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run clang-format with c++-11 style over that

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This commit is contained in:
Greg Landrum
2017-04-22 17:19:10 +02:00
parent 7c0bb0b743
commit 915cf08faa
134 changed files with 917 additions and 1086 deletions
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93
Code/DistGeom/DistGeomUtils.cpp
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@@ -184,8 +184,7 @@ ForceFields::ForceField *constructForceField(
std::map<std::pair<int, int>, double> *extraWeights, double basinSizeTol) {
unsigned int N = mmat.numRows();
CHECK_INVARIANT(N == positions.size(), "");
auto *field =
new ForceFields::ForceField(positions[0]->dimension());
auto *field = new ForceFields::ForceField(positions[0]->dimension());
for (unsigned int i = 0; i < N; i++) {
field->positions().push_back(positions[i]);
}
@@ -208,8 +207,7 @@ ForceFields::ForceField *constructForceField(
includeIt = true;
}
if (includeIt) {
auto *contrib =
new DistViolationContrib(field, i, j, u, l, w);
auto *contrib = new DistViolationContrib(field, i, j, u, l, w);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
}
@@ -217,7 +215,7 @@ ForceFields::ForceField *constructForceField(
// now add chiral constraints
if (weightChiral > 1.e-8) {
for (const auto & cset : csets) {
for (const auto &cset : csets) {
auto *contrib =
new ChiralViolationContrib(field, cset.get(), weightChiral);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
@@ -227,8 +225,7 @@ ForceFields::ForceField *constructForceField(
// finally the contribution from the fourth dimension if we need to
if ((field->dimension() == 4) && (weightFourthDim > 1.e-8)) {
for (unsigned int i = 1; i < N; i++) {
auto *contrib =
new FourthDimContrib(field, i, weightFourthDim);
auto *contrib = new FourthDimContrib(field, i, weightFourthDim);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
}
@@ -248,8 +245,7 @@ ForceFields::ForceField *construct3DForceField(
unsigned int N = mmat.numRows();
CHECK_INVARIANT(N == positions.size(), "");
CHECK_INVARIANT(expTorsionAtoms.size() == expTorsionAngles.size(), "");
auto *field =
new ForceFields::ForceField(positions[0]->dimension());
auto *field = new ForceFields::ForceField(positions[0]->dimension());
for (unsigned int i = 0; i < N; ++i) {
field->positions().push_back(positions[i]);
}
@@ -268,16 +264,15 @@ ForceFields::ForceField *construct3DForceField(
else
atomPairs[j * N + i] = 1;
// expTorsionAngles[t][0] = (signs, V's)
auto *contrib =
new ForceFields::CrystalFF::TorsionAngleContribM6(
field, i, j, k, l, expTorsionAngles[t].second,
expTorsionAngles[t].first);
auto *contrib = new ForceFields::CrystalFF::TorsionAngleContribM6(
field, i, j, k, l, expTorsionAngles[t].second,
expTorsionAngles[t].first);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
} // torsion constraints
// improper torsions / out-of-plane bend / inversion
double oobForceScalingFactor = 10.0;
for (const auto & improperAtom : improperAtoms) {
for (const auto &improperAtom : improperAtoms) {
std::vector<int> n(4);
for (unsigned int i = 0; i < 3; ++i) {
n[1] = 1;
@@ -300,11 +295,10 @@ ForceFields::ForceField *construct3DForceField(
n[3] = 0;
break;
}
auto *contrib =
new ForceFields::UFF::InversionContrib(
field, improperAtom[n[0]], improperAtom[n[1]],
improperAtom[n[2]], improperAtom[n[3]],
improperAtom[4], improperAtom[5], oobForceScalingFactor);
auto *contrib = new ForceFields::UFF::InversionContrib(
field, improperAtom[n[0]], improperAtom[n[1]], improperAtom[n[2]],
improperAtom[n[3]], improperAtom[4], improperAtom[5],
oobForceScalingFactor);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
}
@@ -322,14 +316,13 @@ ForceFields::ForceField *construct3DForceField(
double d = ((*positions[i]) - (*positions[j])).length();
double l = d - 0.01;
double u = d + 0.01;
auto *contrib =
new ForceFields::UFF::DistanceConstraintContrib(field, i, j, l, u,
fdist);
auto *contrib = new ForceFields::UFF::DistanceConstraintContrib(
field, i, j, l, u, fdist);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
// 1,3 distance constraints
for (const auto & angle : angles) {
for (const auto &angle : angles) {
unsigned int i = angle[0];
unsigned int j = angle[1];
unsigned int k = angle[2];
@@ -339,17 +332,15 @@ ForceFields::ForceField *construct3DForceField(
atomPairs[j * N + i] = 1;
// check for triple bonds
if (angle[3]) {
auto *contrib =
new ForceFields::UFF::AngleConstraintContrib(field, i, j, k, 179.0,
180.0, fdist);
auto *contrib = new ForceFields::UFF::AngleConstraintContrib(
field, i, j, k, 179.0, 180.0, fdist);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
} else {
double d = ((*positions[i]) - (*positions[k])).length();
double l = d - 0.01;
double u = d + 0.01;
auto *contrib =
new ForceFields::UFF::DistanceConstraintContrib(field, i, k, l, u,
fdist);
auto *contrib = new ForceFields::UFF::DistanceConstraintContrib(
field, i, k, l, u, fdist);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
}
@@ -361,9 +352,8 @@ ForceFields::ForceField *construct3DForceField(
if (!atomPairs[j * N + i]) {
double l = mmat.getLowerBound(i, j);
double u = mmat.getUpperBound(i, j);
auto *contrib =
new ForceFields::UFF::DistanceConstraintContrib(field, i, j, l, u,
fdist);
auto *contrib = new ForceFields::UFF::DistanceConstraintContrib(
field, i, j, l, u, fdist);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
}
@@ -384,8 +374,7 @@ ForceFields::ForceField *constructPlain3DForceField(
unsigned int N = mmat.numRows();
CHECK_INVARIANT(N == positions.size(), "");
CHECK_INVARIANT(expTorsionAtoms.size() == expTorsionAngles.size(), "");
auto *field =
new ForceFields::ForceField(positions[0]->dimension());
auto *field = new ForceFields::ForceField(positions[0]->dimension());
for (unsigned int i = 0; i < N; ++i) {
field->positions().push_back(positions[i]);
}
@@ -404,10 +393,9 @@ ForceFields::ForceField *constructPlain3DForceField(
else
atomPairs[j * N + i] = 1;
// expTorsionAngles[t][0] = (signs, V's)
auto *contrib =
new ForceFields::CrystalFF::TorsionAngleContribM6(
field, i, j, k, l, expTorsionAngles[t].second,
expTorsionAngles[t].first);
auto *contrib = new ForceFields::CrystalFF::TorsionAngleContribM6(
field, i, j, k, l, expTorsionAngles[t].second,
expTorsionAngles[t].first);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
} // torsion constraints
@@ -424,9 +412,8 @@ ForceFields::ForceField *constructPlain3DForceField(
double d = ((*positions[i]) - (*positions[j])).length();
double l = d - 0.01;
double u = d + 0.01;
auto *contrib =
new ForceFields::UFF::DistanceConstraintContrib(field, i, j, l, u,
fdist);
auto *contrib = new ForceFields::UFF::DistanceConstraintContrib(
field, i, j, l, u, fdist);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
@@ -441,9 +428,8 @@ ForceFields::ForceField *constructPlain3DForceField(
double d = ((*positions[i]) - (*positions[j])).length();
double l = d - 0.01;
double u = d + 0.01;
auto *contrib =
new ForceFields::UFF::DistanceConstraintContrib(field, i, j, l, u,
fdist);
auto *contrib = new ForceFields::UFF::DistanceConstraintContrib(
field, i, j, l, u, fdist);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
@@ -454,9 +440,8 @@ ForceFields::ForceField *constructPlain3DForceField(
if (!atomPairs[j * N + i]) {
double l = mmat.getLowerBound(i, j);
double u = mmat.getUpperBound(i, j);
auto *contrib =
new ForceFields::UFF::DistanceConstraintContrib(field, i, j, l, u,
fdist);
auto *contrib = new ForceFields::UFF::DistanceConstraintContrib(
field, i, j, l, u, fdist);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
}
@@ -472,15 +457,14 @@ ForceFields::ForceField *construct3DImproperForceField(
(void)atomNums;
unsigned int N = mmat.numRows();
CHECK_INVARIANT(N == positions.size(), "");
auto *field =
new ForceFields::ForceField(positions[0]->dimension());
auto *field = new ForceFields::ForceField(positions[0]->dimension());
for (unsigned int i = 0; i < N; ++i) {
field->positions().push_back(positions[i]);
}
// improper torsions / out-of-plane bend / inversion
double oobForceScalingFactor = 10.0;
for (const auto & improperAtom : improperAtoms) {
for (const auto &improperAtom : improperAtoms) {
std::vector<int> n(4);
for (unsigned int i = 0; i < 3; ++i) {
n[1] = 1;
@@ -503,11 +487,10 @@ ForceFields::ForceField *construct3DImproperForceField(
n[3] = 0;
break;
}
auto *contrib =
new ForceFields::UFF::InversionContrib(
field, improperAtom[n[0]], improperAtom[n[1]],
improperAtom[n[2]], improperAtom[n[3]],
improperAtom[4], improperAtom[5], oobForceScalingFactor);
auto *contrib = new ForceFields::UFF::InversionContrib(
field, improperAtom[n[0]], improperAtom[n[1]], improperAtom[n[2]],
improperAtom[n[3]], improperAtom[4], improperAtom[5],
oobForceScalingFactor);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
}