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ost::mol Namespace Reference

Namespaces

 alg
 
 impl
 
 mm
 

Data Structures

class  AtomBase
 
class  AtomHandle
 
class  AtomView
 
class  BondHandle
 
struct  BondTableEntry
 
struct  BondTable
 
class  Builder
 
class  ChainBase
 
class  ChainHandle
 
class  ChainView
 
struct  ChemClass
 
struct  ChemType
 
class  CoordFrame
 
class  CoordGroupHandle
 
class  CoordSource
 
class  EditorBase
 
class  EntityBase
 
class  EntityHandle
 
class  EntityObserver
 
class  EntityPropertyMapper
 
class  EntityView
 
class  EntityVisitor
 
class  EntityViewVisitor
 
class  ICSEditor
 
class  InMemCoordSource
 
class  NotConnectedError
 
struct  Prop
 
struct  PropertyError
 
struct  QueryFlag
 
class  Query
 
struct  QueryErrorDesc
 
class  QueryError
 
class  QueryState
 
class  QueryViewWrapper
 
class  ResidueBase
 
class  ResidueHandle
 
class  ResNum
 
class  ResidueView
 
struct  SecStructure
 
class  SpatialOrganizer
 
class  SurfaceHandle
 
struct  SurfaceVertex
 
struct  SurfaceTri
 
class  TorsionHandle
 
struct  ViewAddFlag
 
class  XCSEditor
 

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_BRANCHED, CHAINTYPE_OLIGOSACCHARIDE,
  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 DLLIMPORT ChainTypeFromString (const StringRef identifier)
 
ChainType DLLIMPORT ChainTypeFromString (const String &identifier)
 
String DLLIMPORT StringFromChainType (ChainType type)
 
String DLLIMPORT EntityTypeFromChainType (ChainType type)
 
String DLLIMPORT EntityPolyTypeFromChainType (ChainType type)
 
String DLLIMPORT BranchedTypeFromChainType (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 DLLEXPORT_OST_MOL PropertyIDFromString (const String &prop)
 
Prop DLLEXPORT_OST_MOL PropertyFromString (const String &prop)
 
String DLLEXPORT_OST_MOL QueryQuoteName (const String &name)
 
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)
 
void DLLIMPORT TransferConnectivity (EntityHandle dest, const std::map< ResidueHandle, ResidueHandle > &to_from)
 
bool operator< (const ResidueHandle &lhs, const ResidueHandle &rhs)
 
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 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 134 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_BRANCHED 

carbohydrate

CHAINTYPE_OLIGOSACCHARIDE 

oligosaccharide (branched carbohydrate, i.e. _entity.type is strictly 'branched')

CHAINTYPE_N_CHAINTYPES 

no. of chain types

Definition at line 36 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 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
String DLLIMPORT ost::mol::BranchedTypeFromChainType ( ChainType  type)

Return pdbx_entity_branch.type consistent with mmCIF dictionary (mmcif_pdbx_v50):

   - oligosaccharide  
Parameters
typeChainType to be translated
Returns
String corresponding to the input, throws a ost::Error on unknown type or if it's not of _entity.type branched
DLLEXPORT_OST_MOL SurfaceHandle ost::mol::BuildSurface ( const EntityView &  ev,
Real  probe_radius,
Real  patch_size 
)
ChainType DLLIMPORT ost::mol::ChainTypeFromString ( const StringRef  identifier)

Create a ChainType item for a given string.

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

Create a ChainType item for a given string.

Parameters
identifierString to be translated
Returns
The ChainType corresponding to the input, throws a ost::Error on unknown type
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, 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 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 (only one bond partner is included in the view) 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 
)
String DLLIMPORT ost::mol::EntityPolyTypeFromChainType ( ChainType  type)

Return _entity_poly.type consistent with mmCIF dictionary (mmcif_pdbx_v50):

   - cyclic-pseudo-peptide  
   - other  
   - peptide nucleic acid   
   - polydeoxyribonucleotide  
   - polydeoxyribonucleotide/polyribonucleotide hybrid  
   - polypeptide(D)   
   - polypeptide(L)   
   - polyribonucleotide

   For consistency with older dictionaries, CHAINTYPE_POLY_SAC_D
   and CHAINTYPE_POLY_SAC_L are still accepted but return "other".
   Older dictionaries still had "polysaccharide(D)" and
   "polysaccharide(L)""
Parameters
typeChainType to be translated
Returns
String corresponding to the input, throws a ost::Error on unknown type or if it's not of _entity.type polymer
String DLLIMPORT ost::mol::EntityTypeFromChainType ( ChainType  type)

Return _entity.type consistent with respective mmCIF vocabulary (mmcif_pdbx_v50):

   - branched
   - macrolide
   - non-polymer
   - polymer
   - water

   For consistency with older vocabularies, CHAINTYPE_POLY_SAC_D
   and CHAINTYPE_POLY_SAC_L return "polymer"
Parameters
typeChainType to be translated
Returns
String corresponding to the input, throws a ost::Error on unknown type
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 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 35 of file __init__.py.

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

Definition at line 33 of file transfer_connectivity.hh.

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

Definition at line 128 of file residue_prop.hh.

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 
)
DLLEXPORT_OST_MOL std::ostream& ost::mol::operator<< ( std::ostream &  os,
const ResidueBase &  residue 
)
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.
String DLLEXPORT_OST_MOL ost::mol::QueryQuoteName ( const String name)
inline

Definition at line 122 of file query.hh.

String DLLIMPORT ost::mol::StringFromChainType ( ChainType  type)

Return the String identifier for a given type.

Parameters
typeChainType 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.