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|
// $Id$
//
// Copyright (C) 2004-2010 Greg Landrum and Rational Discovery LLC
//
// @@ 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/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <GraphMol/RDKitBase.h>
#include <string>
#include <iostream>
#include <GraphMol/FileParsers/MolWriters.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <RDGeneral/FileParseException.h>
#include "RDDepictor.h"
#include "DepictUtils.h"
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <GraphMol/ChemTransforms/ChemTransforms.h>
#include <GraphMol/Conformer.h>
#include <Geometry/point.h>
#include <Geometry/Transform3D.h>
#include <RDGeneral/utils.h>
#include <stdlib.h>
#include <boost/tokenizer.hpp>
typedef boost::tokenizer<boost::char_separator<char> > tokenizer;
using namespace RDKit;
void test1() {
// std::string smiString = "OCC(F)(F)C(F)(F)C(F)(F)C(F)F";
std::string smiString =
"CN([CH](Cc3ccc(OS(c2cccc1c2ccnc1)(=O)=O)cc3)C(=O)N5CCN(c4ccccc4)CC5)S(c7cccc6c7ccnc6)(=O)=O \
C[n](n1)ccc1NC(=O)C(/C#N)=C/c2[s]cc(c2)Br O=C2C1CC3CC(C1)CC2C3 \
c8cc9cc3c5c(c(=O)cc4n1nc6c2c(ccc(c12)c(cc3)c45)cc7c6cc(=O)cc7)c9cc8 \
c1cccc(c1)CCCCNC(=O)C(/C#N)=C/c2ccc(O)c(c2)O \
COc(cc1)ccc1C(=C2)C=C(NC2=C)c3ccc(OC)cc3O \
CC(OC1C(CCCC3)C3C(CCCC2)C2C1OC(C)=O)=O \
Cl.C[N+](C)(C)CCO O=C2C1CC3CC(C1)CC2C3 \
CN3CCC25[CH]4CCC(=O)C5(C)Oc1c(O)ccc(c12)C[CH]34 \
c1ccccc1\\C=C/C=C\\Cl.c1ccccc1C=C(Cl)C1SCCC1.Cl\\C=C1/SCCC1 Cl\\C=C/Br \
c1ccccc1\\C=C/C=C\\C=C/Cl c1ccccc1C=C(Cl)C1SCCC1 Cl\\C=C1/SCCC1 Cl\\C=C/Br \
CN2C3CC(OC(=O)C(CO)c1ccccc1)CC2CC3 \
N2C3CC(OC(=O)C(CO)c1ccccc1)CC2CC3 \
C2C3CC(OC(=O)C(CO)c1ccccc1)CC2CC3 \
ClC=C1SCCC1 C/C=C/C(C1CCCCCC1)=O c1ccccc1\\C=C/C=C\\C=C/Cl \
C[n](n1)ccc1NC(=O)C(/C#N)=C/c2[s]cc(c2)Br \
C1CC(C(Cl)(Br)F)CC1 \
C1(C2)CCC2C=C1 \
OC2C1(C)CCCCC1CCC2 \
CC12CCCC3OC1CCCC23 \
CC(OC1C(CCCC3)C3C(CCCC2)C2C1OC(C)=O)=O \
ON=C(CC1=CC=CC=C1)[CH](C#N)C2=CC=CC=C2 \
COc(cc1)ccc1C(=C2/C#N)\\C=C(NC2=C(C#N)C#N)\\c3ccc(OC)cc3O \
COc(cc1)ccc1C(=C2)C=C(NC2=C)c3ccc(OC)cc3O";
/*C1=CC=CC=C1CCCC2=CC(C=CC=C3)=C3C=C2 C/C=C/C(C1CCCCCC1)=O
C/C=C/C(C1CCCCCC1)=O.c1ccccc1CC(Cl)=O \
[I-].CCC[N+](C)(CCC)CCC C1COCCN2CCOCCN(CCO1)CCOCCOCC2 C1CN2CCN1CC2 \
C(CCCCCCC)(=O)CCCCCC \
ClCCCCCCCCCCCCCCCCCCCCCCCCCCCC(=O)CCCCCCCCCCCCCCCCCCCCCCCCCCF \
C(CCCCCCC)(=O)CCCCCC \
C/C=C/C(C1CCCCCC1)=O C1CC(CC12)C=C2 c1ccccc1\\C=C(Cl)/C#N
N#C\\C=C(Cl)/Cc1ccccc1 \
CN(C)c(cc1)ccc1\\C=C(/C#N)c(n2)c(C#N)c([n]3cccc3)[n]2c(c4)cccc4 \
CCOC(=O)CN1C(=O)/C=C(/C)c(c12)c(C)n[n]2C
C/12=C\\C(=O)c3cc(OC(F)(F)F)ccc3N2C(=O)/C(CC(=O)OC)=C\\1C(=O)OCC \
C/12=C(\\NC(N2)=O)NC(=O)NC1=O F\\C=C/Cl F/C=C/Cl c1ccccc1\\C=C/C
c1ccccc1\\C=C\\C=C\\C=C\\Cl \
c1ccccc1\\C=C/C=C\\C=C/Cl c1ccccc1\\C=C\\C=C(O)\\C=C(Br)\\Cl \
c1ccccc1\\C=C/C=C(O)\\C=C(Br)/Cl \
CC#CCC O=C=O C1=CC=CC=C1 C1CCC1 C1CC1(C#CC) C1CCCCCCC1 C1=CC=CC=C1(CCCCCCC) \
C1=CC=CC=C1(CC(CCC)CCC(C)(C)C) \
C1=CC=CC=C1CCCC2=CC(C=CC=C3)=C3C=C2 \
C1=CC=CC=C1(CC(CCC)CCC(CCC)(CCC)C) \
C1=CC(C=CC=C2)=C2C=C1 C1=CC(C=C2)=C2C=C1 \
C1=CC(CCC2)=C2C=C1 C1(CCC3)CCCC2C1C3CCC2 \
C12=CC=C3C(C4=C(C=CC=C5)C5=C3)C1C(C=C4)=CC=C2 \
C12CCCC3(CCCCC3)C1CCCC2 \
C1CCCC2(CC2)C1 C12C3C4C1C5C2C3C45 \
C2(C=C(C=C5)NC5=C4)=CC(C=C2)=CC1=CC=C(C=C3C=CC4=N3)N1";
*/
std::string rdbase = getenv("RDBASE");
std::string ofile =
rdbase + "/Code/GraphMol/Depictor/test_data/test1.out.sdf";
SDWriter writer(ofile);
boost::char_separator<char> spaceSep(" ");
tokenizer tokens(smiString, spaceSep);
for (tokenizer::iterator token = tokens.begin(); token != tokens.end();
++token) {
std::string smi = *token;
RWMol *m = SmilesToMol(smi, 0, 1);
TEST_ASSERT(m)
RDDepict::compute2DCoords(*m);
writer.write(*m);
delete m;
}
}
void testCollisions() {
std::string smiString =
"CN([CH](Cc3ccc(OS(c2cccc1c2ccnc1)(=O)=O)cc3)C(=O)N5CCN(c4ccccc4)CC5)S(c7cccc6c7ccnc6)(=O)=O \
CC(C)C12CCC(C)(CC1)CC2 \
CC(C)C1CCC2(CC)CCCC1CCC2 \
CC(OC1C(CCCC3)C3C(CCCC2)C2C1OC(C)=O)=O \
OC(=O)C1=C(C=CC=C1)C2=C3C=CC(=O)C(=C3OC4=C2C=CC(=C4Br)O)Br \
CC(CC(=O)OCC(F)(F)C(F)(F)C(F)(F)C(F)F)CC(=O)OCC(F)(F)C(F)(F)C(F)(F)C(F)F \
CC(=O)Nc1ccccc1C(=O)C1CCCC1C1CCCCC1 \
Cc1ccc(C(c2ccc(C)o2)c2ccccc2[N+](=O)[O-])o1 \
CN2C3CC(OC(=O)C(CO)c1ccccc1)CC2CC3";
// this used to be a test, but it's currently failing catastrophically:
// CC(C)(C)O[Si](OCC(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)F)(OCC(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)F)OC(C)(C)C
std::string rdbase = getenv("RDBASE");
std::string ofile =
rdbase + "/Code/GraphMol/Depictor/test_data/collisions.out.sdf";
SDWriter writer(ofile);
boost::char_separator<char> spaceSep(" ");
tokenizer tokens(smiString, spaceSep);
for (tokenizer::iterator token = tokens.begin(); token != tokens.end();
++token) {
std::string smi = *token;
RWMol *m = SmilesToMol(smi, 0, 1);
TEST_ASSERT(m);
unsigned int confId = RDDepict::compute2DCoords(*m);
// check that there are no collisions in the molecules
const Conformer &conf = m->getConformer(confId);
int natms = m->getNumAtoms();
for (int i = 0; i < natms; i++) {
RDGeom::Point3D loci = conf.getAtomPos(i);
for (int j = i + 1; j < natms; j++) {
RDGeom::Point3D locj = conf.getAtomPos(j);
locj -= loci;
CHECK_INVARIANT(locj.length() > 0.35, "");
}
}
writer.write(*m);
delete m;
}
}
void testAddHs() {
// test for issue 193
std::string smi = "F[C@H](Cl)Br";
RWMol *m = SmilesToMol(smi, 0, 1);
MolOps::addHs(*m);
RDDepict::compute2DCoords(*m);
delete m;
}
void testIssue198() {
std::string smi = "Cl.C[N+](C)(C)CCO";
RWMol *m = SmilesToMol(smi, 0, 1);
unsigned int confId = RDDepict::compute2DCoords(*m);
RDKit::ROMol::AtomIterator ai;
const Conformer &conf = m->getConformer(confId);
for (ai = m->beginAtoms(); ai != m->endAtoms(); ai++) {
RDGeom::Point3D loc = conf.getAtomPos((*ai)->getIdx());
CHECK_INVARIANT(loc.x < 100.0, "");
CHECK_INVARIANT(loc.y < 100.0, "");
CHECK_INVARIANT(loc.z < 100.0, "");
}
delete m;
}
void test2() {
std::string rdbase = getenv("RDBASE");
std::string smifile =
rdbase + "/Code/GraphMol/Depictor/test_data/first_200.tpsa.csv";
SmilesMolSupplier smiSup(smifile, ",", 0, -1);
std::string ofile =
rdbase + "/Code/GraphMol/Depictor/test_data/first_200.out.sdf";
SDWriter writer(ofile);
ROMol *mol;
while (1) {
try {
mol = smiSup.next();
std::string mname;
// wmol = static_cast<RWMol *>(mol);
RDDepict::compute2DCoords(*mol);
writer.write(*mol);
} catch (FileParseException &) {
break;
}
}
}
void test3() {
std::string rdbase = getenv("RDBASE");
std::string smifile =
rdbase + "/Code/GraphMol/Depictor/test_data/cis_trans_cases.csv";
SmilesMolSupplier smiSup(smifile, ",", 0, 1);
std::string ofile =
rdbase + "/Code/GraphMol/Depictor/test_data/cis_trans_cpp.out.sdf";
SDWriter writer(ofile);
ROMol *mol;
while (1) {
try {
mol = smiSup.next();
std::string mname;
// wmol = static_cast<RWMol *>(mol);
RDDepict::compute2DCoords(*mol);
writer.write(*mol);
} catch (FileParseException &) {
break;
}
}
}
void _compareCoords(const ROMol *mol1, unsigned int cid1, const ROMol *mol2,
unsigned int cid2, double tol = 0.01) {
unsigned int nat = mol1->getNumAtoms();
CHECK_INVARIANT(nat == mol2->getNumAtoms(), "");
const RDKit::Conformer &conf1 = mol1->getConformer(cid1);
const RDKit::Conformer &conf2 = mol1->getConformer(cid2);
for (unsigned int i = 0; i < nat; i++) {
RDGeom::Point3D pt1 = conf1.getAtomPos(i);
RDGeom::Point3D pt2 = conf2.getAtomPos(i);
pt2 -= pt1;
CHECK_INVARIANT(fabs(pt2.x) < tol, "");
CHECK_INVARIANT(fabs(pt2.y) < tol, "");
// if ((fabs(pt2.x) >= tol) || (fabs(pt2.y) >= tol) ) {
// BOOST_LOG(rdInfoLog)<< pt1 << " " << pt2 << "\n";
//}
}
}
void test4() {
// test prespecified coordinates for various smiles
RDGeom::INT_POINT2D_MAP crdMap;
crdMap[0] = RDGeom::Point2D(3.52, 1.30);
crdMap[1] = RDGeom::Point2D(2.77, 0.0);
crdMap[2] = RDGeom::Point2D(1.27, 0.0);
crdMap[3] = RDGeom::Point2D(0.39, 1.21);
crdMap[4] = RDGeom::Point2D(-1.03, 0.75);
crdMap[5] = RDGeom::Point2D(-1.03, -0.75);
crdMap[6] = RDGeom::Point2D(0.39, -1.21);
// self check
std::string smi = "Cl\\C=C1/SCCC1";
RWMol *m1 = SmilesToMol(smi, 0, 1);
unsigned int cid1 = RDDepict::compute2DCoords(*m1, &crdMap, false);
RWMol *mref = SmilesToMol(smi, 0, 1);
unsigned int cid2 = RDDepict::compute2DCoords(*mref);
MolToMolFile(*mref, "junk.mol");
//_compareCoords(m1, mref);
delete m1;
// now lets remove some of the coordinates
crdMap.erase(crdMap.find(3));
crdMap.erase(crdMap.find(4));
m1 = SmilesToMol(smi, 0, 1);
cid1 = RDDepict::compute2DCoords(*m1, &crdMap, false);
// MolToMolFile(m1, "junk.mol");
//_compareCoords(m1, mref);
delete m1;
// little bit more complicated
smi = "Cl\\C=C1/SCCC1(CC1CC1)";
m1 = SmilesToMol(smi, 0, 1);
cid1 = RDDepict::compute2DCoords(*m1, &crdMap, false);
// MolToMolFile(m1, "junk1.mol");
delete mref;
mref = SmilesToMol(smi, 0, 1);
RDDepict::compute2DCoords(*mref, 0, false);
_compareCoords(m1, cid1, mref, cid2);
delete m1;
// little more complicate we will specify coordinates from half of both the
// rings
crdMap[7] = RDGeom::Point2D(0.85, -2.64);
crdMap[8] = RDGeom::Point2D(-0.15, -3.75);
crdMap[9] = RDGeom::Point2D(-0.46, -5.22);
m1 = SmilesToMol(smi, 0, 1);
cid1 = RDDepict::compute2DCoords(*m1, &crdMap, false);
// MolToMolFile(m1, "junk1.mol");
// MolToMolFile(mref, "junk2.mol");
_compareCoords(m1, cid1, mref, cid2);
delete m1;
// one final test for a case we know is a pain
smi = "C1CCCC2(Cl)(CCCCCC12)";
crdMap.clear();
crdMap[0] = RDGeom::Point2D(-0.83, -3.12);
crdMap[1] = RDGeom::Point2D(0.19, -4.22);
crdMap[2] = RDGeom::Point2D(1.66, -3.88);
crdMap[3] = RDGeom::Point2D(2.10, -2.45);
crdMap[4] = RDGeom::Point2D(1.08, -1.35);
crdMap[5] = RDGeom::Point2D(2.56, -1.12);
crdMap[6] = RDGeom::Point2D(1.73, 0.00);
crdMap[7] = RDGeom::Point2D(1.08, 1.35);
crdMap[8] = RDGeom::Point2D(-0.38, 1.69);
crdMap[9] = RDGeom::Point2D(-1.56, 0.75);
crdMap[10] = RDGeom::Point2D(-1.56, -0.75);
crdMap[11] = RDGeom::Point2D(-0.38, -1.69);
delete mref;
mref = SmilesToMol(smi, 0, 1);
cid2 = RDDepict::compute2DCoords(*mref, 0, false);
crdMap.erase(crdMap.find(5));
// MolToMolFile(mref, "junk1.mol");
m1 = SmilesToMol(smi, 0, 1);
cid1 = RDDepict::compute2DCoords(*m1, &crdMap, false);
_compareCoords(m1, cid1, mref, cid2);
delete m1;
delete mref;
}
void tempTest() {
int i;
RDGeom::Point3D pt1, pt2, pt3;
double cosT, sinT;
RDGeom::Transform3D trans;
RDGeom::Point3D rotnAxis;
double dt;
for (i = 0; i < 100; i++) {
pt1.x = (double)(rand() % 1000);
pt1.y = (double)(rand() % 1000);
pt1.z = (double)(rand() % 1000);
pt1.normalize();
pt2.x = (double)(rand() % 1000);
pt2.y = (double)(rand() % 1000);
pt2.z = (double)(rand() % 1000);
pt2.normalize();
cosT = -pt1.dotProduct(pt2);
sinT = sqrt(1.0 - cosT * cosT);
rotnAxis = pt1.crossProduct(pt2);
rotnAxis.normalize();
trans.setToIdentity();
trans.SetRotation(cosT, sinT, rotnAxis);
pt3 = pt2;
trans.TransformPoint(pt3);
dt = pt1.dotProduct(pt3);
if (fabs(dt + 1.0) > 1.0e-3) {
BOOST_LOG(rdInfoLog) << i << " (" << pt1 << ") (" << pt2 << ") (" << pt3
<< ") (" << rotnAxis << ") " << dt << "\n";
}
}
}
void testIssue248() {
std::string smiString =
"OCC(=O)C1(O)[CH](O)C[CH]2[CH]3CCC4=CC(=O)C=CC4(C)C3(F)[CH](O)CC21C \
CC(C)[CH](OC(C)=O)c1nc2ccccc2c(=O)n1[CH]1CC2(OC1=O)c1c(cccc1)N1C(=O)C(C)(C)N(O)[CH]12 \
CC(CC(=O)OCC(F)(F)C(F)(F)C(F)(F)C(F)F)CC(=O)OCC(F)(F)C(F)(F)C(F)(F)C(F)F \
CC(O[CH]1C(=O)C2(C)[CH](O)C[CH]3OCC3(OC(C)=O)[CH]2[CH](OC(=O)c2ccccc2)C2(O)C[CH](OC([CH](O)[CH](NC(=O)c3ccccc3)c3ccccc3)=O)C(C)=C1C2(C)C)=O \
COc1c2O[CH]3[CH](O)C=C[CH]4C33CCN(C)[CH]4Cc(c32)cc1 \
CN1CCC23[CH]4Oc5c(O)ccc(c25)C[CH]1[CH]3C=C[CH]4O \
CN1C2CCC1C[CH](OC(=O)C(CO)c1ccccc1)C2 \
COC([CH]1C2CCC(C[CH]1OC(c1ccccc1)=O)N2C)=O \
OCC(=O)C1(O)[CH](O)C[CH]2[CH]3CCC4=CC(=O)C=CC4(C)C3(F)[CH](O)CC21C";
// COC12C3Oc4c(O)ccc5c4C33CCN(CC4CC4)[CH](C5)C3(C[CH]1C(O)(C)C(C)(C)C)CC2";
boost::char_separator<char> spaceSep(" ");
tokenizer tokens(smiString, spaceSep);
for (tokenizer::iterator token = tokens.begin(); token != tokens.end();
++token) {
std::string smi = *token;
RWMol *m = SmilesToMol(smi, 0, 1);
unsigned int confId = RDDepict::compute2DCoords(*m);
// check that there are no collisions in the molecules
int natms = m->getNumAtoms();
int i, j;
for (i = 0; i < natms; i++) {
const Conformer &conf = m->getConformer(confId);
RDGeom::Point3D loci = conf.getAtomPos(i);
for (j = i + 1; j < natms; j++) {
RDGeom::Point3D locj = conf.getAtomPos(j);
locj -= loci;
if (locj.length() <= 0.30) {
std::cout << "mismatch: " << i << " " << j << " " << locj.length()
<< std::endl;
std::cout << "\t" << smi << std::endl;
std::cout << MolToMolBlock(*m, true, confId) << std::endl;
}
CHECK_INVARIANT(locj.length() > 0.30, "");
}
}
delete m;
}
}
void testQueries() {
std::string smaString = "C[C,N] c1cc[c,n]cc1C";
boost::char_separator<char> spaceSep(" ");
tokenizer tokens(smaString, spaceSep);
for (tokenizer::iterator token = tokens.begin(); token != tokens.end();
++token) {
std::string sma = *token;
RWMol *m = SmartsToMol(sma);
unsigned int confId = RDDepict::compute2DCoords(*m);
// check that there are no collisions in the molecules
int natms = m->getNumAtoms();
int i, j;
for (i = 0; i < natms; i++) {
const Conformer &conf = m->getConformer(confId);
RDGeom::Point3D loci = conf.getAtomPos(i);
for (j = i + 1; j < natms; j++) {
RDGeom::Point3D locj = conf.getAtomPos(j);
locj -= loci;
if (locj.length() <= 0.30) {
std::cout << "mismatch: " << i << " " << j << " " << locj.length()
<< std::endl;
std::cout << "\t" << sma << std::endl;
std::cout << MolToMolBlock(*m, true, confId) << std::endl;
}
CHECK_INVARIANT(locj.length() > 0.30, "");
}
}
delete m;
}
}
void testRemoveHsCrash() {
std::string rdbase = getenv("RDBASE");
std::string molfile =
rdbase + "/Code/GraphMol/Depictor/test_data/hs_crash.mol";
RWMol *m = MolFileToMol(molfile, true, false);
TEST_ASSERT(m);
ROMol *newM = MolOps::removeHs(*static_cast<ROMol *>(m));
delete m;
RDDepict::compute2DCoords(*newM);
delete newM;
}
void testIssue2091304() {
// the problem here was a crash, so just finishing is success.
RDGeom::INT_POINT2D_MAP crdMap;
crdMap[0] = RDGeom::Point2D(0., 1.50);
std::string smi = "COC";
RWMol *m1 = SmilesToMol(smi);
RDDepict::compute2DCoords(*m1, &crdMap, false);
delete m1;
}
void testIssue2303566() {
RDGeom::INT_POINT2D_MAP crdMap;
crdMap[0] = RDGeom::Point2D(0.0781827, -0.112109);
crdMap[1] = RDGeom::Point2D(1.13205, -0.415657);
crdMap[2] = RDGeom::Point2D(0.676323, -1.51974);
crdMap[3] = RDGeom::Point2D(0.735363, -2.62024);
crdMap[4] = RDGeom::Point2D(0.974216, -1.5726);
crdMap[5] = RDGeom::Point2D(1.02041, -1.56945);
std::string mb =
"\n\
RDKit 2D\n\
\n\
6 7 0 0 0 0 0 0 0 0999 V2000\n\
0.0782 -0.1121 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
1.1321 -0.4157 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
0.6763 -1.5197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
0.7354 -2.6202 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
1.0098 -1.5757 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n\
1.0218 -1.5749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
1 2 1 0\n\
1 3 1 0\n\
3 2 1 0\n\
3 4 1 0\n\
5 6 2 0\n\
2 4 1 0\n\
1 4 1 0\n\
M END\n";
RWMol *m1 = MolBlockToMol(mb);
// in the original bug, this led to a crash, so just having it complete
// means the test passed.
unsigned int cid1 = RDDepict::compute2DCoords(*m1, &crdMap, false);
(void)cid1;
// TEST_ASSERT(cid1>=0);
delete m1;
}
void testIssue2821647() {
{
std::string smi = "CCCCC";
RWMol *m1 = SmilesToMol(smi);
unsigned int cid1 = RDDepict::compute2DCoords(*m1, 0, true);
double xx = 0, yy = 0;
for (unsigned int i = 0; i < m1->getNumAtoms(); i++) {
const Conformer &conf = m1->getConformer(cid1);
RDGeom::Point3D loci = conf.getAtomPos(i);
xx += loci.x * loci.x;
yy += loci.y * loci.y;
}
TEST_ASSERT(xx > yy);
delete m1;
}
{
std::string smi = "c1ccccc1CCCCCC1CC1";
RWMol *m1 = SmilesToMol(smi);
unsigned int cid1 = RDDepict::compute2DCoords(*m1, 0, true);
double xx = 0, yy = 0;
for (unsigned int i = 0; i < m1->getNumAtoms(); i++) {
const Conformer &conf = m1->getConformer(cid1);
RDGeom::Point3D loci = conf.getAtomPos(i);
xx += loci.x * loci.x;
yy += loci.y * loci.y;
}
TEST_ASSERT(xx > yy);
delete m1;
}
{
std::string smi = "c1ccc2c(c1)oc1c3ccccc3oc21";
RWMol *m1 = SmilesToMol(smi);
unsigned int cid1 = RDDepict::compute2DCoords(*m1, 0, true);
double xx = 0, yy = 0;
for (unsigned int i = 0; i < m1->getNumAtoms(); i++) {
const Conformer &conf = m1->getConformer(cid1);
RDGeom::Point3D loci = conf.getAtomPos(i);
xx += loci.x * loci.x;
yy += loci.y * loci.y;
}
TEST_ASSERT(xx > yy);
delete m1;
}
{
std::string smi = "[H]n1c2ccccc2c2n([H])c3ccccc3c12";
RWMol *m1 = SmilesToMol(smi);
unsigned int cid1 = RDDepict::compute2DCoords(*m1, 0, true);
double xx = 0, yy = 0;
for (unsigned int i = 0; i < m1->getNumAtoms(); i++) {
const Conformer &conf = m1->getConformer(cid1);
RDGeom::Point3D loci = conf.getAtomPos(i);
xx += loci.x * loci.x;
yy += loci.y * loci.y;
}
TEST_ASSERT(xx > yy);
delete m1;
}
}
void testIssue2948402() {
{
std::string smi = "C1C2CC3=CC=CC(C2)CC(O3)C1";
RWMol *m1 = SmilesToMol(smi);
unsigned int cid1 = RDDepict::compute2DCoords(*m1, 0, true);
(void)cid1;
// TEST_ASSERT(cid1>=0);
delete m1;
}
}
void testIssue2995724() {
{
// the original problem from Thomas Heller:
std::string smi = "OC(=O)[C@@H]1CCCN1";
RWMol *m1 = SmilesToMol(smi);
unsigned int cid1 = RDDepict::compute2DCoords(*m1, 0, true);
const Conformer &conf = m1->getConformer(cid1);
for (unsigned int i = 0; i < m1->getNumAtoms(); i++) {
RDGeom::Point3D loci = conf.getAtomPos(i);
// we're testing for NaNs here:
TEST_ASSERT(loci.x > -5.0);
TEST_ASSERT(loci.x < 5.0);
TEST_ASSERT(loci.y > -5.0);
TEST_ASSERT(loci.y < 5.0);
}
delete m1;
}
{
// additional test cases from Kirk DeLisle:
std::string smis[] = {"CCC(N1CCN(CC1)C(CC)O)O.Cl[Pt](Cl)(Cl)(Cl)(Cl)Cl",
"CN(C)S(=O)(=O)N1CCN(CC1)S(=O)(=O)N(C)C",
"Cc1ccc(cc1C)Nc2nc(nc(n2)N)CN3CCN(CC3)C",
"CC1(OC(=C(C(=O)O1)C2=NCCC2)O)C"};
for (unsigned int j = 0; j < 4; j++) {
RWMol *m1 = SmilesToMol(smis[j]);
unsigned int cid1 = RDDepict::compute2DCoords(*m1, 0, true);
const Conformer &conf = m1->getConformer(cid1);
for (unsigned int i = 0; i < m1->getNumAtoms(); i++) {
RDGeom::Point3D loci = conf.getAtomPos(i);
TEST_ASSERT(loci.x > -7.0);
TEST_ASSERT(loci.x < 7.0);
TEST_ASSERT(loci.y > -6.0);
TEST_ASSERT(loci.y < 6.0);
}
delete m1;
}
}
}
void testBondLengthChange() {
{
std::string smi = "CC";
RWMol *m1 = SmilesToMol(smi);
unsigned int cid1 = RDDepict::compute2DCoords(*m1, 0, true);
const Conformer &conf = m1->getConformer(cid1);
TEST_ASSERT(feq(conf.getAtomPos(0).x, -0.75));
TEST_ASSERT(feq(conf.getAtomPos(1).x, 0.75));
delete m1;
}
{
std::string smi = "CC";
RWMol *m1 = SmilesToMol(smi);
RDDepict::BOND_LEN = 1.0;
unsigned int cid1 = RDDepict::compute2DCoords(*m1, 0, true);
const Conformer &conf = m1->getConformer(cid1);
TEST_ASSERT(feq(conf.getAtomPos(0).x, -0.5));
TEST_ASSERT(feq(conf.getAtomPos(1).x, 0.5));
delete m1;
}
}
void testIssue3122141() {
{
std::string smi = "ClC1=C(Cl)C2(Cl)C3C(Cl)C=CC3C1(Cl)C2(Cl)Cl";
RWMol *m1 = SmilesToMol(smi);
RDGeom::INT_POINT2D_MAP crdMap;
crdMap[1] = RDGeom::Point2D(1.0, 2.0);
unsigned int cid1 = RDDepict::compute2DCoords(*m1, &crdMap, false);
(void)cid1;
// TEST_ASSERT(cid1>=0);
delete m1;
}
}
void testIssue3135833() {
{
std::string smi =
"N#CC(/C=[N+](/c1cccnc1)c1c2cc(C(=O)c3ncsc3-c3cccnc3)ccc2ccc1)=C(/"
"[NH3+])[S-]";
RWMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
RDGeom::INT_POINT2D_MAP crdMap;
crdMap[32] = RDGeom::Point2D(-2.8518, 1.0270);
crdMap[33] = RDGeom::Point2D(-2.7999, -0.4721);
crdMap[4] = RDGeom::Point2D(-1.4239, -2.6758);
crdMap[11] = RDGeom::Point2D(-1.4757, -1.1767);
crdMap[12] = RDGeom::Point2D(-0.2034, -0.3823);
crdMap[13] = RDGeom::Point2D(1.1208, -1.0869);
crdMap[14] = RDGeom::Point2D(2.3931, -0.2924);
crdMap[15] = RDGeom::Point2D(3.7173, -0.9971);
crdMap[28] = RDGeom::Point2D(2.3412, 1.2067);
crdMap[29] = RDGeom::Point2D(1.0170, 1.9113);
crdMap[30] = RDGeom::Point2D(-0.2553, 1.1168);
crdMap[31] = RDGeom::Point2D(-1.5795, 1.8215);
unsigned int cid1 = RDDepict::compute2DCoords(*m1, &crdMap, false);
(void)cid1;
// TEST_ASSERT(cid1>=0);
delete m1;
}
}
void testIssue3487469() {
{
std::string smi = "C*C";
RWMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
TEST_ASSERT(m1->getAtomWithIdx(1)->getHybridization() == Atom::UNSPECIFIED);
unsigned int cid1 = RDDepict::compute2DCoords(*m1, 0, true);
const Conformer &conf = m1->getConformer(cid1);
RDGeom::Point3D p0 = conf.getAtomPos(0);
RDGeom::Point3D p1 = conf.getAtomPos(1);
RDGeom::Point3D p2 = conf.getAtomPos(2);
RDGeom::Point3D v1 = p0 - p1, v2 = p2 - p1;
v1.normalize();
v2.normalize();
TEST_ASSERT(feq(v1.dotProduct(v2), -0.5, .01))
delete m1;
}
}
void testGitHubIssue8() {
{
std::string smi = "[I-].C[n+]1c(\\C=C\\2/C=CC=CN2CC=C)sc3ccccc13";
RWMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
RWMol *p = SmilesToMol("[I-]");
TEST_ASSERT(p);
ROMol *m2 = deleteSubstructs(*m1, *p);
TEST_ASSERT(m2);
TEST_ASSERT(m2->getNumAtoms() == m1->getNumAtoms() - 1);
unsigned int cid1 = RDDepict::compute2DCoords(*m2);
TEST_ASSERT(cid1 == 0);
delete m1;
delete m2;
delete p;
}
}
void testGitHubIssue78() {
{ // the basic test: the smallest reproducible:
std::string smi = "C3CCCC1C3C(O2)C2CC1";
RWMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
unsigned int cid1 = RDDepict::compute2DCoords(*m1);
const Conformer &conf = m1->getConformer(cid1);
RDGeom::Point3D p5 = conf.getAtomPos(5);
RDGeom::Point3D p6 = conf.getAtomPos(6);
RDGeom::Point3D p7 = conf.getAtomPos(7);
RDGeom::Point3D p8 = conf.getAtomPos(8);
RDGeom::Point3D p9 = conf.getAtomPos(9);
RDGeom::Point3D p87 = p8 - p7;
RDGeom::Point3D p86 = p8 - p6;
RDGeom::Point3D p89 = p8 - p9;
TEST_ASSERT(p87.dotProduct(p86) * p87.dotProduct(p89) < 0);
RDGeom::Point3D p67 = p6 - p7;
RDGeom::Point3D p68 = p6 - p8;
RDGeom::Point3D p65 = p6 - p5;
TEST_ASSERT(p67.dotProduct(p68) * p67.dotProduct(p65) < 0);
delete m1;
}
{ // a collection of previous failures
std::string smis[4] = {"C1=CC=C2C(=C1)C3=CC=CC=C3C4=C2C(C(C5C4O5)O)O",
"CC1=C2C=C(C=CC2=NC3=C1C4=C(O4)C5=CC=CC=C53)CO",
"CC1=C2C=CC3=C(C2=CC4=CC=CC=C14)C5C(O5)C(C3O)O",
"C1=CC=C2C(=C1)C=C3C=CC4=C5C3=C2C6C(C5=CC=C4)O6"};
RWMol *p = SmartsToMol("[#6]~[#6]~1-[#8]-[#6]~1~[#6]");
TEST_ASSERT(p);
for (unsigned int i = 0; i < 4; ++i) {
RWMol *m = SmilesToMol(smis[i]);
TEST_ASSERT(m);
MatchVectType mv;
TEST_ASSERT(SubstructMatch(*m, *p, mv));
TEST_ASSERT(mv.size() == 5);
unsigned int cid1 = RDDepict::compute2DCoords(*m);
const Conformer &conf = m->getConformer(cid1);
RDGeom::Point3D v10 =
conf.getAtomPos(mv[1].second) - conf.getAtomPos(mv[0].second);
RDGeom::Point3D v12 =
conf.getAtomPos(mv[1].second) - conf.getAtomPos(mv[2].second);
RDGeom::Point3D v13 =
conf.getAtomPos(mv[1].second) - conf.getAtomPos(mv[3].second);
TEST_ASSERT(v12.dotProduct(v10) * v12.dotProduct(v13) < 0);
RDGeom::Point3D v31 =
conf.getAtomPos(mv[3].second) - conf.getAtomPos(mv[1].second);
RDGeom::Point3D v32 =
conf.getAtomPos(mv[3].second) - conf.getAtomPos(mv[2].second);
RDGeom::Point3D v34 =
conf.getAtomPos(mv[3].second) - conf.getAtomPos(mv[4].second);
TEST_ASSERT(v32.dotProduct(v32) * v32.dotProduct(v34) < 0);
delete m;
}
delete p;
}
}
void testGitHubIssue910() {
{
// this is a ChEMBL molecule
std::string smiles =
"CSCC[C@H](NC(=O)[C@@H](CCC(N)=O)NC(=O)[C@@H](N)Cc1c[nH]c2ccccc12)C(=O)"
"NCC(=O)N[C@@H](Cc1c[nH]cn1)C(=O)N[C@@H](CO)C(=O)O";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
// add chiral Hs, they were part of the problem
std::vector<unsigned int> chiralAts;
for (RWMol::AtomIterator atIt = m->beginAtoms(); atIt != m->endAtoms();
++atIt) {
if ((*atIt)->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW ||
(*atIt)->getChiralTag() == Atom::CHI_TETRAHEDRAL_CW) {
chiralAts.push_back((*atIt)->getIdx());
}
}
MolOps::addHs(*m, false, false, &chiralAts);
RDDepict::compute2DCoords(*m, NULL, true);
// now look for close contacts.
const Conformer &conf = m->getConformer();
for (unsigned int i = 0; i < conf.getNumAtoms(); ++i) {
for (unsigned int j = i + 1; j < conf.getNumAtoms(); ++j) {
double l = (conf.getAtomPos(i) - conf.getAtomPos(j)).length();
TEST_ASSERT(l > 0.75);
}
}
delete m;
}
}
void testGitHubIssue1073() {
// computeInitialCoords() should call the SSSR code before it calls
// assignStereochemistry()
{
std::string smarts = "[a]12[a][a][a][a][a]1[a][a][a]2";
RWMol *m = SmartsToMol(smarts);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
RingInfo *ri = m->getRingInfo();
TEST_ASSERT(ri->isInitialized());
TEST_ASSERT(ri->isAtomInRingOfSize(0, 6));
TEST_ASSERT(ri->isAtomInRingOfSize(0, 5));
TEST_ASSERT(!ri->isAtomInRingOfSize(0, 9));
delete m;
}
}
int main() {
RDLog::InitLogs();
#if 1
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " test1 \n";
test1();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " testCollisions \n";
testCollisions();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " testAddHs \n";
testAddHs();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " test198 \n";
testIssue198();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " test2 \n";
test2();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " test3 \n";
test3();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " test4 \n";
test4();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " tempTest \n";
tempTest();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " Issue248 \n";
testIssue248();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " Test Queries \n";
testQueries();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " Test crashes associated with RemoveHs \n";
testRemoveHsCrash();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " Test Issue 2091304\n";
testIssue2091304();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " Test Issue 2303566\n";
testIssue2303566();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " Test Issue 2821647\n";
testIssue2821647();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " Test Issue 2948402\n";
testIssue2948402();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " Test Issue 2995724\n";
testIssue2995724();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " Testing a change of the depictor bond length\n";
testBondLengthChange();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " Test Issue 3122141\n";
testIssue3122141();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " Test Issue 3135833\n";
testIssue3135833();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " Test Issue 3487469\n";
testIssue3487469();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " Test GitHub Issue 8\n";
testGitHubIssue8();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
#endif
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " Test GitHub Issue 78\n";
testGitHubIssue78();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " Test GitHub Issue 910\n";
testGitHubIssue910();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
BOOST_LOG(rdInfoLog) << " Test GitHub Issue 1073\n";
testGitHubIssue1073();
BOOST_LOG(rdInfoLog)
<< "***********************************************************\n";
return (0);
}
|
