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#1944-Fullerene and 3D molecules are not represented as 3D in the Miew 3D window #1971

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#1944-Fullerene and 3D molecules are not represented as 3D in the Miew 3D window #1971

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a3acf90
Implemented "xyz" CDXML tag into cdx/cdxml loader and saver.
NayanaGadakh May 27, 2024
362e00d
Resolve reformatting error.
NayanaGadakh May 27, 2024
259f3c2
Added test case for cdxml to mol conversion
NayanaGadakh May 29, 2024
05301c0
Added cdxml to ket test case.
NayanaGadakh May 29, 2024
5cd9a80
Updated output file.
NayanaGadakh May 29, 2024
f06227f
Updated out file
NayanaGadakh May 29, 2024
b677d0e
Updated Reaction outputs.
NayanaGadakh May 30, 2024
dd45ddb
No need of z coord at other places.
NayanaGadakh May 30, 2024
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44 changes: 44 additions & 0 deletions api/tests/integration/ref/formats/mol_to_cdxml.py.out
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Original file line number Diff line number Diff line change
@@ -1,4 +1,48 @@
*** Mol to CDXML ***
1944-3D_Structure.mol
1944-3D_Structure.mol
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE CDXML SYSTEM "http://www.cambridgesoft.com/xml/cdxml.dtd">
<CDXML BondLength="30.000000" LabelFont="3" CaptionFont="4">
<fonttable id="1">
<font id="2" charset="utf-8" name="Arial"/>
<font id="3" charset="utf-8" name="Times New Roman"/>
</fonttable>
<colortable>
<color r="1" g="1" b="1"/>
<color r="0" g="0" b="0"/>
<color r="1" g="0" b="0"/>
<color r="1" g="1" b="0"/>
<color r="0" g="1" b="0"/>
<color r="0" g="1" b="1"/>
<color r="0" g="0" b="1"/>
<color r="1" g="0" b="1"/>
<color r="0.5" g="0.5" b="0.5"/>
</colortable>
<page HeightPages="1" WidthPages="1">
<fragment id="4"/>
<altgroup id="5" Valence="0">
<fragment id="6">
<n id="7" p="168.228012 294.662994" xyz="4.607600 -8.822100 -9.662200"/>
<n id="8" p="202.376999 290.210999" xyz="5.745900 -8.673700 -11.579500"/>
<n id="9" p="186.375000 273.207001" xyz="5.212500 -8.106900 -10.552700"/>
<n id="10" p="200.292007 328.707001" xyz="5.676400 -9.956900 -11.719600"/>
<n id="11" p="166.134003 333.312012" xyz="4.537800 -10.110400 -9.802900"/>
<n id="12" p="182.252991 350.123993" xyz="5.075100 -10.670800 -10.835100"/>
<b id="13" B="9" E="7" Order="2"/>
<b id="14" B="10" E="8" Order="2"/>
<b id="15" B="7" E="11"/>
<b id="16" B="8" E="9"/>
<b id="17" B="11" E="12" Order="2"/>
<b id="18" B="12" E="10"/>
</fragment>
<t p="166.134003 273.207001" InterpretChemically="no">
<s font="3" size="10" face="96">R20</s>
</t>
</altgroup>
</page>
</CDXML>

enhanced_stereo1.mol
enhanced_stereo1.mol
<?xml version="1.0" encoding="UTF-8"?>
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1 change: 1 addition & 0 deletions api/tests/integration/tests/formats/mol_to_cdxml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@

root = joinPathPy("molecules/", __file__)
files = [
"1944-3D_Structure.mol",
"stereo_either-0020.mol",
"enhanced_stereo1.mol",
"enhanced_stereo2.mol",
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31 changes: 31 additions & 0 deletions api/tests/integration/tests/formats/molecules/1944-3D_Structure.mol
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Original file line number Diff line number Diff line change
@@ -0,0 +1,31 @@
$MDL REV 1
$MOL
$HDR
null


$END HDR
$CTAB
0 0 0 0 0 0 0 0 0 0999 V2000
M END
$END CTAB
$RGP
20
$CTAB
6 6 0 0 0 0 0 0 0 0999 V2000
4.6076 -8.8221 -9.6622 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7459 -8.6737 -11.5795 C 0 0 0 0 0 0 0 0 0 0 0 0
5.2125 -8.1069 -10.5527 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6764 -9.9569 -11.7196 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5378 -10.1104 -9.8029 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0751 -10.6708 -10.8351 C 0 0 0 0 0 0 0 0 0 0 0 0
3 1 2 0 0 0
4 2 2 0 0 0
1 5 1 0 0 0
2 3 1 0 0 0
5 6 2 0 0 0
6 4 1 0 0 0
M END
$END CTAB
$END RGP
$END MOL
1 change: 1 addition & 0 deletions core/indigo-core/molecule/src/molecule_cdxml_loader.cpp
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@even1024 even1024 May 27, 2024 •
edited
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This field should be added to parseNode, not to parseText. You don't have cdxml to mol test which would reveal the issue.

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In parseNode, both p and xyz are already present. {"p", pos_lambda},{"xyz", pos_lambda},
I have made changes in parsePos to handle z coord.

Original file line number Diff line number Diff line change
Expand Up @@ -1543,6 +1543,7 @@ void MoleculeCdxmlLoader::_parseText(BaseCDXElement& elem, std::vector<std::pair
auto label_justification_alignment_lambda = [&label_alignment, this](const std::string& data) { label_alignment = data; };

std::unordered_map<std::string, std::function<void(const std::string&)>> text_dispatcher = {{"p", text_coordinates_lambda},
{"xyz", text_coordinates_lambda},
{"BoundingBox", text_bbox_lambda},
{"LabelJustification", label_justification_lambda},
{"LabelAlignment", label_justification_alignment_lambda}};
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50 changes: 50 additions & 0 deletions core/indigo-core/molecule/src/molecule_cdxml_saver.cpp
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6 copy-pastes?

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Removed unnecessary copies where z coord is not required.

Original file line number Diff line number Diff line change
Expand Up @@ -544,6 +544,8 @@ void MoleculeCdxmlSaver::addNodeToFragment(BaseMolecule& mol, XMLElement* fragme
Vec3f pos3 = mol.getAtomXyz(atom_idx);
Vec2f pos(pos3.x, pos3.y);

bool have_z = BaseMolecule::hasZCoord(mol);

pos.add(offset);
if (atom_idx == mol.vertexBegin())
min_coord = max_coord = pos;
Expand Down Expand Up @@ -680,6 +682,14 @@ void MoleculeCdxmlSaver::addNodeToFragment(BaseMolecule& mol, XMLElement* fragme
out.printf("%f %f", pos.x, -pos.y);
buf.push(0);
node->SetAttribute("p", buf.ptr());
if (have_z)
{
QS_DEF(Array<char>, _buf);
ArrayOutput _out(_buf);
_out.printf("%f %f %f", pos3.x, pos3.y, pos3.z);
_buf.push(0);
node->SetAttribute("xyz", _buf.ptr());
}
}

int enh_stereo_type = mol.stereocenters.getType(atom_idx);
Expand Down Expand Up @@ -731,6 +741,14 @@ void MoleculeCdxmlSaver::addNodeToFragment(BaseMolecule& mol, XMLElement* fragme
out.printf("%f %f", pos.x, -pos.y);
buf.push(0);
t->SetAttribute("p", buf.ptr());
if (have_z)
{
QS_DEF(Array<char>, _buf);
ArrayOutput _out(_buf);
_out.printf("%f %f %f", pos3.x, pos3.y, pos3.z);
_buf.push(0);
node->SetAttribute("xyz", _buf.ptr());
}
t->SetAttribute("Justification", "Center");

XMLElement* s = _doc->NewElement("s");
Expand All @@ -752,6 +770,14 @@ void MoleculeCdxmlSaver::addNodeToFragment(BaseMolecule& mol, XMLElement* fragme
out.printf("%f %f", pos.x, -pos.y);
buf.push(0);
t->SetAttribute("p", buf.ptr());
if (have_z)
{
QS_DEF(Array<char>, _buf);
ArrayOutput _out(_buf);
_out.printf("%f %f %f", pos3.x, pos3.y, pos3.z);
_buf.push(0);
node->SetAttribute("xyz", _buf.ptr());
}
t->SetAttribute("LabelJustification", "Left");

XMLElement* s = _doc->NewElement("s");
Expand Down Expand Up @@ -789,6 +815,14 @@ void MoleculeCdxmlSaver::addNodeToFragment(BaseMolecule& mol, XMLElement* fragme
out.printf("%f %f", pos.x, -pos.y);
buf.push(0);
t->SetAttribute("p", buf.ptr());
if (have_z)
{
QS_DEF(Array<char>, _buf);
ArrayOutput _out(_buf);
_out.printf("%f %f %f", pos3.x, pos3.y, pos3.z);
_buf.push(0);
node->SetAttribute("xyz", _buf.ptr());
}
t->SetAttribute("LabelJustification", "Left");

XMLElement* s = _doc->NewElement("s");
Expand Down Expand Up @@ -825,6 +859,14 @@ void MoleculeCdxmlSaver::addNodeToFragment(BaseMolecule& mol, XMLElement* fragme
out.printf("%f %f", pos.x, -pos.y);
buf.push(0);
t->SetAttribute("p", buf.ptr());
if (have_z)
{
QS_DEF(Array<char>, _buf);
ArrayOutput _out(_buf);
_out.printf("%f %f %f", pos3.x, pos3.y, pos3.z);
_buf.push(0);
node->SetAttribute("xyz", _buf.ptr());
}
t->SetAttribute("LabelJustification", "Left");

XMLElement* s = _doc->NewElement("s");
Expand Down Expand Up @@ -868,6 +910,14 @@ void MoleculeCdxmlSaver::addNodeToFragment(BaseMolecule& mol, XMLElement* fragme
out.printf("%f %f", pos.x, -pos.y);
buf.push(0);
t->SetAttribute("p", buf.ptr());
if (have_z)
{
QS_DEF(Array<char>, _buf);
ArrayOutput _out(_buf);
_out.printf("%f %f %f", pos3.x, pos3.y, pos3.z);
_buf.push(0);
node->SetAttribute("xyz", _buf.ptr());
}
t->SetAttribute("LabelJustification", "Left");

XMLElement* s = _doc->NewElement("s");
Expand Down
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