See IMP.atom Overview for more information.

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	AtomType
	The type of an atom. 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	ResidueType
	The type for a residue. More...

class	RigidBodyDiffusion

class	RMSDCalculator
	Used to calculate rmsd between multiple transformation that operate on the same particles. More...

class	SameResiduePairFilter

class	SecondaryStructureResidue
	A decorator for a residue with probability of secondary structure. More...

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	WritePDBOptimizerState

Typedefs
typedef IMP::base::Vector < IMP::base::Pointer < AngleSingletonScore > >	AngleSingletonScores

typedef Key< 8974343, false >	AtomType

typedef IMP::base::Vector < AtomType >	AtomTypes

typedef IMP::base::Vector < IMP::base::Pointer < BerendsenThermostatOptimizerState > >	BerendsenThermostatOptimizerStates

typedef IMP::base::Vector < IMP::base::Pointer < BondedPairFilter > >	BondedPairFilters

typedef IMP::base::Vector < IMP::base::Pointer < BondEndpointsRefiner > >	BondEndpointsRefiners

typedef IMP::base::Vector < IMP::base::Pointer < BondPairContainer > >	BondPairContainers

typedef IMP::base::Vector < IMP::base::Pointer < BondSingletonScore > >	BondSingletonScores

typedef CHARMMConnection< 3 >	CHARMMAngle

typedef IMP::base::Vector < CHARMMAngle >	CHARMMAngles

typedef IMP::base::Vector < CHARMMAtomTopology >	CHARMMAtomTopologies

typedef CHARMMConnection< 2 >	CHARMMBond

typedef IMP::base::Vector < CHARMMBondEndpoint >	CHARMMBondEndpoints

typedef IMP::base::Vector < CHARMMBondParameters >	CHARMMBondParametersList

typedef IMP::base::Vector < CHARMMBond >	CHARMMBonds

typedef CHARMMConnection< 4 >	CHARMMDihedral

typedef IMP::base::Vector < CHARMMDihedralParameters >	CHARMMDihedralParametersList

typedef IMP::base::Vector < CHARMMDihedral >	CHARMMDihedrals

typedef IMP::base::Vector < IMP::base::Pointer < CHARMMIdealResidueTopology > >	CHARMMIdealResidueTopologies

typedef IMP::base::Vector < CHARMMInternalCoordinate >	CHARMMInternalCoordinates

typedef IMP::base::Vector < IMP::base::Pointer < CHARMMParameters > >	CHARMMParametersList

typedef IMP::base::Vector < IMP::base::Pointer < CHARMMPatch > >	CHARMMPatches

typedef IMP::base::Vector < IMP::base::Pointer < CHARMMResidueTopology > >	CHARMMResidueTopologies

typedef IMP::base::Vector < IMP::base::Pointer < CHARMMResidueTopologyBase > >	CHARMMResidueTopologyBases

typedef IMP::base::Vector < IMP::base::Pointer < CHARMMSegmentTopology > >	CHARMMSegmentTopologies

typedef IMP::base::Vector < IMP::base::Pointer < CHARMMTopology > >	CHARMMTopologies

typedef IMP::base::Vector < IMP::base::Pointer < CoulombPairScore > >	CoulombPairScores

typedef IMP::base::Vector < IMP::base::Pointer < CoverBond > >	CoverBonds

typedef IMP::base::Vector < IMP::base::Pointer < DihedralSingletonScore > >	DihedralSingletonScores

typedef boost::graph	HierarchyTree

typedef HierarchyTree::EdgeNameMap	HierarchyTreeConstEdgeName

typedef HierarchyTree::VertexNameMap	HierarchyTreeConstVertexName

typedef HierarchyTree::edge_descriptor	HierarchyTreeEdge

typedef boost::graph_traits < HierarchyTree >	HierarchyTreeTraits

typedef HierarchyTree::vertex_descriptor	HierarchyTreeVertex

typedef IMP::base::Vector < IMP::base::Pointer < ImproperSingletonScore > >	ImproperSingletonScores

typedef IMP::base::Vector < IMP::base::Pointer < LangevinThermostatOptimizerState > >	LangevinThermostatOptimizerStates

typedef IMP::base::Vector < IMP::base::Pointer < LennardJonesPairScore > >	LennardJonesPairScores

typedef IMP::base::Vector < IMP::base::Pointer < PDBSelector > >	PDBSelectors

typedef IMP::base::Vector < IMP::base::Pointer < RemoveRigidMotionOptimizerState > >	RemoveRigidMotionOptimizerStates

typedef IMP::base::Vector < IMP::base::Pointer < RemoveTranslationOptimizerState > >	RemoveTranslationOptimizerStates

typedef Key< 90784334, true >	ResidueType

typedef IMP::base::Vector < ResidueType >	ResidueTypes

typedef IMP::base::Vector < RMSDCalculator >	RMSDCalculators

typedef IMP::base::Vector < Selection >	Selections

typedef IMP::base::Vector < IMP::base::Pointer < Simulator > >	Simulators

typedef IMP::base::Vector < IMP::base::Pointer < VelocityScalingOptimizerState > >	VelocityScalingOptimizerStates

typedef IMP::base::Vector < IMP::base::Pointer < WritePDBOptimizerState > >	WritePDBOptimizerStates

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.

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. More...

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. More...

Bond	create_bond (Bonded a, Bonded b, Bond o)
	Connect the two wrapped particles by a custom bond. More...

Hierarchy	create_clone (Hierarchy d)
	Clone the Hierarchy. More...

Hierarchy	create_clone_one (Hierarchy d)
	Clone the node in the Hierarchy. More...

IMP::core::RigidBody	create_compatible_rigid_body (Hierarchy h, Hierarchy reference)
	Rigidify a molecule or collection of molecules. More...

Restraint *	create_connectivity_restraint (const Selections &s, double k, std::string name="Connectivity%1%")

Restraint *	create_connectivity_restraint (const Selections &s, double x0, double k, std::string name="Connectivity%1%")

core::XYZR	create_cover (const 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. More...

Restraint *	create_distance_restraint (const Selection &n0, const Selection &n1, double x0, double k, std::string name="Distance%1%")

Restraint *	create_excluded_volume_restraint (const Hierarchies &hs, double resolution=-1)

Restraint *	create_excluded_volume_restraint (const Selections &s)

Hierarchy	create_fragment (const Hierarchies &ps)
	Create a fragment containing the specified nodes. More...

Restraint *	create_internal_connectivity_restraint (const Selection &s, double k, std::string name="Connectivity%1%")

Restraint *	create_internal_connectivity_restraint (const Selection &s, double x0, double k, std::string name="Connectivity%1%")

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. More...

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. More...

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

void	destroy (Hierarchy d)
	Delete the Hierarchy. More...

void	destroy_bond (Bond b)
	Destroy the bond connecting to particles. More...

CHARMMParameters *	get_all_atom_CHARMM_parameters ()

Atom	get_atom (Residue rd, AtomType at)
	Return a particle atom from the residue. More...

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. More...

algebra::BoundingBoxD< 3 >	get_bounding_box (const Hierarchy &h)
	Get a bounding box for the Hierarchy. More...

algebra::Sphere3D	get_bounding_sphere (const Hierarchy &h)

Hierarchies	get_by_type (Hierarchy mhd, GetByType t)

Chain	get_chain (Hierarchy h)

Atoms	get_charmm_untyped_atoms (Hierarchy hierarchy)
	Get all atoms in the Hierarchy that do not have CHARMM types. More...

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. More...

std::string	get_data_path (std::string file_name)
	Return the full path to installed data. More...

double	get_diffusion_angle (double D, double dtfs)

double	get_diffusion_coefficient (const algebra::Vector3Ds &displacements, double dt)

double	get_diffusion_coefficient_from_cm2_per_second (double din)

double	get_diffusion_length (double D, double t)

double	get_diffusion_length (double D, double force, double t, double temp=273)

template<class Vector3DsOrXYZs0 , class Vector3DsOrXYZs1 >
double	get_drms (const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)

template<class Vector3DsOrXYZs0 , class Vector3DsOrXYZs1 >
double	get_drmsd (const Vector3DsOrXYZs0 &m0, const Vector3DsOrXYZs1 &m1)
	Calculate the root mean square deviation between two sets of 3D points. More...

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 ()

std::string	get_example_path (std::string file_name)
	Return the path to installed example data for this module. More...

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. More...

bool	get_is_heterogen (Hierarchy h)
	Return true if the piece of hierarchy should be classified as a heterogen. More...

double	get_kd (double na, double nb, double nab, double volume)

double	get_kt (double T)

Hierarchies	get_leaves (const Selection &h)

Hierarchies	get_leaves (Hierarchy h)

Hierarchies	get_leaves (const Hierarchies &h)

double	get_mass (const Selection &s)

double	get_maximum_time_step_estimate (BrownianDynamics *bd)

double	get_molarity (double n, double volume)

template<class Vector3DsOrXYZs0 , class Vector3DsOrXYZs1 >
double	get_native_overlap (const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, double threshold)
	Computes the native overlap between two sets of 3D points. More...

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. More...

Atoms	get_phi_dihedral_atoms (Residue rd)

FloatPair	get_placement_score (const core::XYZs &source, const core::XYZs &target)
	Measure the difference between two placements of the same set of points. More...

Hierarchy	get_previous_residue (Residue rd)

Atoms	get_psi_dihedral_atoms (Residue rd)

double	get_radius_of_gyration (const ParticlesTemp &ps)

double	get_radius_of_gyration (const Selection &s)

Residue	get_residue (Atom d, bool nothrow=false)
	Return the Residue containing this atom. More...

Hierarchy	get_residue (Hierarchy mhd, unsigned int index)
	Get the residue with the specified index. More...

ResidueType	get_residue_type (char c)

template<class Vector3DsOrXYZs0 , class Vector3DsOrXYZs1 >
double	get_rigid_bodies_drms (const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, const IMP::IntRanges &ranges)

template<class Vector3DsOrXYZs0 , class Vector3DsOrXYZs1 >
double	get_rmsd (const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &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. More...

double	get_rmsd (const Selection &s0, const Selection &s1, const IMP::algebra::Transformation3D &tr_for_second=IMP::algebra::get_identity_transformation_3d())

Hierarchy	get_root (Hierarchy h)
	Return the root of the hierarchy. More...

double	get_rotational_diffusion_coefficient (const algebra::Rotation3Ds &displacements, double dt)

Float	get_secondary_structure_match_score (SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2)

double	get_surface_area (const Selection &s)

HierarchyTreeVertexIndex	get_vertex_index (const HierarchyTree &g)

double	get_volume (const Selection &s)

void	remove_charmm_untyped_atoms (Hierarchy hierarchy)
	Remove any atom from the Hierarchy that does not have a CHARMM type. More...

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

void	setup_as_approximation (Hierarchy h)

SecondaryStructureResidue	setup_coarse_secondary_structure_residue (const Particles &ssr_ps, Model *mdl, bool winner_takes_all_per_res=false)

SecondaryStructureResidues	setup_coarse_secondary_structure_residues (const Particles &ssr_ps, Model *mdl, int coarse_factor, int start_res_num, bool winner_takes_all_per_res=false)

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

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

std::string	get_module_name ()

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.
typedef score_functor::DopeType	DopeType

void	add_dope_score_data (atom::Hierarchy h)

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. More...

double	get_mass_from_volume (double v, ProteinDensityReference ref=ALBER)
	Estimate the mass of a protein from its volume. More...

double	get_mass_from_number_of_residues (unsigned int num_aa)
	Estimate the mass of a protein from the number of amino acids. More...

double	get_volume_from_residue_type (ResidueType rt)
	Return an estimate for the volume of a given residue. More...

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. If keep_detailed is true, then the original high resolution structure particles are added as children of the simplified structure.
Hierarchy	create_simplified_along_backbone (Hierarchy input, int num_res, bool keep_detailed=false)

Hierarchy	create_simplified_along_backbone (Chain input, const IntRanges &residue_segments, bool keep_detailed=false)

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)

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)

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 input, Model *model)

void	read_pdb (base::TextInput input, int model, Hierarchy h)

Hierarchy	read_pdb (base::TextInput input, Model model, PDBSelector selector, bool select_first_model=true)

Hierarchies	read_multimodel_pdb (base::TextInput input, Model model, PDBSelector selector)

Hierarchies	read_multimodel_pdb (base::TextInput input, 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 (const Selection &mhd, base::TextOutput out, unsigned int model=0)

void	write_pdb_of_c_alphas (const Selection &mhd, base::TextOutput out, unsigned int model=0)
	Write a hierarchy to a pdb as C_alpha atoms. More...

void	write_multimodel_pdb (const Hierarchies &mhd, base::TextOutput out)

Protein-ligand scoring
`IMP` provides a statistical scoring function for scoring protein-ligand complexes. See the ligand scoring application for more information.
typedef IMP::base::Vector < IMP::base::Pointer < ProteinLigandAtomPairScore > >	ProteinLigandAtomPairScores

typedef IMP::base::Vector < IMP::base::Pointer < ProteinLigandRestraint > >	ProteinLigandRestraints

void	add_protein_ligand_score_data (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)

PSIPRED reading
Reads in PSIPRED results and decorates particles as SecondaryStructureResidues. Currently assuming order of ps matches file.
SecondaryStructureResidues	read_psipred (base::TextInput inf, Model *mdl)

SecondaryStructureResidues	read_psipred (base::TextInput inf, Particles ps)

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)

Typedef Documentation

typedef IMP::base::Vector<IMP::base::Pointer< AngleSingletonScore > > IMP::atom::AngleSingletonScores

Store a set of objects.

Definition at line 39 of file AngleSingletonScore.h.

typedef IMP::base::Vector< AtomType > IMP::atom::AtomTypes

Pass or store a set of AtomType .

Definition at line 28 of file atom/Atom.h.

typedef IMP::base::Vector<IMP::base::Pointer< BerendsenThermostatOptimizerState > > IMP::atom::BerendsenThermostatOptimizerStates

Store a set of objects.

Definition at line 81 of file BerendsenThermostatOptimizerState.h.

typedef IMP::base::Vector<IMP::base::Pointer< BondedPairFilter > > IMP::atom::BondedPairFilters

Store a set of objects.

Definition at line 32 of file BondedPairFilter.h.

typedef IMP::base::Vector<IMP::base::Pointer< BondEndpointsRefiner > > IMP::atom::BondEndpointsRefiners

Store a set of objects.

Definition at line 31 of file BondEndpointsRefiner.h.

typedef IMP::base::Vector<IMP::base::Pointer< BondPairContainer > > IMP::atom::BondPairContainers

Store a set of objects.

Definition at line 59 of file BondPairContainer.h.

typedef IMP::base::Vector<IMP::base::Pointer< BondSingletonScore > > IMP::atom::BondSingletonScores

Store a set of objects.

Definition at line 39 of file BondSingletonScore.h.

typedef IMP::base::Vector< CHARMMAngle > IMP::atom::CHARMMAngles

Pass or store a set of CHARMMAngle .

Definition at line 166 of file charmm_topology.h.

typedef IMP::base::Vector< CHARMMAtomTopology > IMP::atom::CHARMMAtomTopologies

Pass or store a set of CHARMMAtomTopology .

Definition at line 49 of file charmm_topology.h.

typedef IMP::base::Vector< CHARMMBondEndpoint > IMP::atom::CHARMMBondEndpoints

Pass or store a set of CHARMMBondEndpoint .

Definition at line 88 of file charmm_topology.h.

typedef IMP::base::Vector< CHARMMBondParameters > IMP::atom::CHARMMBondParametersList

Pass or store a set of CHARMMBondParameters .

Definition at line 38 of file CHARMMParameters.h.

typedef IMP::base::Vector< CHARMMBond > IMP::atom::CHARMMBonds

Pass or store a set of CHARMMBond .

Definition at line 164 of file charmm_topology.h.

typedef IMP::base::Vector< CHARMMDihedralParameters > IMP::atom::CHARMMDihedralParametersList

Pass or store a set of CHARMMDihedralParameters .

Definition at line 52 of file CHARMMParameters.h.

typedef IMP::base::Vector< CHARMMDihedral > IMP::atom::CHARMMDihedrals

Pass or store a set of CHARMMDihedral .

Definition at line 168 of file charmm_topology.h.

typedef IMP::base::Vector<IMP::base::Pointer< CHARMMIdealResidueTopology > > IMP::atom::CHARMMIdealResidueTopologies

Store a set of objects.

Definition at line 359 of file charmm_topology.h.

typedef IMP::base::Vector< CHARMMInternalCoordinate > IMP::atom::CHARMMInternalCoordinates

Pass or store a set of CHARMMInternalCoordinate .

Definition at line 231 of file charmm_topology.h.

typedef IMP::base::Vector<IMP::base::Pointer< CHARMMParameters > > IMP::atom::CHARMMParametersList

Store a set of objects.

Definition at line 339 of file CHARMMParameters.h.

typedef IMP::base::Vector<IMP::base::Pointer< CHARMMPatch > > IMP::atom::CHARMMPatches

Store a set of objects.

Definition at line 413 of file charmm_topology.h.

typedef IMP::base::Vector<IMP::base::Pointer< CHARMMResidueTopology > > IMP::atom::CHARMMResidueTopologies

Store a set of objects.

Definition at line 467 of file charmm_topology.h.

typedef IMP::base::Vector<IMP::base::Pointer< CHARMMResidueTopologyBase > > IMP::atom::CHARMMResidueTopologyBases

Store a set of objects.

Definition at line 326 of file charmm_topology.h.

typedef IMP::base::Vector<IMP::base::Pointer< CHARMMSegmentTopology > > IMP::atom::CHARMMSegmentTopologies

Store a set of objects.

Definition at line 47 of file charmm_segment_topology.h.

typedef IMP::base::Vector<IMP::base::Pointer< CHARMMTopology > > IMP::atom::CHARMMTopologies

Store a set of objects.

Definition at line 240 of file charmm_segment_topology.h.

typedef IMP::base::Vector<IMP::base::Pointer< CoulombPairScore > > IMP::atom::CoulombPairScores

Store a set of objects.

Definition at line 52 of file CoulombPairScore.h.

typedef IMP::base::Vector<IMP::base::Pointer< CoverBond > > IMP::atom::CoverBonds

Store a set of objects.

Definition at line 32 of file CoverBond.h.

typedef IMP::base::Vector<IMP::base::Pointer< DihedralSingletonScore > > IMP::atom::DihedralSingletonScores

Store a set of objects.

Definition at line 37 of file DihedralSingletonScore.h.

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

A graph for representing a Hierarchy so you can view it nicely.See Graphs in IMP for more information.

Definition at line 154 of file hierarchy_tools.h.

typedef IMP::base::Vector<IMP::base::Pointer< ImproperSingletonScore > > IMP::atom::ImproperSingletonScores

Store a set of objects.

Definition at line 40 of file ImproperSingletonScore.h.

typedef IMP::base::Vector<IMP::base::Pointer< LangevinThermostatOptimizerState > > IMP::atom::LangevinThermostatOptimizerStates

Store a set of objects.

Definition at line 68 of file LangevinThermostatOptimizerState.h.

typedef IMP::base::Vector<IMP::base::Pointer< LennardJonesPairScore > > IMP::atom::LennardJonesPairScores

Store a set of objects.

Definition at line 81 of file LennardJonesPairScore.h.

typedef IMP::base::Vector<IMP::base::Pointer< PDBSelector > > IMP::atom::PDBSelectors

Store a set of objects.

Definition at line 48 of file pdb.h.

typedef IMP::base::Vector<IMP::base::Pointer< ProteinLigandAtomPairScore > > IMP::atom::ProteinLigandAtomPairScores

Store a set of objects.

Definition at line 66 of file protein_ligand_score.h.

typedef IMP::base::Vector<IMP::base::Pointer< ProteinLigandRestraint > > IMP::atom::ProteinLigandRestraints

Store a set of objects.

Definition at line 84 of file protein_ligand_score.h.

typedef IMP::base::Vector<IMP::base::Pointer< RemoveRigidMotionOptimizerState > > IMP::atom::RemoveRigidMotionOptimizerStates

Store a set of objects.

Definition at line 59 of file RemoveRigidMotionOptimizerState.h.

typedef IMP::base::Vector<IMP::base::Pointer< RemoveTranslationOptimizerState > > IMP::atom::RemoveTranslationOptimizerStates

Store a set of objects.

Definition at line 57 of file RemoveTranslationOptimizerState.h.

typedef IMP::base::Vector< ResidueType > IMP::atom::ResidueTypes

Pass or store a set of ResidueType .

Definition at line 27 of file Residue.h.

typedef IMP::base::Vector< RMSDCalculator > IMP::atom::RMSDCalculators

Pass or store a set of RMSDCalculator .

Definition at line 319 of file distance.h.

typedef IMP::base::Vector< Selection > IMP::atom::Selections

Pass or store a set of Selection .

Definition at line 202 of file Selection.h.

typedef IMP::base::Vector<IMP::base::Pointer< Simulator > > IMP::atom::Simulators

Store a set of objects.

Definition at line 125 of file Simulator.h.

typedef IMP::base::Vector<IMP::base::Pointer< VelocityScalingOptimizerState > > IMP::atom::VelocityScalingOptimizerStates

Store a set of objects.

Definition at line 62 of file VelocityScalingOptimizerState.h.

typedef IMP::base::Vector<IMP::base::Pointer< WritePDBOptimizerState > > IMP::atom::WritePDBOptimizerStates

Store a set of objects.

Definition at line 443 of file pdb.h.

Enumeration Type Documentation

enum IMP::atom::GetByType

The different types which can be passed to get_by_type()

Definition at line 356 of file atom/Hierarchy.h.

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 Hovmuller (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

Definition at line 34 of file estimates.h.

Function Documentation

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

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.

Examples:: atom/dope_and_excluded_volume.cpp.

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.

Examples:: atom/dope_and_excluded_volume.cpp.

Hierarchy create_clone ( Hierarchy d )

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 )

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
	)

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.

Restraint * create_connectivity_restraint	(	const Selections &	s,
		double	k,
		std::string	name = `"Connectivity%1%"`
	)

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.

Restraint * create_connectivity_restraint	(	const Selections &	s,
		double	x0,
		double	k,
		std::string	name = `"Connectivity%1%"`
	)

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.

core::XYZR create_cover	(	const 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.

Restraint * create_distance_restraint	(	const Selection &	n0,
		const Selection &	n1,
		double	x0,
		double	k,
		std::string	name = `"Distance%1%"`
	)

Create a distance restraint between the selections.

This restraint applies a harmonic to the minimum distance between a particle in selection n0 and a particle in selection n1.

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

Restraint * 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.

Restraint* IMP::atom::create_excluded_volume_restraint ( const Selections & s )

Create an excluded volume restraint for a list of selections.

Restraint * create_internal_connectivity_restraint	(	const Selection &	s,
		double	k,
		std::string	name = `"Connectivity%1%"`
	)

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,
		std::string	name = `"Connectivity%1%"`
	)

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.

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

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.

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")`
	)

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&)

Hierarchy IMP::atom::create_simplified_along_backbone	(	Hierarchy	input,
		int	num_res,
		bool	keep_detailed = `false`
	)

Simplify every num_res into one particle.

Hierarchy IMP::atom::create_simplified_along_backbone	(	Chain	input,
		const IntRanges &	residue_segments,
		bool	keep_detailed = `false`
	)

Simplify by breaking at the boundaries provided.

void destroy ( Hierarchy d )

All bonds connecting to these atoms are destroyed as are hierarchy links in the Hierarchy and the particles are removed from the Model. If this particle has a parent, it is removed from the parent.

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
	)

The residue must be part of a molecular hierarchy.

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

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

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

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
	)

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

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

Each module has its own data directory, so be sure to use the version of this function in the correct module. To read the data file "data_library" that was placed in the data directory of module "mymodule", do something like

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

This will ensure that the code works when IMP is installed or used via the tools/imppy.sh script.

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 dtfs.

double IMP::atom::get_diffusion_coefficient	(	const algebra::Vector3Ds &	displacements,
		double	dt
	)

Estimate the diffusion coeffient of a particle from a list of displacements each taken after the given time step dt.

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

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

double IMP::atom::get_diffusion_length	(	double	D,
		double	force,
		double	t,
		double	temp = `273`
	)

Return the scale for diffusion under the specified force, the diffusion coefficient D and the time step t.

Parameters

D	diffusion coefficient in Angstrom^2/femtosecond
force	applied force
t	time step in femtoseconds
temp	temperature in Kalvin

template<class Vector3DsOrXYZs0 , class Vector3DsOrXYZs1 >

double IMP::atom::get_drms	(	const Vector3DsOrXYZs0 &	m1,
		const Vector3DsOrXYZs1 &	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

Definition at line 126 of file distance.h.

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template<class Vector3DsOrXYZs0 , class Vector3DsOrXYZs1 >

double IMP::atom::get_drmsd	(	const Vector3DsOrXYZs0 &	m0,
		const Vector3DsOrXYZs1 &	m1
	)

Note: the function assumes correspondence between the two sets of points and does not need rigid alignment. Note that it is different from get_drms().

Definition at line 65 of file distance.h.

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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 and Wikipedia on Viscosity for the values of the viscosity of water used.

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.

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

Each module has its own example directory, so be sure to use the version of this function in the correct module. For example to read the file example_protein.pdb located in the examples directory of the IMP::atom module, do

IMP::atom::read_pdb(IMP::atom::get_example_path("example_protein.pdb", model));

This will ensure that the code works when IMP is installed or used via the tools/imppy.sh script.

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 )

See Also: Bond

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

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_kd	(	double	na,
		double	nb,
		double	nab,
		double	volume
	)

Compute the concentration in molarity from the passed values

Definition at line 99 of file estimates.h.

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double IMP::atom::get_kt ( double T )

Return kT for a given temperature. Value take from Wikipedia.

Definition at line 18 of file atom/constants.h.

Hierarchies get_leaves ( const Selection & h )

Hierarchies get_leaves ( Hierarchy h )

Definition at line 425 of file atom/Hierarchy.h.

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Hierarchies get_leaves ( const Hierarchies & h )

Definition at line 430 of file atom/Hierarchy.h.

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double get_mass ( const Selection & s )

Get the total mass of a hierarchy. In daltons.

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

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`
	)

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

Definition at line 92 of file estimates.h.

template<class Vector3DsOrXYZs0 , class Vector3DsOrXYZs1 >

double IMP::atom::get_native_overlap	(	const Vector3DsOrXYZs0 &	m1,
		const Vector3DsOrXYZs1 &	m2,
		double	threshold
	)

Parameters

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

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

Returns: the native overlap, as a percentage (from 0 to 100)

Definition at line 102 of file distance.h.

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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
	)

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 &	source,
		const core::XYZs &	target
	)

Parameters

[in]	source	The reference placement represented by XYZ coordinates
[in]	target	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 ParticlesTemp & ps )

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.

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

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 Vector3DsOrXYZs0 , class Vector3DsOrXYZs1 >

double IMP::atom::get_rigid_bodies_drms	(	const Vector3DsOrXYZs0 &	m1,
		const Vector3DsOrXYZs1 &	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

Definition at line 159 of file distance.h.

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template<class Vector3DsOrXYZs0 , class Vector3DsOrXYZs1 >

double IMP::atom::get_rmsd	(	const Vector3DsOrXYZs0 &	m1,
		const Vector3DsOrXYZs1 &	m2,
		const IMP::algebra::Transformation3D &	tr_for_second = `IMP::algebra::get_identity_transformation_3d()`
	)

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

Definition at line 28 of file distance.h.

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double IMP::atom::get_rmsd	(	const Selection &	s0,
		const Selection &	s1,
		const IMP::algebra::Transformation3D &	tr_for_second = `IMP::algebra::get_identity_transformation_3d()`
	)

RMSD on a pair of Selections.

Definition at line 48 of file distance.h.

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Hierarchy get_root ( Hierarchy h )

Definition at line 417 of file atom/Hierarchy.h.

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double IMP::atom::get_rotational_diffusion_coefficient	(	const algebra::Rotation3Ds &	displacements,
		double	dt
	)

Estimate the rotational diffusion coeffient of a particle from a list of displacements each taken after the given time step dt.

Float IMP::atom::get_secondary_structure_match_score	(	SecondaryStructureResidue	ssr1,
		SecondaryStructureResidue	ssr2
	)

Compares the secondary structure probabilities of two SecondaryStructureResidues. Returns the RMSD of the three probabilities (lower is better match).

double get_surface_area ( const Selection & s )

Get the total surface area of a hierarchy. In square angstroms. The get_surface_area requires CGAL in order to function.

double get_volume ( const Selection & s )

Get the total volume of a hierarchy. In cubic angstroms. The get_volume requires CGAL in order to function.

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

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 )

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

Hierarchies IMP::atom::read_multimodel_pdb	(	base::TextInput	input,
		Model *	model,
		PDBSelector *	selector
	)

Read all models from the pdb file.

Hierarchies IMP::atom::read_multimodel_pdb	(	base::TextInput	input,
		Model *	model
	)

Read all models from the pdb file.

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

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

void IMP::atom::read_pdb	(	base::TextInput	input,
		int	model,
		Hierarchy	h
	)

Rewrite the coordinates of the passed hierarchy based on the contents of the first model in the pdb file.

The hierarchy must have been created by reading from a pdb file and the atom numbers must correspond between the files. These are not really checked.

A ValueException is thrown if there are insufficient models in the file.

core::RigidMember particles are handled by updating the core::RigidBody algebra::ReferenceFrame3D to align with the loaded particles. Bad things will happen if the loaded coordinates are not a rigid transform of the prior coordinates.

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

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.

SecondaryStructureResidue IMP::atom::setup_coarse_secondary_structure_residue	(	const Particles &	ssr_ps,
		Model *	mdl,
		bool	winner_takes_all_per_res = `false`
	)

Coarsen some SecondaryStructureResidues. Returns a SecondaryStructureResidue whose probabilities reflect those of the underlying residues. Useful if you want to represent the secondary structure contents at a coarser level.

Parameters

[in]	ssr_ps	The SSR-decorated particles to be combined
[in]	mdl	The IMP Model
[in]	winner_takes_all_per_res	Whether to set prob=1.0 for top scoring secondary structure type

SecondaryStructureResidues IMP::atom::setup_coarse_secondary_structure_residues	(	const Particles &	ssr_ps,
		Model *	mdl,
		int	coarse_factor,
		int	start_res_num,
		bool	winner_takes_all_per_res = `false`
	)

Groups SecondaryStructureResidues into segments and then coarsens them. Useful if you have a long sequence and want to make several coarse nodes.

Parameters

[in]	ssr_ps	The SSR-decorated particles to be combined
[in]	mdl	The IMP Model
[in]	coarse_factor	Group size
[in]	start_res_num	Starting residue number for the provided sequence
[in]	winner_takes_all_per_res	Whether to set prob=1.0 for top scoring secondary structure type

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.

void IMP::atom::write_multimodel_pdb	(	const Hierarchies &	mhd,
		base::TextOutput	out
	)

Write the hierarchies one per frame.

void IMP::atom::write_pdb	(	const Selection &	mhd,
		base::TextOutput	out,
		unsigned int	model = `0`
	)

Write some atoms to a PDB.

void IMP::atom::write_pdb_of_c_alphas	(	const Selection &	mhd,
		base::TextOutput	out,
		unsigned int	model = `0`
	)

This method is used to write a non-atomic hierarchy into a pdb in a way that can be read by most programs. If the leaves are Residue particles then the index and residue type will be read from them. Otherwise default values will be used so that each leaf ends up in a separate residue.

Variable Documentation

const ResidueType IMP::atom::UNK

Unknown residue

Classes

Typedefs

Enumerations

Functions

Variables

Standard module methods

Dope scoring

Estimator Functions

Simplification along backbone

Finding information

Mol2 IO

PDB Reading

PDB Writing

Protein-ligand scoring

Python Only

PSIPRED reading

Energy conversions

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation