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Ensure 13 bounds constraints are added to angles that are part of an improper torsion (#7729)

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* make sure 13 bounds constraints are added to angles that are part of an impropper torsion

* make sure angles are constrained with higher force constant to prevent rings from folding

* adapt tests to new behavior

* move comment to correct place

* add min bounds test

* make sure we are not terribly outside of the bounds matrix
This commit is contained in:
nmaeder
2024-08-21 16:06:29 +02:00
committed by GitHub
parent a45d4d9857
commit 168b111fe3
5 changed files with 112 additions and 84 deletions
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16
Code/DistGeom/DistGeomUtils.cpp
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@@ -395,6 +395,8 @@ void add12Terms(ForceFields::ForceField *ff,
distances \param isImproperConstrained bit vector with length of total num
atoms of the molecule where index of every central atom of improper torsion is
set to one \param useBasicKnowledge whether to use basic knowledge terms
\param mmat Bounds matrix from which 13 distances are used in case an angle
is part of an improper torsion
\param numAtoms number of atoms in molecule
*/
@@ -403,7 +405,8 @@ void add13Terms(ForceFields::ForceField *ff,
boost::dynamic_bitset<> &atomPairs,
RDGeom::Point3DPtrVect &positions, double forceConstant,
const boost::dynamic_bitset<> &isImproperConstrained,
bool useBasicKnowledge, unsigned int numAtoms) {
bool useBasicKnowledge, const BoundsMatrix &mmat,
unsigned int numAtoms) {
PRECONDITION(ff, "bad force field");
auto distContribs =
std::make_unique<ForceFields::DistanceConstraintContribs>(ff);
@@ -413,7 +416,6 @@ void add13Terms(ForceFields::ForceField *ff,
unsigned int i = angle[0];
unsigned int j = angle[1];
unsigned int k = angle[2];
if (i < k) {
atomPairs[i * numAtoms + k] = 1;
} else {
@@ -422,7 +424,10 @@ void add13Terms(ForceFields::ForceField *ff,
// check for triple bonds
if (useBasicKnowledge && angle[3]) {
angleContribs->addContrib(i, j, k, 179.0, 180.0, 1);
} else if (!isImproperConstrained[j]) {
} else if (isImproperConstrained[j]) {
distContribs->addContrib(i, k, mmat.getLowerBound(i, k),
mmat.getUpperBound(i, k), forceConstant);
} else {
double d = ((*positions[i]) - (*positions[k])).length();
distContribs->addContrib(i, k, d - KNOWN_DIST_TOL, d + KNOWN_DIST_TOL,
forceConstant);
@@ -511,8 +516,7 @@ ForceFields::ForceField *construct3DForceField(
add12Terms(field, etkdgDetails, atomPairs, positions,
KNOWN_DIST_FORCE_CONSTANT, N);
add13Terms(field, etkdgDetails, atomPairs, positions,
KNOWN_DIST_FORCE_CONSTANT, isImproperConstrained, true, N);
KNOWN_DIST_FORCE_CONSTANT, isImproperConstrained, true, mmat, N);
// minimum distance for all other atom pairs that aren't constrained
addLongRangeDistanceConstraints(field, etkdgDetails, atomPairs, positions,
KNOWN_DIST_FORCE_CONSTANT, mmat, N);
@@ -560,7 +564,7 @@ ForceFields::ForceField *constructPlain3DForceField(
add12Terms(field, etkdgDetails, atomPairs, positions,
KNOWN_DIST_FORCE_CONSTANT, N);
add13Terms(field, etkdgDetails, atomPairs, positions,
KNOWN_DIST_FORCE_CONSTANT, isImproperConstrained, false, N);
KNOWN_DIST_FORCE_CONSTANT, isImproperConstrained, false, mmat, N);
// minimum distance for all other atom pairs that aren't constrained
addLongRangeDistanceConstraints(field, etkdgDetails, atomPairs, positions,
KNOWN_DIST_FORCE_CONSTANT, mmat, N);