rdkit/Code/GraphMol/SLNParse/SLNAttribs.cpp

// $Id$
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//  Copyright (c) 2008, Novartis Institutes for BioMedical Research Inc.
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// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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//  Created by Greg Landrum, Sept. 2006
//

#include <GraphMol/SLNParse/SLNParse.h>
#include <GraphMol/SLNParse/SLNAttribs.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/Invariant.h>

#include <boost/algorithm/string.hpp>
#include <boost/lexical_cast.hpp>

namespace RDKit {
namespace SLNParse {
namespace {
int parseIntAttribVal(std::string attribName, std::string attribVal,
                      int (*defaultFunc)(Atom const *at) = nullptr,
                      Atom *atom = nullptr) {
  PRECONDITION((!defaultFunc) || atom,
               "If a default func is provided, an atom must be as well.");
  int iVal;
  boost::to_lower(attribVal);

  if (defaultFunc && attribVal == "f") {
    iVal = defaultFunc(atom);
  } else {
    try {
      iVal = boost::lexical_cast<int>(attribVal);
    } catch (boost::bad_lexical_cast &) {
      std::stringstream err;
      err << "SLN Parser error: bad integer value (" << attribVal
          << ") provided for property: " << attribName;
      throw SLNParseException(err.str());
    }
  }
  return iVal;
}
}  // end of anonymous namespace

QueryAtom::QUERYATOM_QUERY *makeQueryFromOp(const std::string &op, int val,
                                            int (*func)(Atom const *at),
                                            std::string description) {
  PRECONDITION(func, "bad query function");
  QueryAtom::QUERYATOM_QUERY *res = nullptr;
  if (op == "=") {
    auto *tmp = new ATOM_EQUALS_QUERY;
    tmp->setVal(val);
    tmp->setDataFunc(func);
    tmp->setDescription(description);
    res = tmp;
  } else if (op == "!=") {
    auto *tmp = new ATOM_EQUALS_QUERY;
    tmp->setVal(val);
    tmp->setDataFunc(func);
    tmp->setDescription(description);
    tmp->setNegation(true);
    res = tmp;
  } else if (op == ">") {
    // don't be alarmed by this use of the LessEqual query for >, it's not a
    // bug.
    // The RD GreaterQuery(tgt) returns true if tgt is greater than the thing
    // you
    // compare to. In this case we need to reverse that because we're interested
    // in
    // seeing if the value is greater than the target; this is equiv to asking
    // if
    // the target is < the value.
    auto *tmp = new ATOM_LESS_QUERY;
    tmp->setVal(val);
    tmp->setDataFunc(func);
    tmp->setDescription(description);
    res = tmp;
  } else if (op == ">=") {
    auto *tmp = new ATOM_LESSEQUAL_QUERY;
    tmp->setVal(val);
    tmp->setDataFunc(func);
    tmp->setDescription(description);
    res = tmp;
  } else if (op == "<") {
    auto *tmp = new ATOM_GREATER_QUERY;
    tmp->setVal(val);
    tmp->setDataFunc(func);
    tmp->setDescription(description);
    res = tmp;
  } else if (op == "<=") {
    auto *tmp = new ATOM_GREATEREQUAL_QUERY;
    tmp->setVal(val);
    tmp->setDataFunc(func);
    tmp->setDescription(description);
    res = tmp;
  } else {
    std::stringstream err;
    err << "SLN Parser error: bad attribute operator (" << op << ") provided.";
    throw SLNParseException(err.str());
  }

  POSTCONDITION(res, "bad query");
  return res;
}

void parseAtomAttribs(Atom *atom, AttribListType attribs, bool doingQuery) {
  QueryAtom::QUERYATOM_QUERY *atomQuery = nullptr;
  bool lastWasLowPriAnd = false;
  for (AttribListType::const_iterator it = attribs.begin(); it != attribs.end();
       ++it) {
    QueryAtom::QUERYATOM_QUERY *query = nullptr;
    AttribCombineOp how = it->first;

    boost::shared_ptr<AttribType> attribPtr = it->second;
    std::string attribName = attribPtr->first;
    boost::to_lower(attribName);
    std::string attribVal = attribPtr->second;
    if (attribName == "charge") {
      int chg = 0;
      if (attribVal == "-") {
        chg = -1;
      } else if (attribVal == "+") {
        chg = +1;
      } else {
        chg = parseIntAttribVal(attribName, attribVal);
      }
      if (!doingQuery) {
        atom->setFormalCharge(chg);
      } else {
        query = makeQueryFromOp(attribPtr->op, chg, queryAtomFormalCharge,
                                "AtomFormalCharge");
      }
    } else if (attribName == "i") {
      int val = parseIntAttribVal(attribName, attribVal);
      if (!doingQuery) {
        atom->setIsotope(static_cast<unsigned int>(val));
      } else {
        query = makeQueryFromOp(attribPtr->op, val, queryAtomIsotope,
                                "AtomIsotope");
      }
    } else if (attribName == "r") {
      if (attribVal != "") {
        BOOST_LOG(rdWarningLog)
            << "Query value '" << attribVal << "' ignored for r query\n";
      }
      if (!doingQuery) {
        BOOST_LOG(rdWarningLog) << "Query property '" << attribName
                                << "' ignored on non-query atom\n";
      } else {
        query = makeAtomInRingQuery();
      }
    } else if (attribName == "is") {
      // recursive queries:
      if (!attribPtr->structQuery) {
        throw SLNParseException("failed recursive query");
      }
      query = static_cast<QueryAtom::QUERYATOM_QUERY *>(attribPtr->structQuery);
    } else if (attribName == "s") {
      if (attribPtr->op != "=") {
        std::stringstream err;
        err << "SLN Parser error: comparison operator '" << attribPtr->op
            << "' not supported for chiral attributes.\n";
        throw SLNParseException(err.str());
      }
      boost::to_lower(attribVal);

      if (attribVal[0] == 'i' || attribVal[0] == 'n') {
        if (attribVal.size() > 1 && attribVal[1] == '*') {
          BOOST_LOG(rdWarningLog) << "Chiral modifier * ignored, chiral spec "
                                  << attribVal[0] << " will be used\n";
        }
        if (attribVal.size() > 1 && attribVal[1] == 'm') {
          BOOST_LOG(rdWarningLog) << "Chiral modifier m ignored, chiral spec "
                                  << attribVal[0] << " will be used\n";
        }
      } else {
        BOOST_LOG(rdWarningLog) << "Unsupported stereochemistry specifier '"
                                << attribVal << "' ignored.\n";
      }
    } else {
      // a block of properties that can have "f" values, and so need special
      // handling:
      std::string fTag = "";
      int val = 0;
      if (attribVal == "f" || attribName == "f") {
        fTag = "_SLN_";
        atom->setProp(common_properties::_Unfinished_SLN_, 1);
        val = -666;
      }
      if (attribName == "rbc") {
        if (fTag == "") {
          val = parseIntAttribVal(attribName, attribVal);
        }
        query = makeQueryFromOp(attribPtr->op, val, queryAtomRingBondCount,
                                fTag + "AtomRingBondCount");
      } else if (attribName == "tbo") {
        if (fTag == "") {
          val = parseIntAttribVal(attribName, attribVal);
        }
        query = makeQueryFromOp(attribPtr->op, val, queryAtomTotalValence,
                                fTag + "AtomTotalValence");
      } else if (attribName == "tac") {
        if (fTag == "") {
          val = parseIntAttribVal(attribName, attribVal);
        }
        query = makeQueryFromOp(attribPtr->op, val, queryAtomTotalDegree,
                                fTag + "AtomTotalDegree");
      } else if (attribName == "hc") {
        if (fTag == "") {
          val = parseIntAttribVal(attribName, attribVal);
        }
        query = makeQueryFromOp(attribPtr->op, val, queryAtomHCount,
                                fTag + "AtomHCount");
      } else if (attribName == "hac") {
        if (fTag == "") {
          val = parseIntAttribVal(attribName, attribVal);
        }
        query = makeQueryFromOp(attribPtr->op, val, queryAtomNonHydrogenDegree,
                                fTag + "AtomHeavyAtomDegree");
      } else if (attribName == "f") {
        if (fTag == "") {
          val = parseIntAttribVal(attribName, attribVal);
        }
        query = makeQueryFromOp(
            "=", val, (int (*)(const RDKit::Atom *))(queryAtomAllBondProduct),
            fTag + "AtomBondEnvironment");
      } else {
        // anything we don't know how to deal with we'll just store in raw form:
        atom->setProp(attribName, attribVal);
      }
    }

    // if we've constructed a query from all that, then we need to add it to the
    // atomQuery:
    if (query) {
      if (!doingQuery) {
        BOOST_LOG(rdWarningLog) << "Query property '" << attribName
                                << "' ignored on non-query atom\n";
        delete query;
      } else {
        if (attribPtr->negated) {
          query->setNegation(!query->getNegation());
        }
        if (!atomQuery) {
          // first one is easy:
          atomQuery = query;
        } else {
          QueryAtom::QUERYATOM_QUERY *tQuery;
          switch (how) {
            case AttribAnd:
              // high-priority and:
              tQuery = new ATOM_AND_QUERY;
              tQuery->setDescription("AtomAnd");
              tQuery->addChild(
                  QueryAtom::QUERYATOM_QUERY::CHILD_TYPE(atomQuery));
              tQuery->addChild(QueryAtom::QUERYATOM_QUERY::CHILD_TYPE(query));
              atomQuery = tQuery;
              lastWasLowPriAnd = false;
              break;
            case AttribLowPriAnd:
              tQuery = new ATOM_AND_QUERY;
              tQuery->setDescription("AtomAnd");
              tQuery->addChild(
                  QueryAtom::QUERYATOM_QUERY::CHILD_TYPE(atomQuery));
              tQuery->addChild(QueryAtom::QUERYATOM_QUERY::CHILD_TYPE(query));
              atomQuery = tQuery;
              lastWasLowPriAnd = true;
              break;
            case AttribOr:
              if (lastWasLowPriAnd) {
                // if the last query was a low-priority AND, we need to
                // restructure
                // the tree a bit:
                QueryAtom::QUERYATOM_QUERY *newAndQuery;
                newAndQuery = new ATOM_AND_QUERY;
                newAndQuery->setDescription("AtomAnd");
                auto andChild = atomQuery->beginChildren();
                newAndQuery->addChild(*andChild);
                ++andChild;

                tQuery = new ATOM_OR_QUERY;
                tQuery->setDescription("AtomOr");
                tQuery->addChild(*andChild);

                newAndQuery->addChild(
                    QueryAtom::QUERYATOM_QUERY::CHILD_TYPE(tQuery));
                delete atomQuery;
                atomQuery = newAndQuery;
              } else {
                // otherwise we just do a normal expansion:
                tQuery = new ATOM_OR_QUERY;
                tQuery->setDescription("AtomOr");
                tQuery->addChild(
                    QueryAtom::QUERYATOM_QUERY::CHILD_TYPE(atomQuery));
                tQuery->addChild(QueryAtom::QUERYATOM_QUERY::CHILD_TYPE(query));
                atomQuery = tQuery;
              }
              lastWasLowPriAnd = false;
              break;
            default:
              throw SLNParseException(
                  "unrecognized query composition operator");
          }
        }
      }
    }  // end of query processing
  }  // end of loop over attribs
  if (atomQuery) {
    atom->expandQuery(atomQuery, Queries::COMPOSITE_AND);
  }
}

void parseFinalAtomAttribs(Atom *atom, bool doingQuery) {
  PRECONDITION(atom, "no atom");
  // we need to loop over the atom's query tree and finalize any
  // attributes that had "f" in the original SLN. We will recognize
  // these by the fact that their names start with "_SLN_"
  if (!doingQuery || !atom->hasQuery() ||
      !atom->hasProp(common_properties::_Unfinished_SLN_)) {
    return;
  }
  atom->clearProp(common_properties::_Unfinished_SLN_);
  std::list<QueryAtom::QUERYATOM_QUERY *> q;
  q.push_back(atom->getQuery());
  while (!q.empty()) {
    QueryAtom::QUERYATOM_QUERY *query = q.front();
    q.pop_front();

    std::string description = query->getDescription();
    if (description.size() > 5 && description.substr(0, 5) == "_SLN_") {
      boost::erase_head(description, 5);
      query->setDescription(description);
      static_cast<ATOM_EQUALS_QUERY *>(query)->setVal(
          (int)(query->getDataFunc()(atom)));
    }
    // now add the query's children to the queue and continue:
    for (auto cIt = query->beginChildren(); cIt != query->endChildren();
         ++cIt) {
      q.push_back(const_cast<QueryAtom::QUERYATOM_QUERY *>(cIt->get()));
    }
  }
}

void parseBondAttribs(Bond *bond, AttribListType attribs, bool doingQuery) {
  // FIX: need to do the same query tree reordering here as we did above.
  bool seenTypeQuery = false;
  for (AttribListType::const_iterator it = attribs.begin(); it != attribs.end();
       ++it) {
    Queries::CompositeQueryType how;
    switch (it->first) {
      case AttribAnd:
        how = Queries::COMPOSITE_AND;
        break;
      case AttribOr:
        how = Queries::COMPOSITE_OR;
        break;
      case AttribLowPriAnd:
        how = Queries::COMPOSITE_AND;
        break;
      default:
        throw SLNParseException("unrecognized query composition operator");
    }

    boost::shared_ptr<AttribType> attribPtr = it->second;
    std::string attribName = attribPtr->first;
    boost::to_lower(attribName);
    std::string attribVal = attribPtr->second;
    if (attribName == "type") {
      boost::to_lower(attribVal);
      Bond::BondType bondType;
      if (attribVal == "-" || attribVal == "1") {
        bondType = Bond::SINGLE;
      } else if (attribVal == "=" || attribVal == "2") {
        bondType = Bond::DOUBLE;
      } else if (attribVal == "#" || attribVal == "3") {
        bondType = Bond::TRIPLE;
      } else if (attribVal == ":" || attribVal == "aromatic") {
        bondType = Bond::AROMATIC;
      } else {
        bondType = Bond::OTHER;
        bond->setProp("SLN_Type", attribVal);
      }
      if (!doingQuery) {
        bond->setBondType(bondType);
      } else {
        QueryBond::QUERYBOND_QUERY *query = makeBondOrderEqualsQuery(bondType);
        if (attribPtr->negated) {
          query->setNegation(!query->getNegation());
        }
        if (seenTypeQuery) {
          static_cast<RDKit::QueryBond *>(bond)->expandQuery(query, how, true);
        } else {
          // if this is the first type query, we need to replace any existing
          // bond order queries:
          // FIX: this replaces tooo much, ring queries also get blown out
          bond->setQuery(query);
        }
        seenTypeQuery = true;
      }
    } else if (attribName == "r") {
      if (attribVal != "") {
        BOOST_LOG(rdWarningLog)
            << "Query value '" << attribVal << "' ignored for r query\n";
      }
      if (!doingQuery) {
        BOOST_LOG(rdWarningLog) << "Query property '" << attribName
                                << "' ignored on non-query bond\n";
      } else {
        QueryBond::QUERYBOND_QUERY *query = makeBondIsInRingQuery();
        if (attribPtr->negated) {
          query->setNegation(true);
        }
        static_cast<QueryBond *>(bond)->expandQuery(query, how);
      }
    } else {
      // anything we don't know how to deal with we'll just store in raw form:
      bond->setProp(attribName, attribVal);
    }
  }
}

void parseMolAttribs(ROMol *mol, AttribListType attribs) {
  for (AttribListType::const_iterator it = attribs.begin(); it != attribs.end();
       ++it) {
    CHECK_INVARIANT(it->first == AttribAnd, "bad attrib type");

    boost::shared_ptr<AttribType> attribPtr = it->second;
    std::string attribName = attribPtr->first;
    boost::to_lower(attribName);
    std::string attribVal = attribPtr->second;
    if (attribVal.begin() != attribVal.end() && *(attribVal.begin()) == '"' &&
        *(attribVal.begin()) == *(attribVal.rbegin())) {
      attribVal.erase(attribVal.begin());
      attribVal.erase(--(attribVal.end()));
    }
    if (attribName == "name") {
      mol->setProp(common_properties::_Name, attribVal);
    } else {
      mol->setProp(attribName, attribVal);
    }
  }
}

void adjustAtomChiralities(RWMol *mol) {
  for (auto atom : mol->atoms()) {
    std::string attribVal;
    if (atom->getPropIfPresent(common_properties::_SLN_s, attribVal)) {
      // the atom is marked as chiral, translate the sln chirality into
      // RDKit chirality

      // start with a straight map of the chirality value:
      // as a reminder, here are some SLN <-> SMILES pairs
      //      C[s=n]H(Cl)(F)Br  <->  [C@@H](Cl)(F)Br (CHI_TETRAHEDRAL_CW)
      //      ClC[s=n]H(F)Br  <->  Cl[C@H](F)Br (CHI_TETRAHEDRAL_CCW)
      //      FC[1:s=n](Cl)OCH2@1   <->  F[C@@]1(Cl)OC1 (CHI_TETRAHEDRAL_CW)
      if (attribVal[0] == 'n') {
        atom->setChiralTag(Atom::CHI_TETRAHEDRAL_CW);
      } else if (attribVal[0] == 'i') {
        atom->setChiralTag(Atom::CHI_TETRAHEDRAL_CCW);
      }
      std::list<std::pair<int, int>> neighbors;
      for (auto nbrBond : mol->atomBonds(atom)) {
        neighbors.emplace_back(nbrBond->getOtherAtomIdx(atom->getIdx()),
                               nbrBond->getIdx());
      }

      // std::cerr << "CHIRAL " << (*atomIt)->getIdx();

      // sort by neighbor idx:
      neighbors.sort();
      // figure out the bond ordering:
      std::list<int> bondOrdering;
      for (std::list<std::pair<int, int>>::const_iterator nbrIt =
               neighbors.begin();
           nbrIt != neighbors.end(); ++nbrIt) {
        bondOrdering.push_back(nbrIt->second);
        // std::cerr << " " << nbrIt->second;
      }

      // ok, we now have the ordering of the bonds (used for RDKit chirality),
      // figure out the permutation order relative to the atom numbering
      // (sln chirality):
      int nSwaps = atom->getPerturbationOrder(bondOrdering);

      if (nSwaps % 2) {
        atom->setChiralTag(atom->getChiralTag() == Atom::CHI_TETRAHEDRAL_CW
                               ? Atom::CHI_TETRAHEDRAL_CCW
                               : Atom::CHI_TETRAHEDRAL_CW);
      }
    }
  }
}
}  // namespace SLNParse
}  // namespace RDKit