pdb4dna/include/PDBlib.hh

0001 //
0002 // ********************************************************************
0003 // * License and Disclaimer                                           *
0004 // *                                                                  *
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0017 // *                                                                  *
0018 // * This  code  implementation is the result of  the  scientific and *
0019 // * technical work of the GEANT4 collaboration.                      *
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0023 // * acceptance of all terms of the Geant4 Software license.          *
0024 // ********************************************************************
0025 //
0026 // This example is provided by the Geant4-DNA collaboration
0027 // Any report or published results obtained using the Geant4-DNA software
0028 // shall cite the following Geant4-DNA collaboration publication:
0029 // Med. Phys. 37 (2010) 4692-4708
0030 // Delage et al. PDB4DNA: implementation of DNA geometry from the Protein Data
0031 //                  Bank (PDB) description for Geant4-DNA Monte-Carlo
0032 //                  simulations (submitted to Comput. Phys. Commun.)
0033 // The Geant4-DNA web site is available at http://geant4-dna.org
0034 //
0035 // --------------------------------------------------------------
0036 // Authors: E. Delage
0037 // november 2013
0038 // --------------------------------------------------------------
0039 //
0040 //
0041 /// \file PDBlib.hh
0042 /// \brief Definition of the PDBlib class
0043
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0045
0046 #ifndef PDBlib_h
0047 #  define PDBlib_h 1
0048
0049 #  include "PDBbarycenter.hh"
0050 #  include "PDBmolecule.hh"
0051
0052 //! PDBlib Class
0053 /*!
0054  * This Class define Molecule model ...
0055  */
0056 class PDBlib
0057 {
0058   public:
0059     //! First constructor
0060     PDBlib();
0061     //! Destructor
0062     ~PDBlib() {};
0063
0064     //! Load PDB file into memory
0065     Molecule* Load(const std::string& filename, unsigned short int& isDNA,
0066                    unsigned short int verbose);
0067
0068     // All declarations below are 'DNA specific'
0069     // Just comment those lines if you need to use this code elsewhere.
0070
0071     //! Compute nucleotide barycenter from memory
0072     Barycenter* ComputeNucleotideBarycenters(Molecule* moleculeListTemp);
0073
0074     //! Compute the corresponding bounding volume parameters
0075     void ComputeBoundingVolumeParams(Molecule* moleculeListTemp, double& dX, double& dY,
0076                                      double& dZ,  // Dimensions for bounding volume
0077                                      double& tX, double& tY,
0078                                      double& tZ);  // Translation for bounding volume
0079
0080     //! Compute number of nucleotide per strand
0081     void ComputeNbNucleotidsPerStrand(Molecule* moleculeListTemp);
0082
0083     //! Compute if energy is deposited in per atom
0084     unsigned short int ComputeMatchEdepDNA(Barycenter*, Molecule*, double x, double y, double z,
0085                                            int& numStrand, int& numNucleotid, int& codeResidue);
0086
0087   private:
0088     //! return distance between two 3D points
0089     double DistanceTwo3Dpoints(double xA, double xB, double yA, double yB, double zA, double zB);
0090
0091     //! Number of nucleotid per strand
0092     int fNbNucleotidsPerStrand;
0093 };
0094
0095 #endif
0096
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