mirror of
https://github.com/rdkit/rdkit.git
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262 lines
8.5 KiB
C++
262 lines
8.5 KiB
C++
// $Id$
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//
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// Copyright (C) 2005-2013 Greg Landrum and Rational Discovery LLC
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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 "UniformGrid3D.h"
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#include <DataStructs/DiscreteValueVect.h>
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#include "point.h"
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#include <RDGeneral/Invariant.h>
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#include <RDGeneral/utils.h>
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#include "GridUtils.h"
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#include <iostream>
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#include <sstream>
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#include <fstream>
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#include <ios>
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#include <stdlib.h>
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using namespace RDGeom;
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using namespace RDKit;
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void testUniformGrid1() {
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UniformGrid3D grd(6.0, 5.0, 4.0);
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CHECK_INVARIANT(grd.getSize() == 960, "");
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CHECK_INVARIANT(RDKit::feq(grd.getSpacing(), .5), "");
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CHECK_INVARIANT(grd.getNumX() == 12, "");
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CHECK_INVARIANT(grd.getNumY() == 10, "");
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CHECK_INVARIANT(grd.getNumZ() == 8, "");
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grd.setSphereOccupancy(Point3D(0.0, 0.0, 0.0), 1.5, 0.25);
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CHECK_INVARIANT(grd.getOccupancyVect()->getTotalVal() == 523, "");
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// writeGridToFile(grd, "junk.grd");
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UniformGrid3D grd2(grd);
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CHECK_INVARIANT(grd2.getSize() == 960, "");
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CHECK_INVARIANT(RDKit::feq(grd2.getSpacing(), .5), "");
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CHECK_INVARIANT(grd2.getNumX() == 12, "");
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CHECK_INVARIANT(grd2.getNumY() == 10, "");
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CHECK_INVARIANT(grd2.getNumZ() == 8, "");
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CHECK_INVARIANT(grd2.getOccupancyVect()->getTotalVal() == 523, "");
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// make sure the data are actually decoupled:
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grd.setSphereOccupancy(Point3D(1.0, 1.0, 0.0), 1.5, 0.25);
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CHECK_INVARIANT(grd.getOccupancyVect()->getTotalVal() > 523, "");
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CHECK_INVARIANT(grd2.getOccupancyVect()->getTotalVal() == 523, "");
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}
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void testUniformGrid2() {
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// test distance metrics:
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UniformGrid3D grd(10.0, 10.0, 10.0);
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grd.setSphereOccupancy(Point3D(-2.0, -2.0, 0.0), 1.5, 0.25);
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grd.setSphereOccupancy(Point3D(-2.0, 2.0, 0.0), 1.5, 0.25);
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grd.setSphereOccupancy(Point3D(2.0, -2.0, 0.0), 1.5, 0.25);
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grd.setSphereOccupancy(Point3D(2.0, 2.0, 0.0), 1.5, 0.25);
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writeGridToFile(grd, "junk.grd");
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double dist = tanimotoDistance(grd, grd);
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CHECK_INVARIANT(RDKit::feq(dist, 0.0), "");
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UniformGrid3D grd2(10.0, 10.0, 10.0);
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grd2.setSphereOccupancy(Point3D(-2.0, -2.0, 0.0), 1.5, 0.25);
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grd2.setSphereOccupancy(Point3D(-2.0, 2.0, 0.0), 1.5, 0.25);
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grd2.setSphereOccupancy(Point3D(2.0, -2.0, 0.0), 1.5, 0.25);
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dist = tanimotoDistance(grd, grd2);
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CHECK_INVARIANT(RDKit::feq(dist, 0.25), "");
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dist = protrudeDistance(grd, grd2);
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CHECK_INVARIANT(RDKit::feq(dist, 0.25), "");
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dist = protrudeDistance(grd2, grd);
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CHECK_INVARIANT(RDKit::feq(dist, 0.0), "");
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UniformGrid3D grd3(10.0, 10.0, 10.0);
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grd3.setSphereOccupancy(Point3D(-2.0, -2.0, 0.0), 1.5, 0.25);
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grd3.setSphereOccupancy(Point3D(-2.0, 2.0, 0.0), 1.5, 0.25);
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dist = tanimotoDistance(grd, grd3);
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CHECK_INVARIANT(RDKit::feq(dist, 0.5), "");
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dist = protrudeDistance(grd, grd3);
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CHECK_INVARIANT(RDKit::feq(dist, 0.5), "");
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dist = protrudeDistance(grd3, grd);
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CHECK_INVARIANT(RDKit::feq(dist, 0.0), "");
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UniformGrid3D grd4(10.0, 10.0, 10.0);
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grd4.setSphereOccupancy(Point3D(2.0, 2.0, 0.0), 1.5, 0.25);
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grd4.setSphereOccupancy(Point3D(2.0, -2.0, 0.0), 1.5, 0.25);
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dist = tanimotoDistance(grd3, grd4);
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CHECK_INVARIANT(RDKit::feq(dist, 1.0), "");
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UniformGrid3D grd5(10.0, 10.0, 10.0);
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grd5.setSphereOccupancy(Point3D(-2.0, -2.0, 0.0), 1.5, 0.25);
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dist = tanimotoDistance(grd, grd5);
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CHECK_INVARIANT(RDKit::feq(dist, 0.75), "");
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dist = protrudeDistance(grd, grd5);
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CHECK_INVARIANT(RDKit::feq(dist, 0.75), "");
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dist = protrudeDistance(grd5, grd);
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CHECK_INVARIANT(RDKit::feq(dist, 0.00), "");
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}
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void testUniformGridPickling() {
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{
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// test tanimoto distance
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UniformGrid3D grd(10.0, 10.0, 10.0);
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grd.setSphereOccupancy(Point3D(-2.0, -2.0, 0.0), 1.5, 0.25);
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grd.setSphereOccupancy(Point3D(-2.0, 2.0, 0.0), 1.5, 0.25);
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grd.setSphereOccupancy(Point3D(2.0, -2.0, 0.0), 1.5, 0.25);
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grd.setSphereOccupancy(Point3D(2.0, 2.0, 0.0), 1.5, 0.25);
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UniformGrid3D grd2(grd.toString());
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double dist = tanimotoDistance(grd, grd2);
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CHECK_INVARIANT(RDKit::feq(dist, 0.0), "");
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}
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{
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std::string dirName = getenv("RDBASE");
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dirName += "/Code/Geometry/testData/";
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std::string pklName = dirName + "grid1.bin";
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std::ifstream inS;
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inS.open(pklName.c_str(), std::ios_base::binary);
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unsigned int length;
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inS >> length;
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char *buff = new char[length];
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unsigned int nRead = 0;
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while (nRead < length) {
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nRead += inS.readsome(buff + nRead, length - nRead);
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}
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inS.close();
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std::string pkl(buff, length);
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delete[] buff;
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UniformGrid3D grd(pkl);
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UniformGrid3D grd2(10.0, 10.0, 10.0);
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grd2.setSphereOccupancy(Point3D(-2.0, -2.0, 0.0), 1.5, 0.25);
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grd2.setSphereOccupancy(Point3D(-2.0, 2.0, 0.0), 1.5, 0.25);
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grd2.setSphereOccupancy(Point3D(2.0, -2.0, 0.0), 1.5, 0.25);
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grd2.setSphereOccupancy(Point3D(2.0, 2.0, 0.0), 1.5, 0.25);
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std::string pkl2 = grd2.toString();
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TEST_ASSERT(pkl2.length() == pkl.length());
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TEST_ASSERT(pkl2 == pkl);
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TEST_ASSERT(grd.getSize() == grd2.getSize());
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TEST_ASSERT(grd.getNumX() == grd2.getNumX());
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TEST_ASSERT(grd.getNumY() == grd2.getNumY());
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TEST_ASSERT(grd.getNumZ() == grd2.getNumZ());
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TEST_ASSERT(grd.compareParams(grd2));
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double dist = tanimotoDistance(grd, grd2);
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TEST_ASSERT(RDKit::feq(dist, 0.0));
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}
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}
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void testUniformGridOps() {
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UniformGrid3D grd(10.0, 10.0, 10.0);
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grd.setSphereOccupancy(Point3D(-2.0, -2.0, 0.0), 1.0, 0.25);
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grd.setSphereOccupancy(Point3D(-2.0, 2.0, 0.0), 1.0, 0.25);
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UniformGrid3D grd2(10.0, 10.0, 10.0);
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grd2.setSphereOccupancy(Point3D(2.0, -2.0, 0.0), 1.0, 0.25);
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grd2.setSphereOccupancy(Point3D(2.0, 2.0, 0.0), 1.0, 0.25);
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double dist = tanimotoDistance(grd, grd2);
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CHECK_INVARIANT(RDKit::feq(dist, 1.0), "");
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UniformGrid3D grd3(grd);
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grd3 |= grd2;
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dist = tanimotoDistance(grd3, grd);
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CHECK_INVARIANT(RDKit::feq(dist, 0.5), "");
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dist = tanimotoDistance(grd3, grd2);
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CHECK_INVARIANT(RDKit::feq(dist, 0.5), "");
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UniformGrid3D grd4(10.0, 10.0, 10.0);
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grd4.setSphereOccupancy(Point3D(-2.0, -2.0, 0.0), 1.0, 0.25);
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grd4.setSphereOccupancy(Point3D(-2.0, 2.0, 0.0), 1.0, 0.25);
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grd4.setSphereOccupancy(Point3D(2.0, -2.0, 0.0), 1.0, 0.25);
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UniformGrid3D grd5(grd4);
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grd5 &= grd2;
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dist = tanimotoDistance(grd5, grd);
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CHECK_INVARIANT(RDKit::feq(dist, 1.0), "");
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dist = tanimotoDistance(grd5, grd2);
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CHECK_INVARIANT(RDKit::feq(dist, 0.5), "");
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}
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void testUniformGridIndexing() {
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// test distance metrics:
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UniformGrid3D grd(5.0, 5.0, 5.0);
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{
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unsigned int xi = 3, yi = 3, zi = 3;
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unsigned int idx = grd.getGridIndex(xi, yi, zi);
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unsigned int nxi, nyi, nzi;
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grd.getGridIndices(idx, nxi, nyi, nzi);
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TEST_ASSERT(nxi == xi);
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TEST_ASSERT(nyi == yi);
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TEST_ASSERT(nzi == zi);
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}
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{
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unsigned int xi = 3, yi = 3, zi = 5;
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unsigned int idx = grd.getGridIndex(xi, yi, zi);
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unsigned int nxi, nyi, nzi;
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grd.getGridIndices(idx, nxi, nyi, nzi);
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TEST_ASSERT(nxi == xi);
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TEST_ASSERT(nyi == yi);
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TEST_ASSERT(nzi == zi);
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}
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{
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unsigned int xi = 3, yi = 6, zi = 3;
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unsigned int idx = grd.getGridIndex(xi, yi, zi);
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unsigned int nxi, nyi, nzi;
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grd.getGridIndices(idx, nxi, nyi, nzi);
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TEST_ASSERT(nxi == xi);
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TEST_ASSERT(nyi == yi);
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TEST_ASSERT(nzi == zi);
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}
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{
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unsigned int xi = 0, yi = 0, zi = 0;
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unsigned int idx = grd.getGridIndex(xi, yi, zi);
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unsigned int nxi, nyi, nzi;
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grd.getGridIndices(idx, nxi, nyi, nzi);
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TEST_ASSERT(nxi == xi);
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TEST_ASSERT(nyi == yi);
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TEST_ASSERT(nzi == zi);
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}
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{
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unsigned int xi = 8, yi = 2, zi = 1;
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unsigned int idx = grd.getGridIndex(xi, yi, zi);
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unsigned int nxi, nyi, nzi;
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grd.getGridIndices(idx, nxi, nyi, nzi);
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TEST_ASSERT(nxi == xi);
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TEST_ASSERT(nyi == yi);
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TEST_ASSERT(nzi == zi);
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}
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}
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int main() {
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std::cout << "***********************************************************\n";
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std::cout << "Testing Grid\n";
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std::cout << "\t---------------------------------\n";
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std::cout << "\t testUniformGrid1 \n\n";
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testUniformGrid1();
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std::cout << "\t---------------------------------\n";
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std::cout << "\t testUniformGrid2 \n\n";
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testUniformGrid2();
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std::cout << "\t---------------------------------\n";
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std::cout << "\t testUniformGridPickling \n\n";
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testUniformGridPickling();
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std::cout << "\t---------------------------------\n";
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std::cout << "\t testGridOps \n\n";
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testUniformGridOps();
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std::cout << "\t---------------------------------\n";
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std::cout << "\t testUniformGridIndexing \n\n";
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testUniformGridIndexing();
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return 0;
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}
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