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Prefer wedging ring bonds around atropisomers #7373

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merged 10 commits into from
May 8, 2024
Merged

Prefer wedging ring bonds around atropisomers #7373

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787833c
prefer wedging ring bonds for atropisomers
greglandrum Apr 19, 2024
d2f570d
update expected results
greglandrum Apr 19, 2024
42b0f23
handle 3D as well
greglandrum Apr 19, 2024
f998363
Merge remote-tracking branch 'origin/master' into fix/github7371
greglandrum Apr 26, 2024
9aa3634
prefer wedging to larger rings
greglandrum Apr 26, 2024
e911fcd
extend those changes to 3D
greglandrum Apr 28, 2024
b85b4e9
update tests for those changes
greglandrum May 1, 2024
5f00e87
avoid wedging atropisomers if possible
greglandrum May 3, 2024
1af57c8
Merge remote-tracking branch 'origin/master' into fix/github7371
greglandrum May 3, 2024
e014d6e
Merge branch 'master' into fix/github7371
greglandrum May 7, 2024
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48 changes: 38 additions & 10 deletions Code/GraphMol/Atropisomers.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -860,13 +860,19 @@ bool WedgeBondFromAtropisomerOneBond2d(
}

// did not find a good bond dir - pick one to use
// we would like to have one that is not in a ring, and will be a wedge
// we would like to have one that is in a ring, and will favor it being a
// wedge

// We favor rings here because wedging non-ring bonds makes it too likely that
// we'll end up accidentally creating new atropisomeric bonds. This was github
// issue 7371

const RingInfo *ri = bond->getOwningMol().getRingInfo();

int bestBondEnd = -1, bestBondNumber = -1;
bool bestBondIsSingle = false;
unsigned int bestRingCount = INT_MAX;
unsigned int largestRingSize = 0;
Bond::BondDir bestBondDir = Bond::BondDir::NONE;
for (unsigned int whichEnd = 0; whichEnd < 2; ++whichEnd) {
for (unsigned int whichBond = 0;
Expand Down Expand Up @@ -898,14 +904,24 @@ bool WedgeBondFromAtropisomerOneBond2d(
}
}
auto ringCount = ri->numBondRings(bondToTry->getIdx());
unsigned int ringSize = 0;
if (!ringCount) {
ringCount = 10;
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} else {
// we're going to prefer to put wedges in larger rings, but don't want
// to end up wedging macrocyles if it's avoidable.
ringSize = ri->minBondRingSize(bondToTry->getIdx());
if (ringSize > 8) {
ringSize = 0;
}
}
if (ringCount > bestRingCount) {
continue;
}

else if (ringCount < bestRingCount) {
} else if (ringCount < bestRingCount || ringSize > largestRingSize) {
bestBondEnd = whichEnd;
bestBondNumber = whichBond;
bestRingCount = ringCount;
largestRingSize = ringSize;
bestBondIsSingle = (bondToTry->getBondType() == Bond::BondType::SINGLE);
bestBondDir = getBondDirForAtropisomer2d(bondVecs, bond->getStereo(),
whichEnd, whichBond);
Expand Down Expand Up @@ -939,8 +955,8 @@ bool WedgeBondFromAtropisomerOneBond2d(
}
}

if (bestBondEnd >= 0) // we found a good one
{
if (bestBondEnd >= 0) {
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// we found a good one
// make sure the atoms on the bond are in the right order for the
// wedge/hash the atom on the end of the main bond must be listed
// first for the wedge/has bond
Expand Down Expand Up @@ -1030,6 +1046,7 @@ bool WedgeBondFromAtropisomerOneBond3d(
Bond *bestBond = nullptr;
int bestBondEnd = -1;
unsigned int bestRingCount = UINT_MAX;
unsigned int largestRingSize = 0;
Bond::BondDir bestBondDir = Bond::BondDir::NONE;
bool bestBondIsSingle = false;
for (unsigned int whichEnd = 0; whichEnd < 2; ++whichEnd) {
Expand Down Expand Up @@ -1069,14 +1086,24 @@ bool WedgeBondFromAtropisomerOneBond3d(
}
}
auto ringCount = ri->numBondRings(bondToTry->getIdx());
unsigned int ringSize = 0;
if (!ringCount) {
ringCount = 10;
} else {
// we're going to prefer to put wedges in larger rings, but don't want
// to end up wedging macrocyles if it's avoidable.
ringSize = ri->minBondRingSize(bondToTry->getIdx());
if (ringSize > 8) {
ringSize = 0;
}
}
if (ringCount > bestRingCount) {
continue;
}

else if (ringCount < bestRingCount) {
} else if (ringCount < bestRingCount || ringSize > largestRingSize) {
bestBond = bondToTry;
bestBondEnd = whichEnd;
bestRingCount = ringCount;
largestRingSize = ringSize;
bestBondIsSingle = (bondToTry->getBondType() == Bond::BondType::SINGLE);
bestBondDir = getBondDirForAtropisomer3d(bondToTry, conf);
} else if (bestBondIsSingle &&
Expand Down Expand Up @@ -1106,7 +1133,8 @@ bool WedgeBondFromAtropisomerOneBond3d(
}
}

if (bestBond != nullptr) { // we found a good one
if (bestBond != nullptr) {
// we found a good one

// make sure the atoms on the bond are in the right order for the
// wedge/hash the atom on the end of the main bond must be listed
Expand Down
4 changes: 2 additions & 2 deletions Code/GraphMol/FileParsers/test_data/atropisomers/AtropTest.sdf.expected2.sdf
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ M V30 5 1 5 6
M V30 6 2 6 1
M V30 7 1 1 7
M V30 8 2 7 8
M V30 9 1 8 9 CFG=1
M V30 9 1 8 9
M V30 10 1 9 2
M V30 11 1 7 10
M V30 12 1 10 11
Expand All @@ -64,7 +64,7 @@ M V30 16 1 14 15
M V30 17 2 15 16
M V30 18 1 16 17
M V30 19 2 17 18
M V30 20 1 18 13
M V30 20 1 13 18 CFG=3
M V30 21 1 14 19
M V30 22 1 19 20
M V30 23 1 17 21
Expand Down
4 changes: 2 additions & 2 deletions Code/GraphMol/FileParsers/test_data/atropisomers/JDQ443_3d.sdf.expected2.sdf
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Original file line number Diff line number Diff line change
Expand Up @@ -108,15 +108,15 @@ M V30 32 1 15 47
M V30 33 1 16 20
M V30 34 2 17 18
M V30 35 1 17 21
M V30 36 1 18 19 CFG=3
M V30 36 1 18 19
M V30 37 1 18 22
M V30 38 1 19 23
M V30 39 2 20 24
M V30 40 1 20 48
M V30 41 1 21 49
M V30 42 1 21 50
M V30 43 1 21 51
M V30 44 1 22 25
M V30 44 1 22 25 CFG=3
M V30 45 2 22 26
M V30 46 2 23 27
M V30 47 1 23 28
Expand Down
4 changes: 2 additions & 2 deletions Code/GraphMol/FileParsers/test_data/atropisomers/RP-6306_3d.sdf.expected2.sdf
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ M V30 2 1 1 44
M V30 3 2 2 19
M V30 4 1 3 7
M V30 5 1 3 9
M V30 6 1 3 10 CFG=1
M V30 6 1 3 10
M V30 7 2 4 7
M V30 8 1 4 16
M V30 9 1 5 10
Expand All @@ -69,7 +69,7 @@ M V30 15 1 7 8
M V30 16 1 8 11
M V30 17 2 8 14
M V30 18 2 9 12
M V30 19 1 9 13
M V30 19 1 9 13 CFG=1
M V30 20 2 10 11
M V30 21 1 11 19
M V30 22 1 12 17
Expand Down
4 changes: 2 additions & 2 deletions Code/GraphMol/FileParsers/test_data/atropisomers/RP-6306_atrop1.sdf.expected2.sdf
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ M V30 1 1 1 17
M V30 2 2 2 19
M V30 3 1 3 7
M V30 4 1 3 9
M V30 5 1 3 10 CFG=1
M V30 5 1 3 10
M V30 6 2 4 7
M V30 7 1 4 16
M V30 8 1 5 10
Expand All @@ -44,7 +44,7 @@ M V30 10 1 7 8
M V30 11 1 8 11
M V30 12 2 8 14
M V30 13 2 9 12
M V30 14 1 9 13
M V30 14 1 9 13 CFG=1
M V30 15 2 10 11
M V30 16 1 11 19
M V30 17 1 12 17
Expand Down
4 changes: 2 additions & 2 deletions Code/GraphMol/FileParsers/test_data/atropisomers/RP-6306_atrop2.sdf.expected2.sdf
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ M V30 1 1 1 17
M V30 2 2 2 19
M V30 3 1 3 7
M V30 4 1 3 9
M V30 5 1 3 10 CFG=1
M V30 5 1 3 10
M V30 6 2 4 7
M V30 7 1 4 16
M V30 8 1 5 10
Expand All @@ -44,7 +44,7 @@ M V30 10 1 7 8
M V30 11 1 8 11
M V30 12 2 8 14
M V30 13 2 9 12
M V30 14 1 9 13
M V30 14 1 9 13 CFG=1
M V30 15 2 10 11
M V30 16 1 11 19
M V30 17 1 12 17
Expand Down
4 changes: 2 additions & 2 deletions Code/GraphMol/FileParsers/test_data/atropisomers/RP-6306_atrop3.sdf.expected2.sdf
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ M V30 1 1 1 17
M V30 2 2 2 19
M V30 3 1 3 7
M V30 4 1 3 9
M V30 5 1 3 10 CFG=1
M V30 5 1 3 10
M V30 6 2 4 7
M V30 7 1 4 16
M V30 8 1 5 10
Expand All @@ -44,7 +44,7 @@ M V30 10 1 7 8
M V30 11 1 8 11
M V30 12 2 8 14
M V30 13 2 9 12
M V30 14 1 9 13
M V30 14 1 9 13 CFG=1
M V30 15 2 10 11
M V30 16 1 11 19
M V30 17 1 12 17
Expand Down
4 changes: 2 additions & 2 deletions Code/GraphMol/FileParsers/test_data/atropisomers/RP-6306_atrop4.sdf.expected2.sdf
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ M V30 1 1 1 17
M V30 2 2 2 19
M V30 3 1 3 7
M V30 4 1 3 9
M V30 5 1 3 10 CFG=1
M V30 5 1 3 10
M V30 6 2 4 7
M V30 7 1 4 16
M V30 8 1 5 10
Expand All @@ -44,7 +44,7 @@ M V30 10 1 7 8
M V30 11 1 8 11
M V30 12 2 8 14
M V30 13 2 9 12
M V30 14 1 9 13
M V30 14 1 9 13 CFG=1
M V30 15 2 10 11
M V30 16 1 11 19
M V30 17 1 12 17
Expand Down
4 changes: 2 additions & 2 deletions Code/GraphMol/FileParsers/test_data/atropisomers/RP-6306_atrop5.sdf.expected2.sdf
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ M V30 1 1 1 17
M V30 2 2 2 19
M V30 3 1 3 7
M V30 4 1 3 9
M V30 5 1 3 10 CFG=1
M V30 5 1 3 10
M V30 6 2 4 7
M V30 7 1 4 16
M V30 8 1 5 10
Expand All @@ -44,7 +44,7 @@ M V30 10 1 7 8
M V30 11 1 8 11
M V30 12 2 8 14
M V30 13 2 9 12
M V30 14 1 9 13
M V30 14 1 9 13 CFG=1
M V30 15 2 10 11
M V30 16 1 11 19
M V30 17 1 12 17
Expand Down
4 changes: 2 additions & 2 deletions Code/GraphMol/FileParsers/test_data/atropisomers/ZM374979_atrop1.sdf.expected2.sdf
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Expand Up @@ -52,7 +52,7 @@ M V30 44 C 4.644100 1.443800 0.000000 0
M V30 45 C 3.929600 1.031300 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2 CFG=3
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 4 3 CFG=1
M V30 4 1 4 5
Expand Down Expand Up @@ -93,7 +93,7 @@ M V30 38 1 35 36
M V30 39 1 36 37
M V30 40 3 37 38
M V30 41 2 36 39
M V30 42 1 32 39
M V30 42 1 32 39 CFG=1
M V30 43 1 39 40
M V30 44 1 40 41
M V30 45 1 34 42
Expand Down
4 changes: 2 additions & 2 deletions Code/GraphMol/FileParsers/test_data/atropisomers/ZM374979_atrop2.sdf.expected2.sdf
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Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@ M V30 44 C 4.644100 1.443800 0.000000 0
M V30 45 C 3.929600 1.031300 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2 CFG=3
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 4 3 CFG=1
M V30 4 1 4 5
Expand Down Expand Up @@ -93,7 +93,7 @@ M V30 38 1 35 36
M V30 39 1 36 37
M V30 40 3 37 38
M V30 41 2 36 39
M V30 42 1 32 39
M V30 42 1 32 39 CFG=1
M V30 43 1 39 40
M V30 44 1 40 41
M V30 45 1 34 42
Expand Down
4 changes: 2 additions & 2 deletions Code/GraphMol/FileParsers/test_data/atropisomers/ZM374979_atrop3.sdf.expected2.sdf
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Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@ M V30 44 C 4.644100 1.443800 0.000000 0
M V30 45 C 3.929600 1.031300 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2 CFG=3
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 4 3 CFG=1
M V30 4 1 4 5
Expand Down Expand Up @@ -93,7 +93,7 @@ M V30 38 1 35 36
M V30 39 1 36 37
M V30 40 3 37 38
M V30 41 2 36 39
M V30 42 1 32 39
M V30 42 1 32 39 CFG=1
M V30 43 1 39 40
M V30 44 1 40 41
M V30 45 1 34 42
Expand Down
2 changes: 1 addition & 1 deletion Code/GraphMol/MarvinParse/test_data/JDQ443_3d.mrv.noReapply.expected.mrv
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Large diffs are not rendered by default.

4 changes: 2 additions & 2 deletions Code/GraphMol/MarvinParse/test_data/JDQ443_3d.mrv.noReapply.expected.sdf
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Original file line number Diff line number Diff line change
Expand Up @@ -108,15 +108,15 @@ M V30 32 1 15 47
M V30 33 1 16 20
M V30 34 2 17 18
M V30 35 1 17 21
M V30 36 1 18 19 CFG=3
M V30 36 1 18 19
M V30 37 1 18 22
M V30 38 1 19 23
M V30 39 2 20 24
M V30 40 1 20 48
M V30 41 1 21 49
M V30 42 1 21 50
M V30 43 1 21 51
M V30 44 1 22 25
M V30 44 1 22 25 CFG=3
M V30 45 2 22 26
M V30 46 2 23 27
M V30 47 1 23 28
Expand Down
2 changes: 1 addition & 1 deletion Code/GraphMol/MarvinParse/test_data/RP-6306_3d.mrv.noReapply.expected.mrv
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@@ -1,2 +1,2 @@
<?xml version="1.0" encoding="utf-8"?>
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd"><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="O" x3="-4.84493" y3="1.39393" z3="-1.47056"/><atom id="a2" elementType="O" x3="4.01651" y3="4.2266" z3="-0.04928"/><atom id="a3" elementType="N" x3="0.20832" y3="1.08593" z3="0.538347"/><atom id="a4" elementType="N" x3="0.83608" y3="-1.31367" z3="-0.582773"/><atom id="a5" elementType="N" x3="0.2296" y3="3.55497" z3="1.58667"/><atom id="a6" elementType="N" x3="4.38032" y3="3.23372" z3="2.31635"/><atom id="a7" elementType="C" x3="1.20829" y3="0.06412" z3="-0.05544"/><atom id="a8" elementType="C" x3="2.64283" y3="0.707933" z3="-0.00989333"/><atom id="a9" elementType="C" x3="-1.34773" y3="0.84196" z3="0.683013"/><atom id="a10" elementType="C" x3="0.96712" y3="2.36815" z3="0.963387"/><atom id="a11" elementType="C" x3="2.47669" y3="2.16692" z3="0.63728"/><atom id="a12" elementType="C" x3="-2.32325" y3="1.24833" z3="-0.486453"/><atom id="a13" elementType="C" x3="-1.92304" y3="0.191987" z3="1.99883"/><atom id="a14" elementType="C" x3="3.84963" y3="-0.156333" z3="-0.571013"/><atom id="a15" elementType="C" x3="3.52707" y3="-1.59273" z3="-1.1312"/><atom id="a16" elementType="C" x3="2.0412" y3="-2.09599" z3="-1.10805"/><atom id="a17" elementType="C" x3="-3.87352" y3="1.00473" z3="-0.340667"/><atom id="a18" elementType="C" x3="-3.47349" y3="-0.0516133" z3="2.14461"/><atom id="a19" elementType="C" x3="3.63907" y3="3.26471" z3="0.918587"/><atom id="a20" elementType="C" x3="-1.72536" y3="1.94759" z3="-1.90699"/><atom id="a21" elementType="C" x3="-0.91168" y3="-0.257693" z3="3.27563"/><atom id="a22" elementType="C" x3="-4.44883" y3="0.354573" z3="0.974773"/><atom id="a23" elementType="C" x3="4.77867" y3="-2.54529" z3="-1.73656"/><atom id="a24" elementType="C" x3="1.67981" y3="-3.63617" z3="-1.70688"/><atom id="a25" elementType="H" x3="4.99315" y3="0.287747" z3="-0.564293"/><atom id="a26" elementType="H" x3="-3.94165" y3="-0.556733" z3="3.16157"/><atom id="a27" elementType="H" x3="0.783253" y3="4.50865" z3="1.90493"/><atom id="a28" elementType="H" x3="-0.90216" y3="3.56319" z3="1.77035"/><atom id="a29" elementType="H" x3="-1.15715" y3="3.01831" z3="-1.65835"/><atom id="a30" elementType="H" x3="-2.6096" y3="2.20108" z3="-2.73336"/><atom id="a31" elementType="H" x3="-0.929973" y3="1.18225" z3="-2.4668"/><atom id="a32" elementType="H" x3="-0.0927733" y3="-1.10889" z3="2.90827"/><atom id="a33" elementType="H" x3="-1.5512" y3="-0.753293" z3="4.21307"/><atom id="a34" elementType="H" x3="-0.311733" y3="0.724733" z3="3.72773"/><atom id="a35" elementType="H" x3="-5.65413" y3="0.158387" z3="1.10395"/><atom id="a36" elementType="H" x3="4.88189" y3="-3.59511" z3="-1.09013"/><atom id="a37" elementType="H" x3="5.87029" y3="-1.96457" z3="-1.66413"/><atom id="a38" elementType="H" x3="4.58789" y3="-2.81241" z3="-2.92955"/><atom id="a39" elementType="H" x3="2.27547" y3="-4.50865" z3="-1.06325"/><atom id="a40" elementType="H" x3="1.98072" y3="-3.72428" z3="-2.90304"/><atom id="a41" elementType="H" x3="0.4676" y3="-3.87081" z3="-1.61261"/><atom id="a42" elementType="H" x3="4.11488" y3="2.46745" z3="3.12779"/><atom id="a43" elementType="H" x3="5.21267" y3="3.98412" z3="2.55883"/><atom id="a44" elementType="H" x3="-5.87029" y3="1.14044" z3="-1.16611"/></atomArray><bondArray><bond id="b1" atomRefs2="a1 a17" order="1"/><bond id="b2" atomRefs2="a1 a44" order="1"/><bond id="b3" atomRefs2="a2 a19" order="2"/><bond id="b4" atomRefs2="a3 a7" order="1"/><bond id="b5" atomRefs2="a3 a9" order="1"/><bond id="b6" atomRefs2="a3 a10" order="1"><bondStereo>W</bondStereo></bond><bond id="b7" atomRefs2="a4 a7" order="2"/><bond id="b8" atomRefs2="a4 a16" order="1"/><bond id="b9" atomRefs2="a5 a10" order="1"/><bond id="b10" atomRefs2="a5 a27" order="1"/><bond id="b11" atomRefs2="a5 a28" order="1"/><bond id="b12" atomRefs2="a6 a19" order="1"/><bond id="b13" atomRefs2="a6 a42" order="1"/><bond id="b14" atomRefs2="a6 a43" order="1"/><bond id="b15" atomRefs2="a7 a8" order="1"/><bond id="b16" atomRefs2="a8 a11" order="1"/><bond id="b17" atomRefs2="a8 a14" order="2"/><bond id="b18" atomRefs2="a9 a12" order="2"/><bond id="b19" atomRefs2="a9 a13" order="1"/><bond id="b20" atomRefs2="a10 a11" order="2"/><bond id="b21" atomRefs2="a11 a19" order="1"/><bond id="b22" atomRefs2="a12 a17" order="1"/><bond id="b23" atomRefs2="a12 a20" order="1"/><bond id="b24" atomRefs2="a13 a18" order="2"/><bond id="b25" atomRefs2="a13 a21" order="1"/><bond id="b26" atomRefs2="a14 a15" order="1"/><bond id="b27" atomRefs2="a14 a25" order="1"/><bond id="b28" atomRefs2="a15 a16" order="2"/><bond id="b29" atomRefs2="a15 a23" order="1"/><bond id="b30" atomRefs2="a16 a24" order="1"/><bond id="b31" atomRefs2="a17 a22" order="2"/><bond id="b32" atomRefs2="a18 a22" order="1"/><bond id="b33" atomRefs2="a18 a26" order="1"/><bond id="b34" atomRefs2="a20 a29" order="1"/><bond id="b35" atomRefs2="a20 a30" order="1"/><bond id="b36" atomRefs2="a20 a31" order="1"/><bond id="b37" atomRefs2="a21 a32" order="1"/><bond id="b38" atomRefs2="a21 a33" order="1"/><bond id="b39" atomRefs2="a21 a34" order="1"/><bond id="b40" atomRefs2="a22 a35" order="1"/><bond id="b41" atomRefs2="a23 a36" order="1"/><bond id="b42" atomRefs2="a23 a37" order="1"/><bond id="b43" atomRefs2="a23 a38" order="1"/><bond id="b44" atomRefs2="a24 a39" order="1"/><bond id="b45" atomRefs2="a24 a40" order="1"/><bond id="b46" atomRefs2="a24 a41" order="1"/></bondArray></molecule></MChemicalStruct></MDocument></cml>
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4 changes: 2 additions & 2 deletions Code/GraphMol/MarvinParse/test_data/RP-6306_3d.mrv.noReapply.expected.sdf
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ M V30 2 1 1 44
M V30 3 2 2 19
M V30 4 1 3 7
M V30 5 1 3 9
M V30 6 1 3 10 CFG=1
M V30 6 1 3 10
M V30 7 2 4 7
M V30 8 1 4 16
M V30 9 1 5 10
Expand All @@ -69,7 +69,7 @@ M V30 15 1 7 8
M V30 16 1 8 11
M V30 17 2 8 14
M V30 18 2 9 12
M V30 19 1 9 13
M V30 19 1 9 13 CFG=1
M V30 20 2 10 11
M V30 21 1 11 19
M V30 22 1 12 17
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