atom_base.hh

Go to the documentation of this file.

//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
// Software Foundation; either version 3.0 of the License, or (at your option)
// any later version.
// This library is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
// details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
//------------------------------------------------------------------------------
#ifndef OST_ATOM_BASE_HH
#define OST_ATOM_BASE_HH
 
#include <ost/geom/vec3.hh>
 
#include <ost/mol/module_config.hh>
#include <ost/mol/impl/atom_impl_fw.hh>
#include <ost/generic_property.hh>
 
#include "property_id.hh"
 
namespace ost { namespace mol {
 
class DLLEXPORT_OST_MOL AtomBase: public GenericPropContainer<AtomBase> {
public:
  AtomBase();
  AtomBase(const impl::AtomImplPtr& impl);
public:
 
 
  operator bool() const { return this->IsValid(); }
  bool IsValid() const;
  friend class ConstGenericPropContainer<AtomBase>;  
  const String& GetName() const;
  
  void SetName(const String& atom_name);
    
  const geom::Vec3& GetPos() const;
 
  const geom::Vec3& GetOriginalPos() const;
  geom::Vec3 GetAltPos(const String& alt_group) const;
  Real GetAltBFactor(const String& alt_group) const;
  Real GetAltOcc(const String& alt_group) const;
  
  std::vector<String> GetAltGroupNames() const;
 
    
  String GetQualifiedName() const;
  
  String GetStringProperty(Prop::ID prop_id) const;
                          
  Real GetFloatProperty(Prop::ID prop_id) const;
  
  int GetIntProperty(Prop::ID prop_id) const;
 
  unsigned long GetIndex() const;
 
  Real GetRadius() const;
  
  const String& GetElement() const;
  
  bool IsHetAtom() const;
  
  Real GetBFactor() const;
  
  
  void SetBFactor(Real factor);
  
  void SetOccupancy(Real occ);
  
  
  void SetCharge(Real charge);
  
  void SetMass(Real mass);
  
  void SetHetAtom(bool het);
  
  void SetRadius(Real radius);
  
  void SetIndex (const unsigned long index);
  
  const geom::Mat3& GetAnisou() const;
  
  void SetAnisou(const geom::Mat3& anisou);
  Real GetMass() const;
  
  Real GetCharge() const;
  
  Real GetOccupancy() const;
  
  const impl::AtomImplPtr& Impl() const;
 
  impl::AtomImplPtr& Impl();
 
 
  void SetElement(const String& element);
protected:
  
  GenericPropContainerImpl* GpImpl();
  
  const GenericPropContainerImpl* GpImpl() const;
  
  void CheckValidity() const;
  impl::AtomImplPtr   impl_;
};
 
DLLEXPORT_OST_MOL std::ostream& operator<<(std::ostream& os, 
                                            const AtomBase& atom);
}} // ns
 
#endif // OST_ATOM_BASE_HH