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rdkit/Code/GraphMol/hanoitest.cpp
Greg Landrum da6cd73168 Run clang-format across everything (#7849) 
* run clang-format-18 across Code/*.cpp and Code/*.h

* run clang-format-18 across External
2024-09-26 13:39:02 +02:00

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//
// Copyright (C) 2014 Greg Landrum
//
// @@ 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/test.h>
#include <GraphMol/new_canon.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/hanoiSort.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <iostream>
#include <vector>
#include <random>
#include <cstdlib>
using namespace RDKit;
int pcmp(const void *a, const void *b) {
if ((*(int *)a) < (*(int *)b)) {
return -1;
} else if ((*(int *)a) > (*(int *)b)) {
return 1;
}
return 0;
}
int icmp(int a, int b) {
if (a < b) {
return -1;
} else if (a > b) {
return 1;
}
return 0;
}
class int_compare_ftor {
const int *dp_ints{nullptr};
public:
int_compare_ftor() {};
int_compare_ftor(const int *ints) : dp_ints(ints) {};
int operator()(int i, int j) const {
PRECONDITION(dp_ints, "no ints");
unsigned int ivi = dp_ints[i];
unsigned int ivj = dp_ints[j];
if (ivi < ivj) {
return -1;
} else if (ivi > ivj) {
return 1;
} else {
return 0;
}
}
};
void qs1(const std::vector<std::vector<int>> &vects) {
BOOST_LOG(rdInfoLog) << "sorting (qsort) vectors" << std::endl;
for (auto tv : vects) {
int *data = &tv.front();
qsort(data, tv.size(), sizeof(int), pcmp);
for (unsigned int j = 1; j < tv.size(); ++j) {
TEST_ASSERT(tv[j] >= tv[j - 1]);
}
}
BOOST_LOG(rdInfoLog) << "done: " << vects.size() << std::endl;
}
void hs1(const std::vector<std::vector<int>> &vects) {
BOOST_LOG(rdInfoLog) << "sorting (hanoi sort) vectors" << std::endl;
for (const auto &vect : vects) {
const int *data = &vect.front();
int_compare_ftor icmp(data);
int *indices = (int *)malloc(vect.size() * sizeof(int));
for (unsigned int j = 0; j < vect.size(); ++j) {
indices[j] = j;
}
int *count = (int *)malloc(vect.size() * sizeof(int));
int *changed = (int *)malloc(vect.size() * sizeof(int));
memset(changed, 1, vect.size() * sizeof(int));
RDKit::hanoisort(indices, vect.size(), count, changed, icmp);
for (unsigned int j = 1; j < vect.size(); ++j) {
TEST_ASSERT(data[indices[j]] >= data[indices[j - 1]]);
}
free(count);
free(indices);
free(changed);
}
BOOST_LOG(rdInfoLog) << "done: " << vects.size() << std::endl;
}
void test1() {
BOOST_LOG(rdInfoLog) << "Testing the hanoi sort" << std::endl;
typedef boost::random::mersenne_twister<std::uint32_t, 32, 4, 2, 31,
0x9908b0df, 11, 7, 0x9d2c5680, 15,
0xefc60000, 18, 3346425566U>
rng_type;
typedef boost::uniform_int<> distrib_type;
typedef boost::variate_generator<rng_type &, distrib_type> source_type;
rng_type generator(42u);
const unsigned int nVects = 500000;
const unsigned int vectSize = 50;
const unsigned int nClasses = 15;
distrib_type dist(0, nClasses);
source_type randomSource(generator, dist);
BOOST_LOG(rdInfoLog) << "populating vectors" << std::endl;
std::vector<std::vector<int>> vects(nVects);
for (unsigned int i = 0; i < nVects; ++i) {
vects[i] = std::vector<int>(vectSize);
for (unsigned int j = 0; j < vectSize; ++j) {
vects[i][j] = randomSource();
}
}
// qs1(vects);
hs1(vects);
BOOST_LOG(rdInfoLog) << "Done" << std::endl;
};
class atomcomparefunctor {
Canon::canon_atom *d_atoms{nullptr};
public:
atomcomparefunctor() {};
atomcomparefunctor(Canon::canon_atom *atoms) : d_atoms(atoms) {};
int operator()(int i, int j) const {
PRECONDITION(d_atoms, "no atoms");
unsigned int ivi, ivj;
// always start with the current class:
ivi = d_atoms[i].index;
ivj = d_atoms[j].index;
if (ivi < ivj) {
return -1;
} else if (ivi > ivj) {
return 1;
}
ivi = d_atoms[i].atom->getAtomicNum();
ivj = d_atoms[j].atom->getAtomicNum();
if (ivi < ivj) {
return -1;
} else if (ivi > ivj) {
return 1;
}
return 0;
}
};
class atomcomparefunctor2 {
Canon::canon_atom *d_atoms{nullptr};
public:
atomcomparefunctor2() {};
atomcomparefunctor2(Canon::canon_atom *atoms) : d_atoms(atoms) {};
int operator()(int i, int j) const {
PRECONDITION(d_atoms, "no atoms");
unsigned int ivi, ivj;
// always start with the current class:
ivi = d_atoms[i].index;
ivj = d_atoms[j].index;
if (ivi < ivj) {
return -1;
} else if (ivi > ivj) {
return 1;
}
// start by comparing degree
ivi = d_atoms[i].atom->getDegree();
ivj = d_atoms[j].atom->getDegree();
if (ivi < ivj) {
return -1;
} else if (ivi > ivj) {
return 1;
}
// move onto atomic number
ivi = d_atoms[i].atom->getAtomicNum();
ivj = d_atoms[j].atom->getAtomicNum();
if (ivi < ivj) {
return -1;
} else if (ivi > ivj) {
return 1;
}
return 0;
}
};
void test2() {
BOOST_LOG(rdInfoLog) << "Testing hanoi with a functor." << std::endl;
// make sure that hanoi works with a functor and "molecule data"
{
std::string smi = "FC1C(Cl)C1C";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
std::vector<Canon::canon_atom> atoms(m->getNumAtoms());
std::vector<int> indices(m->getNumAtoms());
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
atoms[i].atom = m->getAtomWithIdx(i);
atoms[i].index = 0;
indices[i] = i;
}
atomcomparefunctor ftor(&atoms.front());
int *data = &indices.front();
int *count = (int *)malloc(atoms.size() * sizeof(int));
int *changed = (int *)malloc(atoms.size() * sizeof(int));
memset(changed, 1, atoms.size() * sizeof(int));
RDKit::hanoisort(data, atoms.size(), count, changed, ftor);
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
// std::cerr<<indices[i]<<" "<<" index: "<<atoms[indices[i]].index<<"
// count: "<<count[indices[i]]<<std::endl;
if (i > 0) {
TEST_ASSERT(atoms[indices[i]].atom->getAtomicNum() >=
atoms[indices[i - 1]].atom->getAtomicNum());
if (atoms[indices[i]].atom->getAtomicNum() !=
atoms[indices[i - 1]].atom->getAtomicNum()) {
TEST_ASSERT(count[indices[i]] != 0);
} else {
TEST_ASSERT(count[indices[i]] == 0);
}
} else {
TEST_ASSERT(count[indices[i]] != 0);
}
}
delete m;
free(count);
free(changed);
}
BOOST_LOG(rdInfoLog) << "Done" << std::endl;
};
void test3() {
BOOST_LOG(rdInfoLog) << "Testing basic partition refinement." << std::endl;
// basic partition refinement
{
std::string smi = "FC1C(Cl)CCC1C";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
std::vector<Canon::canon_atom> atoms(m->getNumAtoms());
initCanonAtoms(*m, atoms, true);
atomcomparefunctor ftor(&atoms.front());
RDKit::Canon::canon_atom *data = &atoms.front();
int *count = (int *)malloc(atoms.size() * sizeof(int));
int *order = (int *)malloc(atoms.size() * sizeof(int));
int activeset;
int *next = (int *)malloc(atoms.size() * sizeof(int));
int *changed = (int *)malloc(atoms.size() * sizeof(int));
memset(changed, 1, atoms.size() * sizeof(int));
char *touched = (char *)malloc(atoms.size() * sizeof(char));
memset(touched, 0, atoms.size() * sizeof(char));
RDKit::Canon::CreateSinglePartition(atoms.size(), order, count, data);
RDKit::Canon::ActivatePartitions(atoms.size(), order, count, activeset,
next, changed);
// std::cerr<<"----------------------------------"<<std::endl;
// for(unsigned int i=0;i<m->getNumAtoms();++i){
// std::cerr<<i<<" "<<atoms[i].index<<" "<<count[i]<<" "<<next[i]<<"
// "<<order[i]<<std::endl;
// }
RDKit::Canon::RefinePartitions(*m, data, ftor, false, order, count,
activeset, next, changed, touched);
// std::cerr<<"----------------------------------"<<std::endl;
// for(unsigned int i=0;i<m->getNumAtoms();++i){
// std::cerr<<i<<" "<<atoms[i].index<<" "<<count[i]<<" "<<next[i]<<"
// "<<order[i]<<std::endl;
// }
// std::cerr<<"----------------------------------"<<std::endl;
// for(unsigned int i=0;i<m->getNumAtoms();++i){
// std::cerr<<order[i]<<" "<<atoms[order[i]].invar<<" index:
// "<<atoms[order[i]].index<<" count: "<<count[order[i]]<<std::endl;
// }
TEST_ASSERT(order[0] == 1);
TEST_ASSERT(order[6] == 0);
TEST_ASSERT(order[7] == 3);
TEST_ASSERT(count[order[0]] == 6);
TEST_ASSERT(count[order[1]] == 0);
TEST_ASSERT(count[order[6]] == 1);
TEST_ASSERT(count[order[7]] == 1);
delete m;
free(count);
free(order);
free(next);
free(changed);
free(touched);
}
{
// this time with smarter invariants
std::string smi = "FC1C(Cl)CCC1C";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
std::vector<Canon::canon_atom> atoms(m->getNumAtoms());
initCanonAtoms(*m, atoms, true);
atomcomparefunctor2 ftor(&atoms.front());
RDKit::Canon::canon_atom *data = &atoms.front();
int *count = (int *)malloc(atoms.size() * sizeof(int));
int *order = (int *)malloc(atoms.size() * sizeof(int));
int activeset;
int *next = (int *)malloc(atoms.size() * sizeof(int));
int *changed = (int *)malloc(atoms.size() * sizeof(int));
memset(changed, 1, atoms.size() * sizeof(int));
char *touched = (char *)malloc(atoms.size() * sizeof(char));
memset(touched, 0, atoms.size() * sizeof(char));
RDKit::Canon::CreateSinglePartition(atoms.size(), order, count, data);
RDKit::Canon::ActivatePartitions(atoms.size(), order, count, activeset,
next, changed);
RDKit::Canon::RefinePartitions(*m, data, ftor, false, order, count,
activeset, next, changed, touched);
// std::cerr<<"----------------------------------"<<std::endl;
// for(unsigned int i=0;i<m->getNumAtoms();++i){
// std::cerr<<order[i]<<" "<<" index: "<<atoms[order[i]].index<<" count:
// "<<count[order[i]]<<std::endl;
// }
TEST_ASSERT(order[0] == 7);
TEST_ASSERT(order[1] == 0);
TEST_ASSERT(order[2] == 3);
TEST_ASSERT(order[3] == 4);
TEST_ASSERT(order[5] == 1);
TEST_ASSERT(count[order[0]] == 1);
TEST_ASSERT(count[order[1]] == 1);
TEST_ASSERT(count[order[2]] == 1);
TEST_ASSERT(count[order[3]] == 2);
TEST_ASSERT(count[order[4]] == 0);
TEST_ASSERT(count[order[5]] == 3);
TEST_ASSERT(count[order[6]] == 0);
delete m;
free(count);
free(order);
free(next);
free(changed);
free(touched);
}
BOOST_LOG(rdInfoLog) << "Done" << std::endl;
};
class atomcomparefunctor3 {
Canon::canon_atom *dp_atoms{nullptr};
const ROMol *dp_mol{nullptr};
unsigned int getAtomNeighborhood(unsigned int i) const {
unsigned int res = 0;
const Atom *at = dp_mol->getAtomWithIdx(i);
std::vector<unsigned int> nbrs(at->getDegree());
unsigned int nbridx = 0;
ROMol::OEDGE_ITER beg, end;
boost::tie(beg, end) = dp_mol->getAtomBonds(at);
while (beg != end) {
const Bond *bond = (*dp_mol)[*beg];
nbrs[nbridx] =
static_cast<unsigned int>(100 * bond->getBondTypeAsDouble()) +
dp_atoms[bond->getOtherAtomIdx(i)].index;
++beg;
++nbridx;
}
std::sort(nbrs.begin(), nbrs.end());
for (nbridx = 0; nbridx < at->getDegree(); ++nbridx) {
res += (nbridx + 1) * 1000 + nbrs[nbridx];
}
return res;
}
int basecomp(int i, int j) const {
PRECONDITION(dp_atoms, "no atoms");
unsigned int ivi, ivj;
// always start with the current class:
ivi = dp_atoms[i].index;
ivj = dp_atoms[j].index;
if (ivi < ivj) {
return -1;
} else if (ivi > ivj) {
return 1;
}
// start by comparing degree
ivi = dp_atoms[i].atom->getDegree();
ivj = dp_atoms[j].atom->getDegree();
if (ivi < ivj) {
return -1;
} else if (ivi > ivj) {
return 1;
}
// move onto atomic number
ivi = dp_atoms[i].atom->getAtomicNum();
ivj = dp_atoms[j].atom->getAtomicNum();
if (ivi < ivj) {
return -1;
} else if (ivi > ivj) {
return 1;
}
return 0;
}
public:
bool df_useNbrs{false};
atomcomparefunctor3() {};
atomcomparefunctor3(Canon::canon_atom *atoms, const ROMol &m)
: dp_atoms(atoms), dp_mol(&m), df_useNbrs(false) {};
int operator()(int i, int j) const {
PRECONDITION(dp_atoms, "no atoms");
PRECONDITION(dp_mol, "no molecule");
int v = basecomp(i, j);
if (v) {
return v;
}
unsigned int ivi, ivj;
if (df_useNbrs) {
ivi = dp_atoms[i].index + 1 + getAtomNeighborhood(i);
ivj = dp_atoms[j].index + 1 + getAtomNeighborhood(j);
// std::cerr<<" "<<i<<"-"<<j<<": "<<ivi<<"
// "<<ivj<<std::endl;
if (ivi < ivj) {
return -1;
} else if (ivi > ivj) {
return 1;
}
}
return 0;
}
};
void test4() {
BOOST_LOG(rdInfoLog) << "Testing partition refinement with neighbors."
<< std::endl;
// partition refinement with neighbors
{
std::string smi = "FC1C(Cl)CCC1C";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
std::vector<Canon::canon_atom> atoms(m->getNumAtoms());
initCanonAtoms(*m, atoms, true);
atomcomparefunctor3 ftor(&atoms.front(), *m);
RDKit::Canon::canon_atom *data = &atoms.front();
int *count = (int *)malloc(atoms.size() * sizeof(int));
int *order = (int *)malloc(atoms.size() * sizeof(int));
int activeset;
int *next = (int *)malloc(atoms.size() * sizeof(int));
int *changed = (int *)malloc(atoms.size() * sizeof(int));
memset(changed, 1, atoms.size() * sizeof(int));
char *touched = (char *)malloc(atoms.size() * sizeof(char));
memset(touched, 0, atoms.size() * sizeof(char));
RDKit::Canon::CreateSinglePartition(atoms.size(), order, count, data);
RDKit::Canon::ActivatePartitions(atoms.size(), order, count, activeset,
next, changed);
// std::cerr<<"1----------------------------------"<<std::endl;
// for(unsigned int i=0;i<m->getNumAtoms();++i){
// std::cerr<<order[i]<<" "<<" index: "<<atoms[order[i]].index<<" count:
// "<<count[order[i]]<<" next: "<<next[order[i]]<<" changed:
// "<<changed[order[i]]<<std::endl;
// }
RDKit::Canon::RefinePartitions(*m, data, ftor, false, order, count,
activeset, next, changed, touched);
// std::cerr<<"2----------------------------------"<<std::endl;
// for(unsigned int i=0;i<m->getNumAtoms();++i){
// std::cerr<<order[i]<<" "<<" index: "<<atoms[order[i]].index<<" count:
// "<<count[order[i]]<<" next: "<<next[order[i]]<<" changed:
// "<<changed[order[i]]<<std::endl;
// }
// std::cerr<<"!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"<<std::endl;
ftor.df_useNbrs = true;
RDKit::Canon::ActivatePartitions(atoms.size(), order, count, activeset,
next, changed);
// std::cerr<<"3----------------------------------"<<std::endl;
// for(unsigned int i=0;i<m->getNumAtoms();++i){
// std::cerr<<order[i]<<" "<<" index: "<<atoms[order[i]].index<<" count:
// "<<count[order[i]]<<" next: "<<next[order[i]]<<" changed:
// "<<changed[order[i]]<<std::endl;
// }
RDKit::Canon::RefinePartitions(*m, data, ftor, true, order, count,
activeset, next, changed, touched);
// std::cerr<<"----------------------------------"<<std::endl;
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
// std::cerr<<order[i]<<" "<<" index: "<<atoms[order[i]].index<<" count:
// "<<count[order[i]]<<std::endl;
TEST_ASSERT(count[order[i]] == 1);
if (i > 0) {
TEST_ASSERT(ftor(order[i], order[i - 1]) >= 0);
}
}
delete m;
free(count);
free(order);
free(next);
free(changed);
free(touched);
}
{
std::string smi = "FC1C(CO)CCC1CC";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
std::vector<Canon::canon_atom> atoms(m->getNumAtoms());
initCanonAtoms(*m, atoms, true);
atomcomparefunctor3 ftor(&atoms.front(), *m);
RDKit::Canon::canon_atom *data = &atoms.front();
int *count = (int *)malloc(atoms.size() * sizeof(int));
int *order = (int *)malloc(atoms.size() * sizeof(int));
int activeset;
int *next = (int *)malloc(atoms.size() * sizeof(int));
int *changed = (int *)malloc(atoms.size() * sizeof(int));
memset(changed, 1, atoms.size() * sizeof(int));
char *touched = (char *)malloc(atoms.size() * sizeof(char));
memset(touched, 0, atoms.size() * sizeof(char));
RDKit::Canon::CreateSinglePartition(atoms.size(), order, count, data);
RDKit::Canon::ActivatePartitions(atoms.size(), order, count, activeset,
next, changed);
RDKit::Canon::RefinePartitions(*m, data, ftor, false, order, count,
activeset, next, changed, touched);
// std::cerr<<"----------------------------------"<<std::endl;
// for(unsigned int i=0;i<m->getNumAtoms();++i){
// std::cerr<<order[i]<<" "<<" index: "<<atoms[order[i]].index<<" count:
// "<<count[order[i]]<<std::endl;
// }
ftor.df_useNbrs = true;
RDKit::Canon::ActivatePartitions(atoms.size(), order, count, activeset,
next, changed);
RDKit::Canon::RefinePartitions(*m, data, ftor, true, order, count,
activeset, next, changed, touched);
// std::cerr<<"----------------------------------"<<std::endl;
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
// std::cerr<<order[i]<<" "<<" index: "<<atoms[order[i]].index<<" count:
// "<<count[order[i]]<<std::endl;
TEST_ASSERT(count[order[i]] == 1);
if (i > 0) {
// std::cerr<<" ftor: "<<ftor(order[i],order[i-1])<<std::endl;
TEST_ASSERT(ftor(order[i], order[i - 1]) >= 0);
}
}
delete m;
free(count);
free(order);
free(next);
free(changed);
free(touched);
}
{
std::string smi = "FC1C(CC)CCC1CC";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
std::vector<Canon::canon_atom> atoms(m->getNumAtoms());
initCanonAtoms(*m, atoms, true);
atomcomparefunctor3 ftor(&atoms.front(), *m);
RDKit::Canon::canon_atom *data = &atoms.front();
int *count = (int *)malloc(atoms.size() * sizeof(int));
int *order = (int *)malloc(atoms.size() * sizeof(int));
int activeset;
int *next = (int *)malloc(atoms.size() * sizeof(int));
int *changed = (int *)malloc(atoms.size() * sizeof(int));
memset(changed, 1, atoms.size() * sizeof(int));
char *touched = (char *)malloc(atoms.size() * sizeof(char));
memset(touched, 0, atoms.size() * sizeof(char));
RDKit::Canon::CreateSinglePartition(atoms.size(), order, count, data);
RDKit::Canon::ActivatePartitions(atoms.size(), order, count, activeset,
next, changed);
// std::cerr<<"----------------------------------"<<std::endl;
// for(unsigned int i=0;i<m->getNumAtoms();++i){
// std::cerr<<order[i]<<" "<<atoms[order[i]].invar<<" index:
// "<<atoms[order[i]].index<<std::endl;
// }
RDKit::Canon::RefinePartitions(*m, data, ftor, false, order, count,
activeset, next, changed, touched);
// std::cerr<<"!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"<<std::endl;
ftor.df_useNbrs = true;
RDKit::Canon::ActivatePartitions(atoms.size(), order, count, activeset,
next, changed);
RDKit::Canon::RefinePartitions(*m, data, ftor, true, order, count,
activeset, next, changed, touched);
// std::cerr<<"----------------------------------"<<std::endl;
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
// std::cerr<<order[i]<<" "<<" index: "<<atoms[order[i]].index<<" count:
// "<<count[order[i]]<<std::endl;
if (i > 0) {
// std::cerr<<" ftor: "<<ftor(order[i],order[i-1])<<std::endl;
TEST_ASSERT(ftor(order[i], order[i - 1]) >= 0);
}
}
// here we can't manage to get everything unique
TEST_ASSERT(order[0] == 4 && count[4] == 2);
TEST_ASSERT(order[1] == 9 && count[9] == 0);
TEST_ASSERT(order[2] == 0 && count[0] == 1);
TEST_ASSERT(order[3] == 3 && count[3] == 2);
TEST_ASSERT(order[4] == 8 && count[8] == 0);
TEST_ASSERT(order[5] == 5 && count[5] == 2);
TEST_ASSERT(order[6] == 6 && count[6] == 0);
TEST_ASSERT(order[7] == 2 && count[2] == 2);
TEST_ASSERT(order[8] == 7 && count[7] == 0);
TEST_ASSERT(order[9] == 1 && count[1] == 1);
delete m;
free(count);
free(order);
free(next);
free(changed);
free(touched);
}
BOOST_LOG(rdInfoLog) << "Done" << std::endl;
};
void test5() {
BOOST_LOG(rdInfoLog) << "testing canonicalization via tie breaking."
<< std::endl;
// canonicalization via tie breaking
{
std::string smi = "FC1C(CC)CCC1CC";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
std::vector<Canon::canon_atom> atoms(m->getNumAtoms());
initCanonAtoms(*m, atoms, true);
atomcomparefunctor3 ftor(&atoms.front(), *m);
RDKit::Canon::canon_atom *data = &atoms.front();
int *count = (int *)malloc(atoms.size() * sizeof(int));
int *order = (int *)malloc(atoms.size() * sizeof(int));
int activeset;
int *next = (int *)malloc(atoms.size() * sizeof(int));
int *changed = (int *)malloc(atoms.size() * sizeof(int));
memset(changed, 1, atoms.size() * sizeof(int));
char *touched = (char *)malloc(atoms.size() * sizeof(char));
memset(touched, 0, atoms.size() * sizeof(char));
RDKit::Canon::CreateSinglePartition(atoms.size(), order, count, data);
RDKit::Canon::ActivatePartitions(atoms.size(), order, count, activeset,
next, changed);
// std::cerr<<"----------------------------------"<<std::endl;
// for(unsigned int i=0;i<m->getNumAtoms();++i){
// std::cerr<<order[i]<<" "<<atoms[order[i]].invar<<" index:
// "<<atoms[order[i]].index<<std::endl;
// }
RDKit::Canon::RefinePartitions(*m, data, ftor, false, order, count,
activeset, next, changed, touched);
// std::cerr<<"!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"<<std::endl;
ftor.df_useNbrs = true;
RDKit::Canon::ActivatePartitions(atoms.size(), order, count, activeset,
next, changed);
RDKit::Canon::RefinePartitions(*m, data, ftor, true, order, count,
activeset, next, changed, touched);
// std::cerr<<"----------------------------------"<<std::endl;
// for(unsigned int i=0;i<m->getNumAtoms();++i){
// std::cerr<<order[i]<<" "<<" index: "<<atoms[order[i]].index<<" count:
// "<<count[order[i]]<<std::endl;
// }
// here we can't manage to get everything unique
TEST_ASSERT(order[0] == 4 && count[4] == 2);
TEST_ASSERT(order[1] == 9 && count[9] == 0);
TEST_ASSERT(order[2] == 0 && count[0] == 1);
TEST_ASSERT(order[3] == 3 && count[3] == 2);
TEST_ASSERT(order[4] == 8 && count[8] == 0);
TEST_ASSERT(order[5] == 5 && count[5] == 2);
TEST_ASSERT(order[6] == 6 && count[6] == 0);
TEST_ASSERT(order[7] == 2 && count[2] == 2);
TEST_ASSERT(order[8] == 7 && count[7] == 0);
TEST_ASSERT(order[9] == 1 && count[1] == 1);
RDKit::Canon::BreakTies(*m, data, ftor, true, order, count, activeset, next,
changed, touched);
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
// std::cerr<<order[i]<<" "<<" index: "<<atoms[order[i]].index<<" count:
// "<<count[order[i]]<<std::endl;
TEST_ASSERT(count[order[i]] == 1);
}
delete m;
free(count);
free(order);
free(next);
free(changed);
free(touched);
}
BOOST_LOG(rdInfoLog) << "Done" << std::endl;
};
void test6() {
BOOST_LOG(rdInfoLog) << "testing canonicalization using the wrapper."
<< std::endl;
// canonicalization using the wrapper
#if 1
{
std::string smi = "FC1C(CC)CCC1CC";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
std::vector<unsigned int> atomRanks;
RDKit::Canon::rankMolAtoms(*m, atomRanks);
boost::dynamic_bitset<> seen(m->getNumAtoms());
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
TEST_ASSERT(!seen[atomRanks[i]]);
seen.set(atomRanks[i], 1);
}
// std::copy(atomRanks.begin(),atomRanks.end(),std::ostream_iterator<unsigned
// int>(std::cerr," "));
// std::cerr<<std::endl;
TEST_ASSERT(atomRanks[0] == 2);
TEST_ASSERT(atomRanks[1] == 9);
TEST_ASSERT(atomRanks[2] == 7);
TEST_ASSERT(atomRanks[3] == 3);
TEST_ASSERT(atomRanks[4] == 0);
TEST_ASSERT(atomRanks[5] == 5);
TEST_ASSERT(atomRanks[6] == 6);
TEST_ASSERT(atomRanks[7] == 8);
TEST_ASSERT(atomRanks[8] == 4);
TEST_ASSERT(atomRanks[9] == 1);
delete m;
}
{
std::string smi = "CC[C@@H]1CCC[C@@H](O1)C(=O)O";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
std::vector<unsigned int> atomRanks;
RDKit::Canon::rankMolAtoms(*m, atomRanks);
boost::dynamic_bitset<> seen(m->getNumAtoms());
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
// std::cerr<<i<<" "<<atomRanks[i]<<std::endl;
TEST_ASSERT(!seen[atomRanks[i]]);
seen.set(atomRanks[i], 1);
}
// for(unsigned int ii=0;ii<atomRanks.size();++ii){
// std::cerr<<ii<<":"<<atomRanks[ii]<<std::endl;
// }
TEST_ASSERT(atomRanks[0] == 0);
TEST_ASSERT(atomRanks[1] == 4);
TEST_ASSERT(atomRanks[2] == 9);
TEST_ASSERT(atomRanks[3] == 5);
TEST_ASSERT(atomRanks[4] == 3);
TEST_ASSERT(atomRanks[5] == 6);
TEST_ASSERT(atomRanks[6] == 10);
TEST_ASSERT(atomRanks[7] == 7);
TEST_ASSERT(atomRanks[8] == 8);
TEST_ASSERT(atomRanks[9] == 1);
TEST_ASSERT(atomRanks[10] == 2);
delete m;
}
{
std::string smi =
"N[C@@H](Cc1c[nH]c2ccccc12)C(=O)N[C@@H](CCCN=C(N)N)C(=O)N[C@@H](Cc3c["
"nH]c4ccccc34)C(=O)OCc5ccccc5";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
std::vector<unsigned int> atomRanks;
RDKit::Canon::rankMolAtoms(*m, atomRanks);
boost::dynamic_bitset<> seen(m->getNumAtoms());
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
// std::cerr<<i<<" "<<atomRanks[i]<<std::endl;
TEST_ASSERT(!seen[atomRanks[i]]);
seen.set(atomRanks[i], 1);
}
// for(unsigned int ii=0;ii<atomRanks.size();++ii){
// std::cerr<<ii<<":"<<atomRanks[ii]<<std::endl;
// }
delete m;
}
#endif
{
std::string smi = "BrC=C1CCC(C(=O)O1)c2cccc3ccccc23";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
std::vector<unsigned int> atomRanks;
RDKit::Canon::rankMolAtoms(*m, atomRanks);
boost::dynamic_bitset<> seen(m->getNumAtoms());
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
// std::cerr<<i<<" "<<atomRanks[i]<<std::endl;
TEST_ASSERT(!seen[atomRanks[i]]);
seen.set(atomRanks[i], 1);
}
// for(unsigned int ii=0;ii<atomRanks.size();++ii){
// std::cerr<<ii<<":"<<atomRanks[ii]<<std::endl;
// }
delete m;
}
{
std::string smi = "CC12CCCC1CCCC2";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
// start w/o tie breaking here; we shouldn't need it.
std::vector<unsigned int> atomRanks;
RDKit::Canon::rankMolAtoms(*m, atomRanks, false);
boost::dynamic_bitset<> seen(m->getNumAtoms());
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
// std::cerr<<" "<<i<<" "<<atomRanks[i]<<std::endl;
TEST_ASSERT(!seen[atomRanks[i]]);
seen.set(atomRanks[i], 1);
}
delete m;
}
{
std::string smi = "CC12CCCC1C1CCC3CC(O)CCC3(C)C1CC2";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
// start w/o tie breaking here; we shouldn't need it.
std::vector<unsigned int> atomRanks;
RDKit::Canon::rankMolAtoms(*m, atomRanks, false);
boost::dynamic_bitset<> seen(m->getNumAtoms());
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
TEST_ASSERT(!seen[atomRanks[i]]);
seen.set(atomRanks[i], 1);
}
delete m;
}
BOOST_LOG(rdInfoLog) << "Done" << std::endl;
};
namespace {
ROMol *_renumber(const ROMol *m, std::vector<unsigned int> &nVect,
const std::string & /*inSmiles*/) {
ROMol *nm = MolOps::renumberAtoms(*m, nVect);
TEST_ASSERT(nm);
TEST_ASSERT(nm->getNumAtoms() == m->getNumAtoms());
TEST_ASSERT(nm->getNumBonds() == m->getNumBonds());
// MolOps::assignStereochemistry(*nm, true, true);
// for (unsigned int ii = 0; ii < nm->getNumAtoms(); ++ii) {
// if (nm->getAtomWithIdx(ii)->hasProp("_CIPCode")) {
// TEST_ASSERT(m->getAtomWithIdx(nVect[ii])->hasProp("_CIPCode"));
// std::string ocip =
// m->getAtomWithIdx(nVect[ii])->getProp<std::string>("_CIPCode");
// std::string ncip =
// nm->getAtomWithIdx(ii)->getProp<std::string>("_CIPCode");
// if (ocip != ncip) {
// std::cerr << " cip mismatch: " << inSmiles << std::endl;
// std::cerr << " " << nVect[ii] << ": " << ocip << " -> " << ii
// << ": " << ncip << std::endl;
// std::cerr << " " << MolToSmiles(*nm, true) << std::endl;
// }
// TEST_ASSERT(ocip == ncip);
// }
// }
return nm;
}
void _renumberTest(const ROMol *m, std::string inSmiles,
unsigned int numRenumbers) {
PRECONDITION(m, "no molecule");
// std::cerr<<">>>>>>>>>>>>>>>>>>>>>>>>>>>"<<std::endl;
std::string osmi = MolToSmiles(*m, true);
std::vector<unsigned int> idxV(m->getNumAtoms());
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
idxV[i] = i;
}
for (unsigned int i = 0; i < numRenumbers; ++i) {
// std::cerr<<"---------------------------------------------------"<<std::endl;
std::vector<unsigned int> nVect(idxV);
std::shuffle(nVect.begin(), nVect.end(), std::mt19937(0xf00d));
// for(unsigned int j=0;j<m->getNumAtoms();++j){
// std::cerr<<"Renumber: "<<nVect[j]<<"->"<<j<<std::endl;
// }
ROMol *nm = _renumber(m, nVect, inSmiles);
nm->setProp(common_properties::_StereochemDone, 1);
std::string smi = MolToSmiles(*nm, true);
if (smi != osmi) {
std::cerr << " input: " << inSmiles << ", Renumbering round: " << i
<< std::endl;
std::cerr << osmi << std::endl;
std::cerr << smi << std::endl;
m->setProp("_Name", "orig");
std::cerr << MolToMolBlock(*m) << std::endl;
nm->setProp("_Name", "renumber");
std::cerr << MolToMolBlock(*nm) << std::endl;
for (unsigned int j = 0; j < m->getNumAtoms(); ++j) {
std::cerr << "Renumber: " << nVect[j] << "->" << j << std::endl;
}
}
delete nm;
TEST_ASSERT(smi == osmi);
}
}
void _renumberTest2(const ROMol *m, std::string inSmiles,
unsigned int numRenumbers) {
PRECONDITION(m, "no molecule");
unsigned int nAtoms = m->getNumAtoms();
std::vector<unsigned int> idxV(m->getNumAtoms());
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
idxV[i] = i;
}
for (unsigned int i = 0; i < numRenumbers; ++i) {
std::vector<unsigned int> nVect(idxV);
std::shuffle(nVect.begin(), nVect.end(), std::mt19937(0xf00d));
ROMol *nm = _renumber(m, nVect, inSmiles);
UINT_VECT ranks(nAtoms);
Canon::rankMolAtoms(*nm, ranks, true);
char *ranksSet = (char *)malloc(nAtoms * sizeof(char));
memset(ranksSet, 0, nAtoms * sizeof(char));
for (unsigned int rank : ranks) {
ranksSet[rank] = 1;
}
for (unsigned int i = 0; i < nAtoms; i++) {
if (ranksSet[i] != 1) {
std::cerr << "Molecule has non unique ranks: " << MolToSmiles(*nm, true)
<< ", Renumbering round: " << i << std::endl;
for (unsigned int i = 0; i < nAtoms; i++) {
std::cerr << "AtomIdx: " << i << " Rank: " << ranks[i] << std::endl;
}
}
TEST_ASSERT(ranksSet[i] == 1);
}
delete nm;
free(ranksSet);
}
}
} // namespace
void test7a() {
BOOST_LOG(rdInfoLog) << "testing some specific ordering problems"
<< std::endl;
std::string rdbase = getenv("RDBASE");
std::string smi1, smi2;
{
std::string fName = rdbase + "/Code/GraphMol/test_data/canon_reorder1.mol";
RWMol *m = MolFileToMol(fName, false, false);
TEST_ASSERT(m);
MolOps::sanitizeMol(*m);
std::vector<unsigned int> atomRanks;
// std::cerr <<"\n\n\n\n\n\n\n\n\n\n\n\n>--------------" << std::endl;
RDKit::Canon::rankMolAtoms(*m, atomRanks, false);
// std::cerr <<"---------------" << std::endl;
// for(unsigned int i=0;i<m->getNumAtoms();++i){
// std::cerr<<" "<<i+1<<" "<<atomRanks[i]<<std::endl;
// }
// std::cerr <<"---------------" << std::endl;
smi1 = MolToSmiles(*m, true);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/test_data/canon_reorder2.mol";
RWMol *m = MolFileToMol(fName, false, false);
TEST_ASSERT(m);
MolOps::sanitizeMol(*m);
std::vector<unsigned int> atomRanks;
// std::cerr <<">--------------" << std::endl;
RDKit::Canon::rankMolAtoms(*m, atomRanks, false);
// std::cerr <<"---------------" << std::endl;
// for(unsigned int i=0;i<m->getNumAtoms();++i){
// std::cerr<<" "<<i+1<<" "<<atomRanks[i]<<std::endl;
// }
// std::cerr <<"---------------" << std::endl;
smi2 = MolToSmiles(*m, true);
delete m;
}
if (smi1 != smi2) {
std::cerr << smi1 << "\n" << smi2 << std::endl;
}
TEST_ASSERT(smi1 == smi2);
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
std::string smis[] = {
"C[C@@H]1CCC[C@H](C)[C@H]1C", "N[C@@]1(C[C@H]([18F])C1)C(=O)O",
"CC12CCCC1C1CCC3CC(O)CCC3(C)C1CC2",
"CC(C)CCCC[C@@H]1C[C@H](/C=C/[C@]2(C)CC[C@H](O)CC2)[C@@H](O)[C@H]1O",
"C[C@@]12CCC[C@H]1[C@@H]1CC[C@H]3C[C@@H](O)CC[C@]3(C)[C@H]1CC2",
"CCCN[C@H]1CC[C@H](NC)CC1",
"O=S(=O)(NC[C@H]1CC[C@H](CNCc2ccc3ccccc3c2)CC1)c1ccc2ccccc2c1",
"CC(C)[C@H]1CC[C@H](C(=O)N[C@H](Cc2ccccc2)C(=O)O)CC1",
"O=[N+]([O-])c1ccccc1S(=O)(=O)NC[C@H]1CC[C@H](CNCC2Cc3ccccc3CC2)CC1",
"Oc1ccc2c(Cc3ccc(OCCN4CCCCC4)cc3)c([C@H]3CC[C@H](O)CC3)sc2c1",
"O=C(c1ccc(OCCN2CCCCC2)cc1)c1c2ccc(O)cc2sc1[C@H]1CC[C@H](O)CC1",
"N#Cc1ccc2c(c1)CCN(CC[C@@H]1CC[C@@H](NC(=O)c3ccnc4ccccc34)CC1)C2",
"COCCOC[C@H](CC1(C(=O)N[C@H]2CC[C@@H](C(=O)O)CC2)CCCC1)C(=O)O",
"c1ccc(CN[C@H]2CC[C@H](Nc3ccc4[nH]ncc4c3)CC2)cc1",
"CCC1=C(C)CN(C(=O)NCCc2ccc(S(=O)(=O)NC(=O)N[C@H]3CC[C@H](C)CC3)cc2)C1=O",
"C[C@H]1C[C@H](C1)N1CCC1", "C[C@H]1C[C@H](C1)N1CCN(C)CC1",
"CN1CCN(CC1)[C@H]1C[C@H](C1)c1ncc2c(N)nccn12",
"CN1CCN(CC1)[C@H]1C[C@H](C1)c1nc(-c2ccc3ccc(nc3c2)-c2ccccc2)c2c(N)nccn12",
"C12C3C1C3C4C5C4C52", "N[C@H]1C2CC3CC1C[C@](O)(C3)C2",
"O=C(CN1CCN(c2ccc(C(F)(F)F)cn2)CC1)N[C@H]1C2CC3CC1C[C@](O)(C3)C2",
"COc1cc([C@H]2[C@H](C)[C@H](C)[C@H]2c2ccc(O)c(OC)c2)ccc1O",
"N[C@@H]1[C@H]2CNC[C@@H]12",
"N[C@@H]1[C@H]2CN(c3nc4c(cc3F)c(=O)c(C(=O)O)cn4C3CC3)C[C@@H]12",
// some examples that came up while doing a torture test in ZINC
"CN1CCCNCCN(C)CCC[NH2+]CC1", "CN1CCC[NH2+]CCN(C)CCC[NH+](C)CC1",
"O=P([O-])([O-])C[NH+]1CCCN(CP(=O)([O-])O)CC[NH+](CP(=O)([O-])[O-])CCC[NH+]"
"(CP(=O)([O-])[O-])CC1",
"O=C(CCNC(=O)Cn1cnc2ccccc2c1=O)NCCc1c[nH]c2ccccc12",
"C1CNCC[NH2+]CC(C2CNCC[NH2+]CCC[NH2+]CCNC2)CNCC[NH2+]C1",
// C60
"C12=C3C4=C5C6=C1C7=C8C9=C1C%10=C%11C(=C29)C3=C2C3=C4C4=C5C5=C9C6=C7C6="
"C7C8=C1C1=C8C%10=C%10C%11=C2C2=C3C3=C4C4=C5C5=C%11C%12=C(C6=C95)C7=C1C1=C%"
"12C5=C%11C4=C3C3=C5C(=C81)C%10=C23",
// C70
"C12=C3C4=C5C6=C7C8=C9C%10=C%11C%12=C%13C%10=C%10C8=C5C1=C%10C1=C%13C5="
"C8C1=C2C1=C3C2=C3C%10=C%13C%14=C3C1=C8C1=C3C5=C%12C5=C8C%11=C%11C9=C7C7="
"C9C6=C4C2=C2C%10=C4C(=C29)C2=C6C(=C8C8=C9C6=C4C%13=C9C(=C%141)C3=C85)C%11="
"C27",
// Bernd's example1
"C12C3C4C3C3C1C2C43",
// Bernd's example2
"C12C3C1C1C4C5C4C4C6C(C6C3C3C1C43)C25",
// doubled house
"C12C3C45C67C8C9C66C14C21C35C78C961", "C12C3C45C6C7C11C27C41C356",
// Problematic round-tripping
"COC(=O)/C=C/C(C)=C/C=C/C(C)=C/C=C/C=C(C)/C=C/C=C(\\C)/C=C/C(=O)[O-]",
"COC(=O)/C=C/C(C)=C/C=C/C(C)=C/C=C/C=C(\\C)/C=C/C=C(\\C)/C=C/C(=O)[O-]",
"c1cc2ccc(ccc3ccc1cc3)cc2", "C13C6C1C2C4C2C3C5C4C56",
"C45C1C6C3C6C5C4C2C3C12", "C45C2C6C3C6C5C4C1C3C12",
"Cl[C@H]1[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H]1Cl",
"N[C@]1(C(=O)O)C[C@H](n2oc(=O)[nH]c2=O)C1", "CC1CC(C)CC(C)C1",
"C[C@H]1C[C@@H](C)C[C@H](C)C1", "C[C@H]1C[C@@H](C)C[C@@H](C)C1",
// Stereochemistry in large rings
"C1[C@@H](C(C)=O)[C@H]2[C@H](C(C)=C1)[C@@H]1O[C@H]2[C@@H](O)C/C=C\\CC1",
// Chembl 20 examples
"COC(=O)CC[C@]12C[C@]13CC[C@]1(C)[C@@H]4[C@@H](C[C@@]1(C)[C@@H]3CC[C@H]2C("
"C)(C)O)O[C@@]1(C[C@@H](C)C(=O)O1)C[C@H]4C",
"C/C=C/"
"[C@H](O)C(C)(C)[C@@H]1CC=CC=CC=C[C@H](OC)Cc2nc(co2)C(=O)O[C@H](C(C)(C)[C@@"
"H](O)/C=C/C)CC=C[C@H]2O[C@H]2C=CC=Cc2nc(co2)C(=O)O1",
"N[C@]1(C(=O)O)C[C@@H](n2oc(=O)[nH]c2=O)C1",
"COc1ccc([C@H]2C3(CO)C4[N@](C)C5C2(CO)C2[N@](C)C3C4(CO)[C@H](c3ccc(OC)cc3)"
"C52CO)cc1",
"NCCNC(=O)[C@]1(O)C[C@@H](O)[C@H](O)[C@H](O)C1",
// CIP renumber problems
// "O=P(O)(O)O[C@@H]1[C@H](OP(=O)(O)O)[C@@H](OP(=O)(O)O)[C@H](OP(=O)(O)O)[C@@H](OP(=O)(O)O[32P](=O)(O)O)[C@@H]1OP(=O)(O)O",
// "O=C(NCCO[C@H]1[C@@H](O)[C@H](OP(=O)(O)O)[C@@H](OP(=O)(O)O)[C@H](O)[C@H]1OP(=O)(O)O)NCCO[C@H]1[C@@H](O)[C@H](OP(=O)(O)O)[C@@H](O[PH](O)(O)O)[C@H](O)[C@H]1OP(=O)(O)O",
// "O=C(NCCO[C@@H]1[C@H](OP(=O)(O)O)[C@@H](OP(=O)(O)O)[C@H](O[PH](O)(O)O)[C@@H](OP(=O)(O)O)[C@@H]1OP(=O)(O)O)NCCO[C@H]1[C@@H](OP(=O)(O)O)[C@H](O)[C@@H](OP(=O)(O)O)[C@H](OP(=O)(O)O)[C@H]1O",
// "O=C(O)[C@H]1[C@@H](C(=O)O)[C@@H](C(=O)O)[C@@H]1C(=O)O",
"C[C@H]1[C@H](C)[C@@H](C)[C@H]1C",
"COc1cc([C@H]2[C@@](NC(=O)c3ccc(NC(=O)C4CCCC4)cc3)(C(=O)O)[C@@H](c3ccc(OC(="
"O)c4cccs4)c(OC)c3)[C@]2(NC(=O)c2ccc(NC(=O)C3CCCC3)cc2)C(=O)O)ccc1OC(=O)"
"c1cccs1",
"COc1cc([C@H]2[C@@](NC(=O)c3ccc(NC(=O)OC(C)(C)C)cc3)(C(=O)O)[C@@H](c3ccc("
"OC(=O)c4cccs4)c(OC)c3)[C@]2(NC(=O)c2ccc(NC(=O)OC(C)(C)C)cc2)C(=O)O)ccc1OC("
"=O)c1cccs1",
"COc1cc([C@H]2[C@](NC(=O)c3ccc(NC(=O)OC(C)(C)C)cc3)(C(=O)O)[C@H](c3ccc(OC(="
"O)c4cccs4)c(OC)c3)[C@]2(NC(=O)c2ccc(NC(=O)OC(C)(C)C)cc2)C(=O)O)ccc1OC(=O)"
"c1cccs1",
"CCC[C@H]1CC[C@H]([C@H]2CC[C@H](OC(=O)[C@H]3[C@@H](c4ccc(O)cc4)[C@H](C(=O)"
"O[C@H]4CC[C@H]([C@H]5CC[C@H](CCC)CC5)CC4)[C@@H]3c3ccc(O)cc3)CC2)CC1",
// test molecules with atom-mapping numbers
"[O:1]=[C:2]([CH2:3][C:4]1=[CH:5][CH:6]=[CH:7][CH:8]=[CH:9]1)[NH2:10]",
// chembl molecules with multiple fragments
// CHEMBL439119
"CCCCCCC1C23C4=c5c6c7c8c9c%10c%11c%12c%13c%14c%15c%16c%17c%18c%19c%20c%21c%"
"22c%23c(c5c5c6c6c8c%11c8c%11c%12c%15c%12c(c%20%16)c%21c%15c%23c5c(c68)c%"
"15c%12%11)C2(C[N+]1(C)C)C%22C%19c1c-%18c2c5c(c13)C4C7C9=C5C1(C2C%17%14)C("
"CCCCCC)[N+](C)(C)CC%10%131.[I-].[I-]",
// CHEMBL1203199
"C[C@H](NC(=O)[C@H]1Cc2c(sc3ccccc23)CN1)c1ccccc1.Cl",
// CHEMBL501667
"CCn1c2ccc3cc2c2cc(ccc21)C(=O)c1ccc(cc1)Cn1cc[n+](c1)Cc1ccc(cc1)-c1cccc(-"
"c2ccc(cc2)C[n+]2ccn(c2)Cc2ccc(cc2)C3=O)c1C(=O)O.[Br-].[Br-]",
// CHEMBL12438
"CCCCCCCCCCCCCCCCCCNC(=O)OC[C@H]1C[C@H]([C@@H2]OC(=O)N(Cc2cccc[n+]2CC)C(C)="
"O)C1.[I-]",
// CHEMBL1172371
"CC.CCCCCCCCCC(C(=O)NCCc1ccc(OP(=S)(Oc2ccc(CCNC(=O)C(CCCCCCCCC)P(=O)([O-])"
"O)cc2)N(C)/N=C/c2ccc(OP3(Oc4ccc(/C=N/"
"N(C)P(=S)(Oc5ccc(CCNC(=O)C(CCCCCCCCC)P(=O)([O-])O)cc5)Oc5ccc(CCNC(=O)C("
"CCCCCCCCC)P(=O)([O-])O)cc5)cc4)=NP(Oc4ccc(/C=N/"
"N(C)P(=S)(Oc5ccc(CCNC(=O)C(CCCCCCCCC)P(=O)([O-])O)cc5)Oc5ccc(CCNC(=O)C("
"CCCCCCCCC)P(=O)([O-])O)cc5)cc4)(Oc4ccc(/C=N/"
"N(C)P(=S)(Oc5ccc(CCNC(=O)C(CCCCCCCCC)P(=O)([O-])O)cc5)Oc5ccc(CCNC(=O)C("
"CCCCCCCCC)P(=O)([O-])O)cc5)cc4)=NP(Oc4ccc(/C=N/"
"N(C)P(=S)(Oc5ccc(CCNC(=O)C(CCCCCCCCC)P(=O)([O-])O)cc5)Oc5ccc(CCNC(=O)C("
"CCCCCCCCC)P(=O)([O-])O)cc5)cc4)(Oc4ccc(/C=N/"
"N(C)P(=S)(Oc5ccc(CCNC(=O)C(CCCCCCCCC)P(=O)([O-])O)cc5)Oc5ccc(CCNC(=O)C("
"CCCCCCCCC)P(=O)([O-])O)cc5)cc4)=N3)cc2)cc1)P(=O)([O-])O.CCCCCCCCCCCCCCCC["
"NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO.CCCCCCCCCCCCCCCC[NH2+]OC(CO)"
"C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO.CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC("
"CO)C(O)C(O)C1O)C(O)CO.CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)"
"C1O)C(O)CO.CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO."
"CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO."
"CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO."
"CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO."
"CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO."
"CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO."
"CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO."
"CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO",
// Examples first reviewer
"C12C3C4C1C3C1C3C4C1C23", // does not initially work
"C12C3C1C1C4C5C(C23)C5C14", "C12C3C4C5C1C1C4C5C3C21",
"C12C3C4C1C2C1C2C4C2C31", "C12C3C4C5C2C2C6C1C(C5C36)C42",
"C12C3C4C5C1C1C3C3C5C1C2C43",
"C12C3C4C5C6C1C1C7C3C3C5C1C1C6C3C2C7C41", // does not initially work
"C12C3C4C5C6C1C1C7C3C3C6C6C4C7C2C3C5C16",
"C12C3C4C5C6C7C8C9C1C6C1C(C37)C9C5C2C8C41",
"C12C3C4C5C6C7C1C1C8C4C4C9C2C2C5C5C1C1C3C(C7C45)C2C8C6C91", // does not
// initially
// work
"C12C3C4C5C6C7C1C1C8C4C4C7C7C3C3C8C8C2C2C5C3C4C(C1C72)C68",
"C12C3C4C5C6C7C8C1C1C9C5C5C%10C2C2C%11C%12C%13C3C3C7C%10C7C4C%11C1C3C(C5C8%"
"12)C(C62)C7C9%13", // does not initially work
// drawn examples first reviewer
"C12C3C4C1CC5C46C7C5C1C57C6C53C1C2", "C1C2C3C4CC5C6C1C17C8C61C5C48C3C27",
// part of github #3490
"C[C@H](C1)C[C@]12CCN2", "EOS"};
void test7() {
BOOST_LOG(rdInfoLog) << "testing stability w.r.t. renumbering." << std::endl;
unsigned int i = 0;
while (smis[i] != "EOS") {
std::string smiles = smis[i++];
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m, true);
//_renumberTest(m, smiles, 1000);
delete m;
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
std::string molbl1 =
"CHEMBL1950780 \n"
" RDKit 2D \n"
" \n"
" 12 12 0 0 0 0 0 0 0 0999 V2000 \n"
" 16.2083 -6.1750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 16.2083 -7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 16.9204 -7.4083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 17.6324 -7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 17.6324 -6.1750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 16.9204 -5.7583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 16.9204 -4.9333 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 18.3480 -5.7646 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 18.3462 -7.4135 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 16.9204 -8.2333 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 15.4945 -7.4135 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 15.4927 -5.7646 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 5 6 1 0 \n"
" 6 7 1 6 \n"
" 1 2 1 0 \n"
" 5 8 1 6 \n"
" 1 6 1 0 \n"
" 4 9 1 6 \n"
" 2 3 1 0 \n"
" 3 10 1 1 \n"
" 3 4 1 0 \n"
" 2 11 1 6 \n"
" 4 5 1 0 \n"
" 1 12 1 6 \n"
"M END";
std::string molbl2 =
"CHEMBL1874247 \n"
" RDKit 2D \n"
" \n"
" 12 12 0 0 0 0 0 0 0 0999 V2000 \n"
" 0.0000 1.6500 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1.4289 0.8250 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -1.4289 0.8250 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1.4289 -0.8250 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -1.4289 -0.8250 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.0000 -1.6500 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.0000 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.7145 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -0.7145 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.0000 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 7 1 1 1 \n"
" 8 2 1 1 \n"
" 9 3 1 1 \n"
" 10 4 1 6 \n"
" 11 5 1 6 \n"
" 12 6 1 1 \n"
" 7 8 1 0 \n"
" 7 9 1 0 \n"
" 8 10 1 0 \n"
" 9 11 1 0 \n"
" 10 12 1 0 \n"
" 11 12 1 0 \n"
"M END";
void test8() {
BOOST_LOG(rdInfoLog) << "testing smiles round-tripping." << std::endl;
std::string rdbase = getenv("RDBASE");
{
std::string fName = rdbase + "/Code/GraphMol/test_data/iChi1b.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
std::string smi1 = MolToSmiles(*m, true);
delete m;
m = SmilesToMol(smi1);
TEST_ASSERT(m);
std::string smi2 = MolToSmiles(*m, true);
if (smi1 != smi2) {
std::cerr << smi1 << "\n" << smi2 << std::endl;
}
TEST_ASSERT(smi1 == smi2);
delete m;
}
{
unsigned int i = 0;
while (smis[i] != "EOS") {
std::string smiles = smis[i++];
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
// std::cerr<<"MolToSMILES 1"<<std::endl;
std::string smi1 = MolToSmiles(*m, true);
delete m;
m = SmilesToMol(smi1);
TEST_ASSERT(m);
// std::cerr<<"MolToSMILES 2"<<std::endl;
std::string smi2 = MolToSmiles(*m, true);
delete m;
if (smi1 != smi2) {
std::cerr << "Input smiles: " << smiles << "\n1. Iter: " << smi1
<< "\n2. Iter: " << smi2 << std::endl;
}
TEST_ASSERT(smi1 == smi2);
}
{
ROMol *m = MolBlockToMol(molbl1);
TEST_ASSERT(m);
std::string smiles = MolToSmiles(*m, true);
delete m;
m = SmilesToMol(smiles);
TEST_ASSERT(m);
// std::cerr<<"MolToSMILES 1"<<std::endl;
std::string smi1 = MolToSmiles(*m, true);
delete m;
if (smiles != smi1) {
std::cerr << smiles << "\n" << smi1 << std::endl;
}
TEST_ASSERT(smiles == smi1);
}
{
ROMol *m = MolBlockToMol(molbl2);
TEST_ASSERT(m);
std::string smiles = MolToSmiles(*m, true);
delete m;
m = SmilesToMol(smiles);
TEST_ASSERT(m);
// std::cerr<<"MolToSMILES 1"<<std::endl;
std::string smi1 = MolToSmiles(*m, true);
delete m;
if (smiles != smi1) {
std::cerr << smiles << "\n" << smi1 << std::endl;
}
TEST_ASSERT(smiles == smi1);
}
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void test9() {
BOOST_LOG(rdInfoLog) << "testing chiral invariants." << std::endl;
std::string rdbase = getenv("RDBASE");
{
std::string smi = "C[C@](F)(Cl)I";
RWMol *m = SmilesToMol(smi, 0, 0);
TEST_ASSERT(m);
MolOps::sanitizeMol(*m);
std::vector<unsigned int> atomRanks;
// std::cerr<<smi<<std::endl;
RDKit::Canon::chiralRankMolAtoms(*m, atomRanks);
// std::copy(atomRanks.begin(),atomRanks.end(),std::ostream_iterator<unsigned
// int>(std::cerr," "));
// std::cerr<<std::endl;
TEST_ASSERT(atomRanks[0] < atomRanks[2]);
TEST_ASSERT(atomRanks[0] < atomRanks[3]);
TEST_ASSERT(atomRanks[0] < atomRanks[4]);
TEST_ASSERT(atomRanks[2] < atomRanks[3]);
TEST_ASSERT(atomRanks[2] < atomRanks[4]);
TEST_ASSERT(atomRanks[3] < atomRanks[4]);
delete m;
}
{
std::string smi = "CC[C@](F)(Cl)C=C";
RWMol *m = SmilesToMol(smi, 0, 0);
TEST_ASSERT(m);
MolOps::sanitizeMol(*m);
std::vector<unsigned int> atomRanks;
// std::cerr<<smi<<std::endl;
RDKit::Canon::chiralRankMolAtoms(*m, atomRanks);
// std::copy(atomRanks.begin(),atomRanks.end(),std::ostream_iterator<unsigned
// int>(std::cerr," "));
// std::cerr<<std::endl;
TEST_ASSERT(atomRanks[1] < atomRanks[3]);
TEST_ASSERT(atomRanks[1] < atomRanks[4]);
TEST_ASSERT(atomRanks[1] < atomRanks[5]);
TEST_ASSERT(atomRanks[3] < atomRanks[4]);
TEST_ASSERT(atomRanks[4] > atomRanks[5]);
TEST_ASSERT(atomRanks[4] > atomRanks[5]);
delete m;
}
{
// make sure we aren't breaking ties
std::string smi = "C[C@](C)(Cl)I";
RWMol *m = SmilesToMol(smi, 0, 0);
TEST_ASSERT(m);
MolOps::sanitizeMol(*m);
std::vector<unsigned int> atomRanks;
// std::cerr<<smi<<std::endl;
RDKit::Canon::chiralRankMolAtoms(*m, atomRanks);
// std::copy(atomRanks.begin(),atomRanks.end(),std::ostream_iterator<unsigned
// int>(std::cerr," "));
// std::cerr<<std::endl;
TEST_ASSERT(atomRanks[0] == atomRanks[2]);
TEST_ASSERT(atomRanks[0] < atomRanks[3]);
TEST_ASSERT(atomRanks[0] < atomRanks[4]);
TEST_ASSERT(atomRanks[2] < atomRanks[3]);
TEST_ASSERT(atomRanks[2] < atomRanks[4]);
TEST_ASSERT(atomRanks[3] < atomRanks[4]);
delete m;
}
{
std::string smi = "N[C@H]1C2CC3CC1C[C@](O)(C3)C2";
RWMol *m = SmilesToMol(smi, 0, 0);
TEST_ASSERT(m);
MolOps::sanitizeMol(*m);
std::vector<unsigned int> atomRanks;
// std::cerr<<smi<<std::endl;
RDKit::Canon::chiralRankMolAtoms(*m, atomRanks);
// std::copy(atomRanks.begin(),atomRanks.end(),std::ostream_iterator<unsigned
// int>(std::cerr," "));
// std::cerr<<std::endl;
TEST_ASSERT(atomRanks[0] > atomRanks[1]);
TEST_ASSERT(atomRanks[0] < atomRanks[9]);
TEST_ASSERT(atomRanks[2] == atomRanks[6]);
TEST_ASSERT(atomRanks[7] == atomRanks[11]);
TEST_ASSERT(atomRanks[3] == atomRanks[5]);
TEST_ASSERT(atomRanks[2] > atomRanks[3]);
TEST_ASSERT(atomRanks[2] > atomRanks[11]);
TEST_ASSERT(atomRanks[3] < atomRanks[11]);
delete m;
}
{
// this one was a chiral ranking problem
std::string smi = "COC(C)CC(C)(C)O";
RWMol *m = SmilesToMol(smi, 0, 0);
TEST_ASSERT(m);
MolOps::sanitizeMol(*m);
std::vector<unsigned int> atomRanks;
// std::cerr<<smi<<std::endl;
RDKit::Canon::chiralRankMolAtoms(*m, atomRanks);
// std::copy(atomRanks.begin(),atomRanks.end(),std::ostream_iterator<unsigned
// int>(std::cerr," "));
// std::cerr<<std::endl;
TEST_ASSERT(atomRanks[1] > atomRanks[8]);
TEST_ASSERT(atomRanks[5] > atomRanks[2]);
delete m;
}
{
// are double bonds being handled correctly?
std::string smi = "OC[C@H](F)C=O";
RWMol *m = SmilesToMol(smi, 0, 0);
TEST_ASSERT(m);
MolOps::sanitizeMol(*m);
std::vector<unsigned int> atomRanks;
// std::cerr<<smi<<std::endl;
RDKit::Canon::chiralRankMolAtoms(*m, atomRanks);
// std::copy(atomRanks.begin(),atomRanks.end(),std::ostream_iterator<unsigned
// int>(std::cerr," "));
// std::cerr<<std::endl;
TEST_ASSERT(atomRanks[0] < atomRanks[5]);
TEST_ASSERT(atomRanks[1] < atomRanks[4]);
delete m;
}
{
// are double bonds being handled correctly?
std::string smi = "O=C[C@H](F)CO";
RWMol *m = SmilesToMol(smi, 0, 0);
TEST_ASSERT(m);
MolOps::sanitizeMol(*m);
std::vector<unsigned int> atomRanks;
// std::cerr<<smi<<std::endl;
RDKit::Canon::chiralRankMolAtoms(*m, atomRanks);
// std::copy(atomRanks.begin(),atomRanks.end(),std::ostream_iterator<unsigned
// int>(std::cerr," "));
// std::cerr<<std::endl;
TEST_ASSERT(atomRanks[0] > atomRanks[5]);
TEST_ASSERT(atomRanks[1] > atomRanks[4]);
delete m;
}
{
// are double bonds being handled correctly?
std::string smi = "CC[C@](C)(CF)C=O";
RWMol *m = SmilesToMol(smi, 0, 0);
TEST_ASSERT(m);
MolOps::sanitizeMol(*m);
std::vector<unsigned int> atomRanks;
// std::cerr<<smi<<std::endl;
RDKit::Canon::chiralRankMolAtoms(*m, atomRanks);
// std::copy(atomRanks.begin(),atomRanks.end(),std::ostream_iterator<unsigned
// int>(std::cerr," "));
// std::cerr<<std::endl;
TEST_ASSERT(atomRanks[4] > atomRanks[6]);
TEST_ASSERT(atomRanks[1] < atomRanks[4]);
delete m;
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void test10() {
BOOST_LOG(rdInfoLog) << "testing unique ranks in w.r.t. renumbering."
<< std::endl;
unsigned int i = 0;
while (smis[i] != "EOS") {
std::string smiles = smis[i++];
// std::cerr<< ">>>Molecule: " << smiles << std::endl;
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m, true);
_renumberTest2(m, smiles, 1);
delete m;
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void test11() {
BOOST_LOG(rdInfoLog) << "testing mol fragments." << std::endl;
{
std::string smi =
"C[C@H]([C@H](c1ccccc1)O)N2CCCCC2.C[C@@H]([C@H](c1ccccc1)O)N2CCCCC2";
ROMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
std::vector<std::string> vfragsmi;
std::vector<std::vector<int>> frags;
unsigned int numFrag = MolOps::getMolFrags(*m, frags);
for (unsigned i = 0; i < numFrag; ++i) {
std::string smii =
MolFragmentToSmiles(*m, frags[i], nullptr, nullptr, nullptr, true);
// std::cout << "Test "<< smii << std::endl;
vfragsmi.push_back(smii);
}
std::string smi1 = MolToSmiles(*m, true);
delete m;
smi = "C[C@@H]([C@H](c1ccccc1)O)N2CCCCC2.C[C@H]([C@H](c1ccccc1)O)N2CCCCC2";
m = SmilesToMol(smi);
TEST_ASSERT(m);
std::string smi2 = MolToSmiles(*m, true);
delete m;
// std::cout << smi1 << "\n" << smi2 << std::endl;
TEST_ASSERT(smi1 == smi2);
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void test12() {
BOOST_LOG(rdInfoLog) << "testing protein round-tripping." << std::endl;
std::string rdbase = getenv("RDBASE");
{
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/2FVD.pdb";
ROMol *m = PDBFileToMol(fName);
TEST_ASSERT(m);
std::string smi1 = MolToSmiles(*m, true);
delete m;
m = SmilesToMol(smi1);
TEST_ASSERT(m);
std::string smi2 = MolToSmiles(*m, true);
delete m;
// std::cout << smi1 << "\n" << smi2 << std::endl;
TEST_ASSERT(smi1 == smi2);
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testGithub1567() {
BOOST_LOG(rdInfoLog)
<< "testing github #1567: Non-canonical result from MolFragmentToSmiles()"
<< std::endl;
{
ROMol *m1 = SmilesToMol("CC1CN(Cc2cccc(C)c2)C1");
TEST_ASSERT(m1);
int m1Ats_a[6] = {1, 12, 3, 4, 5, 11};
std::vector<int> m1Ats(m1Ats_a, m1Ats_a + 6);
int m1Bnds_a[5] = {12, 11, 3, 4, 13};
std::vector<int> m1Bnds(m1Bnds_a, m1Bnds_a + 5);
std::string smi1 = MolFragmentToSmiles(*m1, m1Ats, &m1Bnds);
ROMol *m2 = SmilesToMol("CN(CCC)Cc1cccc(C)c1");
TEST_ASSERT(m2);
int m2Ats_a[6] = {3, 2, 1, 5, 6, 12};
std::vector<int> m2Ats(m2Ats_a, m2Ats_a + 6);
int m2Bnds_a[5] = {2, 1, 4, 5, 12};
std::vector<int> m2Bnds(m2Bnds_a, m2Bnds_a + 5);
std::string smi2 = MolFragmentToSmiles(*m2, m2Ats, &m2Bnds);
TEST_ASSERT(smi1 == smi2);
delete m1;
delete m2;
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testCanonicalDiastereomers() {
// FIX: this is another one that we dno't currently handle properly
#if 0
BOOST_LOG(rdInfoLog) << "testing diastereomer problem." << std::endl;
auto m1 = "F[C@@H](Cl)[C@H](F)Cl"_smiles;
auto m2 = "F[C@H](Cl)[C@@H](F)Cl"_smiles;
auto smi1 = MolToSmiles(*m1);
auto smi2 = MolToSmiles(*m2);
TEST_ASSERT(smi1 != smi2);
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
#endif
}
void testRingsAndDoubleBonds() {
// FIX: we don't currently handle this case properly
#if 0
BOOST_LOG(rdInfoLog)
<< "testing some particular ugly para-stereochemistry examples."
<< std::endl;
std::vector<std::string> smis = {"C/C=C/C=C/C=C/C=C/C", "C/C=C1/C[C@H](O)C1",
"C/C=C1/CC[C@H](O)CC1"};
for (const auto smi : smis) {
SmilesParserParams ps;
ps.sanitize = false;
ps.removeHs = false;
std::unique_ptr<ROMol> mol(SmilesToMol(smi, ps));
TEST_ASSERT(mol);
mol->setProp(common_properties::_StereochemDone, 1);
mol->updatePropertyCache();
MolOps::setBondStereoFromDirections(*mol);
std::cerr << " " << MolToSmiles(*mol) << std::endl;
_renumberTest(mol.get(), smi, 500);
std::cerr << " " << MolToSmiles(*mol) << std::endl;
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
#endif
}
int main() {
RDLog::InitLogs();
boost::logging::enable_logs("rdApp.info");
#if 1
test1();
test2();
test3();
test4();
test5();
test6();
test7a();
test9();
test10();
test11();
test12();
test7();
test8();
testGithub1567();
#endif
testRingsAndDoubleBonds();
testCanonicalDiastereomers();
return 0;
}
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