RDKitSVMainWindow.cc

//
// file RDKitSV.cc
// David Cosgrove
// AstraZeneca
//
// 20th June 2014
//

#include "RDKitSVMainWindow.H"
#include "RDKitSVPanel.H"
#include "RDKitSVSettings.H"
#include "QTGet2Strings.H"
#include "QT4SelectItems.H"

#include <QAction>
#include <QApplication>
#include <QFileDialog>
#include <QFileInfo>
#include <QHBoxLayout>
#include <QMenu>
#include <QMenuBar>
#include <QMessageBox>
#include <QStatusBar>
#include <QString>

#include <boost/algorithm/string.hpp>
#include <boost/algorithm/string/split.hpp>
#include <boost/bind.hpp>
#include <boost/foreach.hpp>
#include <boost/iostreams/device/file.hpp>
#include <boost/iostreams/filtering_stream.hpp>
#include <boost/iostreams/filter/gzip.hpp>
#include <boost/iostreams/stream.hpp>
#include <boost/lexical_cast.hpp>

#include <fstream>
#include <iostream>
#include <list>

#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/FileParsers/MolWriters.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/Substruct/SubstructMatch.h>

using namespace boost;
using namespace std;

namespace RDKitSV {

// ****************************************************************************
RDKitSVMainWindow::RDKitSVMainWindow( int argc , char **argv ) : QMainWindow() {

  build_actions();
  build_menubar();
  build_widget();

  parse_args( argc , argv );

}

// ****************************************************************************
void RDKitSVMainWindow::build_actions() {

  build_file_actions();
  build_smarts_actions();

}

// ****************************************************************************
void RDKitSVMainWindow::build_file_actions() {

  file_exit_ = new QAction( tr( "Exit" ) , this );
  file_exit_->setShortcut( QString( "Ctrl+Q" ) );
  connect( file_exit_ , &QAction::triggered ,
           this , &RDKitSVMainWindow::slot_exit );

  file_read_mols_ = new QAction( tr( "Molecules" ) , this );
  connect( file_read_mols_ , &QAction::triggered ,
           this , &RDKitSVMainWindow::slot_read_mols );

  file_read_smarts_ = new QAction( tr( "SMARTS" ) , this );
  connect( file_read_smarts_ , &QAction::triggered ,
           this , &RDKitSVMainWindow::slot_read_smarts );

  file_write_left_ = new QAction( tr( "Molecules (Left Panel)" ) , this );
  connect( file_write_left_ , &QAction::triggered ,
           this , &RDKitSVMainWindow::slot_write_left_molecules );

  file_write_right_ = new QAction( tr( "Molecules (Right Panel)" ) , this );
  connect( file_write_right_ , &QAction::triggered ,
           this , &RDKitSVMainWindow::slot_write_right_molecules );

  file_write_smarts_ = new QAction( tr( "SMARTS" ) , this );
  connect( file_write_smarts_ , &QAction::triggered ,
           this , &RDKitSVMainWindow::slot_write_smarts );

}

// ****************************************************************************
void RDKitSVMainWindow::build_smarts_actions() {

  smarts_match_ = new QAction( tr( "Match" ) , this );
  smarts_match_->setShortcut( QString( "Ctrl+M" ) );
  connect( smarts_match_ , &QAction::triggered ,
           this , &RDKitSVMainWindow::slot_match_smarts );

  smarts_edit_ = new QAction( tr( "Edit" ) , this );
  connect( smarts_edit_ , &QAction::triggered ,
           this , &RDKitSVMainWindow::slot_edit_smarts );

  smarts_new_ = new QAction( tr( "New" ) , this );
  connect( smarts_new_ , &QAction::triggered ,
           this , &RDKitSVMainWindow::slot_new_smarts );

}

// ****************************************************************************
void RDKitSVMainWindow::build_menubar() {

  QMenu *file_menu = menuBar()->addMenu( tr( "File" ) );
  QMenu *read_menu = file_menu->addMenu( tr( "Read" ) );
  read_menu->addAction( file_read_mols_ );
  read_menu->addAction( file_read_smarts_ );

  QMenu *write_menu = file_menu->addMenu( tr( "Write" ) );
  write_menu->addAction( file_write_left_ );
  write_menu->addAction( file_write_right_ );
  write_menu->addAction( file_write_smarts_ );

  file_menu->addSeparator();
  file_menu->addAction( file_exit_ );

  QMenu *smarts_menu = menuBar()->addMenu( tr( "SMARTS" ) );
  smarts_menu->addAction( smarts_match_ );
  smarts_menu->addAction( smarts_edit_ );
  smarts_menu->addAction( smarts_new_ );

}

// ****************************************************************************
void RDKitSVMainWindow::build_widget() {

  left_panel_ = new RDKitSVPanel;
  right_panel_ = new RDKitSVPanel( false );

  QWidget *cen_wid = new QWidget;
  QHBoxLayout *hbox = new QHBoxLayout;
  hbox->addWidget( left_panel_ );
  hbox->addWidget( right_panel_ );
  right_panel_->hide();

  cen_wid->setLayout( hbox );
  setCentralWidget( cen_wid );

}

// ****************************************************************************
void RDKitSVMainWindow::parse_args( int argc, char **argv ) {

  RDKitSVSettings s( argc , argv );

  vector<string> mol_files = s.mol_files();
  if( !mol_files.empty() ) {
    BOOST_FOREACH( string mf , mol_files ) {
      read_mols( mf );
    }
  }

  string smarts_file = s.smarts_file();
  if( !smarts_file.empty() ) {
    read_smarts( smarts_file );
  }

}

// ****************************************************************************
RDKitSVMainWindow::FILE_TYPE RDKitSVMainWindow::get_filetype( const string &filename ,
                                                              bool &is_compressed ) {

  is_compressed = false;
  if( filename.substr( filename.length() - 3 ) == string( ".gz" ) ) {
    is_compressed = true;
  }

  if( string( ".smi" ) == filename.substr( filename.length() - 4 ) ||
      string( ".smi.gz" ) == filename.substr( filename.length() - 7 ) ||
      string( ".ism" ) == filename.substr( filename.length() - 4 ) ||
      string( ".ism.gz" ) == filename.substr( filename.length() - 7 ) ) {
    return SMILES;
  } else if( string( ".sdf" ) == filename.substr( filename.length() - 4 ) ||
             string( ".sdf.gz" ) == filename.substr( filename.length() - 7 ) ) {
    return SDF;
  }

  return UNKNOWN;

}

// ****************************************************************************
void RDKitSVMainWindow::read_mols( const string &filename ) {

  QApplication::setOverrideCursor( Qt::WaitCursor );
  bool is_compressed;
  FILE_TYPE file_type = get_filetype( filename , is_compressed );

  boost::iostreams::filtering_istream ins;
  if( is_compressed ) {
    ins.push( boost::iostreams::gzip_decompressor() );
  }
  ins.push( boost::iostreams::file_source( filename.c_str() ) );
  if( !ins || !ins.good() ) {
    QMessageBox::warning( this , tr( "File Read Error" ) ,
                          QString( "%1 %2 %3 for reading." ).arg( tr( "Couldn't open" ) ).arg( filename.c_str() ).arg( tr( "for reading." ) ) );
    return;
  }

  vector<RDKit::ROMOL_SPTR> new_mols;
  if( SDF == file_type ) {
    RDKit::MolSupplier *mol_supplier = new RDKit::ForwardSDMolSupplier( &ins , true );
    while( !mol_supplier->atEnd() ) {
      new_mols.push_back( RDKit::ROMOL_SPTR( mol_supplier->next() ) );
      if( !new_mols.back() ) {
        new_mols.pop_back();
        break;
      }
    }
  } else if( SMILES == file_type ) {
    // SmilesMolSupplier doesn't seem to work with compressed streams. It might
    // be because of the use of getline.
    // For now, assume the file is a simple one with no header and just SMILES
    // followed by optional name
    istreambuf_iterator<char> isb( ins ) , eos;

    vector<char> nextline;

    while( isb != eos ) {
      nextline.clear();
      while( isb != eos && *isb != '\n' ) {
        nextline.push_back( *isb );
        ++isb;
      }
      if( '#' != nextline[0] ) {
        vector<string> split_line;
        split( split_line , nextline , is_any_of( " \t" ) );
        string smi( split_line[0] );
        string smi_name;
        if( 1 == split_line.size() ) {
          smi_name = string( "MOL_" ) + lexical_cast<string>( mols_.size() + 1 );
        } else {
          smi_name = string( nextline.begin() + split_line[0].length() + 1 , nextline.end() );
        }
        boost::trim( smi );
        boost::trim( smi_name );
        RDKit::ROMol *mol = RDKit::SmilesToMol( smi );
        if( mol ) {
          mol->setProp( "_Name" , smi_name );
          mols_.push_back( RDKit::ROMOL_SPTR( mol ) );
        }
      }
      ++isb; // get past '\n'
    }
  } else {
    QMessageBox::warning( this , tr( "File Read Error" ) ,
                          QString( "%1 %2." ).arg( tr( "Unrecognised file type for" ) ).arg( filename.c_str() ) );
    return;
  }

  mols_.insert( mols_.end() , new_mols.begin() , new_mols.end() );
  left_panel_->set_molecules( mols_ );

  QApplication::restoreOverrideCursor();

}

// ****************************************************************************
void RDKitSVMainWindow::read_smarts( const string &filename ) {

#ifdef NOTYET
  cout << "reading SMARTS from " << filename << endl;
#endif
  ifstream ifs( filename.c_str() );
  if( !ifs || !ifs.good() ) {
    QMessageBox::warning( this , tr( "File Read Error" ) ,
                          QString( "%1 %2 %3 for reading." ).arg( tr( "Couldn't open" ) ).arg( filename.c_str() ).arg( tr( "for reading." ) ) );
    return;
  }

  while( 1 ) {
    string next_line;
    getline( ifs , next_line );
#ifdef NOTYET
    cout << next_line << "XX" << endl;
#endif
    if( !ifs.good() || ifs.eof() ) {
      break;
    }
    boost::trim( next_line );
    if( next_line.empty() ) {
      continue;
    }
    if( '#' == next_line[0] ) {
      continue; // it's a comment
    }
    list<string> splits;
    boost::split( splits , next_line , boost::is_any_of( " \t" ) );
    string smt , smt_name;
    if( splits.size() >= 2 ) {
      smt = splits.front();
      splits.pop_front();
      boost::trim( smt );
      smt_name = boost::join( splits , " " );
      boost::trim( smt_name );
#ifdef NOTYET
      cout << "smt = " << smt << " name = " << smt_name << endl;
#endif
    } else if( 1 == splits.size() ) {
      smt = splits.front();
      boost::trim( smt );
      smt_name = string( "SMARTS_" ) + lexical_cast<string>( smarts_.size() + 1 );
    }
    smarts_.push_back( make_pair( smt_name , smt ) );
  }
  statusBar()->showMessage( QString( "%1 %2." ).arg( tr( "Number of SMARTS now" ) ).arg( smarts_.size() ) , 2000 );

}

// ****************************************************************************
void RDKitSVMainWindow::write_mols( RDKitSVPanel &panel , const string &filename ) {

  vector<RDKit::ROMOL_SPTR> mols = panel.get_molecules();
  if( mols.empty() ) {
    QMessageBox::information( this , tr( "No molecules." ) ,
                              tr( "Panel contains no molecules, so nothing to write." ) );
    return;
  }

  bool is_compressed;
  FILE_TYPE file_type = get_filetype( filename , is_compressed );

  boost::iostreams::filtering_ostream ons;
  if( is_compressed ) {
    ons.push( boost::iostreams::gzip_compressor() );
  }
  ons.push( boost::iostreams::file_sink( filename.c_str() ) );
  if( !ons || !ons.good() ) {
    QMessageBox::warning( this , tr( "Can't write to file" ) ,
                          QString( "%1 %2." ).arg( tr( "Couldn't write to file" ).arg( filename.c_str() ) ) );
    return;
  }

  RDKit::MolWriter *mw;
  if( SMILES == file_type ) {
    bool ism = filename.substr( filename.length() - 4 ) == ".ism" ||
        filename.substr( filename.length() - 7 ) == ".ism.gz" ? true : false;
    mw = new RDKit::SmilesWriter( &ons , " " , "Name" , true , false , ism );
  } else if( SDF == file_type ) {
    mw = new RDKit::SDWriter( &ons , false );
  } else {
    QMessageBox::warning( this , tr( "File Write Error" ) ,
                          QString( "%1 %2." ).arg( tr( "Unrecognised file type for" ) ).arg( filename.c_str() ) );
    return;
  }

  BOOST_FOREACH( RDKit::ROMOL_SPTR mol , mols ) {
    mw->write( *mol );
  }

  delete mw;

}

// ****************************************************************************
void RDKitSVMainWindow::match_smarts( const vector<pair<string,string> > &smts ) {

  cout << "Matching " << smts.size() << " SMARTS" << endl;
  vector<vector<int> > smarts_match( mols_.size() , vector<int>() );

  QString smts_label;
  for( int i = 0 , is = smts.size() ; i < is ; ++i ) {
    cout << "Matching " << i << " : " << smts[i].second << endl;
    smts_label += QString( "%1 (%2)" ).arg( smts[i].first.c_str() ).arg( smts[i].second.c_str() );
    if( i < is - 1 ) {
      smts_label += "|";
    }
    RDKit::RWMol *q = RDKit::SmartsToMol( smts[i].second );
    for( int j = 0 , js = mols_.size() ; j < js ; ++j ) {
      vector<RDKit::MatchVectType> hits_vect;
      if( RDKit::SubstructMatch( *mols_[j] , *q , hits_vect ) ) {
        // store the numbers of the atoms that matched
        typedef pair<int,int> INTPAIR;
        BOOST_FOREACH( RDKit::MatchVectType hit , hits_vect ) {
          BOOST_FOREACH( INTPAIR ip , hit ) {
            smarts_match[j].push_back( ip.second );
          }
        }
        std::sort( smarts_match[j].begin() , smarts_match[j].end() );
        smarts_match[j].erase( unique( smarts_match[j].begin() , smarts_match[j].end() ) ,
                               smarts_match[j].end() );
      }
    }
    delete q;
  }

  vector<RDKit::ROMOL_SPTR> match_mols , miss_mols;
  vector<vector<int> > match_atom_matches;
  for( int i = 0 , is = mols_.size() ; i < is ; ++i ) {
    if( smarts_match[i].empty() ) {
      miss_mols.push_back( mols_[i] );
    } else {
      match_mols.push_back( mols_[i] );
      match_atom_matches.push_back( smarts_match[i] );
    }
  }

  right_panel_->show();
  left_panel_->set_molecules( match_mols , match_atom_matches );
  // Details, details!!
  if( 1 == match_mols.size() ) {
    left_panel_->set_label( QString( "%1 %2." ).arg( tr( "1 molecule matched." ).arg( smts_label ) ) );
  } else {
    left_panel_->set_label( QString( "%1 %2 %3." ).arg( match_mols.size() ).arg( tr( "molecules matched" ) ).arg( smts_label ) );
  }
  right_panel_->set_molecules( miss_mols );
  if( 1 == miss_mols.size() ) {
    right_panel_->set_label( tr( "1 molecule didn't match" ) );
  } else {
    right_panel_->set_label( QString( "%1 %2" ).arg( miss_mols.size() ).arg( tr( "molecules didn't match." ) ) );
  }

}

// ****************************************************************************
vector<pair<string, string> > RDKitSVMainWindow::select_smarts( bool multi_select ) {

  vector<pair<string,string> > smts_to_use;

  if( smarts_.empty() ) {
    return smts_to_use;
  }

  vector<char> selected_smarts( smarts_.size() , 0 );
  vector<QString> smts;
  for( int i = 0 , is = smarts_.size() ; i < is ; ++i ) {
#ifdef NOTYET
    cout << i << " : " << smarts_[i].first << " :: " << smarts_[i].second << endl;
#endif
    smts.push_back( QString( "%1 (%2)" ).arg( smarts_[i].first.c_str() ).arg( smarts_[i].second.c_str() ) );
  }

  DACLIB::QT4SelectItems si( string( "Select SMARTS to use." ) , smts ,
                             selected_smarts , !multi_select , this );
  if( QDialog::Accepted != si.exec() ) {
    return smts_to_use;
  }
  si.get_results( selected_smarts );

  for( int i = 0 , is = smarts_.size() ; i < is ; ++i ) {
    if( selected_smarts[i] ) {
      smts_to_use.push_back( smarts_[i] );
    }
  }

  return smts_to_use;

}

// ****************************************************************************
void RDKitSVMainWindow::update_smarts( const string &new_name ,
                                       const string &new_val ) {

  vector<pair<string,string> >::iterator p = std::find_if( smarts_.begin() , smarts_.end() ,
                                                           bind( equal_to<string>() , new_name ,
                                                           bind( &pair<string,string>::first , _1 ) ) );
  if( p == smarts_.end() ) {
    smarts_.push_back( make_pair( new_name , new_val ) );
  } else {
    p->second = new_val;
  }

}

// ****************************************************************************
void RDKitSVMainWindow::slot_read_mols() {

  QString filename = QFileDialog::getOpenFileName( this , "Select molecule file" ,
                                                   last_dir_ , "Mol. files (*.smi *.smi.gz *.ism *.ism.gz *.sdf *.sdf.gz)" );
  if( filename.isEmpty() || filename.isNull() ) {
    return;
  }

  QFileInfo fi( filename );
  last_dir_ = fi.absolutePath();

  read_mols( filename.toLocal8Bit().data() );

}

// ****************************************************************************
void RDKitSVMainWindow::slot_read_smarts() {

  QString filename = QFileDialog::getOpenFileName( this , "Select SMARTS file" ,
                                                   last_dir_ , "SMARTS files (*.smt);;Any file (*)" );
  if( filename.isEmpty() || filename.isNull() ) {
    return;
  }

  QFileInfo fi( filename );
  last_dir_ = fi.absolutePath();

  read_smarts( filename.toLocal8Bit().data() );

}

// ****************************************************************************
void RDKitSVMainWindow::slot_exit() {

  exit( 0 );

}

// ****************************************************************************
void RDKitSVMainWindow::slot_match_smarts() {

  vector<pair<string,string> > smts_to_use = select_smarts( true );
  if( smts_to_use.empty() ) {
    return;
  }

  match_smarts( smts_to_use );

}

// ****************************************************************************
void RDKitSVMainWindow::slot_edit_smarts() {

  if( smarts_.empty() ) {
    slot_new_smarts();
  }

  vector<pair<string,string> > smts_to_use = select_smarts( false );
  if( smts_to_use.empty() ) {
    return;
  }

  DACLIB::QTGet2Strings g2s( tr( "SMARTS name" ) , smts_to_use.front().first.c_str() ,
                             tr( "SMARTS value" ) , smts_to_use.front().second.c_str() ,
                             this );
  if( QDialog::Accepted != g2s.exec() ) {
    return;
  }

  QString new_name , new_smarts;
  g2s.get_values( new_name , new_smarts );

  update_smarts( new_name.toLocal8Bit().data() , new_smarts.toLocal8Bit().data() );

}

// ****************************************************************************
void RDKitSVMainWindow::slot_new_smarts() {

  DACLIB::QTGet2Strings g2s( tr( "SMARTS name" ) , QString( "SMARTS_%1" ).arg( smarts_.size() + 1 ) ,
                             tr( "SMARTS value" ) , QString( "" ) ,
                             this );
  if( QDialog::Accepted != g2s.exec() ) {
    return;
  }

  QString new_name , new_smarts;
  g2s.get_values( new_name , new_smarts );

  update_smarts( new_name.toLocal8Bit().data() , new_smarts.toLocal8Bit().data() );

}

// ****************************************************************************
void RDKitSVMainWindow::slot_write_left_molecules() {

  QString filename = QFileDialog::getSaveFileName( this , "File for left panel molecules" ,
                                                   last_dir_ ,
                                                   "Mol. files (*.smi *.smi.gz *.ism *.ism.gz *.sdf *.sdf.gz)" );
  if( filename.isEmpty() ) {
    return;
  }

  QFileInfo fi( filename );
  last_dir_ = fi.absolutePath();

  write_mols( *left_panel_ , filename.toLocal8Bit().data() );

}

// ****************************************************************************
void RDKitSVMainWindow::slot_write_right_molecules() {

  if( right_panel_->isHidden() ) {
    // it's empty, so nothing to do.
    QMessageBox::information( this , tr( "No molecules." ) ,
                              tr( "Right panel is inactive, so nothing to write." ) );
    return;
  }

  QString filename = QFileDialog::getSaveFileName( this , "File for left panel molecules" ,
                                                   last_dir_ ,
                                                   "Mol. files (*.smi *.smi.gz *.ism *.ism.gz *.sdf *.sdf.gz)" );
  if( filename.isEmpty() ) {
    return;
  }

  QFileInfo fi( filename );
  last_dir_ = fi.absolutePath();

  write_mols( *right_panel_ , filename.toLocal8Bit().data() );

}

// ****************************************************************************
void RDKitSVMainWindow::slot_write_smarts() {

  QString filename = QFileDialog::getSaveFileName( this , "File for SMARTS." ,
                                                   last_dir_ ,
                                                   "SMARTS files (*.smt);;Any file (*)" );
  if( filename.isEmpty() ) {
    return;
  }

  QFileInfo fi( filename );
  last_dir_ = fi.absolutePath();

  ofstream ofs( filename.toLocal8Bit().data() );
  if( !ofs || !ofs.good() ) {
    QMessageBox::warning( this , tr( "Can't write to file" ) ,
                          QString( "%1 %2." ).arg( tr( "Couldn't write to file" ).arg( filename ) ) );
    return;
  }

  vector<pair<string,string> > smts_to_use = select_smarts( true );
  if( smts_to_use.empty() ) {
    return;
  }

  typedef pair<string,string> STRINGPAIR;
  BOOST_FOREACH( STRINGPAIR smt , smts_to_use ) {
    ofs << smt.first << " " << smt.second << endl;
  }

}

} // EO namespace RDKitSV