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/**********************************************************************
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
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.
***********************************************************************/
#include "mol.h"
#include "obutil.h"
#include "parsmart.h"
#include "typer.h"
#include "rotor.h"
#include "binary.h"
#include "commandline.h"
#include "version.h"
#include "data.h"
#include <stdio.h>
#ifdef __sgi
#include <iostream.h>
#include <fstream.h>
#else
#include <iostream>
#include <fstream>
#endif
using namespace std;
using namespace OpenBabel;
void usage();
// There isn't a great way to do this -- we need to save argv[0] for usage()
static char *program_name;
int main(int argc,char *argv[])
{
io_type inFileType = UNDEFINED, outFileType = UNDEFINED;
bool gotInType = false, gotOutType = false, removeHydrogens = false;
bool addHydrogens = false;
int arg, inFileArg, outFileArg;
char *ext;
char *formatOptions;
OBFileFormat fileFormat;
// Parse commandline
program_name = argv[0];
inFileArg = 0;
outFileArg = 0;
for (arg = 1; arg <= argc; arg++)
{
if (argv[arg])
{
if (argv[arg][0] == '-')
{
switch (argv[arg][1])
{
case 'v':
{
cout << "Open Babel " << BABEL_VERSION << " -- "
<< __DATE__ << " -- " << __TIME__ << endl;
exit(0);
}
case 'd':
removeHydrogens = true;
break;
case 'h':
addHydrogens = true;
break;
case 'i':
gotInType = true;
ext = argv[arg] + 2;
if (strncasecmp(ext, "MIME", 4) == 0)
outFileType = extab.MIMEToType(ext);
else if (extab.CanReadExtension(ext))
inFileType = extab.FilenameToType(ext);
else
{
cerr << program_name << ": Cannot read input format!" << endl;
usage();
}
break;
case 'o':
gotOutType = true;
ext = argv[arg] + 2;
if (strncasecmp(ext, "MIME", 4) == 0)
outFileType = extab.MIMEToType(ext);
else if (extab.CanWriteExtension(ext))
outFileType = extab.FilenameToType(ext);
else
{
cerr << program_name << ": Cannot write output format!" << endl;
usage();
}
break;
case 'x':
formatOptions = argv[arg];
break;
case '-':
if (inFileArg == 0)
inFileArg = -1;
else
outFileArg = -1;
break;
default:
usage();
break;
}
}
else if (inFileArg == 0)
inFileArg = arg;
else
outFileArg = arg;
}
}
if (inFileArg == 0 || outFileArg == 0
|| (inFileArg < 0 && !gotInType)
|| (outFileArg < 0 && !gotOutType))
usage();
if (!gotInType)
{
if (extab.CanReadExtension(argv[inFileArg]))
inFileType = extab.FilenameToType(argv[inFileArg]);
else
{
cerr << program_name << ": Cannot read input format!" << endl;
usage();
}
}
if (!gotOutType)
{
if (extab.CanWriteExtension(argv[outFileArg]))
outFileType = extab.FilenameToType(argv[outFileArg]);
else
{
cerr << program_name << ": Cannot write output format!" << endl;
usage();
}
}
// Finally, we can do some work!
OBMol mol(inFileType, outFileType);
// read
if (inFileArg > 0)
{
ifstream inFileStream(argv[inFileArg]);
if (!inFileStream)
{
cerr << program_name << ": Cannot read input file!" << endl;
exit (-1);
}
fileFormat.ReadMolecule(inFileStream, mol, argv[inFileArg]);
}
else
fileFormat.ReadMolecule(cin, mol, "STDIN");
// Perform any requested transformations
if (removeHydrogens)
mol.DeleteHydrogens();
if (addHydrogens)
mol.AddHydrogens(false, false);
// write
if (outFileArg > 0)
{
ofstream outFileStream(argv[outFileArg]);
if (!outFileStream)
{
cerr << program_name << ": Cannot write to output file!" << endl;
exit (-1);
}
fileFormat.WriteMolecule(outFileStream, mol, "3D", formatOptions);
}
else
fileFormat.WriteMolecule(cout, mol, "3D", formatOptions);
return(0);
}
void usage()
{
unsigned int i;
cout << "Open Babel " << BABEL_VERSION << " -- " << __DATE__ << " -- "
<< __TIME__ << endl;
cout << "Usage is : " << endl << program_name
<< " [-i<input-type>] <name> [-o<output-type>] <name>" << endl;
cout << endl << "Currently supported input types" << endl;
for (i = 0; i < extab.Count(); i++)
if (extab.IsReadable(i))
cout << "\t" << extab.GetExtension(i) << " -- "
<< extab.GetDescription(i) << " file" << endl;
cout << endl << "Currently supported output types" << endl;
for (i = 0; i < extab.Count(); i++)
if (extab.IsWritable(i))
cout << "\t" << extab.GetExtension(i) << " -- "
<< extab.GetDescription(i) << " file" << endl;
cout << "Additional options : " << endl;
cout << " -d Delete Hydrogens " << endl;
cout << " -h Add Hydrogens " << endl;
cout << " -x[flags] XML.CML options (e.g. -x1ac) " << endl;
cout << " 1 output CML V1.0 (default)" << endl;
cout << " 2 output CML V2.0 (Schema)" << endl;
cout << " a output array format for atoms and bonds (default <atom>)" << endl;
cout << " p prettyprint output (default no indent)" << endl;
cout << " n output namespace (default no namespace)" << endl;
cout << " c use 'cml' as output namespace prefix (else default) (forces n)" << endl;
cout << " d output DOCTYPE (default none)" << endl;
cout << " g debug output" << endl;
exit(0);
}
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