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Misplaced parentheses in shape code (#9222)

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* Move stray bracket.

* Lots of consts.

* Another bad bracket.

* Response to review.
This commit is contained in:
David Cosgrove
2026-04-07 15:59:56 +01:00
committed by GitHub
parent 87a6c7163d
commit eaf546b037
2 changed files with 120 additions and 115 deletions
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205
Code/GraphMol/GaussianShape/SingleConformerAlignment.cpp
View File

@@ -82,13 +82,11 @@ void SingleConformerAlignment::getFinalQuatTrans(
-d_initQuatTrans[4], -d_initQuatTrans[5], -d_initQuatTrans[6]});
RDGeom::Transform3D initialRot;
initialRot.SetRotationFromQuaternion(d_initQuatTrans.data());
auto tt = reverseInitialTrans * tmp * initialRot;
xform = tt;
xform = reverseInitialTrans * tmp * initialRot;
}
std::array<double, 5> SingleConformerAlignment::calcScores(const double *ref,
const double *fit,
bool includeColor) {
std::array<double, 5> SingleConformerAlignment::calcScores(
const double *ref, const double *fit, const bool includeColor) {
std::array<double, 5> scores{0.0, 0.0, 0.0, 0.0, 0.0};
scores[3] = calcVolAndGrads(ref, d_nRefShape, d_refCarbonRadii, fit,
d_nFitShape, d_fitCarbonRadii, d_gradConverters,
@@ -105,13 +103,15 @@ std::array<double, 5> SingleConformerAlignment::calcScores(const double *ref,
return scores;
}
std::array<double, 5> SingleConformerAlignment::calcScores(bool includeColor) {
std::array<double, 5> SingleConformerAlignment::calcScores(
const bool includeColor) {
applyQuatTrans(d_quatTrans);
return calcScores(d_refTemp.data(), d_fitTemp.data(), includeColor);
}
std::array<double, 5> SingleConformerAlignment::calcScores(
const double shapeOvVol, const double colorOvVol, bool includeColor) const {
const double shapeOvVol, const double colorOvVol,
const bool includeColor) const {
std::array<double, 5> scores{0.0, 0.0, 0.0, 0.0, 0.0};
scores[3] = shapeOvVol;
scores[4] = colorOvVol;
@@ -135,31 +135,32 @@ namespace {
// This uses the chain rule: the dV/qQ = (dV/dr) * (dr/dQ) where V is the
// volume overlap and r is the Cartesian space. Assumes gradConverters
// is already the correct size.
void cartToQuatGrads(const double *quat, const double *mol, int numBPts,
std::vector<double> &gradConverters, int gradConvOffset) {
void cartToQuatGrads(const double *quat, const double *mol, const int numBPts,
std::vector<double> &gradConverters,
const int gradConvOffset) {
// for ease of ref
auto q = quat[0];
auto r = quat[1];
auto s = quat[2];
auto u = quat[3];
auto coef = 1.0 / (q * q + r * r + s * s + u * u);
const auto q = quat[0];
const auto r = quat[1];
const auto s = quat[2];
const auto u = quat[3];
const auto coef = 1.0 / (q * q + r * r + s * s + u * u);
for (int i = 0, j = gradConvOffset, k = 12 * gradConvOffset; i < 4 * numBPts;
i += 4, ++j, k += 12) {
auto x = mol[i];
auto y = mol[i + 1];
auto z = mol[i + 2];
auto dx_dq = coef * 2.0 * (q * x + u * y - s * z);
auto dx_dr = coef * 2.0 * (r * x + s * y + u * z);
auto dy_dr = coef * 2.0 * (s * x - r * y + q * z);
auto dx_du = coef * 2.0 * (-u * x + q * y + r * z);
auto dz_ds = dx_dq;
auto dy_du = -dx_dq;
auto dy_ds = dx_dr;
auto dz_du = dx_dr;
auto dx_ds = -dy_dr;
auto dz_dq = dy_dr;
auto dy_dq = dx_du;
auto dz_dr = -dx_du;
const auto x = mol[i];
const auto y = mol[i + 1];
const auto z = mol[i + 2];
const auto dx_dq = coef * 2.0 * (q * x + u * y - s * z);
const auto dx_dr = coef * 2.0 * (r * x + s * y + u * z);
const auto dy_dr = coef * 2.0 * (s * x - r * y + q * z);
const auto dx_du = coef * 2.0 * (-u * x + q * y + r * z);
const auto dz_ds = dx_dq;
const auto dy_du = -dx_dq;
const auto dy_ds = dx_dr;
const auto dz_du = dx_dr;
const auto dx_ds = -dy_dr;
const auto dz_dq = dy_dr;
const auto dy_dq = dx_du;
const auto dz_dr = -dx_du;
gradConverters[k] = dx_dq;
gradConverters[k + 1] = dy_dq;
gradConverters[k + 2] = dz_dq;
@@ -177,17 +178,17 @@ void cartToQuatGrads(const double *quat, const double *mol, int numBPts,
} // namespace
// atoms/shape features
double calcVolAndGrads(const double *ref, int numRefPts,
double calcVolAndGrads(const double *ref, const int numRefPts,
const boost::dynamic_bitset<> *refCarbonRadii,
const double *fit, int numFitPts,
const double *fit, const int numFitPts,
const boost::dynamic_bitset<> *fitCarbonRadii,
std::vector<double> &gradConverters, bool useCutoff,
double distCutoff2, const double *quat,
double *gradients) {
std::vector<double> &gradConverters,
const bool useCutoff, const double distCutoff2,
const double *quat, double *gradients) {
if (gradients) {
cartToQuatGrads(quat, fit, numFitPts, gradConverters, 0);
}
static const double CARBON_A = KAPPA / (1.7 * 1.7);
static constexpr double CARBON_A = KAPPA / (1.7 * 1.7);
static const double CARBON_BIT =
8.0 * pow(std::numbers::pi / (2 * CARBON_A), 1.5);
double vol = 0.0;
@@ -195,31 +196,30 @@ double calcVolAndGrads(const double *ref, int numRefPts,
// If either of the carbon radii flags aren't supplied, treat them
// both as being all carbon. There isn't enough information to do
// otherwise.
bool allCarbon = !refCarbonRadii || !fitCarbonRadii;
const bool allCarbon = !refCarbonRadii || !fitCarbonRadii;
for (int i = 0, i_idx = 0; i < numRefPts * 4; i += 4, i_idx++) {
const auto ai = ref[i + 3];
for (int j = 0, j_idx = 0, k = 0; j < numFitPts * 4;
j += 4, j_idx++, k += 12) {
auto dx = ref[i] - fit[j];
auto dy = ref[i + 1] - fit[j + 1];
auto dz = ref[i + 2] - fit[j + 2];
auto d2 = dx * dx + dy * dy + dz * dz;
const auto dx = ref[i] - fit[j];
const auto dy = ref[i + 1] - fit[j + 1];
const auto dz = ref[i + 2] - fit[j + 2];
const auto d2 = dx * dx + dy * dy + dz * dz;
if (useCutoff && d2 > distCutoff2) {
continue;
}
const auto aj = fit[j + 3];
auto mult = -(ai * aj) / (ai + aj);
auto kij = exp(mult * d2);
if (allCarbon || (!allCarbon && (*refCarbonRadii)[i_idx] &&
(*fitCarbonRadii)[j_idx])) {
const auto mult = -(ai * aj) / (ai + aj);
const auto kij = exp(mult * d2);
if (allCarbon || ((*refCarbonRadii)[i_idx] && (*fitCarbonRadii)[j_idx])) {
vij = kij * CARBON_BIT;
} else {
auto pi_ai_aj = std::numbers::pi / (ai + aj);
const auto pi_ai_aj = std::numbers::pi / (ai + aj);
vij = 8 * kij * pi_ai_aj * std::sqrt(pi_ai_aj);
}
vol += vij;
if (gradients) {
auto r = 2.0 * vij * mult;
const auto r = 2.0 * vij * mult;
// Use the gradient converters to calculate the gradients in quaternion
// space.
// The zeroth gradient is never used, so don't waste time calculating
@@ -247,9 +247,11 @@ double calcVolAndGrads(const double *ref, int numRefPts,
}
// color features
double calcVolAndGrads(const double *ref, int numRefPts, const int *refTypes,
const double *fit, int numFitPts, const int *fitTypes,
int numFitShape, std::vector<double> &gradConverters,
double calcVolAndGrads(const double *ref, const int numRefPts,
const int *refTypes, const double *fit,
const int numFitPts, const int *fitTypes,
const int numFitShape,
std::vector<double> &gradConverters,
const bool useCutoff, const double distCutoff2,
const double *quat, double *gradients) {
double vol = 0.0;
@@ -266,22 +268,22 @@ double calcVolAndGrads(const double *ref, int numRefPts, const int *refTypes,
if (aType != bType) {
continue;
}
auto dx = ref[i] - fit[j];
auto dy = ref[i + 1] - fit[j + 1];
auto dz = ref[i + 2] - fit[j + 2];
auto d2 = dx * dx + dy * dy + dz * dz;
const auto dx = ref[i] - fit[j];
const auto dy = ref[i + 1] - fit[j + 1];
const auto dz = ref[i + 2] - fit[j + 2];
const auto d2 = dx * dx + dy * dy + dz * dz;
if (useCutoff && d2 > distCutoff2) {
continue;
}
const auto aj = fit[j + 3];
auto mult = -(ai * aj) / (ai + aj);
auto kij = exp(mult * d2);
const auto mult = -(ai * aj) / (ai + aj);
const auto kij = exp(mult * d2);
auto pi_ai_aj = std::numbers::pi / (ai + aj);
auto vij = 8 * kij * pi_ai_aj * std::sqrt(pi_ai_aj);
const auto pi_ai_aj = std::numbers::pi / (ai + aj);
const auto vij = 8 * kij * pi_ai_aj * std::sqrt(pi_ai_aj);
vol += vij;
if (gradients) {
auto r = 2.0 * vij * mult;
const auto r = 2.0 * vij * mult;
// Use the converters to calculate the gradients in quaternion space.
// The zeroth gradient is never used, so don't waste time calculating
// it but leave the code here for completeness and possible future use.
@@ -310,7 +312,7 @@ double calcVolAndGrads(const double *ref, int numRefPts, const int *refTypes,
void SingleConformerAlignment::applyQuatTrans(
const std::array<double, 7> &quatTrans) {
// Leave fit at the origin, and move ref to meet it.
RDGeom::Point3D translateA{-quatTrans[4], -quatTrans[5], -quatTrans[6]};
RDGeom::Point3D const translateA{-quatTrans[4], -quatTrans[5], -quatTrans[6]};
translateShape(d_ref.data(), d_refTemp.data(), d_nRefShape + d_nRefColor,
translateA);
// Rotate fit by quaternion
@@ -343,13 +345,13 @@ void SingleConformerAlignment::calcVolumeAndGradients(
d_useCutoff, d_distCutoff2, quatTrans.data(), colorGrads.data());
// The color gradients are normally dwarfed by the shape gradients, so
// normalize them and then mix by the same rule as the final score.
auto shapeSum = sqrt(std::accumulate(
const auto shapeSum = sqrt(std::accumulate(
gradients.begin() + 1, gradients.end(), 0.0,
[](const auto init, const auto g) -> double { return init + g * g; }));
auto colorSum = sqrt(std::accumulate(
const auto colorSum = sqrt(std::accumulate(
colorGrads.begin() + 1, colorGrads.end(), 0.0,
[](const auto init, const auto g) -> double { return init + g * g; }));
auto ratio = shapeSum / colorSum;
const auto ratio = shapeSum / colorSum;
std::transform(
gradients.begin() + 1, gradients.end(), colorGrads.begin(),
gradients.begin() + 1, [&](const auto g1, const auto g2) -> double {
@@ -361,9 +363,9 @@ void SingleConformerAlignment::calcVolumeAndGradients(
}
bool SingleConformerAlignment::doOverlay(std::array<double, 20> &scores,
unsigned int cycle) {
unsigned int maxIters = cycle == 0 ? 10 : d_maxIts - 10;
auto res = optimise(maxIters);
const unsigned int cycle) {
const unsigned int maxIters = cycle == 0 ? 10 : d_maxIts - 10;
const auto res = optimise(maxIters);
// Get the final coords for fit into d_fitTemp, and compute the scores
RDGeom::Transform3D xform;
@@ -373,7 +375,7 @@ bool SingleConformerAlignment::doOverlay(std::array<double, 20> &scores,
applyTransformToShape(d_fit.data(), d_fitTemp.data(),
d_nFitShape + d_nFitColor, xform);
auto tscores = calcScores(d_ref.data(), d_fitTemp.data(), true);
const auto tscores = calcScores(d_ref.data(), d_fitTemp.data(), true);
scores[0] = tscores[0];
scores[1] = tscores[1];
scores[2] = tscores[2];
@@ -398,14 +400,14 @@ bool SingleConformerAlignment::doOverlay(std::array<double, 20> &scores,
}
namespace {
double oneStep(double grad, double stepSize, double quatTrans, double oldGrad,
double oldQuatTrans) {
double oneStep(const double grad, const double stepSize, const double quatTrans,
const double oldGrad, const double oldQuatTrans) {
double step = 0.0;
if (std::signbit(grad) != std::signbit(oldGrad)) {
step = (((quatTrans * fabs(oldGrad)) + (oldQuatTrans * fabs(grad))) /
(fabs(oldGrad) + fabs(grad) + fabs(grad))) -
step = (quatTrans * fabs(oldGrad) + oldQuatTrans * fabs(grad)) /
(fabs(oldGrad) + fabs(grad) + fabs(grad)) -
quatTrans;
double newStep = stepSize * grad;
const double newStep = stepSize * grad;
if (fabs(step) > fabs(newStep)) {
// This is definitely what the PubChem code says! I read it as keeping
// the sign of step, but the value of newStep.
@@ -417,10 +419,11 @@ double oneStep(double grad, double stepSize, double quatTrans, double oldGrad,
return step;
}
void calcStep(std::array<double, 7> &grad, double qStepSize, double tStepSize,
std::array<double, 7> &oldGrad, std::array<double, 7> &quatTrans,
std::array<double, 7> &oldQuatTrans, unsigned int iter,
std::array<double, 7> &step) {
void calcStep(const std::array<double, 7> &grad, const double qStepSize,
const double tStepSize, const std::array<double, 7> &oldGrad,
const std::array<double, 7> &quatTrans,
const std::array<double, 7> &oldQuatTrans,
const unsigned int iter, std::array<double, 7> &step) {
step[0] = 0.0;
if (iter == 0) {
// 1st iteration, use default step sizes
@@ -446,25 +449,25 @@ void calcStep(std::array<double, 7> &grad, double qStepSize, double tStepSize,
}
}
double constrainStep(double maxStep, double *step, bool checkSize) {
double mStep = std::max({fabs(step[0]), fabs(step[1]), fabs(step[2])});
double constrainStep(const double maxStep, double *step, const bool checkSize) {
const double mStep = std::max({fabs(step[0]), fabs(step[1]), fabs(step[2])});
if (mStep > maxStep) {
double scaleFactor = maxStep / mStep;
if (fabs(step[0] > maxStep)) {
const double scaleFactor = maxStep / mStep;
if (fabs(step[0]) > maxStep) {
step[0] *= scaleFactor;
}
if (fabs(step[1] > maxStep)) {
if (fabs(step[1]) > maxStep) {
step[1] *= scaleFactor;
}
if (fabs(step[2] > maxStep)) {
if (fabs(step[2]) > maxStep) {
step[2] *= scaleFactor;
}
}
if (checkSize) {
double quatSquared =
const double quatSquared =
step[0] * step[0] + step[1] * step[1] + step[2] * step[2];
if (quatSquared > 1.0) {
double scaleFactor = 1.0 / (2.0 * quatSquared);
const double scaleFactor = 1.0 / (2.0 * quatSquared);
step[0] *= scaleFactor;
step[1] *= scaleFactor;
step[2] *= scaleFactor;
@@ -490,13 +493,14 @@ std::array<double, 7> combineQuatTrans(const std::array<double, 7> &q1,
return res;
}
double oneReduceStep(double grad, double oldGrad, double quatTrans,
double oldQuatTrans, double stepSize, double step) {
double oneReduceStep(const double grad, const double oldGrad,
const double quatTrans, const double oldQuatTrans,
const double stepSize, double step) {
if (std::signbit(grad) != std::signbit(oldGrad)) {
step = (((quatTrans * fabs(oldGrad)) + (oldQuatTrans * fabs(grad))) /
(fabs(oldGrad + fabs(grad)))) -
step = (quatTrans * fabs(oldGrad) + oldQuatTrans * fabs(grad)) /
(fabs(oldGrad) + fabs(grad)) -
quatTrans;
double newStep = stepSize * grad;
const double newStep = stepSize * grad;
if (fabs(step) > fabs(newStep)) {
step *= fabs(newStep / step);
}
@@ -515,11 +519,12 @@ double oneReduceStep(double grad, double oldGrad, double quatTrans,
return step;
}
void reduceStep(std::array<double, 7> &grad, std::array<double, 7> &oldGrad,
std::array<double, 7> quatTrans,
std::array<double, 7> &oldQuatTrans, unsigned int lineIter,
std::array<double, 7> &step, double &qStepSize,
double &tStepSize) {
void reduceStep(const std::array<double, 7> &grad,
const std::array<double, 7> &oldGrad,
const std::array<double, 7> &quatTrans,
const std::array<double, 7> &oldQuatTrans,
const unsigned int lineIter, std::array<double, 7> &step,
double &qStepSize, double &tStepSize) {
if (lineIter == 2) {
qStepSize *= 0.1;
tStepSize *= 0.1;
@@ -579,7 +584,7 @@ bool SingleConformerAlignment::optimise(unsigned int maxIters) {
iter, step);
// In case we have to backtrack
double oldComboScore = comboScore;
const double oldComboScore = comboScore;
oldQuatTrans = d_quatTrans;
oldGrad = grad;
@@ -588,8 +593,10 @@ bool SingleConformerAlignment::optimise(unsigned int maxIters) {
for (unsigned int lineIter = 0; !converged; lineIter++) {
// Check that the absolute max step size does not go beyond some
// reasonable size
double mqStep = constrainStep(maxQuaternionStep, step.data() + 1, true);
double mtStep = constrainStep(maxTranslationStep, step.data() + 4, false);
const double mqStep =
constrainStep(maxQuaternionStep, step.data() + 1, true);
const double mtStep =
constrainStep(maxTranslationStep, step.data() + 4, false);
if (mqStep <= minQuaternionStep && mtStep <= minTranslationStep) {
converged = true;
comboScore = 0.0; // Make sure we return to the old one.
@@ -597,14 +604,14 @@ bool SingleConformerAlignment::optimise(unsigned int maxIters) {
}
// Calculate the 0th component of the quaternion. Obviously it
// relies on the other 3 components being small
double quatSquared =
const double quatSquared =
step[1] * step[1] + step[2] * step[2] + step[3] * step[3];
step[0] = sqrt(1.0 - quatSquared);
// Update the quaternion with the step, multiplying them.
auto newQuatTrans = combineQuatTrans(d_quatTrans, step);
calcVolumeAndGradients(newQuatTrans, shapeOvlpVol, colorOvlpVol, grad);
auto scores = calcScores(shapeOvlpVol, colorOvlpVol);
comboScore = scores[0];
auto newScores = calcScores(shapeOvlpVol, colorOvlpVol);
comboScore = newScores[0];
// if we made a good step, keep the quaternion and we're done
if (comboScore > oldComboScore) {
d_quatTrans = newQuatTrans;

30
Code/GraphMol/GaussianShape/catch_tests.cpp
View File

@@ -161,7 +161,7 @@ TEST_CASE("basic alignment") {
} else {
CHECK_THAT(scores[0], Catch::Matchers::WithinAbs(0.503, 0.005));
CHECK_THAT(scores[1], Catch::Matchers::WithinAbs(0.761, 0.005));
CHECK_THAT(scores[2], Catch::Matchers::WithinAbs(0.245, 0.005));
CHECK_THAT(scores[2], Catch::Matchers::WithinAbs(0.233, 0.005));
}
// Check that a re-score gives the same answer.
const auto rescores = GaussianShape::ScoreMolecule(
@@ -294,9 +294,9 @@ TEST_CASE("handling molecules with Hs") {
RWMol cp(*probe);
RDGeom::Transform3D xform;
auto scores = GaussianShape::AlignMolecule(*ref, cp);
CHECK_THAT(scores[0], Catch::Matchers::WithinAbs(0.700, 0.005));
CHECK_THAT(scores[0], Catch::Matchers::WithinAbs(0.736, 0.005));
CHECK_THAT(scores[1], Catch::Matchers::WithinAbs(0.834, 0.005));
CHECK_THAT(scores[2], Catch::Matchers::WithinAbs(0.566, 0.005));
CHECK_THAT(scores[2], Catch::Matchers::WithinAbs(0.635, 0.005));
for (auto i = 0u; i < cp.getNumAtoms(); ++i) {
// the failure mode here was that Hs had HUGE coordinates
auto pos = cp.getConformer().getAtomPos(i);
@@ -440,19 +440,18 @@ TEST_CASE("Iressa onto Tagrisso") {
shapeOpts.allCarbonRadii = false;
auto scores = GaussianShape::AlignMolecule(*tagrisso, *iressa, shapeOpts,
shapeOpts, nullptr, opts);
CHECK_THAT(scores[0], Catch::Matchers::WithinAbs(0.332, 0.005));
CHECK_THAT(scores[1], Catch::Matchers::WithinAbs(0.569, 0.005));
CHECK_THAT(scores[2], Catch::Matchers::WithinAbs(0.095, 0.005));
CHECK_THAT(scores[0], Catch::Matchers::WithinAbs(0.331, 0.005));
CHECK_THAT(scores[1], Catch::Matchers::WithinAbs(0.572, 0.005));
CHECK_THAT(scores[2], Catch::Matchers::WithinAbs(0.090, 0.005));
auto rescores = GaussianShape::ScoreMolecule(*tagrisso, *iressa, shapeOpts,
shapeOpts, opts);
CHECK_THAT(scores[0], Catch::Matchers::WithinAbs(rescores[0], 0.005));
CHECK_THAT(scores[1], Catch::Matchers::WithinAbs(rescores[1], 0.005));
CHECK_THAT(scores[2], Catch::Matchers::WithinAbs(rescores[2], 0.005));
auto aligned_iressa =
"COc1cc2ncnc(Nc3ccc(F)c(Cl)c3)c2cc1OCCCN1CCOCC1 |(3.34206,-4.82098,0.224565;2.562,-4.29938,-0.849374;1.40029,-3.66768,-0.520786;0.217637,-4.40844,-0.435429;-0.995315,-3.80966,-0.103538;-2.12266,-4.53841,-0.026421;-3.25097,-3.87666,0.301586;-3.3749,-2.56477,0.559961;-2.22774,-1.8651,0.473675;-2.30832,-0.475114,0.738276;-3.33657,0.464391,0.56286;-4.2686,0.303124,-0.466868;-5.2907,1.23626,-0.641364;-5.38531,2.33529,0.212458;-6.37287,3.22379,0.031359;-4.45782,2.50088,1.24127;-4.5695,3.85508,2.29834;-3.43604,1.56746,1.41601;-0.997368,-2.42737,0.145328;0.187601,-1.67548,0.061391;1.37756,-2.30488,-0.27166;2.52893,-1.56544,-0.352965;2.83995,-1.00034,-1.61907;3.59724,0.302963,-1.40382;2.76275,1.31266,-0.622178;1.52096,1.60458,-1.33518;0.667075,2.50553,-0.54864;-0.616491,2.80465,-1.31789;-0.312021,3.38752,-2.58555;0.491386,2.50505,-3.3701;1.80144,2.19743,-2.65039)|"_smiles;
"COc1cc2ncnc(Nc3ccc(F)c(Cl)c3)c2cc1OCCCN1CCOCC1 |(3.08453,-4.88523,0.170077;2.29914,-4.34091,-0.888589;1.15638,-3.68668,-0.538328;-0.040292,-4.40272,-0.438557;-1.23492,-3.78034,-0.0843727;-2.37618,-4.48548,0.00635958;-3.48492,-3.80191,0.355683;-3.57688,-2.48924,0.623248;-2.41657,-1.81353,0.522875;-2.46344,-0.42373,0.79642;-3.47407,0.538362,0.642364;-4.42522,0.402938,-0.373507;-5.42983,1.35852,-0.526776;-5.48774,2.45427,0.334513;-6.45888,3.36454,0.173853;-4.54106,2.59412,1.34956;-4.60745,3.94414,2.41576;-3.53677,1.63825,1.50308;-1.2037,-2.3998,0.172165;-0.00444866,-1.6727,0.0738388;1.16652,-2.3252,-0.281314;2.33196,-1.60985,-0.376552;2.6352,-1.04403,-1.64422;3.4233,0.241654,-1.43364;2.62275,1.26418,-0.633414;1.37651,1.58654,-1.32523;0.554317,2.50073,-0.520411;-0.734405,2.83149,-1.26777;-0.437359,3.41523,-2.53679;0.334793,2.52057,-3.33873;1.64904,2.18104,-2.64136)|"_smiles;
REQUIRE(aligned_iressa);
checkMolsHaveRoughlySameCoords(*iressa, *aligned_iressa);
CHECK(checkMolsHaveRoughlySameCoords(*iressa, *aligned_iressa));
}
TEST_CASE("Optimise in place") {
@@ -501,9 +500,9 @@ TEST_CASE("Optimise in place") {
ROMol cp(*canon_probe);
auto scores = GaussianShape::AlignMolecule(*pdb_trp_3tmn, cp, shapeOpts,
shapeOpts, nullptr, opts);
CHECK_THAT(scores[0], Catch::Matchers::WithinAbs(0.197, 0.001));
CHECK_THAT(scores[1], Catch::Matchers::WithinAbs(0.361, 0.001));
CHECK_THAT(scores[2], Catch::Matchers::WithinAbs(0.033, 0.001));
CHECK_THAT(scores[0], Catch::Matchers::WithinAbs(0.201, 0.001));
CHECK_THAT(scores[1], Catch::Matchers::WithinAbs(0.364, 0.001));
CHECK_THAT(scores[2], Catch::Matchers::WithinAbs(0.039, 0.001));
}
{
// And with reference as a shape the same
@@ -561,10 +560,9 @@ TEST_CASE("Fragment Mode") {
// Use the smaller molecule as the probe
auto scores = GaussianShape::AlignShape(refShape, probeShape, &xform, opts);
// These are close to the values above for starting from the xtal structures.
CHECK_THAT(scores[0], Catch::Matchers::WithinAbs(0.311, 0.005));
CHECK_THAT(scores[1], Catch::Matchers::WithinAbs(0.408, 0.005));
CHECK_THAT(scores[2], Catch::Matchers::WithinAbs(0.215, 0.005));
MolTransforms::transformConformer(pdb_trp_3tmn->getConformer(), xform);
CHECK_THAT(scores[0], Catch::Matchers::WithinAbs(0.332, 0.005));
CHECK_THAT(scores[1], Catch::Matchers::WithinAbs(0.413, 0.005));
CHECK_THAT(scores[2], Catch::Matchers::WithinAbs(0.251, 0.005));
}
TEST_CASE("custom feature points") {