<commit_before>// $Id: proteinMapper.C,v 1.1 1999/08/26 08:02:45 oliver Exp $

#include <BALL/common.h>
#include <iostream.h>
#include <BALL/SYSTEM/timer.h>
#include <BALL/KERNEL/protein.h>
#include <BALL/KERNEL/PSE.h>
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/STRUCTURE/structureMapper.h>
#include <BALL/MATHS/matrix44.h>
#include <map>

using std::map;
using namespace BALL;

int main(int argc, char** argv) 
{

	// default values
	float upper = 8.0;
	float lower = 4.0;
	float tolerance = 0.6;


	// usage
	if ((argc < 4) || (argc > 7)) 
	{
		cout << argv[0] << " <filenameA> <filenameB> <outfilename> [<upper> [<lower> [<tolerance>]]]" << endl;
		cout << "Maps the backbone of two proteins (Calpha atoms) onto each other." << endl
				 << "Calpha atoms are recognized by their name (CA)." << endl << endl
				 << "Optional parameters:" << endl
				 << "  <upper> (float):" << endl<commit_msg>adapted to new-style ANSI streams<commit_after>// $Id: proteinMapper.C,v 1.2 1999/12/22 16:52:44 oliver Exp $

#include <BALL/common.h>
#include <iostream>
#include <BALL/SYSTEM/timer.h>
#include <BALL/KERNEL/protein.h>
#include <BALL/KERNEL/PSE.h>
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/STRUCTURE/structureMapper.h>
#include <BALL/MATHS/matrix44.h>
#include <map>

using namespace std;
using namespace BALL;

int main(int argc, char** argv) 
{

	// default values
	float upper = 8.0;
	float lower = 4.0;
	float tolerance = 0.6;


	// usage
	if ((argc < 4) || (argc > 7)) 
	{
		cout << argv[0] << " <filenameA> <filenameB> <outfilename> [<upper> [<lower> [<tolerance>]]]" << endl;
		cout << "Maps the backbone of two proteins (Calpha atoms) onto each other." << endl
				 << "Calpha atoms are recognized by their name (CA)." << endl << endl
				 << "Optional parameters:" << endl
				 << "  <upper> (float):" << endl
{'fraction_non_alphanumeric': 0.17843459222769567, 'fraction_numerical': 0.029556650246305417, 'mean_word_length': 3.835978835978836, 'pattern_counts': {'":': 0, '<': 85, '<?xml version=': 0, '>': 37, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1340905', 'n_tokens_mistral': 751, 'n_tokens_neox': 665, 'n_words': 186}