OpenStructure
Namespaces | Data Structures | Typedefs | Enumerations | Functions
ost::mol Namespace Reference

Namespaces

namespace  alg
namespace  impl

Data Structures

class  AtomBase
 base class for AtomHandle and AtomView More...
class  AtomHandle
 Handle to atom datatype. More...
class  AtomView
 definition of AtomView More...
class  BondHandle
 chemical bond More...
struct  BondTableEntry
struct  BondTable
class  ChainBase
 base class for ChainHandle and ChainView More...
class  ChainHandle
 linear chain of residues More...
class  ChainView
 definition of ChainView More...
struct  ChemClass
class  CoordGroupHandle
 coordinate group, for trajectories and such More...
class  CoordSource
 coordinate source More...
class  EditorBase
 base class for entity editors More...
class  EntityBase
 definition of EntityBase More...
class  EntityHandle
 Protein or molecule. More...
class  EntityObserver
class  EntityPropertyMapper
class  EntityView
 definition of EntityView More...
class  EntityVisitor
 EntityVisitor interface. More...
class  EntityViewVisitor
 EntityViewVisitor interface. More...
class  ICSEditor
 editor for internal molecule coordinates More...
class  InMemCoordSource
 in-memory coordinate source More...
class  IterRange
 adaptor to turn iterator into an iterator range More...
class  ChainHandleIter
class  ResidueHandleIter
class  ResidueViewIter
class  AtomHandleIter
class  AtomViewIter
class  NotConnectedError
 Error to indicate that two atoms that are supposed to be connected are not. More...
struct  Prop
struct  PropertyError
struct  QueryFlag
 query flags More...
class  Query
 Selection Query. More...
struct  QueryErrorDesc
class  QueryError
class  QueryState
 Holds state used during query evaluation. More...
class  QueryViewWrapper
class  ResidueBase
 base class for ResidueHandle and ResidueView More...
class  ResidueHandle
 Residue handle. More...
class  ResNum
class  ResidueView
 residue view More...
struct  SecStructure
 Secondary structure types as defined by DSSP. For convenience, the enum values match the characters used in the DSP file format. More...
class  SpatialOrganizer
 spatial organizer More...
class  SurfaceHandle
struct  SurfaceVertex
struct  SurfaceTri
class  TorsionHandle
 Named torsion (dihedral) angle. More...
class  Transform
 basic and essential transformation class, including translation, rotation and center of rotation More...
struct  ViewAddFlag
 Flags to control the behaviour when adding handles to views. More...
class  XCSEditor
 external coordinate system editor More...

Typedefs

typedef std::vector< BondHandleBondHandeList
typedef std::vector< geom::Vec3CoordFrame
typedef boost::shared_ptr
< CoordFrame
CoordFramePtr
typedef std::vector
< CoordFramePtr
CoordFrameList
typedef boost::shared_ptr
< CoordSource
CoordSourcePtr
typedef boost::shared_ptr
< EntityObserver
EntityObserverPtr
typedef std::vector< ChainHandleChainHandleList
typedef std::vector
< ResidueHandle
ResidueHandleList
typedef std::vector< AtomHandleAtomHandleList
typedef std::vector
< TorsionHandle
TorsionHandleList
typedef std::vector< BondHandleBondHandleList
typedef std::vector< EntityHandleEntityHandleList
typedef boost::shared_ptr
< InMemCoordSource
InMemCoordSourcePtr
typedef uint QueryFlags
typedef String ResidueKey
typedef std::vector< SurfaceTriIDSurfaceTriIDList
typedef std::vector
< SurfaceVertexID
SurfaceVertexIDList
typedef std::vector
< SurfaceHandle
SurfaceHandleList
typedef unsigned int SurfaceVertexID
typedef unsigned int SurfaceTriID
typedef std::vector
< SurfaceVertex
SurfaceVertexList
typedef boost::shared_ptr
< AtomViewData > 
AtomViewDataPtr
typedef boost::weak_ptr
< AtomViewData > 
AtomViewDataWeakPtr
typedef std::vector< AtomViewAtomViewList
typedef boost::shared_ptr
< ResidueViewData > 
ResidueViewDataPtr
typedef boost::weak_ptr
< ResidueViewData > 
ResidueViewDataWeakPtr
typedef std::vector< ResidueViewResidueViewList
typedef boost::shared_ptr
< ChainViewData > 
ChainViewDataPtr
typedef boost::weak_ptr
< ChainViewData > 
ChainViewDataWeakPtr
typedef std::vector< ChainViewChainViewList
typedef boost::shared_ptr
< EntityViewData > 
EntityViewDataPtr
typedef boost::weak_ptr
< EntityViewData > 
EntityViewDataWeakPtr
typedef std::vector< EntityViewEntityViewList
typedef std::vector
< QueryViewWrapper
QueryViewWrapperList
typedef int ViewAddFlags

Enumerations

enum  EditMode { BUFFERED_EDIT, UNBUFFERED_EDIT }

Functions

DLLEXPORT_OST_MOL std::ostream & operator<< (std::ostream &os, const AtomBase &atom)
DLLEXPORT_OST_MOL std::ostream & operator<< (std::ostream &os, const BondHandle &bond)
DLLEXPORT_OST_MOL std::ostream & operator<< (std::ostream &os, const ChainBase &chain)
DLLEXPORT_OST_MOL CoordGroupHandle CreateCoordGroup (const AtomHandleList &atoms)
DLLEXPORT_OST_MOL std::ostream & operator<< (std::ostream &os, const EntityBase &ent)
Prop::ID DLLEXPORT_OST_MOL PropertyIDFromString (const String &prop)
Prop DLLEXPORT_OST_MOL PropertyFromString (const String &prop)
DLLEXPORT_OST_MOL std::ostream & operator<< (std::ostream &os, const ResidueBase &residue)
bool DLLEXPORT_OST_MOL InSequence (const ResidueHandle &residue_one, const ResidueHandle &residue_two)
std::ostream & operator<< (std::ostream &os, const ResNum &n)
DLLEXPORT_OST_MOL SurfaceHandle BuildSurface (const EntityView &ev, Real probe_radius, Real patch_size)
DLLEXPORT_OST_MOL SurfaceHandle CreateSurface ()
DLLEXPORT_OST_MOL std::ostream & operator<< (std::ostream &os, const SurfaceHandle &surf)
Real DLLEXPORT_OST_MOL DihedralAngle (const AtomHandle &a1, const AtomHandle &a2, const AtomHandle &a3, const AtomHandle &a4)
DLLEXPORT_OST_MOL std::ostream & operator<< (std::ostream &os, const TorsionHandle &torsion)
std::pair< EntityView,
EntityView > DLLEXPORT_OST_MOL 
CompareViews (const EntityView &view1, const EntityView &view2)
EntityHandle DLLEXPORT_OST_MOL CreateEntityFromView (const EntityView &view, bool include_exlusive_atoms, EntityHandle handle=EntityHandle())
def MergeCoordGroups
create bounding box from entity
geom::Cuboid DLLEXPORT_OST_MOL BoundingBoxFromEntity (const EntityHandle &ent)
geom::Cuboid DLLEXPORT_OST_MOL BoundingBoxFromEntity (const EntityView &ent)
geom::Cuboid DLLEXPORT_OST_MOL BoundingBoxFromAtoms (const AtomHandleList &atoms)

Typedef Documentation

typedef std::vector<AtomHandle> AtomHandleList

Definition at line 30 of file handle_type_fw.hh.

typedef boost::shared_ptr<AtomViewData> AtomViewDataPtr

Definition at line 28 of file view_type_fw.hh.

typedef boost::weak_ptr<AtomViewData> AtomViewDataWeakPtr

Definition at line 30 of file view_type_fw.hh.

typedef std::vector<AtomView> AtomViewList

Definition at line 31 of file view_type_fw.hh.

typedef std::vector<BondHandle> BondHandeList

Definition at line 135 of file bond_handle.hh.

typedef std::vector<BondHandle> BondHandleList

Definition at line 37 of file handle_type_fw.hh.

typedef std::vector<ChainHandle> ChainHandleList

Definition at line 26 of file handle_type_fw.hh.

typedef boost::shared_ptr<ChainViewData> ChainViewDataPtr

Definition at line 40 of file view_type_fw.hh.

typedef boost::weak_ptr<ChainViewData> ChainViewDataWeakPtr

Definition at line 42 of file view_type_fw.hh.

typedef std::vector<ChainView> ChainViewList

Definition at line 43 of file view_type_fw.hh.

typedef std::vector<geom::Vec3> CoordFrame

Definition at line 32 of file coord_frame.hh.

typedef std::vector<CoordFramePtr> CoordFrameList

Definition at line 34 of file coord_frame.hh.

typedef boost::shared_ptr<CoordFrame> CoordFramePtr

Definition at line 33 of file coord_frame.hh.

typedef boost::shared_ptr<CoordSource> CoordSourcePtr

Definition at line 33 of file coord_source.hh.

typedef std::vector<EntityHandle> EntityHandleList

Definition at line 40 of file handle_type_fw.hh.

typedef boost::shared_ptr<EntityObserver> EntityObserverPtr

Definition at line 26 of file entity_observer_fw.hh.

typedef boost::shared_ptr<EntityViewData> EntityViewDataPtr

Definition at line 46 of file view_type_fw.hh.

typedef boost::weak_ptr<EntityViewData> EntityViewDataWeakPtr

Definition at line 48 of file view_type_fw.hh.

typedef std::vector<EntityView> EntityViewList

Definition at line 49 of file view_type_fw.hh.

typedef boost::shared_ptr<InMemCoordSource> InMemCoordSourcePtr

Definition at line 32 of file in_mem_coord_source.hh.

typedef uint QueryFlags

Definition at line 69 of file query.hh.

typedef std::vector<QueryViewWrapper> QueryViewWrapperList

Definition at line 51 of file view_type_fw.hh.

typedef std::vector<ResidueHandle> ResidueHandleList

Definition at line 28 of file handle_type_fw.hh.

typedef String ResidueKey

Definition at line 117 of file residue_prop.hh.

typedef boost::shared_ptr<ResidueViewData> ResidueViewDataPtr

Definition at line 34 of file view_type_fw.hh.

typedef boost::weak_ptr<ResidueViewData> ResidueViewDataWeakPtr

Definition at line 36 of file view_type_fw.hh.

typedef std::vector<ResidueView> ResidueViewList

Definition at line 37 of file view_type_fw.hh.

typedef std::vector<SurfaceHandle> SurfaceHandleList

Definition at line 87 of file surface_handle.hh.

typedef unsigned int SurfaceTriID

Definition at line 63 of file surface_prop.hh.

typedef std::vector<SurfaceTriID> SurfaceTriIDList

Definition at line 35 of file surface_handle.hh.

typedef unsigned int SurfaceVertexID

Definition at line 56 of file surface_prop.hh.

typedef std::vector<SurfaceVertexID> SurfaceVertexIDList

Definition at line 36 of file surface_handle.hh.

typedef std::vector<SurfaceVertex> SurfaceVertexList

Definition at line 65 of file surface_prop.hh.

typedef std::vector<TorsionHandle> TorsionHandleList

Definition at line 34 of file handle_type_fw.hh.

typedef int ViewAddFlags

Definition at line 71 of file view_type_fw.hh.


Enumeration Type Documentation

enum EditMode
Enumerator:
BUFFERED_EDIT 
UNBUFFERED_EDIT 

Definition at line 31 of file editor_type_fw.hh.


Function Documentation

geom::Cuboid DLLEXPORT_OST_MOL ost::mol::BoundingBoxFromAtoms ( const AtomHandleList &  atoms)

create bounding box from atom list

See also:
Bounding Box Example
geom::Cuboid DLLEXPORT_OST_MOL ost::mol::BoundingBoxFromEntity ( const EntityHandle &  ent)

create bounding box from entity handle

See also:
Bounding Box Example
geom::Cuboid DLLEXPORT_OST_MOL ost::mol::BoundingBoxFromEntity ( const EntityView &  ent)

create bounding box from entity view

See also:
Bounding Box Example
DLLEXPORT_OST_MOL SurfaceHandle ost::mol::BuildSurface ( const EntityView &  ev,
Real  probe_radius,
Real  patch_size 
)
std::pair<EntityView, EntityView> DLLEXPORT_OST_MOL ost::mol::CompareViews ( const EntityView &  view1,
const EntityView &  view2 
)

compare two entity views

Exceptions:
IntegrityErrorif trying to compare two views that do not point to the same entity.
Returns:
a pair of views. first contains the elements that are in view1, but not in view2, contains the elements that are in view2 but not in view1
DLLEXPORT_OST_MOL CoordGroupHandle ost::mol::CreateCoordGroup ( const AtomHandleList &  atoms)
EntityHandle DLLEXPORT_OST_MOL ost::mol::CreateEntityFromView ( const EntityView &  view,
bool  include_exlusive_atoms,
EntityHandle  handle = EntityHandle() 
)

create new entity handle from entity view

This function behaves exactly like EntityHandle::Copy(), except that only atoms, residues, chains and bonds that are present in the view will be copied.

Parameters:
viewis the view to be converted to a handle
include_exlusive_atomsif true, atoms that are part of an exclusive bond will also be included in the new entity handle.
handleIf invalid a new entity will be created. If valid, the atoms, residues, chains, bonds and torsions will be added to handle. This is useful to combine several entities into one.
DLLEXPORT_OST_MOL SurfaceHandle ost::mol::CreateSurface ( )
Real DLLEXPORT_OST_MOL ost::mol::DihedralAngle ( const AtomHandle &  a1,
const AtomHandle &  a2,
const AtomHandle &  a3,
const AtomHandle &  a4 
)
bool DLLEXPORT_OST_MOL ost::mol::InSequence ( const ResidueHandle &  residue_one,
const ResidueHandle &  residue_two 
)

Test if two residues are in next in sequence.

Tests whether two residues are next in sequence and if they are connected by a bond. At the moment, this is only implemented for peptides

def ost.mol.MergeCoordGroups (   coord_groups)
Merge several separate coord groups into one. The coord groups must have the 
same number of atoms. In case no coord group is supplied, None will be 
returned.

Definition at line 24 of file __init__.py.

DLLEXPORT_OST_MOL std::ostream& ost::mol::operator<< ( std::ostream &  os,
const EntityBase &  ent 
)
DLLEXPORT_OST_MOL std::ostream& ost::mol::operator<< ( std::ostream &  os,
const ChainBase &  chain 
)
DLLEXPORT_OST_MOL std::ostream& ost::mol::operator<< ( std::ostream &  os,
const SurfaceHandle &  surf 
)
std::ostream& ost::mol::operator<< ( std::ostream &  os,
const ResNum &  n 
)
inline

Definition at line 119 of file residue_prop.hh.

DLLEXPORT_OST_MOL std::ostream& ost::mol::operator<< ( std::ostream &  os,
const TorsionHandle &  torsion 
)
DLLEXPORT_OST_MOL std::ostream& ost::mol::operator<< ( std::ostream &  os,
const BondHandle &  bond 
)
DLLEXPORT_OST_MOL std::ostream& ost::mol::operator<< ( std::ostream &  os,
const ResidueBase &  residue 
)
DLLEXPORT_OST_MOL std::ostream& ost::mol::operator<< ( std::ostream &  os,
const AtomBase &  atom 
)
Prop DLLEXPORT_OST_MOL ost::mol::PropertyFromString ( const String prop)
Returns:
the property. Prop::UNDEF is returned in case the property is not known.
Prop::ID DLLEXPORT_OST_MOL ost::mol::PropertyIDFromString ( const String prop)
Returns:
the property id. Prop::UNDEF is returned in case the property is not known.