simpleBase.h

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// -*- Mode: C++; tab-width: 2: -*-
// vi: set ts=2:
//
//

#ifndef BALL_QSAR_SIMPLEBASE_H
#define BALL_QSAR_SIMPLEBASE_H

#ifndef BALL_QSAR_DESCRIPTOR_H
#include <BALL/QSAR/descriptor.h>
#endif

namespace BALL
{
  class BALL_EXPORT SimpleBase
    : public Descriptor
  {
    public:
  
    SimpleBase();

    SimpleBase(const SimpleBase& sb);

    SimpleBase(const String& name);

    SimpleBase(const String& name, const String& unit);

    virtual ~SimpleBase();
    
    virtual SimpleBase& operator = (const SimpleBase& sb);
    
    
    void computeAllDescriptors(AtomContainer& ac);
    
    void setDataFolder(const char* folder);


    protected:

    /*_ Returns true if the data is calculated already, and the data is still correct,
        otherwise false is returned
        @param molecule to examine
    */
    bool isValid_(AtomContainer& ac);

    /*_ Performs the calculation of some of the simple descriptors.
    */
    void calculate_(AtomContainer& ac);
    
    
    private:
    
    /*_ This method calculates the pmi of the x, y and z axis, return the pmi 
        @param referenced double which holds the pmi x component after calculation
        @param referenced double which holds the pmi y component after calculation
        @param referenced double which holds the pmi z component after calculation
        @param molecule from which the pmi is calculated
    */
    double calcPrincipalMomentOfInertia_(double& pmi_x, double& pmi_y, double& pmi_z, AtomContainer& ac);
    
    /*_ Helper function that reads the atomic polarizabilities 
        from a file from the data section of BALL. It is called from
        getAtomicPolarizability_ and reads into a static variable, hence
        it is read one time per instance.
    */
    void readAtomicPolarizabilities_(std::vector<float>& polarizabilities);

    /*_ Method which returns the atomic polarizability of the element given as parameter
        @param the atomic number of the element
    */
    float getAtomicPolarizability_(int atomic_number);

    /*_ Predicate that returns true if the atom is a carbon and in an
        exclusively aromatic or aliphatic surrounding, means is only
        bound to carbon an hydrogen!
    */
    bool isHydrophobic_(const Atom* atom) const;
    
    String data_folder_;
  };
} // namespace BALL

#endif

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