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#include <iostream>
#include <sstream>
#include <stdexcept>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/FileParsers/MolWriters.h>
#include <GraphMol/Fingerprints/FingerprintUtil.h>
#include <GraphMol/RWMol.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <RDGeneral/BoostEndInclude.h>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/flyweight.hpp>
#include <boost/flyweight/key_value.hpp>
#include <boost/flyweight/no_tracking.hpp>
#include "PubChemShape.hpp"
using namespace std;
#define ERRORTHROW(msg_stream) \
do { \
ostringstream os; \
os << msg_stream; \
throw runtime_error(os.str()); \
} while (0)
// #define DEBUG_MSG(msg_stream) cout << msg_stream << '\n'
#define DEBUG_MSG(msg_stream)
using namespace RDKit;
int main(int argc, char **argv) {
int status = -1;
try {
if (argc != 2)
ERRORTHROW(
"Usage: sdf_align <input.sdf> The first molecule in the SDF "
"is the reference"); //"opt_param
// max_preiters
// max_postiters");
bool useColors = true;
bool sanitize = true;
bool removeHs = false;
SDMolSupplier suppl(argv[1], sanitize, removeHs);
SDWriter writer("sdf_align.out.sdf");
unique_ptr<ROMol> ref{suppl[0]};
if (!ref.get()) {
ERRORTHROW("Failed to read ref conformer");
}
for (auto i = 1u; i < suppl.length(); ++i) {
std::unique_ptr<ROMol> fit{suppl[i]};
if (!fit) {
continue;
}
vector<float> matrix(12, 0.0);
int refConfId = -1;
int fitConfId = -1;
auto [nbr_st, nbr_ct] =
AlignMolecule(*ref, *fit, matrix, refConfId, fitConfId, useColors);
if (i == 1) {
writer.write(*ref, refConfId);
}
writer.write(*fit, fitConfId);
}
status = 0;
} catch (std::exception &e) {
cerr << "Caught std::exception: " << e.what() << '\n';
} catch (...) {
cerr << "Caught unknown exception\n";
}
return status;
}
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