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< 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
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.

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_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.