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#2519 - The length of the arrow becomes 2 bonds after layout but sho…
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…uld be 1 (#2587)

Co-authored-by: Aliakasndr Dziarkach <Aliakasndr.Dziarkach@gmail.com>
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AliaksandrDziarkach and Aliakasndr Dziarkach authored Oct 29, 2024
1 parent 3733529 commit cbc50b4
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Showing 12 changed files with 116 additions and 199 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@
"z": 0.0
},
{
"x": 8.371282,
"x": 6.771282,
"y": 0.0,
"z": 0.0
}
Expand Down Expand Up @@ -93,23 +93,23 @@
{
"label": "O",
"location": [
9.971282,
8.371282,
0.4,
0.0
]
},
{
"label": "C",
"location": [
11.356922,
9.756922,
-0.4,
0.0
]
},
{
"label": "O",
"location": [
12.742563,
11.142563,
0.4,
0.0
]
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
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
110 changes: 55 additions & 55 deletions api/tests/integration/tests/formats/ref/ket_retro_arrow.cdxml
Original file line number Diff line number Diff line change
@@ -1,55 +1,55 @@
<?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">
<n id="5" p="65.569229 36.000000"/>
<n id="6" p="65.569229 -12.000000"/>
<n id="7" p="24.000000 -36.000000"/>
<n id="8" Element="7" NumHydrogens="2" p="107.138428 -36.000000">
<t p="107.138428 -36.000000" LabelJustification="Left">
<s font="3" size="10" face="96">NH</s>
<s font="3" size="10" face="32">2</s>
</t>
</n>
<b id="16" B="5" E="6"/>
<b id="17" B="6" E="7"/>
<b id="18" B="6" E="8"/>
</fragment>
<fragment id="9">
<n id="10" Element="8" NumHydrogens="1" p="299.138458 -12.000000">
<t p="299.138458 -12.000000" LabelJustification="Left">
<s font="3" size="10" face="96">OH</s>
</t>
</n>
<n id="11" p="340.707672 12.000000"/>
<n id="12" Element="8" NumHydrogens="1" p="382.276886 -12.000000">
<t p="382.276886 -12.000000" LabelJustification="Left">
<s font="3" size="10" face="96">OH</s>
</t>
</n>
<b id="19" B="10" E="11"/>
<b id="20" B="11" E="12"/>
</fragment>
<arrow id="13" BoundingBox="251.138443 -0.000000 155.138428 -0.000000" FillType="None" ArrowheadHead="Full" ArrowheadType="Angle" HeadSize="600" ArrowheadCenterSize="600" ArrowheadWidth="150" ArrowShaftSpacing="600" Head3D="251.138443 -0.000000 0.000000" Tail3D="155.138428 -0.000000 0.000000"/>
<graphic id="21" SupersededBy="13" GraphicType="Line" ArrowType="RetroSynthetic" HeadSize="600" BoundingBox="251.138443 -0.000000 155.138428 -0.000000"/>
<scheme>
<step ReactionStepReactants="4" ReactionStepProducts="9" ReactionStepArrows="21"/>
</scheme>
</page>
</CDXML>
<?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">
<n id="5" p="65.569229 36.000000"/>
<n id="6" p="65.569229 -12.000000"/>
<n id="7" p="24.000000 -36.000000"/>
<n id="8" Element="7" NumHydrogens="2" p="107.138428 -36.000000">
<t p="107.138428 -36.000000" LabelJustification="Left">
<s font="3" size="10" face="96">NH</s>
<s font="3" size="10" face="32">2</s>
</t>
</n>
<b id="16" B="5" E="6"/>
<b id="17" B="6" E="7"/>
<b id="18" B="6" E="8"/>
</fragment>
<fragment id="9">
<n id="10" Element="8" NumHydrogens="1" p="251.138443 -12.000000">
<t p="251.138443 -12.000000" LabelJustification="Left">
<s font="3" size="10" face="96">OH</s>
</t>
</n>
<n id="11" p="292.707642 12.000000"/>
<n id="12" Element="8" NumHydrogens="1" p="334.276886 -12.000000">
<t p="334.276886 -12.000000" LabelJustification="Left">
<s font="3" size="10" face="96">OH</s>
</t>
</n>
<b id="19" B="10" E="11"/>
<b id="20" B="11" E="12"/>
</fragment>
<arrow id="13" BoundingBox="203.138458 -0.000000 155.138428 -0.000000" FillType="None" ArrowheadHead="Full" ArrowheadType="Angle" HeadSize="600" ArrowheadCenterSize="600" ArrowheadWidth="150" ArrowShaftSpacing="600" Head3D="203.138458 -0.000000 0.000000" Tail3D="155.138428 -0.000000 0.000000"/>
<graphic id="21" SupersededBy="13" GraphicType="Line" ArrowType="RetroSynthetic" HeadSize="600" BoundingBox="203.138458 -0.000000 155.138428 -0.000000"/>
<scheme>
<step ReactionStepReactants="4" ReactionStepProducts="9" ReactionStepArrows="21"/>
</scheme>
</page>
</CDXML>
6 changes: 3 additions & 3 deletions api/tests/integration/tests/formats/ref/ket_retro_arrow.cml
Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,9 @@
<reactantList>
<molecule>
<atomArray>
<atom id="a0" elementType="O" x2="9.97128" y2="0.4"/>
<atom id="a1" elementType="C" x2="11.3569" y2="-0.4"/>
<atom id="a2" elementType="O" x2="12.7426" y2="0.4"/>
<atom id="a0" elementType="O" x2="8.37128" y2="0.4"/>
<atom id="a1" elementType="C" x2="9.75692" y2="-0.4"/>
<atom id="a2" elementType="O" x2="11.1426" y2="0.4"/>
</atomArray>
<bondArray>
<bond atomRefs2="a0 a1" order="1"/>
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,9 @@ $MOL
-INDIGO-01000000002D

3 2 0 0 0 0 0 0 0 0999 V2000
9.9713 0.4000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
11.3569 -0.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.7426 0.4000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
8.3713 0.4000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
9.7569 -0.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.1426 0.4000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
M END
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,9 @@ M V30 BEGIN REACTANT
M V30 BEGIN CTAB
M V30 COUNTS 3 2 0 0 0
M V30 BEGIN ATOM
M V30 1 O 9.97128 0.4 0.0 0
M V30 2 C 11.3569 -0.4 0.0 0
M V30 3 O 12.7426 0.4 0.0 0
M V30 1 O 8.37128 0.4 0.0 0
M V30 2 C 9.75692 -0.4 0.0 0
M V30 3 O 11.1426 0.4 0.0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
Expand Down
1 change: 1 addition & 0 deletions api/tests/integration/tests/layout/clean2d.py
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
raise

indigo = Indigo()
indigo.resetOptions()
indigo.setOption("molfile-saving-skip-date", "1")
indigo.setOption("treat-x-as-pseudoatom", "1")

Expand Down
108 changes: 12 additions & 96 deletions api/tests/integration/tests/layout/ref/reaction_layout.rdf
Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
$RFMT
$RXN

-INDIGO- 0100000000
Expand Down Expand Up @@ -48,13 +47,13 @@ $MOL
-INDIGO-01000000002D

7 6 0 0 0 0 0 0 0 0999 V2000
22.2851 0.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
23.6708 1.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
25.0564 0.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
26.4420 1.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
27.8277 0.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
29.2133 1.2000 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
25.0564 -1.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
20.6851 0.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
22.0708 1.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
23.4564 0.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
24.8420 1.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
26.2277 0.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
27.6133 1.2000 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
23.4564 -1.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
Expand All @@ -67,96 +66,13 @@ $MOL
-INDIGO-01000000002D

7 7 0 0 0 0 0 0 0 0999 V2000
33.2133 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
31.6133 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
32.4133 1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
34.0133 1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
35.6133 1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
36.4133 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
35.6133 -1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
34.8133 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
34.0133 -1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
38.0133 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 2 0 0 0 0
3 4 1 0 0 0 0
4 5 2 0 0 0 0
5 6 1 0 0 0 0
6 1 2 0 0 0 0
4 7 1 0 0 0 0
M END ref=
$RXN

-INDIGO- 0100000000

2 2
$MOL

-INDIGO-01000000002D

8 7 0 0 0 0 0 0 0 0999 V2000
0.8000 1.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1856 0.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5713 1.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9569 0.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.3426 1.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7282 0.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.1138 1.2000 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
4.9569 -1.2000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
6 7 1 0 0 0 0
4 8 2 0 0 0 0
M END
$MOL

-INDIGO-01000000002D

6 6 0 0 0 0 0 0 0 0999 V2000
13.8995 1.6000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.5138 0.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.5138 -0.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.8995 -1.6000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.2851 -0.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.2851 0.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 2 0 0 0 0
3 4 1 0 0 0 0
4 5 2 0 0 0 0
5 6 1 0 0 0 0
6 1 2 0 0 0 0
M END
$MOL

-INDIGO-01000000002D

7 6 0 0 0 0 0 0 0 0999 V2000
21.6851 0.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
23.0708 1.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
24.4564 0.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
25.8420 1.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
27.2277 0.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
28.6133 1.2000 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
24.4564 -1.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
3 7 1 0 0 0 0
M END
$MOL

-INDIGO-01000000002D

7 7 0 0 0 0 0 0 0 0999 V2000
32.0133 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
32.8133 1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
34.4133 1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
35.2133 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
34.4133 -1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
32.8133 -1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
36.8133 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
32.4133 -1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
36.4133 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 2 0 0 0 0
3 4 1 0 0 0 0
Expand Down
44 changes: 22 additions & 22 deletions api/tests/integration/tests/layout/ref/test1.rxn
Original file line number Diff line number Diff line change
Expand Up @@ -24,28 +24,28 @@ $MOL
-INDIGO-01000000002D

22 22 0 0 0 0 0 0 0 0999 V2000
15.3569 -2.3391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.3569 -0.7391 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
13.9713 0.0609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.5856 -0.7391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.7856 -2.1247 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.9856 -0.7391 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
16.7426 0.0609 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
15.9426 1.4465 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
17.5426 -1.3247 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
18.1282 0.8609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
18.7405 2.3391 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
17.5159 2.3391 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
19.5138 0.0609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
18.9016 -1.4173 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
20.1261 -1.4173 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
20.8995 0.8609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
21.5118 2.3391 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
20.2872 2.3391 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
22.2851 0.0609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
22.2851 -1.5391 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
23.6708 0.8609 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
23.6708 -0.7391 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
13.7569 -2.3391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.7569 -0.7391 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
12.3713 0.0609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.9856 -0.7391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.1856 -2.1247 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.3856 -0.7391 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
15.1426 0.0609 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
14.3426 1.4465 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
15.9426 -1.3247 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
16.5282 0.8609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
17.1405 2.3391 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
15.9159 2.3391 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
17.9138 0.0609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
17.3016 -1.4173 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
18.5261 -1.4173 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
19.2995 0.8609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
19.9118 2.3391 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
18.6872 2.3391 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
20.6851 0.0609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
20.6851 -1.5391 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
22.0708 0.8609 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
22.0708 -0.7391 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
Expand Down
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