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d41752d558
* run clang-tidy with readability-braces-around-statements clang-format the results clean up all the parts that clang-tidy-8 broke * fix problem on windows
304 lines
10 KiB
C++
304 lines
10 KiB
C++
//
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// Copyright (C) 2019 Greg Landrum
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#define CATCH_CONFIG_MAIN // This tells Catch to provide a main() - only do
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// this in one cpp file
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#include "catch.hpp"
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/MolDraw2D/MolDraw2D.h>
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#include <GraphMol/MolDraw2D/MolDraw2DSVG.h>
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#include <GraphMol/MolDraw2D/MolDraw2DUtils.h>
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using namespace RDKit;
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TEST_CASE("prepareAndDrawMolecule", "[drawing]") {
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SECTION("basics") {
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auto m1 = "C1N[C@@H]2OCC12"_smiles;
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REQUIRE(m1);
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// we will be able to recognize that the prep worked because there
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// will be an H in the output:
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MolDraw2DSVG drawer(200, 200);
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MolDraw2DUtils::prepareAndDrawMolecule(drawer, *m1);
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drawer.finishDrawing();
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std::string text = drawer.getDrawingText();
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CHECK(text.find("<tspan>H</tspan>") != std::string::npos);
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}
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}
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TEST_CASE("tag atoms in SVG", "[drawing, SVG]") {
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SECTION("basics") {
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auto m1 = "C1N[C@@H]2OCC12"_smiles;
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REQUIRE(m1);
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MolDraw2DSVG drawer(200, 200);
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MolDraw2DUtils::prepareMolForDrawing(*m1);
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drawer.drawMolecule(*m1);
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std::map<std::string, std::string> actions;
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actions["onclick"] = "alert";
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double radius = 0.2;
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drawer.tagAtoms(*m1, radius, actions);
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drawer.finishDrawing();
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std::string text = drawer.getDrawingText();
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std::ofstream outs("testAtomTags_1.svg");
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outs << text;
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outs.flush();
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CHECK(text.find("<circle") != std::string::npos);
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CHECK(text.find("<circle") != std::string::npos);
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CHECK(text.find("atom-selector") != std::string::npos);
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CHECK(text.find("bond-selector") != std::string::npos);
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}
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}
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TEST_CASE("contour data", "[drawing, conrec]") {
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auto m1 = "C1N[C@@H]2OCC12"_smiles;
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REQUIRE(m1);
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SECTION("grid basics") {
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MolDraw2DSVG drawer(250, 250);
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MolDraw2DUtils::prepareMolForDrawing(*m1);
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const size_t gridSz = 100;
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auto *grid = new double[gridSz * gridSz];
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std::vector<double> xps(gridSz);
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std::vector<double> yps(gridSz);
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double minX = 1000, minY = 1000, maxX = -1000, maxY = -1000;
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const auto conf = m1->getConformer();
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for (size_t i = 0; i < conf.getNumAtoms(); ++i) {
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minX = std::min(minX, conf.getAtomPos(i).x);
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minY = std::min(minY, conf.getAtomPos(i).y);
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maxX = std::max(maxX, conf.getAtomPos(i).x);
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maxY = std::max(maxY, conf.getAtomPos(i).y);
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}
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double x1 = minX - 0.5, y1 = minY - 0.5, x2 = maxX + 0.5, y2 = maxY + 0.5;
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double dx = (x2 - x1) / gridSz, dy = (y2 - y1) / gridSz;
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double maxV = 0.0;
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for (size_t ix = 0; ix < gridSz; ++ix) {
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auto px = x1 + ix * dx;
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xps[ix] = px;
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for (size_t iy = 0; iy < gridSz; ++iy) {
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auto py = y1 + iy * dy;
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if (ix == 0) {
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yps[iy] = py;
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}
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RDGeom::Point2D loc(px, py);
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double val = 0.0;
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for (size_t ia = 0; ia < conf.getNumAtoms(); ++ia) {
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auto dv = loc - RDGeom::Point2D(conf.getAtomPos(ia).x,
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conf.getAtomPos(ia).y);
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auto r = dv.length();
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if (r > 0.1) {
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val += 1 / r;
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}
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}
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maxV = std::max(val, maxV);
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grid[ix * gridSz + iy] = val;
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}
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}
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std::vector<double> levels;
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drawer.clearDrawing();
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MolDraw2DUtils::contourAndDrawGrid(drawer, grid, xps, yps, 10, levels);
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drawer.drawOptions().clearBackground = false;
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drawer.drawMolecule(*m1);
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drawer.finishDrawing();
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std::string text = drawer.getDrawingText();
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std::ofstream outs("contourMol_1.svg");
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outs << text;
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outs.flush();
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delete[] grid;
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}
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SECTION("gaussian basics") {
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MolDraw2DSVG drawer(250, 250);
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MolDraw2DUtils::prepareMolForDrawing(*m1);
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drawer.drawOptions().padding = 0.1;
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const auto conf = m1->getConformer();
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std::vector<Point2D> cents(conf.getNumAtoms());
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std::vector<double> weights(conf.getNumAtoms());
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std::vector<double> widths(conf.getNumAtoms());
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for (size_t i = 0; i < conf.getNumAtoms(); ++i) {
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cents[i] = Point2D(conf.getAtomPos(i).x, conf.getAtomPos(i).y);
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weights[i] = 1;
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widths[i] = 0.4 * PeriodicTable::getTable()->getRcovalent(
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m1->getAtomWithIdx(i)->getAtomicNum());
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}
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std::vector<double> levels;
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drawer.clearDrawing();
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MolDraw2DUtils::contourAndDrawGaussians(drawer, cents, weights, widths, 10,
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levels);
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drawer.drawOptions().clearBackground = false;
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drawer.drawMolecule(*m1);
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drawer.finishDrawing();
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std::string text = drawer.getDrawingText();
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std::ofstream outs("contourMol_2.svg");
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outs << text;
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outs.flush();
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}
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SECTION("gaussian fill") {
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MolDraw2DSVG drawer(250, 250);
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MolDraw2DUtils::prepareMolForDrawing(*m1);
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drawer.drawOptions().padding = 0.1;
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const auto conf = m1->getConformer();
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std::vector<Point2D> cents(conf.getNumAtoms());
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std::vector<double> weights(conf.getNumAtoms());
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std::vector<double> widths(conf.getNumAtoms());
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for (size_t i = 0; i < conf.getNumAtoms(); ++i) {
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cents[i] = Point2D(conf.getAtomPos(i).x, conf.getAtomPos(i).y);
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weights[i] = i % 2 ? -0.5 : 1;
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widths[i] = 0.4 * PeriodicTable::getTable()->getRcovalent(
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m1->getAtomWithIdx(i)->getAtomicNum());
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}
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std::vector<double> levels;
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MolDraw2DUtils::ContourParams cps;
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cps.fillGrid = true;
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drawer.clearDrawing();
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MolDraw2DUtils::contourAndDrawGaussians(drawer, cents, weights, widths, 10,
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levels, cps);
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drawer.drawOptions().clearBackground = false;
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drawer.drawMolecule(*m1);
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drawer.finishDrawing();
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std::string text = drawer.getDrawingText();
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std::ofstream outs("contourMol_3.svg");
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outs << text;
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outs.flush();
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}
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SECTION("gaussian fill 2") {
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auto m2 = "C1N[C@@H]2OCC12C=CC"_smiles;
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REQUIRE(m2);
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MolDraw2DSVG drawer(450, 250);
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MolDraw2DUtils::prepareMolForDrawing(*m2);
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drawer.drawOptions().padding = 0.1;
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const auto conf = m2->getConformer();
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std::vector<Point2D> cents(conf.getNumAtoms());
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std::vector<double> weights(conf.getNumAtoms());
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std::vector<double> widths(conf.getNumAtoms());
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for (size_t i = 0; i < conf.getNumAtoms(); ++i) {
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cents[i] = Point2D(conf.getAtomPos(i).x, conf.getAtomPos(i).y);
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weights[i] = i % 2 ? -0.5 : 1;
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widths[i] = 0.3 * PeriodicTable::getTable()->getRcovalent(
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m2->getAtomWithIdx(i)->getAtomicNum());
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}
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std::vector<double> levels;
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MolDraw2DUtils::ContourParams cps;
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cps.fillGrid = true;
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cps.gridResolution = 0.5;
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drawer.clearDrawing();
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MolDraw2DUtils::contourAndDrawGaussians(drawer, cents, weights, widths, 10,
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levels, cps);
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drawer.drawOptions().clearBackground = false;
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drawer.drawMolecule(*m2);
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drawer.finishDrawing();
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std::string text = drawer.getDrawingText();
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std::ofstream outs("contourMol_4.svg");
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outs << text;
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outs.flush();
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}
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}
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TEST_CASE("dative bonds", "[drawing, organometallics]") {
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SECTION("basics") {
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auto m1 = "N->[Pt]"_smiles;
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REQUIRE(m1);
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MolDraw2DSVG drawer(200, 200);
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MolDraw2DUtils::prepareMolForDrawing(*m1);
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drawer.drawMolecule(*m1);
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drawer.finishDrawing();
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std::string text = drawer.getDrawingText();
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std::ofstream outs("testDativeBonds_1.svg");
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outs << text;
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outs.flush();
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CHECK(text.find("<path class='bond-0' d='M 56.766,102.447 L 50.8587,100 "
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"L 56.766,97.5531") != std::string::npos);
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}
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SECTION("more complex") {
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auto m1 = "N->1[C@@H]2CCCC[C@H]2N->[Pt]11OC(=O)C(=O)O1"_smiles;
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REQUIRE(m1);
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MolDraw2DSVG drawer(200, 200);
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MolDraw2DUtils::prepareMolForDrawing(*m1);
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drawer.drawMolecule(*m1);
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drawer.finishDrawing();
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std::string text = drawer.getDrawingText();
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std::ofstream outs("testDativeBonds_2.svg");
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outs << text;
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outs.flush();
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CHECK(text.find("<path class='bond-7' d='M 95.8183,93.981 "
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"L 94.3351,94.8899 L 94.7412,93.1984") !=
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std::string::npos);
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}
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}
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TEST_CASE("zero-order bonds", "[drawing, organometallics]") {
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SECTION("basics") {
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auto m1 = "N-[Pt]"_smiles;
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REQUIRE(m1);
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m1->getBondWithIdx(0)->setBondType(Bond::ZERO);
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MolDraw2DSVG drawer(200, 200);
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MolDraw2DUtils::prepareMolForDrawing(*m1);
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drawer.drawMolecule(*m1);
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drawer.finishDrawing();
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std::string text = drawer.getDrawingText();
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std::ofstream outs("testZeroOrderBonds_1.svg");
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outs << text;
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outs.flush();
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CHECK(text.find("stroke-dasharray:2,2") != std::string::npos);
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}
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}
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TEST_CASE("copying drawing options", "[drawing]") {
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auto m1 = "C1N[C@@H]2OCC12"_smiles;
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REQUIRE(m1);
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SECTION("foundations") {
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{
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MolDraw2DSVG drawer(200, 200);
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MolDraw2DUtils::prepareAndDrawMolecule(drawer, *m1);
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drawer.finishDrawing();
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std::string text = drawer.getDrawingText();
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CHECK(text.find("fill:#0000FF' ><tspan>NH") != std::string::npos);
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}
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{
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MolDraw2DSVG drawer(200, 200);
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assignBWPalette(drawer.drawOptions().atomColourPalette);
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MolDraw2DUtils::prepareAndDrawMolecule(drawer, *m1);
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drawer.finishDrawing();
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std::string text = drawer.getDrawingText();
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CHECK(text.find("fill:#0000FF' ><tspan>NH") == std::string::npos);
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CHECK(text.find("fill:#000000' ><tspan>NH") != std::string::npos);
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}
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}
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SECTION("test") {
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{
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MolDraw2DSVG drawer(200, 200);
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MolDrawOptions options = drawer.drawOptions();
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assignBWPalette(options.atomColourPalette);
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drawer.drawOptions() = options;
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MolDraw2DUtils::prepareAndDrawMolecule(drawer, *m1);
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drawer.finishDrawing();
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std::string text = drawer.getDrawingText();
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CHECK(text.find("fill:#0000FF' ><tspan>NH") == std::string::npos);
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CHECK(text.find("fill:#000000' ><tspan>NH") != std::string::npos);
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}
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}
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} |