Validate.h

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//
//  Copyright (C) 2018-2021 Susan H. Leung 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.
//
/*! \file Validate.h
 
        \brief Defines the ValidationErrorInfo class and four different
   validation methods: RDKitValidation, MolVSValidation, AllowedAtomsValidation,
   DisallowedAtomsValidation.
 
*/
#include <RDGeneral/export.h>
#ifndef RD_VALIDATE_H
#define RD_VALIDATE_H
 
#include <GraphMol/RDKitBase.h>
#include <GraphMol/ROMol.h>
#include <GraphMol/Atom.h>
#include <iostream>
#include <exception>
#include <string>
#include <utility>
#include <vector>
 
namespace RDKit {
class RWMol;
class ROMol;
class Conformer;
 
namespace MolStandardize {
 
//! The ValidationErrorInfo class is used to store the information returned by a
/// ValidationMethod validate.
using ValidationErrorInfo = std::string;
 
//! The ValidationMethod class is the abstract base class upon which all the
/// four different ValidationMethods inherit from.
class RDKIT_MOLSTANDARDIZE_EXPORT ValidationMethod {
 public:
  ValidationMethod() = default;
  virtual ~ValidationMethod() = default;
 
  virtual std::vector<ValidationErrorInfo> validate(
      const ROMol &mol, bool reportAllFailures) const = 0;
  virtual std::shared_ptr<ValidationMethod> copy() const = 0;
};
 
//! The CompositeValidation class provides a simple way to apply a collection of
// ValidationMethod instances in sequence
class RDKIT_MOLSTANDARDIZE_EXPORT CompositeValidation
    : public ValidationMethod {
 public:
  CompositeValidation(
      const std::vector<std::shared_ptr<ValidationMethod>> &validations)
      : validations(validations) {};
 
  std::vector<ValidationErrorInfo> validate(
      const ROMol &mol, bool reportAllFailures) const override;
 
  std::shared_ptr<ValidationMethod> copy() const override {
    return std::make_shared<CompositeValidation>(*this);
  }
 
 private:
  std::vector<std::shared_ptr<ValidationMethod>> validations;
};
 
//! The RDKitValidation class throws an error when there are no atoms in the
/// molecule or when there is incorrect atom valency.
/*!
 
  <b>Notes:</b>
    - RDKit automatically throws up atom valency issues but this class was made
  for completeness of the project.
*/
class RDKIT_MOLSTANDARDIZE_EXPORT RDKitValidation : public ValidationMethod {
 public:
  RDKitValidation(bool allowEmptyMolecules = false)
      : allowEmptyMolecules(allowEmptyMolecules) {};
 
  std::vector<ValidationErrorInfo> validate(
      const ROMol &mol, bool reportAllFailures) const override;
 
  std::shared_ptr<ValidationMethod> copy() const override {
    return std::make_shared<RDKitValidation>(*this);
  }
 
  bool allowEmptyMolecules;
};
 
//////////////////////////////
/// MolVS Validations
//
 
//! The NoAtomValidation class throws an error if no atoms are present in the
/// molecule.
class RDKIT_MOLSTANDARDIZE_EXPORT NoAtomValidation : public ValidationMethod {
 public:
  std::vector<ValidationErrorInfo> validate(
      const ROMol &mol, bool reportAllFailures) const override;
 
  std::shared_ptr<ValidationMethod> copy() const override {
    return std::make_shared<NoAtomValidation>(*this);
  }
};
 
//! The FragmentValidation class logs if certain fragments are present.
class RDKIT_MOLSTANDARDIZE_EXPORT FragmentValidation : public ValidationMethod {
 public:
  std::vector<ValidationErrorInfo> validate(
      const ROMol &mol, bool reportAllFailures) const override;
 
  std::shared_ptr<ValidationMethod> copy() const override {
    return std::make_shared<FragmentValidation>(*this);
  }
};
 
//! The NeutralValidation class logs if not an overall neutral system.
class RDKIT_MOLSTANDARDIZE_EXPORT NeutralValidation : public ValidationMethod {
 public:
  std::vector<ValidationErrorInfo> validate(
      const ROMol &mol, bool reportAllFailures) const override;
 
  std::shared_ptr<ValidationMethod> copy() const override {
    return std::make_shared<NeutralValidation>(*this);
  }
};
 
//! The IsotopeValidation class logs if molecule contains isotopes.
/*!
  <b>Notes:</b>
  - By default, this class will return an error every time an isotopic
    number is specified. When the `strict` constructor parameter is passed a
    `true` argument, an error is returned only if the specified isotopic number
    is not found in the RDKit periodic table.
*/
class RDKIT_MOLSTANDARDIZE_EXPORT IsotopeValidation : public ValidationMethod {
 public:
  IsotopeValidation(bool strict = false) : strict(strict) {};
  std::vector<ValidationErrorInfo> validate(
      const ROMol &mol, bool reportAllFailures) const override;
 
  std::shared_ptr<ValidationMethod> copy() const override {
    return std::make_shared<IsotopeValidation>(*this);
  }
 
  bool strict;
};
 
////////////////////////////////
//! The MolVSValidation class includes most of the same validations as
/// molvs.validations, namely NoAtomValidation, FragmentValidation,
/// NeutralValidation, IsotopeValidation. MolVS also has IsNoneValidation and
/// DichloroethaneValidation but these were not included here (yet).
class RDKIT_MOLSTANDARDIZE_EXPORT MolVSValidation : public CompositeValidation {
 public:
  // constructor
  MolVSValidation();
  //! overloaded constructor to take in a user-defined list of ValidationMethod
  MolVSValidation(
      const std::vector<std::shared_ptr<ValidationMethod>> &validations);
 
  std::shared_ptr<ValidationMethod> copy() const override {
    return std::make_shared<MolVSValidation>(*this);
  }
};
 
//! The AllowedAtomsValidation class lets the user input a list of atoms,
//! anything not on the list throws an error.
class RDKIT_MOLSTANDARDIZE_EXPORT AllowedAtomsValidation
    : public ValidationMethod {
 public:
  AllowedAtomsValidation(std::vector<std::shared_ptr<Atom>> atoms)
      : d_allowedList(std::move(atoms)) {}
  std::vector<ValidationErrorInfo> validate(
      const ROMol &mol, bool reportAllFailures) const override;
 
  std::shared_ptr<ValidationMethod> copy() const override {
    return std::make_shared<AllowedAtomsValidation>(*this);
  }
 
 private:
  std::vector<std::shared_ptr<Atom>> d_allowedList;
};
 
//! The DisallowedAtomsValidation class lets the user input a list of atoms and
//! as long as there are no atoms from the list it is deemed acceptable.
class RDKIT_MOLSTANDARDIZE_EXPORT DisallowedAtomsValidation
    : public ValidationMethod {
 public:
  DisallowedAtomsValidation(std::vector<std::shared_ptr<Atom>> atoms)
      : d_disallowedList(std::move(atoms)) {}
  std::vector<ValidationErrorInfo> validate(
      const ROMol &mol, bool reportAllFailures) const override;
 
  std::shared_ptr<ValidationMethod> copy() const override {
    return std::make_shared<DisallowedAtomsValidation>(*this);
  }
 
 private:
  std::vector<std::shared_ptr<Atom>> d_disallowedList;
};
 
//! The DisallowedRadicalValidation class reports an error if any
/// unstable radical atoms are found.
/// The allowed radicals are [N]=O and [O]-N.
class RDKIT_MOLSTANDARDIZE_EXPORT DisallowedRadicalValidation
    : public ValidationMethod {
 public:
  std::vector<ValidationErrorInfo> validate(
      const ROMol &mol, bool reportAllFailures) const override;
 
  std::shared_ptr<ValidationMethod> copy() const override {
    return std::make_shared<DisallowedRadicalValidation>(*this);
  }
};
 
//! The FeaturesValidation class reports an error if the input
/// molecule representation includes any undesired features.
class RDKIT_MOLSTANDARDIZE_EXPORT FeaturesValidation : public ValidationMethod {
 public:
  FeaturesValidation(bool allowEnhancedStereo = false,
                     bool allowAromaticBondType = false,
                     bool allowDativeBondType = false,
                     bool allowQueries = false, bool allowDummies = false,
                     bool allowAtomAliases = false)
      : allowEnhancedStereo(allowEnhancedStereo),
        allowAromaticBondType(allowAromaticBondType),
        allowDativeBondType(allowDativeBondType),
        allowQueries(allowQueries),
        allowDummies(allowDummies),
        allowAtomAliases(allowAtomAliases) {};
  std::vector<ValidationErrorInfo> validate(
      const ROMol &mol, bool reportAllFailures) const override;
  std::shared_ptr<ValidationMethod> copy() const override {
    return std::make_shared<FeaturesValidation>(*this);
  }
  bool allowEnhancedStereo;
  bool allowAromaticBondType;
  bool allowDativeBondType;
  bool allowQueries;
  bool allowDummies;
  bool allowAtomAliases;
};
 
//! The Is2DValidation class reports an error if the input
/// molecule representation is designated as 3D or if it includes
/// non-null Z coordinates, and in case all atoms are assigned the
/// same coordinates.
class RDKIT_MOLSTANDARDIZE_EXPORT Is2DValidation : public ValidationMethod {
 public:
  Is2DValidation(double threshold = 1.e-3) : threshold(threshold) {};
  std::vector<ValidationErrorInfo> validate(
      const ROMol &mol, bool reportAllFailures) const override;
  std::shared_ptr<ValidationMethod> copy() const override {
    return std::make_shared<Is2DValidation>(*this);
  }
 
  double threshold;
};
 
//! The Layout2DValidation class reports an error if any atoms are
/// too close to any other atoms or bonds, and in case any bonds are
/// too long.
class RDKIT_MOLSTANDARDIZE_EXPORT Layout2DValidation : public ValidationMethod {
 public:
  Layout2DValidation(double clashLimit = 0.15, double bondLengthLimit = 25.,
                     bool allowLongBondsInRings = true,
                     bool allowAtomBondClashExemption = true,
                     double minMedianBondLength = 1e-3)
      : clashLimit(clashLimit),
        bondLengthLimit(bondLengthLimit),
        allowLongBondsInRings(allowLongBondsInRings),
        allowAtomBondClashExemption(allowAtomBondClashExemption),
        minMedianBondLength(minMedianBondLength) {};
  std::vector<ValidationErrorInfo> validate(
      const ROMol &mol, bool reportAllFailures) const override;
  std::shared_ptr<ValidationMethod> copy() const override {
    return std::make_shared<Layout2DValidation>(*this);
  }
 
  static double squaredMedianBondLength(const ROMol &mol,
                                        const Conformer &conf);
 
  double clashLimit;
  double bondLengthLimit;
  bool allowLongBondsInRings;
  bool allowAtomBondClashExemption;
  double minMedianBondLength;
};
 
//! The StereoValidation class checks various "syntactic" constraints
/// related to the usage of stereo bonds on centers with 4 or 3 substituents,
/// in an attempt to ensure that the associated stereochemical configuration
/// can be interpreted unambiguously.
/// These validation criteria were ported from the AvalonTools STRUCHK software.
class RDKIT_MOLSTANDARDIZE_EXPORT StereoValidation : public ValidationMethod {
 public:
  std::vector<ValidationErrorInfo> validate(
      const ROMol &mol, bool reportAllFailures) const override;
  std::shared_ptr<ValidationMethod> copy() const override {
    return std::make_shared<StereoValidation>(*this);
  }
};
 
//! A convenience function for quickly validating a single SMILES string.
RDKIT_MOLSTANDARDIZE_EXPORT std::vector<ValidationErrorInfo> validateSmiles(
    const std::string &smiles);
 
}  // namespace MolStandardize
}  // namespace RDKit
 
#endif