mirror of
https://github.com/rdkit/rdkit.git
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91212a4eb3
* Fixes #982 also changes bond-wedging algorithm to favor lighter non-ring bonds * prefer wedging bonds to lower-degree atoms * Fixes #983 * small fixes - Fix a problem where a chiral atom is selected to draw a wedge to instead of a ring atom - Fix a problem where two calls to PrepareMolForDrawing() led to two wedged bonds from an atom. * Fixes #985 This isn't the most satisfying solution (the wedged bonds are sometimes a bit too large), but it gives reasonable results on the test cases I've tried.
1581 lines
50 KiB
C++
1581 lines
50 KiB
C++
// $Id$
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//
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// Copyright (C) 2002-2009 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 <GraphMol/RDKitBase.h>
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#include <string>
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#include <iostream>
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#include <fstream>
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#include <sstream>
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#include "MolSupplier.h"
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#include "MolWriters.h"
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#include "FileParsers.h"
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#include <RDGeneral/FileParseException.h>
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#include <RDGeneral/StreamOps.h>
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#include <RDGeneral/RDLog.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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using namespace RDKit;
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void testSmilesWriter() {
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std::string rdbase = getenv("RDBASE");
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std::string fname =
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rdbase + "/Code/GraphMol/FileParsers/test_data/fewSmi.csv";
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SmilesMolSupplier *nSup = new SmilesMolSupplier(fname, ",", 1, 0, false);
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std::string oname =
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rdbase + "/Code/GraphMol/FileParsers/test_data/outSmiles.csv";
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STR_VECT propNames;
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propNames.push_back(std::string("Column_2"));
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SmilesWriter *writer = new SmilesWriter(oname, " ");
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writer->setProps(propNames);
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STR_VECT names;
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STR_VECT props;
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ROMol *mol = nSup->next();
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while (mol) {
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std::string mname, pval;
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mol->getProp(common_properties::_Name, mname);
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mol->getProp("Column_2", pval);
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names.push_back(mname);
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props.push_back(pval);
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writer->write(*mol);
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delete mol;
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try {
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mol = nSup->next();
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} catch (FileParseException &) {
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break;
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}
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}
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writer->flush();
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delete writer;
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delete nSup;
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// now read the molecules back in a check if we have the same properties etc
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nSup = new SmilesMolSupplier(oname);
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int i = 0;
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mol = nSup->next();
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while (mol) {
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std::string mname, pval;
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mol->getProp(common_properties::_Name, mname);
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mol->getProp("Column_2", pval);
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CHECK_INVARIANT(mname == names[i], "");
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CHECK_INVARIANT(pval == props[i], "");
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i++;
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delete mol;
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try {
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mol = nSup->next();
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} catch (FileParseException &) {
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break;
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}
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}
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}
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void testSmilesWriter2() {
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{
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std::stringstream ss;
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SmilesWriter *writer = new SmilesWriter(&ss, " ", "Name", false);
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RWMol *mol;
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mol = SmilesToMol("c1ccccc1");
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// MolOps::Kekulize(*mol);
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writer->write(*mol);
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delete mol;
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mol = SmilesToMol("F[C@H](Cl)Br");
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writer->write(*mol);
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delete mol;
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writer->flush();
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TEST_ASSERT(ss.str() == "c1ccccc1 0\nFC(Cl)Br 1\n");
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delete writer;
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}
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{
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std::stringstream ss;
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SmilesWriter *writer =
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new SmilesWriter(&ss, " ", "Name", false, false, true);
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RWMol *mol;
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mol = SmilesToMol("c1ccccc1");
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MolOps::Kekulize(*mol);
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writer->write(*mol);
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delete mol;
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mol = SmilesToMol("F[C@H](Cl)Br");
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writer->write(*mol);
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delete mol;
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writer->flush();
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TEST_ASSERT(ss.str() == "C1=CC=CC=C1 0\nF[C@H](Cl)Br 1\n");
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delete writer;
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}
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}
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void testSmilesWriterNoNames() {
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std::string rdbase = getenv("RDBASE");
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std::string fname =
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rdbase + "/Code/GraphMol/FileParsers/test_data/fewSmi.csv";
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SmilesMolSupplier *nSup = new SmilesMolSupplier(fname, ",", 1, 0, false);
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std::string oname =
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rdbase + "/Code/GraphMol/FileParsers/test_data/outSmiles.csv";
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STR_VECT propNames;
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propNames.push_back(std::string("Column_2"));
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SmilesWriter *writer = new SmilesWriter(oname, " ", "");
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writer->setProps(propNames);
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STR_VECT props;
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ROMol *mol = nSup->next();
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while (mol) {
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std::string mname, pval;
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mol->getProp("Column_2", pval);
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mol->setProp(common_properties::_Name, "bogus");
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props.push_back(pval);
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writer->write(*mol);
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delete mol;
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try {
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mol = nSup->next();
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} catch (FileParseException &) {
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break;
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}
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}
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writer->flush();
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delete writer;
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delete nSup;
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// now read the molecules back in a check if we have the same properties etc
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nSup = new SmilesMolSupplier(oname, ",", 0, -1);
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int i = 0;
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mol = nSup->next();
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while (mol) {
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std::string mname, pval;
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mol->getProp(common_properties::_Name, mname);
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TEST_ASSERT(mname != "bogus");
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mol->getProp("Column_2", pval);
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TEST_ASSERT(pval == props[i]);
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i++;
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delete mol;
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try {
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mol = nSup->next();
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} catch (FileParseException &) {
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break;
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}
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}
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}
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void testSmilesWriterClose() {
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std::string rdbase = getenv("RDBASE");
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std::string fname =
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rdbase + "/Code/GraphMol/FileParsers/test_data/fewSmi.csv";
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SmilesMolSupplier *nSup = new SmilesMolSupplier(fname, ",", 1, 0, false);
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std::string oname =
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rdbase + "/Code/GraphMol/FileParsers/test_data/outSmiles.csv";
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STR_VECT propNames;
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propNames.push_back(std::string("Column_2"));
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SmilesWriter *writer = new SmilesWriter(oname, " ", "");
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writer->setProps(propNames);
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STR_VECT props;
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ROMol *mol = nSup->next();
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while (mol) {
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std::string mname, pval;
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mol->getProp("Column_2", pval);
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mol->setProp(common_properties::_Name, "bogus");
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props.push_back(pval);
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writer->write(*mol);
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delete mol;
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try {
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mol = nSup->next();
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} catch (FileParseException &) {
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break;
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}
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}
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writer->close();
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delete nSup;
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// now read the molecules back in a check if we have the same properties etc
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nSup = new SmilesMolSupplier(oname, ",", 0, -1);
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int i = 0;
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mol = nSup->next();
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while (mol) {
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std::string mname, pval;
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mol->getProp(common_properties::_Name, mname);
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TEST_ASSERT(mname != "bogus");
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mol->getProp("Column_2", pval);
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TEST_ASSERT(pval == props[i]);
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i++;
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delete mol;
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try {
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mol = nSup->next();
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} catch (FileParseException &) {
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break;
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}
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}
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}
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void testSDWriter() {
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std::string rdbase = getenv("RDBASE");
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std::string fname =
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rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf";
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SDMolSupplier sdsup(fname);
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std::string ofile =
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rdbase + "/Code/GraphMol/FileParsers/test_data/outNCI_few.sdf";
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SDWriter *writer = new SDWriter(ofile);
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STR_VECT names;
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while (!sdsup.atEnd()) {
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ROMol *mol = sdsup.next();
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std::string mname;
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mol->getProp(common_properties::_Name, mname);
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names.push_back(mname);
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writer->write(*mol);
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delete mol;
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}
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writer->flush();
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CHECK_INVARIANT(writer->numMols() == 16, "");
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// make sure we can close() the writer and delete it:
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writer->close();
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delete writer;
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// now read in the file we just finished writing
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SDMolSupplier reader(ofile);
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int i = 0;
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while (!reader.atEnd()) {
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ROMol *mol = reader.next();
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std::string mname;
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mol->getProp(common_properties::_Name, mname);
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CHECK_INVARIANT(mname == names[i], "");
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delete mol;
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i++;
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}
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// now read in a file with aromatic information on the bonds
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std::string infile =
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rdbase + "/Code/GraphMol/FileParsers/test_data/outNCI_arom.sdf";
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SDMolSupplier nreader(infile);
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i = 0;
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while (!nreader.atEnd()) {
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ROMol *mol = nreader.next();
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std::string mname;
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mol->getProp(common_properties::_Name, mname);
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CHECK_INVARIANT(mname == names[i], "");
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i++;
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delete mol;
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}
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}
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void testTDTWriter() {
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std::string rdbase = getenv("RDBASE");
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std::string fname =
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rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf";
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SDMolSupplier sdsup(fname);
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std::string ofile =
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rdbase + "/Code/GraphMol/FileParsers/test_data/outNCI_few.tdt";
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TDTWriter *writer = new TDTWriter(ofile);
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STR_VECT names;
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while (!sdsup.atEnd()) {
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ROMol *mol = sdsup.next();
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std::string mname;
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mol->getProp("CAS_RN", mname);
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names.push_back(mname);
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writer->write(*mol);
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delete mol;
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}
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writer->flush();
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TEST_ASSERT(writer->numMols() == 16);
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delete writer;
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// now read in the file we just finished writing
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TDTMolSupplier reader(ofile);
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int i = 0;
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while (!reader.atEnd()) {
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ROMol *mol = reader.next();
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if (mol) {
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std::string mname;
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mol->getProp("CAS_RN", mname);
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CHECK_INVARIANT(mname == names[i], "");
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delete mol;
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}
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i++;
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}
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TEST_ASSERT(i == 16);
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}
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void testSmilesWriterStrm() {
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std::string rdbase = getenv("RDBASE");
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std::string fname =
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rdbase + "/Code/GraphMol/FileParsers/test_data/fewSmi.csv";
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SmilesMolSupplier *nSup = new SmilesMolSupplier(fname, ",", 1, 0, false);
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std::string oname =
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rdbase + "/Code/GraphMol/FileParsers/test_data/outSmiles.csv";
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std::ofstream *oStream = new std::ofstream(oname.c_str());
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STR_VECT propNames;
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propNames.push_back(std::string("Column_2"));
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SmilesWriter *writer = new SmilesWriter(oStream, " ");
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writer->setProps(propNames);
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STR_VECT names;
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STR_VECT props;
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ROMol *mol = nSup->next();
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while (mol) {
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std::string mname, pval;
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mol->getProp(common_properties::_Name, mname);
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mol->getProp("Column_2", pval);
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names.push_back(mname);
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props.push_back(pval);
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writer->write(*mol);
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delete mol;
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try {
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mol = nSup->next();
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} catch (FileParseException &) {
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break;
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}
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}
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writer->flush();
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delete writer;
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delete nSup;
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// now read the molecules back in a check if we have the same properties etc
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nSup = new SmilesMolSupplier(oname);
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int i = 0;
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mol = nSup->next();
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while (mol) {
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std::string mname, pval;
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mol->getProp(common_properties::_Name, mname);
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mol->getProp("Column_2", pval);
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CHECK_INVARIANT(mname == names[i], "");
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CHECK_INVARIANT(pval == props[i], "");
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i++;
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delete mol;
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try {
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mol = nSup->next();
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} catch (FileParseException &) {
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break;
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}
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}
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}
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void testSDWriterStrm() {
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std::string rdbase = getenv("RDBASE");
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{
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std::string fname =
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rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf";
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SDMolSupplier sdsup(fname);
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std::string ofile =
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rdbase + "/Code/GraphMol/FileParsers/test_data/outNCI_few.sdf";
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std::ofstream *oStream = new std::ofstream(ofile.c_str());
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SDWriter *writer = new SDWriter(oStream);
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STR_VECT names;
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while (!sdsup.atEnd()) {
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ROMol *mol = sdsup.next();
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std::string mname;
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mol->getProp(common_properties::_Name, mname);
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names.push_back(mname);
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writer->write(*mol);
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delete mol;
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}
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writer->flush();
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CHECK_INVARIANT(writer->numMols() == 16, "");
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delete writer;
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// now read in the file we just finished writing
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SDMolSupplier reader(ofile);
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int i = 0;
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while (!reader.atEnd()) {
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ROMol *mol = reader.next();
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std::string mname;
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mol->getProp(common_properties::_Name, mname);
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CHECK_INVARIANT(mname == names[i], "");
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delete mol;
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i++;
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}
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}
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{
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// now read in a file with aromatic information on the bonds
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std::string infile =
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rdbase + "/Code/GraphMol/FileParsers/test_data/outNCI_arom.sdf";
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SDMolSupplier nreader(infile);
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unsigned int i = 0;
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while (!nreader.atEnd()) {
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ROMol *mol = nreader.next();
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TEST_ASSERT(mol);
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++i;
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delete mol;
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}
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TEST_ASSERT(i == 16);
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}
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}
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void testTDTWriterStrm() {
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std::string rdbase = getenv("RDBASE");
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std::string fname =
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rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf";
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SDMolSupplier sdsup(fname);
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std::string ofile =
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rdbase + "/Code/GraphMol/FileParsers/test_data/outNCI_few.tdt";
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std::ofstream *oStream = new std::ofstream(ofile.c_str());
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TDTWriter *writer = new TDTWriter(oStream);
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STR_VECT names;
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while (!sdsup.atEnd()) {
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ROMol *mol = sdsup.next();
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std::string mname;
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mol->getProp("CAS_RN", mname);
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names.push_back(mname);
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writer->write(*mol);
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delete mol;
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}
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writer->flush();
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TEST_ASSERT(writer->numMols() == 16);
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delete writer;
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// now read in the file we just finished writing
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TDTMolSupplier reader(ofile);
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int i = 0;
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while (!reader.atEnd()) {
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ROMol *mol = reader.next();
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if (mol) {
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std::string mname;
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mol->getProp("CAS_RN", mname);
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CHECK_INVARIANT(mname == names[i], "");
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delete mol;
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}
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i++;
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}
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TEST_ASSERT(i == 16);
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}
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void testSDMemoryCorruption() {
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std::string rdbase = getenv("RDBASE");
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std::string fname = rdbase + "/Data/NCI/first_200.props.sdf";
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SDMolSupplier sdsup(fname, true);
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std::string ofile =
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rdbase +
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"/Code/GraphMol/FileParsers/test_data/outNCI_first_200.props.sdf";
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std::ostream *os = new std::ofstream(ofile.c_str());
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// std::ostream *os=new std::stringstream();
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SDWriter *writer = new SDWriter(os, false);
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STR_VECT names;
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#if 1
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ROMol *m1 = sdsup.next();
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MolOps::sanitizeMol(*(RWMol *)m1);
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#else
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ROMol *m1 = SmilesToMol("C1CC1");
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TEST_ASSERT(m1);
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#endif
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sdsup.reset();
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int nDone = 0;
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while (!sdsup.atEnd()) {
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// std::cerr<<nDone<<std::endl;
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ROMol *mol = sdsup.next();
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// std::cerr<<"m:"<<mol<<std::endl;
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TEST_ASSERT(mol);
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std::string mname;
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mol->getProp(common_properties::_Name, mname);
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names.push_back(mname);
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// std::cerr<<" w"<<std::endl;
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writer->write(*mol);
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// std::cerr<<" ok"<<std::endl;
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delete mol;
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nDone++;
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}
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CHECK_INVARIANT(nDone == 200, "");
|
|
writer->flush();
|
|
CHECK_INVARIANT(writer->numMols() == 200, "");
|
|
|
|
delete writer;
|
|
#if 1
|
|
// now read in the file we just finished writing
|
|
SDMolSupplier reader(ofile);
|
|
int i = 0;
|
|
while (!reader.atEnd()) {
|
|
ROMol *mol = reader.next();
|
|
std::string mname;
|
|
mol->getProp(common_properties::_Name, mname);
|
|
CHECK_INVARIANT(mname == names[i], "");
|
|
|
|
delete mol;
|
|
i++;
|
|
}
|
|
#endif
|
|
}
|
|
|
|
void testIssue3525000() {
|
|
{
|
|
std::string rdbase = getenv("RDBASE");
|
|
std::string fname =
|
|
rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3525000.sdf";
|
|
RWMol *mol = MolFileToMol(fname);
|
|
TEST_ASSERT(mol);
|
|
|
|
std::string cip;
|
|
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(0)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "R");
|
|
TEST_ASSERT(mol->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(3)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "R");
|
|
TEST_ASSERT(mol->getAtomWithIdx(6)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(6)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "R");
|
|
TEST_ASSERT(mol->getAtomWithIdx(8)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(8)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "R");
|
|
TEST_ASSERT(mol->getAtomWithIdx(9)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(9)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "R");
|
|
TEST_ASSERT(mol->getAtomWithIdx(10)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(10)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "S");
|
|
TEST_ASSERT(mol->getAtomWithIdx(14)->hasProp(common_properties::_CIPCode));
|
|
// FIX: Marvin disagrees about this one:
|
|
mol->getAtomWithIdx(14)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "R");
|
|
TEST_ASSERT(mol->getAtomWithIdx(15)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(15)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "R");
|
|
|
|
std::string mb = MolToMolBlock(*mol);
|
|
delete mol;
|
|
mol = MolBlockToMol(mb);
|
|
TEST_ASSERT(mol);
|
|
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(0)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "R");
|
|
TEST_ASSERT(mol->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(3)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "R");
|
|
TEST_ASSERT(mol->getAtomWithIdx(6)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(6)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "R");
|
|
TEST_ASSERT(mol->getAtomWithIdx(8)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(8)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "R");
|
|
TEST_ASSERT(mol->getAtomWithIdx(9)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(9)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "R");
|
|
TEST_ASSERT(mol->getAtomWithIdx(10)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(10)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "S");
|
|
TEST_ASSERT(mol->getAtomWithIdx(14)->hasProp(common_properties::_CIPCode));
|
|
// FIX: Marvin disagrees about this one:
|
|
mol->getAtomWithIdx(14)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "R");
|
|
TEST_ASSERT(mol->getAtomWithIdx(15)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(15)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "R");
|
|
}
|
|
{
|
|
std::string rdbase = getenv("RDBASE");
|
|
std::string fname =
|
|
rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3525000b.sdf";
|
|
RWMol *mol = MolFileToMol(fname);
|
|
TEST_ASSERT(mol);
|
|
MolOps::assignChiralTypesFrom3D(*mol);
|
|
MolOps::assignStereochemistry(*mol);
|
|
std::string cip;
|
|
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(0)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "S");
|
|
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "S");
|
|
TEST_ASSERT(mol->getAtomWithIdx(2)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(2)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "R");
|
|
TEST_ASSERT(mol->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(3)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "R");
|
|
TEST_ASSERT(mol->getAtomWithIdx(4)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(4)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "S");
|
|
|
|
std::string mb = MolToMolBlock(*mol);
|
|
delete mol;
|
|
mol = MolBlockToMol(mb);
|
|
TEST_ASSERT(mol);
|
|
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(0)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "S");
|
|
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "S");
|
|
TEST_ASSERT(mol->getAtomWithIdx(2)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(2)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "R");
|
|
TEST_ASSERT(mol->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(3)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "R");
|
|
TEST_ASSERT(mol->getAtomWithIdx(4)->hasProp(common_properties::_CIPCode));
|
|
mol->getAtomWithIdx(4)->getProp(common_properties::_CIPCode, cip);
|
|
TEST_ASSERT(cip == "S");
|
|
}
|
|
}
|
|
|
|
void testIssue265() {
|
|
{
|
|
ROMol *m1 = SmilesToMol("C1ON1");
|
|
TEST_ASSERT(m1);
|
|
Conformer *conf = new Conformer(m1->getNumAtoms());
|
|
RDGeom::Point3D p1(0, 0, 0);
|
|
RDGeom::Point3D p2(1, 0, 0);
|
|
RDGeom::Point3D p3(0, 1, 0);
|
|
conf->setAtomPos(0, p1);
|
|
conf->setAtomPos(1, p2);
|
|
conf->setAtomPos(2, p3);
|
|
m1->addConformer(conf);
|
|
|
|
std::stringstream sstream;
|
|
TDTWriter writer(&sstream);
|
|
writer.write(*m1);
|
|
writer.flush();
|
|
std::string otext = sstream.str();
|
|
TEST_ASSERT(otext == "$SMI<C1NO1>\n3D<0,0,0,0,1,0,1,0,0;>\n");
|
|
}
|
|
}
|
|
|
|
void testMolFileChiralFlag() {
|
|
{
|
|
ROMol *m1 = SmilesToMol("C[C@H](Cl)F");
|
|
TEST_ASSERT(m1);
|
|
|
|
std::string mb = MolToMolBlock(*m1);
|
|
delete m1;
|
|
m1 = MolBlockToMol(mb);
|
|
TEST_ASSERT(!m1->hasProp(common_properties::_MolFileChiralFlag));
|
|
}
|
|
{
|
|
ROMol *m1 = SmilesToMol("C[C@H](Cl)F");
|
|
TEST_ASSERT(m1);
|
|
m1->setProp(common_properties::_MolFileChiralFlag,
|
|
static_cast<unsigned int>(1));
|
|
std::string mb = MolToMolBlock(*m1);
|
|
delete m1;
|
|
m1 = MolBlockToMol(mb);
|
|
TEST_ASSERT(m1->hasProp(common_properties::_MolFileChiralFlag));
|
|
}
|
|
}
|
|
|
|
void testMolFileTotalValence() {
|
|
BOOST_LOG(rdInfoLog) << "testing handling of mol file valence flags"
|
|
<< std::endl;
|
|
|
|
{
|
|
RWMol *m1 = SmilesToMol("[Na]");
|
|
std::string mb = MolToMolBlock(*m1);
|
|
delete m1;
|
|
m1 = MolBlockToMol(mb);
|
|
TEST_ASSERT(m1);
|
|
TEST_ASSERT(m1->getNumAtoms() == 1);
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->getNoImplicit());
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->getNumExplicitHs() == 0);
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->getNumRadicalElectrons() == 1);
|
|
delete m1;
|
|
}
|
|
{
|
|
RWMol *m1 = SmilesToMol("[CH]");
|
|
std::string mb = MolToMolBlock(*m1);
|
|
delete m1;
|
|
m1 = MolBlockToMol(mb);
|
|
TEST_ASSERT(m1);
|
|
TEST_ASSERT(m1->getNumAtoms() == 1);
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->getNoImplicit());
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->getNumExplicitHs() == 1);
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->getNumRadicalElectrons() == 1);
|
|
|
|
delete m1;
|
|
}
|
|
{
|
|
RWMol *m1 = SmilesToMol("[CH2]");
|
|
std::string mb = MolToMolBlock(*m1);
|
|
delete m1;
|
|
m1 = MolBlockToMol(mb);
|
|
TEST_ASSERT(m1);
|
|
TEST_ASSERT(m1->getNumAtoms() == 1);
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->getNoImplicit());
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->getNumExplicitHs() == 2);
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->getNumRadicalElectrons() == 2);
|
|
delete m1;
|
|
}
|
|
{
|
|
RWMol *m1 = SmilesToMol("[CH3]");
|
|
std::string mb = MolToMolBlock(*m1);
|
|
delete m1;
|
|
m1 = MolBlockToMol(mb);
|
|
TEST_ASSERT(m1);
|
|
TEST_ASSERT(m1->getNumAtoms() == 1);
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->getNoImplicit());
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->getNumExplicitHs() == 3);
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->getNumRadicalElectrons() == 1);
|
|
delete m1;
|
|
}
|
|
|
|
BOOST_LOG(rdInfoLog) << "done" << std::endl;
|
|
}
|
|
|
|
void testMolFileWithRxn() {
|
|
BOOST_LOG(rdInfoLog) << "testing handling of mol files with reactions"
|
|
<< std::endl;
|
|
std::string rdbase = getenv("RDBASE");
|
|
rdbase += "/Code/GraphMol/FileParsers/test_data/";
|
|
|
|
{
|
|
std::string fName;
|
|
fName = rdbase + "rxn1.mol";
|
|
ROMol *m = MolFileToMol(fName);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumAtoms() == 18);
|
|
TEST_ASSERT(m->getNumBonds() == 16);
|
|
|
|
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::molRxnRole));
|
|
TEST_ASSERT(
|
|
m->getAtomWithIdx(0)->getProp<int>(common_properties::molRxnRole) == 1);
|
|
TEST_ASSERT(
|
|
m->getAtomWithIdx(0)->hasProp(common_properties::molRxnComponent));
|
|
TEST_ASSERT(m->getAtomWithIdx(0)->getProp<int>(
|
|
common_properties::molRxnComponent) == 1);
|
|
|
|
TEST_ASSERT(m->getAtomWithIdx(17)->hasProp(common_properties::molRxnRole));
|
|
TEST_ASSERT(m->getAtomWithIdx(17)->getProp<int>(
|
|
common_properties::molRxnRole) == 2);
|
|
TEST_ASSERT(
|
|
m->getAtomWithIdx(17)->hasProp(common_properties::molRxnComponent));
|
|
TEST_ASSERT(m->getAtomWithIdx(17)->getProp<int>(
|
|
common_properties::molRxnComponent) == 3);
|
|
|
|
std::string mb = MolToMolBlock(*m);
|
|
delete m;
|
|
m = MolBlockToMol(mb);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumAtoms() == 18);
|
|
TEST_ASSERT(m->getNumBonds() == 16);
|
|
|
|
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::molRxnRole));
|
|
TEST_ASSERT(
|
|
m->getAtomWithIdx(0)->getProp<int>(common_properties::molRxnRole) == 1);
|
|
TEST_ASSERT(
|
|
m->getAtomWithIdx(0)->hasProp(common_properties::molRxnComponent));
|
|
TEST_ASSERT(m->getAtomWithIdx(0)->getProp<int>(
|
|
common_properties::molRxnComponent) == 1);
|
|
|
|
TEST_ASSERT(m->getAtomWithIdx(17)->hasProp(common_properties::molRxnRole));
|
|
TEST_ASSERT(m->getAtomWithIdx(17)->getProp<int>(
|
|
common_properties::molRxnRole) == 2);
|
|
TEST_ASSERT(
|
|
m->getAtomWithIdx(17)->hasProp(common_properties::molRxnComponent));
|
|
TEST_ASSERT(m->getAtomWithIdx(17)->getProp<int>(
|
|
common_properties::molRxnComponent) == 3);
|
|
delete m;
|
|
}
|
|
BOOST_LOG(rdInfoLog) << "done" << std::endl;
|
|
}
|
|
|
|
void testSDWriterOptions() {
|
|
BOOST_LOG(rdInfoLog) << "testing SDWriter options" << std::endl;
|
|
{
|
|
std::stringstream ss;
|
|
SDWriter writer(&ss, false);
|
|
RWMol *mol = SmilesToMol("c1ccccc1");
|
|
writer.write(*mol);
|
|
delete mol;
|
|
writer.flush();
|
|
CHECK_INVARIANT(writer.numMols() == 1, "");
|
|
|
|
std::string txt = ss.str();
|
|
TEST_ASSERT(txt.find("V2000") != std::string::npos);
|
|
TEST_ASSERT(txt.find("V3000") == std::string::npos);
|
|
}
|
|
{
|
|
std::stringstream ss;
|
|
SDWriter writer(&ss, false);
|
|
RWMol *mol = SmilesToMol("c1ccccc1");
|
|
writer.setForceV3000(true);
|
|
writer.write(*mol);
|
|
delete mol;
|
|
writer.flush();
|
|
CHECK_INVARIANT(writer.numMols() == 1, "");
|
|
|
|
std::string txt = ss.str();
|
|
TEST_ASSERT(txt.find("V2000") == std::string::npos);
|
|
TEST_ASSERT(txt.find("V3000") != std::string::npos);
|
|
}
|
|
{
|
|
std::stringstream ss;
|
|
SDWriter writer(&ss, false);
|
|
RWMol *mol = SmilesToMol("c1ccccc1");
|
|
writer.write(*mol);
|
|
writer.setForceV3000(true);
|
|
writer.write(*mol);
|
|
delete mol;
|
|
writer.flush();
|
|
CHECK_INVARIANT(writer.numMols() == 2, "");
|
|
|
|
std::string txt = ss.str();
|
|
TEST_ASSERT(txt.find("V2000") != std::string::npos);
|
|
TEST_ASSERT(txt.find("V3000") != std::string::npos);
|
|
TEST_ASSERT(txt.find("V2000") < txt.find("V3000"));
|
|
}
|
|
{
|
|
std::stringstream ss;
|
|
SDWriter writer(&ss, false);
|
|
RWMol *mol = SmilesToMol("c1ccccc1");
|
|
writer.setForceV3000(true);
|
|
writer.write(*mol);
|
|
writer.setForceV3000(false);
|
|
writer.write(*mol);
|
|
delete mol;
|
|
writer.flush();
|
|
CHECK_INVARIANT(writer.numMols() == 2, "");
|
|
|
|
std::string txt = ss.str();
|
|
TEST_ASSERT(txt.find("V2000") != std::string::npos);
|
|
TEST_ASSERT(txt.find("V3000") != std::string::npos);
|
|
TEST_ASSERT(txt.find("V2000") > txt.find("V3000"));
|
|
}
|
|
{
|
|
// kekulization
|
|
std::stringstream ss;
|
|
SDWriter writer(&ss, false);
|
|
RWMol *mol = SmilesToMol("c1ccccc1");
|
|
writer.write(*mol);
|
|
delete mol;
|
|
writer.flush();
|
|
CHECK_INVARIANT(writer.numMols() == 1, "");
|
|
|
|
std::string txt = ss.str();
|
|
TEST_ASSERT(txt.find(" 1 2 2") != std::string::npos);
|
|
TEST_ASSERT(txt.find(" 1 2 4") == std::string::npos);
|
|
}
|
|
{
|
|
// kekulization
|
|
std::stringstream ss;
|
|
SDWriter writer(&ss, false);
|
|
RWMol *mol = SmilesToMol("c1ccccc1");
|
|
writer.setKekulize(false);
|
|
writer.write(*mol);
|
|
delete mol;
|
|
writer.flush();
|
|
CHECK_INVARIANT(writer.numMols() == 1, "");
|
|
|
|
std::string txt = ss.str();
|
|
TEST_ASSERT(txt.find(" 1 2 2") == std::string::npos);
|
|
TEST_ASSERT(txt.find(" 1 2 4") != std::string::npos);
|
|
}
|
|
{
|
|
// kekulization
|
|
std::stringstream ss;
|
|
SDWriter writer(&ss, false);
|
|
RWMol *mol = SmilesToMol("c1ccccc1");
|
|
writer.write(*mol);
|
|
writer.setKekulize(false);
|
|
writer.write(*mol);
|
|
delete mol;
|
|
writer.flush();
|
|
CHECK_INVARIANT(writer.numMols() == 2, "");
|
|
|
|
std::string txt = ss.str();
|
|
TEST_ASSERT(txt.find(" 1 2 2") != std::string::npos);
|
|
TEST_ASSERT(txt.find(" 1 2 4") != std::string::npos);
|
|
TEST_ASSERT(txt.find(" 1 2 2") < txt.find(" 1 2 4"));
|
|
}
|
|
{
|
|
// kekulization
|
|
std::stringstream ss;
|
|
SDWriter writer(&ss, false);
|
|
RWMol *mol = SmilesToMol("c1ccccc1");
|
|
writer.setKekulize(false);
|
|
writer.write(*mol);
|
|
writer.setKekulize(true);
|
|
writer.write(*mol);
|
|
delete mol;
|
|
writer.flush();
|
|
CHECK_INVARIANT(writer.numMols() == 2, "");
|
|
|
|
std::string txt = ss.str();
|
|
TEST_ASSERT(txt.find(" 1 2 2") != std::string::npos);
|
|
TEST_ASSERT(txt.find(" 1 2 4") != std::string::npos);
|
|
TEST_ASSERT(txt.find(" 1 2 2") > txt.find(" 1 2 4"));
|
|
}
|
|
BOOST_LOG(rdInfoLog) << "done" << std::endl;
|
|
}
|
|
|
|
void testZBO() {
|
|
BOOST_LOG(rdInfoLog) << "testing handling of ZBO specs" << std::endl;
|
|
std::string rdbase = getenv("RDBASE");
|
|
rdbase += "/Code/GraphMol/FileParsers/test_data/";
|
|
{
|
|
std::string fName;
|
|
fName = rdbase + "FeCO5.mol";
|
|
ROMol *m = MolFileToMol(fName);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumAtoms() == 11);
|
|
TEST_ASSERT(m->getNumBonds() == 10);
|
|
TEST_ASSERT(m->getBondWithIdx(0)->getBondType() == Bond::ZERO);
|
|
TEST_ASSERT(m->getBondWithIdx(1)->getBondType() == Bond::ZERO);
|
|
TEST_ASSERT(m->getBondWithIdx(2)->getBondType() == Bond::ZERO);
|
|
TEST_ASSERT(m->getBondWithIdx(6)->getBondType() == Bond::ZERO);
|
|
TEST_ASSERT(m->getBondWithIdx(7)->getBondType() == Bond::ZERO);
|
|
|
|
std::string mb = MolToMolBlock(*m);
|
|
delete m;
|
|
std::cerr << "MOLBLOCK:\n" << mb << "------\n";
|
|
m = MolBlockToMol(mb);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumAtoms() == 11);
|
|
TEST_ASSERT(m->getNumBonds() == 10);
|
|
TEST_ASSERT(m->getBondWithIdx(0)->getBondType() == Bond::ZERO);
|
|
TEST_ASSERT(m->getBondWithIdx(1)->getBondType() == Bond::ZERO);
|
|
TEST_ASSERT(m->getBondWithIdx(2)->getBondType() == Bond::ZERO);
|
|
TEST_ASSERT(m->getBondWithIdx(6)->getBondType() == Bond::ZERO);
|
|
TEST_ASSERT(m->getBondWithIdx(7)->getBondType() == Bond::ZERO);
|
|
|
|
delete m;
|
|
}
|
|
|
|
{
|
|
std::string fName;
|
|
fName = rdbase + "H3BNH3.mol";
|
|
ROMol *m = MolFileToMol(fName);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumAtoms() == 2);
|
|
TEST_ASSERT(m->getNumBonds() == 1);
|
|
TEST_ASSERT(m->getBondWithIdx(0)->getBondType() == Bond::ZERO);
|
|
TEST_ASSERT(m->getAtomWithIdx(0)->getFormalCharge() == 0);
|
|
TEST_ASSERT(m->getAtomWithIdx(1)->getFormalCharge() == 0);
|
|
TEST_ASSERT(m->getAtomWithIdx(0)->getNumExplicitHs() == 3);
|
|
TEST_ASSERT(m->getAtomWithIdx(1)->getNumExplicitHs() == 0);
|
|
TEST_ASSERT(m->getAtomWithIdx(0)->getTotalNumHs() == 3);
|
|
TEST_ASSERT(m->getAtomWithIdx(1)->getTotalNumHs() == 3);
|
|
|
|
std::string mb = MolToMolBlock(*m);
|
|
delete m;
|
|
// std::cerr<<"MOLBLOCK:\n"<<mb<<"------\n";
|
|
m = MolBlockToMol(mb);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumAtoms() == 2);
|
|
TEST_ASSERT(m->getNumBonds() == 1);
|
|
TEST_ASSERT(m->getBondWithIdx(0)->getBondType() == Bond::ZERO);
|
|
TEST_ASSERT(m->getAtomWithIdx(0)->getFormalCharge() == 0);
|
|
TEST_ASSERT(m->getAtomWithIdx(1)->getFormalCharge() == 0);
|
|
TEST_ASSERT(m->getAtomWithIdx(0)->getNumExplicitHs() == 3);
|
|
TEST_ASSERT(m->getAtomWithIdx(1)->getNumExplicitHs() == 3);
|
|
TEST_ASSERT(m->getAtomWithIdx(0)->getTotalNumHs() == 3);
|
|
TEST_ASSERT(m->getAtomWithIdx(1)->getTotalNumHs() == 3);
|
|
|
|
delete m;
|
|
}
|
|
BOOST_LOG(rdInfoLog) << "done" << std::endl;
|
|
}
|
|
|
|
void testV3000WriterDetails() {
|
|
BOOST_LOG(rdInfoLog) << "testing details of v3000 writing" << std::endl;
|
|
std::string rdbase = getenv("RDBASE");
|
|
rdbase += "/Code/GraphMol/FileParsers/test_data/";
|
|
{
|
|
std::string fName = rdbase + "chebi_57262.v3k.mol";
|
|
RWMol *m = MolFileToMol(fName);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumAtoms() == 22);
|
|
TEST_ASSERT(m->getNumBonds() == 21);
|
|
TEST_ASSERT(m->getAtomWithIdx(18)->getAtomicNum() == 0);
|
|
TEST_ASSERT(!m->getAtomWithIdx(18)->hasQuery());
|
|
TEST_ASSERT(m->getAtomWithIdx(18)->getIsotope() == 1);
|
|
TEST_ASSERT(m->getAtomWithIdx(21)->getAtomicNum() == 0);
|
|
TEST_ASSERT(!m->getAtomWithIdx(21)->hasQuery());
|
|
TEST_ASSERT(m->getAtomWithIdx(21)->getIsotope() == 2);
|
|
|
|
std::string mb = MolToMolBlock(*m, true, -1, true, true);
|
|
TEST_ASSERT(mb.find("MASS=1") != std::string::npos);
|
|
TEST_ASSERT(mb.find("MASS=2") != std::string::npos);
|
|
|
|
delete m;
|
|
m = MolBlockToMol(mb);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumAtoms() == 22);
|
|
TEST_ASSERT(m->getNumBonds() == 21);
|
|
TEST_ASSERT(m->getAtomWithIdx(18)->getAtomicNum() == 0);
|
|
TEST_ASSERT(!m->getAtomWithIdx(18)->hasQuery());
|
|
TEST_ASSERT(m->getAtomWithIdx(18)->getIsotope() == 1);
|
|
TEST_ASSERT(m->getAtomWithIdx(21)->getAtomicNum() == 0);
|
|
TEST_ASSERT(!m->getAtomWithIdx(21)->hasQuery());
|
|
TEST_ASSERT(m->getAtomWithIdx(21)->getIsotope() == 2);
|
|
|
|
// repeat that one more time to make sure we're really solid:
|
|
mb = MolToMolBlock(*m, true, -1, true, true);
|
|
TEST_ASSERT(mb.find("MASS=1") != std::string::npos);
|
|
TEST_ASSERT(mb.find("MASS=2") != std::string::npos);
|
|
|
|
delete m;
|
|
m = MolBlockToMol(mb);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumAtoms() == 22);
|
|
TEST_ASSERT(m->getNumBonds() == 21);
|
|
TEST_ASSERT(m->getAtomWithIdx(18)->getAtomicNum() == 0);
|
|
TEST_ASSERT(!m->getAtomWithIdx(18)->hasQuery());
|
|
TEST_ASSERT(m->getAtomWithIdx(18)->getIsotope() == 1);
|
|
TEST_ASSERT(m->getAtomWithIdx(21)->getAtomicNum() == 0);
|
|
TEST_ASSERT(!m->getAtomWithIdx(21)->hasQuery());
|
|
TEST_ASSERT(m->getAtomWithIdx(21)->getIsotope() == 2);
|
|
|
|
delete m;
|
|
}
|
|
|
|
BOOST_LOG(rdInfoLog) << "done" << std::endl;
|
|
}
|
|
|
|
void testGithub187() {
|
|
BOOST_LOG(rdInfoLog) << "testing github issue 187: A not written to mol block"
|
|
<< std::endl;
|
|
std::string rdbase = getenv("RDBASE");
|
|
rdbase += "/Code/GraphMol/FileParsers/test_data/";
|
|
|
|
{
|
|
std::string fName = rdbase + "github187.mol";
|
|
RWMol *m = MolFileToMol(fName);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumAtoms() == 1);
|
|
TEST_ASSERT(m->getNumBonds() == 0);
|
|
TEST_ASSERT(m->getAtomWithIdx(0)->hasQuery());
|
|
std::string mb = MolToMolBlock(*m);
|
|
TEST_ASSERT(mb.find(" A 0") != std::string::npos);
|
|
|
|
// try the v3000 version:
|
|
mb = MolToMolBlock(*m, true, -1, true, true);
|
|
TEST_ASSERT(mb.find("V30 1 A 0") != std::string::npos);
|
|
|
|
delete m;
|
|
}
|
|
|
|
{
|
|
std::string fName = rdbase + "github187.v3k.mol";
|
|
RWMol *m = MolFileToMol(fName);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumAtoms() == 1);
|
|
TEST_ASSERT(m->getNumBonds() == 0);
|
|
TEST_ASSERT(m->getAtomWithIdx(0)->hasQuery());
|
|
std::string mb = MolToMolBlock(*m);
|
|
TEST_ASSERT(mb.find(" A 0") != std::string::npos);
|
|
|
|
// try the v3000 version:
|
|
mb = MolToMolBlock(*m, true, -1, true, true);
|
|
TEST_ASSERT(mb.find("V30 1 A 0") != std::string::npos);
|
|
|
|
delete m;
|
|
}
|
|
|
|
{
|
|
std::string fName = rdbase + "github187.2.mol";
|
|
RWMol *m = MolFileToMol(fName);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumAtoms() == 1);
|
|
TEST_ASSERT(m->getNumBonds() == 0);
|
|
TEST_ASSERT(m->getAtomWithIdx(0)->hasQuery());
|
|
std::string mb = MolToMolBlock(*m);
|
|
TEST_ASSERT(mb.find(" Q 0") != std::string::npos);
|
|
|
|
// try the v3000 version:
|
|
mb = MolToMolBlock(*m, true, -1, true, true);
|
|
TEST_ASSERT(mb.find("V30 1 \"NOT [C,H]\" 0") != std::string::npos);
|
|
|
|
delete m;
|
|
}
|
|
|
|
BOOST_LOG(rdInfoLog) << "done" << std::endl;
|
|
}
|
|
|
|
void testGithub186() {
|
|
BOOST_LOG(rdInfoLog)
|
|
<< "testing github issue 186: chiral S not written to ctab" << std::endl;
|
|
std::string rdbase = getenv("RDBASE");
|
|
rdbase += "/Code/GraphMol/FileParsers/test_data/";
|
|
|
|
{
|
|
std::string fName = rdbase + "github186.mol";
|
|
RWMol *m = MolFileToMol(fName);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumAtoms() == 11);
|
|
TEST_ASSERT(m->getNumBonds() == 10);
|
|
TEST_ASSERT(m->getAtomWithIdx(6)->getChiralTag() != Atom::CHI_UNSPECIFIED &&
|
|
m->getAtomWithIdx(6)->getChiralTag() != Atom::CHI_OTHER);
|
|
|
|
std::string mb = MolToMolBlock(*m);
|
|
delete m;
|
|
m = MolBlockToMol(mb);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumAtoms() == 11);
|
|
TEST_ASSERT(m->getNumBonds() == 10);
|
|
TEST_ASSERT(m->getAtomWithIdx(6)->getChiralTag() != Atom::CHI_UNSPECIFIED &&
|
|
m->getAtomWithIdx(6)->getChiralTag() != Atom::CHI_OTHER);
|
|
|
|
delete m;
|
|
}
|
|
}
|
|
|
|
void testGithub189() {
|
|
BOOST_LOG(rdInfoLog)
|
|
<< "testing github issue 189: Problems round-tripping Al2Cl6 via CTAB"
|
|
<< std::endl;
|
|
std::string rdbase = getenv("RDBASE");
|
|
rdbase += "/Code/GraphMol/FileParsers/test_data/";
|
|
|
|
{
|
|
std::string fName = rdbase + "github189.mol";
|
|
RWMol *m = MolFileToMol(fName);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumAtoms() == 8);
|
|
TEST_ASSERT(m->getNumBonds() == 8);
|
|
TEST_ASSERT(m->getAtomWithIdx(2)->getNoImplicit());
|
|
TEST_ASSERT(m->getAtomWithIdx(2)->getTotalValence() == 4);
|
|
|
|
std::string mb = MolToMolBlock(*m);
|
|
delete m;
|
|
m = MolBlockToMol(mb);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumAtoms() == 8);
|
|
TEST_ASSERT(m->getNumBonds() == 8);
|
|
TEST_ASSERT(m->getAtomWithIdx(2)->getNoImplicit());
|
|
TEST_ASSERT(m->getAtomWithIdx(2)->getTotalValence() == 4);
|
|
|
|
// try v3k
|
|
mb = MolToMolBlock(*m, true, -1, true, true);
|
|
delete m;
|
|
m = MolBlockToMol(mb);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumAtoms() == 8);
|
|
TEST_ASSERT(m->getNumBonds() == 8);
|
|
TEST_ASSERT(m->getAtomWithIdx(2)->getNoImplicit());
|
|
TEST_ASSERT(m->getAtomWithIdx(2)->getTotalValence() == 4);
|
|
|
|
delete m;
|
|
}
|
|
}
|
|
|
|
void testGithub266() {
|
|
BOOST_LOG(rdInfoLog)
|
|
<< "testing github issue 266: Bond query information written to CTAB"
|
|
<< std::endl;
|
|
std::string rdbase = getenv("RDBASE");
|
|
rdbase += "/Code/GraphMol/FileParsers/test_data/";
|
|
|
|
{
|
|
std::string fName = rdbase + "bond-query.mol";
|
|
RWMol *m = MolFileToMol(fName);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumBonds() == 4);
|
|
TEST_ASSERT(m->getBondWithIdx(1)->hasQuery());
|
|
TEST_ASSERT(m->getBondWithIdx(1)->getQuery()->getDescription() == "BondOr");
|
|
|
|
std::string mb = MolToMolBlock(*m);
|
|
RWMol *m2 = MolBlockToMol(mb);
|
|
TEST_ASSERT(m2->getNumBonds() == 4);
|
|
TEST_ASSERT(m2->getBondWithIdx(1)->hasQuery());
|
|
TEST_ASSERT(m2->getBondWithIdx(1)->getQuery()->getDescription() ==
|
|
"BondOr");
|
|
|
|
// try v3k
|
|
mb = MolToMolBlock(*m, true, -1, true, true);
|
|
delete m2;
|
|
m2 = MolBlockToMol(mb);
|
|
TEST_ASSERT(m2->getNumBonds() == 4);
|
|
TEST_ASSERT(m2->getBondWithIdx(1)->hasQuery());
|
|
TEST_ASSERT(m2->getBondWithIdx(1)->getQuery()->getDescription() ==
|
|
"BondOr");
|
|
|
|
delete m;
|
|
}
|
|
|
|
{
|
|
std::string fName = rdbase + "bond-query2.mol";
|
|
RWMol *m = MolFileToMol(fName);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumBonds() == 4);
|
|
TEST_ASSERT(m->getBondWithIdx(1)->hasQuery());
|
|
TEST_ASSERT(m->getBondWithIdx(1)->getQuery()->getDescription() == "BondOr");
|
|
|
|
std::string mb = MolToMolBlock(*m);
|
|
RWMol *m2 = MolBlockToMol(mb);
|
|
TEST_ASSERT(m2->getNumBonds() == 4);
|
|
TEST_ASSERT(m2->getBondWithIdx(1)->hasQuery());
|
|
TEST_ASSERT(m2->getBondWithIdx(1)->getQuery()->getDescription() ==
|
|
"BondOr");
|
|
|
|
// try v3k
|
|
mb = MolToMolBlock(*m, true, -1, true, true);
|
|
delete m2;
|
|
m2 = MolBlockToMol(mb);
|
|
TEST_ASSERT(m2->getNumBonds() == 4);
|
|
TEST_ASSERT(m2->getBondWithIdx(1)->hasQuery());
|
|
TEST_ASSERT(m2->getBondWithIdx(1)->getQuery()->getDescription() ==
|
|
"BondOr");
|
|
|
|
delete m;
|
|
}
|
|
|
|
{
|
|
std::string fName = rdbase + "bond-query3.mol";
|
|
RWMol *m = MolFileToMol(fName);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumBonds() == 4);
|
|
TEST_ASSERT(m->getBondWithIdx(1)->hasQuery());
|
|
TEST_ASSERT(m->getBondWithIdx(1)->getQuery()->getDescription() == "BondOr");
|
|
|
|
std::string mb = MolToMolBlock(*m);
|
|
RWMol *m2 = MolBlockToMol(mb);
|
|
TEST_ASSERT(m2->getNumBonds() == 4);
|
|
TEST_ASSERT(m2->getBondWithIdx(1)->hasQuery());
|
|
TEST_ASSERT(m2->getBondWithIdx(1)->getQuery()->getDescription() ==
|
|
"BondOr");
|
|
|
|
// try v3k
|
|
mb = MolToMolBlock(*m, true, -1, true, true);
|
|
delete m2;
|
|
m2 = MolBlockToMol(mb);
|
|
TEST_ASSERT(m2->getNumBonds() == 4);
|
|
TEST_ASSERT(m2->getBondWithIdx(1)->hasQuery());
|
|
TEST_ASSERT(m2->getBondWithIdx(1)->getQuery()->getDescription() ==
|
|
"BondOr");
|
|
|
|
delete m;
|
|
}
|
|
|
|
{
|
|
ROMol *m = SmartsToMol("C-CN");
|
|
TEST_ASSERT(m);
|
|
std::string mb = MolToMolBlock(*m);
|
|
RWMol *m2 = MolBlockToMol(mb);
|
|
TEST_ASSERT(m2->getNumBonds() == 2);
|
|
TEST_ASSERT(!m2->getAtomWithIdx(0)->hasQuery());
|
|
TEST_ASSERT(!m2->getAtomWithIdx(1)->hasQuery());
|
|
TEST_ASSERT(!m2->getAtomWithIdx(2)->hasQuery());
|
|
TEST_ASSERT(m2->getAtomWithIdx(0)->getAtomicNum() == 6);
|
|
TEST_ASSERT(m2->getAtomWithIdx(1)->getAtomicNum() == 6);
|
|
TEST_ASSERT(m2->getAtomWithIdx(2)->getAtomicNum() == 7);
|
|
TEST_ASSERT(!m2->getBondWithIdx(0)->hasQuery());
|
|
TEST_ASSERT(m2->getBondWithIdx(1)->hasQuery());
|
|
TEST_ASSERT(m2->getBondWithIdx(1)->getQuery()->getDescription() ==
|
|
"BondOr");
|
|
}
|
|
}
|
|
|
|
void testGithub268() {
|
|
BOOST_LOG(rdInfoLog)
|
|
<< "testing github issue 268: Bond topology information written to CTAB"
|
|
<< std::endl;
|
|
std::string rdbase = getenv("RDBASE");
|
|
rdbase += "/Code/GraphMol/FileParsers/test_data/";
|
|
|
|
{
|
|
std::string fName = rdbase + "bond-query4.mol";
|
|
RWMol *m = MolFileToMol(fName);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumBonds() == 4);
|
|
TEST_ASSERT(m->getBondWithIdx(1)->hasQuery());
|
|
TEST_ASSERT(m->getBondWithIdx(1)->getQuery()->getDescription() ==
|
|
"BondAnd");
|
|
|
|
std::string mb = MolToMolBlock(*m);
|
|
RWMol *m2 = MolBlockToMol(mb);
|
|
TEST_ASSERT(m2->getNumBonds() == 4);
|
|
TEST_ASSERT(m2->getBondWithIdx(1)->hasQuery());
|
|
TEST_ASSERT(m2->getBondWithIdx(1)->getQuery()->getDescription() ==
|
|
"BondAnd");
|
|
|
|
// try v3k
|
|
mb = MolToMolBlock(*m, true, -1, true, true);
|
|
delete m2;
|
|
m2 = MolBlockToMol(mb);
|
|
TEST_ASSERT(m2->getNumBonds() == 4);
|
|
TEST_ASSERT(m2->getBondWithIdx(1)->hasQuery());
|
|
TEST_ASSERT(m2->getBondWithIdx(1)->getQuery()->getDescription() ==
|
|
"BondAnd");
|
|
|
|
delete m;
|
|
}
|
|
}
|
|
|
|
void testGithub357() {
|
|
BOOST_LOG(rdInfoLog) << "testing github issue 357: Hydrogens in mol blocks "
|
|
"have a valence value set"
|
|
<< std::endl;
|
|
{
|
|
ROMol *m1 = SmilesToMol("O");
|
|
TEST_ASSERT(m1);
|
|
ROMol *m2 = MolOps::addHs(*m1);
|
|
TEST_ASSERT(m2);
|
|
delete m1;
|
|
std::string mb = MolToMolBlock(*m2);
|
|
TEST_ASSERT(
|
|
mb.find(" 0.0000 0.0000 0.0000 H 0 0 0 0 0 1") ==
|
|
std::string::npos);
|
|
}
|
|
}
|
|
|
|
void testNeedsUpdatePropertyCacheSDWriter() {
|
|
BOOST_LOG(rdInfoLog)
|
|
<< "testing test needsUpdatePropertyCache functionality in SDwriter"
|
|
<< std::endl;
|
|
{
|
|
ROMol *m1 = SmilesToMol("c1ccccc1[NH]C(=O)", 0, false);
|
|
TEST_ASSERT(m1);
|
|
TEST_ASSERT(m1->needsUpdatePropertyCache() == true);
|
|
std::string mb = MolToMolBlock(*m1);
|
|
delete m1;
|
|
ROMol *m2 = MolBlockToMol(mb);
|
|
TEST_ASSERT(m2);
|
|
delete m2;
|
|
}
|
|
}
|
|
|
|
void testGithub488() {
|
|
BOOST_LOG(rdInfoLog) << "testing github issue 488: SmilesWriter not creating "
|
|
"automatic name values for molecules read from CTABs"
|
|
<< std::endl;
|
|
{
|
|
ROMol *m1 = SmilesToMol("O");
|
|
TEST_ASSERT(m1);
|
|
m1->setProp("_Name", "");
|
|
std::stringstream ss;
|
|
SmilesWriter w(&ss);
|
|
w.write(*m1);
|
|
m1->setProp("_Name", "foo");
|
|
w.write(*m1);
|
|
m1->clearProp("_Name");
|
|
w.write(*m1);
|
|
m1->setProp("_Name", " ");
|
|
w.write(*m1);
|
|
w.close();
|
|
std::string txt = ss.str();
|
|
TEST_ASSERT(txt.find("O 0") != std::string::npos);
|
|
TEST_ASSERT(txt.find("O foo") != std::string::npos);
|
|
TEST_ASSERT(txt.find("O 2") != std::string::npos);
|
|
TEST_ASSERT(txt.find("O \n") != std::string::npos);
|
|
}
|
|
}
|
|
|
|
void testGithub611() {
|
|
BOOST_LOG(rdInfoLog) << "testing github issue 611: If wedged bonds are "
|
|
"already present, write them to mol blocks"
|
|
<< std::endl;
|
|
std::string rdbase = getenv("RDBASE");
|
|
rdbase += "/Code/GraphMol/FileParsers/test_data/";
|
|
{
|
|
std::string fName = rdbase + "Github611.mol";
|
|
RWMol *m = MolFileToMol(fName);
|
|
TEST_ASSERT(m);
|
|
std::string mb = MolToMolBlock(*m);
|
|
TEST_ASSERT(mb.find("3 5 1 1") != std::string::npos);
|
|
|
|
m->getBondWithIdx(2)->setBondDir(Bond::BEGINWEDGE);
|
|
mb = MolToMolBlock(*m);
|
|
TEST_ASSERT(mb.find("3 5 1 1") == std::string::npos);
|
|
TEST_ASSERT(mb.find("3 4 1 1") != std::string::npos);
|
|
}
|
|
}
|
|
|
|
void testGetSDText() {
|
|
BOOST_LOG(rdInfoLog) << "testing SDWriter::getText()" << std::endl;
|
|
std::string rdbase = getenv("RDBASE");
|
|
rdbase += "/Code/GraphMol/FileParsers/test_data/";
|
|
{
|
|
std::string fname = rdbase + "NCI_aids_few.sdf";
|
|
SDMolSupplier sdsup(fname);
|
|
|
|
while (!sdsup.atEnd()) {
|
|
ROMol *mol = sdsup.next();
|
|
TEST_ASSERT(mol);
|
|
std::string sdf = SDWriter::getText(*mol);
|
|
SDMolSupplier tsupp;
|
|
tsupp.setData(sdf);
|
|
ROMol *mol2 = tsupp[0];
|
|
TEST_ASSERT(mol2);
|
|
std::string csmi1 = MolToSmiles(*mol, true);
|
|
std::string csmi2 = MolToSmiles(*mol2, true);
|
|
TEST_ASSERT(csmi1 == csmi2);
|
|
STR_VECT pns = mol->getPropList(false, false);
|
|
BOOST_FOREACH (const std::string &pn, pns) {
|
|
TEST_ASSERT(mol2->hasProp(pn));
|
|
TEST_ASSERT(mol->getProp<std::string>(pn) ==
|
|
mol2->getProp<std::string>(pn));
|
|
}
|
|
delete mol;
|
|
delete mol2;
|
|
}
|
|
}
|
|
}
|
|
|
|
int main() {
|
|
RDLog::InitLogs();
|
|
#if 1
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testSmilesWriter()\n";
|
|
testSmilesWriter();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testSmilesWriter2()\n";
|
|
testSmilesWriter2();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testSmilesWriterNoNames()\n";
|
|
testSmilesWriterNoNames();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testSmilesWriterClose()\n";
|
|
testSmilesWriterNoNames();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testSDWriter()\n";
|
|
testSDWriter();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testTDTWriter()\n";
|
|
testTDTWriter();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testSmilesWriterStrm()\n";
|
|
testSmilesWriterStrm();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testSDWriterStrm()\n";
|
|
testSDWriterStrm();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testTDTWriterStrm()\n";
|
|
testTDTWriterStrm();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testSDMemoryCorruption()\n";
|
|
testSDMemoryCorruption();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testIssue265()\n";
|
|
testIssue265();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testMolFileChiralFlag()\n";
|
|
testMolFileChiralFlag();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
testMolFileTotalValence();
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
testMolFileWithRxn();
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
testZBO();
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
testSDWriterOptions();
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
testV3000WriterDetails();
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
testGithub187();
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
testGithub186();
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
testGithub189();
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
testGithub266();
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
testGithub268();
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
testGithub357();
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
testNeedsUpdatePropertyCacheSDWriter();
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
#endif
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testIssue3525000()\n";
|
|
testIssue3525000();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
testGithub488();
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
testGithub611();
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
testGetSDText();
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
}
|