Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

#2747 Incorrect substituent position #2773

Merged
merged 5 commits into from
Mar 6, 2025
Merged

#2747 Incorrect substituent position #2773

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
0eb1d3e
epam#2747 set position of node to its parent node
jblack-mestre Feb 4, 2025
399d3ff
#2747 remove wrong code
jblack-mestre Feb 12, 2025
a92dd60
assign superatom coordinates based on parent node coordinates
jblack-mestre Feb 17, 2025
cd99644
epam#2747 add regression test
jblack-mestre Feb 17, 2025
9ac5c54
Merge branch 'master' into 2747_substituent_position
jblack-mestre Mar 4, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions api/tests/integration/ref/rendering/render_reactions.py.out
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,3 +17,5 @@ issue 2513 elliptical-arc-arrow render error
issue_2513.png rendering status: OK
issue 2741 missing stereochemistry
missing_stereochemistry_2741.png rendering status: OK
issue 2747 incorrect substituent position
incorrect_substituent_position_2747.png rendering status: OK
149 changes: 149 additions & 0 deletions api/tests/integration/tests/rendering/reactions/incorrect_substituent_position_2747.cdxml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,149 @@
<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE CDXML SYSTEM "https://static.chemistry.revvitycloud.com/cdxml/CDXML.dtd" >
<CDXML CreationProgram="ChemDraw 23.1.1.3" Name="incorrect_substituent_position_2747.cdxml" BoundingBox="22.14 17.56 470.71 283.26" WindowPosition="0 0" WindowSize="-2147483648 0" WindowIsZoomed="yes" FractionalWidths="yes" InterpretChemically="yes" ShowAtomQuery="yes" ShowAtomStereo="no" ShowAtomEnhancedStereo="yes" ShowAtomNumber="no" ShowResidueID="no" ShowBondQuery="yes" ShowBondRxn="yes" ShowBondStereo="no" ShowTerminalCarbonLabels="no" ShowNonTerminalCarbonLabels="no" HideImplicitHydrogens="no" Magnification="1333" LabelFont="3" LabelSize="10" LabelFace="96" CaptionFont="20" CaptionSize="10" HashSpacing="2.50" MarginWidth="1.60" LineWidth="0.60" BoldWidth="2" BondLength="14.40" BondSpacing="18" ChainAngle="120" LabelJustification="Auto" CaptionJustification="Left" AminoAcidTermini="HOH" ShowSequenceTermini="yes" ShowSequenceBonds="yes" ShowSequenceUnlinkedBranches="no" ResidueWrapCount="40" ResidueBlockCount="10" PrintMargins="36 36 36 36" MacPrintInfo="0003000001200120000000000B6608A0FF84FF880BE309180367052703FC0002000001200120000000000B6608A0000100000064000000010001010100000001270F000100010000000000000000000000000002001901900000000000600000000000000000000100000000000000000000000000000000" ChemPropName="" ChemPropFormula="Chemical Formula: " ChemPropExactMass="Exact Mass: " ChemPropMolWt="Molecular Weight: " ChemPropMOverZ="m/z: " ChemPropAnalysis="Elemental Analysis: " ChemPropBoilingPt="Boiling Point: " ChemPropMeltingPt="Melting Point: " ChemPropCritTemp="Critical Temp: " ChemPropCritPres="Critical Pres: " ChemPropCritVol="Critical Vol: " ChemPropGibbs="Gibbs Energy: " ChemPropLogP="Log P: " ChemPropMR="MR: " ChemPropHenry="Henry&apos;s Law: " ChemPropEForm="Heat of Form: " ChemProptPSA="tPSA: " ChemPropCLogP="CLogP: " ChemPropCMR="CMR: " ChemPropLogS="LogS: " ChemPropPKa="pKa: " ChemPropID="" ChemPropFragmentLabel="" color="0" bgcolor="1" RxnAutonumberStart="1" RxnAutonumberConditions="no" RxnAutonumberStyle="Roman" RxnAutonumberFormat="(#)">
<colortable>
<color r="1" g="1" b="1"/>
<color r="0" g="0" b="0"/>
</colortable>
<fonttable>
<font id="3" charset="iso-8859-1" name="Arial"/>
<font id="20" charset="iso-8859-1" name="Times New Roman"/>
</fonttable>
<page id="895" BoundingBox="0 0 3780 2159.25" HeaderPosition="36" FooterPosition="36" PrintTrimMarks="yes" HeightPages="3" WidthPages="7">
<fragment id="3" BoundingBox="22.14 17.56 202.59 283.26" Z="97">
<n id="4" p="96.36 201.38" Z="98" AS="N" AtomID="1"/>
<n id="5" p="61.06 221.75" Z="99" Element="7" NumHydrogens="0" NeedsClean="yes" AS="N" AtomID="2">
<t p="57.45 225.65" BoundingBox="57.45 217.31 64.67 225.65" LabelJustification="Left">
<s font="3" size="10" color="0" face="96">N</s>
</t>
</n>
<n id="6" p="25.75 201.38" Z="100" AS="N" AtomID="3"/>
<n id="7" p="25.75 160.61" Z="101" Element="7" NumHydrogens="0" NeedsClean="yes" AS="N" AtomID="4">
<t p="22.14 164.51" BoundingBox="22.14 156.17 29.36 164.51" LabelJustification="Left">
<s font="3" size="10" color="0" face="96">N</s>
</t>
</n>
<n id="8" p="61.06 140.22" Z="102" AS="N" AtomID="5"/>
<n id="9" p="96.36 160.61" Z="103" AS="N" AtomID="6"/>
<n id="10" p="131.67 221.75" Z="104" AS="N" AtomID="7"/>
<n id="11" p="166.98 201.38" Z="105" AS="N" AtomID="8"/>
<n id="12" p="202.29 221.75" Z="106" AS="N" AtomID="9"/>
<n id="13" p="202.29 262.53" Z="107" AS="N" AtomID="10"/>
<n id="14" p="166.98 282.91" Z="108" AS="N" AtomID="11"/>
<n id="15" p="131.67 262.53" Z="109" AS="N" AtomID="12"/>
<n id="16" p="61.06 99.45" Z="110" AS="N" AtomID="13"/>
<n id="17" p="25.75 79.06" Z="111" AS="N" AtomID="14"/>
<n id="18" p="25.75 38.30" Z="112" AS="N" AtomID="15"/>
<n id="19" p="61.06 17.91" Z="113" AS="N" AtomID="16"/>
<n id="20" p="96.36 38.30" Z="114" AS="N" AtomID="17"/>
<n id="21" p="96.36 79.06" Z="115" AS="N" AtomID="18"/>
<n id="22" p="131.67 140.22" Z="116" NodeType="Fragment" AS="N" AtomID="19">
<fragment id="896">
<n id="24" p="153.81 1284.85" Z="117"/>
<n id="25" p="171.49 1295.06" Z="118" NodeType="ExternalConnectionPoint" ExternalConnectionNum="1"/>
<n id="27" p="118.56 1299.63" Z="119" Element="7" NumHydrogens="0" NeedsClean="yes">
<t p="92.81 -994.91" BoundingBox="92.81 -1003.26 100.03 -994.91" LabelJustification="Left">
<s font="3" size="10" color="0" face="96">N</s>
</t>
</n>
<b id="26" Z="120" B="25" E="24"/>
<b id="28" Z="121" B="24" E="27" Order="3"/>
</fragment>
<t p="123.01 149.67" BoundingBox="123.01 129.37 157.67 149.97" LabelJustification="Left" LabelAlignment="Left">
<s font="3" size="24">CN</s>
</t>
</n>
<b id="107" Z="122" B="4" E="5" Order="2" BS="N" BondCircularOrdering="113 112 108 0"/>
<b id="108" Z="123" B="5" E="6" BS="N"/>
<b id="109" Z="124" B="6" E="7" Order="2" BS="N" BondCircularOrdering="0 108 110 0"/>
<b id="110" Z="125" B="7" E="8" BS="N"/>
<b id="111" Z="126" B="8" E="9" Order="2" BS="N" BondCircularOrdering="120 110 112 29"/>
<b id="112" Z="127" B="9" E="4" BS="N"/>
<b id="113" Z="128" B="4" E="10" BS="N"/>
<b id="114" Z="129" B="10" E="11" Order="2" BS="N" BondCircularOrdering="113 119 115 0"/>
<b id="115" Z="130" B="11" E="12" BS="N"/>
<b id="116" Z="131" B="12" E="13" Order="2" BS="N" BondCircularOrdering="0 115 117 0"/>
<b id="117" Z="132" B="13" E="14" BS="N"/>
<b id="118" Z="133" B="14" E="15" Order="2" BS="N" BondCircularOrdering="0 117 119 0"/>
<b id="119" Z="134" B="15" E="10" BS="N"/>
<b id="120" Z="135" B="8" E="16" BS="N"/>
<b id="121" Z="136" B="16" E="17" Order="2" BS="N" BondCircularOrdering="120 126 122 0"/>
<b id="122" Z="137" B="17" E="18" BS="N"/>
<b id="123" Z="138" B="18" E="19" Order="2" BS="N" BondCircularOrdering="0 122 124 0"/>
<b id="124" Z="139" B="19" E="20" BS="N"/>
<b id="125" Z="140" B="20" E="21" Order="2" BS="N" BondCircularOrdering="0 124 126 0"/>
<b id="126" Z="141" B="21" E="16" BS="N"/>
<b id="29" Z="142" B="9" E="22" BS="N"/>
</fragment>
<fragment id="217" BoundingBox="289.87 17.74 470.71 283.07" Z="144">
<n id="218" p="364.28 201.38" Z="145" AS="N" AtomID="20"/>
<n id="219" p="328.98 221.75" Z="146" Element="7" NumHydrogens="0" NeedsClean="yes" AS="N" AtomID="21">
<t p="325.37 225.65" BoundingBox="325.37 217.31 332.59 225.65" LabelJustification="Left">
<s font="3" size="10" color="0" face="96">N</s>
</t>
</n>
<n id="220" p="293.69 201.74" Z="147" AS="N" AtomID="22"/>
<n id="221" p="293.48 160.98" Z="148" Element="7" NumHydrogens="0" NeedsClean="yes" AS="N" AtomID="23">
<t p="289.87 164.88" BoundingBox="289.87 156.54 297.09 164.88" LabelJustification="Left">
<s font="3" size="10" color="0" face="96">N</s>
</t>
</n>
<n id="222" p="328.67 140.40" Z="149" AS="N" AtomID="24"/>
<n id="223" p="364.05 160.61" Z="150" AS="N" AtomID="25"/>
<n id="224" p="399.58 221.77" Z="151" AS="N" AtomID="26"/>
<n id="225" p="434.89 201.38" Z="152" AS="N" AtomID="27"/>
<n id="226" p="470.18 221.37" Z="153" AS="N" AtomID="28"/>
<n id="227" p="470.41 262.14" Z="154" AS="N" AtomID="29"/>
<n id="228" p="435.22 282.72" Z="155" AS="N" AtomID="30"/>
<n id="229" p="399.81 262.52" Z="156" AS="N" AtomID="31"/>
<n id="230" p="328.67 99.64" Z="157" AS="N" AtomID="32"/>
<n id="231" p="293.36 79.25" Z="158" AS="N" AtomID="33"/>
<n id="232" p="293.07 38.67" Z="159" AS="N" AtomID="34"/>
<n id="233" p="328.27 18.09" Z="160" AS="N" AtomID="35"/>
<n id="234" p="363.64 38.31" Z="161" AS="N" AtomID="36"/>
<n id="235" p="363.85 79.08" Z="162" AS="N" AtomID="37"/>
<n id="236" p="399.37 140.22" Z="163" NodeType="Fragment" AS="N" AtomID="38">
<fragment id="897">
<n id="238" p="1334.90 -544.58" Z="164"/>
<n id="239" p="1353.59 -536.33" Z="165" NodeType="ExternalConnectionPoint" ExternalConnectionNum="1"/>
<n id="240" p="1297.68 -561" Z="166" Element="7" NumHydrogens="0" NeedsClean="yes">
<t p="1294.07 -557.10" BoundingBox="1294.07 -565.45 1301.29 -557.10" LabelJustification="Left">
<s font="3" size="10" color="0" face="96">N</s>
</t>
</n>
<b id="241" Z="167" B="239" E="238"/>
<b id="242" Z="168" B="238" E="240" Order="3"/>
</fragment>
<t p="390.70 149.67" BoundingBox="390.70 129.37 425.37 149.97" LabelJustification="Left" LabelAlignment="Left">
<s font="3" size="24">CN</s>
</t>
</n>
<b id="297" Z="169" B="218" E="219" Order="2" BS="N" BondCircularOrdering="303 302 298 0"/>
<b id="298" Z="170" B="219" E="220" BS="N"/>
<b id="299" Z="171" B="220" E="221" Order="2" BS="N" BondCircularOrdering="0 298 300 0"/>
<b id="300" Z="172" B="221" E="222" BS="N"/>
<b id="301" Z="173" B="222" E="223" Order="2" BS="N" BondCircularOrdering="310 300 302 317"/>
<b id="302" Z="174" B="223" E="218" BS="N"/>
<b id="303" Z="175" B="218" E="224" BS="N"/>
<b id="304" Z="176" B="224" E="225" Order="2" BS="N" BondCircularOrdering="303 309 305 0"/>
<b id="305" Z="177" B="225" E="226" BS="N"/>
<b id="306" Z="178" B="226" E="227" Order="2" BS="N" BondCircularOrdering="0 305 307 0"/>
<b id="307" Z="179" B="227" E="228" BS="N"/>
<b id="308" Z="180" B="228" E="229" Order="2" BS="N" BondCircularOrdering="0 307 309 0"/>
<b id="309" Z="181" B="229" E="224" BS="N"/>
<b id="310" Z="182" B="222" E="230" BS="N"/>
<b id="311" Z="183" B="230" E="231" Order="2" BS="N" BondCircularOrdering="310 316 312 0"/>
<b id="312" Z="184" B="231" E="232" BS="N"/>
<b id="313" Z="185" B="232" E="233" Order="2" BS="N" BondCircularOrdering="0 312 314 0"/>
<b id="314" Z="186" B="233" E="234" BS="N"/>
<b id="315" Z="187" B="234" E="235" Order="2" BS="N" BondCircularOrdering="0 314 316 0"/>
<b id="316" Z="188" B="235" E="230" BS="N"/>
<b id="317" Z="189" B="223" E="236" BS="N"/>
</fragment>
<graphic id="893" SupersededBy="898" BoundingBox="266.95 150.41 224.12 150.41" Z="143" GraphicType="Line" ArrowType="FullHead" HeadSize="1000"/>
<scheme id="899">
<step id="900" ReactionStepReactants="3" ReactionStepProducts="217" ReactionStepArrows="893"/>
</scheme>
<arrow id="898" BoundingBox="224.12 147.91 266.95 151.91" Z="143" FillType="None" ArrowheadHead="Full" ArrowheadType="Solid" HeadSize="1000" ArrowheadCenterSize="875" ArrowheadWidth="250" Head3D="266.95 150.41 0" Tail3D="224.12 150.41 0" Center3D="428.87 238.91 0" MajorAxisEnd3D="455.75 238.91 0" MinorAxisEnd3D="428.87 265.80 0"/>
</page>
</CDXML>
Binary file added ...s/integration/tests/rendering/ref/linux/incorrect_substituent_position_2747.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added ...sts/integration/tests/rendering/ref/mac/incorrect_substituent_position_2747.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added ...sts/integration/tests/rendering/ref/win/incorrect_substituent_position_2747.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
10 changes: 10 additions & 0 deletions api/tests/integration/tests/rendering/render_reactions.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -127,6 +127,16 @@ def renderRxnfile(filename, outfile):
renderer.renderToFile(rxn, joinPathPy("out/" + png_fname, __file__))
print(checkImageSimilarity(png_fname))

print("issue 2747 incorrect substituent position")
indigo.resetOptions()
indigo.setOption("render-output-format", "png")
fname = "incorrect_substituent_position_2747"
png_fname = fname + ".png"
cdxml_fname = joinPathPy("reactions/%s.cdxml" % fname, __file__)
rxn = indigo.loadReactionFromFile(cdxml_fname)
renderer.renderToFile(rxn, joinPathPy("out/" + png_fname, __file__))
print(checkImageSimilarity(png_fname))

if isIronPython():
renderer.Dispose()
indigo.Dispose()
1 change: 1 addition & 0 deletions core/indigo-core/molecule/molecule_cdxml_loader.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -174,6 +174,7 @@ namespace indigo
int repeat_pattern;
std::string label;
bool is_superatom;
Vec3f superatom_position;
};

struct CdxmlText
Expand Down
2 changes: 2 additions & 0 deletions core/indigo-core/molecule/molecule_sgroups.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -195,6 +195,8 @@ namespace indigo
};
Array<_BondConnection> bond_connections; // SBV in Molfile format

Vec3f display_position;

private:
Superatom(const Superatom&);
};
Expand Down
1 change: 1 addition & 0 deletions core/indigo-core/molecule/src/base_molecule.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -227,6 +227,7 @@ void BaseMolecule::mergeSGroupsWithSubmolecule(BaseMolecule& mol, Array<int>& ma
ap.apid.copy(supersa.attachment_points[j].apid);
}
}
sa.display_position.copy(supersa.display_position);
}
else if (sg.sgroup_type == SGroup::SG_TYPE_SRU)
{
Expand Down
6 changes: 6 additions & 0 deletions core/indigo-core/molecule/src/molecule_cdxml_loader.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -721,6 +721,11 @@ void MoleculeCdxmlLoader::_parseCDXMLElements(BaseCDXElement& first_elem, bool n
}
}
this->_parseLabel(elem, bracket.label);
if (fragment_start_idx - 1 > 0 && fragment_start_idx - 1 < static_cast<int>(nodes.size()))
{
auto parentNode = this->nodes[fragment_start_idx - 1];
bracket.superatom_position.copy(parentNode.pos);
}
this->brackets.push_back(bracket);
}
else
Expand Down Expand Up @@ -1000,6 +1005,7 @@ void MoleculeCdxmlLoader::_addBracket(BaseMolecule& mol, const CdxmlBracket& bra
Superatom& sa = (Superatom&)sgroup;
sa.contracted = DisplayOption::Contracted;
sa.subscript.readString(bracket.label.c_str(), true);
sa.display_position.copy(bracket.superatom_position);
}
else
switch (bracket.usage)
Expand Down
1 change: 1 addition & 0 deletions core/indigo-core/molecule/src/molecule_sgroups.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -105,6 +105,7 @@ Superatom::Superatom() : unresolved(false)
seqid = -1;
attachment_points.clear();
bond_connections.clear();
display_position.clear();
}

Superatom::~Superatom()
Expand Down
43 changes: 31 additions & 12 deletions core/render2d/src/render_internal.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -823,13 +823,23 @@ void MoleculeRenderInternal::_prepareSGroups(bool collapseAtLeastOneSuperatom)
if (sgroup.sgroup_type == SGroup::SG_TYPE_SUP)
{
const Superatom& group = (Superatom&)sgroup;
Vec3f displayPosition = group.display_position;
bool useDisplayPosition = false;
if (fabs(displayPosition.x) > EPSILON || fabs(displayPosition.y) > EPSILON || fabs(displayPosition.z) > EPSILON)
{
useDisplayPosition = true;
}

Vec3f centre;
for (int j = 0; j < group.atoms.size(); ++j)
if (!useDisplayPosition)
{
int atomID = group.atoms[j];
centre.add(mol.getAtomXyz(atomID));
for (int j = 0; j < group.atoms.size(); ++j)
{
int atomID = group.atoms[j];
centre.add(mol.getAtomXyz(atomID));
}
centre.scale(1.0f / group.atoms.size());
}
centre.scale(1.0f / group.atoms.size());
int superAtomID = -1;

if (mol.isQueryMolecule())
Expand All @@ -854,15 +864,16 @@ void MoleculeRenderInternal::_prepareSGroups(bool collapseAtLeastOneSuperatom)
{
int atomID = group.atoms[0];
const Vertex& v = mol.getVertex(atomID);
bool posCounted = false;
for (int j = v.neiBegin(); j < v.neiEnd(); j = v.neiNext(j))
{
int neighboringAtomID = v.neiVertex(j);
if (!groupAtoms.find(neighboringAtomID))
{
pos.add(mol.getAtomXyz(atomID));
posCounted = true;
posCnt++;
if (!useDisplayPosition)
{
pos.add(mol.getAtomXyz(atomID));
posCnt++;
}
int neighboringBondID = v.neiEdge(j), bondID = -1;
if (mol.findEdgeIndex(neighboringAtomID, superAtomID) < 0)
{
Expand Down Expand Up @@ -890,15 +901,23 @@ void MoleculeRenderInternal::_prepareSGroups(bool collapseAtLeastOneSuperatom)
}
mol.removeAtom(atomID);
}
if (posCnt == 0)

if (useDisplayPosition)
{
pos.copy(centre);
mol.setAtomXyz(superAtomID, displayPosition.x, displayPosition.y, displayPosition.z);
}
else
{
pos.scale(1.f / posCnt);
if (posCnt == 0)
{
pos.copy(centre);
}
else
{
pos.scale(1.f / posCnt);
}
mol.setAtomXyz(superAtomID, pos.x, pos.y, pos.z);
}
mol.setAtomXyz(superAtomID, pos.x, pos.y, pos.z);
}
}
}
Expand Down
Loading