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rdkit/Code/GraphMol/Trajectory/trajectoryTest.cpp
Greg Landrum 5712176605 Implement the two deprecations that were planned for the 2020.09 release cycle (#3047) 
* Deprecation: planned removal of .message() and .getMessage() methods

* Deprecation: planned removal of old MolHash code

* document deprecations

* output the diffs when the psql tests fail

* remove .message() from SWIG wrappers

note that the KeyError doesn't work properly. We should clean up the the exceptions here anyway

* typo
2020-04-01 14:30:07 +02:00

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// $Id$
//
// Copyright (C) 2016 Sereina Riniker, Paolo Tosco
//
// @@ 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/test.h>
#include "Trajectory.h"
#include <Geometry/point.h>
#include <GraphMol/ROMol.h>
#include <GraphMol/Conformer.h>
#include <GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h>
#include <GraphMol/ForceFieldHelpers/MMFF/Builder.h>
#include <ForceField/ForceField.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolWriters.h>
#include <RDGeneral/Invariant.h>
using namespace RDKit;
void testSnapshot() {
{
boost::shared_array<double> pos;
Snapshot s(pos);
bool e = false;
try {
s.getPoint2D(12);
} catch (...) {
e = true;
}
TEST_ASSERT(e);
}
{
boost::shared_array<double> pos(new double[3]());
Snapshot s(pos);
bool e = false;
try {
s.getPoint2D(0);
} catch (...) {
e = true;
}
TEST_ASSERT(e);
}
}
void testTrajectory2D() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "testTrajectory2D" << std::endl;
const unsigned int dim = 2;
const unsigned int np = 10;
const unsigned int ns = 5;
Trajectory traj(dim, np);
CHECK_INVARIANT(traj.dimension() == dim, "");
CHECK_INVARIANT(traj.numPoints() == np, "");
boost::shared_array<double> c(new double[np * dim]);
for (unsigned int i = 0; i < np * dim; ++i) {
c[i] = static_cast<double>(i);
}
for (unsigned int i = 0; i < ns; ++i) {
traj.addSnapshot(Snapshot(c, static_cast<double>(i)));
}
TEST_ASSERT(traj.size() == ns);
{
bool e = false;
try {
traj.getSnapshot(ns);
} catch (...) {
e = true;
}
TEST_ASSERT(e);
}
{
bool e = false;
try {
traj.getSnapshot(0).getPoint2D(np);
} catch (...) {
e = true;
}
TEST_ASSERT(e);
}
for (unsigned int i = 0; i < np; ++i) {
TEST_ASSERT(RDKit::feq(std::round(traj.getSnapshot(0).getPoint2D(i).x),
static_cast<double>(i * dim)));
TEST_ASSERT(RDKit::feq(std::round(traj.getSnapshot(0).getPoint2D(i).y),
static_cast<double>(i * dim + 1)));
bool e = false;
try {
TEST_ASSERT(
RDKit::feq(std::round(traj.getSnapshot(0).getPoint3D(i).z), 0.0));
} catch (...) {
e = true;
}
TEST_ASSERT(!e);
}
for (unsigned int i = 0; i < ns; ++i) {
TEST_ASSERT(RDKit::feq(std::round(traj.getSnapshot(i).getEnergy()),
static_cast<double>(i)));
}
traj.removeSnapshot(0);
TEST_ASSERT(traj.size() == ns - 1);
for (unsigned int i = 0; i < ns - 1; ++i) {
TEST_ASSERT(RDKit::feq(std::round(traj.getSnapshot(i).getEnergy()),
static_cast<double>(i + 1)));
}
traj.insertSnapshot(0, Snapshot(c, 999.0));
TEST_ASSERT(traj.size() == ns);
Snapshot copySnapshot(traj.getSnapshot(0));
traj.addSnapshot(copySnapshot);
TEST_ASSERT(traj.size() == ns + 1);
TEST_ASSERT(RDKit::feq(std::round(traj.getSnapshot(0).getEnergy()), 999.0));
TEST_ASSERT(RDKit::feq(std::round(traj.getSnapshot(1).getEnergy()), 1.0));
TEST_ASSERT(RDKit::feq(
std::round(traj.getSnapshot(traj.size() - 1).getEnergy()), 999.0));
Trajectory traj2(traj);
BOOST_LOG(rdErrorLog) << "done" << std::endl;
}
void testTrajectory3D() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "testTrajectory3D" << std::endl;
const unsigned int dim = 3;
const unsigned int np = 10;
const unsigned int ns = 5;
Trajectory traj(dim, np);
CHECK_INVARIANT(traj.dimension() == dim, "");
CHECK_INVARIANT(traj.numPoints() == np, "");
boost::shared_array<double> c(new double[np * dim]);
for (unsigned int i = 0; i < np * dim; ++i) {
c[i] = static_cast<double>(i);
}
for (unsigned int i = 0; i < ns; ++i) {
traj.addSnapshot(Snapshot(c, static_cast<double>(i)));
}
TEST_ASSERT(traj.size() == ns);
{
bool e = false;
try {
traj.getSnapshot(ns);
} catch (...) {
e = true;
}
TEST_ASSERT(e);
}
{
bool e = false;
try {
traj.getSnapshot(0).getPoint2D(np);
} catch (...) {
e = true;
}
TEST_ASSERT(e);
}
for (unsigned int i = 0; i < np; ++i) {
TEST_ASSERT(RDKit::feq(std::round(traj.getSnapshot(0).getPoint3D(i).x),
static_cast<double>(i * dim)));
TEST_ASSERT(RDKit::feq(std::round(traj.getSnapshot(0).getPoint3D(i).y),
static_cast<double>(i * dim + 1)));
TEST_ASSERT(RDKit::feq(std::round(traj.getSnapshot(0).getPoint3D(i).z),
static_cast<double>(i * dim + 2)));
if (!i) {
bool e = false;
try {
traj.getSnapshot(0).getPoint2D(i);
} catch (...) {
e = true;
}
TEST_ASSERT(e);
}
}
for (unsigned int i = 0; i < ns; ++i) {
TEST_ASSERT(RDKit::feq(std::round(traj.getSnapshot(i).getEnergy()),
static_cast<double>(i)));
}
traj.removeSnapshot(0);
TEST_ASSERT(traj.size() == ns - 1);
for (unsigned int i = 0; i < ns - 1; ++i) {
TEST_ASSERT(RDKit::feq(std::round(traj.getSnapshot(i).getEnergy()),
static_cast<double>(i + 1)));
}
traj.insertSnapshot(0, Snapshot(c, 999.0));
TEST_ASSERT(traj.size() == ns);
Snapshot copySnapshot(traj.getSnapshot(0));
traj.addSnapshot(copySnapshot);
TEST_ASSERT(traj.size() == ns + 1);
TEST_ASSERT(RDKit::feq(std::round(traj.getSnapshot(0).getEnergy()), 999.0));
TEST_ASSERT(RDKit::feq(std::round(traj.getSnapshot(1).getEnergy()), 1.0));
TEST_ASSERT(RDKit::feq(
std::round(traj.getSnapshot(traj.size() - 1).getEnergy()), 999.0));
Trajectory traj2(traj);
BOOST_LOG(rdErrorLog) << "done" << std::endl;
}
void testReadAmber() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "testReadAmber" << std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName = rdbase + "/Code/GraphMol/test_data/water_coords_bad.trx";
{
Trajectory traj(2, 0);
bool ok = false;
try {
readAmberTrajectory(fName, traj);
} catch (...) {
ok = true;
}
TEST_ASSERT(ok);
}
{
Trajectory traj(3, 3);
bool ok = false;
try {
readAmberTrajectory(fName, traj);
} catch (ValueErrorException &e) {
BOOST_LOG(rdErrorLog) << e.what() << std::endl;
ok = true;
}
TEST_ASSERT(ok);
}
fName = rdbase + "/Code/GraphMol/test_data/water_coords_bad2.trx";
{
bool ok = false;
try {
Trajectory traj(3, 3);
readAmberTrajectory(fName, traj);
} catch (ValueErrorException &e) {
BOOST_LOG(rdErrorLog) << e.what() << std::endl;
ok = true;
}
TEST_ASSERT(ok);
}
fName = rdbase + "/Code/GraphMol/test_data/water_coords.trx";
{
Trajectory traj(3, 3);
readAmberTrajectory(fName, traj);
TEST_ASSERT(traj.size() == 1);
}
fName = rdbase + "/Code/GraphMol/test_data/water_coords2.trx";
{
Trajectory traj(3, 3);
readAmberTrajectory(fName, traj);
TEST_ASSERT(traj.size() == 2);
Trajectory trajCopy(traj);
}
BOOST_LOG(rdErrorLog) << "done" << std::endl;
}
void testReadGromos() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "testReadGromos" << std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName = rdbase + "/Code/GraphMol/test_data/water_coords_bad.trc";
{
Trajectory traj(2, 0);
bool ok = false;
try {
readGromosTrajectory(fName, traj);
} catch (...) {
ok = true;
}
TEST_ASSERT(ok);
}
{
Trajectory traj(3, 3);
bool ok = false;
try {
readGromosTrajectory(fName, traj);
} catch (ValueErrorException &e) {
BOOST_LOG(rdErrorLog) << e.what() << std::endl;
ok = true;
}
TEST_ASSERT(ok);
}
fName = rdbase + "/Code/GraphMol/test_data/water_coords_bad2.trc";
{
bool ok = false;
try {
Trajectory traj(3, 3);
readGromosTrajectory(fName, traj);
} catch (ValueErrorException &e) {
BOOST_LOG(rdErrorLog) << e.what() << std::endl;
ok = true;
}
TEST_ASSERT(ok);
}
fName = rdbase + "/Code/GraphMol/test_data/water_coords.trc";
{
Trajectory traj(3, 3);
readGromosTrajectory(fName, traj);
TEST_ASSERT(traj.size() == 1);
}
fName = rdbase + "/Code/GraphMol/test_data/water_coords2.trc";
{
Trajectory traj(3, 3);
readGromosTrajectory(fName, traj);
TEST_ASSERT(traj.size() == 2);
Trajectory trajCopy(traj);
}
BOOST_LOG(rdErrorLog) << "done" << std::endl;
}
void testAddConformersFromTrajectory() {
BOOST_LOG(rdInfoLog) << "-----------------------\n";
BOOST_LOG(rdInfoLog) << "Testing adding conformers from a trajectory"
<< std::endl;
std::string molBlock =
"\n"
" RDKit 3D\n"
"\n"
" 71 74 0 0 0 0 0 0 0 0999 V2000\n"
" 8.2543 3.1901 -0.3005 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 7.4558 1.9712 0.0938 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 7.3934 1.0441 -0.9483 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 6.6660 -0.0533 -0.4641 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 5.1928 0.2346 -0.4609 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 4.3713 -0.9410 -0.5770 N 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.1852 -1.0034 -1.2291 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.2914 0.1276 -1.6316 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.9308 -0.4468 -1.9908 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.1417 -0.7821 -0.7545 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -0.1848 0.3695 0.0456 N 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -1.5661 0.7686 -0.0745 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -2.4768 -0.0640 0.8206 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -3.8874 0.1143 0.3941 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -4.6333 -0.9984 0.0264 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -6.0127 -0.9516 -0.0400 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -6.7062 0.1599 0.3963 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -8.0408 0.4828 -0.1977 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -7.7914 1.1180 -1.5591 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -8.7622 1.4403 0.7265 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -8.8409 -0.7397 -0.4395 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -8.9121 -1.6637 0.4258 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -9.7414 -0.7636 -1.5059 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -5.9736 1.2357 0.8565 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -4.5843 1.2252 0.8530 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.6263 1.4884 -0.3942 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.0541 1.0258 -0.4230 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.9225 -2.3317 -1.2963 N 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.6061 -2.9745 -0.3180 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.3554 -4.1536 0.3735 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.7653 -4.2712 1.6948 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 4.8254 -3.4613 2.0796 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 5.1978 -2.3436 1.3419 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 4.5694 -2.0799 0.1305 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 9.3138 3.1372 0.0031 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 7.8117 4.0754 0.1798 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 8.2358 3.3535 -1.4074 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 6.4027 2.2146 0.3634 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 7.9270 1.5444 1.0040 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 7.0677 -0.2415 0.5615 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 6.9530 -0.9105 -1.1025 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 4.9578 0.7259 0.5137 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 4.9985 0.9430 -1.3033 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.7171 0.7264 -2.4494 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.3994 0.2339 -2.6810 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1.1342 -1.4171 -2.5076 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -0.7632 -1.3370 -1.0391 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.7845 -1.4394 -0.1311 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.0125 0.1989 1.0673 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -1.6672 1.8215 0.2925 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -1.8705 0.7271 -1.1337 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -2.3045 0.3159 1.8590 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -2.1980 -1.1367 0.7635 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -4.1513 -1.9468 -0.2114 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -6.6138 -1.7460 -0.4718 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -7.0727 0.4399 -2.0858 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -7.3144 2.1076 -1.4482 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -8.7609 1.1720 -2.1135 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -8.3137 2.4504 0.5729 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -8.6170 1.0817 1.7580 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -9.8244 1.4444 0.4200 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -6.4629 2.0541 1.3719 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -4.0445 2.0563 1.3058 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.3329 1.8224 -1.3991 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.4920 2.3164 0.3160 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.2025 0.3766 0.4766 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.7945 1.8369 -0.3969 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.4404 -4.6964 0.1303 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.3157 -5.0055 2.3587 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 5.4272 -3.7654 2.9380 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 5.5668 -1.5069 1.9380 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1 2 1 0\n"
" 2 3 1 0\n"
" 3 4 1 0\n"
" 4 5 1 0\n"
" 5 6 1 0\n"
" 6 7 1 0\n"
" 7 8 1 0\n"
" 8 9 1 0\n"
" 9 10 1 0\n"
" 10 11 1 0\n"
" 11 12 1 0\n"
" 12 13 1 0\n"
" 13 14 1 0\n"
" 14 15 2 0\n"
" 15 16 1 0\n"
" 16 17 2 0\n"
" 17 18 1 0\n"
" 18 19 1 0\n"
" 18 20 1 0\n"
" 18 21 1 0\n"
" 21 22 2 0\n"
" 21 23 1 0\n"
" 17 24 1 0\n"
" 24 25 2 0\n"
" 11 26 1 0\n"
" 26 27 1 0\n"
" 7 28 2 0\n"
" 28 29 1 0\n"
" 29 30 2 0\n"
" 30 31 1 0\n"
" 31 32 2 0\n"
" 32 33 1 0\n"
" 33 34 2 0\n"
" 34 6 1 0\n"
" 27 8 1 0\n"
" 34 29 1 0\n"
" 25 14 1 0\n"
" 1 35 1 0\n"
" 1 36 1 0\n"
" 1 37 1 0\n"
" 2 38 1 0\n"
" 2 39 1 0\n"
" 4 40 1 0\n"
" 4 41 1 0\n"
" 5 42 1 0\n"
" 5 43 1 0\n"
" 8 44 1 0\n"
" 9 45 1 0\n"
" 9 46 1 0\n"
" 10 47 1 0\n"
" 10 48 1 0\n"
" 11 49 1 0\n"
" 12 50 1 0\n"
" 12 51 1 0\n"
" 13 52 1 0\n"
" 13 53 1 0\n"
" 15 54 1 0\n"
" 16 55 1 0\n"
" 19 56 1 0\n"
" 19 57 1 0\n"
" 19 58 1 0\n"
" 20 59 1 0\n"
" 20 60 1 0\n"
" 20 61 1 0\n"
" 24 62 1 0\n"
" 25 63 1 0\n"
" 26 64 1 0\n"
" 26 65 1 0\n"
" 27 66 1 0\n"
" 27 67 1 0\n"
" 30 68 1 0\n"
" 31 69 1 0\n"
" 32 70 1 0\n"
" 33 71 1 0\n"
"M CHG 2 11 1 23 -1\n"
"M END\n";
RWMol *mol = MolBlockToMol(molBlock, true, false);
const unsigned int everySteps = 10;
const unsigned int maxIts = 1000;
double gradTol = 0.01;
std::string rdbase = getenv("RDBASE");
std::string fName =
rdbase + "/Code/GraphMol/test_data/bilastine_trajectory.sdf";
SDWriter w(fName);
ForceFields::ForceField *field = MMFF::constructForceField(*mol);
field->initialize();
auto *sv = new SnapshotVect;
int res = field->minimize(everySteps, sv, maxIts, gradTol);
TEST_ASSERT(res == 0);
Trajectory traj(3, mol->getNumAtoms(), sv);
mol->removeConformer(0);
traj.addConformersToMol(*mol);
for (unsigned int nConf = 0; nConf < mol->getNumConformers(); ++nConf) {
std::stringstream ss;
ss << std::fixed << std::setprecision(4)
<< traj.getSnapshot(nConf).getEnergy();
mol->setProp("ENERGY", ss.str(), false);
w.write(*mol, nConf);
}
w.close();
traj.clear();
unsigned int n1 = mol->getNumConformers();
traj.addConformersToMol(*mol);
unsigned int n2 = mol->getNumConformers();
TEST_ASSERT(n1 == n2);
// getSnapshot should raise exception after Clear()
bool ok = false;
try {
traj.getSnapshot(0);
} catch (Invar::Invariant &e) {
BOOST_LOG(rdErrorLog) << e.what() << std::endl;
ok = true;
}
TEST_ASSERT(ok);
delete field;
delete mol;
}
void testAddConformersFromAmberTrajectory() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "testAddConformersFromAmberTrajectory" << std::endl;
ROMol *mol = SmilesToMol("CCC");
std::string rdbase = getenv("RDBASE");
std::string fName = rdbase + "/Code/GraphMol/test_data/water_coords.trx";
{
Trajectory traj(3, mol->getNumAtoms());
readAmberTrajectory(fName, traj);
TEST_ASSERT(traj.size() == 1);
for (unsigned int i = 0; i < 2; ++i) {
traj.addConformersToMol(*mol);
TEST_ASSERT(mol->getNumConformers() == i + 1);
TEST_ASSERT(mol->getConformer(i).getNumAtoms() == 3);
TEST_ASSERT(RDKit::feq(mol->getConformer(i).getAtomPos(0).x, 0.1941767));
TEST_ASSERT(RDKit::feq(mol->getConformer(i).getAtomPos(2).z, -0.4088006));
}
mol->clearConformers();
bool e = false;
try {
traj.addConformersToMol(*mol, 1);
} catch (...) {
e = true;
}
TEST_ASSERT(e);
TEST_ASSERT(mol->getNumConformers() == 0);
}
fName = rdbase + "/Code/GraphMol/test_data/water_coords2.trx";
{
Trajectory traj(3, mol->getNumAtoms());
readAmberTrajectory(fName, traj);
TEST_ASSERT(traj.size() == 2);
traj.addConformersToMol(*mol);
TEST_ASSERT(mol->getNumConformers() == 2);
mol->clearConformers();
traj.addConformersToMol(*mol, 0, 0);
TEST_ASSERT(mol->getNumConformers() == 1);
traj.addConformersToMol(*mol, 1);
TEST_ASSERT(mol->getNumConformers() == 2);
}
delete mol;
BOOST_LOG(rdErrorLog) << "done" << std::endl;
}
void testAddConformersFromGromosTrajectory() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "testAddConformersFromGromosTrajectory" << std::endl;
ROMol *mol = SmilesToMol("CCC");
std::string rdbase = getenv("RDBASE");
std::string fName = rdbase + "/Code/GraphMol/test_data/water_coords.trc";
{
Trajectory traj(3, mol->getNumAtoms());
readGromosTrajectory(fName, traj);
TEST_ASSERT(traj.size() == 1);
for (unsigned int i = 0; i < 2; ++i) {
traj.addConformersToMol(*mol);
TEST_ASSERT(mol->getNumConformers() == i + 1);
TEST_ASSERT(mol->getConformer(i).getNumAtoms() == 3);
TEST_ASSERT(RDKit::feq(mol->getConformer(i).getAtomPos(0).x, 1.941767));
TEST_ASSERT(RDKit::feq(mol->getConformer(i).getAtomPos(2).z, -4.088006));
}
mol->clearConformers();
bool e = false;
try {
traj.addConformersToMol(*mol, 1);
} catch (...) {
e = true;
}
TEST_ASSERT(e);
TEST_ASSERT(mol->getNumConformers() == 0);
}
fName = rdbase + "/Code/GraphMol/test_data/water_coords2.trc";
{
Trajectory traj(3, mol->getNumAtoms());
readGromosTrajectory(fName, traj);
TEST_ASSERT(traj.size() == 2);
traj.addConformersToMol(*mol);
TEST_ASSERT(mol->getNumConformers() == 2);
mol->clearConformers();
traj.addConformersToMol(*mol, 0, 0);
TEST_ASSERT(mol->getNumConformers() == 1);
mol->clearConformers();
traj.addConformersToMol(*mol, 1);
TEST_ASSERT(mol->getNumConformers() == 1);
}
delete mol;
BOOST_LOG(rdErrorLog) << "done" << std::endl;
}
int main() {
BOOST_LOG(rdErrorLog)
<< "***********************************************************\n";
BOOST_LOG(rdErrorLog) << "Testing Trajectory\n";
testSnapshot();
testTrajectory2D();
testTrajectory3D();
testReadAmber();
testReadGromos();
testAddConformersFromTrajectory();
testAddConformersFromAmberTrajectory();
testAddConformersFromGromosTrajectory();
return 0;
}
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