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|
//
// Copyright (C) 2018 Susan H. Leung
//
// @@ 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 "Validate.h"
#include <RDGeneral/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/ROMol.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <iostream>
using namespace RDKit;
using namespace std;
using namespace MolStandardize;
void testRDKitValidation() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing RDKit validation"
<< std::endl;
string smi1, smi2, smi3, smi4;
RDKitValidation vm;
// testing RDKitDefault
smi1 = "CO(C)C";
unique_ptr<ROMol> m1(SmilesToMol(smi1, 0, false));
vector<ValidationErrorInfo> errout1 = vm.validate(*m1, true);
for (auto &query : errout1) {
std::string msg = query.message();
TEST_ASSERT(msg ==
"INFO: [ValenceValidation] Explicit valence for atom # 1 O, 3, "
"is greater than permitted");
}
// testing for molecule with no atoms
smi2 = "";
unique_ptr<ROMol> m2(SmilesToMol(smi2, 0, false));
vector<ValidationErrorInfo> errout2 = vm.validate(*m2, true);
for (auto &query : errout2) {
std::string msg = query.message();
TEST_ASSERT(msg == "ERROR: [NoAtomValidation] Molecule has no atoms");
}
// testing molecule with multiple valency errors
smi3 = "CO(C)CCN(=O)=O";
unique_ptr<ROMol> m3(SmilesToMol(smi3, 0, false));
vector<ValidationErrorInfo> errout3 = vm.validate(*m3, true);
std::vector<string> msgs1;
std::vector<string> ans1 = {
"INFO: [ValenceValidation] Explicit valence for atom # 1 O, 3, is "
"greater than permitted",
"INFO: [ValenceValidation] Explicit valence for atom # 5 N, 5, is "
"greater than permitted"};
for (auto &query : errout3) {
msgs1.push_back(query.message());
}
TEST_ASSERT(msgs1 == ans1);
// testing molecule with multiple valency errors and only outputting
// first error
smi4 = "CO(C)CCN(=O)=O";
unique_ptr<ROMol> m4(SmilesToMol(smi4, 0, false));
vector<ValidationErrorInfo> errout4 = vm.validate(*m4, false);
std::vector<string> msgs2;
std::vector<string> ans2 = {
"INFO: [ValenceValidation] Explicit valence for atom # 1 O, 3, is "
"greater than permitted"};
for (auto &query : errout4) {
msgs2.push_back(query.message());
}
TEST_ASSERT(msgs2 == ans2);
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testMolVSValidation() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing MolVS validation"
<< std::endl;
string smi1, smi2, smi3, smi4, smi5, smi6;
MolVSValidation vm;
// testing MolVSDefault
// testing for molecule with no atoms
smi1 = "";
unique_ptr<ROMol> m1(SmilesToMol(smi1, 0, false));
vector<ValidationErrorInfo> errout1 = vm.validate(*m1, true);
for (auto &query : errout1) {
std::string msg = query.message();
TEST_ASSERT(msg == "ERROR: [NoAtomValidation] Molecule has no atoms");
}
smi2 = "O=C([O-])c1ccccc1";
unique_ptr<ROMol> m2(SmilesToMol(smi2, 0, false));
vector<ValidationErrorInfo> errout2 = vm.validate(*m2, true);
for (auto &query : errout2) {
std::string msg = query.message();
TEST_ASSERT(msg ==
"INFO: [NeutralValidation] Not an overall neutral system (-1)");
}
smi3 = "CN=[NH+]CN=N";
unique_ptr<ROMol> m3(SmilesToMol(smi3, 0, false));
vector<ValidationErrorInfo> errout3 = vm.validate(*m3, true);
for (auto &query : errout3) {
std::string msg = query.message();
TEST_ASSERT(
msg ==
"INFO: [NeutralValidation] Not an overall neutral system (+1)"); // fix
// to
// show
// +
// sign
}
smi4 = "[13CH4]";
unique_ptr<ROMol> m4(SmilesToMol(smi4, 0, false));
vector<ValidationErrorInfo> errout4 = vm.validate(*m4, true);
for (auto &query : errout4) {
std::string msg = query.message();
TEST_ASSERT(msg ==
"INFO: [IsotopeValidation] Molecule contains isotope 13C");
}
smi5 = "[2H]C(Cl)(Cl)Cl";
unique_ptr<ROMol> m5(SmilesToMol(smi5, 0, false));
vector<ValidationErrorInfo> errout5 = vm.validate(*m5, true);
for (auto &query : errout5) {
std::string msg = query.message();
TEST_ASSERT(msg ==
"INFO: [IsotopeValidation] Molecule contains isotope 2H");
}
smi6 = "[2H]OC([2H])([2H])[2H]";
unique_ptr<ROMol> m6(SmilesToMol(smi6, 0, false));
vector<ValidationErrorInfo> errout6 = vm.validate(*m6, true);
for (auto &query : errout6) {
std::string msg = query.message();
TEST_ASSERT(msg ==
"INFO: [IsotopeValidation] Molecule contains isotope 2H");
}
std::string smi7 = "COc1cccc(C=N[N-]C(N)=O)c1[O-].O.O.O.O=[U+2]=O";
unique_ptr<ROMol> m7(SmilesToMol(smi7, 0, false));
vector<ValidationErrorInfo> errout7 = vm.validate(*m7, true);
TEST_ASSERT(errout7.size() != 0);
for (auto &query : errout7) {
std::string msg = query.message();
TEST_ASSERT(msg == "INFO: [FragmentValidation] water/hydroxide is present");
}
std::string smi8 = "CC(=O)O.NCC(=O)NCCCCCCCCCCNC(=O)CN";
unique_ptr<ROMol> m8(SmilesToMol(smi8, 0, false));
vector<ValidationErrorInfo> errout8 = vm.validate(*m8, true);
TEST_ASSERT(errout8.size() != 0);
for (auto &query : errout8) {
std::string msg = query.message();
TEST_ASSERT(msg ==
"INFO: [FragmentValidation] acetate/acetic acid is present");
}
std::string smi9 = "N#CC(Br)(Br)C#N.[Br-].[K+]";
unique_ptr<ROMol> m9(SmilesToMol(smi9, 0, false));
vector<ValidationErrorInfo> errout9 = vm.validate(*m9, true);
std::vector<std::string> ans = {
"INFO: [FragmentValidation] bromine is present",
"INFO: [FragmentValidation] potassium is present"};
TEST_ASSERT(errout9.size() == ans.size());
for (size_t i = 0; i < errout9.size(); ++i) {
TEST_ASSERT(errout9[i].message() == ans[i]);
}
std::string smi10 = "C1COCCO1.O=C(NO)NO";
unique_ptr<ROMol> m10(SmilesToMol(smi10, 0, false));
vector<ValidationErrorInfo> errout10 = vm.validate(*m10, true);
std::vector<std::string> ans10 = {
"INFO: [FragmentValidation] 1,2-dimethoxyethane is present",
"INFO: [FragmentValidation] 1,4-dioxane is present"};
TEST_ASSERT(errout10.size() == ans10.size());
for (size_t i = 0; i < errout10.size(); ++i) {
TEST_ASSERT(errout10[i].message() == ans10[i]);
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testMolVSOptions() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing MolVS Options"
<< std::endl;
vector<boost::shared_ptr<MolVSValidations>> validations = {
boost::make_shared<IsotopeValidation>()};
MolVSValidation vm(validations);
// testing MolVSDefault
// testing for molecule with no atoms
string smi1 = "";
unique_ptr<ROMol> m1(SmilesToMol(smi1, 0, false));
vector<ValidationErrorInfo> errout1 = vm.validate(*m1, true);
for (auto &query : errout1) {
std::string msg = query.message();
// TEST_ASSERT(msg == "ERROR: [NoAtomValidation] Molecule has no atoms");
TEST_ASSERT(msg == "");
}
string smi2 = "O=C([O-])c1ccccc1";
unique_ptr<ROMol> m2(SmilesToMol(smi2, 0, false));
vector<ValidationErrorInfo> errout2 = vm.validate(*m2, true);
for (auto &query : errout2) {
std::string msg = query.message();
// TEST_ASSERT(msg ==
// "INFO: [NeutralValidation] Not an overall neutral system
// (-1)");
TEST_ASSERT(msg == "");
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testAllowedAtomsValidation() {
BOOST_LOG(rdInfoLog)
<< "-----------------------\n Testing AllowedAtoms validation"
<< std::endl;
// std::vector<string> atoms = {"C", "N", "O"};
std::vector<unsigned int> atoms = {6, 7, 8};
std::vector<shared_ptr<Atom>> atomList;
for (auto &atom : atoms) {
shared_ptr<Atom> a(new Atom(atom));
atomList.push_back(a);
}
AllowedAtomsValidation vm(atomList);
std::string smi1;
smi1 = "CC(=O)CF";
unique_ptr<ROMol> m1(SmilesToMol(smi1));
vector<ValidationErrorInfo> errout1 = vm.validate(*m1, true);
for (auto &query : errout1) {
std::string msg = query.message();
std::cout << msg << std::endl;
TEST_ASSERT(
msg ==
"INFO: [AllowedAtomsValidation] Atom F is not in allowedAtoms list");
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testDisallowedAtomsValidation() {
BOOST_LOG(rdInfoLog)
<< "-----------------------\n Testing DisallowedAtoms validation"
<< std::endl;
// std::vector<string> atoms = {"F", "Cl", "Br"};
std::vector<unsigned int> atoms = {9, 17, 35};
std::vector<shared_ptr<Atom>> atomList;
for (auto &atom : atoms) {
shared_ptr<Atom> a(new Atom(atom));
atomList.push_back(a);
}
DisallowedAtomsValidation vm(atomList);
std::string smi1;
smi1 = "CC(=O)CF";
unique_ptr<ROMol> m1(SmilesToMol(smi1));
vector<ValidationErrorInfo> errout1 = vm.validate(*m1, true);
for (auto &query : errout1) {
std::string msg = query.message();
std::cout << msg << std::endl;
TEST_ASSERT(
msg ==
"INFO: [DisallowedAtomsValidation] Atom F is in disallowedAtoms list");
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testFragment() {
BOOST_LOG(rdInfoLog)
<< "-----------------------\n Testing fragment validation" << std::endl;
string smi1, smi2, smi3, smi4, smi5, smi6;
MolVSValidation vm;
// testing MolVSValidation fragmentValidation
// FragmentValidation should identify 1,2-dichloroethane.
smi1 = "ClCCCl.c1ccccc1O";
unique_ptr<ROMol> m1(SmilesToMol(smi1, 0, false));
vector<ValidationErrorInfo> errout1 = vm.validate(*m1, true);
for (auto &query : errout1) {
std::string msg = query.message();
std::cout << msg << std::endl;
TEST_ASSERT(msg ==
"INFO: [FragmentValidation] 1,2-dichloroethane is present");
}
smi2 = "COCCOC.CCCBr";
unique_ptr<ROMol> m2(SmilesToMol(smi2, 0, false));
vector<ValidationErrorInfo> errout2 = vm.validate(*m2, true);
for (auto &query : errout2) {
std::string msg = query.message();
std::cout << msg << std::endl;
TEST_ASSERT(msg ==
"INFO: [FragmentValidation] 1,2-dimethoxyethane is present");
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testValidateSmiles() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing ValidateSmiles"
<< std::endl;
// an invalid smiles should throw a ValueErrorException error
try {
vector<ValidationErrorInfo> errout1 = validateSmiles("3478q439g98h");
} catch (const ValueErrorException &e) {
std::cout << e.message() << std::endl;
TEST_ASSERT(e.message() ==
"SMILES Parse Error: syntax error for input: 3478q439g98h")
};
vector<ValidationErrorInfo> errout2 = validateSmiles("");
for (auto &query : errout2) {
std::string msg = query.message();
std::cout << msg << std::endl;
TEST_ASSERT(msg == "ERROR: [NoAtomValidation] Molecule has no atoms");
}
vector<ValidationErrorInfo> errout3 = validateSmiles("ClCCCl.c1ccccc1O");
for (auto &query : errout3) {
std::string msg = query.message();
TEST_ASSERT(msg ==
"INFO: [FragmentValidation] 1,2-dichloroethane is present");
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
int main() {
testRDKitValidation();
testMolVSValidation();
testMolVSOptions();
testAllowedAtomsValidation();
testDisallowedAtomsValidation();
testFragment();
testValidateSmiles();
return 0;
}
|
