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//
// Depictions with highlights - example17.cpp
#include <fstream>
#include <string>
#include <vector>
#include <GraphMol/GraphMol.h>
#include <GraphMol/Depictor/RDDepictor.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/MolDraw2D/MolDraw2DSVG.h>
using namespace RDKit;
std::vector<int> get_all_hit_atoms(ROMol &mol, const std::string &smt) {
std::vector<int> hit_atoms;
RWMol *query = SmartsToMol(smt);
std::vector<MatchVectType> hits_vect;
SubstructMatch(mol, *query, hits_vect);
for (size_t i = 0; i < hits_vect.size(); ++i) {
for (size_t j = 0; j < hits_vect[i].size(); ++j) {
hit_atoms.emplace_back(hits_vect[i][j].second);
}
}
delete query;
return hit_atoms;
}
std::vector<int> get_all_hit_bonds(ROMol &mol,
const std::vector<int> &hit_atoms) {
std::vector<int> hit_bonds;
for (int i : hit_atoms) {
for (int j : hit_atoms) {
if (i > j) {
Bond *bnd = mol.getBondBetweenAtoms(i, j);
if (bnd) {
hit_bonds.emplace_back(bnd->getIdx());
}
}
}
}
return hit_bonds;
}
void update_colour_map(const std::vector<int> &ats, DrawColour col,
std::map<int, std::vector<DrawColour>> &ha_map) {
for (auto h : ats) {
auto ex = ha_map.find(h);
if (ex == ha_map.end()) {
std::vector<DrawColour> cvec(1, col);
ha_map.insert(make_pair(h, cvec));
} else {
if (ex->second.end() == find(ex->second.begin(), ex->second.end(), col)) {
ex->second.emplace_back(col);
}
}
}
}
int main() {
std::string file_root = getenv("RDBASE");
file_root += "/Docs/Book/images/";
auto mol = "CO[C@@H](O)C1=C(O[C@H](F)Cl)C(C#N)=C1ONNC[NH3+]"_smiles;
std::vector<int> hit1_atoms = get_all_hit_atoms(*mol, "CONN");
std::vector<int> hit1_bonds = get_all_hit_bonds(*mol, hit1_atoms);
{
// all atoms and bonds highlighted the same colour
std::ofstream outs(file_root + "example_17_1.svg");
MolDraw2DSVG drawer(500, 500, outs);
drawer.drawMolecule(*mol, &hit1_atoms, &hit1_bonds);
drawer.finishDrawing();
outs.flush();
}
{
// individual colours for each highlight
std::ofstream outs(file_root + "example_17_2.svg");
MolDraw2DSVG drawer(500, 500, outs);
std::map<int, DrawColour> atom_cols;
atom_cols.insert(std::make_pair(13, DrawColour(1.0, 0.0, 0.0)));
atom_cols.insert(std::make_pair(14, DrawColour(0.0, 1.0, 0.0)));
atom_cols.insert(std::make_pair(15, DrawColour(0.0, 0.0, 1.0)));
atom_cols.insert(std::make_pair(16, DrawColour(1.0, 0.55, 0.0)));
std::map<int, DrawColour> bond_cols;
bond_cols.insert(std::make_pair(13, DrawColour(0.8, 0.8, 0.0)));
bond_cols.insert(std::make_pair(14, DrawColour(0.0, 1.0, 1.0)));
bond_cols.insert(std::make_pair(15, DrawColour(1.0, 0.0, 1.0)));
drawer.drawMolecule(*mol, &hit1_atoms, &hit1_bonds, &atom_cols, &bond_cols);
drawer.finishDrawing();
outs.flush();
}
std::vector<int> hit2_atoms = get_all_hit_atoms(*mol, "N#CC~CO");
std::vector<int> hit2_bonds = get_all_hit_bonds(*mol, hit2_atoms);
std::vector<int> hit3_atoms = get_all_hit_atoms(*mol, "C=CON");
std::vector<int> hit3_bonds = get_all_hit_bonds(*mol, hit3_atoms);
std::vector<int> hit4_atoms = get_all_hit_atoms(*mol, "CONNCN");
std::vector<int> hit4_bonds = get_all_hit_bonds(*mol, hit4_atoms);
std::map<int, std::vector<DrawColour>> ha_map;
update_colour_map(hit1_atoms, DrawColour(1.0, 0.0, 0.0), ha_map);
update_colour_map(hit2_atoms, DrawColour(0.0, 1.0, 0.0), ha_map);
update_colour_map(hit3_atoms, DrawColour(0.0, 0.0, 1.0), ha_map);
update_colour_map(hit4_atoms, DrawColour(1.0, 0.55, 0.0), ha_map);
std::map<int, std::vector<DrawColour>> hb_map;
update_colour_map(hit1_bonds, DrawColour(1.0, 0.0, 0.0), hb_map);
update_colour_map(hit2_bonds, DrawColour(0.0, 1.0, 0.0), hb_map);
update_colour_map(hit3_bonds, DrawColour(0.0, 0.0, 1.0), hb_map);
update_colour_map(hit4_bonds, DrawColour(1.0, 0.55, 0.0), hb_map);
std::map<int, double> h_rads;
std::map<int, int> h_lw_mult;
{
// atoms and bonds can have multiple highlights
std::ofstream outs(file_root + "example_17_3.svg");
MolDraw2DSVG drawer(500, 500, outs);
drawer.drawOptions().fillHighlights = false;
drawer.drawOptions().continuousHighlight = true;
drawer.drawOptions().atomHighlightsAreCircles = true;
drawer.drawMoleculeWithHighlights(*mol, "Test 1", ha_map, hb_map, h_rads,
h_lw_mult);
drawer.finishDrawing();
outs.flush();
}
}
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