MMFF/AtomTyper.h

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//
//  Copyright (C) 2013-2016 Paolo Tosco
//
//  Copyright (C) 2004-2006 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/export.h>
#ifndef _RD_MMFFATOMTYPER_H__
#define _RD_MMFFATOMTYPER_H__
 
#include <vector>
#include <string>
#include <iostream>
#include <ForceField/MMFF/Params.h>
#include <cstdint>
 
namespace RDKit {
class ROMol;
class RWMol;
class Atom;
class Bond;
 
namespace MMFF {
 
namespace DefaultParameters {
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFPropCollection *
getMMFFProp();
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFAromCollection *
getMMFFArom();
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFDefCollection *
getMMFFDef();
RDKIT_FORCEFIELDHELPERS_EXPORT const
    ForceFields::MMFF::MMFFHerschbachLaurieCollection *
    getMMFFHerschbachLaurie();
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFPBCICollection *
getMMFFPBCI();
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFAngleCollection *
getMMFFAngle();
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFStbnCollection *
getMMFFStbn();
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFDfsbCollection *
getMMFFDfsb();
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFTorCollection *
getMMFFTor(const bool isMMFFs);
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFOopCollection *
getMMFFOop(const bool isMMFFs);
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFVdWCollection *
getMMFFVdW();
}  // namespace DefaultParameters
 
class RingMembershipSize;
using namespace ForceFields::MMFF;
class RDKIT_FORCEFIELDHELPERS_EXPORT MMFFAtomProperties {
 public:
  MMFFAtomProperties() {}
  ~MMFFAtomProperties() = default;
  std::uint8_t mmffAtomType{0};
  double mmffFormalCharge{0.0};
  double mmffPartialCharge{0.0};
};
 
typedef boost::shared_ptr<MMFFAtomProperties> MMFFAtomPropertiesPtr;
enum { CONSTANT = 1, DISTANCE = 2 };
enum {
  MMFF_VERBOSITY_NONE = 0,
  MMFF_VERBOSITY_LOW = 1,
  MMFF_VERBOSITY_HIGH = 2
};
class RDKIT_FORCEFIELDHELPERS_EXPORT MMFFMolProperties {
 public:
  MMFFMolProperties(ROMol &mol, const std::string &mmffVariant = "MMFF94",
                    std::uint8_t verbosity = MMFF_VERBOSITY_NONE,
                    std::ostream &oStream = std::cout);
  ~MMFFMolProperties() = default;
  unsigned int getMMFFBondType(const Bond *bond);
  unsigned int getMMFFAngleType(const ROMol &mol, const unsigned int idx1,
                                const unsigned int idx2,
                                const unsigned int idx3);
  const std::pair<unsigned int, unsigned int> getMMFFTorsionType(
      const ROMol &mol, const unsigned int idx1, const unsigned int idx2,
      const unsigned int idx3, const unsigned int idx4);
  void computeMMFFCharges(const ROMol &mol);
  const ForceFields::MMFF::MMFFTor *getMMFFTorsionEmpiricalRuleParams(
      const ROMol &mol, unsigned int idx2, unsigned int idx3);
  const ForceFields::MMFF::MMFFBond *getMMFFBondStretchEmpiricalRuleParams(
      const ROMol &mol, const Bond *bond);
  std::uint8_t getMMFFAtomType(const unsigned int idx) {
    URANGE_CHECK(idx, this->d_MMFFAtomPropertiesPtrVect.size());
 
    return this->d_MMFFAtomPropertiesPtrVect[idx]->mmffAtomType;
  }
  double getMMFFFormalCharge(const unsigned int idx) {
    URANGE_CHECK(idx, this->d_MMFFAtomPropertiesPtrVect.size());
 
    return this->d_MMFFAtomPropertiesPtrVect[idx]->mmffFormalCharge;
  }
  double getMMFFPartialCharge(const unsigned int idx) {
    URANGE_CHECK(idx, this->d_MMFFAtomPropertiesPtrVect.size());
 
    return this->d_MMFFAtomPropertiesPtrVect[idx]->mmffPartialCharge;
  }
  void setMMFFBondTerm(const bool state) { this->d_bondTerm = state; }
  bool getMMFFBondTerm() { return this->d_bondTerm; }
  void setMMFFAngleTerm(const bool state) { this->d_angleTerm = state; }
  bool getMMFFAngleTerm() { return this->d_angleTerm; }
  void setMMFFStretchBendTerm(const bool state) {
    this->d_stretchBendTerm = state;
  }
  bool getMMFFStretchBendTerm() { return this->d_stretchBendTerm; }
  void setMMFFOopTerm(const bool state) { this->d_oopTerm = state; }
  bool getMMFFOopTerm() { return this->d_oopTerm; }
  void setMMFFTorsionTerm(const bool state) { this->d_torsionTerm = state; }
  bool getMMFFTorsionTerm() { return this->d_torsionTerm; }
  void setMMFFVdWTerm(const bool state) { this->d_vdWTerm = state; }
  bool getMMFFVdWTerm() { return this->d_vdWTerm; }
  void setMMFFEleTerm(const bool state) { this->d_eleTerm = state; }
  bool getMMFFEleTerm() { return this->d_eleTerm; }
  void setMMFFVariant(const std::string &mmffVariant) {
    PRECONDITION((mmffVariant == "MMFF94") || (mmffVariant == "MMFF94s"),
                 "bad MMFF variant");
 
    this->d_mmffs = mmffVariant == "MMFF94s";
  }
  const std::string getMMFFVariant() {
    return (this->d_mmffs ? "MMFF94s" : "MMFF94");
  }
  void setMMFFDielectricConstant(const double dielConst) {
    PRECONDITION(dielConst > 0.0, "bad dielectric constant");
 
    this->d_dielConst = dielConst;
  }
  double getMMFFDielectricConstant() { return this->d_dielConst; }
  void setMMFFDielectricModel(std::uint8_t dielModel) {
    this->d_dielModel = dielModel;
  }
  std::uint8_t getMMFFDielectricModel() { return this->d_dielModel; }
  void setMMFFVerbosity(std::uint8_t verbosity) {
    this->d_verbosity = verbosity;
  }
  std::uint8_t getMMFFVerbosity() { return this->d_verbosity; }
  void setMMFFOStream(std::ostream *oStream) { this->d_oStream = oStream; }
  std::ostream &getMMFFOStream() { return *(this->d_oStream); }
  bool isValid() { return d_valid; }
  bool getMMFFBondStretchParams(const ROMol &mol, const unsigned int idx1,
                                const unsigned int idx2, unsigned int &bondType,
                                MMFFBond &mmffBondStretchParams);
  bool getMMFFAngleBendParams(const ROMol &mol, const unsigned int idx1,
                              const unsigned int idx2, const unsigned int idx3,
                              unsigned int &angleType,
                              MMFFAngle &mmffAngleBendParams);
  bool getMMFFStretchBendParams(const ROMol &mol, const unsigned int idx1,
                                const unsigned int idx2,
                                const unsigned int idx3,
                                unsigned int &stretchBendType,
                                MMFFStbn &mmffStretchBendParams,
                                MMFFBond mmffBondStretchParams[2],
                                MMFFAngle &mmffAngleBendParams);
  bool getMMFFTorsionParams(const ROMol &mol, const unsigned int idx1,
                            const unsigned int idx2, const unsigned int idx3,
                            const unsigned int idx4, unsigned int &torsionType,
                            MMFFTor &mmffTorsionParams);
  bool getMMFFOopBendParams(const ROMol &mol, const unsigned int idx1,
                            const unsigned int idx2, const unsigned int idx3,
                            const unsigned int idx4,
                            MMFFOop &mmffOopBendParams);
  bool getMMFFVdWParams(const unsigned int idx1, const unsigned int idx2,
                        MMFFVdWRijstarEps &mmffVdWParams);
 
 private:
  void setMMFFHeavyAtomType(const RingMembershipSize &rmSize, const Atom *atom);
  void setMMFFHydrogenType(const Atom *atom);
  void setMMFFFormalCharge(const unsigned int idx, const double fChg) {
    URANGE_CHECK(idx, this->d_MMFFAtomPropertiesPtrVect.size());
 
    this->d_MMFFAtomPropertiesPtrVect[idx]->mmffFormalCharge = fChg;
  }
  void setMMFFPartialCharge(const unsigned int idx, const double pChg) {
    URANGE_CHECK(idx, this->d_MMFFAtomPropertiesPtrVect.size());
 
    this->d_MMFFAtomPropertiesPtrVect[idx]->mmffPartialCharge = pChg;
  }
  bool d_valid;
  bool d_mmffs;
  bool d_bondTerm;
  bool d_angleTerm;
  bool d_stretchBendTerm;
  bool d_oopTerm;
  bool d_torsionTerm;
  bool d_vdWTerm;
  bool d_eleTerm;
  double d_dielConst;        //!< the dielectric constant
  std::uint8_t d_dielModel;  //!< the dielectric model (1 = constant, 2 =
  // distance-dependent)
  std::uint8_t d_verbosity;
  std::ostream *d_oStream;
  std::vector<MMFFAtomPropertiesPtr> d_MMFFAtomPropertiesPtrVect;
};
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int isAngleInRingOfSize3or4(
    const ROMol &mol, const unsigned int idx1, const unsigned int idx2,
    const unsigned int idx3);
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int isTorsionInRingOfSize4or5(
    const ROMol &mol, const unsigned int idx1, const unsigned int idx2,
    const unsigned int idx3, const unsigned int idx4);
RDKIT_FORCEFIELDHELPERS_EXPORT bool isRingAromatic(
    const ROMol &mol, const INT_VECT &ringIndxVect);
RDKIT_FORCEFIELDHELPERS_EXPORT bool isAtomInAromaticRingOfSize(
    const Atom *atom, const unsigned int ringSize);
RDKIT_FORCEFIELDHELPERS_EXPORT bool isAtomNOxide(const Atom *atom);
RDKIT_FORCEFIELDHELPERS_EXPORT bool areAtomsInSameAromaticRing(
    const ROMol &mol, const unsigned int idx1, const unsigned int idx2);
RDKIT_FORCEFIELDHELPERS_EXPORT bool areAtomsInSameRingOfSize(
    const ROMol &mol, const unsigned int ringSize, const unsigned int numAtoms,
    ...);
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int sanitizeMMFFMol(RWMol &mol);
//! \deprecated, please use MolOps::setMMFFAromaticity instead
RDKIT_FORCEFIELDHELPERS_EXPORT void setMMFFAromaticity(RWMol &mol);
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int getMMFFStretchBendType(
    const unsigned int angleType, const unsigned int bondType1,
    const unsigned int bondType2);
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int getPeriodicTableRow(
    const int atomicNum);
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFAngle *
getMMFFAngleBendEmpiricalRuleParams(
    const ROMol &mol, const ForceFields::MMFF::MMFFAngle *oldMMFFAngleParams,
    const ForceFields::MMFF::MMFFProp *mmffPropParamsCentralAtom,
    const ForceFields::MMFF::MMFFBond *mmffBondParams1,
    const ForceFields::MMFF::MMFFBond *mmffBondParams2, unsigned int idx1,
    unsigned int idx2, unsigned int idx3);
}  // namespace MMFF
}  // namespace RDKit
 
#endif