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rdkit/Code/GraphMol/FileParsers/testMol2ToMol.cpp
Ric 6224a42516 Build warnings revisited (#2318) 
* unused vars in bison parser cleanup

* initialization order in TopologicalTorsionGenerator

* unused params in SLN bison

* sln flex unused params

* throwing destructor in TDTWriter

* signed comparison in substructmethods

* unused input param in smiles/smarts bison

* unused ms param in sln bison

* signed comparison in FingerprintGenerator

* store return of fscanf in StructCheckerOptions

* unreferenced var in catch

* uninitialized value in FileParserUtils

* avoid override overload warning in MolDraw2DSVG

* non-final overrides in Validate.h

* unused static var in Avalon

* unused vars in catch blocks

* make AvalonTools avalonSimilarityBits & avalonSSSBits const int

* assert fscanf result in StructCheckerOptions
2019-03-08 16:42:54 +01:00

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//
// Copyright (c) 2008, Novartis Institutes for BioMedical Research Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior
// written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// created by Nik Stiefl May 2008
//
#include <RDGeneral/test.h>
#include <RDGeneral/RDLog.h>
#include <GraphMol/RDKitBase.h>
#include "FileParsers.h"
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <RDGeneral/FileParseException.h>
#include <RDGeneral/BadFileException.h>
#include <string>
using namespace RDKit;
void testGeneral(std::string rdbase) {
BOOST_LOG(rdInfoLog) << "---------------------------------------"
<< std::endl;
BOOST_LOG(rdInfoLog) << "-- testing general mol2 file parsing --"
<< std::endl;
BOOST_LOG(rdInfoLog) << "---------------------------------------"
<< std::endl;
{
bool ok = false;
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/nonExistFile.mol2";
try {
RWMol *m = Mol2FileToMol(fName);
delete m;
} catch (const BadFileException &) {
ok = true;
}
TEST_ASSERT(ok);
}
{
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/pyrazole_pyridine.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 5);
// this was sf.net issue 2727976:
TEST_ASSERT(m->getNumConformers() == 1);
TEST_ASSERT(m->getConformer().is3D());
TEST_ASSERT(feq(m->getConformer().getAtomPos(0).x, 1.5019));
TEST_ASSERT(feq(m->getConformer().getAtomPos(0).y, 1.0435));
TEST_ASSERT(feq(m->getConformer().getAtomPos(0).z, 0.0000));
delete m;
}
{
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/benzene.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 6);
delete m;
}
{
bool ok = false;
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/mol_noatoms.mol2";
try {
RWMol *m = Mol2FileToMol(fName);
delete m;
} catch (const FileParseException &) {
ok = true;
}
TEST_ASSERT(ok);
}
{
bool ok = false;
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/mol_nomol.mol2";
try {
RWMol *m = Mol2FileToMol(fName);
delete m;
} catch (const FileParseException &) {
ok = true;
}
TEST_ASSERT(ok);
}
{
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/lonePairMol.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 5 && m->getNumBonds() == 4);
delete m;
}
{
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/symmetricGuanidine.mol2";
RWMol *m = Mol2FileToMol(fName, false);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getFormalCharge() == 1);
TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge() == 1);
delete m;
}
{
std::string fName =
rdbase +
"/Code/GraphMol/FileParsers/test_data/highlySymmetricGuanidine.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(4)->getFormalCharge() == 1);
TEST_ASSERT(m->getAtomWithIdx(12)->getFormalCharge() == 1);
TEST_ASSERT(m->getAtomWithIdx(20)->getFormalCharge() == 1);
delete m;
}
{
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/Noxide.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge() == 1);
TEST_ASSERT(m->getAtomWithIdx(9)->getFormalCharge() == -1);
delete m;
}
{
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/Noxide.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge() == 1);
TEST_ASSERT(m->getAtomWithIdx(9)->getFormalCharge() == -1);
delete m;
}
{
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/fusedRing.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getFormalCharge() == 0);
TEST_ASSERT(m->getAtomWithIdx(5)->getFormalCharge() == 0);
TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge() == 0);
TEST_ASSERT(m->getAtomWithIdx(13)->getFormalCharge() == 0);
delete m;
}
{
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/pyridiniumPhenyl.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(5)->getFormalCharge() == 1);
TEST_ASSERT(m->getAtomWithIdx(6)->getFormalCharge() == 0);
delete m;
}
{
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/sulfonAmide.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getFormalCharge() == 0);
delete m;
}
{
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/chargedAmidineRWH.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(6)->getFormalCharge() == 1);
delete m;
}
{
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/chargedAmidineEC.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(3)->getFormalCharge() == 1);
delete m;
}
{
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/chargedAmidine.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(9)->getFormalCharge() == 1);
delete m;
}
{
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/dbtranslateCharged.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge() == 1);
delete m;
}
{
std::string fName =
rdbase +
"/Code/GraphMol/FileParsers/test_data/dbtranslateUncharged.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge() == 0);
delete m;
}
{
std::string fName =
rdbase +
"/Code/GraphMol/FileParsers/test_data/dbtranslateUnchargedRing.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(2)->getFormalCharge() == 0);
delete m;
}
#if 0
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Sulfonate.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
BOOST_LOG(rdInfoLog) <<MolToSmiles(*m)<<std::endl;
delete m;
}
#endif
BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "-- DONE general mol2 file parsing --" << std::endl;
BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
}
void testAromaticChargedFail(std::string rdbase) {
BOOST_LOG(rdInfoLog) << "---------------------------------------"
<< std::endl;
BOOST_LOG(rdInfoLog) << "-- testing subst arom groups in mol2 --"
<< std::endl;
BOOST_LOG(rdInfoLog) << "---------------------------------------"
<< std::endl;
// this one checks on substituted aromatic groups that need to be charged,
// e.g. c1ccccn1C which
// should convert to c1cccc[n+]1C
{
// this one is supposed to have a sanitisation error!
// have to fix that one next ...
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/badSubstPyridine.mol2";
RWMol *m = Mol2FileToMol(fName);
if (m) {
delete m;
}
}
BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "-- DONE subst arom groups in mol2 --" << std::endl;
BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
}
void testIssue3399798(std::string rdbase) {
BOOST_LOG(rdInfoLog) << "---------------------------------------"
<< std::endl;
BOOST_LOG(rdInfoLog) << "-- testing issue 3399798 --"
<< std::endl;
BOOST_LOG(rdInfoLog) << "---------------------------------------"
<< std::endl;
{
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3399798.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag() == Atom::CHI_UNSPECIFIED);
TEST_ASSERT(m->getAtomWithIdx(3)->getChiralTag() == Atom::CHI_UNSPECIFIED);
delete m;
}
{
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3399798.2.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag() == Atom::CHI_UNSPECIFIED);
TEST_ASSERT(m->getAtomWithIdx(3)->getChiralTag() != Atom::CHI_UNSPECIFIED);
delete m;
}
BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "-- DONE --" << std::endl;
BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
}
// Test the following GitHub issue: https://github.com/rdkit/rdkit/issues/114
void testIssue114(std::string rdbase) {
BOOST_LOG(rdInfoLog) << "-----------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "-- testing GitHub issue #114 --" << std::endl;
BOOST_LOG(rdInfoLog) << "-----------------------------------" << std::endl;
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/EZ_mol2_issue114.mol2";
RWMol *mol = Mol2FileToMol(fName);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOZ);
delete mol;
BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "-- DONE --" << std::endl;
BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
}
void testGithub438(std::string rdbase) {
BOOST_LOG(rdInfoLog) << "-----------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "-- testing GitHub issue #438: problems with metals in mol2 files --"
<< std::endl;
BOOST_LOG(rdInfoLog) << "-----------------------------------" << std::endl;
{
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/github438_1.mol2";
RWMol *mol = Mol2FileToMol(fName);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->getFormalCharge() == 1);
delete mol;
}
{
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/github438_2.mol2";
RWMol *mol = Mol2FileToMol(fName);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->getFormalCharge() == 2);
delete mol;
}
BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "-- DONE --" << std::endl;
BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
}
void testDisableCleanup(std::string rdbase) {
BOOST_LOG(rdInfoLog) << "-----------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "-- testing disabling cleanup of substructures in Mol2 parsing --"
<< std::endl;
BOOST_LOG(rdInfoLog) << "-----------------------------------" << std::endl;
{
std::string fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/3505.mol2";
bool sanitize = true, removeHs = true;
Mol2Type variant = CORINA;
{
bool cleanupSubstructures = true; // the default
std::unique_ptr<ROMol> mol(Mol2FileToMol(fName, sanitize, removeHs,
variant, cleanupSubstructures));
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondBetweenAtoms(3, 12));
TEST_ASSERT(mol->getBondBetweenAtoms(3, 12)->getBondType() ==
Bond::SINGLE);
TEST_ASSERT(mol->getAtomWithIdx(12)->getFormalCharge() == 0);
}
{
bool cleanupSubstructures = false;
std::unique_ptr<ROMol> mol(Mol2FileToMol(fName, sanitize, removeHs,
variant, cleanupSubstructures));
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondBetweenAtoms(3, 12));
TEST_ASSERT(mol->getBondBetweenAtoms(3, 12)->getBondType() ==
Bond::DOUBLE);
TEST_ASSERT(mol->getAtomWithIdx(12)->getFormalCharge() == 1);
}
}
BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "-- DONE --" << std::endl;
BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
}
// FIX still missing chirality by 3D structure
// still missing input std::string
int main(int argc, char *argv[]) {
(void)argc;
(void)argv;
RDLog::InitLogs();
std::string rdbase = getenv("RDBASE");
testGeneral(rdbase);
testAromaticChargedFail(rdbase);
testIssue3399798(rdbase);
testIssue114(rdbase);
testGithub438(rdbase);
testDisableCleanup(rdbase);
return 0;
}
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