99 lines
4.1 KiB
C++
99 lines
4.1 KiB
C++
//
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// ********************************************************************
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// * License and Disclaimer *
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// * *
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// * The Geant4 software is copyright of the Copyright Holders of *
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// * the Geant4 Collaboration. It is provided under the terms and *
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// * conditions of the Geant4 Software License, included in the file *
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// * LICENSE and available at http://cern.ch/geant4/license . These *
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// * include a list of copyright holders. *
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// * *
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// * Neither the authors of this software system, nor their employing *
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// * institutes,nor the agencies providing financial support for this *
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// * work make any representation or warranty, express or implied, *
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// * regarding this software system or assume any liability for its *
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// * use. Please see the license in the file LICENSE and URL above *
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// * for the full disclaimer and the limitation of liability. *
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// * *
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// * This code implementation is the result of the scientific and *
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// * technical work of the GEANT4 collaboration. *
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// * By using, copying, modifying or distributing the software (or *
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// * any work based on the software) you agree to acknowledge its *
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// * use in resulting scientific publications, and indicate your *
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// * acceptance of all terms of the Geant4 Software license. *
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// ********************************************************************
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//
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/// \file PDBlib.hh
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/// \brief Definition of the PDBlib class
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// This example is provided by the Geant4-DNA collaboration
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// Any report or published results obtained using the Geant4-DNA software
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// shall cite the following Geant4-DNA collaboration publication:
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// Med. Phys. 37 (2010) 4692-4708
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// Delage et al. PDB4DNA: implementation of DNA geometry from the Protein Data
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// Bank (PDB) description for Geant4-DNA Monte-Carlo
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// simulations (submitted to Comput. Phys. Commun.)
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// The Geant4-DNA web site is available at http://geant4-dna.org
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//
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// --------------------------------------------------------------
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// Authors: E. Delage
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// november 2013
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// --------------------------------------------------------------
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//
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//
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//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
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#ifndef PDBlib_h
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# define PDBlib_h 1
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# include "PDBbarycenter.hh"
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# include "PDBmolecule.hh"
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//! PDBlib Class
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/*!
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* This Class define Molecule model ...
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*/
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class PDBlib
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{
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public:
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//! First constructor
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PDBlib();
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//! Destructor
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~PDBlib() {};
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//! Load PDB file into memory
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Molecule* Load(const std::string& filename, unsigned short int& isDNA,
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unsigned short int verbose);
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// All declarations below are 'DNA specific'
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// Just comment those lines if you need to use this code elsewhere.
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//! Compute nucleotide barycenter from memory
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Barycenter* ComputeNucleotideBarycenters(Molecule* moleculeListTemp);
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//! Compute the corresponding bounding volume parameters
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void ComputeBoundingVolumeParams(Molecule* moleculeListTemp, double& dX, double& dY,
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double& dZ, // Dimensions for bounding volume
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double& tX, double& tY,
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double& tZ); // Translation for bounding volume
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//! Compute number of nucleotide per strand
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void ComputeNbNucleotidsPerStrand(Molecule* moleculeListTemp);
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//! Compute if energy is deposited in per atom
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unsigned short int ComputeMatchEdepDNA(Barycenter*, Molecule*, double x, double y, double z,
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int& numStrand, int& numNucleotid, int& codeResidue);
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private:
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//! return distance between two 3D points
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double DistanceTwo3Dpoints(double xA, double xB, double yA, double yB, double zA, double zB);
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//! Number of nucleotid per strand
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int fNbNucleotidsPerStrand;
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};
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#endif
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//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
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