ost::mol Namespace Reference

Namespaces

namespace  alg
namespace  impl
namespace  mm

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  Builder
class  ChainBase
 base class for ChainHandle and ChainView More...
class  ChainHandle
 linear chain of residues More...
class  ChainView
 definition of ChainView More...
struct  ChemClass
struct  ChemType
class  CoordFrame
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  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...
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 boost::shared_ptr
< CoordFrame
CoordFramePtr
typedef std::vector
< CoordFramePtr
CoordFrameList
typedef boost::shared_ptr
< CoordSource
CoordSourcePtr
typedef boost::shared_ptr
< EntityObserver
EntityObserverPtr
typedef std::pair< EntityView,
EntityView
EntityViewPair
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< ResNumResNumList
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 geom::Transform Transform
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  ChainType {
  CHAINTYPE_POLY, CHAINTYPE_NON_POLY, CHAINTYPE_WATER, CHAINTYPE_POLY_PEPTIDE_D,
  CHAINTYPE_POLY_PEPTIDE_L, CHAINTYPE_POLY_DN, CHAINTYPE_POLY_RN, CHAINTYPE_POLY_SAC_D,
  CHAINTYPE_POLY_SAC_L, CHAINTYPE_POLY_DN_RN, CHAINTYPE_UNKNOWN, CHAINTYPE_MACROLIDE,
  CHAINTYPE_CYCLIC_PSEUDO_PEPTIDE, CHAINTYPE_POLY_PEPTIDE_DN_RN, CHAINTYPE_N_CHAINTYPES
}
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)
ChainType DLLEXPORT_OST_MOL ChainTypeFromString (const StringRef identifier)
ChainType DLLEXPORT_OST_MOL ChainTypeFromString (const String &identifier)
String DLLEXPORT_OST_MOL StringFromChainType (ChainType type)
DLLEXPORT_OST_MOL CoordFrame CreateCoordFrame (const geom::Vec3List &atom_pos, const geom::Vec3 &cell_size=geom::Vec3(), const geom::Vec3 &cell_angles=geom::Vec3())
DLLEXPORT_OST_MOL void GetIndices (const EntityView &sele, std::vector< unsigned long > &indices)
DLLEXPORT_OST_MOL void GetMasses (const EntityView &sele, std::vector< Real > &masses)
DLLEXPORT_OST_MOL void GetIndicesAndMasses (const EntityView &sele, std::vector< unsigned long > &indices, std::vector< Real > &masses)
DLLEXPORT_OST_MOL void GetPositions (const EntityView &sele, std::vector< geom::Vec3 > &ref_pos)
DLLEXPORT_OST_MOL void GetCaIndices (const EntityView &segment, std::vector< unsigned long > &indices_ca)
DLLEXPORT_OST_MOL void GetCaCONIndices (const EntityView &segment, std::vector< unsigned long > &indices_ca, std::vector< unsigned long > &indices_c, std::vector< unsigned long > &indices_o, std::vector< unsigned long > &indices_n)
DLLEXPORT_OST_MOL CoordGroupHandle CreateCoordGroup (const AtomHandleList &atoms)
DLLEXPORT_OST_MOL std::ostream & operator<< (std::ostream &os, const EntityBase &ent)
Prop::ID DLLIMPORT PropertyIDFromString (const String &prop)
Prop DLLIMPORT PropertyFromString (const String &prop)
DLLIMPORT std::ostream & operator<< (std::ostream &os, const ResidueBase &residue)
bool DLLIMPORT InSequence (const ResidueHandle &residue_one, const ResidueHandle &residue_two)
std::ostream & operator<< (std::ostream &os, const ResNum &n)
DLLIMPORT SurfaceHandle BuildSurface (const EntityView &ev, Real probe_radius, Real patch_size)
DLLIMPORT SurfaceHandle CreateSurface ()
DLLIMPORT std::ostream & operator<< (std::ostream &os, const SurfaceHandle &surf)
Real DLLIMPORT DihedralAngle (const AtomHandle &a1, const AtomHandle &a2, const AtomHandle &a3, const AtomHandle &a4)
DLLIMPORT std::ostream & operator<< (std::ostream &os, const TorsionHandle &torsion)
void DLLIMPORT TransferConnectivity (EntityHandle dest, const std::map< ResidueHandle, ResidueHandle > &to_from)
bool operator< (const ResidueHandle &lhs, const ResidueHandle &rhs)
std::pair< EntityView,
EntityView > DLLIMPORT 
CompareViews (const EntityView &view1, const EntityView &view2)
EntityHandle DLLIMPORT CreateEntityFromView (const EntityView &view, bool include_exlusive_atoms, EntityHandle handle=EntityHandle())
def Transform
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<CoordFramePtr> CoordFrameList

Definition at line 207 of file coord_frame.hh.

typedef boost::shared_ptr<CoordFrame> CoordFramePtr

Definition at line 206 of file coord_frame.hh.

typedef boost::shared_ptr<CoordSource> CoordSourcePtr

Definition at line 37 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 std::pair<EntityView, EntityView> EntityViewPair

Definition at line 349 of file entity_view.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 125 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<ResNum> ResNumList

Definition at line 126 of file residue_prop.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.

Definition at line 5 of file transform.hh.

typedef int ViewAddFlags

Definition at line 71 of file view_type_fw.hh.


Enumeration Type Documentation

enum ChainType
Enumerator:
CHAINTYPE_POLY 

polymer

CHAINTYPE_NON_POLY 

non-polymer

CHAINTYPE_WATER 

water

CHAINTYPE_POLY_PEPTIDE_D 

(D) amino acid sequence

CHAINTYPE_POLY_PEPTIDE_L 

(L) amino acid sequence

CHAINTYPE_POLY_DN 

polydeoxyribonucleotide

CHAINTYPE_POLY_RN 

polyribonucleotide

CHAINTYPE_POLY_SAC_D 

polysaccharide(D)

CHAINTYPE_POLY_SAC_L 

polysaccharide(L)

CHAINTYPE_POLY_DN_RN 

polydeoxyribonucleotide/ -ribonucleotide hybrid

CHAINTYPE_UNKNOWN 

guess what

CHAINTYPE_MACROLIDE 

macrolide

CHAINTYPE_CYCLIC_PSEUDO_PEPTIDE 

cyclic-pseudo-peptide

CHAINTYPE_POLY_PEPTIDE_DN_RN 

peptide nucleic acid

CHAINTYPE_N_CHAINTYPES 

no. of chain types

Definition at line 31 of file chain_type.hh.

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 EntityView &  ent  ) 

create bounding box from entity view

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
DLLIMPORT SurfaceHandle ost::mol::BuildSurface ( const EntityView &  ev,
Real  probe_radius,
Real  patch_size 
)
ChainType DLLEXPORT_OST_MOL ost::mol::ChainTypeFromString ( const String identifier  ) 

Create a ChainType item for a given string.

Parameters:
identifier String to be translated
Returns:
The ChainType corresponding to the input, throws a ost::Error on unknown type
ChainType DLLEXPORT_OST_MOL ost::mol::ChainTypeFromString ( const StringRef  identifier  ) 

Create a ChainType item for a given string.

Parameters:
identifier StringRef to be translated
Returns:
The ChainType corresponding to the input, throws a ost:Error on unknown type
std::pair<EntityView, EntityView> DLLIMPORT ost::mol::CompareViews ( const EntityView &  view1,
const EntityView &  view2 
)

compare two entity views

Exceptions:
IntegrityError if 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, second contains the elements that are in view2 but not in view1
DLLEXPORT_OST_MOL CoordFrame ost::mol::CreateCoordFrame ( const geom::Vec3List atom_pos,
const geom::Vec3 cell_size = geom::Vec3(),
const geom::Vec3 cell_angles = geom::Vec3() 
)
DLLEXPORT_OST_MOL CoordGroupHandle ost::mol::CreateCoordGroup ( const AtomHandleList &  atoms  ) 
EntityHandle DLLIMPORT 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:
view is the view to be converted to a handle
include_exlusive_atoms if true, atoms that are part of an exclusive bond (only one bond partner is included in the view) will also be included in the new entity handle.
handle If 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.
DLLIMPORT SurfaceHandle ost::mol::CreateSurface (  ) 
Real DLLIMPORT ost::mol::DihedralAngle ( const AtomHandle &  a1,
const AtomHandle &  a2,
const AtomHandle &  a3,
const AtomHandle &  a4 
)
DLLEXPORT_OST_MOL void ost::mol::GetCaCONIndices ( const EntityView &  segment,
std::vector< unsigned long > &  indices_ca,
std::vector< unsigned long > &  indices_c,
std::vector< unsigned long > &  indices_o,
std::vector< unsigned long > &  indices_n 
)

Writes the backbone indices of all residues in the EntityView into the provided list.

DLLEXPORT_OST_MOL void ost::mol::GetCaIndices ( const EntityView &  segment,
std::vector< unsigned long > &  indices_ca 
)

Writes the indices of all atoms in the EntityView into the provided list.

DLLEXPORT_OST_MOL void ost::mol::GetIndices ( const EntityView &  sele,
std::vector< unsigned long > &  indices 
)

This function returns a vector containing the atom indices of the atoms in an EntityView; it is used to accelerate the extraction of information from a trajectory

DLLEXPORT_OST_MOL void ost::mol::GetIndicesAndMasses ( const EntityView &  sele,
std::vector< unsigned long > &  indices,
std::vector< Real > &  masses 
)

conveniece for GetIndices and GetMasses in one call

DLLEXPORT_OST_MOL void ost::mol::GetMasses ( const EntityView &  sele,
std::vector< Real > &  masses 
)

This function returns a vector containing the atom masses of the atoms in an EntityView; it is used together with GetIndices to accelerate the extraction of RMSD from a trajectory

DLLEXPORT_OST_MOL void ost::mol::GetPositions ( const EntityView &  sele,
std::vector< geom::Vec3 > &  ref_pos 
)

Writes the positions of all atoms in the EntityView into the provided vec3 list.

bool DLLIMPORT 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 35 of file __init__.py.

bool ost::mol::operator< ( const ResidueHandle &  lhs,
const ResidueHandle &  rhs 
)

Definition at line 33 of file transfer_connectivity.hh.

DLLIMPORT std::ostream& ost::mol::operator<< ( std::ostream &  os,
const TorsionHandle &  torsion 
)
DLLIMPORT 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 128 of file residue_prop.hh.

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

Return the String identifier for a given type.

Parameters:
type ChainType to be translated
Returns:
String corresponding to the input, throws a ost::Error on unknown type
void DLLIMPORT ost::mol::TransferConnectivity ( EntityHandle  dest,
const std::map< ResidueHandle, ResidueHandle > &  to_from 
)
def ost::mol::Transform (   tf = None  ) 

Definition at line 24 of file __init__.py.

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