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entity_impl.hh 8.32 KiB
//------------------------------------------------------------------------------
// 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_ENTITY_IMPL_HH
#define OST_ENTITY_IMPL_HH
#include <map>
#include <vector>
#include <boost/enable_shared_from_this.hpp>
#include <ost/mol/module_config.hh>
#include <ost/geom/geom.hh>
#include <ost/mol/impl/entity_impl_fw.hh>
#include <ost/mol/entity_view.hh>
#include <ost/mol/transform.hh>
#include <ost/mol/residue_prop.hh>
#include <ost/mol/impl/atom_impl_fw.hh>
#include <ost/mol/impl/residue_impl_fw.hh>
#include <ost/mol/impl/chain_impl_fw.hh>
#include <ost/mol/impl/connector_impl_fw.hh>
#include <ost/mol/impl/torsion_impl_fw.hh>
#include <ost/mol/impl/fragment_impl_fw.hh>
#include <ost/mol/entity_visitor_fw.hh>
#include <ost/mol/entity_observer_fw.hh>
#include <ost/mol/entity_view.hh>
#include <ost/mol/entity_handle.hh>
#include <ost/mol/spatial_organizer.hh>
#include <ost/generic_property.hh>
namespace ost { namespace mol { namespace impl {
/// \internal
typedef std::map<AtomImpl*,AtomImplPtr> AtomImplMap;
/// \internal
typedef std::map<ResidueImpl*,ResidueImplPtr> ResidueImplMap;
/// \internal
typedef std::vector<ChainImplPtr> ChainImplList;
/// \internal
typedef std::map<ConnectorImpl*,ConnectorImplP> ConnectorImplMap;
/// \internal
typedef std::map<TorsionImpl*,TorsionImplP> TorsionImplMap;
/// \internal
typedef std::vector<FragmentImplP> FragmentImplList;
/// \internal
typedef std::map<EntityObserver*,EntityObserverPtr> EntityObserverMap;
/// \internal
typedef SpatialOrganizer<AtomImplPtr> SpatialAtomOrganizer;
/// \internal
typedef enum {
DirtyICS=1,
DirtyXCS=2,
// dirty trace (implies dirty ICS)
DirtyTrace=DirtyICS+4,
DirtyOrganizer=8,
DisableICS=16,
} EntityDirtyFlags;
/// \internal
class EntityImpl: public GenericPropContainerImpl,
public boost::enable_shared_from_this<EntityImpl>
{
public:
EntityImpl();
~EntityImpl();
/// \brief copy entity
EntityImplPtr Copy();
Real GetMass() const;
geom::Vec3 GetCenterOfMass() const;
geom::Vec3 GetCenterOfAtoms() const;
geom::Vec3 GetGeometricCenter() const;
geom::Vec3 GetGeometricStart() const;
geom::Vec3 GetGeometricEnd() const;
geom::Vec3 GetBoundarySize() const;
// default copy ctor and assignment op should work for now
AtomImplPtr CreateAtom(const ResidueImplPtr& rp, const String& name,
const geom::Vec3& pos, const AtomProp& prop);
ResidueImplPtr CreateResidue(const ChainImplPtr& cp,
const ResNum& n,
const ResidueKey& k);
ChainImplPtr InsertChain(const String& cname);
/// \brief insert a new chain based on parameters of the given chain
///
/// The chain will have no residues and atoms
ChainImplPtr InsertChain(const ChainImplPtr& chain);
ConnectorImplP Connect(const AtomImplPtr& first, const AtomImplPtr& second,
Real len, Real theta, Real phi,
unsigned char bond_order);
TorsionImplP AddTorsion(const String& name, const AtomImplPtr& a1,
const AtomImplPtr& a2, const AtomImplPtr& a3,
const AtomImplPtr& a4);
void TraceDirectionality();
//! Search for torsion.
TorsionImplP FindTorsion(const AtomImplPtr& a1,
const AtomImplPtr& a2,
const AtomImplPtr& a3,
const AtomImplPtr& a4) const;
void RenameChain(ChainImplPtr chain, const String& new_name);
bool SetAngle(const AtomImplPtr& a1, const AtomImplPtr& a2,
const AtomImplPtr& a3, Real angle);
Real GetAngle(const AtomImplPtr& a1, const AtomImplPtr& a2,
const AtomImplPtr& a3) const;
Real GetAngleXCS(const AtomImplPtr& a1, const AtomImplPtr& a2,
const AtomImplPtr& a3) const;
Real GetAngleICS(const AtomImplPtr& a1, const AtomImplPtr& a2,
const AtomImplPtr& a3) const;
// update positions from internal coordinate system void UpdateFromICS();
// update internal coordinate system from positions
void UpdateFromXCS();
void Apply(EntityVisitor& v);
void ApplyTransform(const geom::Mat4 transfmat);
void SetTransform(const geom::Mat4 transfmat);
void AttachObserver(const EntityObserverPtr& o);
void DetachObserver(const EntityObserverPtr& o);
void NotifyObserver();
void UpdateOrganizer();
AtomImplList FindWithin(const geom::Vec3& pos, Real radius) const;
EntityView Select(const EntityHandle& h, const Query& q,
QueryFlags flags) const;
EntityView CreateFullView(const EntityHandle& h) const;
/// Get chain by name. Returns an invalid ChainImplPtr if no chain with the
/// given name exists.
ChainImplPtr FindChain(const String& name) const;
ResidueImplPtr FindResidue(const String& chain_name,
const ResNum& residue) const;
AtomImplPtr FindAtom(const String& chain_name,
const ResNum& residue,
const String& atom_name) const;
/*
this is a deep-swap which will exchange the internal structure
of two implementations, which by design affects _all_ entity handles
that point two either of these two implementations
*/
void Swap(EntityImpl& impl);
//! Get total number of atoms of all chains belonging to this entity
int GetAtomCount() const;
//! Get total number of bonds belonging to this entity
int GetBondCount() const;
//! Get list of bonds
mol::BondHandleList GetBondList() const;
//! Get total number of residues of all chains belonging to this entity
int GetResidueCount() const;
//! Get number of chains
int GetChainCount() const;
//! Get transformation matrix
const geom::Mat4& GetTransfMatrix() const;
//! Get inverse transformation matrix
const geom::Mat4& GetInvTransfMatrix() const;
bool IsTransfIdentity() const;
const ChainImplList& GetChainList() const { return chain_list_; }
ChainImplList& GetChainList() { return chain_list_; }
void DeleteFromConnMap(const ConnectorImplP& conn);
void DeleteChain(const ChainImplPtr& chain);
void DeleteAtom(const AtomImplPtr& atom);
void IncXCSEditorCount();
void DecXCSEditorCount();
void IncICSEditorCount();
void DecICSEditorCount();
TorsionImplMap& GetTorsionMap();
void UpdateXCSIfNeeded();
void UpdateICSIfNeeded();
void UpdateOrganizerIfNeeded();
void EnableICS();
bool HasICS() const;
bool IsXCSDirty() const;
void MarkXCSDirty();
void MarkICSDirty();
void MarkTraceDirty();
void MarkOrganizerDirty();
void UpdateTransformedPos();
const String& GetName() const;
impl::ChainImplList::iterator GetChain(const String& name);
void SetName(const String& ent_name);
private:
void DoCopy(EntityImplPtr dest);
void ReplicateHierarchy(EntityImplPtr dest);
void DoCopyBondsAndTorsions(EntityImplPtr dest);
AtomImplMap atom_map_;
ChainImplList chain_list_;
ConnectorImplMap connector_map_;
TorsionImplMap torsion_map_;
geom::Mat4 transformation_matrix_;
geom::Mat4 inverse_transformation_matrix_;
bool identity_transf_;
SpatialAtomOrganizer atom_organizer_;
FragmentImplList fragment_list_;
EntityObserverMap observer_map_;
int xcs_editor_count_;
int ics_editor_count_;
int dirty_flags_;
String name_;
unsigned long next_index_;
template <bool always_true>
EntityView do_selection(const EntityHandle&, const Query&, QueryFlags) const;
};
}}} // ns
#endif