mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-06 22:39:55 +08:00
399 lines
12 KiB
C++
399 lines
12 KiB
C++
//
|
|
// Copyright (C) 2015 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/utils.h>
|
|
#include <RDGeneral/Invariant.h>
|
|
#include <RDGeneral/RDLog.h>
|
|
#include <GraphMol/RDKitBase.h>
|
|
#include <GraphMol/SmilesParse/SmilesParse.h>
|
|
#include <GraphMol/FileParsers/MolSupplier.h>
|
|
#include <GraphMol/Depictor/RDDepictor.h>
|
|
#include <GraphMol/FileParsers/MolFileStereochem.h>
|
|
|
|
#include <GraphMol/MolDraw2D/MolDraw2D.h>
|
|
#include <GraphMol/MolDraw2D/MolDraw2DSVG.h>
|
|
#include <iostream>
|
|
#include <fstream>
|
|
#include <sstream>
|
|
|
|
using namespace RDKit;
|
|
|
|
void test1(){
|
|
std::cout << " ----------------- Test 1" << std::endl;
|
|
{
|
|
std::string smiles="CO[C@@H](O)C1=C(O[C@H](F)Cl)C=C1ONNC[NH3+]";
|
|
ROMol *m = SmilesToMol(smiles);
|
|
TEST_ASSERT(m);
|
|
RDDepict::compute2DCoords(*m);
|
|
WedgeMolBonds(*m,&(m->getConformer()));
|
|
std::ofstream outs("test1_1.svg");
|
|
MolDraw2DSVG drawer(300,300,outs);
|
|
drawer.drawMolecule(*m);
|
|
drawer.finishDrawing();
|
|
outs.flush();
|
|
delete m;
|
|
}
|
|
{
|
|
// make sure this works with the stringstream too:
|
|
std::string smiles="CO[C@@H](O)C1=C(O[C@H](F)Cl)C=C1ONNC[NH3+]";
|
|
ROMol *m = SmilesToMol(smiles);
|
|
TEST_ASSERT(m);
|
|
RDDepict::compute2DCoords(*m);
|
|
WedgeMolBonds(*m,&(m->getConformer()));
|
|
MolDraw2DSVG drawer(300,300);
|
|
drawer.drawMolecule(*m);
|
|
drawer.finishDrawing();
|
|
std::string text = drawer.getDrawingText();
|
|
TEST_ASSERT(text.find("<svg:svg")!=std::string::npos);
|
|
TEST_ASSERT(text.find("</svg:svg>")!=std::string::npos);
|
|
delete m;
|
|
}
|
|
{
|
|
std::string smiles="Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
|
|
ROMol *m = SmilesToMol(smiles);
|
|
TEST_ASSERT(m);
|
|
RDDepict::compute2DCoords(*m);
|
|
WedgeMolBonds(*m,&(m->getConformer()));
|
|
std::ofstream outs("test1_2.svg");
|
|
MolDraw2DSVG drawer(300,300,outs);
|
|
drawer.drawMolecule(*m);
|
|
drawer.finishDrawing();
|
|
outs.flush();
|
|
delete m;
|
|
}
|
|
{
|
|
std::string smiles="Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
|
|
ROMol *m = SmilesToMol(smiles);
|
|
TEST_ASSERT(m);
|
|
RDDepict::compute2DCoords(*m);
|
|
WedgeMolBonds(*m,&(m->getConformer()));
|
|
std::ofstream outs("test1_3.svg");
|
|
MolDraw2DSVG drawer(300,300,outs);
|
|
std::vector<int> highlights;
|
|
highlights.push_back(0);
|
|
highlights.push_back(4);
|
|
highlights.push_back(5);
|
|
drawer.drawMolecule(*m,&highlights);
|
|
drawer.finishDrawing();
|
|
outs.flush();
|
|
delete m;
|
|
}
|
|
std::cout << " Done" << std::endl;
|
|
}
|
|
|
|
#ifdef RDK_CAIRO_BUILD
|
|
#include <cairo.h>
|
|
#include "MolDraw2DCairo.h"
|
|
void test2(){
|
|
std::cout << " ----------------- Test 2" << std::endl;
|
|
{
|
|
std::string smiles="CO[C@@H](O)C1=C(O[C@H](F)Cl)C=C1ONNC[NH3+]";
|
|
ROMol *m = SmilesToMol(smiles);
|
|
TEST_ASSERT(m);
|
|
RDDepict::compute2DCoords(*m);
|
|
WedgeMolBonds(*m,&(m->getConformer()));
|
|
|
|
cairo_surface_t *surface =
|
|
cairo_image_surface_create (CAIRO_FORMAT_ARGB32, 300, 300);
|
|
cairo_t *cr = cairo_create (surface);
|
|
|
|
MolDraw2DCairo drawer(300,300,cr);
|
|
drawer.drawMolecule(*m);
|
|
drawer.finishDrawing();
|
|
|
|
cairo_destroy (cr);
|
|
cairo_surface_write_to_png (surface, "test2_1.png");
|
|
cairo_surface_destroy (surface);
|
|
delete m;
|
|
}
|
|
{
|
|
std::string smiles="Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
|
|
ROMol *m = SmilesToMol(smiles);
|
|
TEST_ASSERT(m);
|
|
RDDepict::compute2DCoords(*m);
|
|
WedgeMolBonds(*m,&(m->getConformer()));
|
|
|
|
cairo_surface_t *surface =
|
|
cairo_image_surface_create (CAIRO_FORMAT_ARGB32, 300, 300);
|
|
cairo_t *cr = cairo_create (surface);
|
|
|
|
MolDraw2DCairo drawer(300,300,cr);
|
|
drawer.drawMolecule(*m);
|
|
drawer.finishDrawing();
|
|
|
|
cairo_destroy (cr);
|
|
cairo_surface_write_to_png (surface, "test2_2.png");
|
|
cairo_surface_destroy (surface);
|
|
delete m;
|
|
}
|
|
{
|
|
std::string smiles="Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
|
|
ROMol *m = SmilesToMol(smiles);
|
|
TEST_ASSERT(m);
|
|
RDDepict::compute2DCoords(*m);
|
|
WedgeMolBonds(*m,&(m->getConformer()));
|
|
|
|
cairo_surface_t *surface =
|
|
cairo_image_surface_create (CAIRO_FORMAT_ARGB32, 300, 300);
|
|
cairo_t *cr = cairo_create (surface);
|
|
|
|
MolDraw2DCairo drawer(300,300,cr);
|
|
std::vector<int> highlights;
|
|
highlights.push_back(0);
|
|
highlights.push_back(4);
|
|
highlights.push_back(5);
|
|
drawer.drawMolecule(*m,&highlights);
|
|
drawer.finishDrawing();
|
|
|
|
cairo_destroy (cr);
|
|
cairo_surface_write_to_png (surface, "test2_3.png");
|
|
cairo_surface_destroy (surface);
|
|
delete m;
|
|
}
|
|
std::cout << " Done" << std::endl;
|
|
}
|
|
#else // RDK_CAIRO_BUILD
|
|
void test2(){
|
|
}
|
|
#endif
|
|
|
|
|
|
void test3(){
|
|
std::cout << " ----------------- Test 3" << std::endl;
|
|
{
|
|
std::string smiles="C1CC1CC1ON1";
|
|
std::string nameBase="test3_1";
|
|
ROMol *m = SmilesToMol(smiles);
|
|
TEST_ASSERT(m);
|
|
RDDepict::compute2DCoords(*m);
|
|
WedgeMolBonds(*m,&(m->getConformer()));
|
|
static const int ha[] = {0,3,4,5};
|
|
std::vector<int> highlight_atoms(ha, ha+sizeof(ha)/sizeof(int));
|
|
std::map<int,std::string> atomLabels;
|
|
atomLabels[2]="C1";
|
|
atomLabels[1]="a<sub>3</sub><sup>4</sup>";
|
|
|
|
#ifdef RDK_CAIRO_BUILD
|
|
{
|
|
cairo_surface_t *surface =
|
|
cairo_image_surface_create (CAIRO_FORMAT_ARGB32, 300, 300);
|
|
cairo_t *cr = cairo_create (surface);
|
|
|
|
MolDraw2DCairo drawer(300,300,cr);
|
|
drawer.drawOptions().atomLabels = &atomLabels;
|
|
drawer.drawMolecule(*m,&highlight_atoms);
|
|
drawer.finishDrawing();
|
|
|
|
cairo_destroy (cr);
|
|
cairo_surface_write_to_png (surface, (nameBase+".png").c_str());
|
|
cairo_surface_destroy (surface);
|
|
}
|
|
#endif
|
|
{
|
|
std::ofstream outs((nameBase+".svg").c_str());
|
|
MolDraw2DSVG drawer(300,300,outs);
|
|
drawer.drawOptions().atomLabels = &atomLabels;
|
|
drawer.drawMolecule(*m,&highlight_atoms);
|
|
drawer.finishDrawing();
|
|
outs.flush();
|
|
}
|
|
delete m;
|
|
}
|
|
{
|
|
std::string smiles="C1CC1CC1ON1";
|
|
std::string nameBase="test3_2";
|
|
ROMol *m = SmilesToMol(smiles);
|
|
TEST_ASSERT(m);
|
|
RDDepict::compute2DCoords(*m);
|
|
WedgeMolBonds(*m,&(m->getConformer()));
|
|
static const int ha[] = {0,3,4,5};
|
|
std::vector<int> highlight_atoms(ha, ha+sizeof(ha)/sizeof(int));
|
|
|
|
#ifdef RDK_CAIRO_BUILD
|
|
{
|
|
cairo_surface_t *surface =
|
|
cairo_image_surface_create (CAIRO_FORMAT_ARGB32, 300, 300);
|
|
cairo_t *cr = cairo_create (surface);
|
|
|
|
MolDraw2DCairo drawer(300,300,cr);
|
|
drawer.drawOptions().circleAtoms=false;
|
|
drawer.drawMolecule(*m,&highlight_atoms);
|
|
drawer.finishDrawing();
|
|
|
|
cairo_destroy (cr);
|
|
cairo_surface_write_to_png (surface, (nameBase+".png").c_str());
|
|
cairo_surface_destroy (surface);
|
|
}
|
|
#endif
|
|
{
|
|
std::ofstream outs((nameBase+".svg").c_str());
|
|
MolDraw2DSVG drawer(300,300,outs);
|
|
drawer.drawOptions().circleAtoms=false;
|
|
drawer.drawMolecule(*m,&highlight_atoms);
|
|
drawer.finishDrawing();
|
|
outs.flush();
|
|
}
|
|
delete m;
|
|
}
|
|
{
|
|
std::string smiles="Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
|
|
std::string nameBase="test3_3";
|
|
ROMol *m = SmilesToMol(smiles);
|
|
TEST_ASSERT(m);
|
|
RDDepict::compute2DCoords(*m);
|
|
WedgeMolBonds(*m,&(m->getConformer()));
|
|
static const int ha[] = {11,12,13,14,15,16};
|
|
std::vector<int> highlight_atoms(ha, ha+sizeof(ha)/sizeof(int));
|
|
std::map<int,DrawColour> highlight_colors;
|
|
highlight_colors[12]=DrawColour(0,0,1);
|
|
highlight_colors[13]=DrawColour(0,1,0);
|
|
|
|
#ifdef RDK_CAIRO_BUILD
|
|
{
|
|
cairo_surface_t *surface =
|
|
cairo_image_surface_create (CAIRO_FORMAT_ARGB32, 300, 300);
|
|
cairo_t *cr = cairo_create (surface);
|
|
|
|
MolDraw2DCairo drawer(300,300,cr);
|
|
drawer.drawOptions().circleAtoms=true;
|
|
drawer.drawMolecule(*m,&highlight_atoms,&highlight_colors);
|
|
drawer.finishDrawing();
|
|
|
|
cairo_destroy (cr);
|
|
cairo_surface_write_to_png (surface, (nameBase+".png").c_str());
|
|
cairo_surface_destroy (surface);
|
|
}
|
|
#endif
|
|
{
|
|
std::ofstream outs((nameBase+".svg").c_str());
|
|
MolDraw2DSVG drawer(300,300,outs);
|
|
drawer.drawOptions().circleAtoms=true;
|
|
drawer.drawMolecule(*m,&highlight_atoms,&highlight_colors);
|
|
drawer.finishDrawing();
|
|
outs.flush();
|
|
}
|
|
delete m;
|
|
}
|
|
{
|
|
std::string smiles="Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
|
|
std::string nameBase="test3_4";
|
|
ROMol *m = SmilesToMol(smiles);
|
|
TEST_ASSERT(m);
|
|
RDDepict::compute2DCoords(*m);
|
|
WedgeMolBonds(*m,&(m->getConformer()));
|
|
static const int ha[] = {11,12,13,14,15,16,3};
|
|
std::vector<int> highlight_atoms(ha, ha+sizeof(ha)/sizeof(int));
|
|
std::map<int,DrawColour> highlight_colors;
|
|
highlight_colors[12]=DrawColour(.5,.5,1);
|
|
highlight_colors[13]=DrawColour(.5,1,.5);
|
|
MolDrawOptions options;
|
|
options.circleAtoms=true;
|
|
options.highlightColour=DrawColour(1,.5,.5);
|
|
options.continuousHighlight=true;
|
|
|
|
#ifdef RDK_CAIRO_BUILD
|
|
{
|
|
cairo_surface_t *surface =
|
|
cairo_image_surface_create (CAIRO_FORMAT_ARGB32, 300, 300);
|
|
cairo_t *cr = cairo_create (surface);
|
|
|
|
MolDraw2DCairo drawer(300,300,cr);
|
|
drawer.drawOptions() = options;
|
|
drawer.drawMolecule(*m,&highlight_atoms,&highlight_colors);
|
|
drawer.finishDrawing();
|
|
cairo_destroy (cr);
|
|
cairo_surface_write_to_png (surface, (nameBase+".png").c_str());
|
|
cairo_surface_destroy (surface);
|
|
}
|
|
#endif
|
|
{
|
|
std::ofstream outs((nameBase+".svg").c_str());
|
|
MolDraw2DSVG drawer(300,300,outs);
|
|
drawer.drawOptions() = options;
|
|
drawer.drawMolecule(*m,&highlight_atoms,&highlight_colors);
|
|
drawer.finishDrawing();
|
|
outs.flush();
|
|
}
|
|
delete m;
|
|
}
|
|
std::cout << " Done" << std::endl;
|
|
}
|
|
|
|
#ifdef RDK_TEST_MULTITHREADED
|
|
#include <boost/thread.hpp>
|
|
namespace {
|
|
void runblock(const std::vector<ROMol *> &mols,const std::vector<std::string> &refData,
|
|
unsigned int count,unsigned int idx){
|
|
for(unsigned int j=0;j<500;j++){
|
|
for(unsigned int i=0;i<mols.size();++i){
|
|
if(i%count != idx) continue;
|
|
ROMol *mol = mols[i];
|
|
MolDraw2DSVG drawer(300,300);
|
|
drawer.drawMolecule(*mol);
|
|
drawer.finishDrawing();
|
|
std::string text = drawer.getDrawingText();
|
|
TEST_ASSERT(text==refData[i]);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
void testMultiThreaded(){
|
|
std::cout << " ----------------- Test multi-threaded drawing" << std::endl;
|
|
std::string fName = getenv("RDBASE");
|
|
fName += "/Data/NCI/first_200.props.sdf";
|
|
RDKit::SDMolSupplier suppl(fName);
|
|
std::cerr<<"reading molecules"<<std::endl;
|
|
std::vector<ROMol *> mols;
|
|
while(!suppl.atEnd()&&mols.size()<100){
|
|
ROMol *mol=0;
|
|
try{
|
|
mol=suppl.next();
|
|
} catch(...){
|
|
continue;
|
|
}
|
|
if(!mol) continue;
|
|
mols.push_back(mol);
|
|
}
|
|
|
|
std::cerr<<"generating reference drawings"<<std::endl;
|
|
std::vector<std::string> refData(mols.size());
|
|
for(unsigned int i=0;i<mols.size();++i){
|
|
MolDraw2DSVG drawer(300,300);
|
|
drawer.drawMolecule(*(mols[i]));
|
|
drawer.finishDrawing();
|
|
refData[i]=drawer.getDrawingText();
|
|
TEST_ASSERT(refData[i].find("<svg:svg")!=std::string::npos);
|
|
TEST_ASSERT(refData[i].find("</svg:svg>")!=std::string::npos);
|
|
}
|
|
|
|
boost::thread_group tg;
|
|
unsigned int count=4;
|
|
std::cerr<<"processing"<<std::endl;
|
|
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,refData,count,i));
|
|
}
|
|
tg.join_all();
|
|
std::cerr<<" Done"<<std::endl;
|
|
}
|
|
#else
|
|
void testMultiThreaded(){
|
|
}
|
|
#endif
|
|
|
|
int main(){
|
|
RDLog::InitLogs();
|
|
test1();
|
|
test2();
|
|
test3();
|
|
testMultiThreaded();
|
|
}
|