != null && options.contains(Option.ALLOW_SINGLETON)) {
Expand Down Expand Up @@ -597,12 +601,11 @@ public List<Sgroup> generate(final IAtomContainer mol,
}

// ensure we don't abbreviate stereochemistry
for (IStereoElement<?,?> se : mol.stereoElements()) {
for (IStereoElement<?, ?> se : mol.stereoElements()) {
IChemObject chemObject = se.getFocus();
if (chemObject instanceof IAtom) {
usedAtoms.add((IAtom) chemObject);
}
else if (chemObject instanceof IBond) {
} else if (chemObject instanceof IBond) {
usedAtoms.add(((IBond) chemObject).getBegin());
usedAtoms.add(((IBond) chemObject).getEnd());
}
Expand Down Expand Up @@ -638,26 +641,23 @@ else if (chemObject instanceof IBond) {
Sgroup sgroup = new Sgroup();
sgroup.setType(SgroupType.CtabAbbreviation);
sgroup.setSubscript(label);

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

if (!splitsAtomSet(atomSets, sgroup))
newSgroups.add(sgroup);
for (int i = 1; i < numAtoms; i++)
sgroup.addAtom(frag.getAtom(i));
if (!isAcceptableSet(atomSets, sgroup))
continue;
usedAtoms.addAll(sgroup.getAtoms());
newSgroups.add(sgroup);
allSgroups.add(sgroup);

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

if (!options.contains(Option.AUTO_CONTRACT_HETERO) &&
!options.contains(Option.AUTO_CONTRACT_TERMINAL))
!options.contains(Option.AUTO_CONTRACT_TERMINAL))
return newSgroups;

// collect adjacency info and terminal crossing bonds
Expand All @@ -672,27 +672,27 @@ else if (chemObject instanceof IBond) {

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

boolean okay = false;
if (attach.getAtomicNumber() != IAtom.C &&
options.contains(Option.AUTO_CONTRACT_HETERO))
okay = true;
else if (effectiveDegree(attach, allCrossingBonds) <= 1 &&
options.contains(Option.AUTO_CONTRACT_TERMINAL))
options.contains(Option.AUTO_CONTRACT_TERMINAL))
okay = true;
if (!okay)
continue;

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

Map<String,AdjacentGroup> adjGroupMap = new LinkedHashMap<>();
Map<String, AdjacentGroup> adjGroupMap = new LinkedHashMap<>();

for (final Sgroup sgroup : sgroupAdjs.getOrDefault(attach, Collections.emptyList())) {
if (containsChargeChar(sgroup.getSubscript()))
Expand All @@ -704,7 +704,7 @@ else if (effectiveDegree(attach, allCrossingBonds) <= 1 &&
xatoms.addAll(sgroup.getAtoms());
adjGroupMap.computeIfAbsent(sgroup.getSubscript(),
k -> new AdjacentGroup(sgroup))
.add(sgroup);
.add(sgroup);
}


Expand All @@ -714,16 +714,16 @@ else if (effectiveDegree(attach, allCrossingBonds) <= 1 &&

// can only contract terminal bonds
if (!usedAtoms.contains(nbr) &&
mol.getConnectedBondsCount(nbr) == 1) {
mol.getConnectedBondsCount(nbr) == 1) {

if (nbr.getMassNumber() != null ||
(nbr.getFormalCharge() != null && nbr.getFormalCharge() != 0) ||
isNonMethylTerminalCarbon(nbr)) {
(nbr.getFormalCharge() != null && nbr.getFormalCharge() != 0) ||
isNonMethylTerminalCarbon(nbr)) {
newbonds.add(bond);
} else if (nbr.getAtomicNumber() == 1) {
hcount++;
xatoms.add(nbr);
} else if (nbr.getAtomicNumber() > 0){
} else if (nbr.getAtomicNumber() > 0) {
String symbol = newSymbol(nbr.getAtomicNumber(), nbr.getImplicitHydrogenCount(), false);
adjGroupMap.computeIfAbsent(symbol, k -> new AdjacentGroup(k, nbr)).add();
xatoms.add(nbr);
Expand Down Expand Up @@ -762,9 +762,9 @@ else if (effectiveDegree(attach, allCrossingBonds) <= 1 &&
// reject if no bonds (<1), except if all symbols are identical... (HashSet.size==1)
// reject if more than 2 bonds
if (adjGroupMap.isEmpty() ||
newbonds.size() < 1 && !options.contains(Option.ALLOW_SINGLETON) ||
newbonds.size() > 1 && !options.contains(Option.AUTO_CONTRACT_LINKERS) ||
newbonds.size() > 2)
newbonds.size() < 1 && !options.contains(Option.ALLOW_SINGLETON) ||
newbonds.size() > 1 && !options.contains(Option.AUTO_CONTRACT_LINKERS) ||
newbonds.size() > 2)
continue;

if (isCC(attach, xbonds, adjGroupMap))
Expand All @@ -776,7 +776,7 @@ else if (effectiveDegree(attach, allCrossingBonds) <= 1 &&

// create the symbol
StringBuilder sb = new StringBuilder();
String prev = "{!no_match!}";
String prev = "{!no_match!}";

// We are going to reorder and select a possible prefix, so we
// work on a copy. Later we need to remove all the old Sgroups
Expand Down Expand Up @@ -822,7 +822,7 @@ else if (effectiveDegree(attach, allCrossingBonds) <= 1 &&
for (IAtom atom : xatoms)
newSgroup.addAtom(atom);

if (!splitsAtomSet(atomSets, newSgroup)) {
if (isAcceptableSet(atomSets, newSgroup)) {
// remove previous contractions
for (AdjacentGroup group : adjGroupsAll)
newSgroups.removeAll(group.sgroups);
Expand All @@ -837,7 +837,7 @@ else if (effectiveDegree(attach, allCrossingBonds) <= 1 &&
}

if (options.contains(Option.ALLOW_SINGLETON) &&
options.contains(Option.AUTO_CONTRACT_TERMINAL)) {
options.contains(Option.AUTO_CONTRACT_TERMINAL)) {

// recompute the adjacency and crossing bond info
sgroupAdjs = getSgroupAdjacency(allSgroups);
Expand All @@ -861,7 +861,7 @@ else if (effectiveDegree(attach, allCrossingBonds) <= 1 &&
for (IAtom atom : endAbbrs.get(0).getAtoms())
newSgroup.addAtom(atom);

if (!splitsAtomSet(atomSets, newSgroup)) {
if (isAcceptableSet(atomSets, newSgroup)) {
newSgroups.removeAll(begAbbrs);
newSgroups.removeAll(endAbbrs);
newSgroups.add(newSgroup);
Expand All @@ -886,7 +886,7 @@ else if (isTrivial(endLabel))
for (IAtom atom : endAbbrs.get(0).getAtoms())
newSgroup.addAtom(atom);

if (!splitsAtomSet(atomSets, newSgroup)) {
if (isAcceptableSet(atomSets, newSgroup)) {
newSgroups.removeAll(begAbbrs);
newSgroups.removeAll(endAbbrs);
newSgroups.add(newSgroup);
Expand All @@ -899,27 +899,23 @@ else if (isTrivial(endLabel))
}

/**
* Determine if a Sgroup splits a set of atoms the user has requested are
* kept together.
* Determine if a Sgroup is acceptable based on the provided atomsets. An
* Sgroup is acceptable if all atoms are in the same 'set' (as marked by
* the {@code atomSets} argument).
*
* @param atomSets the atom set indications, atom -> set_id
* @param sgroup the sgroup to test
* @param sgroup the sgroup to test
* @return the sgroup splits an atom set and should not be contracted
*/
private static boolean splitsAtomSet(Map<IAtom, Integer> atomSets, Sgroup sgroup) {
if (atomSets.isEmpty())
private static boolean isAcceptableSet(Map<IAtom, Integer> atomSets, Sgroup sgroup) {
if (sgroup == null)
return false;
if (atomSets.isEmpty())
return true;
Set<Integer> visitSets = new HashSet<>();

// if a crossing bond has atoms in the same group, then this new sgroup
// "splits" the set as part will be contracted and part will not
for (IBond bond : sgroup.getBonds())
if (atomSets.getOrDefault(bond.getBegin(), -1)
.equals(atomSets.getOrDefault(bond.getEnd(), -2)))
return true;
for (IAtom atom : sgroup.getAtoms())
visitSets.add(atomSets.getOrDefault(atom, -1));
return visitSets.size() != 1;
return visitSets.size() == 1;
}

private static boolean isNonMethylTerminalCarbon(IAtom nbr) {
Expand Down Expand Up @@ -981,15 +977,15 @@ private static boolean isCC(IAtom attach, Set<IBond> xbonds, Map<String, Adjacen
return attach.getAtomicNumber() == IAtom.C &&
nbrSymbols.size() == 1 &&
(nbrSymbols.values().iterator().next().symbol.equals("Me") ||
nbrSymbols.values().iterator().next().symbol.equals("CH"));
nbrSymbols.values().iterator().next().symbol.equals("CH"));
}

private int effectiveDegree(IAtom attach, Set<IBond> xbonds) {
int degree = 0;
for (IBond bond : attach.bonds()) {
IAtom nbor = bond.getOther(attach);
if (nbor.getBondCount() != 1 &&
!xbonds.contains(bond))
!xbonds.contains(bond))
degree++;
}
return degree;
Expand All @@ -1010,7 +1006,7 @@ private Sgroup getAbbr(IAtomContainer part) throws CDKException {
}
} else {
cansmi = usmigen.create(part);
label = disconnectedAbbreviations.get(cansmi);
label = disconnectedAbbreviations.get(cansmi);
if (label != null && !disabled.contains(label)) {
Sgroup sgroup = new Sgroup();
sgroup.setType(SgroupType.CtabAbbreviation);
Expand All @@ -1037,7 +1033,7 @@ private boolean containsChargeChar(String str) {
* Check if last char is a digit.
*/
private boolean digitAtEnd(String str) {
return Character.isDigit(str.charAt(str.length()-1));
return Character.isDigit(str.charAt(str.length() - 1));
}

private String newSymbol(int atomnum, int hcount, boolean prefix) {
Expand Down Expand Up @@ -1113,12 +1109,12 @@ public int apply(final IAtomContainer mol) {
* in/out of the contraction. If there are more atoms contracted than not
* it is not applied.
*
* @param mol molecule
* @param mol molecule
* @param atomSets atoms, keep these atoms together
* @return number of new abbreviations
* @see #generate(IAtomContainer, Map)
*/
public int apply(final IAtomContainer mol, final Map<IAtom,Integer> atomSets) {
public int apply(final IAtomContainer mol, final Map<IAtom, Integer> atomSets) {
List<Sgroup> newSgroups = generate(mol, atomSets);
List<Sgroup> sgroups = mol.getProperty(CDKConstants.CTAB_SGROUPS);

Expand Down Expand Up @@ -1149,10 +1145,11 @@ private static int countRingAtoms(IAtomContainer mol) {
private boolean shouldContract(Sgroup sgroup, int nAtoms, int nRingAtoms) {
if (sgroup.getBonds().isEmpty())
return true; // no crossing bonds, normally an agent etc
int nAbbrRingAtoms = 0;
int nAbbrRingAtoms = 0;
for (IAtom atom : sgroup.getAtoms()) {
if (atom.isInRing())
nAbbrRingAtoms++;;
nAbbrRingAtoms++;
;
}
int nOtherRingAtoms = nRingAtoms - nAbbrRingAtoms;
if (nAbbrRingAtoms != 0)
Expand Down
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