FileParserUtils.h

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//
//  Copyright (C) 2010-2025 Greg Landrum and other RDKit contributors
//
//   @@ 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/export.h>
#ifndef RD_FILEPARSERUTILS_H
#define RD_FILEPARSERUTILS_H
 
#include <string>
#include <iostream>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/lexical_cast.hpp>
#include <boost/algorithm/string.hpp>
#include <boost/format.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include "FileParsers.h"
#include <string_view>
 
namespace RDKit {
class RWMol;
class Conformer;
 
namespace FileParserUtils {
RDKIT_FILEPARSERS_EXPORT inline std::string_view strip(
    std::string_view orig, std::string stripChars = " \t\r\n") {
  std::string_view res = orig;
  auto start = res.find_first_not_of(stripChars);
  if (start != std::string_view::npos) {
    auto end = res.find_last_not_of(stripChars) + 1;
    res = res.substr(start, end - start);
  } else {
    res = "";
  }
  return res;
}
 
template <typename T>
T stripSpacesAndCast(std::string_view input, bool acceptSpaces = false) {
  auto trimmed = strip(input, " ");
  if (acceptSpaces && trimmed.empty()) {
    return 0;
  } else {
    return boost::lexical_cast<T>(trimmed);
  }
}
template <typename T>
T stripSpacesAndCast(const std::string &input, bool acceptSpaces = false) {
  return stripSpacesAndCast<T>(std::string_view(input.c_str()), acceptSpaces);
}
RDKIT_FILEPARSERS_EXPORT int toInt(const std::string &input,
                                   bool acceptSpaces = true);
RDKIT_FILEPARSERS_EXPORT unsigned int toUnsigned(const std::string &input,
                                                 bool acceptSpaces = true);
RDKIT_FILEPARSERS_EXPORT double toDouble(const std::string &input,
                                         bool acceptSpaces = true);
RDKIT_FILEPARSERS_EXPORT int toInt(const std::string_view input,
                                   bool acceptSpaces = true);
RDKIT_FILEPARSERS_EXPORT unsigned int toUnsigned(std::string_view input,
                                                 bool acceptSpaces = true);
RDKIT_FILEPARSERS_EXPORT double toDouble(const std::string_view input,
                                         bool acceptSpaces = true);
 
// gets a V3000 CTAB for a molecule
RDKIT_FILEPARSERS_EXPORT std::string getV3000CTAB(
    const ROMol &tmol, const boost::dynamic_bitset<> &wasAromatic,
    int confId = -1, unsigned int precision = 6);
//! \overload
inline std::string getV3000CTAB(const ROMol &tmol, int confId = -1,
                                unsigned int precision = 6) {
  boost::dynamic_bitset<> wasAromatic(tmol.getNumBonds());
  return getV3000CTAB(tmol, wasAromatic, confId, precision);
};
// reads a line from an MDL v3K CTAB
RDKIT_FILEPARSERS_EXPORT std::string getV3000Line(std::istream *inStream,
                                                  unsigned int &line);
 
// nAtoms and nBonds are ignored on input, set on output
RDKIT_FILEPARSERS_EXPORT bool ParseV3000CTAB(
    std::istream *inStream, unsigned int &line, RWMol *mol, Conformer *&conf,
    bool &chiralityPossible, unsigned int &nAtoms, unsigned int &nBonds,
    bool strictParsing = true, bool expectMEND = true,
    bool expectMacroAtoms = false);
 
// nAtoms and nBonds are used
RDKIT_FILEPARSERS_EXPORT bool ParseV2000CTAB(
    std::istream *inStream, unsigned int &line, RWMol *mol, Conformer *&conf,
    bool &chiralityPossible, unsigned int &nAtoms, unsigned int &nBonds,
    bool strictParsing = true);
 
//! finishes up the processing (sanitization, etc.) of a molecule read from
//! CTAB
RDKIT_FILEPARSERS_EXPORT void finishMolProcessing(
    RWMol *res, bool chiralityPossible,
    const v2::FileParsers::MolFileParserParams &ps);
//! \overload
inline void finishMolProcessing(RWMol *res, bool chiralityPossible,
                                bool sanitize, bool removeHs) {
  v2::FileParsers::MolFileParserParams ps;
  ps.sanitize = sanitize;
  ps.removeHs = removeHs;
  finishMolProcessing(res, chiralityPossible, ps);
}
 
//! Deprecated, please use QueryOps::replaceAtomWithQueryAtom instead
RDKIT_FILEPARSERS_EXPORT Atom *replaceAtomWithQueryAtom(RWMol *mol, Atom *atom);
 
//! applies a particular property to the atoms as an atom property list
template <typename T, typename U>
void applyMolListProp(ROMol &mol, const std::string &pn,
                      const std::string &prefix,
                      const std::string &missingValueMarker, size_t nItems,
                      U getter) {
  std::string itempn = pn.substr(prefix.size());
  std::string strVect = mol.getProp<std::string>(pn);
  std::vector<std::string> tokens;
  boost::split(tokens, strVect, boost::is_any_of(" \t\n"),
               boost::token_compress_on);
  std::string mv = missingValueMarker;
  size_t first_token = 0;
  if (tokens.size() == nItems + 1 && tokens[0].front() == '[' &&
      tokens[0].back() == ']') {
    mv = std::string(tokens[0].begin() + 1, tokens[0].end() - 1);
    first_token = 1;
  }
  if (mv.empty()) {
    BOOST_LOG(rdWarningLog) << "Missing value marker for property " << pn
                            << " is empty." << std::endl;
  }
  if(tokens.size() - first_token != nItems) {
    BOOST_LOG(rdWarningLog) << "Property list " << pn << " has incompatible size, "
                            << tokens.size() << " elements found; expecting "
                            << nItems << ". Ignoring it." << std::endl;
    return;
  }
  for (size_t i = first_token; i < tokens.size(); ++i) {
    if (tokens[i] != mv) {
      unsigned int itemid = i - first_token;
      try {
        T apv = boost::lexical_cast<T>(tokens[i]);
        getter(itemid)->setProp(itempn, apv);
      } catch (const boost::bad_lexical_cast &) {
        BOOST_LOG(rdWarningLog)
            << "Value " << tokens[i] << " for property " << pn << " of item "
            << itemid << " can not be parsed. Ignoring it." << std::endl;
      }
    }
  }
}
 
//! applies a particular property to the atoms as an atom property list
template <typename T>
[[deprecated("use applyMolListProp instead")]]
void applyMolListPropToAtoms(ROMol &mol, const std::string &pn,
                             const std::string &prefix,
                             const std::string &missingValueMarker = "n/a") {
  auto getter = [&mol](size_t which) { return mol.getAtomWithIdx(which); };
  applyMolListProp<T>(mol, pn, prefix, missingValueMarker, mol.getNumAtoms(),
                      getter);
}
 
template <typename T, typename U>
void applyMolListProps(ROMol &mol, const std::string &prefix, size_t nItems,
                       U getter, const std::string missingValueMarker = "n/a") {
  for (auto pn : mol.getPropList()) {
    if (pn.find(prefix) == 0 && pn.length() > prefix.length()) {
      applyMolListProp<T>(mol, pn, prefix, missingValueMarker, nItems, getter);
    }
  }
}
 
//! applies all properties matching a particular prefix as an atom property
//! list
template <typename T>
[[deprecated("use applyMolListProps instead")]]
void applyMolListPropsToAtoms(ROMol &mol, const std::string &prefix,
                              const std::string missingValueMarker = "n/a") {
  auto getter = [&mol](size_t which) { return mol.getAtomWithIdx(which); };
  auto nItems = mol.getNumAtoms();
  for (auto pn : mol.getPropList()) {
    if (pn.find(prefix) == 0 && pn.length() > prefix.length()) {
      applyMolListProp<T>(mol, pn, prefix, missingValueMarker, nItems, getter);
    }
  }
}
 
static constexpr std::string_view atomPropPrefixView = "atom.";
static constexpr size_t atomPropPrefixLength = atomPropPrefixView.length();
static const std::string atomPropPrefix = std::string(atomPropPrefixView);
static constexpr std::string_view bondPropPrefixView = "bond.";
static constexpr size_t bondPropPrefixLength = bondPropPrefixView.length();
static const std::string bondPropPrefix = std::string(bondPropPrefixView);
 
//! if the property name matches our rules for atom property lists, we'll
//! apply it to the atoms
inline void processMolPropertyList(
    ROMol &mol, const std::string &pn,
    const std::string &missingValueMarker = "n/a") {
  auto propSetter = [&](const std::string &propPrefix, auto getter,
                        size_t nItems) {
    std::string prefix = propPrefix + "prop.";
    if (pn.find(prefix) == 0 && pn.length() > prefix.length()) {
      applyMolListProp<std::string>(mol, pn, prefix, missingValueMarker, nItems,
                                    getter);
    } else {
      prefix = propPrefix + "iprop.";
      if (pn.find(prefix) == 0 && pn.length() > prefix.length()) {
        applyMolListProp<int>(mol, pn, prefix, missingValueMarker, nItems,
                              getter);
      } else {
        prefix = propPrefix + "dprop.";
        if (pn.find(prefix) == 0 && pn.length() > prefix.length()) {
          applyMolListProp<double>(mol, pn, prefix, missingValueMarker, nItems,
                                   getter);
        } else {
          prefix = propPrefix + "bprop.";
          if (pn.find(prefix) == 0 && pn.length() > prefix.length()) {
            applyMolListProp<bool>(mol, pn, prefix, missingValueMarker, nItems,
                                   getter);
          }
        }
      }
    }
  };
 
  if (pn.find(atomPropPrefix) == 0 && pn.length() > atomPropPrefixLength) {
    propSetter(
        atomPropPrefix,
        [&mol](size_t which) { return mol.getAtomWithIdx(which); },
        mol.getNumAtoms());
  } else if (pn.find(bondPropPrefix) == 0 &&
             pn.length() > bondPropPrefixLength) {
    propSetter(
        bondPropPrefix,
        [&mol](size_t which) { return mol.getBondWithIdx(which); },
        mol.getNumBonds());
  }
}
//! loops over all properties and applies the ones that match the rules for
//! atom property lists to the atoms and bonds
inline void processMolPropertyLists(
    ROMol &mol, const std::string &missingValueMarker = "n/a") {
  for (const auto &pn : mol.getPropList()) {
    processMolPropertyList(mol, pn, missingValueMarker);
  }
}
 
static constexpr unsigned int DEFAULT_LINESIZE = 190;
 
template <typename T, typename U>
std::string getPropertyList(U getter, const std::string &propName,
                            std::string missingValueMarker = "",
                            unsigned int lineSize = DEFAULT_LINESIZE) {
  std::string res;
  std::string propVal;
  if (!missingValueMarker.empty()) {
    propVal += boost::str(boost::format("[%s] ") % missingValueMarker);
  } else {
    missingValueMarker = "n/a";
  }
  for (const auto item : getter()) {
    std::string apVal = missingValueMarker;
    T tVal;
    if (item->getPropIfPresent(propName, tVal)) {
      apVal = boost::lexical_cast<std::string>(tVal);
    }
    if (propVal.length() + apVal.length() + 1 >= lineSize) {
      // remove trailing space:
      propVal.pop_back();
      res += propVal + "\n";
      propVal = "";
    }
    propVal += apVal + " ";
  }
  if (!propVal.empty()) {
    // remove the trailing space:
    propVal.pop_back();
    res += propVal;
  }
  return res;
}
 
template <typename T>
[[deprecated("use getPropertyList() instead")]]
std::string getAtomPropertyList(ROMol &mol, const std::string &atomPropName,
                                std::string missingValueMarker = "",
                                unsigned int lineSize = DEFAULT_LINESIZE) {
  return getPropertyList<T>([&mol]() { return mol.atoms(); }, atomPropName,
                            missingValueMarker, lineSize);
}
 
template <typename T, typename U>
void createPropertyList(ROMol &mol, U getter, const std::string &prefix,
                        const std::string &typeMarker,
                        const std::string &propName,
                        const std::string &missingValueMarker = "",
                        unsigned int lineSize = DEFAULT_LINESIZE) {
  std::string molPropName = prefix + "." + typeMarker + "." + propName;
  mol.setProp(molPropName, getPropertyList<T>(getter, propName,
                                              missingValueMarker, lineSize));
}
 
inline void createAtomIntPropertyList(
    ROMol &mol, const std::string &atomPropName,
    const std::string &missingValueMarker = "",
    unsigned int lineSize = DEFAULT_LINESIZE) {
  createPropertyList<int>(
      mol, [&mol]() { return mol.atoms(); }, "atom", "iprop", atomPropName,
      missingValueMarker, lineSize);
}
inline void createAtomDoublePropertyList(
    ROMol &mol, const std::string &atomPropName,
    const std::string &missingValueMarker = "",
    unsigned int lineSize = DEFAULT_LINESIZE) {
  createPropertyList<double>(
      mol, [&mol]() { return mol.atoms(); }, "atom", "dprop", atomPropName,
      missingValueMarker, lineSize);
}
inline void createAtomBoolPropertyList(
    ROMol &mol, const std::string &atomPropName,
    const std::string &missingValueMarker = "",
    unsigned int lineSize = DEFAULT_LINESIZE) {
  createPropertyList<bool>(
      mol, [&mol]() { return mol.atoms(); }, "atom", "bprop", atomPropName,
      missingValueMarker, lineSize);
}
inline void createAtomStringPropertyList(
    ROMol &mol, const std::string &atomPropName,
    const std::string &missingValueMarker = "",
    unsigned int lineSize = DEFAULT_LINESIZE) {
  createPropertyList<std::string>(
      mol, [&mol]() { return mol.atoms(); }, "atom", "prop", atomPropName,
      missingValueMarker, lineSize);
}
 
inline void createBondIntPropertyList(
    ROMol &mol, const std::string &bondPropName,
    const std::string &missingValueMarker = "",
    unsigned int lineSize = DEFAULT_LINESIZE) {
  createPropertyList<int>(
      mol, [&mol]() { return mol.bonds(); }, "bond", "iprop", bondPropName,
      missingValueMarker, lineSize);
}
inline void createBondDoublePropertyList(
    ROMol &mol, const std::string &bondPropName,
    const std::string &missingValueMarker = "",
    unsigned int lineSize = DEFAULT_LINESIZE) {
  createPropertyList<double>(
      mol, [&mol]() { return mol.bonds(); }, "bond", "dprop", bondPropName,
      missingValueMarker, lineSize);
}
inline void createBondBoolPropertyList(
    ROMol &mol, const std::string &bondPropName,
    const std::string &missingValueMarker = "",
    unsigned int lineSize = DEFAULT_LINESIZE) {
  createPropertyList<bool>(
      mol, [&mol]() { return mol.bonds(); }, "bond", "bprop", bondPropName,
      missingValueMarker, lineSize);
}
inline void createBondStringPropertyList(
    ROMol &mol, const std::string &bondPropName,
    const std::string &missingValueMarker = "",
    unsigned int lineSize = DEFAULT_LINESIZE) {
  createPropertyList<std::string>(
      mol, [&mol]() { return mol.bonds(); }, "bond", "prop", bondPropName,
      missingValueMarker, lineSize);
}
 
RDKIT_FILEPARSERS_EXPORT void moveAdditionalPropertiesToSGroups(RWMol &mol);
 
}  // namespace FileParserUtils
}  // namespace RDKit
 
#endif