<commit_before>// $Id$
//
//  Copyright (C) 2006-2012 <NAME>
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
#include <RDGeneral/utils.h>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <GraphMol/RDKitQueries.h>
#include <RDGeneral/Exceptions.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <boost/dynamic_bitset.hpp>
#include <boost/tokenizer.hpp>
#include <boost/algorithm/string/trim.hpp>
#include <boost/algorithm/string.hpp>
#include <vector>
#include <algorithm>
#include <iostream>
#include <fstream>
#include <sstream>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <RDGeneral/StreamOps.h>
#include <RDGeneral/FileParseException.h>
#include <RDGeneral/BadFileException.h>
#include <GraphMol/ChemTransforms/ChemTransforms.h>

namespace RDKit{
  namespace {
    void updateSubMolConfs(const ROMol &mol,RWMol &res,
                           boost::dynamic_bitset<> &removedAtoms){
      // update conformer information:
      res.clearConformers();
      for(ROMol::ConstConformerIterator citer=mol.beginConformers();
          citer!=mol.endConformers();++citer){
        Conformer *newConf=new Conformer(res.getNumAtoms());
        newConf->setId((*citer)->getId());
        int aIdx=0;
        for(unsigned int i=0;i<mol.getNumAtoms();++i){
          if(!removedAtoms[i]){
            newConf->setAtomPos(aIdx,(*citer)->getAtomPos(i));
            ++aIdx;<commit_msg>this was a similar bug to #584<commit_after>// $Id$
//
//  Copyright (C) 2006-2012 <NAME>
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
#include <RDGeneral/utils.h>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <GraphMol/RDKitQueries.h>
#include <RDGeneral/Exceptions.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <boost/dynamic_bitset.hpp>
#include <boost/tokenizer.hpp>
#include <boost/algorithm/string/trim.hpp>
#include <boost/algorithm/string.hpp>
#include <vector>
#include <algorithm>
#include <iostream>
#include <fstream>
#include <sstream>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <RDGeneral/StreamOps.h>
#include <RDGeneral/FileParseException.h>
#include <RDGeneral/BadFileException.h>
#include <GraphMol/ChemTransforms/ChemTransforms.h>

namespace RDKit{
  namespace {
    void updateSubMolConfs(const ROMol &mol,RWMol &res,
                           boost::dynamic_bitset<> &removedAtoms){
      // update conformer information:
      res.clearConformers();
      for(ROMol::ConstConformerIterator citer=mol.beginConformers();
          citer!=mol.endConformers();++citer){
        Conformer *newConf=new Conformer(res.getNumAtoms());
        newConf->setId((*citer)->getId());
        newConf->set3D((*citer)->is3D());
        int aIdx=0;
        for(unsigned int i=0;i<mol.getNumAtoms();++i){
          if(!removedAtoms[i]){
            newConf->setAtomPos(aIdx,(*citer)->getAtomPos(i));
            ++aIdx;
{'fraction_non_alphanumeric': 0.14483589280337247, 'fraction_numerical': 0.007527853056308341, 'mean_word_length': 3.8425655976676385, 'pattern_counts': {'":': 0, '<': 51, '<?xml version=': 0, '>': 59, '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': '7550092', 'n_tokens_mistral': 1159, 'n_tokens_neox': 1126, 'n_words': 234}