Crippen.h

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//
//  Copyright (C) 2004-2007 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.
//
 
/*! \file Crippen.h
 
  \brief Use MolDescriptors.h in client code.
 
*/
#include <RDGeneral/export.h>
#ifndef __RD_CRIPPEN_H__
#define __RD_CRIPPEN_H__
 
#include <string>
#include <vector>
#include <boost/smart_ptr.hpp>
 
namespace RDKit {
class ROMol;
namespace Descriptors {
const std::string crippenVersion = "1.2.0";
 
//! generate atomic contributions to the Wildman-Crippen LogP and MR
//! estimates for a molecule
/*!
  Uses an atom-based scheme based on the values in the paper:
    S. A. Wildman and G. M. Crippen JCICS 39 868-873 (1999)
 
  \param mol           the molecule of interest
  \param logpContribs  used to return the logp contributions, must
                       be equal in length to the number of atoms
  \param mrContribs    used to return the MR contributions, must
                       be equal in length to the number of atoms
  \param force         forces the value to be recalculated instead
                       of pulled from the cache
  \param atomTypes     if provided will be used to return the indices
                       of the atom types, should be as long as the
                       number of atoms
  \param atomTypeLabels   if provided will be used to return the labels
                          of the atom types, should be as long as the
                          number of atoms
 
*/
RDKIT_DESCRIPTORS_EXPORT void getCrippenAtomContribs(
    const ROMol &mol, std::vector<double> &logpContribs,
    std::vector<double> &mrContribs, bool force = false,
    std::vector<unsigned int> *atomTypes = nullptr,
    std::vector<std::string> *atomTypeLabels = nullptr);
 
//! generate Wildman-Crippen LogP and MR estimates for a molecule
/*!
  Uses an atom-based scheme based on the values in the paper:
    S. A. Wildman and G. M. Crippen JCICS 39 868-873 (1999)
 
  \param mol        the molecule of interest
  \param logp       used to return the logp estimate
  \param mr         used to return the MR estimate
  \param includeHs  (optional) if this is true (the default), a
      copy of \c mol is made and Hs are added to it.  If false,
      Hs that are not explicitly present in the graph will not
      be included.
  \param force      forces the value to be recalculated instead of
                    pulled from the cache
 
*/
RDKIT_DESCRIPTORS_EXPORT void calcCrippenDescriptors(const ROMol &mol,
                                                     double &logp, double &mr,
                                                     bool includeHs = true,
                                                     bool force = false);
 
//! a class used to store Crippen parameters
class RDKIT_DESCRIPTORS_EXPORT CrippenParams {
 public:
  boost::shared_ptr<const ROMol> dp_pattern;
  unsigned int idx;
  std::string label;
  std::string smarts;
  double logp;
  double mr;
  ~CrippenParams();
};
 
const std::string CrippenClogPVersion = crippenVersion;
//! calculate the default Wildman-Crippen LogP for a molecule
/*!
  See calcCrippenDescriptors
    \param mol        the molecule of interest
 */
RDKIT_DESCRIPTORS_EXPORT double calcClogP(const ROMol &mol);
 
const std::string CrippenMRVersion = crippenVersion;
//! calculate the default Wildman-Crippen MR Estimate for a molecule
/*!
  See calcCrippenDescriptors
    \param mol        the molecule of interest
 */
RDKIT_DESCRIPTORS_EXPORT double calcMR(const ROMol &mol);
 
//! singleton class for retrieving Crippen parameters
/*!
  Use the singleton like this:
 
  \verbatim
  CrippenParamCollection *params=CrippenParamCollection::getParams();
  \endverbatim
 
  If you have your own parameter data, it can be supplied as a string:
  \verbatim
  CrippenParamCollection *params=CrippenParamCollection::getParams(myParamData);
  \endverbatim
  You are responsible for making sure that the data is in the correct
  format (see Crippen.cpp for an example).
 
*/
class RDKIT_DESCRIPTORS_EXPORT CrippenParamCollection {
 public:
  typedef std::vector<CrippenParams> ParamsVect;
  static const CrippenParamCollection *getParams(
      const std::string &paramData = "");
  ParamsVect::const_iterator begin() const { return d_params.begin(); }
  ParamsVect::const_iterator end() const { return d_params.end(); }
 
  CrippenParamCollection(const std::string &paramData);
 
 private:
  ParamsVect d_params;  //!< the parameters
};
}  // end of namespace Descriptors
}  // namespace RDKit
 
#endif