Fitting atomic structures into a cryo-electron microscopy density map. More...

Detailed Description

Fitting atomic structures into a cryo-electron microscopy density map.

MultiFit is a computational method for simultaneously fitting atomic structures of components into their assembly density map at resolutions as low as 25Å. The component positions and orientations are optimized with respect to a scoring function that includes the quality-of-fit of components in the map, the protrusion of components from the map envelope, as well as the shape complementarity between pairs of components. The scoring function is optimized by an exact inference optimizer DOMINO that efficiently finds the global minimum in a discrete sampling space.

For more information please see the MultiFit website.

See the IMP::cnmultifit module for a similar protocol for handling symmetric complexes.

multifit: command line tool

Generally, this module is not used directly; instead, the multifit command line tool is used. For an example, see Modeling of 3sfd.

Web server

A webserver that uses both this module and the IMP::cnmultifit module is also available.

complex_to_anchor_graph

Build an anchor graph from a PDB file.

Info

Author(s): Keren Lasker

Maintainer: benmwebb

License: LGPL This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Publications:

See main IMP papers list.
K. Lasker, M. Topf, A. Sali, H. J. Wolfson, "Inferential optimization for simultaneous fitting of multiple components into a cryoEM map of their assembly", J Mol Biol 388, 2009

Classes
class	AnchorsData
	Storage of anchors (points and edges) More...

class	AssemblyHeader
	Holds data about the assembly density needed for optimization. More...

class	ComplementarityRestraint
	Compute the complementarity between two molecules. More...

class	ComponentHeader
	Holds data about a component needed for optimization. More...

class	DataPointsAssignment

class	DensityDataPoints
	Stores density voxels as a vector of Array1D. More...

class	DummyRestraint
	A simple Restraint that always returns a score of zero. More...

class	Ensemble
	An ensemble of fitting solutions. More...

class	FFTFitting
	Fit a molecule inside its density by local or global FFT. More...

class	FFTFittingOutput
	Storage of the results from an FFT fit. More...

class	FittingSolutionRecord
	A fitting solution record. More...

class	FittingStates

class	GeometricHash
	Geometric Hash table. More...

class	MergeTreeBuilder
	Utility class for building merge trees. More...

class	ProbabilisticAnchorGraph
	Probabilistic anchor graph. More...

class	ProteinsAnchorsSamplingSpace
	stores the anchors sampling space for each protein More...

class	ProteomicsData
	Storage of proteomics data. More...

class	ProteomicsEMAlignmentAtomic
	Align proteomics graph to EM density map. More...

class	RadiusOfGyrationRestraint
	Ensure the radius of gyration of particles fits the predicted one. More...

class	SettingsData
	Holds header data for optimization. More...

class	WeightedExcludedVolumeRestraint
	Calculate score based on fit to EM map. More...

Typedefs
typedef IMP::Vector < AlignmentParams >	AlignmentParamsList

typedef IMP::Vector< AnchorsData >	AnchorsDataList

typedef std::map< IntPair, int >	CEdges

typedef IMP::Vector < ComplementarityParams >	ComplementarityParamsList

typedef IMP::Vector < IMP::Pointer < ComponentHeader > >	ComponentHeaders

typedef IMP::Vector < IMP::WeakPointer < ComponentHeader > >	ComponentHeadersTemp

typedef IMP::Vector < ConnectivityParams >	ConnectivityParamsList

typedef IMP::algebra::DenseGrid3D < double >	DensGrid

typedef IMP::Vector < IMP::Pointer < DensityDataPoints > >	DensityDataPointsList

typedef IMP::Vector < IMP::WeakPointer < DensityDataPoints > >	DensityDataPointsListTemp

typedef IMP::Vector< DominoParams >	DominoParamsList

typedef IMP::Vector < IMP::Pointer< Ensemble > >	Ensembles

typedef IMP::Vector < IMP::WeakPointer< Ensemble > >	EnsemblesTemp

typedef IMP::Vector< EVParams >	EVParamsList

typedef IMP::Vector < FiltersParams >	FiltersParamsList

typedef IMP::Vector < FittingParams >	FittingParamsList

typedef IMP::Vector < FittingSolutionRecord >	FittingSolutionRecords

typedef IMP::Vector < FragmentsParams >	FragmentsParamsList

typedef IMP::Vector < IMP::Pointer < ProbabilisticAnchorGraph > >	ProbabilisticAnchorGraphs

typedef IMP::Vector < IMP::WeakPointer < ProbabilisticAnchorGraph > >	ProbabilisticAnchorGraphsTemp

typedef IMP::Vector < ProteinRecordData >	ProteinRecordDataList

typedef IMP::Vector < ProteinsAnchorsSamplingSpace >	ProteinsAnchorsSamplingSpaces

typedef IMP::Vector < IMP::Pointer < ProteomicsEMAlignmentAtomic > >	ProteomicsEMAlignmentAtomics

typedef IMP::Vector < IMP::WeakPointer < ProteomicsEMAlignmentAtomic > >	ProteomicsEMAlignmentAtomicsTemp

typedef IMP::Vector< RogParams >	RogParamsList

typedef IMP::Vector< XlinkParams >	XlinkParamsList

Functions
void	add_surface_index (core::Hierarchy mhd, Float apix, FloatKey shell_key=FloatKey("surf_ind"), FloatKey radius_key=core::XYZR::get_radius_key(), FloatKey weight_key=atom::Mass::get_mass_key())
	Add shell index to leaves. More...

FittingSolutionRecords	convert_em_to_multifit_format (const em::FittingSolutions &em_fits)

algebra::Transformation3Ds	convert_multifit_format_to_transformations (const FittingSolutionRecords &recs)

em::FittingSolutions	convert_multifit_to_em_format (const FittingSolutionRecords &multifit_fits)

FittingSolutionRecords	convert_transformations_to_multifit_format (const algebra::Transformation3Ds &trans)

atom::Hierarchy	create_coarse_molecule_from_density (em::DensityMap dmap, float dens_threshold, int num_beads, Model mdl, float bead_radius)
	Coarsen a density map based on voxels clustering. More...

atom::Hierarchy	create_coarse_molecule_from_molecule (const atom::Hierarchy &mh, int num_beads, Model *mdl, float bead_radius, bool add_conn_restraint=false)
	Coarsen a molecule based on atom clustering. More...

atom::Hierarchies	create_coarse_molecules_from_molecules (const atom::Hierarchies &mhs, int frag_len, Model *mdl, float bead_radius, bool add_conn_restraint=false)
	Coarsen molecules based on atom clustering. More...

em::DensityMap *	create_hit_map (core::RigidBody rb, Refiner rb_ref, const FittingSolutionRecords &sols, em::DensityMap damp)

IMP::Restraint *	create_weighted_excluded_volume_restraint (core::RigidBody rb1, core::RigidBody rb2, FloatKey shell_key=FloatKey("surf_ind"))
	Create a weighted excluded volume restraint between two rigid bodies. More...

multifit::FittingSolutionRecords	fft_based_rigid_fitting (atom::Hierarchy mol2fit, em::DensityMap *dmap, double density_threshold, double angle_sampling_interval_rad)
	FFT fit of a molecule in the density. More...

float	get_actual_radius_of_gyration (ParticlesTemp ps)

IntsList	get_anchor_indices_matching_secondary_structure (const AnchorsData &ad, const atom::SecondaryStructureResidues &ssrs, Float max_rmsd=0.7)
	Get lists of anchors that match a sequence of secondary structures. More...

void	get_anchors_for_density (em::DensityMap *dmap, int number_of_means, float density_threshold, std::string pdb_filename, std::string cmm_filename, std::string seg_filename, std::string txt_filename)
	Generate anchors in several formats for a given density map. More...

float	get_approximated_radius (int len)

float	get_approximated_radius_of_gyration (int len)

FittingSolutionRecords	get_close_to_point (const FittingSolutionRecords &fit_sols, atom::Hierarchy mh, IMP::Particle *ap, Float dist)
	prune solutions by distance to an anchor point More...

IntsList	get_connected_components (em::DensityMap *dmap, float threshold, float edge_threshold)
	Return connected components based on density values. More...

ProteinsAnchorsSamplingSpace	get_part_of_sampling_space (const ProteinsAnchorsSamplingSpace &prots_ss, const Strings &prot_names)
	Get the sampling space of few of the proteins. More...

multifit::SettingsData *	get_partial_assembly_setting_data (multifit::SettingsData *prots_sd, const Strings &prot_names)
	Get the assembly data for a few of the proteins. More...

ProteomicsData *	get_partial_proteomics_data (const ProteomicsData *pd, const Strings &prot_names)

algebra::Vector3Ds	get_points_close_to_molecule (const atom::Hierarchy &mh, const algebra::Vector3Ds points, Float max_dist)

algebra::Vector3Ds	get_points_far_from_molecule (const atom::Hierarchy &mh, const algebra::Vector3Ds points, Float max_dist)

algebra::Vector3D	get_segment_maximum (const DataPointsAssignment &dpa, em::DensityMap *dmap, int segment_id)

algebra::Vector3D	get_segment_maximum (const DataPointsAssignment &dpa, DensGrid *dmap, int segment_id)

void	get_segmentation (em::DensityMap *dmap, double apix, double density_threshold, int num_means, const std::string pdb_filename, const std::string cmm_filename, const std::string seg_filename, const std::string txt_filename)
	Segment a density map using the anchor graph. More...

em::DensityMap *	grid2map (const DensGrid &dg, float spacing)

Ensemble *	load_ensemble (multifit::SettingsData sd, Model mdl, const ProteinsAnchorsSamplingSpace &mapping_data)

AnchorsData	molecule2anchors (atom::Hierarchy mh, int k)

em::FittingSolutions	pca_based_rigid_fitting (core::RigidBody rb, Refiner rb_refiner, em::DensityMap em_map, Float threshold, FloatKey wei_key=atom::Mass::get_mass_key(), algebra::PrincipalComponentAnalysis dens_pca_input=algebra::PrincipalComponentAnalysis())
	Compute fitting scores for a given set of rigid transformations. More...

em::FittingSolutions	pca_based_rigid_fitting (ParticlesTemp ps, em::DensityMap *em_map, Float threshold, FloatKey wei_key=atom::Mass::get_mass_key(), algebra::PrincipalComponentAnalysis dens_pca_input=algebra::PrincipalComponentAnalysis())
	Compute fitting scores for a given set of rigid transformations. More...

AnchorsData	read_anchors_data (const char *txt_filename)

std::pair< algebra::Vector3Ds, CEdges >	read_cmm (const std::string &cmm_filename)

FittingSolutionRecords	read_fitting_solutions (const char *fitting_fn)
	Fitting solutions reader. More...

IntsList	read_paths (const char *txt_filename, int max_paths=INT_MAX)
	Read paths. More...

ProteinsAnchorsSamplingSpace	read_protein_anchors_mapping (multifit::ProteomicsData *prots, const std::string &anchors_prot_map_fn, int max_paths=INT_MAX)

ProteomicsData *	read_proteomics_data (const char *proteomics_fn)
	Proteomics reader. More...

SettingsData *	read_settings (const char *filename)

em::DensityMap *	remove_background (em::DensityMap *dmap, float threshold, float edge_threshold)
	Returns a map containing all density without the background. More...

void	write_chimera (const std::string &chimera_filename, const DataPointsAssignment &dpa)

void	write_cmm (const std::string &cmm_filename, const std::string &marker_set_name, const AnchorsData &dpa)

void	write_connolly_surface (atom::Atoms atoms, TextOutput fn, float density, float probe_radius)
	Write the Connolly surface for a set of atoms to a file. More...

void	write_fitting_solutions (const char *fitting_fn, const FittingSolutionRecords &fit_sols, int num_sols=-1)
	Write fitting solutions to a file. More...

void	write_markers (const algebra::PrincipalComponentAnalysisD< 3 > &pca, std::ostream &out)

void	write_paths (const IntsList &paths, const std::string &txt_filename)

void	write_pdb (const std::string &pdb_filename, const DataPointsAssignment &dpa)

void	write_protein_anchors_mapping (const std::string &anchors_prot_map_fn, const std::string &anchors_fn, const std::vector< std::pair< String, String > > &prot_paths)

void	write_protein_anchors_mapping (const std::string &anchors_prot_map_fn, const ProteinsAnchorsSamplingSpace &pa, const Strings &prot_names)

void	write_segment_as_mrc (em::DensityMap *dmap, const DataPointsAssignment &dpa, int segment_id, Float resolution, Float apix, const std::string &filename)

void	write_segment_as_pdb (const DataPointsAssignment &dpa, int segment_id, const std::string &filename)

void	write_segments_as_mrc (em::DensityMap *dmap, const DataPointsAssignment &dpa, Float resolution, Float apix, Float threshold, const std::string &filename)
	Write segments in MRC format. More...

void	write_segments_as_pdb (const DataPointsAssignment &dpa, const std::string &filename)

void	write_settings (const char filename, const SettingsData sd)

void	write_txt (const std::string &txt_filename, const AnchorsData &ad)

Standard module functions
All `IMP` modules have a set of standard functions to help get information about the module and about files associated with the module.
std::string	get_module_version ()

std::string	get_module_name ()

std::string	get_data_path (std::string file_name)
	Return the full path to one of this module's data files. More...

std::string	get_example_path (std::string file_name)
	Return the full path to one of this module's example files. More...

Typedef Documentation

typedef IMP::Vector< AlignmentParams > IMP::multifit::AlignmentParamsList

Pass or store a set of AlignmentParams .

Definition at line 322 of file AlignmentParams.h.

typedef IMP::Vector< AnchorsData > IMP::multifit::AnchorsDataList

Pass or store a set of AnchorsData .

Definition at line 89 of file anchors_reader.h.

typedef IMP::Vector< ComplementarityParams > IMP::multifit::ComplementarityParamsList

Pass or store a set of ComplementarityParams .

Definition at line 269 of file AlignmentParams.h.

typedef IMP::Vector<IMP::Pointer< ComponentHeader > > IMP::multifit::ComponentHeaders

Store a set of objects.

Definition at line 73 of file SettingsData.h.

typedef IMP::Vector<IMP::WeakPointer< ComponentHeader > > IMP::multifit::ComponentHeadersTemp

Pass a set of objects.

See Also: ComponentHeader

Definition at line 73 of file SettingsData.h.

typedef IMP::Vector< ConnectivityParams > IMP::multifit::ConnectivityParamsList

Pass or store a set of ConnectivityParams .

Definition at line 95 of file AlignmentParams.h.

typedef IMP::Vector<IMP::Pointer< DensityDataPoints > > IMP::multifit::DensityDataPointsList

Store a set of objects.

Definition at line 60 of file DensityDataPoints.h.

typedef IMP::Vector<IMP::WeakPointer< DensityDataPoints > > IMP::multifit::DensityDataPointsListTemp

Pass a set of objects.

See Also: DensityDataPoints

Definition at line 60 of file DensityDataPoints.h.

typedef IMP::Vector< DominoParams > IMP::multifit::DominoParamsList

Pass or store a set of DominoParams .

Definition at line 48 of file AlignmentParams.h.

typedef IMP::Vector<IMP::Pointer< Ensemble > > IMP::multifit::Ensembles

Store a set of objects.

Definition at line 49 of file ensemble_analysis.h.

typedef IMP::Vector<IMP::WeakPointer< Ensemble > > IMP::multifit::EnsemblesTemp

Pass a set of objects.

See Also: Ensemble

Definition at line 49 of file ensemble_analysis.h.

typedef IMP::Vector< EVParams > IMP::multifit::EVParamsList

Pass or store a set of EVParams .

Definition at line 186 of file AlignmentParams.h.

typedef IMP::Vector< FiltersParams > IMP::multifit::FiltersParamsList

Pass or store a set of FiltersParams .

Definition at line 209 of file AlignmentParams.h.

typedef IMP::Vector< FittingParams > IMP::multifit::FittingParamsList

Pass or store a set of FittingParams .

Definition at line 235 of file AlignmentParams.h.

typedef IMP::Vector< FittingSolutionRecord > IMP::multifit::FittingSolutionRecords

Pass or store a set of FittingSolutionRecord .

Definition at line 84 of file FittingSolutionRecord.h.

typedef IMP::Vector< FragmentsParams > IMP::multifit::FragmentsParamsList

Pass or store a set of FragmentsParams .

Definition at line 123 of file AlignmentParams.h.

typedef IMP::Vector<IMP::Pointer< ProbabilisticAnchorGraph > > IMP::multifit::ProbabilisticAnchorGraphs

Store a set of objects.

Definition at line 67 of file anchor_graph.h.

typedef IMP::Vector<IMP::WeakPointer< ProbabilisticAnchorGraph > > IMP::multifit::ProbabilisticAnchorGraphsTemp

Pass a set of objects.

See Also: ProbabilisticAnchorGraph

Definition at line 67 of file anchor_graph.h.

typedef IMP::Vector< ProteinRecordData > IMP::multifit::ProteinRecordDataList

Pass or store a set of ProteinRecordData .

Definition at line 68 of file proteomics_reader.h.

typedef IMP::Vector< ProteinsAnchorsSamplingSpace > IMP::multifit::ProteinsAnchorsSamplingSpaces

Pass or store a set of ProteinsAnchorsSamplingSpace .

Definition at line 65 of file protein_anchors_mapping_reader.h.

typedef IMP::Vector<IMP::Pointer< ProteomicsEMAlignmentAtomic > > IMP::multifit::ProteomicsEMAlignmentAtomics

Store a set of objects.

Definition at line 116 of file proteomics_em_alignment_atomic.h.

typedef IMP::Vector<IMP::WeakPointer< ProteomicsEMAlignmentAtomic > > IMP::multifit::ProteomicsEMAlignmentAtomicsTemp

Pass a set of objects.

See Also: ProteomicsEMAlignmentAtomic

Definition at line 116 of file proteomics_em_alignment_atomic.h.

typedef IMP::Vector< RogParams > IMP::multifit::RogParamsList

Pass or store a set of RogParams .

Definition at line 143 of file AlignmentParams.h.

typedef IMP::Vector< XlinkParams > IMP::multifit::XlinkParamsList

Pass or store a set of XlinkParams .

Definition at line 72 of file AlignmentParams.h.

Function Documentation

void IMP::multifit::add_surface_index	(	core::Hierarchy	mhd,
		Float	apix,
		FloatKey	shell_key = `FloatKey("surf_ind")`,
		FloatKey	radius_key = `core::XYZR::get_radius_key()`,
		FloatKey	weight_key = `atom::Mass::get_mass_key()`
	)

Add shell index to leaves.

Parameters

[in]	mhd	the Hierarchy to modify
[in]	apix	the resolution of the surface
[in]	shell_key	the Key used to store the shell index
[in]	radius_key	the Key used for particle radius
[in]	weight_key	the Key used for particle weight (e.g. mass)

Note: we assume that the leaves are xyz particles

atom::Hierarchy IMP::multifit::create_coarse_molecule_from_density	(	em::DensityMap *	dmap,
		float	dens_threshold,
		int	num_beads,
		Model *	mdl,
		float	bead_radius
	)

Coarsen a density map based on voxels clustering.

Parameters

[in]	dmap	the density map to coarsen
[in]	dens_threshold	use only voxels above this threshold for clustering
[in]	num_beads	the number of beads
[in]	mdl	model to add the new molecule to
[in]	bead_radius	bead radius

atom::Hierarchy IMP::multifit::create_coarse_molecule_from_molecule	(	const atom::Hierarchy &	mh,
		int	num_beads,
		Model *	mdl,
		float	bead_radius,
		bool	add_conn_restraint = `false`
	)

Coarsen a molecule based on atom clustering.

Deprecated:

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Unused and will be removed.

Parameters

[in]	mh	the molecule to coarsen
[in]	num_beads	the output number of beads
[in]	mdl	model to add the new molecule to
[in]	bead_radius	bead radius
[in]	add_conn_restraint	if true a connectivity restraint between the particles of the new molecule is added

atom::Hierarchies IMP::multifit::create_coarse_molecules_from_molecules	(	const atom::Hierarchies &	mhs,
		int	frag_len,
		Model *	mdl,
		float	bead_radius,
		bool	add_conn_restraint = `false`
	)

Coarsen molecules based on atom clustering.

Deprecated:

As of IMP release 2.5. See the IMP Deprecation Policy for more information about deprecation in IMP. Unused and will be removed.

Parameters

[in]	mhs	the molecules to coarsen
[in]	frag_len	the number of beads for each molecule will be its number of residues / frag_len
[in]	mdl	model to add the new molecule to
[in]	bead_radius	bead radius
[in]	add_conn_restraint	if true a connectivity restraint between the particles of the new molecule is added

IMP::Restraint* IMP::multifit::create_weighted_excluded_volume_restraint	(	core::RigidBody	rb1,
		core::RigidBody	rb2,
		FloatKey	shell_key = `FloatKey("surf_ind")`
	)

Create a weighted excluded volume restraint between two rigid bodies.

Parameters

[in]	rb1	the first rigid body
[in]	rb2	the second rigid body
[in]	shell_key	the attribute that stored the particles surface level with respect to its molecule

multifit::FittingSolutionRecords IMP::multifit::fft_based_rigid_fitting	(	atom::Hierarchy	mol2fit,
		em::DensityMap *	dmap,
		double	density_threshold,
		double	angle_sampling_interval_rad
	)

FFT fit of a molecule in the density.

Parameters

[in]	mol2fit	a rigid body molecule to fit
[in]	dmap	the map to fit into
[in]	density_threshold	ignore density below this value
[in]	angle_sampling_interval_rad	sampling internal in radians

IntsList IMP::multifit::get_anchor_indices_matching_secondary_structure	(	const AnchorsData &	ad,
		const atom::SecondaryStructureResidues &	ssrs,
		Float	max_rmsd = `0.7`
	)

Get lists of anchors that match a sequence of secondary structures.

Parameters

[in]	ad	The AnchorsData
[in]	ssrs	The SecondaryStructureResidue particles to match
[in]	max_rmsd	SecondaryStructureResidue match must be below this value (0.816 is rmsd of known SSE to random)

void IMP::multifit::get_anchors_for_density	(	em::DensityMap *	dmap,
		int	number_of_means,
		float	density_threshold,
		std::string	pdb_filename,
		std::string	cmm_filename,
		std::string	seg_filename,
		std::string	txt_filename
	)

Generate anchors in several formats for a given density map.

FittingSolutionRecords IMP::multifit::get_close_to_point	(	const FittingSolutionRecords &	fit_sols,
		atom::Hierarchy	mh,
		IMP::Particle *	ap,
		Float	dist
	)

prune solutions by distance to an anchor point

Parameters

[in]	fit_sols	initial fitting solutions
[in]	mh	the molecule the fitting solutions apply for
[in]	ap	anchor point for which the transformed mh (fit) should be close to
[in]	dist	all fits such that the distance between ap and the fit center is smaller than dist will be included

Returns: the pruned fitting solutions

IntsList IMP::multifit::get_connected_components	(	em::DensityMap *	dmap,
		float	threshold,
		float	edge_threshold
	)

Return connected components based on density values.

Parameters

[in]	dmap	the density map to analyze
[in]	threshold	consider only voxels above this threshold
[in]	edge_threshold	an edge is added between two neighboring voxels if their density difference is below this threshold

Returns: List of indexes for each connected component

std::string IMP::multifit::get_data_path ( std::string file_name )

Return the full path to one of this module's data files.

To read the data file "data_library" that was placed in the data directory of this module, do something like

std::ifstream in(IMP::multifit::get_data_path("data_library"));

This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.

Note: Each module has its own data directory, so be sure to use this function from the correct module.

std::string IMP::multifit::get_example_path ( std::string file_name )

Return the full path to one of this module's example files.

To read the example file "example_protein.pdb" that was placed in the examples directory of this module, do something like

std::ifstream in(IMP::multifit::get_example_path("example_protein.pdb"));

This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.

Note: Each module has its own example directory, so be sure to use this function from the correct module.

ProteinsAnchorsSamplingSpace IMP::multifit::get_part_of_sampling_space	(	const ProteinsAnchorsSamplingSpace &	prots_ss,
		const Strings &	prot_names
	)

Get the sampling space of few of the proteins.

multifit::SettingsData* IMP::multifit::get_partial_assembly_setting_data	(	multifit::SettingsData *	prots_sd,
		const Strings &	prot_names
	)

Get the assembly data for a few of the proteins.

algebra::Vector3Ds IMP::multifit::get_points_close_to_molecule	(	const atom::Hierarchy &	mh,
		const algebra::Vector3Ds	points,
		Float	max_dist
	)

Given a molecule and a set of points, return the indexes of the points that are close to the molecule (up to max_dist) and the res

void IMP::multifit::get_segmentation	(	em::DensityMap *	dmap,
		double	apix,
		double	density_threshold,
		int	num_means,
		const std::string	pdb_filename,
		const std::string	cmm_filename,
		const std::string	seg_filename,
		const std::string	txt_filename
	)

Segment a density map using the anchor graph.

All voxels above the threshold are segmented into the given number of clusters, and neighboring clusters are linked.

Parameters

[in]	dmap	the density map to segment
[in]	apix	the map spacing in angstroms per pixel
[in]	density_threshold	consider only voxels over this threshold
[in]	num_means	the number of segments to generate
[in]	pdb_filename	write cluster centers as CA atoms in PDB format
[in]	cmm_filename	if not empty, write clusters in CMM format
[in]	seg_filename	if not empty, write segments in MRC format
[in]	txt_filename	if not empty, write anchors in text format

em::FittingSolutions IMP::multifit::pca_based_rigid_fitting	(	core::RigidBody	rb,
		Refiner *	rb_refiner,
		em::DensityMap *	em_map,
		Float	threshold,
		FloatKey	wei_key = `atom::Mass::get_mass_key()`,
		algebra::PrincipalComponentAnalysis	dens_pca_input = `algebra::PrincipalComponentAnalysis()`
	)

Compute fitting scores for a given set of rigid transformations.

Fit a protein to its density by principal component matching

Parameters

[in]	rb	The rigid body to be fitted
[in]	rb_refiner	The rigid body refiner
[in]	em_map	The density map to fit to
[in]	threshold	Use voxels above this threshold for PCA calculations
[in]	wei_key	The weight key of the particles in the rigid body
[in]	dens_pca_input	provide precalculated em_map PCA is available

Returns: fitting solutions

Note: the function assumes the density map holds its density

em::FittingSolutions IMP::multifit::pca_based_rigid_fitting	(	ParticlesTemp	ps,
		em::DensityMap *	em_map,
		Float	threshold,
		FloatKey	wei_key = `atom::Mass::get_mass_key()`,
		algebra::PrincipalComponentAnalysis	dens_pca_input = `algebra::PrincipalComponentAnalysis()`
	)

Compute fitting scores for a given set of rigid transformations.

Fit a protein to its density by principal component matching

Parameters

[in]	ps	The particles to fit (treated as rigid)
[in]	em_map	The density map to fit to
[in]	threshold	Use voxels above this threshold for PCA calculations
[in]	wei_key	The weight key of the particles in the rigid body
[in]	dens_pca_input	precalculated em_map PCA

Returns: fitting solutions

Note: the function assumes the density map holds its density

FittingSolutionRecords IMP::multifit::read_fitting_solutions ( const char * fitting_fn )

Fitting solutions reader.

IntsList IMP::multifit::read_paths	(	const char *	txt_filename,
		int	max_paths = `INT_MAX`
	)

Read paths.

Note: Notice that for the function to read the last line it should end with

ProteomicsData* IMP::multifit::read_proteomics_data ( const char * proteomics_fn )

Proteomics reader.

em::DensityMap* IMP::multifit::remove_background	(	em::DensityMap *	dmap,
		float	threshold,
		float	edge_threshold
	)

Returns a map containing all density without the background.

Parameters

[in]	dmap	the density map to segment
[in]	threshold	consider only voxels above this threshold
[in]	edge_threshold	consider only voxels above this threshold

Returns: the segmented map

void IMP::multifit::write_connolly_surface	(	atom::Atoms	atoms,
		TextOutput	fn,
		float	density,
		float	probe_radius
	)

Write the Connolly surface for a set of atoms to a file.

void IMP::multifit::write_fitting_solutions	(	const char *	fitting_fn,
		const FittingSolutionRecords &	fit_sols,
		int	num_sols = `-1`
	)

Write fitting solutions to a file.

Parameters

[in]	fitting_fn	the fitting filename
[in]	fit_sols	the fitting solutions to write to file
[in]	num_sols	optional, only write the first num_sols fits.

void IMP::multifit::write_segments_as_mrc	(	em::DensityMap *	dmap,
		const DataPointsAssignment &	dpa,
		Float	resolution,
		Float	apix,
		Float	threshold,
		const std::string &	filename
	)

Write segments in MRC format.

Note: segments are written as filename_0.mrc; an additional file filename.cmd is generated for easy loading of all segments

Detailed Description

multifit: command line tool

Web server

complex_to_anchor_graph

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Standard module functions

Typedef Documentation

Function Documentation