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< BondHandle >	BondHandeList

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< ChainHandle >	ChainHandleList

typedef std::vector < ResidueHandle >	ResidueHandleList

typedef std::vector< AtomHandle >	AtomHandleList

typedef std::vector < TorsionHandle >	TorsionHandleList

typedef std::vector< BondHandle >	BondHandleList

typedef std::vector< EntityHandle >	EntityHandleList

typedef boost::shared_ptr < InMemCoordSource >	InMemCoordSourcePtr

typedef uint	QueryFlags

typedef String	ResidueKey

typedef std::vector< ResNum >	ResNumList

typedef std::vector< SurfaceTriID >	SurfaceTriIDList

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< AtomView >	AtomViewList

typedef boost::shared_ptr < ResidueViewData >	ResidueViewDataPtr

typedef boost::weak_ptr < ResidueViewData >	ResidueViewDataWeakPtr

typedef std::vector< ResidueView >	ResidueViewList

typedef boost::shared_ptr < ChainViewData >	ChainViewDataPtr

typedef boost::weak_ptr < ChainViewData >	ChainViewDataWeakPtr

typedef std::vector< ChainView >	ChainViewList

typedef boost::shared_ptr < EntityViewData >	EntityViewDataPtr

typedef boost::weak_ptr < EntityViewData >	EntityViewDataWeakPtr

typedef std::vector< EntityView >	EntityViewList

typedef std::vector < QueryViewWrapper >	QueryViewWrapperList

typedef int	ViewAddFlags

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.

typedef geom::Transform Transform

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

type	ChainType 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

identifier StringRef 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

identifier String 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

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 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

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.

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

type	ChainType 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

type	ChainType 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

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.

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 }

Namespaces

Data Structures

Typedefs

Enumerations

Functions

Typedef Documentation

Enumeration Type Documentation

Function Documentation