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molecule_1h_nmr.cpp

// molecule_1h_nmr.cpp - Molecule's implementation of (more) functions

#include <qobject.h>
#include <qlist.h>
#include <qstring.h>
#include <qregexp.h>
#include <qmessagebox.h>
#include <iostream>

using std::cout;
using std::endl;

#include "graphdialog.h"
#include "molinfodialog.h"
#include "moldata.h"
#include "render2d.h"
#include "drawable.h"
#include "molecule.h"
#include "dpoint.h"
#include "defs.h"

// SSSR (see comments in this file)
#include "molecule_sssr.h"

QStringList Molecule::Calc1HNMR(bool show_dialog) {
  QStringList peak_list;
  int c1, c2, c3, mul, inten;
  double shift1;
  QString n1, nfull, ntemp;

  // get list of unique points
  up = AllPoints();
  // find aromatic rings
  MakeSSSR();
  // add hydrogens
  cout << bonds.count() << endl;
  AddNMRprotons();
  up = AllPoints();  // need to re-run after adding protons
  cout << bonds.count() << endl;
  // assign magnetic environment
  ProtonEnvironment();
  // determine multiplicity and chirality
  Multiplicity_1HNMR();
  // sort lists and calculate spectrum
  Calc1HMultiplicityAndIntensity();
  // remove added hydrogens
  RemoveNMRprotons();
  cout << bonds.count() << endl;

  GraphDialog *g = new GraphDialog(r, tr("Predicted 1H-NMR"));

  peaklist.clear();

  // print (for now) list of NMR values
  for ( QStringList::Iterator it = protonFinalList.begin(); 
      it != protonFinalList.end(); ++it ) {
    ntemp = *it;
    c1 = ntemp.find(',');
    c2 = ntemp.find(',', c1 + 1);
    c3 = ntemp.find(',', c2 + 1);
    shift1 = ntemp.mid(0, c1).toDouble();
    nfull = "";
    n1.setNum(shift1);
    nfull = n1 + " ppm";
    nfull = nfull + tr(" Intensity: ") + ntemp.mid(c1 + 1, c2 - c1 - 1);
    nfull = nfull + tr(" Multiplicity: ") + ntemp.mid(c2 + 1, c3 - c2 - 1);
    inten = ntemp.mid(c1 + 1, c2 - c1 - 1).toInt();
    mul = ntemp.mid(c2 + 1, c3 - c2 - 1).toInt();
    tmp_peak = new Peak;
    tmp_peak->value = shift1;
    tmp_peak->intensity = inten;
    tmp_peak->multiplicity = mul;
    tmp_peak->comment = nfull;
    peaklist.append(tmp_peak);
    g->AddPeak(shift1, mul, QColor(0,0,0), QString("peak"), nfull);
  }
  if (show_dialog == true) g->show();

  return protonFinalList;
}

void Molecule::AddNMRprotons() {
  DPoint *new_proton;
  int h, ct, sumbonds;
  QString orig_element;
  double ox, oy;
  for (tmp_pt = up.first(); tmp_pt != NULL; tmp_pt = up.next()) {
    orig_element = tmp_pt->element;
    ox = tmp_pt->x; oy = tmp_pt->y;
    if (orig_element == "H") continue;
    if (orig_element == "") orig_element = "C";
    sumbonds = 0; h = 0;
    // remove protons and charges
    for (ct = 0; ct < orig_element.length(); ct++) {
      if (orig_element[ct] == 'H') {
      orig_element.remove(ct, 1);
      ct = 0;
      }
      if (orig_element[ct] == '+') {
      orig_element.remove(ct, 1);
      ct = 0;
      }
      if (orig_element[ct] == '-') {
      orig_element.remove(ct, 1);
      ct = 0;
      }
      if (orig_element[ct].isNumber() == true) {
      orig_element.remove(ct, 1);
      ct = 0;
      }
    }
    // find order of bonds
    for (tmp_bond = bonds.first(); tmp_bond!=NULL; tmp_bond = bonds.next()) {
      if (tmp_bond->Find(tmp_pt)) {
      if (tmp_bond->Order() < 4)
        sumbonds += tmp_bond->Order();
      else
        sumbonds += 1; // order 5 and 7 (stereo) and order 1 bonds
      }
    }
    h = MolData::Hydrogens(orig_element) - sumbonds;
    if (h < 0) h = 0;
    for (ct = 0; ct < h; ct++) {
      tmp_bond = new Bond(r);
      new_proton = new DPoint;
      new_proton->element = "H";
      new_proton->nmr_proton = true;
      new_proton->x = ox; new_proton->y = oy;
      tmp_bond->setPoints(tmp_pt, new_proton);
      bonds.append(tmp_bond);
    }
  }
}

void Molecule::RemoveNMRprotons() {
  for (tmp_bond = bonds.first(); tmp_bond!=NULL; tmp_bond = bonds.next()) {
    if (tmp_bond->End()->nmr_proton == true) {
      bonds.remove(tmp_bond);
      delete tmp_bond;
      tmp_bond = bonds.first();
    }
  }
}

// Do depth-first search to identify magnetic environment
// Essentially, assign a HOSE-style code to each proton.
void Molecule::ProtonEnvironment() {
  QListIterator<DPoint> it(up);
  int adj_protons;
  DPoint *depth1_pt, *depth2_pt, *depth3_pt;
  QList<DPoint> search_stack; // depth 2 atoms
  QString nearest, r1, r2, r3, r_current, depth3_str;
  QStringList rgroups, depth3list;
  int rnext = 0;
  protonMagEnvList.clear();

  for (tmp_pt = up.first(); tmp_pt != NULL; tmp_pt = up.next()) {
    tmp_pt->protonHOSECode = "";
    rgroups.clear();
    r1 = "";
    r2 = "";
    r3 = "";
    r_current = "";
    rnext = 0;
    adj_protons = 1;
    tmp_pt->H1_multiplicity = 0;
    search_stack.clear();
    if (tmp_pt->element != "H") continue;
    // first, find atom this proton is connected to (depth 1)
    for (tmp_bond = bonds.first(); tmp_bond != NULL; tmp_bond = bonds.next()){
      if (tmp_bond->Find(tmp_pt)) {
      depth1_pt = tmp_bond->otherPoint(tmp_pt);
      nearest = depth1_pt->baseElement();
      if ( (depth1_pt->inring == true) &&
           (depth1_pt->aromatic == true) )
        nearest.append("A");
      if ( (depth1_pt->inring == true) &&
           (depth1_pt->aromatic == false) )
        nearest.append("R");
      break;
      }
    }
    // now, find depth 2 atoms and put in list
    for (tmp_bond = bonds.first(); tmp_bond != NULL; tmp_bond = bonds.next()){
      if (tmp_bond->Find(depth1_pt)) {
      depth2_pt = tmp_bond->otherPoint(depth1_pt);
      //cout << "DEPTH2: "<< depth2_pt->element << endl;
      if (depth2_pt == tmp_pt) continue;
      search_stack.append(depth2_pt);
      depth2_pt->serial = tmp_bond->Order();
      }
    }
    // determine R groups
    for (depth2_pt = search_stack.first(); depth2_pt != NULL;
       depth2_pt = search_stack.next()) {
      r_current = "";
      if ( (depth2_pt->serial == 2) && (depth2_pt->aromatic == false) )
      r_current = "=";
      if (depth2_pt->serial == 3) r_current = "#";
      r_current.append(depth2_pt->baseElement());
      if (depth2_pt->aromatic == true)
      r_current.append("A");
      depth3list.clear();
      for (tmp_bond = bonds.first(); tmp_bond != NULL; 
         tmp_bond = bonds.next()){
      if (tmp_bond->Find(depth2_pt)) {
        depth3_pt = tmp_bond->otherPoint(depth2_pt);
        if (depth3_pt == depth1_pt) continue;
        //cout << "DEPTH3: "<< depth3_pt->element << endl;
        depth3_str = "";
        if ( (tmp_bond->Order() == 2) &&
             (depth3_pt->aromatic == false) )
             depth3_str = "=";
        if (tmp_bond->Order() == 3) depth3_str = "#";
        depth3_str.append(depth3_pt->baseElement());
        depth3list.append(depth3_str);
      }      
      }
      depth3list.sort();
      for ( QStringList::Iterator it1 = depth3list.begin(); 
          it1 != depth3list.end(); ++it1 ) {
      r_current.append(*it1);
      } 
      rgroups.append(r_current);
    }
    rgroups.sort();
    for ( QStringList::Iterator it2 = rgroups.begin(); 
        it2 != rgroups.end(); ++it2 ) {
      nearest.append("(");
      nearest.append(*it2);
      nearest.append(")");
      if (r1 == "") {
      r1 = *it2;
      continue;
      }
      if (r2 == "") {
      r2 = *it2;
      continue;
      }
      if (r3 == "") {
      r3 = *it2;
      continue;
      }
    } 
    // check for chirality
    if ( (r1 != r2) && (r2 != r3) && (r1 != r3) && (r1 != "H") &&
       (r1 != "") && (r2 != "") && (r3 != "") &&
       (r2 != "H") && (r3 != "H") && (nearest.left(1) == "C") &&
       (nearest.left(2) != "CA") ) {
      nearest.prepend("*");
    }
    tmp_pt->protonHOSECode = nearest;
    cout << "env:" << nearest << endl;
  }
}

// Do depth-first search to find adjacent protons (H at depth 2 and 3)
void Molecule::Multiplicity_1HNMR() {
  QListIterator<DPoint> it(up);
  int adj_protons;
  bool split, chiral;
  DPoint *depth1_pt, *depth2_pt, *depth3_pt;
  QString new_magenv;
  QList<DPoint> search_stack; // depth 2 atoms

  for (tmp_pt = up.first(); tmp_pt != NULL; tmp_pt = up.next()) {
    // chiral atoms should implicitly be split...
    if (tmp_pt->protonHOSECode.contains("*") > 0) {
      protonMagEnvList.append(tmp_pt->protonHOSECode);
      continue;
    }
    adj_protons = 1;
    split = false; chiral = false;
    tmp_pt->H1_multiplicity = 0;
    search_stack.clear();
    if (tmp_pt->element != "H") continue;
    // first, find atom this proton is connected to (depth 1)
    for (tmp_bond = bonds.first(); tmp_bond != NULL; tmp_bond = bonds.next()){
      if (tmp_bond->Find(tmp_pt)) {
      depth1_pt = tmp_bond->otherPoint(tmp_pt);
      break;
      }
    }
    // now, find depth 2 atoms and put in list
    for (tmp_bond = bonds.first(); tmp_bond != NULL; tmp_bond = bonds.next()){
      if (tmp_bond->Find(depth1_pt)) {
      depth2_pt = tmp_bond->otherPoint(depth1_pt);
      //cout << "DEPTH2: "<< depth2_pt->element << endl;
      if (depth2_pt->element == "H")
        adj_protons += 0;
      else
        search_stack.append(depth2_pt);
      }
    }
    //cout << "Stack: " << search_stack.count() << endl;
    // now find depth 3 protons
    for (depth2_pt = search_stack.first(); depth2_pt != NULL;
       depth2_pt = search_stack.next()) {
      for (tmp_bond = bonds.first(); tmp_bond != NULL; 
         tmp_bond = bonds.next()){
      if (tmp_bond->Find(depth2_pt)) {
        depth3_pt = tmp_bond->otherPoint(depth2_pt);
        //cout << "DEPTH3: "<< depth3_pt->element << endl;
        if (depth3_pt->element == "H") {
          adj_protons++;
          if (depth3_pt->protonHOSECode != tmp_pt->protonHOSECode)
            split = true;
        }
      }      
      }
    }
    tmp_pt->H1_multiplicity = adj_protons;
    cout << "1H_mult = " << adj_protons << endl;
    new_magenv = tmp_pt->protonHOSECode;
    if (split) { 
      new_magenv.prepend("+");
    } else {
      new_magenv.prepend("-");
    }
    protonMagEnvList.append(new_magenv);
   
    cout << "Magnetic environment: " << new_magenv << endl;
  } // for (tmp_pt...)
}

void Molecule::Calc1HMultiplicityAndIntensity() {
  QString current_nmr, tmp_nmr, rev_nmr, n1, chiralnote;
  int int_count = 1, multi = 0;
  bool first_time = true;
  protonFinalList.clear();
  protonMagEnvList.sort();
  for ( QStringList::Iterator it2 = protonMagEnvList.begin(); 
      it2 != protonMagEnvList.end(); ++it2 ) {
    tmp_nmr = *it2;
    if (first_time == true) {
      first_time = false;
      current_nmr = tmp_nmr;
      continue;
    }
    if (tmp_nmr != current_nmr) {
      rev_nmr = current_nmr;
      rev_nmr.replace( QRegExp("\\(H\\)"), "" );
      cout << "rev_nmr = " << rev_nmr << endl;
      multi = rev_nmr.contains('H', true) + 1;
      if (rev_nmr.contains('-') > 0)
      multi = 1;
      // chirality?
      chiralnote = "";
      if (rev_nmr.contains('*') > 0) {
      cout << "Oh no! Chiral center!" << endl;
      chiralnote = " (chiral)";
      }
      rev_nmr = current_nmr;
      rev_nmr.prepend(",");
      rev_nmr.prepend(chiralnote);
      n1.setNum(multi);
      rev_nmr.prepend(n1);
      n1.setNum(int_count);
      rev_nmr.prepend(",");
      rev_nmr.prepend(n1);
      rev_nmr.prepend(",");
      n1.setNum(Calc1HShift(current_nmr));
      rev_nmr.prepend(n1);
      protonFinalList.append(rev_nmr);
      current_nmr = tmp_nmr;
      int_count = 1;
    } else {
      int_count++;
    }
  }
  rev_nmr = current_nmr;
  rev_nmr.replace( QRegExp("\\(H\\)"), "" );
  multi = rev_nmr.contains('H', true) + 1;
  if (rev_nmr.contains('-') > 0)
    multi = 1;
  // chirality?
  chiralnote = "";
  if (rev_nmr.contains('*') > 0) {
    cout << "Oh no! Chiral center!" << endl;
    chiralnote = " (chiral)";
  }
  rev_nmr = current_nmr;
  rev_nmr.prepend(",");
  rev_nmr.prepend(chiralnote);
  n1.setNum(multi);
  rev_nmr.prepend(n1);
  n1.setNum(int_count);
  rev_nmr.prepend(",");
  rev_nmr.prepend(n1);
  rev_nmr.prepend(",");
  n1.setNum(Calc1HShift(current_nmr));
  rev_nmr.prepend(n1);
  protonFinalList.append(rev_nmr);
  current_nmr = tmp_nmr;
  int_count = 0;
  
  cout << endl << "Proton final list:" << endl;
  for ( QStringList::Iterator it = protonFinalList.begin(); 
      it != protonFinalList.end(); ++it ) {
    cout << *it << endl;
  }  
}

//
// everything below this point probably belongs in a separate file.
//
// proton types used in identification
#define PROTON_CH 10
#define PROTON_CH_AROMATIC 20
#define PROTON_CH2 30
#define PROTON_CH2_RING 40
#define PROTON_CH3 50
#define PROTON_NH 60
#define PROTON_NH2 70
#define PROTON_OH 80
#define PROTON_SH 90

double Molecule::Calc1HShift(QString phc) {
  QString substr, nearest, r1, r2, r3;
  int l1, l2, rcount, nearest_code, protons;
  double base_shift;

  l1 = phc.find('+');
  if (l1 < 0)
    l1 = phc.find('-');
  if (l1 < 0)
    l1 = phc.find('*');
  substr = phc.mid(l1 + 1);

  cout << "1H shift of " << substr << endl;

  // identify base type:  extract primary atom and R groups
  rcount = 0;
  nearest_code = 0;
  protons = 0;
  l1 = substr.find("(");

  nearest = substr.left(l1);
  l2 = substr.find(")", l1);
  r1 = substr.mid(l1 + 1, l2 - l1 - 1);
  rcount++;
  l1 = substr.find("(", l2);
  if (l1 > 0) {
    l2 = substr.find(")", l1);
    r2 = substr.mid(l1 + 1, l2 - l1 - 1);
    rcount++;
    l1 = substr.find("(", l2);
    if (l1 > 0) {
      l2 = substr.find(")", l1);
      r3 = substr.mid(l1 + 1, l2 - l1 - 1);
      rcount++;
    }
  }

  if (r1 == "H") protons++;
  if (r2 == "H") protons++;
  if (r3 == "H") protons++;

  if (nearest == "C") {
    if (protons == 0) nearest_code = PROTON_CH;
    if (protons == 1) nearest_code = PROTON_CH2;
    if (protons == 2) nearest_code = PROTON_CH3;
  }
  if (nearest == "CA") {
    nearest_code = PROTON_CH_AROMATIC;
  }
  if (nearest == "CR") {
    if (protons == 0) nearest_code = PROTON_CH;
    if (protons == 1) nearest_code = PROTON_CH2_RING;
  }
  if (nearest == "N") {
    if (protons == 0) nearest_code = PROTON_NH;
    if (protons == 1) nearest_code = PROTON_NH2;
  }
  if (nearest == "O") {
    nearest_code = PROTON_OH;
  }
  if (nearest == "S") {
    nearest_code = PROTON_SH;
  }

  // start with a base shift based on proton type
  switch (nearest_code) {
  case PROTON_CH:
    base_shift = 2.1;
    if ( (r1 == "=O") && (r2 == "OC") ) return 8.1;  // -O-CHO
    if (r1 == "=O") return 9.7;  // -CHO
    break;
  case PROTON_CH_AROMATIC:
    base_shift = 7.5;
    break;
  case PROTON_CH2:
    base_shift = 1.8;
    if ( (r1 == "C=OC") && (r2 == "C=OC") ) return 3.7; // -CO-CH2-CO-
    if ( (r1 == "C=OC") && (r3 == "OC") ) return 4.75; // -CO-CH2-O-
    if ( (r2 == "OC") && (r3 == "OC") ) return 5.5; // -S-CH2-S-
    if ( (r2 == "SC") && (r3 == "SC") ) return 3.75; // -S-CH2-S-
    if ( (r2 == "OC") && (r3 == "SC") ) return 4.9; // -O-CH2-S-
    if ( (r2.left(1) == "N") && (r3.left(1) == "N") ) return 4.3; // -N-CH2-N-
    break;
  case PROTON_CH2_RING:
    base_shift = 1.8;
    break;
  case PROTON_CH3:
    base_shift = 0.8;
    if (r3 == "OC") return 3.6;  // CH3-O-
    if (r3.left(1) == "N") return 2.6;  // CH3-N-
    if (r3.left(1) == "S") return 2.2;  // CH3-S-
    if (r1.left(2) == "CA") return 2.5; // CH3-Ar
    if (r1.left(3) == "C=O") return 2.1; // CH3-CO-
    break;
  case PROTON_NH:
    base_shift = 1.8;
    if (r1.left(2) == "CA") return 5.0;  // Ar-NH-
    break;
  case PROTON_NH2:
    base_shift = (double)(phc.length() % 10);
    break;
  case PROTON_OH:
    base_shift = 3.0;  // R-OH
    if (r1.left(2) == "CA") return 5.8;  // Ar-OH
    if (r1 == "C=OC") return 11.5;  // carboxylic acid characteristic
    break;
  case PROTON_SH:
    base_shift = 2.0;
    if (r1.left(2) == "CA") return 4.0;  // Ar-SH
    break;
  }

  return base_shift;
}

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