Detailed Description

This module contains functionality for dealing with atoms and proteins.

This module provides a variety of functionality for loading, creating, manipulating and scoring atomic structures. Molecules and collections of molecules are represented using Hierarchy particles. Whenever possible, one should prefer to use IMP::atom::Selection and related helper functions to manipulate molecules as that provides a simple and biologically relevant way of describing parts of molecules of interest.

Conventions

The name "residue index" is used to refer to the index of the residue in the conventional description of the protein, as opposed to its index among the set of residues which are found in the current molecule. The same concept is know as the "residue number" in pdb files. This index is not necessarily unique within a Chain, however, the combination of the residue index and insertion code should be.

Examples:

Author(s): Daniel Russel, Ben Webb, Dina Schneidman, Javier Velázquez-Muriel

Version: SVN.r12662 with Boost.FileSystem, cgal

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:

Daniel Russel, Keren Lasker, Ben Webb, Dina Schneidman, Javier Velázquez-Muriel, Andrej Sali, “Putting the pieces together: integrative structure determination of macromolecular assemblies”, PLoS Biology, 2012. This paper provides an overview of the key concepts in IMP and how to apply them to biological problems.
Frank Alber, Friedrich Foerster, Dmitry Korkin, Maya Topf, Andrej Sali, “Integrating diverse data for structure determination of macromolecular assemblies”, Annual Review of Biochemistry, 2008. This paper provides a review of the integrative structure determination methodology and various data sources that can be used.

Classes
class	AllMol2Selector
	Read all atoms. More...
class	AllPDBSelector
	Defines a selector that will pick every ATOM and HETATM record. More...
class	AndPDBSelector
	Select atoms which are selected by both selectors. More...
class	Angle
	A particle that describes an angle between three particles. More...
class	AngleSingletonScore
	Score the angle based on a UnaryFunction,. More...
class	Atom
	A decorator for a particle representing an atom. More...
class	ATOMPDBSelector
	Select all non-alternative ATOM records. More...
class	BerendsenThermostatOptimizerState
	Maintains temperature during molecular dynamics. More...
class	Bond
	A decorator for wrapping a particle representing a molecular bond. More...
class	Bonded
	A decorator for a particle which has bonds. More...
class	BondedPairFilter
	A filter for bonds. More...
class	BondEndpointsRefiner
	Return the endpoints of a bond. More...
class	BondGeometry
	Display an Bond particle as a segment. More...
class	BondGraph
	Represent a bond graph as a boost graph. More...
class	BondPairContainer
	A container that returns pairs of the endpoints of the bonds. More...
class	BondsGeometry
	Display an IMP::SingletonContainer of Bond particles as segments. More...
class	BondSingletonScore
	Score the bond based on a UnaryFunction,. More...
class	BrownianDynamics
	Simple Brownian dynamics optimizer. More...
class	CAlphaPDBSelector
	Select all CA ATOM records. More...
class	CBetaPDBSelector
	Select all CB ATOM records. More...
class	Chain
	Store info for a chain of a protein. More...
class	ChainPDBSelector
	Select all ATOM and HETATMrecords with the given chain ids. More...
class	Charged
	A decorator for a point particle that has an electrostatic charge. More...
class	CHARMMAtom
	A decorator for an atom that has a defined CHARMM type. More...
class	CHARMMAtomTopology
	A single atom in a CHARMM topology. More...
class	CHARMMBondEndpoint
	The end of a bond, angle, dihedral, improper, or internal coordinate. More...
struct	CHARMMBondParameters
	The parameters for a CHARMM bond or angle. More...
class	CHARMMConnection
	A connection (bond, angle, dihedral) between some number of endpoints. More...
struct	CHARMMDihedralParameters
	The parameters for a CHARMM dihedral or improper. More...
class	CHARMMIdealResidueTopology
	The ideal topology of a single residue. More...
class	CHARMMInternalCoordinate
	A geometric relationship between four atoms. More...
class	CHARMMParameters
	CHARMM force field parameters. More...
class	CHARMMPatch
	A CHARMM patch residue. More...
class	CHARMMResidueTopology
	The topology of a single residue in a model. More...
class	CHARMMResidueTopologyBase
	Base class for all CHARMM residue-based topology. More...
class	CHARMMSegmentTopology
	The topology of a single CHARMM segment in a model. More...
class	CHARMMStereochemistryRestraint
	Enforce CHARMM stereochemistry on the given Hierarchy. More...
class	CHARMMTopology
	The topology of a complete CHARMM model. More...
class	Copy
	A decorator for keeping track of copies of a molecule. More...
class	CoulombPairScore
	Coulomb (electrostatic) score between a pair of particles. More...
class	CoverBond
	Cover a bond with a sphere. More...
class	CPDBSelector
	Select all C (not CA or CB) ATOM records. More...
class	Diffusion
	A decorator for a diffusing particle. More...
class	Dihedral
	A particle that describes a dihedral angle between four particles. More...
class	DihedralSingletonScore
	Score the dihedral angle. More...
class	Domain
	A decorator to associate a particle with a part of a protein. More...
class	DopePairScore
class	ElementTable
class	ForceFieldParameters
	Storage and access to force field. More...
class	ForceSwitch
	Smooth interaction scores by switching the derivatives (force switch). More...
class	Fragment
	A decorator to associate a particle with a part of a protein/DNA/RNA. More...
class	HierarchiesGeometry
	Display an IMP::SingletonContainer of IMP::atom::Hierarchy particles as balls. More...
class	Hierarchy
	The standard decorator for manipulating molecular structures. More...
class	HierarchyGeometry
	Display an IMP::atom::Hierarchy particle as balls. More...
class	HydrogenPDBSelector
	Select all hydrogen ATOM and HETATM records. More...
class	ImproperSingletonScore
	Score the improper dihedral based on a UnaryFunction,. More...
class	LangevinThermostatOptimizerState
	Maintains temperature during molecular dynamics. More...
class	LennardJones
	A decorator for a particle that has a Lennard-Jones potential well. More...
class	LennardJonesPairScore
	Lennard-Jones score between a pair of particles. More...
class	Mass
	Add mass to a particle. More...
class	Mol2Selector
	A base class for choosing which Mol2 atoms to read. More...
class	MolecularDynamics
	Simple molecular dynamics optimizer. More...
class	Molecule
	A decorator for a molecule. More...
class	NonAlternativePDBSelector
	Select all ATOM and HETATM records which are not alternatives. More...
class	NonHydrogenMol2Selector
	Defines a selector that will pick only non-hydrogen atoms. More...
class	NonWaterNonHydrogenPDBSelector
	Select non water and non hydrogen atoms. More...
class	NonWaterPDBSelector
	Select all non-water non-alternative ATOM and HETATM records. More...
class	NotPDBSelector
	Select atoms which not selected by a given selector. More...
class	NPDBSelector
	Select all N ATOM records. More...
class	OrPDBSelector
	Select atoms which are selected by either selector. More...
class	PDBSelector
	Select which atoms to read from a PDB file. More...
class	PPDBSelector
	Select all P ATOM records. More...
class	ProteinLigandAtomPairScore
class	ProteinLigandRestraint
class	RemoveRigidMotionOptimizerState
	Removes rigid translation and rotation from the particles. More...
class	RemoveTranslationOptimizerState
	Removes rigid translation from the particles. More...
class	Residue
	A decorator for a residue. More...
class	RigidBodyDiffusion
class	RMSDCalculator
class	SameResiduePairFilter
class	Selection
class	SelectionGeometry
	Display a Selection. More...
class	Simulator
	The base class for simulators. More...
class	SmoothingFunction
	Base class for smoothing nonbonded interactions as a function of distance. More...
class	StereochemistryPairFilter
	A filter that excludes bonds, angles and dihedrals. More...
class	VelocityScalingOptimizerState
	Maintains temperature during molecular dynamics by velocity scaling. More...
class	WaterPDBSelector
	Select all non-water ATOM and HETATMrecords. More...
class	WritePDBFailureHandler
class	WritePDBOptimizerState
Estimator Functions
These functions allow you to estimate physical quantities relating to biomolecules.
enum	ProteinDensityReference { ALBER, HARPAZ, ANDERSSON, TSAI, QUILLIN, SQUIRE }
double	get_protein_density_from_reference (ProteinDensityReference densityReference)
double	get_volume_from_mass (double m, ProteinDensityReference ref=ALBER)
	Estimate the volume of a protein from its mass.
double	get_mass_from_volume (double v, ProteinDensityReference ref=ALBER)
	Estimate the mass of a protein from its volume.
double	get_mass_from_number_of_residues (unsigned int num_aa)
	Estimate the mass of a protein from the number of amino acids.
double	get_volume_from_residue_type (ResidueType rt)
	Return an estimate for the volume of a given residue.
PDB Reading
The read PDB methods produce a hierarchy that looks as follows: One Atom per ATOM or HETATM record in the PDB. All Atom particles have a parent which is a Residue. All Residue particles have a parent which is a Chain. Waters are currently dropped if they are ATOM records. This can be fixed. The read_pdb() functions should successfully parse all valid pdb files. It can produce warnings on files which are not valid. It will attempt to read such files, but all bets are off. When reading PDBs, PDBSelector objects can be used to choose to only process certain record types. See the class documentation for more information. When no PDB selector is supplied for reading, the NonWaterPDBSelector is used. Set the IMP::LogLevel to VERBOSE to see details of parse errors.
Hierarchy	read_pdb (base::TextInput in, Model *model)
Hierarchy	read_pdb (base::TextInput in, Model model, PDBSelector selector, bool select_first_model=true)
Hierarchies	read_multimodel_pdb (base::TextInput in, Model model, PDBSelector selector)
Hierarchies	read_multimodel_pdb (base::TextInput in, Model *model)
PDB Writing
The methods to write a PDBs expects a Hierarchy that looks as follows: all leaves are Atom particles all Atom particles have Residue particles as parents All Residue particles that have a Chain particle as an ancestor are considered part of a protein, DNA or RNA, ones without are considered heterogens. The functions produce files that are not valid PDB files, eg only ATOM/HETATM lines are printed for all Atom particles in the hierarchy. Complain if your favorite program can't read them and we might fix it.
void	write_pdb (Hierarchy mhd, base::TextOutput out, unsigned int model=0)
void	write_pdb (const Hierarchies &mhd, base::TextOutput out, unsigned int model=0)
void	write_multimodel_pdb (const Hierarchies &mhd, base::TextOutput out)
Simplification along backbone
These two methods create a simplified version of a molecule by merging residues sequentially. In one case every n residues are merged, in the other, the intervals are passed manually. The resulting molecule is not optimized by default and has no restraints automatically created. At the moment, the calls only support unmodified hierarchies loaded by read_pdb() which have only protein or DNA members. They return Hierarchy() if the input chain is empty.
Hierarchy	create_simplified_along_backbone (Chain in, int num_res)
Hierarchy	create_simplified_along_backbone (Chain in, const IntRanges &residue_segments)
Finding information
Get the attribute of the given particle or throw a ValueException if it is not applicable. The particle with the given information must be above the passed node.
std::string	get_molecule_name (Hierarchy h)
Ints	get_residue_indexes (Hierarchy h)
ResidueType	get_residue_type (Hierarchy h)
int	get_chain_id (Hierarchy h)
AtomType	get_atom_type (Hierarchy h)
std::string	get_domain_name (Hierarchy h)
int	get_copy_index (Hierarchy h)
Python Only
The following functions are only availale in Python as the equivalent C++ functionality is provided via template functions or in other ways that don't directly map to python.
void	show_molecular_hiearchy (Hierarchy h)
Mol2 IO
`IMP` can also read and write Mol2 files. As with read_pdb(), selector objects are used to determine which atoms are read. The read function produces a hierarchy containing the molecule. The write hierarchy writes all the Residue types in the hierarchy to the file.
Hierarchy	read_mol2 (base::TextInput mol2_file, Model model, Mol2Selector mol2sel=nullptr)
void	write_mol2 (Hierarchy rhd, base::TextOutput file_name)
Energy conversions
The native energy units in `IMP` are difficult to do any sort of math with. One can convert the quantities into more useful ones.
double	get_energy_in_femto_joules (double energy_in_kcal_per_mol)
double	get_force_in_femto_newtons (double force_in_kcal_per_mol_per_angstrom)
double	get_spring_constant_in_femto_newtons_per_angstrom (double k_in_kcal_per_mol_per_angstrom_square)
Protein-ligand scoring
`IMP` provides a statistical scoring function for scoring protein-ligand complexes. See the ligand scoring application for more information.
void	add_protein_ligand_score_data (Hierarchy h)
Dope scoring
`IMP` provides the DOPE scoring function for scoring proteins. Note: These are quite large objects as they store the whole DOPE lookup table. It is much better to share them between restraints than to create separate instances.
void	add_dope_score_data (atom::Hierarchy h)
Typedefs
typedef Key< 8974343, false >	AtomType
typedef CHARMMConnection< 3 >	CHARMMAngle
typedef CHARMMConnection< 2 >	CHARMMBond
typedef CHARMMConnection< 4 >	CHARMMDihedral
typedef boost::graph	HierarchyTree
typedef Key< 90784334, true >	ResidueType
Enumerations
enum	Element { UNKNOWN_ELEMENT = 0, H = 1, He = 2, Li = 3, Be = 4, B = 5, C = 6, N = 7, O = 8, F = 9, Ne = 10, Na = 11, Mg = 12, Al = 13, Si = 14, P = 15, S = 16, Cl = 17, Ar = 18, K = 19, Ca = 20, Sc = 21, Ti = 22, V = 23, Cr = 24, Mn = 25, Fe = 26, Co = 27, Ni = 28, Cu = 29, Zn = 30, Ga = 31, Ge = 32, As = 33, Se = 34, Br = 35, Kr = 36, Rb = 37, Sr = 38, Y = 39, Zr = 40, Nb = 41, Mo = 42, Tc = 43, Ru = 44, Rh = 45, Pd = 46, Ag = 47, Cd = 48, In = 49, Sn = 50, Sb = 51, Te = 52, I = 53, Xe = 54, Cs = 55, Ba = 56, La = 57, Ce = 58, Pr = 59, Nd = 60, Pm = 61, Sm = 62, Eu = 63, Gd = 64, Tb = 65, Dy = 66, Ho = 67, Er = 68, Tm = 69, Yb = 70, Lu = 71, Hf = 72, Ta = 73, W = 74, Re = 75, Os = 76, Ir = 77, Pt = 78, Au = 79, Hg = 80, Tl = 81, Pb = 82, Bi = 83, Po = 84, At = 85, Rn = 86, Fr = 87, Ra = 88, Ac = 89, Th = 90, Pa = 91, U = 92, Np = 93, Pu = 94, Am = 95, Cm = 96, Bk = 97, Cf = 98, Es = 99, Fm = 100, Md = 101, No = 102, Lr = 103, Db = 104, Jl = 105, Rf = 106 }
	The various elements currently supported/known. More...
enum	GetByType { ATOM_TYPE, RESIDUE_TYPE, CHAIN_TYPE, DOMAIN_TYPE, FRAGMENT_TYPE, XYZ_TYPE, XYZR_TYPE, MASS_TYPE }
Functions
AtomType	add_atom_type (std::string name, Element e)
	Create a new AtomType.
void	add_bonds (Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters())
void	add_radii (Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters(), FloatKey radius_key=FloatKey("radius"))
Bond	create_bond (Bonded a, Bonded b, Int t)
	Connect the two wrapped particles by a bond.
Bond	create_bond (Bonded a, Bonded b, Bond o)
	Connect the two wrapped particles by a custom bond.
Hierarchy	create_clone (Hierarchy d)
	Clone the Hierarchy.
Hierarchy	create_clone_one (Hierarchy d)
	Clone the node in the Hierarchy.
IMP::core::RigidBody	create_compatible_rigid_body (Hierarchy h, Hierarchy reference)
	Rigidify a molecule or collection of molecules.
Restraint *	create_connectivity_restraint (const Selections &s, double k)
Restraint *	create_connectivity_restraint (const Selections &s, double x0, double k)
core::XYZR	create_cover (Selection s, std::string name=std::string())
Bond	create_custom_bond (Bonded a, Bonded b, Float length, Float stiffness=-1)
	Connect the two wrapped particles by a custom bond.
Restraint *	create_distance_restraint (const Selection &n0, const Selection &n1, double x0, double k)
Restraint *	create_excluded_volume_restraint (const Hierarchies &hs, double resolution=-1)
Restraint *	create_excluded_volume_restraint (Selections ss)
Hierarchy	create_fragment (const Hierarchies &ps)
	Create a fragment containing the specified nodes.
Restraint *	create_internal_connectivity_restraint (const Selection &s, double k)
Restraint *	create_internal_connectivity_restraint (const Selection &s, double x0, double k)
Hierarchy	create_protein (Model *m, std::string name, double resolution, int number_of_residues, int first_residue_index=0, double volume=-1)
	Create a coarse grained molecule.
Hierarchy	create_protein (Model *m, std::string name, double resolution, const Ints domain_boundaries)
IMP::core::RigidBody	create_rigid_body (const Hierarchies &h, std::string name=std::string("created rigid body"))
	Rigidify a molecule or collection of molecules.
IMP::core::RigidBody	create_rigid_body (Hierarchy h)
void	destroy (Hierarchy d)
	Delete the Hierarchy.
void	destroy_bond (Bond b)
	Destroy the bond connecting to particles.
CHARMMParameters *	get_all_atom_CHARMM_parameters ()
Atom	get_atom (Residue rd, AtomType at)
	Return a particle atom from the residue.
bool	get_atom_type_exists (std::string name)
	Return true if that atom type already exists.
Bond	get_bond (Bonded a, Bonded b)
	Get the bond between two particles.
algebra::BoundingBoxD< 3 >	get_bounding_box (const Hierarchy &h)
	Get a bounding box for the Hierarchy.
algebra::Sphere3D	get_bounding_sphere (const Hierarchy &h)
Hierarchies	get_by_type (Hierarchy mhd, GetByType t)
Chain	get_chain (Hierarchy h)
Chain	get_chain (Residue rd, bool nothrow=false)
Atoms	get_charmm_untyped_atoms (Hierarchy hierarchy)
	Get all atoms in the Hierarchy that do not have CHARMM types.
FloatPair	get_component_placement_score (const core::XYZs &ref1, const core::XYZs &ref2, const core::XYZs &mdl1, const core::XYZs &mdl2)
	Measure the difference between two placements of the same set of points.
double	get_d_from_cm2_per_second (double din)
double	get_diffusion_angle (double D, double dtfs)
double	get_diffusion_length (double D, double t)
double	get_diffusion_length (double D, double force, double t)
template<class Vecto3DsOrXYZs0 , class Vecto3DsOrXYZs1 >
double	get_drms (const Vecto3DsOrXYZs0 &m1, const Vecto3DsOrXYZs1 &m2)
double	get_einstein_diffusion_coefficient (double r)
double	get_einstein_rotational_diffusion_coefficient (double r)
Element	get_element_for_atom_type (AtomType at)
ElementTable &	get_element_table ()
CHARMMParameters *	get_heavy_atom_CHARMM_parameters ()
HierarchyTree	get_hierarchy_tree (Hierarchy h)
Bonds	get_internal_bonds (Hierarchy mhd)
	Get the bonds internal to this tree.
bool	get_is_heterogen (Hierarchy h)
	Return true if the piece of hierarchy should be classified as a heterogen.
double	get_kb_t (double temperature)
	get kt
double	get_kd (double na, double nb, double nab, double volume)
Hierarchies	get_leaves (Hierarchy h)
Hierarchies	get_leaves (const Hierarchies &h)
double	get_mass (Selection h)
double	get_maximum_time_step_estimate (BrownianDynamics *bd)
double	get_molarity (double n, double volume)
template<class Vecto3DsOrXYZs0 , class Vecto3DsOrXYZs1 >
double	get_native_overlap (const Vecto3DsOrXYZs0 &m1, const Vecto3DsOrXYZs1 &m2, double threshold)
	Computes the native overlap between two sets of 3D points.
Hierarchy	get_next_residue (Residue rd)
char	get_one_letter_code (ResidueType c)
double	get_pairwise_rmsd_score (const core::XYZs &ref1, const core::XYZs &ref2, const core::XYZs &mdl1, const core::XYZs &mdl2)
	Measure the RMSD between two placements of the same set of points.
Atoms	get_phi_dihedral_atoms (Residue rd)
FloatPair	get_placement_score (const core::XYZs &from, const core::XYZs &to)
	Measure the difference between two placements of the same set of points.
Hierarchy	get_previous_residue (Residue rd)
Atoms	get_psi_dihedral_atoms (Residue rd)
double	get_radius_of_gyration (const ParticlesTemp &ps)
	Return the radius of gyration of a set of points.
double	get_radius_of_gyration (Selection h)
Residue	get_residue (Atom d, bool nothrow=false)
	Return the Residue containing this atom.
Hierarchy	get_residue (Hierarchy mhd, unsigned int index)
	Get the residue with the specified index.
ResidueType	get_residue_type (char c)
template<class Vecto3DsOrXYZs0 , class Vecto3DsOrXYZs1 >
double	get_rigid_bodies_drms (const Vecto3DsOrXYZs0 &m1, const Vecto3DsOrXYZs1 &m2, const IMP::IntRanges &ranges)
template<class Vecto3DsOrXYZs0 , class Vecto3DsOrXYZs1 >
double	get_rmsd (const Vecto3DsOrXYZs0 &m1, const Vecto3DsOrXYZs1 &m2, const IMP::algebra::Transformation3D &tr_for_second=IMP::algebra::get_identity_transformation_3d())
	Calculate the root mean square deviation between two sets of 3D points.
Hierarchy	get_root (Hierarchy h)
	Return the root of the hierarchy.
void	remove_charmm_untyped_atoms (Hierarchy hierarchy)
	Remove any atom from the Hierarchy that does not have a CHARMM type.
void	setup_as_approximation (Particle *h, const ParticlesTemp &other)
void	setup_as_approximation (Hierarchy h)
void	show (Hierarchy h, std::ostream &out=std::cout)
	Print out a molecular hierarchy.
void	transform (Hierarchy h, const algebra::Transformation3D &tr)
Variables
const ResidueType	UNK

Typedef Documentation

typedef boost::graph IMP::atom::HierarchyTree

A graph for representing a Hierarchy so you can view it nicely.

Enumeration Type Documentation

enum IMP::atom::Element

The various elements currently supported/known.

enum IMP::atom::GetByType

The different types which can be passed to get_by_type()

enum IMP::atom::ProteinDensityReference

Several protein density value references that have been proposed in the literature.

ALBER et al. (structure 2005) Estimated value 0.625 (1/1.60) Da/A3
HARPAZ et al. (1994) Computed value 0.826446=1/1.21 Da/A3
ANDERSSON and Hovm�ller (1998) Computed value 1.22 g/cm3 ~ 0.7347 Da/A3
TSAI et al. (1999) Computed value 1.40 g/cm3 ~ 0.84309 Da/A3
QUILLIN and Matthews (2000) Computed value 1.43 g/cm3 ~ 0.86116 Da/A3
SQUIRE and Himmel (1979), Gekko and Noguchi (1979) Experimental value 1.37 g/cm3 ~ 0.82503 Da/A3

Function Documentation

AtomType IMP::atom::add_atom_type	(	std::string	name,
		Element	e
	)

Create a new AtomType.

This creates a new AtomType (returned) and sets up the mapping between the AtomType and the proper element.

Note:: This method has not been tested. If you use it, please write a test and remove this comment.

See also:: atom_type_exists()

void add_bonds	(	Hierarchy	d,
		const ForceFieldParameters *	ffp = `get_all_atom_CHARMM_parameters()`
	)

Add bonds using definitions from given force field parameters. Note that, at the moment, all added bonds are reported as IMP::Bond::SINGLE, whether or not they actually are.

void IMP::atom::add_dope_score_data ( atom::Hierarchy h )

Add the dope atom types to the atoms in the hierarchy.

void add_radii	(	Hierarchy	d,
		const ForceFieldParameters *	ffp = `get_all_atom_CHARMM_parameters()`,
		FloatKey	radius_key = `FloatKey("radius")`
	)

Add vdW radius from given force field.

Hierarchy create_clone ( Hierarchy d )

Clone the Hierarchy.

This method copies the Bond, Bonded, Atom, Residue, and Domain data and the particle name to the new copies in addition to the Hierarchy relationships.

Hierarchy create_clone_one ( Hierarchy d )

Clone the node in the Hierarchy.

This method copies the Atom, Residue, Chain and Domain data and the particle name.

IMP::core::RigidBody IMP::atom::create_compatible_rigid_body	(	Hierarchy	h,
		Hierarchy	reference
	)

Rigidify a molecule or collection of molecules.

This method is identical to create_rigid_body() except that the chosen reference frame is aligned with that of reference (which must have exactly the same set of particles). This allows one to make sure the rigid body is equivalent when you have several copies of the same molecule.

IMP::atom::create_connectivity_restraint	(	const Selections &	s,
		double	k
	)

Create a restraint connecting the selections.

If one or more of the selections is a rigid body, this will be used to accelerate the computation.

Examples: dependency graph, setup, nup84 cg, nup84 rb

Restraint * create_connectivity_restraint	(	const Selections &	s,
		double	x0,
		double	k
	)

Create a restraint connecting the selections. The particles are allowed to be appart by x0 and still count as connected.

If one or more of the selections is a rigid body, this will be used to accelerate the computation.

IMP::atom::create_cover	(	Selection	s,
		std::string	name = `std::string()`
	)

Create an XYZR particle which always includes the particles in the selection in its bounding volume. If all the particles in the selection are part of the same rigid body, then the created particle is added as part of that rigid body. Otherwise it uses an IMP::core::Cover to maintain the cover property.

Doing this can be a useful way to accelerate computations when it is OK to replace a potential complicated set of geometry represented by the selection with a much simpler one.

Examples: markers

IMP::atom::create_distance_restraint	(	const Selection &	n0,
		const Selection &	n1,
		double	x0,
		double	k
	)

Create a distance restraint between the selections.

If one or more of the selections is a rigid body, this will be used to accelerate the computation.

Examples: dependency graph, rigid brownian dynamics, setup, nup84 cg, nup84 rb

IMP::atom::create_excluded_volume_restraint	(	const Hierarchies &	hs,
		double	resolution = `-1`
	)

Create an excluded volume restraint for the included molecules. If a value is provided for resolution, then something less than the full resolution representation will be used.

If one or more of the selections is a rigid body, this will be used to accelerate the computation.

Examples: dependency graph, setup, nup84 cg, nup84 rb

Restraint* IMP::atom::create_excluded_volume_restraint ( Selections ss )

Create an excluded volume restraint for a list of selections.

Restraint * create_internal_connectivity_restraint	(	const Selection &	s,
		double	k
	)

Create a restraint connecting the selection.

If one or more of the selections is a rigid body, this will be used to accelerate the computation.

Restraint * create_internal_connectivity_restraint	(	const Selection &	s,
		double	x0,
		double	k
	)

Create a restraint connecting the selection. The particles are allowed to be appart by x0 and still count as connected.

If one or more of the selections is a rigid body, this will be used to accelerate the computation.

IMP::atom::create_protein	(	Model *	m,
		std::string	name,
		double	resolution,
		int	number_of_residues,
		int	first_residue_index = `0`,
		double	volume = `-1`
	)

Create a coarse grained molecule.

The coarse grained model is created with a number of spheres based on the resolution and the volume. If the volume is not provided it is estimated based on the number of residues. The protein is created as a molecular hierarchy rooted at p. The leaves are Domain particles with appropriate residue indexes stored and are XYZR particles.

Volume is, as usual, in cubic anstroms.

Currently the function creates a set of balls with radii no greater than resolution which overlap by 20% and have a volume of their union equal to the passed volume.

The coordinates of the balls defining the protein are optimized by default, and have garbage coordinate values.

Warning: create_protein has not been well tested yet: Use with caution and please report any bugs found.

Warning: create_protein has not been stabilized and is likely to change without notice.

Examples: dependency graph, setup, nup84 cg, nup84 rb

Hierarchy IMP::atom::create_protein	(	Model *	m,
		std::string	name,
		double	resolution,
		const Ints	domain_boundaries
	)

Like the former create_protein(), but it enforces domain splits at the provide domain boundairs. The domain boundaries should be the start of the first domain, any boundies, and then one past the end of the last domain.

IMP::core::RigidBody IMP::atom::create_rigid_body	(	const Hierarchies &	h,
		std::string	name = `std::string("created rigid body")`
	)

Rigidify a molecule or collection of molecules.

The rigid body created has all the leaves as members and a member rigid body for each internal node in the tree. The particle created to be the rigid body is returned.

A name can be passed as it is not easy to automatically pick a decent name.

See also:: create_aligned_rigid_body()

IMP::core::RigidBody IMP::atom::create_rigid_body ( Hierarchy h )

See also:: create_rigid_body(const Hierarchies&)

IMP::atom::create_simplified_along_backbone	(	Chain	in,
		int	num_res
	)

Simplify every num_res into one particle.

Examples: dependency graph, displaying ensembles, cg pdb, molecular hierarchy, setup, nup84 rb

Hierarchy IMP::atom::create_simplified_along_backbone	(	Chain	in,
		const IntRanges &	residue_segments
	)

Simplify by breaking at the boundaries provided.

IMP::atom::destroy ( Hierarchy d )

Delete the Hierarchy.

All bonds connecting to these atoms are destroyed as are hierarchy links in the Hierarchy and the particles are removed from the Model.

Examples: dependency graph, displaying ensembles, cg pdb, molecular hierarchy, setup, nup84 rb

CHARMMParameters* IMP::atom::get_all_atom_CHARMM_parameters ( )

The default CHARMM parameters support normal amino acid and nucleic acid residues and the atoms found in them. To use CHARMM with heterogens or non-standard residues, a different CHARMM parameters file must be used.

See also:: get_heavy_atom_CHARMM_parameters()

Atom get_atom	(	Residue	rd,
		AtomType	at
	)

Return a particle atom from the residue.

The residue must be part of a molecular hierarchy.

bool IMP::atom::get_atom_type_exists ( std::string name )

Return true if that atom type already exists.

algebra::BoundingBoxD< 3 > IMP::atom::get_bounding_box ( const Hierarchy & h )

Get a bounding box for the Hierarchy.

This bounding box is that of the highest (in the CS sense of a tree growing down from the root) cut through the tree where each node in the cut has x,y,z, and r. That is, if the root has x,y,z,r then it is the bounding box of that sphere. If only the leaves have radii, it is the bounding box of the leaves. If no such cut exists, the behavior is undefined.

algebra::Sphere3D get_bounding_sphere ( const Hierarchy & h )

See get_bounding_box() for more details.

Chain IMP::atom::get_chain ( Hierarchy h )

Get the containing chain or Chain() if there is none

Chain get_chain	(	Residue	rd,
		bool	nothrow = `false`
	)

Return the chain containing the residue.

Exceptions:

ValueException if no residue is found, unless nothrow is true.

Atoms IMP::atom::get_charmm_untyped_atoms ( Hierarchy hierarchy )

Get all atoms in the Hierarchy that do not have CHARMM types.

Returns:: a list of every Atom in the given Hierarchy that is not also a CHARMMAtom.

See also:: remove_charmm_untyped_atoms

FloatPair IMP::atom::get_component_placement_score	(	const core::XYZs &	ref1,
		const core::XYZs &	ref2,
		const core::XYZs &	mdl1,
		const core::XYZs &	mdl2
	)

Measure the difference between two placements of the same set of points.

Parameters:

[in]	ref1	The reference placement of the first component represented by XYZ coordinates
[in]	ref2	The reference placement of the second component represented by XYZ coordinates
[in]	mdl1	The modeled placement of the first component represented by XYZ coordinates
[in]	mdl2	The modeled placement of the second component represented by XYZ coordinates

Returns:: the function returns (distance score,angle score)

Note:: The measure quantifies the difference between the relative placements of two components compared to a reference relative placement. First, the two compared structures are brought into the same frame of reference by superposing the first pair of equivalent domains (ref1 and mdl1). Next, the distance and angle scores are calculated for the second component using placement_score.; see Topf, Lasker et al Structure, 2008 for details

double IMP::atom::get_diffusion_angle	(	double	D,
		double	dtfs
	)

Get the standard deviation of the diffusion angle change given the rigid body diffusion coefficient and the time step.

double IMP::atom::get_diffusion_length	(	double	D,
		double	t
	)

Return the standard deviation for the Brownian step given the diffusion coefficient and the time step.

double IMP::atom::get_diffusion_length	(	double	D,
		double	force,
		double	t
	)

Return the scale for diffusion under the specified force.

template<class Vecto3DsOrXYZs0 , class Vecto3DsOrXYZs1 >

double IMP::atom::get_drms	(	const Vecto3DsOrXYZs0 &	m1,
		const Vecto3DsOrXYZs1 &	m2
	)

Distance-RMS between two sets of points, defined as: sqrt( sum[ (d1ij**2 - d2ij**2)**2]/(4 * sum[d1ij**2]) ) (Levitt, 1992) d1ij - distance between points i and j in set m1 (the "reference" set) d2ij - distance between points i and j in set m2

Parameters:

[in]	m1	set of points
[in]	m2	set of points

double IMP::atom::get_einstein_diffusion_coefficient ( double r )

Return the prediction diffusion coefficient in Angstrom squared per femtosecond given a radius in angstrom. See wikipedia for a reference.

double IMP::atom::get_einstein_rotational_diffusion_coefficient ( double r )

Return the prediction diffusion coefficient in radians squared per femtosecond given a radius in angstrom.

CHARMMParameters* IMP::atom::get_heavy_atom_CHARMM_parameters ( )

The default CHARMM parameters support normal amino acid and nucleic acid residues and the atoms found in them. To use CHARMM with heterogens or non-standard residues, a different CHARMM parameters file must be used.

No hydrogen parameters are read.

See also:: get_all_atom_CHARMM_parameters();

HierarchyTree get_hierarchy_tree ( Hierarchy h )

Get a graph for the passed Hierarchy. This can be used, for example, to graphically display the hierarchy in 2D.

Bonds get_internal_bonds ( Hierarchy mhd )

Get the bonds internal to this tree.

See also:: Bond

bool IMP::atom::get_is_heterogen ( Hierarchy h )

Return true if the piece of hierarchy should be classified as a heterogen.

For the purposes of classification, a heterogen is anything that

is a heterogen atom (one whose name starts with HET:)
is or is part of a Residue that is not a normal protein, rna or dna residue
or is not part of a Chain For the moment, this can only be called on residues or atoms.

double IMP::atom::get_kb_t ( double temperature )

get kt

double IMP::atom::get_kd	(	double	na,
		double	nb,
		double	nab,
		double	volume
	)

Compute the concentration in molarity from the passed values

IMP::atom::get_leaves ( Hierarchy h )

Examples: dependency graph, displaying ensembles, adding data, shared functions, dock with crosslinks, collision cross section, pdb, setup, nup84 cg, nup84 rb, analyze 0

Hierarchies get_leaves ( const Hierarchies & h )

double get_mass ( Selection h )

Get the total mass of a hierarchy. In daltons.

double IMP::atom::get_mass_from_number_of_residues ( unsigned int num_aa )

Estimate the mass of a protein from the number of amino acids.

We use an estimate of 110 Daltons per residue, following Chimera.

The mass is in Daltons.

double IMP::atom::get_mass_from_volume	(	double	v,
		ProteinDensityReference	ref = `ALBER`
	)

Estimate the mass of a protein from its volume.

Parameters:

[in]	v	the volume for which we want to output the corresponding mass
[in]	ref	the protein density reference used in the computation. As a default ref is the estimate published in Alber et. al, Structure 2005.

double IMP::atom::get_maximum_time_step_estimate ( BrownianDynamics * bd )

Repeatedly run the current model with brownian dynamics at different time steps to try to find the maximum time step that can be used without the model exploding.

double IMP::atom::get_molarity	(	double	n,
		double	volume
	)

Compute the concentration in molarity from the passed values

template<class Vecto3DsOrXYZs0 , class Vecto3DsOrXYZs1 >

double IMP::atom::get_native_overlap	(	const Vecto3DsOrXYZs0 &	m1,
		const Vecto3DsOrXYZs1 &	m2,
		double	threshold
	)

Computes the native overlap between two sets of 3D points.

Parameters:

[in]	m1	first set
[in]	m2	second set
[in]	threshold	threshold distance (amstrongs) for the calculation

Note:: The result is returned as a percentage (from 0 to 100); the function assumes correspondence between two sets of points and does not perform rigid alignment.

Hierarchy get_next_residue ( Residue rd )

Return the residue from the same chain with one higher index, or Hierarchy().

Note:: Currently, this function only works if the parent of rd is the chain. This should be fixed later. Ask if you need it.

The return type is Hierarchy since the particle representing the next residue might not be a Residue particle.

char IMP::atom::get_one_letter_code ( ResidueType c )

Get the 1-letter amino acid code from the residue type.

double IMP::atom::get_pairwise_rmsd_score	(	const core::XYZs &	ref1,
		const core::XYZs &	ref2,
		const core::XYZs &	mdl1,
		const core::XYZs &	mdl2
	)

Measure the RMSD between two placements of the same set of points.

Parameters:

[in]	ref1	The reference placement of the first component represented by XYZ coordinates
[in]	ref2	The reference placement of the second component represented by XYZ coordinates
[in]	mdl1	The modeled placement of the first component represented by XYZ coordinates
[in]	mdl2	The modeled placement of the second component represented by XYZ coordinates

Note:: The measure quantifies the RMSD between the relative placements of two components compared to a reference relative placement. First, the two compared structures are brought into the same frame of reference by superposing the first pair of equivalent domains (ref1 and mdl1). Next, the RMSD is calculated for the second component; see Lasker et al JMB, 2009 for details

Atoms get_phi_dihedral_atoms ( Residue rd )

Return the atoms comprising the phi dihedral. If all atoms cannot be found, an empty list is returned.

FloatPair IMP::atom::get_placement_score	(	const core::XYZs &	from,
		const core::XYZs &	to
	)

Measure the difference between two placements of the same set of points.

Parameters:

[in]	from	The reference placement represented by XYZ coordinates
[in]	to	The modeled placement represented by XYZ coordinates

Note:: The measure quantifies the difference between placements of the same structure. A rigid transformation that brings mdl1 to ref1 is reported.

Returns:: (d,a), A transformation from mdl to ref represented by a a distance (d) and an angle (a). d is the distance bewteen the centroids of the two placements and a is the axis angle of the rotation matrix between the two placements

Note:: see Lasker,Topf et al JMB, 2009 for details

Hierarchy get_previous_residue ( Residue rd )

Return the residue from the same chain with one lower index, or Hierarchy().

See also:: get_next_residue

double IMP::atom::get_protein_density_from_reference ( ProteinDensityReference densityReference )

returns the protein density value (in Da/A^3) associated with a given reference

Atoms get_psi_dihedral_atoms ( Residue rd )

Return the atoms comprising the psi dihedral. If all atoms cannot be found, an empty list is returned.

double IMP::atom::get_radius_of_gyration ( const Vector3Ds & ps )

Return the radius of gyration of a set of points.

Compute the radius of gyration of a set of particles with (optional) radii and mass and (non-optional) coordinates. Either all particles must have mass or none of them.

See also:: IMP::atom::get_radius_of_gyration()

Residue get_residue	(	Atom	d,
		bool	nothrow = `false`
	)

Return the Residue containing this atom.

The atom must be part of a molecular hierarchy.

Exceptions:

ValueException if no residue is found, unless nothrow is true.

ResidueType IMP::atom::get_residue_type ( char c )

Get the residue type from the 1-letter amino acid code.

Exceptions:

ValueException if an invalid character is passed.

template<class Vecto3DsOrXYZs0 , class Vecto3DsOrXYZs1 >

double IMP::atom::get_rigid_bodies_drms	(	const Vecto3DsOrXYZs0 &	m1,
		const Vecto3DsOrXYZs1 &	m2,
		const IMP::IntRanges &	ranges
	)

DRMS between to sets of rigid bodies. Points ij belonging to the same rigid body are not evaluated, as they are the same in both sets

Parameters:

[in]	m1	set of points
[in]	m2	set of points
[in]	ranges	of points considered to be the same rigid body. Eg, (0-29,30-49) means two rigid bodies, first with the 30 first atoms, second with the last 20

template<class Vecto3DsOrXYZs0 , class Vecto3DsOrXYZs1 >

double IMP::atom::get_rmsd	(	const Vecto3DsOrXYZs0 &	m1,
		const Vecto3DsOrXYZs1 &	m2,
		const IMP::algebra::Transformation3D &	tr_for_second = `IMP::algebra::get_identity_transformation_3d()`
	)

Calculate the root mean square deviation between two sets of 3D points.

Note:: the function assumes correspondence between the two sets of points and does not perform rigid alignment.

Hierarchy get_root ( Hierarchy h )

Return the root of the hierarchy.

double IMP::atom::get_volume_from_mass	(	double	m,
		ProteinDensityReference	ref = `ALBER`
	)

Estimate the volume of a protein from its mass.

Parameters:

[in]	m	the mass for which we want to output the corresponding volume
[in]	ref	the protein density reference used in the computation. As a default ref is the estimate published in Alber et. al, Structure 2005.

double IMP::atom::get_volume_from_residue_type ( ResidueType rt )

Return an estimate for the volume of a given residue.

The volume estimates are taken from Pontius J, Richelle J, Wodak SJ., Deviations from standard atomic volumes as a quality measure for protein crystal structures, J Mol Biol. 1996 Nov 22;264(1):121-36.

Exceptions:

ValueException if a non-standard residue type is passed

IMP::atom::read_pdb	(	base::TextInput	in,
		Model *	model
	)

Read a all the molecules in the first model of the pdb file.

Examples: cover particles, dependency graph, charmm forcefield verbose, generate density map of fixed dimension, profile, displaying ensembles, rigid bodies, score protein with ligand, markers, cg pdb, adding data, dock with crosslinks, profile fit, pdb, pdb2density, molecular hierarchy, charmm forcefield, local fitting, assess dope, rigid body excluded volume, setup, fit restraint, nup84 rb, load protein restrain bonds

void IMP::atom::remove_charmm_untyped_atoms ( Hierarchy hierarchy )

Remove any atom from the Hierarchy that does not have a CHARMM type.

See also:: get_charmm_untyped_atoms, CHARMMTopology::add_missing_atoms

void IMP::atom::setup_as_approximation	(	Particle *	h,
		const ParticlesTemp &	other
	)

Set the mass, radius, residues, and coordinates to approximate the passed particles.

void setup_as_approximation ( Hierarchy h )

Set the mass, radius, residues, and coordinates to approximate the passed particle based on the leaves of h.

void show	(	Hierarchy	h,
		std::ostream &	out = `std::cout`
	)

Print out a molecular hierarchy.

void IMP::atom::show_molecular_hiearchy ( Hierarchy h )

Print out the molecular hierarchy. Equivalent to

IMP::core::show(h);

void IMP::atom::transform	(	Hierarchy	h,
		const algebra::Transformation3D &	tr
	)

Transform a hierarchy. This is aware of rigid bodies.

IMP::atom::write_pdb	(	Hierarchy	mhd,
		base::TextOutput	out,
		unsigned int	model = `0`
	)

Examples: cg pdb, dock with crosslinks, local fitting, structure from sequence

Variable Documentation

const ResidueType IMP::atom::UNK

Unknown residue

Detailed Description

Conventions

Classes

Estimator Functions

PDB Reading

PDB Writing

Simplification along backbone

Finding information

Python Only

Mol2 IO

Energy conversions

Protein-ligand scoring

Dope scoring

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation