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stage
include
ost
mol
entity_view.hh
Go to the documentation of this file.
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//------------------------------------------------------------------------------
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// This file is part of the OpenStructure project <www.openstructure.org>
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//
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// Copyright (C) 2008-2011 by the OpenStructure authors
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//
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// This library is free software; you can redistribute it and/or modify it under
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// the terms of the GNU Lesser General Public License as published by the Free
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// Software Foundation; either version 3.0 of the License, or (at your option)
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// any later version.
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// This library is distributed in the hope that it will be useful, but WITHOUT
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// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
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// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
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// details.
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//
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// You should have received a copy of the GNU Lesser General Public License
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// along with this library; if not, write to the Free Software Foundation, Inc.,
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// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
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//------------------------------------------------------------------------------
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#ifndef OST_ENTITY_VIEW_HN
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#define OST_ENTITY_VIEW_HN
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/*
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Author: Marco Biasini
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*/
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#include <
ost/mol/module_config.hh
>
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#include <
ost/mol/residue_prop.hh
>
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#include <
ost/mol/entity_base.hh
>
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#include <
ost/mol/view_type_fw.hh
>
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#include <
ost/mol/impl/entity_impl_fw.hh
>
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#include <
ost/mol/entity_visitor_fw.hh
>
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#include <
ost/mol/handle_type_fw.hh
>
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#include <
ost/mol/query.hh
>
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#include <
ost/mol/iterator_fw.hh
>
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#include <
ost/mol/property_id.hh
>
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#include <
ost/geom/geom.hh
>
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#ifdef _MSC_VER
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# ifdef FindAtom
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# undef FindAtom
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# endif
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# ifdef AddAtom
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# undef AddAtom
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# endif
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#endif
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namespace
ost {
namespace
mol {
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class
DLLEXPORT_OST_MOL
EntityView
:
public
EntityBase
{
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friend
class
AtomView
;
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friend
class
ResidueView
;
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public
:
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EntityView
();
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explicit
EntityView
(
const
EntityHandle
& entity,
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ViewAddFlags
flags=0);
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operator
bool()
const
{
return
this->IsValid(); }
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bool
IsValid
()
const
{
return
data_.get()!=0; }
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Real
GetMass()
const
;
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geom::Vec3
GetCenterOfMass()
const
;
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geom::Vec3
GetCenterOfAtoms()
const
;
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geom::AlignedCuboid
GetBounds()
const
;
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public
:
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EntityView
(
const
EntityViewDataPtr
& data,
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const
impl::EntityImplPtr
impl);
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const
EntityViewDataPtr
& ViewData()
const
;
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EntityViewDataPtr
& ViewData();
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public
:
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EntityView
Copy()
const
;
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ChainView
AddChain(
const
ChainHandle
& chain_handle,
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ViewAddFlags
flags=0);
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ChainView
AddChain(
const
ChainView
& chain_view,
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ViewAddFlags
flags=0);
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ResidueView
AddResidue(
const
ResidueHandle
& residue_handle,
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ViewAddFlags
flags=0);
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ResidueView
AddResidue(
const
ResidueView
& residue_view,
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ViewAddFlags
flags=0);
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AtomView
AddAtom(
const
AtomHandle
& atom_handle,
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ViewAddFlags
flags=0);
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AtomView
AddAtom(
const
AtomView
& atom_view,
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ViewAddFlags
flags=0);
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EntityView
Select(
const
String
& query_string,
QueryFlags
flags=0)
const
;
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EntityView
Select(
const
Query
& query,
QueryFlags
flags=0)
const
;
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bool
AddBond(
const
BondHandle
& bond_handle);
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int
GetAtomCount()
const
;
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int
GetResidueCount()
const
;
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int
GetChainCount()
const
;
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ChainView
FindChain(
const
String
& chain_name)
const
;
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ResidueView
FindResidue(
const
ResidueHandle
& residue)
const
;
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ResidueView
FindResidue(
const
String
& chain,
const
ResNum
& num)
const
;
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ResidueView
ViewForHandle(
const
ResidueHandle
& residue)
const
;
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AtomView
FindAtom(
const
AtomHandle
& atom)
const
;
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AtomView
ViewForHandle(
const
AtomHandle
& atom)
const
;
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AtomView
FindAtom(
const
String
& chain_name,
const
ResNum
& num,
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const
String
& atom_name)
const
;
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ChainView
FindChain(
const
ChainHandle
& chain)
const
;
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ChainView
ViewForHandle(
const
ChainHandle
& chain)
const
;
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bool
IsChainIncluded(
const
ChainHandle
& chain)
const
;
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void
RemoveAtom(
AtomView
view);
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void
RemoveResidue(
ResidueView
view);
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void
RemoveChain(
ChainView
view);
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void
AddAllInclusiveBonds();
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const
BondHandleList
& GetBondList()
const
;
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AtomViewList
FindWithin(
const
geom::Vec3
& center,
Real
radius)
const
;
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int
GetBondCount()
const
;
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const
ChainViewList
& GetChainList()
const
;
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AtomViewIter
AtomsBegin()
const
;
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AtomViewIter
AtomsEnd()
const
;
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ResidueViewIter
ResiduesBegin()
const
;
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ResidueViewIter
ResiduesEnd()
const
;
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ResidueViewList
GetResidueList()
const
;
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AtomViewList
GetAtomList()
const
;
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void
Apply(
EntityVisitor
& visitor);
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void
Apply(
EntityViewVisitor
& visitor);
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EntityHandle
GetHandle()
const
;
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std::pair<Real,Real> GetMinMax(
const
String
& prop,
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Prop::Level
hint=
Prop::UNSPECIFIED
)
const
;
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Real
GetAngle(
const
AtomHandle
& a1,
const
AtomHandle
& a2,
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const
AtomHandle
& a3)
const
;
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Real
GetAngle(
const
AtomView
& a1,
const
AtomView
& a2,
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const
AtomView
& a3)
const
;
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EntityView
ExtendViewToResidues()
const
;
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EntityView
ExtendViewToSurrounding(
Real
gap)
const
;
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String
Dump()
const
;
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EntityView
CreateFullView()
const
;
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EntityView
CreateEmptyView()
const
;
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#ifdef _MSC_VER
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// alternative routines for msvc
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AtomView
AddXAtom(
const
AtomHandle
& ah,
ViewAddFlags
flags=0);
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AtomView
FindXAtom(
const
AtomHandle
& ah);
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#endif
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void
RemoveBond(
const
BondHandle
& bond);
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protected
:
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void
AddAtomInternal(
const
AtomView
& av);
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void
RemoveAtomInternal(
const
AtomView
& av);
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private
:
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EntityViewDataPtr
data_;
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};
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typedef
std::pair<EntityView, EntityView>
EntityViewPair
;
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}}
// ns
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#endif // OST_ENTITY_VIEW_HH
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