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/**********************************************************************
addhtest.cpp - Test adding hydrogens
Copyright (C) 2019 David R. Koes
This file is part of the Open Babel project.
For more information, see <http://openbabel.org/>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
***********************************************************************/
// used to set import/export for Cygwin DLLs
#ifdef WIN32
#define USING_OBDLL
#endif
#include <cstdlib>
#include <openbabel/babelconfig.h>
#include <openbabel/mol.h>
#include <openbabel/obconversion.h>
#include <openbabel/atom.h>
#include <openbabel/bond.h>
#include <openbabel/obiter.h>
#include <openbabel/elements.h>
#include <openbabel/generic.h>
#include <stdio.h>
#include <iostream>
#include <fstream>
#if defined(__sun)
#include <alloca.h>
#endif
using namespace std;
using namespace OpenBabel;
//add hydrogens and then perform some sanity checks
void addh_check(OBMol *mol)
{
unsigned len = mol->NumAtoms();
unsigned *vcnts = (unsigned*)alloca(len*sizeof(unsigned));
memset(vcnts, 0, sizeof(unsigned)*len);
//chemistry is weird, so can't rely on MaxBonds in general
//we recod the valence count before adding hydrogens
FOR_ATOMS_OF_MOL(atom, mol) {
int total_valence = atom->GetExplicitValence();
assert(atom->GetIndex() < len);
vcnts[atom->GetIndex()] = total_valence;
}
mol->AddHydrogens();
//check valences and bond lengths
FOR_ATOMS_OF_MOL(atom, mol) {
int total_valence = atom->GetTotalValence();
if(atom->GetIndex() >= len) {
assert(total_valence == 1); //H
continue;
}
int maxval = max(OBElements::GetMaxBonds(atom->GetAtomicNum()), vcnts[atom->GetIndex()]);
if(total_valence > maxval) {
cerr << "Hydrogens added when already greater than MaxBonds " << total_valence << " vs "
<< OBElements::GetMaxBonds(atom->GetAtomicNum()) << " for atom "
<< atom->GetId() << " " << OBElements::GetSymbol(atom->GetAtomicNum()) << "\n";
//exit(-1);
}
}
FOR_BONDS_OF_MOL(bond, mol) {
if(bond->GetLength() > 5) {
cerr << "Bond length between " << bond->GetBeginAtom()->GetId()
<< " and " << bond->GetEndAtom()->GetId() << " is too long: "
<< bond->GetLength() << "\n";
//exit(-1);
}
}
}
// 1
// reads addh.in, which has a file name on each line,
// reads molecule, adds hydrogens
int addhtest(int argc, char* argv[])
{
int choice = 1;
if (argc > 1) {
if(sscanf(argv[1], "%d", &choice) != 1) {
printf("Couldn't parse that input as a number\n");
return -1;
}
}
if(choice != 1) //eh, not bothering to split this up
{
cout << "Test number " << choice << " does not exist!\n";
return -1;
}
cout << endl << "# Testing addh handling... " << endl;
#ifdef TESTDATADIR
string testdatadir(TESTDATADIR);
string infile = testdatadir + "addh.in";
#else
string infile = "files/addh.in";
#endif
#ifdef FORMATDIR
char env[BUFF_SIZE];
snprintf(env, BUFF_SIZE, "BABEL_LIBDIR=%s", FORMATDIR);
putenv(env);
#endif
ifstream ifs(infile.c_str());
if (!ifs)
{
cout << "Bail out! Cannot read " << infile << endl;
return(-1);
}
//gzip.in specifies what files to read and their canonical smiles
string line;
string filepath;
vector<string> correctResults; //read from file
OBConversion conv;
OBMol mol;
while(getline(ifs, line))
{
if(line.length() == 0)
continue; //ignore blank lines
if(line[0] != '#')
{
stringstream str(line);
string fname;
str >> fname;
OBFormat *format = conv.FormatFromExt(fname.c_str());
conv.SetInFormat(format);
#ifdef TESTDATADIR
filepath = testdatadir + fname;
#else
filepath = "files/" + fname;
#endif
conv.ReadFile(&mol,filepath);
cerr << filepath << "\n";
addh_check(&mol);
}
}
return(0);
}
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