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5618819c64e3d06b2c82d457aaf76e3410cceee2
rdkit/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp
Greg Landrum 5618819c64 merge #641
2015-11-14 05:03:24 +01:00

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//
// Copyright (C) 2004-2008 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 <GraphMol/RDKitBase.h>
#include <string>
#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;
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() {
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();
TEST_ASSERT(e1>100.0);
TEST_ASSERT(e1<300.0);
delete ff;
ff=UFF::constructForceField(m2, 100, *ci);
ff->initialize();
double e2=ff->calcEnergy();
TEST_ASSERT(feq(e1,e2));
}
}
#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;
}
}
}
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
#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) << "*******************************************************\n";
return(0);
}
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