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Backmegre: #2422 - Indigo functions doesn't work prorerly: Aromatize, Dearomatize, Layout, Clean Up, Hydrogens, Auto-Mapping Tool #2548

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merged 7 commits into from
Oct 14, 2024
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Backmegre: #2422 - Indigo functions doesn't work prorerly: Aromatize, Dearomatize, Layout, Clean Up, Hydrogens, Auto-Mapping Tool #2548

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b589dc8
pathway operations
even1024 Oct 10, 2024
bfdd984
pathway operations
even1024 Oct 11, 2024
9f26510
pathway operations
even1024 Oct 11, 2024
d465d58
pathway operations
even1024 Oct 11, 2024
e0cebcd
pathway operations
even1024 Oct 11, 2024
8f9188e
Merge branch 'master' of github.com:epam/Indigo into 2422-pathway-ope…
even1024 Oct 11, 2024
79cfbe8
pathway operations
even1024 Oct 11, 2024
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10 changes: 8 additions & 2 deletions api/c/indigo/src/indigo_layout.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -108,6 +108,7 @@ CEXPORT int indigoLayout(int object)
if (rxn.isPathwayReaction())
{
PathwayLayout pl(static_cast<PathwayReaction&>(rxn), self.layout_options);
pl.setPreserveMoleculeLayout(false);
pl.make();
}
else
Expand Down Expand Up @@ -184,10 +185,15 @@ CEXPORT int indigoClean2d(int object)
if (IndigoBaseReaction::is(obj))
{
BaseReaction& rxn = obj.getBaseReaction();
for (int i = rxn.begin(); i < rxn.end(); i = rxn.next(i))
if (rxn.isPathwayReaction())
{
MoleculeCleaner2d::clean(rxn.getBaseMolecule(i));
auto& pwr = rxn.asPathwayReaction();
for (int i = 0; i < pwr.getMoleculeCount(); i++)
MoleculeCleaner2d::clean(pwr.getMolecule(i));
}
else
for (int i = rxn.begin(); i < rxn.end(); i = rxn.next(i))
MoleculeCleaner2d::clean(rxn.getBaseMolecule(i));
}
else
throw IndigoError("Clean2d can be executed only for molecules but %s was provided", obj.debugInfo());
Expand Down
122 changes: 94 additions & 28 deletions api/c/indigo/src/indigo_misc.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -507,24 +507,53 @@ CEXPORT int indigoUnfoldHydrogens(int item)
{
BaseReaction& rxn = obj.getBaseReaction();
bool has_coords = false;
bool only_selected = false;
for (int i = rxn.begin(); i != rxn.end(); i = rxn.next(i))
if (MoleculeHasCoords(rxn.getBaseMolecule(i)))
bool selected_only = false;
if (rxn.isPathwayReaction())
{
auto& pwr = rxn.asPathwayReaction();
for (int i = 0; i < pwr.getMoleculeCount(); ++i)
{
has_coords = true;
break;
if (MoleculeHasCoords(pwr.getMolecule(i)))
{
has_coords = true;
break;
}
}

for (int i = rxn.begin(); i != rxn.end(); i = rxn.next(i))
if (rxn.getBaseMolecule(i).countSelectedAtoms() > 0)
for (int i = 0; i < pwr.getMoleculeCount(); ++i)
{
only_selected = true;
break;
if (pwr.getMolecule(i).countSelectedAtoms() > 0)
{
selected_only = true;
break;
}
}

for (int i = rxn.begin(); i != rxn.end(); i = rxn.next(i))
for (int i = 0; i < pwr.getMoleculeCount(); ++i)
{
UnfoldAndLayoutHydrogens(pwr.getMolecule(i), selected_only, has_coords);
}
}
else
{
UnfoldAndLayoutHydrogens(rxn.getBaseMolecule(i), only_selected, has_coords);
for (int i = rxn.begin(); i != rxn.end(); i = rxn.next(i))
if (MoleculeHasCoords(rxn.getBaseMolecule(i)))
{
has_coords = true;
break;
}

for (int i = rxn.begin(); i != rxn.end(); i = rxn.next(i))
if (rxn.getBaseMolecule(i).countSelectedAtoms() > 0)
{
selected_only = true;
break;
}

for (int i = rxn.begin(); i != rxn.end(); i = rxn.next(i))
{
UnfoldAndLayoutHydrogens(rxn.getBaseMolecule(i), selected_only, has_coords);
}
}
}
else
Expand Down Expand Up @@ -566,18 +595,39 @@ CEXPORT int indigoFoldUnfoldHydrogens(int item)
else if (IndigoBaseReaction::is(obj))
{
BaseReaction& brxn = obj.getBaseReaction();
for (int i = brxn.begin(); i != brxn.end(); i = brxn.next(i))
if (brxn.getBaseMolecule(i).countSelectedAtoms() > 0)
{
selected_only = true;
break;
}
for (int i = brxn.begin(); i != brxn.end(); i = brxn.next(i))
if (hasConvertableToImplicitHydrogen(brxn.getBaseMolecule(i), selected_only))
if (brxn.isPathwayReaction())
{
auto& pwr = brxn.asPathwayReaction();
for (int i = 0; i < pwr.getMoleculeCount(); ++i)
{
fold = true;
break;
if (pwr.getMolecule(i).countSelectedAtoms() > 0)
{
selected_only = true;
break;
}
}
for (int i = 0; i < pwr.getMoleculeCount(); ++i)
if (hasConvertableToImplicitHydrogen(pwr.getMolecule(i), selected_only))
{
fold = true;
break;
}
}
else
{
for (int i = brxn.begin(); i != brxn.end(); i = brxn.next(i))
if (brxn.getBaseMolecule(i).countSelectedAtoms() > 0)
{
selected_only = true;
break;
}
for (int i = brxn.begin(); i != brxn.end(); i = brxn.next(i))
if (hasConvertableToImplicitHydrogen(brxn.getBaseMolecule(i), selected_only))
{
fold = true;
break;
}
}
}
else
{
Expand Down Expand Up @@ -634,18 +684,34 @@ CEXPORT int indigoFoldHydrogens(int item)
}
else if (IndigoBaseReaction::is(obj))
{
int i;
BaseReaction& rxn = obj.getBaseReaction();
bool selected_only = false;
for (i = rxn.begin(); i != rxn.end(); i = rxn.next(i))
if (rxn.getBaseMolecule(i).countSelectedAtoms() > 0)
if (rxn.isPathwayReaction())
{
auto& pwr = rxn.asPathwayReaction();
for (int i = 0; i < pwr.getMoleculeCount(); ++i)
{
selected_only = true;
break;
if (pwr.getMolecule(i).countSelectedAtoms() > 0)
{
selected_only = true;
break;
}
}
for (int i = 0; i < pwr.getMoleculeCount(); ++i)
_removeHydrogens(pwr.getMolecule(i), selected_only);
}
else
{
for (int i = rxn.begin(); i != rxn.end(); i = rxn.next(i))
if (rxn.getBaseMolecule(i).countSelectedAtoms() > 0)
{
selected_only = true;
break;
}

for (i = rxn.begin(); i != rxn.end(); i = rxn.next(i))
_removeHydrogens(rxn.getBaseMolecule(i), selected_only);
for (int i = rxn.begin(); i != rxn.end(); i = rxn.next(i))
_removeHydrogens(rxn.getBaseMolecule(i), selected_only);
}
}
else
throw IndigoError("indigoFoldHydrogens(): %s given", obj.debugInfo());
Expand Down
5 changes: 2 additions & 3 deletions api/c/indigo/src/indigo_savers.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -918,10 +918,9 @@ CEXPORT int indigoSaveCdx(int item, int output)
if (IndigoBaseReaction::is(obj))
{
ReactionCdxmlSaver saver(out, true);
if (obj.type == IndigoObject::REACTION)
if (obj.type == IndigoObject::REACTION || obj.type == IndigoObject::PATHWAY_REACTION)
{
Reaction& rxn = obj.getReaction();
saver.saveReaction(rxn);
saver.saveReaction(obj.getBaseReaction());
}
else if (obj.type == IndigoObject::QUERY_REACTION)
{
Expand Down
11 changes: 11 additions & 0 deletions api/tests/integration/ref/reaction/pathway_ops.py.out
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
*** PATHWAY AROMATIZE/DEAROMATIZE ***
pathway1.rdf:SUCCEED
pathway2.rdf:SUCCEED
pathway3.rdf:SUCCEED
pathway4.rdf:SUCCEED
pathway5.rdf:SUCCEED
pathway6.rdf:SUCCEED
pathway7.rdf:SUCCEED
pathway8.rdf:SUCCEED
pathway9.rdf:SUCCEED
pathway10.rdf:SUCCEED
87 changes: 42 additions & 45 deletions api/tests/integration/tests/formats/ref/pathway1.cdxml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,24 +24,24 @@
<n id="8" p="98.053192 -172.899597"/>
<n id="9" p="15.000010 -172.683609"/>
<n id="10" p="56.711403 -148.923965"/>
<b id="59" B="7" E="5" Order="2"/>
<b id="60" B="5" E="9"/>
<b id="61" B="9" E="10" Order="2"/>
<b id="62" B="10" E="8"/>
<b id="63" B="8" E="6" Order="2"/>
<b id="64" B="6" E="7"/>
<b id="58" B="7" E="5" Order="2"/>
<b id="59" B="5" E="9"/>
<b id="60" B="9" E="10" Order="2"/>
<b id="61" B="10" E="8"/>
<b id="62" B="8" E="6" Order="2"/>
<b id="63" B="6" E="7"/>
</fragment>
<fragment id="11">
<n id="12" p="56.526604 -73.923943"/>
<n id="13" p="80.545532 -0.000000"/>
<n id="14" p="95.391754 -45.421871"/>
<n id="15" p="32.512493 -0.000000"/>
<n id="16" p="17.661453 -45.421871"/>
<b id="65" B="12" E="16"/>
<b id="66" B="16" E="15" Order="2"/>
<b id="67" B="15" E="13"/>
<b id="68" B="13" E="14" Order="2"/>
<b id="69" B="14" E="12"/>
<b id="64" B="12" E="16"/>
<b id="65" B="16" E="15" Order="2"/>
<b id="66" B="15" E="13"/>
<b id="67" B="13" E="14" Order="2"/>
<b id="68" B="14" E="12"/>
</fragment>
<fragment id="17">
<n id="18" p="495.132690 -140.943573"/>
Expand All @@ -51,13 +51,13 @@
<n id="22" p="578.272705 -140.943573"/>
<n id="23" p="536.700317 -164.943359"/>
<n id="24" p="619.840393 -164.943359"/>
<b id="70" B="23" E="18"/>
<b id="71" B="18" E="19"/>
<b id="72" B="19" E="20"/>
<b id="73" B="20" E="21"/>
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<b id="75" B="22" E="23"/>
<b id="76" B="22" E="24"/>
<b id="69" B="23" E="18"/>
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<b id="71" B="19" E="20"/>
<b id="72" B="20" E="21"/>
<b id="73" B="21" E="22"/>
<b id="74" B="22" E="23"/>
<b id="75" B="22" E="24"/>
</fragment>
<fragment id="25">
<n id="26" p="552.919373 -496.768616"/>
Expand All @@ -67,13 +67,13 @@
<n id="30" p="514.053833 -468.266327"/>
<n id="31" p="552.919373 -544.768555"/>
<n id="32" p="600.919250 -544.768555"/>
<b id="77" B="26" E="30"/>
<b id="78" B="30" E="29" Order="2"/>
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<b id="80" B="27" E="28" Order="2"/>
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<b id="77" B="30" E="29" Order="2"/>
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<b id="80" B="28" E="26"/>
<b id="81" B="26" E="31" Order="2"/>
<b id="82" B="31" E="32"/>
</fragment>
<fragment id="33">
<n id="34" p="528.083740 -318.203552"/>
Expand All @@ -84,14 +84,14 @@
<n id="39" p="612.449646 -250.623489"/>
<n id="40" p="565.711426 -239.943359"/>
<n id="41" p="481.719940 -330.626129"/>
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</fragment>
<fragment id="42">
<n id="43" p="1058.488403 -341.341309"/>
Expand All @@ -103,18 +103,15 @@
<n id="49" p="1016.919678 -269.104889"/>
<n id="50" p="1066.259766 -235.403503"/>
<n id="51" p="1175.485596 -259.379883"/>
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</fragment>
<scheme>
<step ReactionStepReactants="4 11 17" ReactionStepProducts="25" ReactionStepArrows="58"/>
</scheme>
</page>
</CDXML>
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