ost::mol::alg Namespace Reference

Namespaces
namespace	views

Data Structures
struct	SecStructureSegment
	a consecutive secondary structure element More...
struct	SuperpositionResult
	stores the number of cycles and the two final EntityViews (in case IterativeSuperposition was applied), the root mean square deviation of the two superposed objects and the transformation matrix (geom::Mat4) to superpose input1 onto input2. More...
class	SuperposerSVD
	effiently superpose a bunch of models with the same number of atoms Choose either two EntityViews or two AtomViewLists. More...

Typedefs
typedef std::vector < SecStructureSegment >	SecStructureSegments

Functions
EntityView DLLEXPORT_OST_MOL_ALG	FilterClashes (const EntityView &ent, Real tolerance=0.1, bool always_remove_bb=false)
EntityView DLLEXPORT_OST_MOL_ALG	FilterClashes (const EntityHandle &ent, Real tolerance=0.1, bool always_remove_bb=false)
Real DLLEXPORT_OST_MOL_ALG	LocalDistTest (const EntityView &mdl, const EntityView &ref, Real cutoff, Real max_dist)
Real DLLEXPORT_OST_MOL_ALG	LocalDistTest (const ost::seq::AlignmentHandle &aln, Real cutoff, Real max_dist, int ref_index=0, int mdl_index=1)
CoordGroupHandle DLLEXPORT_OST_MOL_ALG	SuperposeFrames (CoordGroupHandle cg, EntityView sel, int begin=0, int end=-1, int ref=-1)
SuperpositionResult DLLEXPORT_OST_MOL_ALG	SuperposeAtoms (const mol::AtomViewList &atoms1, const mol::AtomViewList &atoms2, bool apply_transform)
SuperpositionResult DLLEXPORT_OST_MOL_ALG	SuperposeSVD (const mol::EntityView &ev1, const mol::EntityView &ev2, bool apply_transform)
SuperpositionResult DLLEXPORT_OST_MOL_ALG	SuperposeSVD (const std::vector< geom::Vec3 > &pl1, const std::vector< geom::Vec3 > &pl2)
SuperpositionResult DLLEXPORT_OST_MOL_ALG	IterativeSuperposition (mol::EntityView &ev1, mol::EntityView &ev2, int ncycles, Real distance_threshold, bool apply_transform)
Real DLLEXPORT_OST_MOL_ALG	CalculateRMSD (const mol::EntityView &ev1, const mol::EntityView &ev2, const geom::Mat4 &transformation)

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Typedef Documentation

typedef std::vector<SecStructureSegment> SecStructureSegments

Definition at line 46 of file sec_structure_segments.hh.

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Function Documentation

Real DLLEXPORT_OST_MOL_ALG ost::mol::alg::CalculateRMSD	(	const mol::EntityView &	ev1,
		const mol::EntityView &	ev2,
		const geom::Mat4 &	transformation
	)

calculates RMSD for two entity view

EntityView DLLEXPORT_OST_MOL_ALG ost::mol::alg::FilterClashes	(	const EntityView &	ent,
		Real	tolerance = 0.1,
		bool	always_remove_bb = false
	)

EntityView DLLEXPORT_OST_MOL_ALG ost::mol::alg::FilterClashes	(	const EntityHandle &	ent,
		Real	tolerance = 0.1,
		bool	always_remove_bb = false
	)

SuperpositionResult DLLEXPORT_OST_MOL_ALG ost::mol::alg::IterativeSuperposition	(	mol::EntityView &	ev1,
		mol::EntityView &	ev2,
		int	ncycles,
		Real	distance_threshold,
		bool	apply_transform
	)

iterative superposition

Real DLLEXPORT_OST_MOL_ALG ost::mol::alg::LocalDistTest	(	const EntityView &	mdl,
		const EntityView &	ref,
		Real	cutoff,
		Real	max_dist
	)

Real DLLEXPORT_OST_MOL_ALG ost::mol::alg::LocalDistTest	(	const ost::seq::AlignmentHandle &	aln,
		Real	cutoff,
		Real	max_dist,
		int	ref_index = 0,
		int	mdl_index = 1
	)

SuperpositionResult DLLEXPORT_OST_MOL_ALG ost::mol::alg::SuperposeAtoms	(	const mol::AtomViewList &	atoms1,
		const mol::AtomViewList &	atoms2,
		bool	apply_transform
	)

takes the corresponding atoms and superposes them

CoordGroupHandle DLLEXPORT_OST_MOL_ALG ost::mol::alg::SuperposeFrames	(	CoordGroupHandle	cg,
		EntityView	sel,
		int	begin = 0,
		int	end = -1,
		int	ref = -1
	)

returns a superposed version of coord group

SuperpositionResult DLLEXPORT_OST_MOL_ALG ost::mol::alg::SuperposeSVD	(	const mol::EntityView &	ev1,
		const mol::EntityView &	ev2,
		bool	apply_transform
	)

superposes two entity views

SuperpositionResult DLLEXPORT_OST_MOL_ALG ost::mol::alg::SuperposeSVD	(	const std::vector< geom::Vec3 > &	pl1,
		const std::vector< geom::Vec3 > &	pl2
	)

superposes two pointlists