rdkit/Code/GraphMol/Descriptors/MolDescriptors.cpp

// $Id$
//
//  Copyright (C) 2005-2012 Greg Landrum and Rational Discovery LLC
//
//   @@ 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/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include "MolDescriptors.h"
#include <map>
#include <list>
#include <algorithm>
#include <sstream>

namespace RDKit {
namespace Descriptors {

const std::string amwVersion = "1.0.0";
double calcAMW(const ROMol &mol, bool onlyHeavy) {
  double res = 0.0;
  for (ROMol::ConstAtomIterator atomIt = mol.beginAtoms();
       atomIt != mol.endAtoms(); ++atomIt) {
    int atNum = (*atomIt)->getAtomicNum();
    if (atNum != 1 || !onlyHeavy) {
      res += (*atomIt)->getMass();
    }

    // add our implicit Hs if we need to:
    if (!onlyHeavy) {
      const PeriodicTable *table = PeriodicTable::getTable();
      res += (*atomIt)->getTotalNumHs() * table->getAtomicWeight(1);
    }
  }
  return res;
}

const std::string exactmwVersion = "1.1.0";
double calcExactMW(const ROMol &mol, bool onlyHeavy) {
  double res = 0.0;
  int nHsToCount = 0;
  const PeriodicTable *table = PeriodicTable::getTable();
  for (ROMol::ConstAtomIterator atomIt = mol.beginAtoms();
       atomIt != mol.endAtoms(); ++atomIt) {
    int atNum = (*atomIt)->getAtomicNum();
    if (atNum != 1 || !onlyHeavy) {
      if (!(*atomIt)->getIsotope()) {
        res += table->getMostCommonIsotopeMass(atNum);
      } else {
        res += (*atomIt)->getMass();
      }
      res -= constants::electronMass * (*atomIt)->getFormalCharge();
    }

    // add our implicit Hs if we need to:
    if (!onlyHeavy) {
      nHsToCount += (*atomIt)->getTotalNumHs(false);
    }
  }
  if (!onlyHeavy) {
    res += nHsToCount * table->getMostCommonIsotopeMass(1);
  }
  return res;
}

namespace {
bool HillCompare(const std::pair<unsigned int, std::string> &v1,
                 const std::pair<unsigned int, std::string> &v2) {
  bool nCompare = (v1.first < v2.first);

  // special cases: Cs, Hs, Ds, and Ts go at the beginning
  if (v1.second == "C") {
    if (v2.second != "C") return true;
    return nCompare;
  } else if (v2.second == "C")
    return false;

  if (v1.second == "H") {
    if (v2.second != "H") return true;
    return nCompare;
  } else if (v2.second == "H")
    return false;

  if (v1.second == "D")
    return true;
  else if (v2.second == "D")
    return false;

  if (v1.second == "T")
    return true;
  else if (v2.second == "T")
    return false;

  // finally, just compare the symbols and the isotopes:
  if (v1 != v2)
    return v1 < v2;
  else
    return nCompare;
}
}

static std::string _molFormulaVersion = "1.3.0";
std::string calcMolFormula(const ROMol &mol, bool separateIsotopes,
                           bool abbreviateHIsotopes) {
  std::ostringstream res;
  std::map<std::pair<unsigned int, std::string>, unsigned int> counts;
  int charge = 0;
  unsigned int nHs = 0;
  const PeriodicTable *table = PeriodicTable::getTable();
  for (ROMol::ConstAtomIterator atomIt = mol.beginAtoms();
       atomIt != mol.endAtoms(); ++atomIt) {
    int atNum = (*atomIt)->getAtomicNum();
    std::pair<unsigned int, std::string> key =
        std::make_pair(0, table->getElementSymbol(atNum));
    if (separateIsotopes) {
      unsigned int isotope = (*atomIt)->getIsotope();
      if (abbreviateHIsotopes && atNum == 1 && (isotope == 2 || isotope == 3)) {
        if (isotope == 2)
          key.second = "D";
        else
          key.second = "T";
      } else {
        key.first = isotope;
      }
    }
    if (counts.find(key) != counts.end()) {
      counts[key] += 1;
    } else {
      counts[key] = 1;
    }
    nHs += (*atomIt)->getTotalNumHs();
    charge += (*atomIt)->getFormalCharge();
  }

  if (nHs) {
    std::pair<unsigned int, std::string> key = std::make_pair(0, "H");
    if (counts.find(key) != counts.end()) {
      counts[key] += nHs;
    } else {
      counts[key] = nHs;
    }
  }
  std::list<std::pair<unsigned int, std::string> > ks;
  for (std::map<std::pair<unsigned int, std::string>,
                unsigned int>::const_iterator countIt = counts.begin();
       countIt != counts.end(); ++countIt) {
    ks.push_back(countIt->first);
  }
  ks.sort(HillCompare);

  for (std::list<std::pair<unsigned int, std::string> >::const_iterator kIter =
           ks.begin();
       kIter != ks.end(); ++kIter) {
    const std::pair<unsigned int, std::string> &key = *kIter;
    if (key.first > 0) {
      res << "[" << key.first << key.second << "]";
    } else {
      res << key.second;
    }
    if (counts[key] > 1) res << counts[key];
  }
  if (charge > 0) {
    res << "+";
    if (charge > 1) res << charge;
  } else if (charge < 0) {
    res << "-";
    if (charge < -1) res << -1 * charge;
  }
  return res.str();
}

}  // end of namespace Descriptors
}  // end of namespace RDKit