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openbabel/tools/obabel.cpp
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Julien Nabet bc917de223 Fixes #1282: check format input is provided 
to avoid a segfault
2018-04-14 14:18:18 +02:00

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/**********************************************************************
main.cpp - Main conversion program, command-line handling.
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison
Some portions Copyright (C) 2004-2010 by Chris Morley
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 <openbabel/babelconfig.h>
#include <iostream>
#include <fstream>
#include <sstream>
#include <string>
#include <map>
#if HAVE_CONIO_H
#include <conio.h>
#endif
#include <cstdlib> // for exit() on Linux
#if !HAVE_STRNCASECMP
extern "C" int strncasecmp(const char *s1, const char *s2, size_t n);
#endif
#include <openbabel/obconversion.h>
#include <openbabel/plugin.h>
using namespace std;
using namespace OpenBabel;
void DoOption(const char* p, OBConversion& Conv, OBConversion::Option_type typ,
int& arg, int argc, char *argv[]);
void usage();
void help();
// 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[])
{
OBConversion Conv(&cin, &cout); //default input and output are console
OBFormat* pInFormat = NULL;
OBFormat* pOutFormat = NULL;
bool outGzip = false;
vector<string> FileList, OutputFileList;
string OutputFileName;
// Parse commandline
bool gotInType = false, gotOutType = false;
bool SplitOrBatch=false;
char *oext = NULL;
char *iext = NULL;
//Save name of program without its path (and .exe)
string pn(argv[0]);
string::size_type pos;
#ifdef _WIN32
pos = pn.find(".exe");
if(pos!=string::npos)
argv[0][pos]='\0';
#endif
pos = pn.find_last_of("/\\");
if(pos==string::npos)
program_name=argv[0];
else
program_name=argv[0]+pos+1;
const char* p;
int arg;
for (arg = 1; arg < argc; ++arg)
{
if (argv[arg])
{
if (argv[arg][0] == '-')
{
char opchar[2]="?";
opchar[0]=argv[arg][1];
switch (opchar[0])
{
case 'V':
{
cout << "Open Babel " << BABEL_VERSION << " -- "
<< __DATE__ << " -- " << __TIME__ << endl;
exit(0);
}
case 'i':
//Parameter is the input format which overrides any file extensions
gotInType = true;
iext = argv[arg] + 2;
if(!*iext)
iext = argv[++arg]; //space left after -i: use next argument
if (iext && strncasecmp(iext, "MIME", 4) == 0)
{
// get the MIME type from the next argument
iext = argv[++arg];
pInFormat = Conv.FormatFromMIME(iext);
}
else
pInFormat = Conv.FindFormat(iext);
if(pInFormat==NULL)
{
cerr << program_name << ": cannot read input format!" << endl;
usage();
}
break;
case 'o':
//Parameter is the output format which overrides any file extension
gotOutType = true;
oext = argv[arg] + 2;
if(!*oext)
oext = argv[++arg]; //space left after -i: use next argument
if (oext && strncasecmp(oext, "MIME", 4) == 0)
{
// get the MIME type from the next argument
oext = argv[++arg];
pOutFormat = Conv.FormatFromMIME(oext);
}
else
pOutFormat = Conv.FindFormat(oext);
if(pOutFormat==NULL)
{
cerr << program_name << ": cannot write output format!" << endl;
usage();
}
break;
case 'O':
OutputFileName = argv[arg] + 2;
if(OutputFileName.size()<3)
OutputFileName = argv[++arg]; //space left after -O: use next argument
break;
case 'L': //display a list of plugin type or classes
{
const char* param=NULL;
if(argc>arg+1)
param = argv[arg+2];
// First assume first arg is a plugin type and
// param is a subtype, like babel -L ops gen3D
// or first arg is a plugin ID, like babel -L cml
OBPlugin* plugin;
if ((OBPlugin::GetPlugin("plugins", argv[arg+1]) &&
(plugin = OBPlugin::GetPlugin(argv[arg+1], param))) ||
(plugin = OBPlugin::GetPlugin(NULL, argv[arg+1])))
{
//Output details of subtype
string txt;
plugin->Display(txt, "verbose", argv[arg+1]);
cout << "One of the " << plugin->TypeID() << '\n' << txt << endl;
return 0;
}
//...otherwise assume it is a plugin type, like babel -L forcefields
//Output list of subtypes
OBPlugin::List(argv[arg+1], param);
return 0;
}
case '?':
case 'H':
if(isalnum(argv[arg][2]) || arg==argc-2)
{
if(strncasecmp(argv[arg]+2,"all",3))
{
OBFormat* pFormat
= (arg==argc-2) ? Conv.FindFormat(argv[arg+1]) : Conv.FindFormat(argv[arg]+2);
if(pFormat)
{
cout << argv[arg]+2 << " " << pFormat->Description() << endl;
if(pFormat->Flags() & NOTWRITABLE)
cout << " This format is Read-only" << endl;
if(pFormat->Flags() & NOTREADABLE)
cout << " This format is Write-only" << endl;
if(strlen(pFormat->SpecificationURL()))
cout << "Specification at: " << pFormat->SpecificationURL() << endl;
}
else
cout << "Format type: " << argv[arg]+2 << " was not recognized" <<endl;
}
else
{
OBPlugin::List("formats","verbose");
}
}
else
help();
return 0;
case '-': //long option --name text
{
//Option's text is in the next and subsequent args, until one starts with -
char* nam = argv[arg]+2;
if(!strcasecmp(nam, "help")) //special case handled here
{
help();
return 0;
}
if(*nam != '\0') //Do nothing if name is empty
{
string txt;
while(arg<argc-1 && *argv[arg+1]!='-')
{
//use text from subsequent args
if(!txt.empty())txt += ' '; //..space separated if more than one
txt += argv[++arg];
}
// If a API directive, e.g.---errorlevel
// send to the pseudoformat "obapi" (without any leading -)
if(*nam=='-')
{
OBConversion apiConv;
OBFormat* pAPI= OBConversion::FindFormat("obapi");
if(pAPI)
{
apiConv.SetOutFormat(pAPI);
apiConv.AddOption(nam+1, OBConversion::GENOPTIONS, txt.c_str());
apiConv.Write(NULL, &std::cout);
}
}
else
// Is a normal long option name, e.g --addtotitle
Conv.AddOption(nam,OBConversion::GENOPTIONS,txt.c_str());
}
}
break;
case 'm': //multiple output files
SplitOrBatch=true;
break;
case 'a': //single character input option
p = argv[arg]+2;
DoOption(p,Conv,OBConversion::INOPTIONS,arg,argc,argv);
break;
case 'x': //single character output option
p = argv[arg]+2;
DoOption(p,Conv,OBConversion::OUTOPTIONS,arg,argc,argv);
break;
//Not essential, but allows these options to be before input filenames
//since we know they take one parameter, and are the most likely options to be misplaced
case 'f':
case 'l':
p = argv[arg] + 2;
if(!*p)
p = argv[++arg]; //space left after -f: use next argument
Conv.AddOption(opchar, OBConversion::GENOPTIONS, p);
break;
case ':':
//e.g. -:c1ccccc1. SMILES passed as a file name and handled in OBConversion
FileList.push_back(argv[arg]);
break;
default: //single character general option
p = argv[arg]+1;
DoOption(p,Conv,OBConversion::GENOPTIONS,arg,argc,argv);
break;
}
}
else //filenames
FileList.push_back(argv[arg]);
}
}
#if defined(_WIN32) && defined(USING_DYNAMIC_LIBS)
//Expand wildcards in input filenames and add to FileList
vector<string> tempFileList(FileList);
FileList.clear();
vector<string>::iterator itr;
for(itr=tempFileList.begin();itr!=tempFileList.end();++itr)
{
if((*itr)[0]=='-')
FileList.push_back(*itr);
else
DLHandler::findFiles (FileList, *itr);
}
#endif
if (!gotInType)
{
if(FileList.empty())
{
cerr << "No input file or format spec or possibly a misplaced option.\n"
"Most options must come after the input files. (-i -o -O -m can be anywhwere.)\n" <<endl;
usage();
}
}
if (!gotOutType)
{
//check there is a valid output format, but the extension will be re-interpreted in OBConversion
pOutFormat = Conv.FormatFromExt(OutputFileName.c_str(), outGzip);
if(OutputFileName.empty() || pOutFormat==NULL)
{
cerr << "Missing or unknown output file or format spec or possibly a misplaced option.\n"
"Options, other than -i -o -O -m, must come after the input files.\n" <<endl;
usage();
}
}
if(!Conv.SetInFormat(pInFormat)) //rely on autodetection for gzipped input
{
cerr << "Invalid input format" << endl;
usage();
}
if(!Conv.SetOutFormat(pOutFormat, outGzip))
{
cerr << "Invalid output format" << endl;
usage();
}
if(SplitOrBatch)
{
//Put * into output file name before extension (or ext.gz)
if(OutputFileName.empty())
{
OutputFileName = "*.";
OutputFileName += oext;
}
else
{
string::size_type pos = OutputFileName.rfind(".gz");
if(pos==string::npos)
pos = OutputFileName.rfind('.');
else
pos = OutputFileName.rfind('.',pos-1);
if(pos==string::npos)
OutputFileName += '*';
else
OutputFileName.insert(pos,"*");
}
}
int count = Conv.FullConvert(FileList, OutputFileName, OutputFileList);
Conv.ReportNumberConverted(count);
if(OutputFileList.size()>1)
{
clog << OutputFileList.size() << " files output. The first is " << OutputFileList[0] <<endl;
}
//std::string messageSummary = obErrorLog.GetMessageSummary();
//if (messageSummary.size())
// {
// clog << messageSummary << endl;
// }
#ifdef _DEBUG
//CM keep window open
cout << "Press any key to finish" <<endl;
getch();
#endif
return 0;
}
void DoOption(const char* p, OBConversion& Conv,
OBConversion::Option_type typ, int& arg, int argc, char *argv[])
{
//Unlike babel, cannot have multiple concatenated single char options
//accepts: -sCCC -s CCC -s"CCC" -s CCC red -sCCC red
char ch[2]="?";
*ch = *p++;
std::string txt;
//Get the option text
if(*p)
txt = p; //use text immediately following the option letter, and keep looking
while(arg<argc-1 && *argv[arg+1]!='-')
{
//use text from subsequent args
if(!txt.empty())txt += ' '; //..space separated if more than one
txt += argv[++arg];
}
Conv.AddOption(ch, typ, txt.c_str());
}
void usage()
{
cout << "Open Babel " << BABEL_VERSION << " -- " << __DATE__ << " -- "
<< __TIME__ << endl;
cout << "Usage:\n" << program_name
<< " [-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options]" << endl;
cout << "Try -H option for more information." << endl;
#ifdef _DEBUG
//CM keep window open
cout << "Press any key to finish" <<endl;
getch();
#endif
exit (0);
}
void help()
{
cout << "Open Babel converts chemical structures from one file format to another"<< endl << endl;
cout << "Usage: " << endl;
cout << program_name << "[-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options]" << endl;
cout << "The extension of a file decides the format, unless it is overridden" <<endl;
cout << " by -i or -o options, e.g. -icml, or -o smi" << endl;
cout << "See below for available format-types, which are the same as the " << endl;
cout << "file extensions and are case independent." << endl;
cout << "If no input or output file is given stdin or stdout are used instead." << endl << endl;
cout << "More than one input file can be specified and their names can contain" <<endl;
cout << "wildcard chars (* and ?). The format of each file can be different unless" <<endl;
cout << "the -i option has been used, when they are all the same." <<endl;
cout << "By default, the molecules are aggregated in the output file," << endl;
cout << " but see -m option, Splitting, below.\n" << endl;
cout << "Options, other than -i -o -O -m, must come after the input files.\n" <<endl;
cout << OBConversion::Description(); // Conversion options
cout << "-H Outputs this help text" << endl;
cout << "-Hxxx (xxx is file format ID e.g. -Hcml) gives format info" <<endl;
cout << "-Hall Outputs details of all formats" <<endl;
cout << "-V Outputs version number" <<endl;
cout << "-L <category> Lists plugin classes of this category, e.g. <formats>" << endl;
cout << " Use just -L for a list of plugin categories." << endl;
cout << " Use -L <ID> e.g. -L sdf for details of a format or other plugin." << endl;
cout << "-m Produces multiple output files, to allow:" <<endl;
cout << " Splitting: e.g. " << program_name << " infile.mol -O new.smi -m" <<endl;
cout << " puts each molecule into new1.smi new2.smi etc" <<endl;
cout << " Batch conversion: e.g. " << program_name << " *.mol -osmi -m" <<endl;
cout << " converts each input file to a .smi file" << endl;
#ifdef _WIN32
cout << " In Windows these can also be done using the forms" <<endl;
cout << " " << program_name << " infile.mol -O new*.smi and " << program_name << " *.mol -O *.smi respectively.\n" <<endl;
#endif
OBFormat* pDefault = OBConversion::GetDefaultFormat();
if(pDefault)
cout << pDefault->TargetClassDescription();// some more options probably for OBMol
OBFormat* pAPI= OBConversion::FindFormat("obapi");
if(pAPI)
cout << pAPI->Description();
cout << "To see a list of recognized file formats use\n babel -L formats [read] [write]\n"
<< "To see details and specific options for a particular format, e.g CML, use\n babel -L cml\n"
<< endl;
//cout << "The following file formats are recognized:" << endl;
//OBPlugin::List("formats");
//cout << "\nSee further specific info and options using -H<format-type>, e.g. -Hcml" << endl;
}
/* OpenBabel man page*/
/** \page babel a converter for chemistry and molecular modeling data files
*
* \n
* \par SYNOPSIS
*
* \b babel [-H<help-options>] [-V] [-m] [-d] [-h] [-p] [-s<SMARTS-pattern>] [-v<SMARTS-pattern>] [-f<#> -l<#>] [-c] [-x<format-options>] [-i<input-type>] \<infile\> [-o<output-type>] -O\<outfile\>
*
* \par DESCRIPTION
*
* Open Babel is a program designed to interconvert a number of
* file formats currently used in molecular modeling software. \n\n
*
* Note that Open Babel can also be used as a library to interconvert
* many file formats and to provide standard chemistry software routines.
* See the Open Babel web pages (http://openbabel.org) for more
* information.
*
* \par OPTIONS
*
* If only input and output files are given, Open Babel will guess
* the file type from the filename extension. \n\n
*
* \b -V :
* Output version number and exit \n\n
* \b -H :
* Output usage information \n\n
* \b -H\<format-ID\> :
* Output formatting information and options for format specified\n\n
* \b -Hall :
* Output formatting information and options for all formats\n\n
* \b -i :
* Specifies input format, see below for the available formats \n\n
* \b -o :
* Specifies output format, see below for the available formats \n\n
* \b -m :
* Produce multiple output files, to allow:\n
* * Splitting one input file - put each molecule into consecutively numbered output files \n
* * Batch conversion - convert each of multiple input files into a specified output format \n
* See examples below \n\n
* \b -d :
* Delete Hydrogens \n\n
* \b -h :
* Add Hydrogens \n\n
* \b -p :
* Add Hydrogens appropriate for pH (use transforms in phmodel.txt) \n\n
* \b -t :
* All input files describe a single molecule \n\n
* \b -f\<#\> :
* For multiple entries input, start import at molecule # \n\n
* \b -l\<#\> :
* For multiple entries input, stop import at molecule # \n\n
* \b -c :
* Center atomic coordinates at (0,0,0) \n\n
* \b -s\<SMARTS\> :
* Convert only molecules matching the SMARTS pattern specified \n\n
* \b -v\<SMARTS\> :
* Convert only molecules \b NOT matching SMARTS pattern specified \n\n
*
* \par FILE FORMATS
*
* The following formats are currently supported by Open Babel:
* \n alc -- Alchemy format
* \n bgf -- BGF format
* \n box -- Dock 3.5 Box format
* \n bs -- Ball and Stick format
* \n c3d1 -- Chem3D Cartesian 1 format
* \n c3d2 -- Chem3D Cartesian2 format
* \n caccrt -- Cacao format
* \n cache -- CAChe format [Writeonly]
* \n cacint -- CacaoInternal format [Writeonly]
* \n car -- MSI Biosym/Insight II CAR format [Readonly]
* \n ccc -- CCC format [Readonly]
* \n cht -- ChemTool format [Writeonly]
* \n cml -- Chemical Markup Language
* \n crk2d -- Chemical Resource Kit diagram format (2D)
* \n crk3d -- Chemical Resource Kit 3D format
* \n csr -- CSR format [Writeonly]
* \n cssr -- CSD CSSR format [Writeonly]
* \n ct -- ChemDraw Connection Table format
* \n dmol -- DMol3 coordinates format
* \n ent -- Protein Data Bank format
* \n feat -- Feature format
* \n fh -- Fenske-Hall Z-Matrix format [Writeonly]
* \n fix -- FIX format [Writeonly]
* \n g03 -- Gaussian98/03 Cartesian [Writeonly]
* \n g98 -- Gaussian98/03 Cartesian [Writeonly]
* \n gam -- GAMESS Output
* \n gamout -- GAMESS Output
* \n gau -- Gaussian98/03 Cartesian [Writeonly]
* \n gpr -- Ghemical format
* \n gr96 -- GROMOS96 format [Writeonly]
* \n hin -- HyperChem Input format
* \n ins -- ShelX format [Readonly]
* \n jout -- Jaguar output format
* \n mdl -- MDL MOL format
* \n mm1gp -- Ghemical format
* \n mm3 -- MM3 format [Writeonly]
* \n mmd -- MacroMod format
* \n mmod -- MacroMod format
* \n mol -- MDL MOL format
* \n mol2 -- Sybyl Mol2 format
* \n mopcrt -- MOPAC Cartesian format
* \n mopout -- MOPAC Output format [Readonly]
* \n mpqc -- MPQC format [Readonly]
* \n nwo -- NWChem format
* \n pdb -- Protein Data Bank format
* \n pov -- POV-Ray input format [Writeonly]
* \n pqs -- Parallel Quantum Solutions format
* \n prep -- Amber Prep format [Readonly]
* \n qcout -- QChem output format
* \n qm1gp -- Ghemical format
* \n report -- Report format [Writeonly]
* \n res -- ShelX format [Readonly]
* \n rxn -- MDL RXN format
* \n sd -- MDL MOL format
* \n sdf -- MDL MOL format
* \n smi -- SMILES format
* \n tmol -- TurboMole Coordinate format
* \n txyz -- Tinker format [Writeonly]
* \n unixyz -- UniChem XYZ format
* \n vmol -- ViewMol format
* \n xed -- XED format [Writeonly]
* \n xyz -- XYZ cartesian coordinates format
* \n zin -- ZINDO input format [Writeonly]
*
* \par FORMAT OPTIONS
* Individual file formats may have additional formatting options. \n
* Input format options are preceded by 'a', e.g. -as \n
* Output format options are preceded by 'x', e.g. -xn \n
* For further specific information and options, use -H<format-type> \n
* e.g., -Hcml
*
* \par EXAMPLES
* - Standard conversion \n
* babel -ixyz ethanol.xyz -opdb ethanol.pdb \n
* - Conversion from a SMI file in STDIN to a Mol2 file written to STDOUT \n
* babel -ismi -omol2 \n
* - Split a multi-molecule file into new1.smi, new2.smi, etc. \n
* babel infile.mol new.smi -m \n
*
* \par AUTHORS
*
* Open Babel is currently maintained by \b Geoff \b Hutchison, \b Chris \b Morley and \b Michael \b Banck.
*
* For more contributors to Open Babel, see http://openbabel.org/THANKS.shtml
*
* \par COPYRIGHT
* Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
* Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison \n \n
* 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.\n \n
* 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.
*
* \par SEE ALSO
* The web pages for Open Babel can be found at http://openbabel.org/
**/
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