rdkit/Code/GraphMol/FileParsers/XYZFileParserCatchTest.cpp

#include "RDGeneral/test.h"
#include "catch.hpp"
#include <RDGeneral/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/QueryAtom.h>
#include <GraphMol/MolPickler.h>
#include <GraphMol/Chirality.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/FileParsers/MolFileStereochem.h>
#include <RDGeneral/FileParseException.h>

using namespace RDKit;

TEST_CASE("xyz file parser") {
  SECTION("basics") {
    std::string rdbase = getenv("RDBASE");
    std::string fName = rdbase +
                        "/Code/GraphMol/FileParsers/test_data/"
                        "acetate.xyz";
    std::unique_ptr<RWMol> mol(XYZFileToMol(fName));
    REQUIRE(mol);

    REQUIRE(mol->getNumAtoms() == 7);

    size_t ind = 0;
    for (auto a : {6, 6, 1, 1, 1, 8, 8}) {
      CHECK(mol->getAtomWithIdx(ind)->getAtomicNum() == a);
      ind++;
    }

    RDGeom::POINT3D_VECT positions = {
        RDGeom::Point3D{-4.71686, 0.89919, 0.05714},
        RDGeom::Point3D{-3.24898, 0.98400, -0.22830},
        RDGeom::Point3D{-5.04167, 1.74384, 0.67862},
        RDGeom::Point3D{-5.01710, -0.02205, 0.56344},
        RDGeom::Point3D{-5.21076, 0.96874, -0.91208},
        RDGeom::Point3D{-2.65909, 2.05702, -0.34025},
        RDGeom::Point3D{-2.63413, -0.18702, -0.48679}};

    CHECK(mol->hasProp("_FileComments"));
    CHECK(mol->getProp<std::string>("_FileComments") == "charge=-1=");

    auto conf = &mol->getConformer();
    REQUIRE(conf);
    REQUIRE(conf->getNumAtoms() == 7);

    ind = 0;
    for (auto p : positions) {
      CHECK(conf->getAtomPos(ind).x == Approx(p.x).margin(1e-6));
      CHECK(conf->getAtomPos(ind).y == Approx(p.y).margin(1e-6));
      CHECK(conf->getAtomPos(ind).z == Approx(p.z).margin(1e-6));
      ind++;
    }
  }
  SECTION("basics w/o comment and w/ nonstandard spacing") {
    std::string rdbase = getenv("RDBASE");
    std::string fName = rdbase +
                        "/Code/GraphMol/FileParsers/test_data/"
                        "ethane.xyz";
    std::unique_ptr<RWMol> mol(XYZFileToMol(fName));
    REQUIRE(mol);

    REQUIRE(mol->getNumAtoms() == 8);

    size_t ind = 0;
    for (auto a : {6, 6, 1, 1, 1, 1, 1, 1}) {
      CHECK(mol->getAtomWithIdx(ind)->getAtomicNum() == a);
      ind++;
    }

    RDGeom::POINT3D_VECT positions = {
        RDGeom::Point3D{-4.58735, 0.92696, 0.00000},
        RDGeom::Point3D{-3.11050, 0.92696, 0.00000},
        RDGeom::Point3D{-4.93786, 1.78883, 0.58064},
        RDGeom::Point3D{-4.93786, -0.00682, 0.45608},
        RDGeom::Point3D{-4.93786, 0.99888, -1.03672},
        RDGeom::Point3D{-2.75999, 0.85505, 1.03672},
        RDGeom::Point3D{-2.75998, 1.86075, -0.45608},
        RDGeom::Point3D{-2.75998, 0.06509, -0.58064}};

    CHECK(!mol->hasProp("_FileComments"));

    auto conf = &mol->getConformer();
    REQUIRE(conf);
    REQUIRE(conf->getNumAtoms() == 8);

    ind = 0;
    for (auto p : positions) {
      CHECK(conf->getAtomPos(ind).x == Approx(p.x).margin(1e-6));
      CHECK(conf->getAtomPos(ind).y == Approx(p.y).margin(1e-6));
      CHECK(conf->getAtomPos(ind).z == Approx(p.z).margin(1e-6));
      ind++;
    }
  }
  SECTION("zero atoms") {
    std::string rdbase = getenv("RDBASE");
    std::string fName = rdbase +
                        "/Code/GraphMol/FileParsers/test_data/"
                        "nonexistant.xyz";

    std::unique_ptr<RWMol> mol(XYZFileToMol(fName));
    REQUIRE(mol);
    REQUIRE(mol->getNumAtoms() == 0);
  }
  SECTION("empty file") {
    std::string rdbase = getenv("RDBASE");
    std::string fName = rdbase +
                        "/Code/GraphMol/FileParsers/test_data/"
                        "empty.xyz";

    std::unique_ptr<RWMol> mol(XYZFileToMol(fName));
    REQUIRE(!mol);
  }
}

TEST_CASE("xyz block parser") {
  SECTION("basics") {
    std::string xyzblock = R"XYZ(5
        methane
        C      0.000000    0.000000    0.000000
        H     -0.635000   -0.635000    0.635000
        H     -0.635000    0.635000   -0.635000
        H      0.635000   -0.635000   -0.635000
        H      0.635000    0.635000    0.635000
        )XYZ";
    std::unique_ptr<RWMol> mol(XYZBlockToMol(xyzblock));
    REQUIRE(mol);

    REQUIRE(mol->getNumAtoms() == 5);

    size_t ind = 0;
    for (auto a : {6, 1, 1, 1, 1}) {
      CHECK(mol->getAtomWithIdx(ind)->getAtomicNum() == a);
      ind++;
    }

    RDGeom::POINT3D_VECT positions = {RDGeom::Point3D{0.000, 0.000, 0.000},
                                      RDGeom::Point3D{-0.635, -0.635, 0.635},
                                      RDGeom::Point3D{-0.635, 0.635, -0.635},
                                      RDGeom::Point3D{0.635, -0.635, -0.635},
                                      RDGeom::Point3D{0.635, 0.635, 0.635}};

    CHECK(mol->hasProp("_FileComments"));
    CHECK(mol->getProp<std::string>("_FileComments") == "        methane");

    auto conf = &mol->getConformer();
    REQUIRE(conf);
    REQUIRE(conf->getNumAtoms() == 5);

    ind = 0;
    for (auto p : positions) {
      CHECK(conf->getAtomPos(ind).x == Approx(p.x).margin(1e-6));
      CHECK(conf->getAtomPos(ind).y == Approx(p.y).margin(1e-6));
      CHECK(conf->getAtomPos(ind).z == Approx(p.z).margin(1e-6));
      ind++;
    }
  }
}