rdkit/Code/GraphMol/Atom.cpp

// $Id$
//
//  Copyright (C) 2001-2010 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 <math.h>

#include "ROMol.h"
#include "Atom.h"
#include "PeriodicTable.h"
#include "SanitException.h"
#include "QueryOps.h"
#include "MonomerInfo.h"

#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/types.h>
#include <RDGeneral/Dict.h>

namespace RDKit {
  namespace {
    // Determine whether or not a molecule is to the left of Carbon
    bool isEarlyAtom(int atomicNum){
      return (4 - PeriodicTable::getTable()->getNouterElecs(atomicNum)) > 0;
    }
  }
Atom::Atom(){
  d_atomicNum=0;
  initAtom();
}

Atom::Atom(unsigned int num) {
  d_atomicNum = num;
  initAtom();
};

Atom::Atom(std::string what) {
  d_atomicNum = PeriodicTable::getTable()->getAtomicNumber(what);
  initAtom();
};

Atom::Atom( const Atom & other){
  // NOTE: we do *not* copy ownership!
  d_atomicNum = other.d_atomicNum;
  dp_mol = 0;
  d_index=0;
  d_formalCharge = other.d_formalCharge;
  df_noImplicit = other.df_noImplicit;
  df_isAromatic = other.df_isAromatic;
  d_dativeFlag = other.d_dativeFlag;
  d_numExplicitHs = other.d_numExplicitHs;
  d_numRadicalElectrons = other.d_numRadicalElectrons;
  d_mass = other.d_mass;
  d_isotope = other.d_isotope;
  //d_pos = other.d_pos;
  d_chiralTag=other.d_chiralTag;
  d_hybrid = other.d_hybrid;
  d_implicitValence=other.d_implicitValence;
  d_explicitValence=other.d_explicitValence;
  if(other.dp_props){
    dp_props = new Dict(*other.dp_props);
  } else {
    dp_props = new Dict();
    STR_VECT computed;
    dp_props->setVal(detail::computedPropName, computed);
  }
  if(other.dp_monomerInfo){
    dp_monomerInfo = other.dp_monomerInfo->copy();
  } else {
    dp_monomerInfo=0;
  }

}
void Atom::initAtom(){
  df_isAromatic = false;
  df_noImplicit = false;
  d_dativeFlag=0;
  d_numExplicitHs = 0;
  d_numRadicalElectrons=0;
  d_formalCharge = 0;
  d_index = 0;
  if(d_atomicNum){
    d_mass = PeriodicTable::getTable()->getAtomicWeight(d_atomicNum);
  } else{
    d_mass = 0.0;
  }
  d_isotope=0;
  d_chiralTag=CHI_UNSPECIFIED;
  d_hybrid = UNSPECIFIED;
  dp_mol = 0;
  dp_props = new Dict();
  dp_monomerInfo = 0;

  d_implicitValence=-1;
  d_explicitValence=-1;

}

Atom::~Atom()
{
  if(dp_props){
    delete dp_props;
    dp_props = 0;
  }
  if(dp_monomerInfo){
    delete dp_monomerInfo;
  }
}

Atom *Atom::copy() const {
  Atom *res = new Atom(*this);
  return res;
}


void Atom::setOwningMol(ROMol *other)
{
  // NOTE: this operation does not update the topology of the owning
  // molecule (i.e. this atom is not added to the graph).  Only
  // molecules can add atoms to themselves.
  dp_mol = other;
}


std::string Atom::getSymbol() const {
  std::string res;
  // handle dummies differently:
  if(d_atomicNum != 0 || !hasProp("dummyLabel") ){
    res = PeriodicTable::getTable()->getElementSymbol(d_atomicNum);
  } else {
    res=getProp<std::string>("dummyLabel");
  }
  return res;
}

unsigned int Atom::getDegree() const {
  PRECONDITION(dp_mol,"degree not defined for atoms not associated with molecules");
  return getOwningMol().getAtomDegree(this);
}

unsigned int Atom::getTotalDegree() const {
  PRECONDITION(dp_mol,"degree not defined for atoms not associated with molecules");
  unsigned int res=this->getTotalNumHs(false)+this->getDegree();
  return res;
}

//
//  If includeNeighbors is set, we'll loop over our neighbors
//   and include any of them that are Hs in the count here
//
unsigned int Atom::getTotalNumHs(bool includeNeighbors) const {
  PRECONDITION(dp_mol,"valence not defined for atoms not associated with molecules")
  int res = getNumExplicitHs() + getNumImplicitHs();
  if(includeNeighbors){
    ROMol::ADJ_ITER begin,end;
    const ROMol *parent = &getOwningMol();
    boost::tie(begin,end) = parent->getAtomNeighbors(this);
    while(begin!=end){
      const Atom *at = parent->getAtomWithIdx(*begin);
      if(at->getAtomicNum()==1) res++;
      ++begin;
    }
  }
  return res;
}

unsigned int Atom::getNumImplicitHs() const {
  if(df_noImplicit) return 0;
  
  PRECONDITION(d_implicitValence>-1,
               "getNumImplicitHs() called without preceding call to calcImplicitValence()");
  return getImplicitValence();
}

int Atom::getExplicitValence() const {
  PRECONDITION(dp_mol,"valence not defined for atoms not associated with molecules");
  PRECONDITION(d_explicitValence>-1,
               "getExplicitValence() called without call to calcExplicitValence()");
  return d_explicitValence;
}

unsigned int Atom::getTotalValence() const {
  PRECONDITION(dp_mol,"valence not defined for atoms not associated with molecules");
  return getExplicitValence()+getImplicitValence();
}
  
int Atom::calcExplicitValence(bool strict) {
  PRECONDITION(dp_mol,"valence not defined for atoms not associated with molecules");
  unsigned int res;
  // FIX: contributions of bonds to valence are being done at best
  // approximately
  double accum=0;
  ROMol::OEDGE_ITER beg,end;
  boost::tie(beg,end) = getOwningMol().getAtomBonds(this);
  while(beg!=end){
    accum += getOwningMol()[*beg]->getValenceContrib(this);
    ++beg;
  }
  accum += getNumExplicitHs();

  bool valenceOk=true;
  
  // check accum is greater than the default valence
  int chr = getFormalCharge();
  if(d_atomicNum>1){
    int dv = PeriodicTable::getTable()->getDefaultValence(d_atomicNum-chr);
    if (accum > dv && this->getIsAromatic()){
      // this needs some explanation : if the atom is aromatic and
      // accum > (dv + chr) we assume that no hydrogen can be added
      // to this atom.  We set x = (v + chr) such that x is the
      // closest possible integer to "accum" but less than
      // "accum".
      //
      // "v" here is one of the allowed valences. For example:
      //    sulfur here : O=c1ccs(=O)cc1
      //    nitrogen here : c1cccn1C
    
      int pval = dv;
      const INT_VECT &valens = PeriodicTable::getTable()->getValenceList(d_atomicNum-chr);
      for (INT_VECT_CI vi = valens.begin(); vi != valens.end() && *vi!=-1; ++vi) {
        int val = (*vi);
        if (val > accum) {
          break;
        } else {
          pval = val;
        }
      }
      accum = pval;
    }
    // despite promising to not to blame it on him - this a trick Greg
    // came up with: if we have a bond order sum of x.5 (i.e. 1.5, 2.5
    // etc) we would like it to round to the higher integer value -- 
    // 2.5 to 3 instead of 2 -- so we will add 0.1 to accum.
    // this plays a role in the number of hydrogen that are implicitly
    // added. This will only happen when the accum is a non-integer
    // value and less than the default valence (otherwise the above if
    // statement should have caught it). An example of where this can
    // happen is the following smiles:
    //    C1ccccC1
    // Daylight accepts this smiles and we should be able to Kekulize
    // correctly.
    accum += 0.1;

    res = static_cast<int>(round(accum));

    if(strict){
      int effectiveValence=res;
      const INT_VECT &valens = PeriodicTable::getTable()->getValenceList(d_atomicNum-chr);
      int maxValence=*(valens.rbegin());
      // maxValence == -1 signifies that we'll take anything at the high end
      if( maxValence>0 &&effectiveValence>maxValence){
        valenceOk=false;
      }
    }
  } else if(d_atomicNum==0){
    res = static_cast<int>(round(accum));
    valenceOk=1;
  } else {
    // it's H
    res = static_cast<int>(round(accum));
    if(strict){
      switch(chr){
      case 0:
        valenceOk=(res<2);
        break;
      case 1:
      case -1:
        valenceOk=(res==0);
        break;
      default:
        valenceOk=false;
      }
    }
  }
  if(strict && !valenceOk){
    // the explicit valence is greater than any
    // allowed valence for the atoms - raise an error
    std::ostringstream errout;
    errout << "Explicit valence for atom # " << getIdx() 
           << " " << PeriodicTable::getTable()->getElementSymbol(d_atomicNum)
           << ", " << res <<", is greater than permitted";
    std::string msg = errout.str();
    BOOST_LOG(rdErrorLog) << msg << std::endl;
    throw MolSanitizeException(msg);
  }

  d_explicitValence = res;

  return res;
}

int Atom::getImplicitValence() const {
  PRECONDITION(dp_mol,"valence not defined for atoms not associated with molecules");
  if(df_noImplicit) return 0;
  return d_implicitValence;
}

// NOTE: this uses the explicitValence, so it will call
// calcExplictValence() if it hasn't already been called
int Atom::calcImplicitValence(bool strict) {
  PRECONDITION(dp_mol,"valence not defined for atoms not associated with molecules");
  if(df_noImplicit) return 0;
  if(d_explicitValence==-1) this->calcExplicitValence(strict);
  // this is basically the difference between the allowed valence of
  // the atom and the explicit valence already specified - tells how
  // many Hs to add
  // 
  int res;

  // catch anything without a default valence:
  if (PeriodicTable::getTable()->getDefaultValence(d_atomicNum)==-1) {
    d_implicitValence = 0;
    return 0;
  }

  if(d_atomicNum==1){
    // H special case:
    if(getFormalCharge()==0){
      int explicitPlusRadV = getExplicitValence() + getNumRadicalElectrons();
      switch(explicitPlusRadV){
      case 0:
        res=1;
        break;
      case 1:
        res=0;
        break;
      default:
        if(strict){
          std::ostringstream errout;
          errout << "Hydrogen # " << getIdx() 
                 << " has valence greater than permitted: "<< explicitPlusRadV;
          std::string msg = errout.str();
          BOOST_LOG(rdErrorLog) << msg << std::endl;
          throw MolSanitizeException(msg);
        }
      }
    } else {
      res=0;
    }
    d_implicitValence = res;
    return res;
  }
  
  // here is how we are going to deal with the possibility of
  // multiple valences
  // - check the explicit valence "ev"
  // - if it is already equal to one of the allowed valences for the
  //    atom return 0
  // - otherwise take return difference between next larger allowed
  //   valence and "ev"
  // if "ev" is greater than all allowed valences for the atom raise an exception
  // finally aromatic cases are dealt with differently - these atoms are allowed
  // only default valences
  int explicitPlusRadV = getExplicitValence() + getNumRadicalElectrons();
  int chg = getFormalCharge();

  // if we have an aromatic case treat it differently
  if (getIsAromatic()) {
    int dv=PeriodicTable::getTable()->getDefaultValence(d_atomicNum-chg);
    if (explicitPlusRadV <= dv) {
      res = dv - explicitPlusRadV;
    }
    else {
      // As we assume when finding the explicitPlusRadValence if we are
      // aromatic we should not be adding any hydrogen and already
      // be at an accepted valence state,

      // FIX: this is just ERROR checking and probably moot - the
      // explicitPlusRadValence function called above should assure us that
      // we satisfy one of the accepted valence states for the
      // atom. The only diff I can think of is in the way we handle
      // formal charge here vs the explicit valence function.
      bool satis = false;
      const INT_VECT &valens = PeriodicTable::getTable()->getValenceList(d_atomicNum-chg);
      for (INT_VECT_CI vi = valens.begin();
	   vi!=valens.end() && *vi>0; ++vi) {
        if (explicitPlusRadV == (*vi) ) {
          satis = true;
          break;
        }
      }
      if (strict && !satis) {
        std::ostringstream errout;
        errout << "Explicit valence for aromatic atom # " << getIdx() 
               << " not equal to any accepted valence\n";
        std::string msg = errout.str();
        BOOST_LOG(rdErrorLog) << msg << std::endl;
        throw MolSanitizeException(msg);
      }
      res = 0;
    }
  }
  else {
    // non-aromatic case we are allowed to have non default valences
    // and be able to add hydrogens
    const INT_VECT &valens = PeriodicTable::getTable()->getValenceList(d_atomicNum-chg);
    if(valens.size()==1 && valens[0]==-1){
      // no default valence, set res to zero
      res = 0;
    } else {
      res = -1;
      for (INT_VECT_CI vi = valens.begin();
           vi != valens.end() && *vi>=0; ++vi) {
        int tot = (*vi);
        if (explicitPlusRadV <= tot) {
          res = tot - explicitPlusRadV;
          break;
        }
      }
    }
    if (res < 0) {
      if(strict){
        // this means that the explicit valence is greater than any
        // allowed valence for the atoms - raise an error
        std::ostringstream errout;
        errout << "Explicit valence for atom # " << getIdx() 
               << " " << PeriodicTable::getTable()->getElementSymbol(d_atomicNum)
               << ", " << res <<", greater than permitted";
        std::string msg = errout.str();
        BOOST_LOG(rdErrorLog) << msg << std::endl;
        throw MolSanitizeException(msg);
      } else {
        res = 0;
      }
    }
  }
      
  d_implicitValence = res;
  return res;
}

void Atom::setIsotope(unsigned int what){
  d_isotope=what;
  if(d_isotope){
    d_mass=PeriodicTable::getTable()->getMassForIsotope(d_atomicNum,d_isotope);
  } else {
    d_mass = PeriodicTable::getTable()->getAtomicWeight(d_atomicNum);
  }
}

void Atom::setQuery(Atom::QUERYATOM_QUERY *what) {
  //  Atoms don't have complex queries so this has to fail
  PRECONDITION(0,"plain atoms have no Query");
}
Atom::QUERYATOM_QUERY *Atom::getQuery() const {
  return NULL;
};
void Atom::expandQuery(Atom::QUERYATOM_QUERY *what,
                       Queries::CompositeQueryType how,
                       bool maintainOrder) {
  PRECONDITION(0,"plain atoms have no Query");
}

bool Atom::Match(Atom const *what) const {
  PRECONDITION(what,"bad query atom");
  bool res = getAtomicNum() == what->getAtomicNum();
  // special dummy--dummy match case:
  //   [*] matches [*],[1*],[2*],etc.
  //   [1*] only matches [*] and [1*]
  if(res){
    if(!getAtomicNum()){
      // this is the new behavior, based on the isotopes:
      int tgt=this->getIsotope();
      int test=what->getIsotope();
      if(tgt && test && tgt!=test){
        res = false;
      }
    } else {
      // standard atom-atom match: The general rule here is that if this atom has a property that
      // deviates from the default, then the other atom should match that value.
      if( (this->getFormalCharge() && this->getFormalCharge()!=what->getFormalCharge()) ||
          (this->getIsotope() && this->getIsotope()!=what->getIsotope()) ){
        res=false;
      }
    }
  }
  return res;
}
bool Atom::Match(const Atom::ATOM_SPTR what) const {
  return Match(what.get());
}

void Atom::updatePropertyCache(bool strict) {
  calcExplicitValence(strict);
  calcImplicitValence(strict);
}

// returns the number of swaps required to convert the ordering
// of the probe list to match the order of our incoming bonds:
//
//  e.g. if our incoming bond order is: [0,1,2,3]:
//   getPerturbationOrder([1,0,2,3]) = 1
//   getPerturbationOrder([1,2,3,0]) = 3
//   getPerturbationOrder([1,2,0,3]) = 2
int Atom::getPerturbationOrder(INT_LIST probe) const{
  PRECONDITION(dp_mol,"perturbation order not defined for atoms not associated with molecules")
  INT_LIST ref;
  ROMol::OEDGE_ITER beg,end;
  boost::tie(beg,end) = getOwningMol().getAtomBonds(this);
  while(beg!=end){
    ref.push_back(getOwningMol()[*beg]->getIdx());
    ++beg;
  }
  int nSwaps=static_cast<int>(countSwapsToInterconvert(ref,probe));
  return nSwaps;
}

void Atom::invertChirality(){
  switch(getChiralTag()){
  case CHI_TETRAHEDRAL_CW:
    setChiralTag(CHI_TETRAHEDRAL_CCW);
    break;
  case CHI_TETRAHEDRAL_CCW:
    setChiralTag(CHI_TETRAHEDRAL_CW);
    break;
  case CHI_OTHER:
  case CHI_UNSPECIFIED:
    break;
  }
}
} // end o' namespace RDKit

std::ostream & operator<<(std::ostream& target, const RDKit::Atom &at){
  target << at.getIdx() << " " << at.getAtomicNum() << " " << at.getSymbol();
  target << " chg: " << at.getFormalCharge();
  target << "  deg: " << at.getDegree();
  target << " exp: ";
  try {
    int explicitValence = at.getExplicitValence();
    target << explicitValence;
  } catch (...){
    target << "N/A";
  }
  target << " imp: ";
  try {
    int implicitValence = at.getImplicitValence();
    target << implicitValence;
  } catch (...){
    target << "N/A";
  }
  target << " hyb: " << at.getHybridization();
  target << " arom?: " << at.getIsAromatic();
  target << " chi: " << at.getChiralTag();
  if(at.getNumRadicalElectrons()){
    target << " rad: " << at.getNumRadicalElectrons();
  }
  if(at.getIsotope()){
    target << " iso: " << at.getIsotope();
  }
  return target;
};