atom_impl.hh

//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2010 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_IMPL_HH
#define OST_ATOM_IMPL_HH

#include <boost/enable_shared_from_this.hpp>

#include <ost/mol/module_config.hh>
#include <ost/geom/geom.hh>
#include <ost/mol/entity_visitor_fw.hh>
#include <ost/mol/atom_prop.hh>

#include <ost/mol/impl/atom_impl_fw.hh>
#include <ost/mol/impl/residue_impl_fw.hh>
#include <ost/mol/impl/connector_impl_fw.hh>
#include <ost/mol/impl/fragment_impl_fw.hh>
#include <ost/mol/impl/entity_impl_fw.hh>

#include <ost/generic_property.hh>
#include <ost/mol/property_id.hh>

namespace ost { namespace mol { namespace impl {

/// \brief Atom implementation.
/// 
/// \section Connectors
/// each atom distinguishes between two types of connectors: primary and
/// secondary. each atoms has at most one primary connector: this connects the
/// atom with the atom that serves as the frame of reference for the internal
/// coordinates. the secondary connectors connect this atom with the atoms that
/// themselves depend on the coordinate system of this atom.
/// \internal
class AtomImpl: public GenericPropContainerImpl,
                public boost::enable_shared_from_this<AtomImpl> {
public:
   AtomImpl(const EntityImplPtr& ent, const ResidueImplPtr& res,
            const String& name, const geom::Vec3& pos, const AtomProp& prop,
            unsigned long index);

  ~AtomImpl();
  void Apply(EntityVisitor& h);

  const String& GetName() const {return name_;}

  void SetName(const String& atom_name) { 
    name_=atom_name; 
  }


  const geom::Vec3& GetPos() const {return tf_pos_;}

  const geom::Vec3& GetOriginalPos() const {return pos_;}

  void SetTransformedPos(const geom::Vec3& pos) { tf_pos_=pos; }

  void SetOriginalPos(const geom::Vec3& pos) { pos_=pos; }
  
  const AtomProp& GetAtomProps() const {return prop_;}
  
  AtomProp& GetAtomProps() {return prop_;}
  
  ResidueImplPtr GetResidue() const;

  void SetPrimaryConnector(const ConnectorImplP& bp) {
    prim_connector_=bp;
  }
  
  const ConnectorImplP& GetPrimaryConnector() const {
    return prim_connector_;
  }

  const ConnectorImplList& GetSecondaryConnectors() const {
    return connector_list_;
  }

  void AddSecondaryConnector(const ConnectorImplP& bp);
  
  // updates position and then follows secondary connectors
  void UpdateFromICS();

  // derive internal coordinates from position and linkage
  void UpdateFromXCS();
  
  String GetQualifiedName() const;
  
  EntityImplPtr GetEntity() const;
  
  int GetConnectorCount() const {
    return connector_list_.size()+(prim_connector_ ? 1 : 0);
  }

  void SetVisited(bool f) {set_state_bit(0,f);}
  bool IsVisited() const {return get_state_bit(0);}

  void SetTraced(bool f) {set_state_bit(1,f);}
  bool IsTraced() const {return get_state_bit(1);}

  unsigned int GetState() const {
    return state_;
  }
  
  void SetState(int state) {
    state_=state;
  }
  
  void ClearDirectionality();
  /// \brief trace directionality
  void TraceDirectionality(FragmentImplP frag, ConnectorImplP conn,  
                           int n, unsigned int& c);

  bool HasPrevious() const {return prim_connector_.get()!=NULL;}

  void DeleteAllConnectors();
  
  void DeleteConnector(const ConnectorImplP& conn, 
                       bool delete_other=true);

  void DeleteAllTorsions();
  
  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 {return index_;}
  void SetIndex(unsigned long index) {index_=index;}
                     
private:
  ResidueImplW res_;
  String name_;
  geom::Vec3 pos_;
  geom::Vec3 tf_pos_;
  AtomProp prop_;

  ConnectorImplP prim_connector_;
  ConnectorImplList connector_list_;
  FragmentImplP fragment_;
  
  /// total rotation matrix. used to optimise recursive traversal. Do not rely
  /// on its value!
  geom::Mat3 total_rot_;
  
  /// state used by many algorithms that need to associate data with an
  /// atom
  unsigned int state_;

  void set_state_bit(unsigned int bit, bool state) 
  {
    unsigned int mask = 0x1<<bit;
    if(state) {
      state_ |= mask;
    } else {
      state_ &= ~mask;
    }
  }

  bool get_state_bit(unsigned int bit) const {
    unsigned int mask = 0x1<<bit;
    return (state_ & mask)!=0;
  }

  unsigned long index_;
};

/// \internal
std::ostream& operator<<(std::ostream& o, const AtomImplPtr ap);

/// \internal
bool ConnectorExists(const AtomImplPtr& a, const AtomImplPtr& b);

/// \internal
ConnectorImplP GetConnector(const AtomImplPtr& a, const AtomImplPtr& b);

}}} // ns

#endif