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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/FORMAT/molFileFactory.h>
#include <BALL/FORMAT/dockResultFile.h>
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/KERNEL/molecule.h>
#include <BALL/FORMAT/commandlineParser.h>
#include "version.h"
using namespace BALL;
using namespace std;
void validateParameters(CommandlineParser& params)
{
String formats = MolFileFactory::getSupportedFormats();
vector<String> v;
formats.split(v,",");
String input_format = params.get("if");
String output_format = params.get("of");
bool correct_input_format = false;
bool correct_output_format = false;
for (Size i=0; i<v.size(); i++)
{
if (input_format == v[i])
{
correct_input_format = true;
}
if (output_format == v[i])
{
correct_output_format = true;
}
}
if (!correct_input_format)
{
Log.error() << "Input file format " << input_format << " is not supported\nSupported formats are " << formats << endl;
exit(1);
}
if (!correct_output_format)
{
Log.error() << "Output file format " << output_format << " is not supported\nSupported formats are " << formats << endl;
exit(1);
}
}
int main(int argc, char* argv[])
{
CommandlineParser parpars("Converter", "interconvert molecular file-formats", VERSION, String(__DATE__), "Convert, combine and store");
parpars.registerMandatoryInputFile("i", "input filename");
parpars.registerMandatoryStringParameter("if", "input format");
parpars.registerMandatoryOutputFile("o", "output filename");
parpars.registerMandatoryStringParameter("of", "output format");
parpars.registerFlag("rm", "remove input file when finished");
// the available formats
String formats = MolFileFactory::getSupportedFormats();
// we support: mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz,
// mol2.gz, sdf.gz, drf.gz, pdb.gz, ac.gz, ent.gz, brk.gz, hin.gz, mol.gz, xyz.gz.
String man = String("This tool can be used to convert between different molecular file-formats.\nSupported formats are ") + formats + String(". File extensions of input and output filenames are ignored.");
parpars.setToolManual(man);
parpars.setSupportedFormats("i",MolFileFactory::getSupportedFormats());
parpars.setSupportedFormats("o",MolFileFactory::getSupportedFormats());
vector<String> v;
formats.split(v,",");
list<String> format_list;
for (Size i=0; i<v.size(); i++)
{
format_list.push_back(v[i]);
}
parpars.setParameterRestrictions("if",format_list);
parpars.setParameterRestrictions("of",format_list);
parpars.parse(argc, argv);
validateParameters(parpars);
//String default_format = "mol2";
String input_format = parpars.get("if");
String output_format = parpars.get("of");
GenericMolFile* input = MolFileFactory::open(parpars.get("i"), ios::in, input_format, true);
GenericMolFile* output = MolFileFactory::open(parpars.get("o"), ios::out, output_format, true);
DockResultFile* drf_output = dynamic_cast<DockResultFile*>(output);
if (drf_output)
{
drf_output->setToolInfo(parpars.getStartCommand(), parpars.getStartTime());
}
Molecule* mol;
int no_written = 0;
int no_ignored = 0;
while ((mol = input->read()))
{
bool b;
if (output_format == "pdb")
{
PDBInfo *pdbi = new PDBInfo();
System* mol_sys = new System();
pdbi->setName(mol->getName());
String compnd_line = String(80, PDB::FORMAT_COMPND, 1, mol->getName().c_str());
pdbi->getSkippedRecords().push_back(String("COMPND") + compnd_line);
mol_sys->insert(*mol);
b = (dynamic_cast<PDBFile*>(output))->write(*mol_sys, *pdbi);
}
else
{
b = output->write(*mol);
}
if (b) no_written++;
else no_ignored++;
delete mol;
String smf[] = {"pdb", "pdb.gz", "ac", "ac.gz", "brk", "brk.gz", "mol", "mol.gz"};
set<String> single_molecule_formats (smf,smf+8);
if (single_molecule_formats.count(output_format) > 0)
{
if (no_written > 0)
{
Log.error() << "Output format " << output_format << " only writes one molecule per file. Only first molecule written.\nYou can use LigandFileSplitter to split input file first." << endl;
input->close();
output->close();
delete input;
delete output;
exit(1);
}
}
if (no_written%50 == 0)
{
Log.level(5) << "\r" << no_written << "molecules";
Log.flush();
}
}
Log.level(20) << "\r";
if (no_ignored > 0) Log.level(20) << "ignored " << no_ignored << " identical molecules!" << endl;
Log.level(20) << "wrote " << no_written << " molecules." << endl;
input->close();
output->close();
delete input;
delete output;
if (parpars.has("rm"))
{
File::remove(parpars.get("i"));
Log.level(20) << parpars.get("i") << " removed." << endl;
}
}
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