mirror of
https://github.com/rdkit/rdkit.git
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a45d4d9857
* add angles and distances * add Inversions * add torsiona angle contribs * use new contribs in test * use new inversion and torsion contribs in dg * use new distance contribs in dg * use new angle constraints in dg * use new constraints in FF tests * update docstrings * remove unused import * include new contribs * cleanup includes * make changes requested by @greglandrum * use std::move instead of release
239 lines
7.5 KiB
C++
239 lines
7.5 KiB
C++
//
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// Copyright (C) 2015 Sereina Riniker
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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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#include <RDGeneral/test.h>
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#include <RDGeneral/utils.h>
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#include <Geometry/point.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <ForceField/MMFF/Params.h>
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#include <ForceField/MMFF/TorsionAngle.h>
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#include <GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.h>
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#include <GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h>
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#include <GraphMol/MolOps.h>
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#include <GraphMol/MolTransforms/MolTransforms.h>
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#include <ForceField/ForceField.h>
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#include <iostream>
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#include <string>
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#include <cmath>
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using namespace RDGeom;
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using namespace RDKit;
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void testTorsionAngleContribs() {
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std::cerr << "-------------------------------------" << std::endl;
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std::cerr << " Test CrystalFF torsional term." << std::endl;
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ForceFields::ForceField ff;
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Point3D p1, p2, p3, p4;
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RDGeom::PointPtrVect &ps = ff.positions();
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ps.push_back(&p1);
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ps.push_back(&p2);
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ps.push_back(&p3);
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ps.push_back(&p4);
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// ------- ------- ------- ------- ------- ------- -------
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// Basic SP3 - SP3
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// ------- ------- ------- ------- ------- ------- -------
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// [!#1:1][CX4H2:2]!@[CX4H2:3][!#1:4] 1 0.0 1 0.0 1 4.0 1 0.0 1 0.0 1 0.0
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std::vector<int> signs(6, 1);
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std::vector<double> v(6, 0.0);
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v[2] = 4.0;
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auto contrib = new ForceFields::CrystalFF::TorsionAngleContribs(&ff);
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contrib->addContrib(0, 1, 2, 3, v, signs);
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ff.contribs().emplace_back(contrib);
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p1.x = 0;
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p1.y = 1.5;
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p1.z = 0;
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p2.x = 0.0;
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p2.y = 0.0;
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p2.z = 0.0;
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p3.x = 1.5;
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p3.y = 0.0;
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p3.z = 0.0;
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p4.x = 1.5;
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p4.y = 0.0;
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p4.z = 1.5;
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ff.initialize();
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ff.minimize(10, 1e-8, 1e-8);
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double cosPhi = ForceFields::MMFF::Utils::calcTorsionCosPhi(
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*(RDGeom::Point3D *)ff.positions()[0],
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*(RDGeom::Point3D *)ff.positions()[1],
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*(RDGeom::Point3D *)ff.positions()[2],
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*(RDGeom::Point3D *)ff.positions()[3]);
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TEST_ASSERT(RDKit::feq(cosPhi, 0.5, 1e-4));
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// ------- ------- ------- ------- ------- ------- -------
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// Basic SP2 - SP2
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// ------- ------- ------- ------- ------- ------- -------
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signs[1] = -1;
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v[2] = 0.0;
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v[1] = 7.0;
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ff.contribs().pop_back();
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contrib = new ForceFields::CrystalFF::TorsionAngleContribs(&ff);
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contrib->addContrib(0, 1, 2, 3, v, signs);
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ff.contribs().emplace_back(contrib);
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p1.x = 0;
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p1.y = 1.5;
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p1.z = 0.1;
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p2.x = 0.0;
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p2.y = 0.0;
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p2.z = 0.0;
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p3.x = 1.5;
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p3.y = 0.0;
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p3.z = 0.0;
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p4.x = 1.5;
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p4.y = 0.2;
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p4.z = 1.5;
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ff.initialize();
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ff.minimize(10, 1e-8, 1e-8);
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cosPhi = ForceFields::MMFF::Utils::calcTorsionCosPhi(
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*(RDGeom::Point3D *)ff.positions()[0],
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*(RDGeom::Point3D *)ff.positions()[1],
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*(RDGeom::Point3D *)ff.positions()[2],
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*(RDGeom::Point3D *)ff.positions()[3]);
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TEST_ASSERT(RDKit::feq(cosPhi, 1.0, 1e-4));
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}
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void testTorsionPrefs() {
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ROMol *mol;
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mol = SmilesToMol("CCCC");
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TEST_ASSERT(mol);
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ForceFields::CrystalFF::CrystalFFDetails details;
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ForceFields::CrystalFF::getExperimentalTorsions(*mol, details, true, false,
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false, false, 1, false);
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TEST_ASSERT(details.expTorsionAtoms.size() == 1);
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TEST_ASSERT(details.expTorsionAngles.size() == 1);
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TEST_ASSERT(details.expTorsionAtoms[0][0] == 0);
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TEST_ASSERT(details.expTorsionAtoms[0][3] == 3);
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TEST_ASSERT(details.expTorsionAngles[0].first.size() == 6);
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TEST_ASSERT(details.expTorsionAngles[0].second.size() == 6);
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std::vector<std::tuple<unsigned int, std::vector<unsigned int>,
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const ForceFields::CrystalFF::ExpTorsionAngle *>>
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torsionBonds;
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ForceFields::CrystalFF::getExperimentalTorsions(
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*mol, details, torsionBonds, true, false, false, false, 2, false);
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TEST_ASSERT(torsionBonds.size() == 1);
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TEST_ASSERT(std::get<0>(torsionBonds[0]) == 1);
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TEST_ASSERT(std::get<2>(torsionBonds[0])->smarts ==
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"[!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]");
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TEST_ASSERT(std::get<2>(torsionBonds[0])->torsionIdx == 229);
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delete mol;
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mol = SmilesToMol("CCCCC");
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TEST_ASSERT(mol);
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ForceFields::CrystalFF::getExperimentalTorsions(
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*mol, details, torsionBonds, true, false, false, false, 2, false);
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TEST_ASSERT(details.expTorsionAtoms.size() == 2);
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TEST_ASSERT(details.expTorsionAngles.size() == 2);
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TEST_ASSERT(torsionBonds.size() == 2);
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TEST_ASSERT(std::get<0>(torsionBonds[0]) == 1);
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TEST_ASSERT(std::get<0>(torsionBonds[1]) == 2);
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delete mol;
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}
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void testTorsionPrefsSmallRings() {
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ROMol *mol;
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ForceFields::CrystalFF::CrystalFFDetails details;
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mol = SmilesToMol("C1COCC1");
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TEST_ASSERT(mol);
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// small ring torsion turned off
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ForceFields::CrystalFF::getExperimentalTorsions(*mol, details, true, false,
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false, false, 1, false);
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TEST_ASSERT(details.expTorsionAtoms.size() == 0);
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TEST_ASSERT(details.expTorsionAngles.size() == 0);
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// small ring torsion turned on
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ForceFields::CrystalFF::getExperimentalTorsions(*mol, details, true, true,
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false, false, 1, false);
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TEST_ASSERT(details.expTorsionAtoms.size() > 0);
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TEST_ASSERT(details.expTorsionAngles.size() > 0);
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delete mol;
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}
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void testTorsionPrefsBridgedSmallRings() {
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// test bridged system does not trigger any small ring torsion
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ROMol *mol;
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ForceFields::CrystalFF::CrystalFFDetails details;
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mol = SmilesToMol("O[C@H]1C[C@H]2CC[C@]1(C)C2(C)C");
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TEST_ASSERT(mol);
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// small ring torsion turned off
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ForceFields::CrystalFF::getExperimentalTorsions(*mol, details, true, true,
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false, false, 1, false);
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TEST_ASSERT(details.expTorsionAtoms.size() == 0);
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TEST_ASSERT(details.expTorsionAngles.size() == 0);
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delete mol;
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}
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void testTorsionPrefsMacrocycles() {
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ROMol *mol;
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ForceFields::CrystalFF::CrystalFFDetails details;
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mol = SmilesToMol("C1COCCCCCCC1");
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TEST_ASSERT(mol);
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// macrocycle ring torsion turned off
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ForceFields::CrystalFF::getExperimentalTorsions(*mol, details, true, false,
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false, false, 1, false);
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TEST_ASSERT(details.expTorsionAtoms.size() == 0);
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TEST_ASSERT(details.expTorsionAngles.size() == 0);
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// macrocycle ring torsion turned on
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ForceFields::CrystalFF::getExperimentalTorsions(*mol, details, true, false,
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true, false, 1, false);
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TEST_ASSERT(details.expTorsionAtoms.size() > 0);
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TEST_ASSERT(details.expTorsionAngles.size() > 0);
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delete mol;
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}
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int main() {
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RDLog::InitLogs();
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BOOST_LOG(rdInfoLog)
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<< "********************************************************\n";
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BOOST_LOG(rdInfoLog) << "Testing Crystal ForceField\n";
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BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
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BOOST_LOG(rdInfoLog) << "\t SMARTS parsing\n";
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testTorsionAngleContribs();
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BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
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BOOST_LOG(rdInfoLog) << "\t Seeing if non-ring torsions are applied\n";
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testTorsionPrefs();
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BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
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BOOST_LOG(rdInfoLog) << "\t Seeing if small ring torsions are applied\n";
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testTorsionPrefsSmallRings();
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BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
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BOOST_LOG(rdInfoLog) << "\t Seeing if macrocycle ring torsions are applied\n";
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testTorsionPrefsMacrocycles();
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return 0;
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}
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