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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
{
/** QSAR molecular simple descriptors base class, this
class implements some methods to calculate simple
descriptors.
\\
*/
class BALL_EXPORT SimpleBase
: public Descriptor
{
public:
/** @name Constructors and Destructors
*/
//@{
/** Default constructor
*/
SimpleBase();
/** Copy constructor
*/
SimpleBase(const SimpleBase& sb);
/** Named constructor
*/
SimpleBase(const String& name);
/** Named unit constructor
*/
SimpleBase(const String& name, const String& unit);
/** Destructor
*/
virtual ~SimpleBase();
//@}
/** @name Assignment
*/
//@{
/** Assignment operator
*/
virtual SimpleBase& operator = (const SimpleBase& sb);
/** @name Accessors
*/
//@{
void computeAllDescriptors(AtomContainer& ac);
/** allows to set the data-folder without using BALL_DATA_PATH enviroment variable, which is useful for standalone applications */
void setDataFolder(const char* folder);
//@}
protected:
/** @name Predicates
*/
//@{
/*_ 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);
//@}
/** @name Accessors
*/
//@{
/*_ Performs the calculation of some of the simple descriptors.
*/
void calculate_(AtomContainer& ac);
//@}
private:
/** @name Accessors
*/
//@{
/*_ 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);
//@}
/** @name Predicates
*/
//@{
/*_ 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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