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Prefer wedging ring bonds around atropisomers (#7373)
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* prefer wedging ring bonds for atropisomers

* update expected results

* handle 3D as well

* prefer wedging to larger rings

wedging bonds in 5 rings make later attempts at improving kekulization very difficult

update expected results

* extend those changes to 3D

* update tests for those changes

* avoid wedging atropisomers if possible

response to review
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@greglandrum
greglandrum committed May 8, 2024
1 parent a2b149a commit 18d1ff5
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Showing 51 changed files with 405 additions and 92 deletions.
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;
} 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) {
// 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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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_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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Original file line number Diff line number Diff line change
@@ -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" 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4 changes: 2 additions & 2 deletions Code/GraphMol/MarvinParse/test_data/RP-6306_3d.mrv.noReapply.expected.sdf
View file
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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