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5f7e04fe5db3d59d2b2f4763fa22642d74fcfe29
rdkit/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp
Greg Landrum 5f7e04fe5d Fix github1240 (#1396) 
* add a test (currently fails, of course)

* backup, not really working

* Fixes #1240

* a bit more parameter tweaking to get some more structures to embed
2017-04-18 02:33:23 -04:00

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//
// Copyright (C) 2004-2017 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/RDLog.h>
#include <RDGeneral/versions.h>
#include <GraphMol/RDKitBase.h>
#include <string>
#include <vector>
#include <iostream>
#include <DistGeom/BoundsMatrix.h>
#include <DistGeom/DistGeomUtils.h>
#include <DistGeom/TriangleSmooth.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <iostream>
#include "BoundsMatrixBuilder.h"
#include "Embedder.h"
#include <stdlib.h>
#include <GraphMol/FileParsers/MolWriters.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/ROMol.h>
#include <ForceField/ForceField.h>
#include <GraphMol/ForceFieldHelpers/UFF/Builder.h>
#include <RDGeneral/FileParseException.h>
#include <ForceField/ForceField.h>
#include <GraphMol/MolAlign/AlignMolecules.h>
#include <math.h>
#include <RDGeneral/Exceptions.h>
#include <boost/tokenizer.hpp>
typedef boost::tokenizer<boost::char_separator<char> > tokenizer;
using namespace RDKit;
void test1() {
std::string smiString =
"CC1=C(C(C)=CC=C2)C2=CC=C1 c1ccccc1C C/C=C/CC \
C/12=C(\\CSC2)Nc3cc(n[n]3C1=O)c4ccccc4 C1CCCCS1(=O)(=O) c1ccccc1 \
C1CCCC1 C1CCCCC1 \
C1CC1(C)C C12(C)CC1CC2";
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/DistGeomHelpers/test_data/initCoords.sdf";
SDMolSupplier sdsup(fname);
// SDWriter writer("foo.sdf");
boost::char_separator<char> spaceSep(" ");
tokenizer tokens(smiString, spaceSep);
for (tokenizer::iterator token = tokens.begin(); token != tokens.end();
++token) {
std::string smi = *token;
RWMol *m = SmilesToMol(smi, 0, 1);
int cid = DGeomHelpers::EmbedMolecule(*m, 10, 1, true, false, 2, true, 1, 0,
1e-2);
CHECK_INVARIANT(cid >= 0, "");
ROMol *m2 = sdsup.next();
// BOOST_LOG(rdInfoLog) << ">>> " << smi << std::endl;
// writer.write(*m);
// writer.flush();
// ROMol *m2 = NULL;
if (m2) {
unsigned int nat = m->getNumAtoms();
const Conformer &conf1 = m->getConformer(0);
const Conformer &conf2 = m2->getConformer(0);
#if 0
BOOST_LOG(rdInfoLog) << "-----------------------" << std::endl;
BOOST_LOG(rdInfoLog) << MolToMolBlock(*m2) << std::endl;
BOOST_LOG(rdInfoLog) << "---" << std::endl;
BOOST_LOG(rdInfoLog) << MolToMolBlock(*m) << std::endl;
BOOST_LOG(rdInfoLog) << "-----------------------" << std::endl;
#endif
for (unsigned int i = 0; i < nat; i++) {
RDGeom::Point3D pt1i = conf1.getAtomPos(i);
RDGeom::Point3D pt2i = conf2.getAtomPos(i);
for (unsigned int j = i + 1; j < nat; j++) {
RDGeom::Point3D pt1j = conf1.getAtomPos(j);
RDGeom::Point3D pt2j = conf2.getAtomPos(j);
double d1 = (pt1j - pt1i).length();
double d2 = (pt2j - pt2i).length();
if (m->getBondBetweenAtoms(i, j)) {
// BOOST_LOG(rdInfoLog) << ">1> " <<i<<","<<j<<":"<< d1 << " " << d2
// << std::endl;
TEST_ASSERT(fabs(d1 - d2) / d1 < 0.06);
} else {
// BOOST_LOG(rdInfoLog) << ">2> " <<i<<","<<j<<":"<< d1 << " " << d2
// << " "<<fabs(d1-d2)/d1<<std::endl;
TEST_ASSERT(fabs(d1 - d2) / d1 < 0.12);
}
}
}
}
delete m;
delete m2;
}
}
void computeDistMat(const RDGeom::PointPtrVect &origCoords,
RDNumeric::DoubleSymmMatrix &distMat) {
unsigned int N = origCoords.size();
CHECK_INVARIANT(N == distMat.numRows(), "");
unsigned int i, j;
RDGeom::Point3D pti, ptj;
double d;
for (i = 1; i < N; i++) {
pti = *(RDGeom::Point3D *)origCoords[i];
for (j = 0; j < i; j++) {
ptj = *(RDGeom::Point3D *)origCoords[j];
ptj -= pti;
d = ptj.length();
distMat.setVal(i, j, d);
}
}
}
void computeMolDmat(ROMol &mol, RDNumeric::DoubleSymmMatrix &distMat) {
RDGeom::PointPtrVect origCoords;
unsigned int i, nat = mol.getNumAtoms();
Conformer &conf = mol.getConformer(0);
for (i = 0; i < nat; i++) {
origCoords.push_back(&conf.getAtomPos(i));
}
computeDistMat(origCoords, distMat);
}
void test2() {
// check for in ring distances, and distances containing two bonds in a ring
std::string smi = "Cc1c(C=CC(C)N2)c2[nH]n1";
ROMol *mol = SmilesToMol(smi, 0, 1);
DistGeom::BoundsMatPtr bm;
RDNumeric::DoubleSymmMatrix *dmat;
int cid;
unsigned int nat = mol->getNumAtoms();
#if 1
bm.reset(new DistGeom::BoundsMatrix(nat));
DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
DGeomHelpers::setTopolBounds(*mol, bm);
std::cerr << "go" << std::endl;
cid = DGeomHelpers::EmbedMolecule(*mol, 10, 1);
TEST_ASSERT(cid > -1);
dmat = new RDNumeric::DoubleSymmMatrix(nat, 0.0);
computeMolDmat(*mol, *dmat);
TEST_ASSERT((bm->getUpperBound(0, 9) - bm->getLowerBound(0, 9)) < 0.13);
TEST_ASSERT((bm->getUpperBound(0, 9) - dmat->getVal(0, 9) > -0.1) &&
(bm->getLowerBound(0, 9) - dmat->getVal(0, 9) < 0.10));
TEST_ASSERT((bm->getUpperBound(10, 7) - bm->getLowerBound(10, 7)) < 0.13);
TEST_ASSERT((bm->getUpperBound(10, 7) - dmat->getVal(10, 7) > -0.1) &&
(bm->getLowerBound(10, 7) - dmat->getVal(10, 7) < 0.10));
TEST_ASSERT((bm->getUpperBound(2, 5) - bm->getLowerBound(2, 5)) < 0.20);
TEST_ASSERT((bm->getUpperBound(2, 5) - dmat->getVal(2, 5) > -0.1) &&
(bm->getLowerBound(2, 5) - dmat->getVal(2, 5) < 0.10));
TEST_ASSERT((bm->getUpperBound(8, 4) - bm->getLowerBound(8, 4)) > 1.);
TEST_ASSERT((bm->getUpperBound(8, 4) - bm->getLowerBound(8, 4)) < 1.2);
TEST_ASSERT((bm->getUpperBound(8, 4) - dmat->getVal(8, 4) > -0.1) &&
(bm->getLowerBound(8, 4) - dmat->getVal(8, 4) < 0.10));
TEST_ASSERT((bm->getUpperBound(8, 6) - bm->getLowerBound(8, 6)) > 1.0);
TEST_ASSERT((bm->getUpperBound(8, 6) - bm->getLowerBound(8, 6)) < 1.2);
TEST_ASSERT((bm->getUpperBound(8, 6) - dmat->getVal(8, 6) > -0.1) &&
(bm->getLowerBound(8, 6) - dmat->getVal(8, 6) < 0.10));
delete mol;
delete dmat;
// chain of singles
smi = "CCCC";
mol = SmilesToMol(smi, 0, 1);
nat = mol->getNumAtoms();
bm.reset(new DistGeom::BoundsMatrix(nat));
DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
DGeomHelpers::setTopolBounds(*mol, bm);
cid = DGeomHelpers::EmbedMolecule(*mol, 10, 1);
TEST_ASSERT(cid > -1);
dmat = new RDNumeric::DoubleSymmMatrix(nat, 0.0);
computeMolDmat(*mol, *dmat);
TEST_ASSERT((bm->getUpperBound(0, 3) - bm->getLowerBound(0, 3)) > 1.0);
TEST_ASSERT((bm->getUpperBound(0, 3) - bm->getLowerBound(0, 3)) < 1.3);
TEST_ASSERT((bm->getUpperBound(0, 3) - dmat->getVal(0, 3) > -0.1) &&
(bm->getLowerBound(0, 3) - dmat->getVal(0, 3) < 0.10));
delete mol;
delete dmat;
smi = "C=C=C=C";
mol = SmilesToMol(smi, 0, 1);
nat = mol->getNumAtoms();
bm.reset(new DistGeom::BoundsMatrix(nat));
DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
DGeomHelpers::setTopolBounds(*mol, bm);
cid = DGeomHelpers::EmbedMolecule(*mol, 10, 1);
TEST_ASSERT(cid > -1);
dmat = new RDNumeric::DoubleSymmMatrix(nat, 0.0);
computeMolDmat(*mol, *dmat);
TEST_ASSERT((bm->getUpperBound(0, 3) - bm->getLowerBound(0, 3)) < .13);
TEST_ASSERT(bm->getUpperBound(0, 3) > dmat->getVal(0, 3));
// this is kinda goofy but this linear molecule doesn't satisfy the bounds
// completely
TEST_ASSERT(fabs(bm->getLowerBound(0, 3) - dmat->getVal(0, 3)) < 0.2);
delete mol;
delete dmat;
#endif
std::cerr << "-------------------------------------\n\n";
smi = "C/C=C/C";
mol = SmilesToMol(smi, 0, 1);
nat = mol->getNumAtoms();
bm.reset(new DistGeom::BoundsMatrix(nat));
DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
DGeomHelpers::setTopolBounds(*mol, bm);
cid = DGeomHelpers::EmbedMolecule(*mol, 10, 1);
TEST_ASSERT(cid > -1);
dmat = new RDNumeric::DoubleSymmMatrix(nat, 0.0);
// std::cerr << "\n-----\n" << MolToMolBlock(mol,false,cid) << std::endl;;
computeMolDmat(*mol, *dmat);
TEST_ASSERT((bm->getUpperBound(0, 3) - bm->getLowerBound(0, 3)) < .13);
// std::cerr << bm->getUpperBound(0,3) << " " << dmat->getVal(0,3) << " " <<
// bm->getLowerBound(0,3) << std::endl;
TEST_ASSERT((bm->getUpperBound(0, 3) - dmat->getVal(0, 3) > -0.1) &&
(bm->getLowerBound(0, 3) - dmat->getVal(0, 3) < 0.1));
delete mol;
delete dmat;
smi = "C/C=C\\C";
mol = SmilesToMol(smi, 0, 1);
nat = mol->getNumAtoms();
bm.reset(new DistGeom::BoundsMatrix(nat));
DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
DGeomHelpers::setTopolBounds(*mol, bm);
cid = DGeomHelpers::EmbedMolecule(*mol, 10, 1);
TEST_ASSERT(cid > -1);
dmat = new RDNumeric::DoubleSymmMatrix(nat, 0.0);
computeMolDmat(*mol, *dmat);
TEST_ASSERT((bm->getUpperBound(0, 3) - bm->getLowerBound(0, 3)) < .13);
TEST_ASSERT((bm->getUpperBound(0, 3) - dmat->getVal(0, 3) > -0.1) &&
(bm->getLowerBound(0, 3) - dmat->getVal(0, 3) < 0.10));
delete mol;
delete dmat;
smi = "CC=CC";
mol = SmilesToMol(smi, 0, 1);
nat = mol->getNumAtoms();
bm.reset(new DistGeom::BoundsMatrix(nat));
DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
DGeomHelpers::setTopolBounds(*mol, bm);
cid = DGeomHelpers::EmbedMolecule(*mol, 10, 1);
TEST_ASSERT(cid > -1);
dmat = new RDNumeric::DoubleSymmMatrix(nat, 0.0);
computeMolDmat(*mol, *dmat);
TEST_ASSERT((bm->getUpperBound(0, 3) - bm->getLowerBound(0, 3)) < 1.13);
TEST_ASSERT((bm->getUpperBound(0, 3) - bm->getLowerBound(0, 3)) > 1.);
TEST_ASSERT((bm->getUpperBound(0, 3) - dmat->getVal(0, 3) > -0.1) &&
(bm->getLowerBound(0, 3) - dmat->getVal(0, 3) < 0.10));
delete mol;
delete dmat;
smi = "O=S-S=O";
mol = SmilesToMol(smi, 0, 1);
nat = mol->getNumAtoms();
bm.reset(new DistGeom::BoundsMatrix(nat));
DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
DGeomHelpers::setTopolBounds(*mol, bm);
cid = DGeomHelpers::EmbedMolecule(*mol, 10, 1);
TEST_ASSERT(cid > -1);
dmat = new RDNumeric::DoubleSymmMatrix(nat, 0.0);
computeMolDmat(*mol, *dmat);
TEST_ASSERT((bm->getUpperBound(0, 3) - bm->getLowerBound(0, 3)) < .13);
TEST_ASSERT((bm->getUpperBound(0, 3) - dmat->getVal(0, 3) > -0.1) &&
(bm->getLowerBound(0, 3) - dmat->getVal(0, 3) < 0.10));
delete mol;
delete dmat;
#if 0
// this next block of tests all handle the special case that led to Issue284
smi = "COC=O";
mol = SmilesToMol(smi, 0, 1);
nat = mol->getNumAtoms();
bm.reset(new DistGeom::BoundsMatrix(nat));
DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
DGeomHelpers::setTopolBounds(*mol, bm);
cid = DGeomHelpers::EmbedMolecule(*mol, 10, 1);
TEST_ASSERT(cid>-1);
dmat = new RDNumeric::DoubleSymmMatrix(nat, 0.0);
computeMolDmat(*mol, *dmat);
//TEST_ASSERT( (bm->getUpperBound(0,3) - bm->getLowerBound(0,3)) < .13);
double x,y,z;
x = bm->getUpperBound(0,3);
y = bm->getLowerBound(0,3);
z = dmat->getVal(0,3);
//TEST_ASSERT( (bm->getUpperBound(0,3) - dmat->getVal(0,3) > -0.1)
// && (bm->getLowerBound(0,3) - dmat->getVal(0,3) < 0.10 ));
delete mol;
delete dmat;
smi = "C[NH]C=O";
mol = SmilesToMol(smi, 0, 1);
nat = mol->getNumAtoms();
bm.reset(new DistGeom::BoundsMatrix(nat));
DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
DGeomHelpers::setTopolBounds(*mol, bm);
cid = DGeomHelpers::EmbedMolecule(*mol, 10, 1);
TEST_ASSERT(cid>-1);
dmat = new RDNumeric::DoubleSymmMatrix(nat, 0.0);
computeMolDmat(*mol, *dmat);
TEST_ASSERT( (bm->getUpperBound(0,3) - bm->getLowerBound(0,3)) < .13);
//TEST_ASSERT( (bm->getUpperBound(0,3) - dmat->getVal(0,3) > -0.1)
// && (bm->getLowerBound(0,3) - dmat->getVal(0,3) < 0.10));
delete mol;
delete dmat;
#endif
}
void test3() {
// check embedding based based on distances calculated from previous created
// (good) coordinates
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/DistGeomHelpers/test_data/combi_coords.sdf";
SDMolSupplier sdsup(fname);
unsigned int i, j, nat;
bool gotCoords;
while (!sdsup.atEnd()) {
ROMol *mol = sdsup.next();
std::string mname;
mol->getProp(common_properties::_Name, mname);
RDGeom::PointPtrVect origCoords, newCoords;
nat = mol->getNumAtoms();
Conformer &conf = mol->getConformer(0);
for (i = 0; i < nat; i++) {
origCoords.push_back(&conf.getAtomPos(i));
}
RDNumeric::DoubleSymmMatrix distMat(nat, 0.0);
computeDistMat(origCoords, distMat);
gotCoords = DistGeom::computeInitialCoords(distMat, origCoords);
CHECK_INVARIANT(gotCoords, "");
RDNumeric::DoubleSymmMatrix distMatNew(nat, 0.0);
computeDistMat(origCoords, distMatNew);
for (i = 1; i < nat; i++) {
for (j = 0; j < i; j++) {
CHECK_INVARIANT(
RDKit::feq(distMat.getVal(i, j), distMatNew.getVal(i, j), 0.01),
"");
}
}
}
}
void test4() {
std::string smi =
"c1cc(C(F)(F)F)ccc1/C=N/NC(=O)c(n2)c[n]3cc(C(F)(F)F)cc(c23)Cl";
ROMol *m = SmilesToMol(smi, 0, 1);
DGeomHelpers::EmbedMolecule(*m, 10, 1); // etCoords(*m, iter);
std::string fname = "test.mol";
MolToMolFile(*m, fname);
delete m;
}
void test5() {
// some real CDK2 molecules lets see how many fail
std::string rdbase = getenv("RDBASE");
std::string smifile =
rdbase + "/Code/GraphMol/DistGeomHelpers/test_data/cis_trans_cases.csv";
SmilesMolSupplier smiSup(smifile, ",", 0, 1);
ROMol *mol;
int i = 0;
int cid;
while (1) {
try {
i++;
mol = smiSup.next();
cid = DGeomHelpers::EmbedMolecule(*mol, 10, 1); // getCoords(*mol, iter);
TEST_ASSERT(cid > -1);
delete mol;
} catch (FileParseException &) {
break;
}
}
}
void test6() {
std::string smi;
ROMol *m;
DistGeom::BoundsMatPtr bm;
m = SmilesToMol("CC");
TEST_ASSERT(m);
bm.reset(new DistGeom::BoundsMatrix(m->getNumAtoms()));
TEST_ASSERT(bm);
DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
TEST_ASSERT(feq(bm->getLowerBound(0, 1), 0.0));
TEST_ASSERT(feq(bm->getLowerBound(1, 0), 0.0));
TEST_ASSERT(feq(bm->getUpperBound(0, 1), 1000.0));
TEST_ASSERT(feq(bm->getUpperBound(1, 0), 1000.0));
DGeomHelpers::setTopolBounds(*m, bm);
TEST_ASSERT(bm->getLowerBound(0, 1) > 0.0);
TEST_ASSERT(bm->getUpperBound(0, 1) < 1000.0);
TEST_ASSERT(bm->getLowerBound(0, 1) < bm->getUpperBound(0, 1));
delete m;
}
void testIssue215() {
std::string smi;
ROMol *m;
DistGeom::BoundsMatPtr bm;
bool ok;
m = SmilesToMol("C=C1C2CC1C2");
TEST_ASSERT(m);
bm.reset(new DistGeom::BoundsMatrix(m->getNumAtoms()));
TEST_ASSERT(bm);
DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
DGeomHelpers::setTopolBounds(*m, bm);
// this was the specific problem:
TEST_ASSERT(bm->getUpperBound(0, 4) < 100.0);
ok = DistGeom::triangleSmoothBounds(bm);
TEST_ASSERT(ok);
delete m;
}
void _computeStats(const std::vector<double> &vals, double &mean,
double &stdDev) {
unsigned int N = vals.size();
mean = 0.0;
double sqSum = 0.0;
stdDev = 0.0;
std::vector<double>::const_iterator vci;
for (vci = vals.begin(); vci != vals.end(); vci++) {
mean += (*vci);
sqSum += (*vci) * (*vci);
}
mean /= N;
sqSum /= N;
stdDev = sqrt(sqSum - (mean * mean));
}
void testTemp() {
// ROMol *m =
// SmilesToMol("CN(C)c(cc1)ccc1\\C=C(/C#N)c(n2)c(C#N)c([n]3cccc3)[n]2c(c4)cccc4");
// ROMol *m =
// SmilesToMol("C12C(=O)N(Cc3ccccc3)C(=O)C1C(C(=O)OC)(NC2c4ccc(Cl)c(c4)[N+]([O-])=O)Cc5c6ccccc6[nH]c5");
// c1(n2cccc2)n(c3ccccc3)ncc1
// ROMol *m = SmilesToMol("N#CCc1c(C#N)cn(C)n1");
// ROMol *m = SmilesToMol("Cc1c(C#N)cn(C)n1");
std::string rdbase = getenv("RDBASE");
std::string smifile =
rdbase + "/Code/GraphMol/DistGeomHelpers/test_data/cis_trans_cases.csv";
SmilesMolSupplier smiSup(smifile, ",", 0, 1);
ROMol *m;
unsigned int cnt = 0;
while (!smiSup.atEnd()) {
m = smiSup.next();
unsigned int i;
std::vector<double> energies;
double energy;
for (i = 0; i < 20; i++) {
int cid = DGeomHelpers::EmbedMolecule(*m, 10, 1, false);
if (cid >= 0) {
ForceFields::ForceField *ff = UFF::constructForceField(*m, 10, cid);
ff->initialize();
energy = ff->calcEnergy();
energies.push_back(energy);
delete ff;
}
}
double mean, stdDev;
_computeStats(energies, mean, stdDev);
std::string mname;
cnt++;
m->getProp(common_properties::_Name, mname);
BOOST_LOG(rdDebugLog) << cnt << "," << mname << "," << mean << "," << stdDev
<< "\n";
delete m;
}
}
void test15Dists() {
ROMol *m = SmilesToMol("c1ccccc1C");
unsigned int nat = m->getNumAtoms();
DistGeom::BoundsMatrix *mat = new DistGeom::BoundsMatrix(nat);
DGeomHelpers::initBoundsMat(mat);
DistGeom::BoundsMatPtr mmat(mat);
DGeomHelpers::setTopolBounds(*m, mmat);
CHECK_INVARIANT(RDKit::feq(mmat->getUpperBound(2, 6), 4.32, 0.01), "");
CHECK_INVARIANT(RDKit::feq(mmat->getLowerBound(2, 6), 4.16, 0.01), "");
delete m;
m = SmilesToMol("CC1=C(C(C)=CC=C2)C2=CC=C1");
nat = m->getNumAtoms();
mmat.reset(new DistGeom::BoundsMatrix(nat));
DGeomHelpers::initBoundsMat(mmat);
DGeomHelpers::setTopolBounds(*m, mmat);
CHECK_INVARIANT(RDKit::feq(mmat->getLowerBound(0, 4), 2.31, 0.01), "");
CHECK_INVARIANT(RDKit::feq(mmat->getUpperBound(0, 4), 2.47, 0.01), "");
CHECK_INVARIANT(RDKit::feq(mmat->getLowerBound(4, 11), 4.11, 0.01), "");
CHECK_INVARIANT(RDKit::feq(mmat->getUpperBound(4, 11), 4.27, 0.01), "");
delete m;
m = SmilesToMol("C/C=C/C=C/C", 0, 1);
nat = m->getNumAtoms();
mmat.reset(new DistGeom::BoundsMatrix(nat));
DGeomHelpers::initBoundsMat(mmat);
DGeomHelpers::setTopolBounds(*m, mmat);
CHECK_INVARIANT(RDKit::feq(mmat->getLowerBound(0, 4), 4.1874), "");
CHECK_INVARIANT(RDKit::feq(mmat->getUpperBound(0, 4), 4.924), "");
CHECK_INVARIANT(RDKit::feq(mmat->getLowerBound(1, 5), 4.1874), "");
CHECK_INVARIANT(RDKit::feq(mmat->getUpperBound(1, 5), 4.924), "");
delete m;
m = SmilesToMol("NCc(c1)cccc1");
delete m;
}
void testMultipleConfs() {
std::string smi = "CC(C)(C)c(cc1)ccc1c(cc23)n[n]3C(=O)/C(=C\\N2)C(=O)OCC";
ROMol *m = SmilesToMol(smi, 0, 1);
INT_VECT cids =
DGeomHelpers::EmbedMultipleConfs(*m, 10, 30, 100, true, false, -1);
INT_VECT_CI ci;
// SDWriter writer("junk.sdf");
double energy;
for (ci = cids.begin(); ci != cids.end(); ci++) {
// writer.write(*m, *ci);
ForceFields::ForceField *ff = UFF::constructForceField(*m, 10, *ci);
ff->initialize();
energy = ff->calcEnergy();
// BOOST_LOG(rdInfoLog) << energy << std::endl;
TEST_ASSERT(energy > 100.0);
TEST_ASSERT(energy < 300.0);
delete ff;
}
}
void testMultipleConfsExpTors() {
std::string smi = "CC(C)(C)c(cc1)ccc1c(cc23)n[n]3C(=O)/C(=C\\N2)C(=O)OCC";
ROMol *m = SmilesToMol(smi, 0, 1);
INT_VECT cids = DGeomHelpers::EmbedMultipleConfs(
*m, 10, 30, 100, true, false, -1, true, 1, -1.0, 0, 1e-3, false, true,
true, true, false);
INT_VECT_CI ci;
// SDWriter writer("junk.sdf");
double energy;
for (ci = cids.begin(); ci != cids.end(); ci++) {
// writer.write(*m, *ci);
ForceFields::ForceField *ff = UFF::constructForceField(*m, 10, *ci);
ff->initialize();
energy = ff->calcEnergy();
// BOOST_LOG(rdInfoLog) << energy << std::endl;
TEST_ASSERT(energy > 50.0);
TEST_ASSERT(energy < 300.0);
delete ff;
}
}
void testOrdering() {
std::string smi = "CC(C)(C)C(=O)NC(C1)CC(N2C)CCC12";
ROMol *m = SmilesToMol(smi, 0, 1);
unsigned int nat = m->getNumAtoms();
DistGeom::BoundsMatrix *mat = new DistGeom::BoundsMatrix(nat);
DGeomHelpers::initBoundsMat(mat);
DistGeom::BoundsMatPtr mmat(mat);
DGeomHelpers::setTopolBounds(*m, mmat);
delete m;
std::string smi2 = "CN1C2CCC1CC(NC(=O)C(C)(C)C)C2";
ROMol *m2 = SmilesToMol(smi2, 0, 1);
DistGeom::BoundsMatrix *mat2 = new DistGeom::BoundsMatrix(nat);
DGeomHelpers::initBoundsMat(mat2);
DistGeom::BoundsMatPtr mmat2(mat2);
DGeomHelpers::setTopolBounds(*m2, mmat2);
delete m2;
}
#if 1
void testIssue227() {
std::string smi =
"CCOP1(OCC)=CC(c2ccccc2)=C(c2ccc([N+]([O-])=O)cc2)N=C1c1ccccc1";
ROMol *m = SmilesToMol(smi, 0, 1);
unsigned int nat = m->getNumAtoms();
DistGeom::BoundsMatrix *mat = new DistGeom::BoundsMatrix(nat);
DistGeom::BoundsMatPtr bm(mat);
DGeomHelpers::initBoundsMat(bm);
DGeomHelpers::setTopolBounds(*m, bm);
bool ok = DistGeom::triangleSmoothBounds(bm);
TEST_ASSERT(ok);
delete m;
smi = "OC(=O)c1cc2cc(c1)-c1c(O)c(ccc1)-c1cc(C(O)=O)cc(c1)OCCOCCO2";
m = SmilesToMol(smi, 0, 1);
nat = m->getNumAtoms();
DistGeom::BoundsMatrix *nmat = new DistGeom::BoundsMatrix(nat);
bm.reset(nmat);
DGeomHelpers::initBoundsMat(bm);
DGeomHelpers::setTopolBounds(*m, bm);
ok = DistGeom::triangleSmoothBounds(bm);
TEST_ASSERT(ok);
delete m;
}
#endif
void testIssue236() {
std::string smi =
"Cn1c2n(-c3ccccc3)c(=O)c3c(nc4ccc([N+]([O-])=O)cc4c3)c2c(=O)n(C)c1=O";
ROMol *m = SmilesToMol(smi, 0, 1);
unsigned int nat = m->getNumAtoms();
DistGeom::BoundsMatrix *mat = new DistGeom::BoundsMatrix(nat);
DistGeom::BoundsMatPtr bm(mat);
DGeomHelpers::initBoundsMat(bm);
DGeomHelpers::setTopolBounds(*m, bm);
bool ok = DistGeom::triangleSmoothBounds(bm);
TEST_ASSERT(ok);
smi = "Cc1cccc2c1c(C3=CCC3)c(C)cc2";
m = SmilesToMol(smi, 0, 1);
nat = m->getNumAtoms();
DistGeom::BoundsMatrix *nmat = new DistGeom::BoundsMatrix(nat);
bm.reset(nmat);
DGeomHelpers::initBoundsMat(bm);
DGeomHelpers::setTopolBounds(*m, bm);
ok = DistGeom::triangleSmoothBounds(bm);
TEST_ASSERT(ok);
delete m;
}
void testIssue244() {
// the bug here was a crash during the setting of the topological
// bounds, so just completing the calls to setTopolBounds() indicates
// success
std::string smi = "NC1C(=O)N2C1SCC(Cl)=C2C(O)=O";
ROMol *m = SmilesToMol(smi, 0, 1);
unsigned int nat = m->getNumAtoms();
DistGeom::BoundsMatrix *mat = new DistGeom::BoundsMatrix(nat);
DistGeom::BoundsMatPtr bm(mat);
DGeomHelpers::initBoundsMat(bm);
DGeomHelpers::setTopolBounds(*m, bm);
delete m;
smi = "NC1C(=O)N2C1SCC(Cl)=C2C(O)=O";
m = SmilesToMol(smi, 0, 1);
nat = m->getNumAtoms();
bm.reset(new DistGeom::BoundsMatrix(nat));
DGeomHelpers::initBoundsMat(bm);
DGeomHelpers::setTopolBounds(*m, bm);
delete m;
smi = "CC1(C)SC2N(C1C(O)=O)C(=O)C2N";
m = SmilesToMol(smi, 0, 1);
nat = m->getNumAtoms();
bm.reset(new DistGeom::BoundsMatrix(nat));
DGeomHelpers::initBoundsMat(bm);
DGeomHelpers::setTopolBounds(*m, bm);
delete m;
}
void testIssue251() {
std::string smi = "COC=O";
ROMol *m = SmilesToMol(smi, 0, 1);
unsigned int nat = m->getNumAtoms();
DistGeom::BoundsMatrix *mat = new DistGeom::BoundsMatrix(nat);
DistGeom::BoundsMatPtr bm(mat);
DGeomHelpers::initBoundsMat(bm);
DGeomHelpers::setTopolBounds(*m, bm);
TEST_ASSERT(RDKit::feq(bm->getLowerBound(0, 3), 2.67, 0.01));
TEST_ASSERT(RDKit::feq(bm->getUpperBound(0, 3), 2.79, 0.01));
delete m;
}
void testIssue276() {
bool ok;
std::string smi = "CP1(C)=CC=CN=C1C";
ROMol *m = SmilesToMol(smi, 0, 1);
unsigned int nat = m->getNumAtoms();
DistGeom::BoundsMatrix *mat = new DistGeom::BoundsMatrix(nat);
DistGeom::BoundsMatPtr bm(mat);
DGeomHelpers::initBoundsMat(bm);
DGeomHelpers::setTopolBounds(*m, bm);
#if 0
for(unsigned int i=0;i<nat;i++){
for(unsigned int j=0;j<nat;j++){
if(i<j) std::cout << bm->getUpperBound(i,j) << " ";
else if(i>j) std::cout << bm->getLowerBound(i,j) << " ";
else std::cout << "0.00000" << " ";
}
std::cout << std::endl;
}
std::cout << std::endl;
#endif
ok = DistGeom::triangleSmoothBounds(bm);
TEST_ASSERT(ok);
delete m;
}
void testIssue284() {
bool ok;
std::string smi = "CNC(=O)C";
ROMol *m = SmilesToMol(smi, 0, 1);
TEST_ASSERT(m);
unsigned int nat = m->getNumAtoms();
DistGeom::BoundsMatrix *mat = new DistGeom::BoundsMatrix(nat);
DistGeom::BoundsMatPtr bm(mat);
DGeomHelpers::initBoundsMat(bm);
DGeomHelpers::setTopolBounds(*m, bm);
ok = DistGeom::triangleSmoothBounds(bm);
TEST_ASSERT(ok);
// amide bonds are cis-oid:
TEST_ASSERT(bm->getLowerBound(0, 3) < 3.0);
TEST_ASSERT(bm->getUpperBound(0, 3) < 3.0);
delete m;
smi = "CN(C)C(=O)C";
m = SmilesToMol(smi, 0, 1);
TEST_ASSERT(m);
nat = m->getNumAtoms();
DistGeom::BoundsMatrix *mat2 = new DistGeom::BoundsMatrix(nat);
DistGeom::BoundsMatPtr bm2(mat2);
DGeomHelpers::initBoundsMat(bm2);
DGeomHelpers::setTopolBounds(*m, bm2);
ok = DistGeom::triangleSmoothBounds(bm2);
TEST_ASSERT(ok);
// we've got no information to tell us cis-oid vs trans-oid here, so
// the windows are huge:
TEST_ASSERT(bm2->getLowerBound(0, 4) < 3.0);
TEST_ASSERT(bm2->getUpperBound(0, 4) > 3.5);
TEST_ASSERT(bm2->getLowerBound(2, 4) < 3.0);
TEST_ASSERT(bm2->getUpperBound(2, 4) > 3.5);
TEST_ASSERT(bm->getLowerBound(0, 3) < bm2->getLowerBound(0, 4));
TEST_ASSERT(bm->getUpperBound(0, 3) < bm2->getUpperBound(0, 4));
TEST_ASSERT(bm->getLowerBound(0, 3) < bm2->getLowerBound(2, 4));
TEST_ASSERT(bm->getUpperBound(0, 3) < bm2->getUpperBound(2, 4));
delete m;
}
void testIssue285() {
bool ok;
std::string smi = "CNC(=O)C";
ROMol *m = SmilesToMol(smi, 0, 1);
TEST_ASSERT(m);
unsigned int nat = m->getNumAtoms();
DistGeom::BoundsMatrix *mat = new DistGeom::BoundsMatrix(nat);
DistGeom::BoundsMatPtr bm(mat);
DGeomHelpers::initBoundsMat(bm);
DGeomHelpers::setTopolBounds(*m, bm);
ok = DistGeom::triangleSmoothBounds(bm);
TEST_ASSERT(ok);
unsigned int tgtNumber = 10;
INT_VECT cids = DGeomHelpers::EmbedMultipleConfs(*m, tgtNumber);
TEST_ASSERT(cids.size() == tgtNumber);
std::vector<std::string> molBlocks;
for (INT_VECT_CI cid = cids.begin(); cid != cids.end(); ++cid) {
molBlocks.push_back(MolToMolBlock(*m, true, *cid));
}
for (std::vector<std::string>::const_iterator mbI = molBlocks.begin();
mbI != molBlocks.end(); ++mbI) {
for (std::vector<std::string>::const_iterator mbJ = mbI + 1;
mbJ != molBlocks.end(); ++mbJ) {
TEST_ASSERT((*mbI) != (*mbJ));
}
// std::cerr << (*mbI) << "\n$$$$\n";
}
delete m;
}
void testIssue355() {
bool ok;
std::string smi = "CNC(=O)C";
ROMol *m = SmilesToMol(smi, 0, 1);
TEST_ASSERT(m);
unsigned int nat = m->getNumAtoms();
DistGeom::BoundsMatrix *mat = new DistGeom::BoundsMatrix(nat);
DistGeom::BoundsMatPtr bm(mat);
DGeomHelpers::initBoundsMat(bm);
DGeomHelpers::setTopolBounds(*m, bm);
TEST_ASSERT(bm->getLowerBound(0, 3) < 3.0);
TEST_ASSERT(bm->getUpperBound(0, 3) < 3.0);
TEST_ASSERT(bm->getUpperBound(0, 4) > 3.2);
TEST_ASSERT(bm->getLowerBound(0, 4) > 3.2);
ok = DistGeom::triangleSmoothBounds(bm);
TEST_ASSERT(ok);
delete m;
smi = "CNC(=O)NC";
m = SmilesToMol(smi, 0, 1);
TEST_ASSERT(m);
bm.reset(new DistGeom::BoundsMatrix(m->getNumAtoms()));
DGeomHelpers::initBoundsMat(bm);
DGeomHelpers::setTopolBounds(*m, bm);
TEST_ASSERT(bm->getLowerBound(0, 3) < 3.0);
TEST_ASSERT(bm->getUpperBound(0, 3) < 3.0);
TEST_ASSERT(bm->getUpperBound(0, 4) > 3.2);
TEST_ASSERT(bm->getLowerBound(0, 4) > 3.2);
TEST_ASSERT(bm->getLowerBound(5, 3) < 3.0);
TEST_ASSERT(bm->getUpperBound(5, 3) < 3.0);
TEST_ASSERT(bm->getUpperBound(5, 1) > 3.2);
TEST_ASSERT(bm->getLowerBound(5, 1) > 3.2);
delete m;
smi = "CNC(=O)Nc1ccccc1";
m = SmilesToMol(smi, 0, 1);
TEST_ASSERT(m);
bm.reset(new DistGeom::BoundsMatrix(m->getNumAtoms()));
DGeomHelpers::initBoundsMat(bm);
DGeomHelpers::setTopolBounds(*m, bm);
TEST_ASSERT(bm->getLowerBound(0, 3) < 3.0);
TEST_ASSERT(bm->getUpperBound(0, 3) < 3.0);
TEST_ASSERT(bm->getUpperBound(0, 4) > 3.2);
TEST_ASSERT(bm->getLowerBound(0, 4) > 3.2);
TEST_ASSERT(bm->getLowerBound(5, 3) < 3.0);
TEST_ASSERT(bm->getUpperBound(5, 3) < 3.0);
TEST_ASSERT(bm->getUpperBound(5, 1) > 3.2);
TEST_ASSERT(bm->getLowerBound(5, 1) > 3.2);
delete m;
}
void testRandomCoords() {
std::string smiString =
"CC1=C(C(C)=CC=C2)C2=CC=C1 c1ccccc1C C/C=C/CC \
C/12=C(\\CSC2)Nc3cc(n[n]3C1=O)c4ccccc4 C1CCCCS1(=O)(=O) c1ccccc1 \
C1CCCC1 C1CCCCC1 \
C1CC1(C)C C12(C)CC1CC2";
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/DistGeomHelpers/test_data/initCoords.random.sdf";
SDMolSupplier sdsup(fname, true, false);
// SDWriter writer("foo.sdf");
// SDWriter writer(fname);
boost::char_separator<char> spaceSep(" ");
tokenizer tokens(smiString, spaceSep);
for (tokenizer::iterator token = tokens.begin(); token != tokens.end();
++token) {
std::string smi = *token;
// std::cerr << "SMI: " << smi << std::endl;
ROMol *m = SmilesToMol(smi, 0, 1);
RWMol *m2 = (RWMol *)MolOps::addHs(*m);
delete m;
m = m2;
int cid =
DGeomHelpers::EmbedMolecule(*m, 10, 1, true, true, 2, true, 1, 0, 1e-2);
CHECK_INVARIANT(cid >= 0, "");
// writer.write(*m);
// writer.flush();
#if 1
m2 = static_cast<RWMol *>(sdsup.next());
// ROMol *m2 = NULL;
if (m2) {
TEST_ASSERT(m->getNumAtoms() == m2->getNumAtoms());
unsigned int nat = m->getNumAtoms();
const Conformer &conf1 = m->getConformer(0);
const Conformer &conf2 = m2->getConformer(0);
#if 0
BOOST_LOG(rdInfoLog) << "-----------------------" << std::endl;
BOOST_LOG(rdInfoLog) << MolToMolBlock(*m2) << std::endl;
BOOST_LOG(rdInfoLog) << "---" << std::endl;
BOOST_LOG(rdInfoLog) << MolToMolBlock(*m) << std::endl;
BOOST_LOG(rdInfoLog) << "-----------------------" << std::endl;
#endif
for (unsigned int i = 0; i < nat; i++) {
RDGeom::Point3D pt1i = conf1.getAtomPos(i);
RDGeom::Point3D pt2i = conf2.getAtomPos(i);
for (unsigned int j = i + 1; j < nat; j++) {
RDGeom::Point3D pt1j = conf1.getAtomPos(j);
RDGeom::Point3D pt2j = conf2.getAtomPos(j);
double d1 = (pt1j - pt1i).length();
double d2 = (pt2j - pt2i).length();
if (m->getBondBetweenAtoms(i, j)) {
TEST_ASSERT(fabs(d1 - d2) / d1 < 0.05);
} else {
TEST_ASSERT(fabs(d1 - d2) / d1 < 0.1);
}
}
}
}
delete m2;
#endif
delete m;
}
}
void testIssue1989539() {
{
std::string smi = "c1ccccc1.Cl";
ROMol *m = SmilesToMol(smi, 0, 1);
RWMol *m2 = (RWMol *)MolOps::addHs(*m);
delete m;
m = m2;
int cid = DGeomHelpers::EmbedMolecule(*m);
TEST_ASSERT(cid >= 0);
std::vector<int> cids = DGeomHelpers::EmbedMultipleConfs(*m, 10);
TEST_ASSERT(cids.size() == 10);
TEST_ASSERT(std::find(cids.begin(), cids.end(), -1) == cids.end());
delete m;
}
{
std::string smi = "[Cl-].c1ccccc1C[NH3+]";
RWMol *m = SmilesToMol(smi, 0, 1);
int cid = DGeomHelpers::EmbedMolecule(*m);
TEST_ASSERT(cid >= 0);
std::vector<int> cids = DGeomHelpers::EmbedMultipleConfs(*m, 10);
TEST_ASSERT(cids.size() == 10);
TEST_ASSERT(std::find(cids.begin(), cids.end(), -1) == cids.end());
delete m;
}
}
void testConstrainedEmbedding() {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/DistGeomHelpers/test_data/constrain1.sdf";
SDMolSupplier sdsup(fname);
ROMol *ref = sdsup.next();
{
ROMol *test = new ROMol(*ref);
std::map<int, RDGeom::Point3D> coords;
coords[0] = ref->getConformer().getAtomPos(0);
coords[1] = ref->getConformer().getAtomPos(1);
coords[2] = ref->getConformer().getAtomPos(2);
coords[3] = ref->getConformer().getAtomPos(3);
coords[4] = ref->getConformer().getAtomPos(4);
#if 1
int cid = DGeomHelpers::EmbedMolecule(*test, 30, 22, true, false, 2., true,
1, &coords);
TEST_ASSERT(cid > -1);
MatchVectType alignMap;
alignMap.push_back(std::make_pair(0, 0));
alignMap.push_back(std::make_pair(1, 1));
alignMap.push_back(std::make_pair(2, 2));
alignMap.push_back(std::make_pair(3, 3));
alignMap.push_back(std::make_pair(4, 4));
double ssd = MolAlign::alignMol(*test, *ref, -1, -1, &alignMap);
BOOST_LOG(rdInfoLog) << "ssd: " << ssd << std::endl;
TEST_ASSERT(ssd < 0.1);
#endif
delete test;
}
{
ROMol *test = sdsup.next();
std::map<int, RDGeom::Point3D> coords;
coords[4] = ref->getConformer().getAtomPos(0);
coords[5] = ref->getConformer().getAtomPos(1);
coords[6] = ref->getConformer().getAtomPos(2);
coords[7] = ref->getConformer().getAtomPos(3);
coords[8] = ref->getConformer().getAtomPos(4);
int cid = DGeomHelpers::EmbedMolecule(*test, 30, 22, true, false, 2., true,
1, &coords);
TEST_ASSERT(cid > -1);
MatchVectType alignMap;
alignMap.push_back(std::make_pair(4, 0));
alignMap.push_back(std::make_pair(5, 1));
alignMap.push_back(std::make_pair(6, 2));
alignMap.push_back(std::make_pair(7, 3));
alignMap.push_back(std::make_pair(8, 4));
double ssd = MolAlign::alignMol(*test, *ref, -1, -1, &alignMap);
BOOST_LOG(rdInfoLog) << "ssd: " << ssd << std::endl;
TEST_ASSERT(ssd < 0.1);
delete test;
}
}
void testIssue2091864() {
{
std::string smi = "C1C2CC12";
RWMol *m = SmilesToMol(smi);
int cid = DGeomHelpers::EmbedMolecule(*m);
TEST_ASSERT(cid >= 0);
delete m;
}
{
std::string smi = "C1CC2C3C1C23";
RWMol *m = SmilesToMol(smi);
int cid = DGeomHelpers::EmbedMolecule(*m);
TEST_ASSERT(cid >= 0);
std::vector<int> cids = DGeomHelpers::EmbedMultipleConfs(*m, 10);
TEST_ASSERT(cids.size() == 10);
TEST_ASSERT(std::find(cids.begin(), cids.end(), -1) == cids.end());
delete m;
}
{
std::string smi = "c1ccc2c(c1)C1C3C2C13";
RWMol *m = SmilesToMol(smi);
int cid = DGeomHelpers::EmbedMolecule(*m);
TEST_ASSERT(cid >= 0);
std::vector<int> cids = DGeomHelpers::EmbedMultipleConfs(*m, 10);
TEST_ASSERT(cids.size() == 10);
TEST_ASSERT(std::find(cids.begin(), cids.end(), -1) == cids.end());
delete m;
}
}
void testIssue2091974() {
{
std::string smi = "CCOC(OCC)(OCC)OCC";
ROMol *m = SmilesToMol(smi);
ROMol *m2 = MolOps::addHs(*m);
delete m;
int cid = DGeomHelpers::EmbedMolecule(*m2);
TEST_ASSERT(cid >= 0);
delete m2;
}
{
std::string smi = "O=N(=O)OCC(CON(=O)=O)(CON(=O)=O)CON(=O)=O";
ROMol *m = SmilesToMol(smi);
ROMol *m2 = MolOps::addHs(*m);
delete m;
int cid = DGeomHelpers::EmbedMolecule(*m2);
TEST_ASSERT(cid >= 0);
delete m2;
}
}
void testIssue2835784() {
#if 1
{
std::string smi = "C1C=C1";
RWMol *m = SmilesToMol(smi);
int cid = DGeomHelpers::EmbedMolecule(*m);
TEST_ASSERT(cid >= 0);
std::vector<int> cids = DGeomHelpers::EmbedMultipleConfs(*m, 10);
TEST_ASSERT(cids.size() == 10);
TEST_ASSERT(std::find(cids.begin(), cids.end(), -1) == cids.end());
delete m;
}
{
std::string smi = "C1C=C1";
ROMol *m = SmilesToMol(smi);
ROMol *m2 = MolOps::addHs(*m);
delete m;
int cid = DGeomHelpers::EmbedMolecule(*m2);
TEST_ASSERT(cid >= 0);
std::vector<int> cids = DGeomHelpers::EmbedMultipleConfs(*m2, 10);
TEST_ASSERT(cids.size() == 10);
TEST_ASSERT(std::find(cids.begin(), cids.end(), -1) == cids.end());
delete m2;
}
{
std::string smi = "C12=CCC1C2";
RWMol *m = SmilesToMol(smi);
int cid = DGeomHelpers::EmbedMolecule(*m);
TEST_ASSERT(cid >= 0);
std::vector<int> cids = DGeomHelpers::EmbedMultipleConfs(*m, 10);
TEST_ASSERT(cids.size() == 10);
TEST_ASSERT(std::find(cids.begin(), cids.end(), -1) == cids.end());
delete m;
}
#endif
{
std::string smi = "C12=CCC1C2";
ROMol *m = SmilesToMol(smi);
ROMol *m2 = MolOps::addHs(*m);
delete m;
int cid = DGeomHelpers::EmbedMolecule(*m2);
TEST_ASSERT(cid >= 0);
std::vector<int> cids = DGeomHelpers::EmbedMultipleConfs(*m2, 10);
TEST_ASSERT(cids.size() == 10);
TEST_ASSERT(std::find(cids.begin(), cids.end(), -1) == cids.end());
delete m2;
}
}
void testIssue3019283() {
{
std::string smi = "C1=C2C1C1CC21";
RWMol *m = SmilesToMol(smi);
int cid = DGeomHelpers::EmbedMolecule(*m);
TEST_ASSERT(cid >= 0);
std::vector<int> cids = DGeomHelpers::EmbedMultipleConfs(*m, 10);
TEST_ASSERT(cids.size() == 10);
TEST_ASSERT(std::find(cids.begin(), cids.end(), -1) == cids.end());
delete m;
}
}
void testIssue3238580() {
{
std::string smi = "C1CCC2=CC12";
RWMol *m = SmilesToMol(smi);
DistGeom::BoundsMatrix *mat = new DistGeom::BoundsMatrix(m->getNumAtoms());
DistGeom::BoundsMatPtr bm(mat);
DGeomHelpers::initBoundsMat(bm);
DGeomHelpers::setTopolBounds(*m, bm);
// if we get here it indicates everything was fine.
// do bounds smoothing just to be sure:
bool ok = DistGeom::triangleSmoothBounds(bm);
TEST_ASSERT(ok);
delete m;
}
{
std::string rdbase = getenv("RDBASE");
std::string molfile =
rdbase + "/Code/GraphMol/DistGeomHelpers/test_data/Issue3238580.1.mol";
RWMol *m = MolFileToMol(molfile);
DistGeom::BoundsMatrix *mat = new DistGeom::BoundsMatrix(m->getNumAtoms());
DistGeom::BoundsMatPtr bm(mat);
DGeomHelpers::initBoundsMat(bm);
DGeomHelpers::setTopolBounds(*m, bm);
// if we get here it indicates everything was fine.
// do bounds smoothing just to be sure:
bool ok = DistGeom::triangleSmoothBounds(bm);
TEST_ASSERT(ok);
delete m;
}
{
std::string rdbase = getenv("RDBASE");
std::string molfile =
rdbase + "/Code/GraphMol/DistGeomHelpers/test_data/Issue3238580.2.mol";
RWMol *m = MolFileToMol(molfile);
DistGeom::BoundsMatrix *mat = new DistGeom::BoundsMatrix(m->getNumAtoms());
DistGeom::BoundsMatPtr bm(mat);
DGeomHelpers::initBoundsMat(bm);
DGeomHelpers::setTopolBounds(*m, bm);
// if we get here it indicates everything was fine.
// do bounds smoothing just to be sure:
bool ok = DistGeom::triangleSmoothBounds(bm);
TEST_ASSERT(ok);
delete m;
}
{
std::string rdbase = getenv("RDBASE");
std::string molfile =
rdbase + "/Code/GraphMol/DistGeomHelpers/test_data/Issue3238580.3.mol";
RWMol *m = MolFileToMol(molfile);
DistGeom::BoundsMatrix *mat = new DistGeom::BoundsMatrix(m->getNumAtoms());
DistGeom::BoundsMatPtr bm(mat);
DGeomHelpers::initBoundsMat(bm);
DGeomHelpers::setTopolBounds(*m, bm);
// if we get here it indicates everything was fine.
// do bounds smoothing just to be sure:
bool ok = DistGeom::triangleSmoothBounds(bm);
TEST_ASSERT(ok);
delete m;
}
}
void testIssue3483968() {
{
std::string rdbase = getenv("RDBASE");
std::string molfile =
rdbase + "/Code/GraphMol/DistGeomHelpers/test_data/Issue3483968.mol";
RWMol *m = MolFileToMol(molfile);
TEST_ASSERT(m);
int cid = DGeomHelpers::EmbedMolecule(*m, 0, -1, true, false, 2.0, true, 1,
0, 1e-3, true);
TEST_ASSERT(cid >= 0);
std::vector<int> cids = DGeomHelpers::EmbedMultipleConfs(
*m, 10, 30, 1, true, false, 2.0, true, 1, -1.0, 0, 1e-3, true);
TEST_ASSERT(cids.size() == 10);
TEST_ASSERT(std::find(cids.begin(), cids.end(), -1) == cids.end());
delete m;
}
}
#ifdef RDK_TEST_MULTITHREADED
namespace {
void runblock(const std::vector<ROMol *> &mols,
const std::vector<double> &energies, unsigned int count,
unsigned int idx) {
for (unsigned int j = 0; j < 100; j++) {
for (unsigned int i = 0; i < mols.size(); ++i) {
if (i % count != idx) continue;
ROMol mol(*mols[i]);
std::vector<int> cids =
DGeomHelpers::EmbedMultipleConfs(mol, 10, 30, 0xFEED);
TEST_ASSERT(cids.size() == 10);
ForceFields::ForceField *field = 0;
try {
field = UFF::constructForceField(mol, 100.0, cids[0]);
} catch (...) {
field = 0;
}
TEST_ASSERT(field);
field->initialize();
double eng = field->calcEnergy();
if (!feq(eng, energies[i])) {
std::cerr << i << " iter " << j << " " << energies[i] << " != " << eng
<< std::endl;
}
TEST_ASSERT(feq(eng, energies[i]));
delete field;
}
}
};
}
#include <RDGeneral/BoostStartInclude.h>
#include <boost/thread.hpp>
#include <RDGeneral/BoostEndInclude.h>
void testMultiThread() {
std::cerr << "building molecules" << std::endl;
// std::string smi="C/12=C(\\CSC2)Nc3cc(n[n]3C1=O)c4ccccc4";
std::string smi = "c1ccc2c(c1)C1C3C2C13";
std::vector<ROMol *> mols;
for (unsigned int i = 0; i < 100; ++i) {
RWMol *m = SmilesToMol(smi);
mols.push_back(m);
}
std::cerr << "generating reference data" << std::endl;
std::vector<double> energies(mols.size(), 0.0);
for (unsigned int i = 0; i < mols.size(); ++i) {
ROMol mol(*mols[i]);
std::vector<int> cids =
DGeomHelpers::EmbedMultipleConfs(mol, 10, 30, 0xFEED);
TEST_ASSERT(cids.size() == 10);
ForceFields::ForceField *field = 0;
try {
field = UFF::constructForceField(mol, 100.0, cids[0]);
} catch (...) {
field = 0;
}
TEST_ASSERT(field);
field->initialize();
double eng = field->calcEnergy();
TEST_ASSERT(eng != 0.0);
energies[i] = eng;
delete field;
}
std::cerr << "validating reference data" << std::endl;
for (unsigned int i = 0; i < mols.size(); ++i) {
ROMol mol(*mols[i]);
std::vector<int> cids =
DGeomHelpers::EmbedMultipleConfs(mol, 10, 30, 0xFEED);
TEST_ASSERT(cids.size() == 10);
ForceFields::ForceField *field = 0;
try {
field = UFF::constructForceField(mol, 100.0, cids[0]);
} catch (...) {
field = 0;
}
TEST_ASSERT(field);
field->initialize();
double eng = field->calcEnergy();
TEST_ASSERT(feq(eng, energies[i]));
delete field;
}
boost::thread_group tg;
std::cerr << "processing" << std::endl;
unsigned int count = 4;
for (unsigned int i = 0; i < count; ++i) {
std::cerr << " launch :" << i << std::endl;
std::cerr.flush();
tg.add_thread(new boost::thread(runblock, mols, energies, count, i));
}
tg.join_all();
for (unsigned int i = 0; i < mols.size(); ++i) delete mols[i];
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
#else
void testMultiThread() {}
#endif
void testGithub55() {
{
std::string smiles = "c1cnco1";
RWMol *core = SmilesToMol(smiles);
TEST_ASSERT(core);
int cid = DGeomHelpers::EmbedMolecule(*core);
TEST_ASSERT(cid >= 0);
smiles = "o1cncc1C";
RWMol *mol = SmilesToMol(smiles);
TEST_ASSERT(mol);
std::map<int, RDGeom::Point3D> coords;
coords[0] = core->getConformer().getAtomPos(4);
coords[1] = core->getConformer().getAtomPos(3);
coords[2] = core->getConformer().getAtomPos(2);
coords[3] = core->getConformer().getAtomPos(1);
coords[4] = core->getConformer().getAtomPos(0);
cid = DGeomHelpers::EmbedMolecule(*mol, 50, 22, true, false, 2., true, 1,
&coords);
TEST_ASSERT(cid > -1);
delete core;
delete mol;
}
{
std::string smiles = "c1cncs1";
RWMol *core = SmilesToMol(smiles);
TEST_ASSERT(core);
int cid = DGeomHelpers::EmbedMolecule(*core);
TEST_ASSERT(cid >= 0);
smiles = "s1cncc1C";
RWMol *mol = SmilesToMol(smiles);
TEST_ASSERT(mol);
std::map<int, RDGeom::Point3D> coords;
coords[0] = core->getConformer().getAtomPos(4);
coords[1] = core->getConformer().getAtomPos(3);
coords[2] = core->getConformer().getAtomPos(2);
coords[3] = core->getConformer().getAtomPos(1);
coords[4] = core->getConformer().getAtomPos(0);
cid = DGeomHelpers::EmbedMolecule(*mol, 50, 22, true, false, 2., true, 1,
&coords);
TEST_ASSERT(cid > -1);
delete core;
delete mol;
}
}
void testGithub256() {
{
RWMol *mol = new RWMol();
TEST_ASSERT(mol);
bool ok = false;
try {
DGeomHelpers::EmbedMolecule(*mol);
ok = false;
} catch (const ValueErrorException &e) {
ok = true;
}
TEST_ASSERT(ok);
delete mol;
}
}
#ifdef RDK_TEST_MULTITHREADED
void testMultiThreadMultiConf() {
boost::char_separator<char> sep("|");
tokenizer tokens(std::string(RDKit::rdkitBuild), sep);
std::vector<std::string> tokenVect(tokens.begin(), tokens.end());
const double ENERGY_TOLERANCE = ((tokenVect[2] != "MINGW") ? 1.0e-6 : 1.0);
const double MSD_TOLERANCE = ((tokenVect[2] != "MINGW") ? 1.0e-6 : 1.0e-5);
std::string smi = "CC(C)(C)c(cc1)ccc1c(cc23)n[n]3C(=O)/C(=C\\N2)C(=O)OCC";
ROMol *m = SmilesToMol(smi, 0, 1);
INT_VECT cids;
ROMol m2(*m);
DGeomHelpers::EmbedMultipleConfs(*m, cids, 200, 1, 30, 100, true, false, -1);
DGeomHelpers::EmbedMultipleConfs(m2, cids, 200, 0, 30, 100, true, false, -1);
INT_VECT_CI ci;
for (ci = cids.begin(); ci != cids.end(); ci++) {
ForceFields::ForceField *ff = UFF::constructForceField(*m, 100, *ci);
ff->initialize();
double e1 = ff->calcEnergy();
const RDGeom::PointPtrVect &pVect = ff->positions();
TEST_ASSERT(e1 > 100.0);
TEST_ASSERT(e1 < 300.0);
ForceFields::ForceField *ff2 = UFF::constructForceField(m2, 100, *ci);
ff2->initialize();
double e2 = ff2->calcEnergy();
const RDGeom::PointPtrVect &p2Vect = ff2->positions();
TEST_ASSERT(RDKit::feq(e1, e2, ENERGY_TOLERANCE));
TEST_ASSERT(pVect.size() == p2Vect.size());
double msd = 0.0;
for (unsigned int i = 0; i < pVect.size(); ++i) {
const RDGeom::Point3D *p =
dynamic_cast<const RDGeom::Point3D *>(pVect[i]);
const RDGeom::Point3D *p2 =
dynamic_cast<const RDGeom::Point3D *>(p2Vect[i]);
TEST_ASSERT(p && p2);
msd += (*p - *p2).lengthSq();
}
msd /= static_cast<double>(pVect.size());
TEST_ASSERT(msd < MSD_TOLERANCE);
delete ff;
delete ff2;
}
}
#endif
void testGithub563() {
{
std::string smi = "[H][C@]1(C[NH3+])CC[C@]([H])(CNC)CC1";
ROMol *m = SmilesToMol(smi);
std::string csmi = MolToSmiles(*m, true);
std::cerr << csmi << std::endl;
for (unsigned int i = 1; i < 100; ++i) {
ROMol m2 = ROMol(*m);
MolOps::addHs(m2);
DGeomHelpers::EmbedMolecule(m2, 50, i);
MolOps::assignChiralTypesFrom3D(m2);
MolOps::removeHs(m2);
std::string smi = MolToSmiles(m2, true);
TEST_ASSERT(smi == csmi);
}
delete m;
}
}
void testGithub568() {
{
// sample molecules (either from ChEMBL or derived from ChEMBL) that were
// problematic
std::string smis[] = {
"C1CN2C[C@@H]1[C@@]1(CN=CO1)C2",
"OC(=O)[C@@H]1[C@H]2CC[C@H](O2)[C@@H]1C(=O)O",
"O=C(CCc1ccccc1)OC[C@H]2C[C@@H]3O[C@H]2[C@@H]4[C@H]3C(=O)OC4=O",
"Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c5ccccc15",
"Nc1ncnc2c1ncn2[C@@H]3C=C(CO)[C@@H](O)[C@H]3O",
"CO[C@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O",
"CO[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O",
"CCS[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O",
"CCCCC[C@H](O)\\C=C\\[C@@]1(F)[C@H](O)C[C@H](O)[C@@H]1C\\C=C/"
"CCCC(=O)OC",
"CCCCC[C@@H](O)\\C=C\\[C@]1(F)[C@@H](O)C[C@@H](O)[C@H]1C\\C=C/"
"CCCC(=O)OC",
"CNC(=O)Oc1cccc2[C@@H]3[C@@H](CCN3C)COc12",
"CNC(=O)Oc1ccc2OC[C@@H]3CCN(C)[C@@H]3c2c1",
"CN1CC[C@H]2COc3c(O)cccc3[C@@H]12",
"CC(=O)C[C@@]12CCC[C@H]1[C@@H]3CCC4=CC(=O)CC[C@@H]4[C@H]3CC2",
"OC(=O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1",
"COc1ccc2[C@H](O)[C@@H](COc2c1)N3CCC(O)(CC3)c4ccc(F)cc4",
"O[C@@H]1[C@@H](COc2cc(O)ccc12)N3CCC(Cc4ccccc4)CC3",
"O[C@H]1[C@H](COc2cc(O)ccc12)N3CCC(O)(CC3)c4ccccc4",
"CC(=O)c1ccc2C[C@@H]3[C@@H]4CCCC[C@]4(CCN3CC5CC5)c2c1",
"CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5OCOc5cc4[C@@H]3C[C@@H]2C1",
"COc1cc2CCN3C[C@H]4CC[C@@H](O)C[C@H]4C[C@H]3c2cc1OC",
"O[C@H]1C[C@H]2C[C@@H]3N(CCc4cc5OCOc5cc34)C[C@H]2C[C@H]1C#N",
"COC(=O)[C@@H]1C[C@@](C)(NC(=O)N1)C(=O)O",
"CC(=O)OC1=C(C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1)Sc5ccccc5",
"Nc1ncnc2c1ncn2[C@H]3C[C@H](O)[C@@H](CO)C3",
"C[C@@H](N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc4ccc(OCc5cccc(F)c5)cc34)C(=O)N",
"CN1C(=O)CC[C@@]2(C)C1=CCc3cc(Cl)ccc23",
"Cc1nc(COc2ccc3OC[C@H](Cc4cccnc4)[C@H](O)c3c2)ccc1[N+](=O)[O-]", "EOS"};
for (unsigned int idx = 0; smis[idx] != "EOS"; ++idx) {
ROMol *m = SmilesToMol(smis[idx]);
std::string csmi = MolToSmiles(*m, true);
std::cerr << csmi << std::endl;
for (unsigned int i = 1; i < 20;
++i) { // increase the limit here to make this a real torture test
RWMol m2 = ROMol(*m);
MolOps::addHs(m2);
int cid = DGeomHelpers::EmbedMolecule(m2, 50, i);
TEST_ASSERT(cid >= 0);
MolOps::assignChiralTypesFrom3D(m2);
// m2.setProp("_Name",smis[idx]);
// std::cerr<<MolToMolBlock(m2)<<std::endl;
// TEST_ASSERT(0);
MolOps::removeHs(m2);
std::string smi = MolToSmiles(m2, true);
if (smi != csmi) {
std::cerr << "-------------" << std::endl;
std::cerr << smis[idx] << " " << i << std::endl;
std::cerr << smi << "\n" << csmi << std::endl;
m2.setProp("_Name", smis[idx]);
std::cerr << MolToMolBlock(m2) << std::endl;
}
TEST_ASSERT(smi == csmi);
}
delete m;
}
}
}
void testGithub696() {
{
std::string smi = "COc1ccc2CCCCCCCCCCc3ccc(OC)c(c3)-c1c2";
ROMol *m = SmilesToMol(smi);
// m->debugMol(std::cerr);
DistGeom::BoundsMatPtr bm;
bm.reset(new DistGeom::BoundsMatrix(m->getNumAtoms()));
DGeomHelpers::initBoundsMat(bm);
DGeomHelpers::setTopolBounds(*m, bm, false, false);
TEST_ASSERT(bm->getUpperBound(2, 19) > bm->getLowerBound(2, 19));
TEST_ASSERT(bm->getLowerBound(2, 19) > 2.0);
TEST_ASSERT(bm->getUpperBound(2, 19) > 2.5);
bool ok = DistGeom::triangleSmoothBounds(bm);
TEST_ASSERT(ok);
delete m;
}
}
void testGithub697() {
{ // a group of chembl molecules (and things derived from them), all of which
// contain a c1cscn1 heterocycle
std::string smis[] = {
"C1SC2=NC1CCCCCC2", "C1CCCc2nc(CC1)cs2", "C1Cc2coc(n2)-c2coc(C1)n2",
"C1Cc2coc(n2)-c2csc(C1)n2", "C1CCc2nc(cs2)-c2nc(C1)co2",
"C1Cc2nc(co2)-c2nc(cs2)-c2nc1co2",
"C1Cc2nc(co2)-c2nc(co2)-c2nc(cs2)-c2nc(co2)-c2nc1co2",
"C1CNCc2coc(n2)-c2coc(n2)-c2csc(n2)-c2coc(n2)-c2coc(CNCCN1)n2",
"C=C1NC(=O)C(C(C)C)NC(=O)C(C(C)CC)NC(=O)c2nc(oc2-c2ccccc2)-c2coc(n2)-"
"c2csc(n2)-c2coc(n2)-c2coc1n2",
"CCC(C)C1NC(=O)c2nc(oc2-c2ccccc2)-c2coc(n2)-c2csc(n2)-c2coc(n2)-c2coc("
"n2)"
"CNC(=O)C(C(C)C)NC1=O",
"CCC(C)C1NC(=O)c2nc(oc2-c2ccccc2)-c2coc(n2)-c2csc(n2)-c2coc(n2)-c2coc("
"n2)"
"C(COC(C)=O)NC(=O)C(C(C)C)NC1=O",
"CCC(C)C1NC(=O)c2nc(oc2-c2ccccc2)-c2coc(n2)-c2csc(n2)-c2coc(n2)-c2coc("
"n2)"
"C(COC(=O)COCCOCCOC)NC(=O)C(C(C)C)NC1=O",
"C=C1NC(=O)C(C(C)C)NC(=O)C(C(C)CC)NC(=O)c2nc(oc2-c2ccccc2)-c2coc(n2)-"
"c2csc(n2)-c2coc(n2)-c2nc1oc2C",
"C=C1NC(=O)C(C(C)C)NC(=O)C(C(C)CC)NC(=O)c2nc(oc2-c2ccccc2)-c2nc(oc2C)-"
"c2csc(n2)-c2coc(n2)-c2nc1oc2C",
"CCC(C)C1NC(=O)c2nc(oc2-c2ccccc2)-c2coc(n2)-c2csc(n2)-c2coc(n2)-c2coc("
"n2)"
"C(COC(=O)COCCOC)NC(=O)C(C(C)C)NC1=O",
"C=C1NC(=O)C(C(C)C)NC(=O)C(C(C)CC)NC(=O)c2nc(oc2-c2ccccc2)-c2nc(oc2C)-"
"c2csc(n2)-c2coc(n2)-c2coc1n2",
"CCC(C)C1NC(=O)c2nc(oc2-c2ccccc2)-c2coc(n2)-c2csc(n2)-c2coc(n2)-c2coc("
"n2)"
"C(COC(=O)C(N)CCCNC(=N)N)NC(=O)C(C(C)C)NC1=O",
"EOS"};
for (unsigned int idx = 0; smis[idx] != "EOS"; ++idx) {
ROMol *m = SmilesToMol(smis[idx]);
TEST_ASSERT(m);
DistGeom::BoundsMatPtr bm;
bm.reset(new DistGeom::BoundsMatrix(m->getNumAtoms()));
DGeomHelpers::initBoundsMat(bm);
DGeomHelpers::setTopolBounds(*m, bm, false, false);
bool ok = DistGeom::triangleSmoothBounds(bm);
if (!ok) {
m->debugMol(std::cerr);
std::cerr << " FAILED: " << smis[idx] << std::endl;
}
TEST_ASSERT(ok);
delete m;
}
}
}
namespace {
void compareConfs(const ROMol *m, const ROMol *expected, int molConfId = -1,
int expectedConfId = -1) {
PRECONDITION(m, "bad pointer");
PRECONDITION(expected, "bad pointer");
TEST_ASSERT(m->getNumAtoms() == expected->getNumAtoms());
const Conformer &conf1 = m->getConformer(molConfId);
const Conformer &conf2 = expected->getConformer(expectedConfId);
for (unsigned int i = 0; i < m->getNumAtoms(); i++) {
TEST_ASSERT(m->getAtomWithIdx(i)->getAtomicNum() ==
expected->getAtomWithIdx(i)->getAtomicNum());
RDGeom::Point3D pt1i = conf1.getAtomPos(i);
RDGeom::Point3D pt2i = conf2.getAtomPos(i);
TEST_ASSERT((pt1i - pt2i).length() < 10e-4);
}
}
}
void testGithub971() {
{
// sample molecule found by Sereina
std::string smi = "C/C(=C\\c1ccccc1)CN1C2CC[NH2+]CC1CC2";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::addHs(*m);
int cid = DGeomHelpers::EmbedMolecule(*m, 0, 0xf00d);
TEST_ASSERT(cid >= 0);
MolOps::removeHs(*m);
std::string expectedMb =
"\n RDKit 3D\n\n 19 21 0 0 0 0 0 0 0 0999 V2000\n "
" 1.1258 -1.3888 0.9306 C 0 0 0 0 0 0 0 0 0 0 0 "
"0\n 1.0779 -0.1065 0.1565 C 0 0 0 0 0 0 0 0 0 0 0 "
" 0\n 2.2519 0.2795 -0.3483 C 0 0 0 0 0 0 0 0 0 0 "
"0 0\n 3.5245 -0.0901 0.2817 C 0 0 0 0 0 0 0 0 0 0 "
" 0 0\n 4.2551 0.9456 0.8411 C 0 0 0 0 0 0 0 0 0 "
"0 0 0\n 5.6137 0.8099 1.0965 C 0 0 0 0 0 0 0 0 0 "
" 0 0 0\n 6.2293 -0.3871 0.7552 C 0 0 0 0 0 0 0 0 "
"0 0 0 0\n 5.4107 -1.4793 0.4938 C 0 0 0 0 0 0 0 0 "
" 0 0 0 0\n 4.2354 -1.1874 -0.1873 C 0 0 0 0 0 0 0 "
"0 0 0 0 0\n -0.0943 0.0572 -0.7601 C 0 0 0 0 0 0 0 "
" 0 0 0 0 0\n -1.3242 0.2903 -0.0524 N 0 0 0 0 0 0 "
"0 0 0 0 0 0\n -2.1468 1.1490 -0.9044 C 0 0 0 0 0 0 "
" 0 0 0 0 0 0\n -3.1678 1.9193 -0.1239 C 0 0 0 0 0 "
"0 0 0 0 0 0 0\n -2.9879 1.6714 1.3508 C 0 0 0 0 0 "
" 0 0 0 0 0 0 0\n -3.3579 0.3480 1.7662 N 0 0 0 0 "
"0 0 0 0 0 0 0 0\n -3.4586 -0.6011 0.7007 C 0 0 0 0 "
" 0 0 0 0 0 0 0 0\n -2.1733 -0.8977 -0.0058 C 0 0 0 "
"0 0 0 0 0 0 0 0 0\n -2.5650 -1.1467 -1.4589 C 0 0 0 "
" 0 0 0 0 0 0 0 0 0\n -2.7401 0.2591 -1.9624 C 0 0 "
"0 0 0 0 0 0 0 0 0 0\n 1 2 1 0\n 2 3 2 0\n 3 4 1 "
"0\n 4 5 2 0\n 5 6 1 0\n 6 7 2 0\n 7 8 1 0\n 8 9 2 "
"0\n 2 10 1 0\n 10 11 1 0\n 11 12 1 0\n 12 13 1 0\n 13 14 1 "
"0\n 14 15 1 0\n 15 16 1 0\n 16 17 1 0\n 17 18 1 0\n 18 19 1 "
"0\n 9 4 1 0\n 17 11 1 0\n 19 12 1 0\nM CHG 1 15 1\nM "
"END\n";
RWMol *expected = MolBlockToMol(expectedMb);
unsigned int nat = expected->getNumAtoms();
TEST_ASSERT(nat == m->getNumAtoms());
compareConfs(m, expected, 0, 0);
delete m;
delete expected;
}
}
void testEmbedParameters() {
std::string rdbase = getenv("RDBASE");
{
std::string fname =
rdbase +
"/Code/GraphMol/DistGeomHelpers/test_data/simple_torsion.dg.mol";
RWMol *ref = MolFileToMol(fname, true, false);
TEST_ASSERT(ref);
RWMol *mol = SmilesToMol("OCCC");
TEST_ASSERT(mol);
MolOps::addHs(*mol);
TEST_ASSERT(ref->getNumAtoms() == mol->getNumAtoms());
DGeomHelpers::EmbedParameters params;
params.randomSeed = 42;
DGeomHelpers::EmbedMolecule(*mol, params);
compareConfs(ref, mol);
delete ref;
delete mol;
}
{
std::string fname =
rdbase +
"/Code/GraphMol/DistGeomHelpers/test_data/simple_torsion.etdg.mol";
RWMol *ref = MolFileToMol(fname, true, false);
TEST_ASSERT(ref);
RWMol *mol = SmilesToMol("OCCC");
TEST_ASSERT(mol);
MolOps::addHs(*mol);
TEST_ASSERT(ref->getNumAtoms() == mol->getNumAtoms());
DGeomHelpers::EmbedParameters params;
params.randomSeed = 42;
params.useExpTorsionAnglePrefs = true;
DGeomHelpers::EmbedMolecule(*mol, params);
compareConfs(ref, mol);
delete ref;
delete mol;
}
{
std::string fname =
rdbase +
"/Code/GraphMol/DistGeomHelpers/test_data/simple_torsion.etkdg.mol";
RWMol *ref = MolFileToMol(fname, true, false);
TEST_ASSERT(ref);
RWMol *mol = SmilesToMol("OCCC");
TEST_ASSERT(mol);
MolOps::addHs(*mol);
TEST_ASSERT(ref->getNumAtoms() == mol->getNumAtoms());
DGeomHelpers::EmbedParameters params;
params.randomSeed = 42;
params.useExpTorsionAnglePrefs = true;
params.useBasicKnowledge = true;
DGeomHelpers::EmbedMolecule(*mol, params);
compareConfs(ref, mol);
delete ref;
delete mol;
}
{
std::string fname =
rdbase +
"/Code/GraphMol/DistGeomHelpers/test_data/simple_torsion.kdg.mol";
RWMol *ref = MolFileToMol(fname, true, false);
TEST_ASSERT(ref);
RWMol *mol = SmilesToMol("OCCC");
TEST_ASSERT(mol);
MolOps::addHs(*mol);
TEST_ASSERT(ref->getNumAtoms() == mol->getNumAtoms());
DGeomHelpers::EmbedParameters params;
params.randomSeed = 42;
params.useBasicKnowledge = true;
DGeomHelpers::EmbedMolecule(*mol, params);
compareConfs(ref, mol);
delete ref;
delete mol;
}
//------------
// using the pre-defined parameter sets
{
std::string fname =
rdbase +
"/Code/GraphMol/DistGeomHelpers/test_data/simple_torsion.etdg.mol";
RWMol *ref = MolFileToMol(fname, true, false);
TEST_ASSERT(ref);
RWMol *mol = SmilesToMol("OCCC");
TEST_ASSERT(mol);
MolOps::addHs(*mol);
TEST_ASSERT(ref->getNumAtoms() == mol->getNumAtoms());
DGeomHelpers::EmbedParameters params(DGeomHelpers::ETDG);
params.randomSeed = 42;
DGeomHelpers::EmbedMolecule(*mol, params);
compareConfs(ref, mol);
delete ref;
delete mol;
}
{
std::string fname =
rdbase +
"/Code/GraphMol/DistGeomHelpers/test_data/simple_torsion.etkdg.mol";
RWMol *ref = MolFileToMol(fname, true, false);
TEST_ASSERT(ref);
RWMol *mol = SmilesToMol("OCCC");
TEST_ASSERT(mol);
MolOps::addHs(*mol);
TEST_ASSERT(ref->getNumAtoms() == mol->getNumAtoms());
DGeomHelpers::EmbedParameters params(DGeomHelpers::ETKDG);
params.randomSeed = 42;
DGeomHelpers::EmbedMolecule(*mol, params);
compareConfs(ref, mol);
delete ref;
delete mol;
}
{
std::string fname =
rdbase +
"/Code/GraphMol/DistGeomHelpers/test_data/simple_torsion.kdg.mol";
RWMol *ref = MolFileToMol(fname, true, false);
TEST_ASSERT(ref);
RWMol *mol = SmilesToMol("OCCC");
TEST_ASSERT(mol);
MolOps::addHs(*mol);
TEST_ASSERT(ref->getNumAtoms() == mol->getNumAtoms());
DGeomHelpers::EmbedParameters params(DGeomHelpers::KDG);
params.randomSeed = 42;
DGeomHelpers::EmbedMolecule(*mol, params);
compareConfs(ref, mol);
delete ref;
delete mol;
}
}
void testGithub1227() {
{
RWMol *m = SmilesToMol("CC");
TEST_ASSERT(m);
MolOps::addHs(*m);
TEST_ASSERT(m->getNumAtoms() == 8);
INT_VECT cids;
DGeomHelpers::EmbedParameters params(DGeomHelpers::ETKDG);
params.randomSeed = 0xf00d;
cids = DGeomHelpers::EmbedMultipleConfs(*m, 10, params);
TEST_ASSERT(cids.size() == 10);
params.pruneRmsThresh = 0.5;
cids = DGeomHelpers::EmbedMultipleConfs(*m, 10, params);
TEST_ASSERT(cids.size() == 1);
params.onlyHeavyAtomsForRMS = false; // the old default behavior
cids = DGeomHelpers::EmbedMultipleConfs(*m, 10, params);
TEST_ASSERT(cids.size() == 6);
delete m;
}
}
void testGithub1240() {
{
RWMol *mol = SmilesToMol("C1CCCCCCC1");
TEST_ASSERT(mol);
MolOps::addHs(*mol);
DGeomHelpers::EmbedParameters params;
params.randomSeed = 42;
params.maxIterations = 1;
int cid = DGeomHelpers::EmbedMolecule(*mol, params);
TEST_ASSERT(cid >= 0);
delete mol;
}
{
RWMol *mol = SmilesToMol("C1C3CC2CC(CC1C2)C3");
TEST_ASSERT(mol);
MolOps::addHs(*mol);
DGeomHelpers::EmbedParameters params;
params.randomSeed = 42;
params.maxIterations = 1;
int cid = DGeomHelpers::EmbedMolecule(*mol, params);
TEST_ASSERT(cid >= 0);
delete mol;
}
{
RWMol *mol = SmilesToMol("c1ccccccccc1");
TEST_ASSERT(mol);
MolOps::addHs(*mol);
TEST_ASSERT(mol->getNumAtoms() == 20);
DGeomHelpers::EmbedParameters params;
params.randomSeed = 0xf00d;
params.maxIterations = 1; // we should get this in one iteration
int cid = DGeomHelpers::EmbedMolecule(*mol, params);
TEST_ASSERT(cid >= 0);
// std::cerr << MolToMolBlock(*mol) << std::endl;
delete mol;
}
{
RWMol *mol = SmilesToMol("c1ccccccc1");
TEST_ASSERT(mol);
MolOps::addHs(*mol);
TEST_ASSERT(mol->getNumAtoms() == 16);
DGeomHelpers::EmbedParameters params;
params.randomSeed = 0xf00d;
params.maxIterations = 1; // we should get this in one iteration
int cid = DGeomHelpers::EmbedMolecule(*mol, params);
TEST_ASSERT(cid >= 0);
// std::cerr << MolToMolBlock(*mol) << std::endl;
delete mol;
}
{
RWMol *mol = SmilesToMol("c1ccccccccccc1");
TEST_ASSERT(mol);
MolOps::addHs(*mol);
TEST_ASSERT(mol->getNumAtoms() == 24);
DGeomHelpers::EmbedParameters params;
params.randomSeed = 0xf00d;
params.maxIterations = 1; // we should get this in one iteration
int cid = DGeomHelpers::EmbedMolecule(*mol, params);
TEST_ASSERT(cid >= 0);
// std::cerr << MolToMolBlock(*mol) << std::endl;
delete mol;
}
{
// CHEMBL307150
RWMol *mol =
SmilesToMol("Cc1cc2ccn(C)c2c3c4C(=O)NC(=O)c4c5c6ccccc6[nH]c5c13");
TEST_ASSERT(mol);
MolOps::addHs(*mol);
DGeomHelpers::EmbedParameters params;
params.randomSeed = 0xf00d;
int cid = DGeomHelpers::EmbedMolecule(*mol, params);
TEST_ASSERT(cid >= 0);
params = DGeomHelpers::ETKDG;
params.randomSeed = 0xf00d;
cid = DGeomHelpers::EmbedMolecule(*mol, params);
TEST_ASSERT(cid >= 0);
// std::cerr << MolToMolBlock(*mol) << std::endl;
delete mol;
}
{
// CHEMBL43398
RWMol *mol =
SmilesToMol("C[C@@H]1[C@@H]2Cc3ccc(O)cc3[C@]1(C)CCN2CCN4CCCC4");
TEST_ASSERT(mol);
MolOps::addHs(*mol);
DGeomHelpers::EmbedParameters params;
params.randomSeed = 0xf00d;
int cid = DGeomHelpers::EmbedMolecule(*mol, params);
TEST_ASSERT(cid >= 0);
params = DGeomHelpers::ETKDG;
params.randomSeed = 0xf00d;
cid = DGeomHelpers::EmbedMolecule(*mol, params);
TEST_ASSERT(cid >= 0);
delete mol;
}
{
// CHEMBL290986
// std::cerr << "-----------------------------------" << std::endl;
RWMol *mol = SmilesToMol(
"COc1c(O)ccc2O[C@@H]([C@@H]3CCCC(=C3)C)c4c(ccc5NC(C)(C)C=C(C)c45)c12");
TEST_ASSERT(mol);
MolOps::addHs(*mol);
DGeomHelpers::EmbedParameters params;
params.randomSeed = 0xf00d;
int cid = DGeomHelpers::EmbedMolecule(*mol, params);
TEST_ASSERT(cid >= 0);
// std::cerr << "-----------------------------------" << std::endl;
params = DGeomHelpers::ETKDG;
params.randomSeed = 0xf00d;
cid = DGeomHelpers::EmbedMolecule(*mol, params);
TEST_ASSERT(cid >= 0);
// std::cerr << MolToMolBlock(*mol) << std::endl;
delete mol;
}
}
int main() {
RDLog::InitLogs();
BOOST_LOG(rdInfoLog)
<< "********************************************************\n";
BOOST_LOG(rdInfoLog) << "Testing DistGeomHelpers\n";
#if 1
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test2 \n\n";
test2();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test3 \n\n";
test3();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test4 \n\n";
test4();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test5 \n\n";
test5();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test6 \n\n";
test6();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test15Dists \n\n";
test15Dists();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test Issue 215 \n\n";
testIssue215();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t testMultipleConfs \n\n";
testMultipleConfs();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t testMultipleConfsExpTors \n\n";
testMultipleConfsExpTors();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t testIssue227 \n\n";
testIssue227();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t testIssue236 \n\n";
testIssue236();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t testOrdering \n\n";
testOrdering();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t testIssue244 \n\n";
testIssue244();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t testIssue251 \n\n";
testIssue251();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t testIssue276 \n";
testIssue276();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t testIssue284 \n\n";
testIssue284();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t testIssue285 \n\n";
testIssue285();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t testIssue355 \n\n";
testIssue355();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t testRandomCoords \n\n";
testRandomCoords();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test sf.net issue 1989539 \n\n";
testIssue1989539();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test sf.net issue 2091864 \n\n";
testIssue2091864();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test constrained embedding \n\n";
testConstrainedEmbedding();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test sf.net issue 2091974 \n\n";
testIssue2091974();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test sf.net issue 2835784 \n\n";
testIssue2835784();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test sf.net issue 3019283 \n\n";
testIssue3019283();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test sf.net issue 3238580 \n\n";
testIssue3238580();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test sf.net issue 3483968 \n\n";
testIssue3483968();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test github issue 55 \n\n";
testGithub55();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test1 \n\n";
test1();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test multi-threading \n\n";
testMultiThread();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog)
<< "\t test github issue 256: handling of zero-atom molecules\n\n";
testGithub256();
#ifdef RDK_TEST_MULTITHREADED
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test multi-threaded multi-conf embedding \n\n";
testMultiThreadMultiConf();
#endif
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test github issue 563: Incorrect ring "
"stereochemistry after embedding\n\n";
testGithub563();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test github issue 568: Incorrect stereochemistry "
"after embedding\n\n";
testGithub568();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test github issue 696: Bad 1-4 bounds matrix "
"elements in highly constrained system\n";
testGithub696();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog)
<< "\t More ChEMBL molecules failing bounds smoothing.\n";
testGithub697();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t ugly conformations can be generated for highly "
"constrained ring systems.\n";
testGithub971();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test embed parameters structure.\n";
testEmbedParameters();
#endif
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog)
<< "\t test github 1227: Hs being used in RMSD filtering.\n";
testGithub1227();
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t Failure to embed larger aromatic rings.\n";
testGithub1240();
BOOST_LOG(rdInfoLog)
<< "*******************************************************\n";
return (0);
}
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