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IMP Reference Guide
2.11.1
The Integrative Modeling Platform
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Functionality for loading, creating, manipulating and scoring atomic structures. More...
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.
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 known 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.
Several helper programs are also provided. They all take the name of the PDB file as the first argument:
Check a PDB file for problems.
Score ligand poses. To score the poses, use the ligand_score command line tool.
Two different scoring files are provided:
The rank score is used by default.
They are both located in the IMP.atom data directory. This directory is available within IMP python scripts via the IMP::atom::get_data_path() function. From the command line, the files can be found at build/data/atom if IMP is not installed or something like /usr/share/imp/data/atom if it is installed.
Score ligand poses from docking output. Like the ligand_score tool, this scores ligand poses, but unlike that tool, it does not score the current pose; instead, it scores each pose corresponding to a transformation in a docking program output file. The transformation file has a simple format (it is a subset of the PatchDock output); the 7 space-separated columns should be the transformation number followed by the ligand translation and rotation.
Author(s): Daniel Russel, Ben Webb, Dina Schneidman, Javier Velázquez-Muriel, Hao Fan
Maintainer: benmwebb
License: LGPL This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
Publications:
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 | AngularVelocity |
| A particle with angular velocity. 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 | AtomTypePDBSelector |
| Select all atoms of the given types. More... | |
| class | BackbonePDBSelector |
| Select all backbone (N,CA,C,O) 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 a 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 simulator. More... | |
| class | BrownianDynamicsTAMD |
| Simple Brownian dynamics simulator. More... | |
| class | CAAngleRestraint |
| Angle restraint between three residues in CA-only representation. More... | |
| class | CADihedralRestraint |
| Dihedral restraint between five residues in CA-only representation. More... | |
| class | CAlphaPDBSelector |
| Select all CA ATOM records. More... | |
| class | CBetaPDBSelector |
| Select all CB ATOM records. More... | |
| class | CenterOfMass |
| A particle that is the center of mass of other particles. More... | |
| class | Chain |
| Store info for a chain of a protein. More... | |
| class | ChainPDBSelector |
| Select all ATOM and HETATM records with the given chain ids. More... | |
| class | ChainType |
| The type for a chain. 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 with a diffusion coefficient. 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 | EzRestraint |
| Ez Potential restraint. More... | |
| 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 | HelixRestraint |
| Restraint a set of residues to use ideal helix dihedrals and bonds. 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 | LinearVelocity |
| A particle with linear (XYZ) velocity. 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 | NonHydrogenPDBSelector |
| Select 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 are not selected by a given selector. More... | |
| class | NPDBSelector |
| Select all N ATOM records. More... | |
| class | OrientedSoapPairScore |
| Score a pair of atoms using an orientation-dependent SOAP score. More... | |
| class | OrPDBSelector |
| Select atoms which are selected by either or both selectors. More... | |
| class | PDBSelector |
| Select which atoms to read from a PDB file. More... | |
| class | PPDBSelector |
| Select all P (= phosphate) ATOM records. More... | |
| class | ProteinLigandAtomPairScore |
| class | ProteinLigandRestraint |
| Score a pair of molecules. More... | |
| class | RemoveRigidMotionOptimizerState |
| Removes rigid translation and rotation from the particles. More... | |
| class | RemoveTranslationOptimizerState |
| Removes rigid translation from the particles. More... | |
| class | Representation |
| A decorator for a representation. More... | |
| class | Residue |
| A decorator for a residue. More... | |
| class | ResidueType |
| The type for a residue. More... | |
| class | ResidueTypePDBSelector |
| Select all atoms in residues of the given types. More... | |
| class | RigidBodyDiffusion |
| class | SameResiduePairFilter |
| class | SecondaryStructureResidue |
| A decorator for a residue with probability of secondary structure. More... | |
| class | Selection |
| Select hierarchy particles identified by the biological name. More... | |
| 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 | SoapPairFilter |
| Filter atom pairs for SOAP. More... | |
| class | State |
| Associate an integer "state" index with a hierarchy node. More... | |
| class | StereochemistryPairFilter |
| A filter that excludes bonds, angles and dihedrals. More... | |
| class | StructureSource |
| Store strings describing the source of this structure fragment. More... | |
| class | TAMDCentroid |
| class | TAMDParticle |
| class | VelocityScalingOptimizerState |
| Maintains temperature during molecular dynamics by velocity scaling. More... | |
| class | WaterPDBSelector |
| Select all non-water ATOM and HETATM records. More... | |
| class | WritePDBOptimizerState |
| class | XorPDBSelector |
| Select atoms which are selected by either selector but not both. More... | |
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, MOLECULE_TYPE, DOMAIN_TYPE, FRAGMENT_TYPE, XYZ_TYPE, XYZR_TYPE, MASS_TYPE, STATE_TYPE } |
| The different types which can be passed to get_by_type() More... | |
| enum | RepresentationType { BALLS = 0, DENSITIES = 1 } |
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... | |
| 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%") |
| Create a restraint connecting the selections. More... | |
| Restraint * | create_connectivity_restraint (const Selections &s, double x0, double k, std::string name="Connectivity%1%") |
| Create a restraint connecting the selections. More... | |
| 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) |
| Create an excluded volume restraint for a list of selections. More... | |
| Restraint * | create_internal_connectivity_restraint (const Selection &s, double k, std::string name="Connectivity%1%") |
| Create a restraint connecting the selection. More... | |
| Restraint * | create_internal_connectivity_restraint (const Selection &s, double x0, double k, std::string name="Connectivity%1%") |
| Create a restraint connecting the selection. More... | |
| Hierarchy | create_protein (Model *m, std::string name, double target_radius, 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 target_radius, 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) |
| Hierarchy | create_simplified_assembly_from_volume (Hierarchy h, double resolution) |
| Hierarchy | create_simplified_from_volume (Hierarchy h, double resolution) |
| void | destroy_bond (Bond b) |
| Destroy the bond connecting two 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. More... | |
| Bond | get_bond (Bonded a, Bonded b) |
| Get the bond between two particles. More... | |
| Chain | get_chain (Hierarchy h) |
| Get the containing chain or Chain() if there is none. More... | |
| std::string | get_chain_id (Hierarchy h) |
| Walk up the hierarchy to determine the chain id. More... | |
| 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... | |
| int | get_copy_index (Hierarchy h) |
| Walk up the hierarchy to find the current copy index. More... | |
| double | get_diffusion_angle (double D, double dtfs) |
| double | get_diffusion_coefficient (const algebra::Vector3Ds &displacements, double dt) |
| double | get_diffusion_coefficient (const algebra::Vector3Ds &displacements, const Floats &dts) |
| 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=-1) |
| 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 distance the root mean square deviation between two sets of 3D points. More... | |
| template<class Vector3DsOrXYZs0 , class Vector3DsOrXYZs1 > | |
| double | get_drmsd_Q (const Vector3DsOrXYZs0 &m0, const Vector3DsOrXYZs1 &m1, double threshold) |
| double | get_einstein_diffusion_coefficient (double r, double temp=-1) |
| double | get_einstein_rotational_diffusion_coefficient (double r, double temp=-1) |
| Element | get_element_for_atom_type (AtomType at) |
| ElementTable & | get_element_table () |
| CHARMMParameters * | get_heavy_atom_CHARMM_parameters () |
| HierarchyTree | get_hierarchy_tree (Hierarchy h) |
| Get a graph for the passed Hierarchy. More... | |
| double | get_kd (double na, double nb, double nab, double volume) |
| double | get_kt (double T) |
| Return kT for a given temperature in units of [kcal/mol]. More... | |
| Hierarchies | get_leaves (const Selection &h) |
| double | get_mass (ResidueType c) |
| Get the mass from the residue type. More... | |
| double | get_mass (const Selection &s) |
| Get the total mass of a hierarchy, in Daltons. More... | |
| double | get_maximum_time_step_estimate (BrownianDynamics *bd) |
| double | get_molarity (double n, double volume) |
| std::string | get_molecule_name (Hierarchy h) |
| 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) |
| Return the residue from the same chain with one higher index. More... | |
| char | get_one_letter_code (ResidueType c) |
| Get the 1-letter amino acid code from the residue type. More... | |
| 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) |
| Return the atoms comprising the phi dihedral. More... | |
| 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) |
| Return the residue from the same chain with one lower index. More... | |
| Atoms | get_psi_dihedral_atoms (Residue rd) |
| Return the atoms comprising the psi dihedral. More... | |
| double | get_radius_of_gyration (const ParticlesTemp &ps, bool weighted=true) |
| double | get_radius_of_gyration (const Selection &s) |
| Representation | get_representation (Hierarchy h, bool nothrow=false) |
| Return the Representation object containing this hierarchy. More... | |
| Residue | get_residue (Atom d, bool nothrow=false) |
| Return the Residue containing this atom. More... | |
| ResidueType | get_residue_type (char c) |
| Get the residue type from the 1-letter amino acid code. More... | |
| double | get_resolution (Model *m, ParticleIndex pi) |
| Estimate the resolution of the hierarchy as used by Representation. More... | |
| double | get_resolution (Hierarchy h) |
| template<class Vector3DsOrXYZs0 , class Vector3DsOrXYZs1 > | |
| double | get_rigid_bodies_drms (const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, const IMP::IntRanges &ranges) |
| DRMS between two sets of rigid bodies. More... | |
| double | get_rmsd (const core::XYZs &s0, const core::XYZs &s1) |
| double | get_rmsd (const Selection &s0, const Selection &s1) |
| double | get_rmsd_transforming_first (const IMP::algebra::Transformation3D &tr, const core::XYZs &s0, const core::XYZs &s1) |
| double | get_rmsd_transforming_first (const algebra::Transformation3D &tr, const Selection &s0, const Selection &s1) |
| double | get_rotational_diffusion_coefficient (const algebra::Rotation3Ds &orientations, double dt) |
| Float | get_secondary_structure_match_score (SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2) |
| Compares the secondary structure probabilities of two residues. More... | |
| int | get_state_index (Hierarchy h) |
| Walk up the hierarchy to find the current state. More... | |
| double | get_surface_area (const Selection &s) |
| Get the total surface area of a hierarchy, in square angstroms. More... | |
| algebra::Transformation3D | get_transformation_aligning_first_to_second (const Selection &s1, const Selection &s2) |
| Get the transformation to align two selections. More... | |
| HierarchyTreeVertexIndex | get_vertex_index (const HierarchyTree &g) |
| double | get_volume (const Selection &s) |
| Get the total volume of a hierarchy, in cubic angstroms. More... | |
| Hierarchy | read_mmcif (TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector()) |
| Read all the molecules in the first model of the mmCIF file. More... | |
| Hierarchies | read_multimodel_mmcif (TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector()) |
| Read all models from the mmCIF file. More... | |
| 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) |
| Coarsen some SecondaryStructureResidues. More... | |
| 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_as_graphviz (const HierarchyTree &name, TextOutput out) |
| void | show_with_representations (Hierarchy h, std::ostream &out=std::cout) |
| Traverse through the tree and show atom info, including representations. More... | |
| void | transform (Hierarchy h, const algebra::Transformation3D &tr) |
| Transform a hierarchy. This is aware of rigid bodies. More... | |
Variables | |
| const double | ALL_RESOLUTIONS |
| const AtomType | AT_CA |
| const AtomType | AT_N |
| const AtomType | AT_UNKNOWN |
| const ChainType | DNA |
| Shorthand for IMP::atom::Polydeoxyribonucleotide. More... | |
| const ChainType | DPolypeptide |
| Polypeptide(D) More... | |
| const ChainType | DPolysaccharide |
| Polysaccharide(D) More... | |
| const ResidueType | GLY |
| const ChainType | LPolypeptide |
| Polypeptide(L) More... | |
| const ChainType | LPolysaccharide |
| Polysaccharide(L) More... | |
| const ChainType | Polydeoxyribonucleotide |
| DNA. More... | |
| const ChainType | Polyribonucleotide |
| RNA. More... | |
| const ChainType | Protein |
| Shorthand for IMP::atom::LPolypeptide. More... | |
| const ChainType | RNA |
| Shorthand for IMP::atom::Polyribonucleotide. More... | |
| const ResidueType | UNK |
| Unknown residue. More... | |
| const ChainType | UnknownChainType |
| Unknown chain type. More... | |
Standard module functions | |
All | |
| std::string | get_module_version () |
| std::string | get_module_name () |
| std::string | get_data_path (std::string file_name) |
| Return the full path to one of this module's data files. More... | |
| std::string | get_example_path (std::string file_name) |
| Return the full path to one of this module's example files. More... | |
Dope scoring | |
| |
| 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... | |
Energy conversions | |
| 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) |
| Convert force from kcal/mol/A to femtonewtons. More... | |
| double | get_spring_constant_in_femto_newtons_per_angstrom (double k_in_kcal_per_mol_per_angstrom_square) |
| Convert spring constant from kcal/mol/A^2 to femtonewton/A. 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. | |
| Ints | get_residue_indexes (Hierarchy h) |
| ResidueType | get_residue_type (Hierarchy h) |
| AtomType | get_atom_type (Hierarchy h) |
| std::string | get_domain_name (Hierarchy h) |
Mol2 IO | |
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 (TextInput mol2_file, Model *model, Mol2Selector *mol2sel=nullptr) |
| Create a hierarchy from a Mol2 file. More... | |
| void | write_mol2 (Hierarchy rhd, TextOutput file_name) |
| Write a ligand hierarchy as a mol2 file. More... | |
PDB Reading | |
The read PDB methods produce a hierarchy that looks as follows:
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. In order to track the provenance of IMP-generated models, the provenance of any PDB files read in here - for example, the PDB id, or detail about a comparative model - needs to also be tracked. This is done using the PDB headers:
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. | |
| PDBSelector * | get_default_pdb_selector () |
| Hierarchy | read_pdb (TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true) |
| Read all the molecules in the first model of the PDB file. More... | |
| void | read_pdb (TextInput input, int model, Hierarchy h) |
| Hierarchies | read_multimodel_pdb (TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector()) |
PDB Writing | |
The methods to write a PDB expects a Hierarchy that looks as follows: 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, TextOutput out, unsigned int model=1) |
| void | write_pdb_of_c_alphas (const Selection &mhd, TextOutput out, unsigned int model=1) |
| Write a hierarchy to a PDB as C_alpha atoms. More... | |
| void | write_multimodel_pdb (const Hierarchies &mhd, TextOutput out) |
Protein-ligand scoring | |
| |
| typedef Key< 783462 > | ProteinLigandType |
| typedef IMP::Vector < ProteinLigandType > | ProteinLigandTypes |
| typedef IMP::Vector < IMP::Pointer < ProteinLigandAtomPairScore > > | ProteinLigandAtomPairScores |
| typedef IMP::Vector < IMP::WeakPointer < ProteinLigandAtomPairScore > > | ProteinLigandAtomPairScoresTemp |
| typedef IMP::Vector < IMP::Pointer < ProteinLigandRestraint > > | ProteinLigandRestraints |
| typedef IMP::Vector < IMP::WeakPointer < ProteinLigandRestraint > > | ProteinLigandRestraintsTemp |
| void | add_protein_ligand_score_data (Hierarchy h) |
Python Only | |
The following functions are only available 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_hierarchy (Hierarchy h) |
| Print out the molecular hierarchy. More... | |
PSIPRED reading | |
Reads in PSIPRED results and decorates particles as SecondaryStructureResidues. Currently assuming order of ps matches file. | |
| SecondaryStructureResidues | read_psipred (TextInput inf, Model *mdl) |
| SecondaryStructureResidues | read_psipred (TextInput inf, Particles ps) |
A vector of reference-counting object pointers.
Definition at line 45 of file AngleSingletonScore.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 45 of file AngleSingletonScore.h.
| typedef IMP::Vector< AtomType > IMP::atom::AtomTypes |
Pass or store a set of AtomType .
Definition at line 29 of file atom/Atom.h.
| typedef IMP::Vector<IMP::Pointer< BerendsenThermostatOptimizerState > > IMP::atom::BerendsenThermostatOptimizerStates |
A vector of reference-counting object pointers.
Definition at line 67 of file BerendsenThermostatOptimizerState.h.
| typedef IMP::Vector<IMP::WeakPointer< BerendsenThermostatOptimizerState > > IMP::atom::BerendsenThermostatOptimizerStatesTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 67 of file BerendsenThermostatOptimizerState.h.
A vector of reference-counting object pointers.
Definition at line 38 of file BondedPairFilter.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 38 of file BondedPairFilter.h.
A vector of reference-counting object pointers.
Definition at line 37 of file BondEndpointsRefiner.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 37 of file BondEndpointsRefiner.h.
A vector of reference-counting object pointers.
Definition at line 61 of file BondPairContainer.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 61 of file BondPairContainer.h.
A vector of reference-counting object pointers.
Definition at line 42 of file BondSingletonScore.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 42 of file BondSingletonScore.h.
| typedef IMP::Vector< ChainType > IMP::atom::ChainTypes |
| typedef IMP::Vector< CHARMMAngle > IMP::atom::CHARMMAngles |
Pass or store a set of CHARMMAngle .
Definition at line 169 of file charmm_topology.h.
Pass or store a set of CHARMMAtomTopology .
Definition at line 50 of file charmm_topology.h.
Pass or store a set of CHARMMBondEndpoint .
Definition at line 90 of file charmm_topology.h.
Pass or store a set of CHARMMBondParameters .
Definition at line 38 of file CHARMMParameters.h.
| typedef IMP::Vector< CHARMMBond > IMP::atom::CHARMMBonds |
Pass or store a set of CHARMMBond .
Definition at line 167 of file charmm_topology.h.
Pass or store a set of CHARMMDihedralParameters .
Definition at line 52 of file CHARMMParameters.h.
| typedef IMP::Vector< CHARMMDihedral > IMP::atom::CHARMMDihedrals |
Pass or store a set of CHARMMDihedral .
Definition at line 171 of file charmm_topology.h.
| typedef IMP::Vector<IMP::Pointer< CHARMMIdealResidueTopology > > IMP::atom::CHARMMIdealResidueTopologies |
A vector of reference-counting object pointers.
Definition at line 358 of file charmm_topology.h.
| typedef IMP::Vector<IMP::WeakPointer< CHARMMIdealResidueTopology > > IMP::atom::CHARMMIdealResidueTopologiesTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 358 of file charmm_topology.h.
Pass or store a set of CHARMMInternalCoordinate .
Definition at line 239 of file charmm_topology.h.
A vector of reference-counting object pointers.
Definition at line 345 of file CHARMMParameters.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 345 of file CHARMMParameters.h.
| typedef IMP::Vector<IMP::Pointer< CHARMMPatch > > IMP::atom::CHARMMPatches |
A vector of reference-counting object pointers.
Definition at line 413 of file charmm_topology.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 413 of file charmm_topology.h.
A vector of reference-counting object pointers.
Definition at line 465 of file charmm_topology.h.
| typedef IMP::Vector<IMP::WeakPointer< CHARMMResidueTopology > > IMP::atom::CHARMMResidueTopologiesTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 465 of file charmm_topology.h.
| typedef IMP::Vector<IMP::Pointer< CHARMMResidueTopologyBase > > IMP::atom::CHARMMResidueTopologyBases |
A vector of reference-counting object pointers.
Definition at line 324 of file charmm_topology.h.
| typedef IMP::Vector<IMP::WeakPointer< CHARMMResidueTopologyBase > > IMP::atom::CHARMMResidueTopologyBasesTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 324 of file charmm_topology.h.
A vector of reference-counting object pointers.
Definition at line 48 of file charmm_segment_topology.h.
| typedef IMP::Vector<IMP::WeakPointer< CHARMMSegmentTopology > > IMP::atom::CHARMMSegmentTopologiesTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 48 of file charmm_segment_topology.h.
| typedef IMP::Vector<IMP::Pointer< CHARMMTopology > > IMP::atom::CHARMMTopologies |
A vector of reference-counting object pointers.
Definition at line 244 of file charmm_segment_topology.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 244 of file charmm_segment_topology.h.
A vector of reference-counting object pointers.
Definition at line 58 of file CoulombPairScore.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 58 of file CoulombPairScore.h.
| typedef IMP::Vector<IMP::Pointer< CoverBond > > IMP::atom::CoverBonds |
A vector of reference-counting object pointers.
Definition at line 39 of file CoverBond.h.
| typedef IMP::Vector<IMP::WeakPointer< CoverBond > > IMP::atom::CoverBondsTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 39 of file CoverBond.h.
A vector of reference-counting object pointers.
Definition at line 42 of file DihedralSingletonScore.h.
| typedef IMP::Vector<IMP::WeakPointer< DihedralSingletonScore > > IMP::atom::DihedralSingletonScoresTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 42 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 164 of file hierarchy_tools.h.
A vector of reference-counting object pointers.
Definition at line 50 of file ImproperSingletonScore.h.
| typedef IMP::Vector<IMP::WeakPointer< ImproperSingletonScore > > IMP::atom::ImproperSingletonScoresTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 50 of file ImproperSingletonScore.h.
| typedef IMP::Vector<IMP::Pointer< LangevinThermostatOptimizerState > > IMP::atom::LangevinThermostatOptimizerStates |
A vector of reference-counting object pointers.
Definition at line 56 of file LangevinThermostatOptimizerState.h.
| typedef IMP::Vector<IMP::WeakPointer< LangevinThermostatOptimizerState > > IMP::atom::LangevinThermostatOptimizerStatesTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 56 of file LangevinThermostatOptimizerState.h.
A vector of reference-counting object pointers.
Definition at line 89 of file LennardJonesPairScore.h.
| typedef IMP::Vector<IMP::WeakPointer< LennardJonesPairScore > > IMP::atom::LennardJonesPairScoresTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 89 of file LennardJonesPairScore.h.
| typedef IMP::Vector<IMP::Pointer< PDBSelector > > IMP::atom::PDBSelectors |
A vector of weak (non reference-counting) pointers to specified objects.
| typedef IMP::Vector<IMP::Pointer< ProteinLigandAtomPairScore > > IMP::atom::ProteinLigandAtomPairScores |
A vector of reference-counting object pointers.
Definition at line 65 of file protein_ligand_score.h.
| typedef IMP::Vector<IMP::WeakPointer< ProteinLigandAtomPairScore > > IMP::atom::ProteinLigandAtomPairScoresTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 65 of file protein_ligand_score.h.
A vector of reference-counting object pointers.
Definition at line 80 of file protein_ligand_score.h.
| typedef IMP::Vector<IMP::WeakPointer< ProteinLigandRestraint > > IMP::atom::ProteinLigandRestraintsTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 80 of file protein_ligand_score.h.
| typedef Key<783462> IMP::atom::ProteinLigandType |
The marker to identify the atom types.
Definition at line 34 of file protein_ligand_score.h.
Pass or store a set of ProteinLigandType .
Definition at line 39 of file protein_ligand_score.h.
| typedef IMP::Vector<IMP::Pointer< RemoveRigidMotionOptimizerState > > IMP::atom::RemoveRigidMotionOptimizerStates |
A vector of reference-counting object pointers.
Definition at line 42 of file RemoveRigidMotionOptimizerState.h.
| typedef IMP::Vector<IMP::WeakPointer< RemoveRigidMotionOptimizerState > > IMP::atom::RemoveRigidMotionOptimizerStatesTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 42 of file RemoveRigidMotionOptimizerState.h.
| typedef IMP::Vector<IMP::Pointer< RemoveTranslationOptimizerState > > IMP::atom::RemoveTranslationOptimizerStates |
A vector of reference-counting object pointers.
Definition at line 43 of file RemoveTranslationOptimizerState.h.
| typedef IMP::Vector<IMP::WeakPointer< RemoveTranslationOptimizerState > > IMP::atom::RemoveTranslationOptimizerStatesTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 43 of file RemoveTranslationOptimizerState.h.
| typedef IMP::Vector< ResidueType > IMP::atom::ResidueTypes |
Pass or store a set of ResidueType .
| typedef IMP::Vector< Selection > IMP::atom::Selections |
Pass or store a set of Selection .
Definition at line 241 of file Selection.h.
| typedef IMP::Vector<IMP::Pointer< Simulator > > IMP::atom::Simulators |
A vector of reference-counting object pointers.
Definition at line 218 of file Simulator.h.
| typedef IMP::Vector<IMP::WeakPointer< Simulator > > IMP::atom::SimulatorsTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 218 of file Simulator.h.
| typedef IMP::Vector<IMP::Pointer< VelocityScalingOptimizerState > > IMP::atom::VelocityScalingOptimizerStates |
A vector of reference-counting object pointers.
Definition at line 52 of file VelocityScalingOptimizerState.h.
| typedef IMP::Vector<IMP::WeakPointer< VelocityScalingOptimizerState > > IMP::atom::VelocityScalingOptimizerStatesTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 52 of file VelocityScalingOptimizerState.h.
| enum IMP::atom::Element |
| enum IMP::atom::GetByType |
The different types which can be passed to get_by_type()
Definition at line 324 of file atom/Hierarchy.h.
Several protein density value references that have been proposed in the literature.
Definition at line 33 of file estimates.h.
Eventually, other types of representation will be supported
Definition at line 25 of file Representation.h.
| AtomType IMP::atom::add_atom_type | ( | std::string | name, |
| Element | e | ||
| ) |
| void IMP::atom::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 IMP::atom::add_protein_ligand_score_data | ( | Hierarchy | h | ) |
Add the data needed to use ProteinLigandAtomPairScore with the passed Hierarchy.
| void IMP::atom::add_radii | ( | Hierarchy | d, |
| const ForceFieldParameters * | ffp = get_all_atom_CHARMM_parameters(), |
||
| FloatKey | radius_key = FloatKey("radius") |
||
| ) |
Add vdW radius from given force field.
| 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.
| Restraint* IMP::atom::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* IMP::atom::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 apart 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 IMP::atom::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 potentially complicated set of geometries represented by the selection with a much simpler one.
| Restraint* IMP::atom::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* 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.
| Restraint* IMP::atom::create_excluded_volume_restraint | ( | const Selections & | s | ) |
Create an excluded volume restraint for a list of selections.
| Restraint* IMP::atom::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* IMP::atom::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 apart 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 IMP::atom::create_protein | ( | Model * | m, |
| std::string | name, | ||
| double | target_radius, | ||
| 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 angstroms.
Currently the function creates a set of balls with radii no greater than target_radius 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 not optimized by default, and have garbage coordinate values.
| Hierarchy IMP::atom::create_protein | ( | Model * | m, |
| std::string | name, | ||
| double | target_radius, | ||
| const Ints | domain_boundaries | ||
| ) |
Like the former create_protein(), but it enforces domain splits at the provided domain boundaries. The domain boundaries should be the start of the first domain, any boundaries, 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.
| IMP::core::RigidBody IMP::atom::create_rigid_body | ( | Hierarchy | h | ) |
| 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.
| Hierarchy IMP::atom::create_simplified_assembly_from_volume | ( | Hierarchy | h, |
| double | resolution | ||
| ) |
Create a new hierarchy that approximates the volume occupied by the old one.
This function is like create_simplified_from_volume() except that the result is divided into Chain and Molecule bits. It assumes that all geometry is rooted under a chain or a molecule.
| Hierarchy IMP::atom::create_simplified_from_volume | ( | Hierarchy | h, |
| double | resolution | ||
| ) |
Create a new hierarchy that approximates the volume occupied by the old one.
The new hierarchy will contain a number of Fragment particles whose surface (and hence volume) approximates the input hierarchy in the sense of IMP::algebra::get_simplified_from_volume().
The resulting representation has approximately the desired resolution in the sense of get_resolution().
Residue indexes are assigned to the created Fragments from the original residue indexes, and particles containing adjacent residues are connected by bonds.
| 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.
| Atom IMP::atom::get_atom | ( | Residue | rd, |
| AtomType | at | ||
| ) |
| bool IMP::atom::get_atom_type_exists | ( | std::string | name | ) |
Return true if that atom type already exists.
| Chain IMP::atom::get_chain | ( | Hierarchy | h | ) |
Get the containing chain or Chain() if there is none.
| std::string IMP::atom::get_chain_id | ( | Hierarchy | h | ) |
Walk up the hierarchy to determine the chain id.
| Atoms IMP::atom::get_charmm_untyped_atoms | ( | Hierarchy | hierarchy | ) |
Get all atoms in the Hierarchy that do not have CHARMM types.
| 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.
| [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 |
| int IMP::atom::get_copy_index | ( | Hierarchy | h | ) |
Walk up the hierarchy to find the current copy index.
| std::string IMP::atom::get_data_path | ( | std::string | file_name | ) |
Return the full path to one of this module's data files.
To read the data file "data_library" that was placed in the data directory of this module, do something like
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.
| double IMP::atom::get_diffusion_angle | ( | double | D, |
| double | dtfs | ||
| ) |
Get the standard deviation of the diffusion angle change in radians given the rigid body diffusion coefficient in A^2/fs and the time step dtfs in fs.
| double IMP::atom::get_diffusion_coefficient | ( | const algebra::Vector3Ds & | displacements, |
| double | dt | ||
| ) |
Estimate the diffusion coefficient of a particle in A^2/fs from a list of displacements each taken after the given time step dt. Removes any non-random motion component (under the simplifying assumption it is constant over time)
| displacements | displacement vectors in Angstroms |
| dt | time step in femtoseconds |
| double IMP::atom::get_diffusion_coefficient | ( | const algebra::Vector3Ds & | displacements, |
| const Floats & | dts | ||
| ) |
Estimate the diffusion coefficient of a particle in A^2/fs from a list of displacements each taken after the given time step dt. Removes any non-random motion component (under the simplifying assumption it is constant over time)
| displacements | displacement vectors in Angstroms |
| dts | corresponding time steps in femtoseconds, expected to sum to more than zero |
| double IMP::atom::get_diffusion_length | ( | double | D, |
| double | t | ||
| ) |
Return the standard deviation for the Brownian step in Angstroms given the diffusion coefficient D in A^2/fs and the time step t in fs.
| double IMP::atom::get_diffusion_length | ( | double | D, |
| double | force, | ||
| double | t, | ||
| double | temp = -1 |
||
| ) |
Return the scale for diffusion in Angstroms given the specified force, the diffusion coefficient D and the time step t.
| D | diffusion coefficient in Angstrom^2/femtosecond |
| force | applied force in kcal/mol/A |
| t | time step in femtoseconds |
| temp | temperature in Kelvin (negative = default IMP temperature of 297.15K) |
| 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
| [in] | m1 | set of points |
| [in] | m2 | set of points |
Definition at line 147 of file atom/distance.h.
Here is the call graph for this function:| double IMP::atom::get_drmsd | ( | const Vector3DsOrXYZs0 & | m0, |
| const Vector3DsOrXYZs1 & | m1 | ||
| ) |
Calculate distance the root mean square deviation between two sets of 3D points.
See generic geometry for more information.
Definition at line 49 of file atom/distance.h.
Here is the call graph for this function:| double IMP::atom::get_drmsd_Q | ( | const Vector3DsOrXYZs0 & | m0, |
| const Vector3DsOrXYZs1 & | m1, | ||
| double | threshold | ||
| ) |
Calculate the distance root mean square deviation between two sets of 3D points with a distance threshold
See generic geometry for more information.
Definition at line 85 of file atom/distance.h.
Here is the call graph for this function:| double IMP::atom::get_einstein_diffusion_coefficient | ( | double | r, |
| double | temp = -1 |
||
| ) |
Return the predicted diffusion coefficient in Angstrom squared per femtosecond at the specified radius and temperature.
| particle | radius in angstroms |
| temp | temperature in Kelvin (negative = default IMP temperature of 297.15K) |
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, |
| double | temp = -1 |
||
| ) |
Return the predicted diffusion coefficient in radians squared per femtosecond at the specified radius and temeprature.
| particle | radius in angstroms |
| temp | temperature in Kelvin (negative = default IMP temperature of 297.15K) |
| std::string IMP::atom::get_example_path | ( | std::string | file_name | ) |
Return the full path to one of this module's example files.
To read the example file "example_protein.pdb" that was placed in the examples directory of this module, do something like
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.
| double IMP::atom::get_force_in_femto_newtons | ( | double | force_in_kcal_per_mol_per_angstrom | ) |
Convert force from kcal/mol/A to femtonewtons.
| 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.
| HierarchyTree IMP::atom::get_hierarchy_tree | ( | Hierarchy | h | ) |
| 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 101 of file estimates.h.
Here is the call graph for this function:| double IMP::atom::get_kt | ( | double | T | ) |
Return kT for a given temperature in units of [kcal/mol].
Definition at line 18 of file atom/constants.h.
| Hierarchies IMP::atom::get_leaves | ( | const Selection & | h | ) |
| double IMP::atom::get_mass | ( | ResidueType | c | ) |
Get the mass from the residue type.
| double IMP::atom::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 | ) |
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.
| [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.
| std::string IMP::atom::get_molecule_name | ( | Hierarchy | h | ) |
Walk up the hierarchy to determine the molecule name.
| double IMP::atom::get_native_overlap | ( | const Vector3DsOrXYZs0 & | m1, |
| const Vector3DsOrXYZs1 & | m2, | ||
| double | threshold | ||
| ) |
Computes the native overlap between two sets of 3D points.
| [in] | m1 | first set |
| [in] | m2 | second set |
| [in] | threshold | threshold distance (angstroms) for the calculation |
Definition at line 124 of file atom/distance.h.
Here is the call graph for this function:| Hierarchy IMP::atom::get_next_residue | ( | Residue | rd | ) |
Return the residue from the same chain with one higher index.
If no such residue exists, return Hierarchy().
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.
| [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 |
| Atoms IMP::atom::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 | ||
| ) |
Measure the difference between two placements of the same set of points.
| [in] | source | The reference placement represented by XYZ coordinates |
| [in] | target | The modeled placement represented by XYZ coordinates |
| Hierarchy IMP::atom::get_previous_residue | ( | Residue | rd | ) |
Return the residue from the same chain with one lower index.
If no such residue exists, return Hierarchy().
| 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 IMP::atom::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, |
| bool | weighted = true |
||
| ) |
Compute the radius of gyration $R_g$ of a set of particles. It is assumed the particles has coordinates (XYZ decorator), and optionally, the $R_g$ may be weighted by mass or radius^3.
| ps | the particles |
| weighted | If true then $R_g$ is weighted by either mass or radius^3, in this order of preference. If none exists, an unweighted $R_g$ is computed. If weighted is true, then it is is assumed that either all particles have mass/radius or none of them do. |
| double IMP::atom::get_radius_of_gyration | ( | const Selection & | s | ) |
| Representation IMP::atom::get_representation | ( | Hierarchy | h, |
| bool | nothrow = false |
||
| ) |
Return the Representation object containing this hierarchy.
| Residue IMP::atom::get_residue | ( | Atom | d, |
| bool | nothrow = false |
||
| ) |
Return the Residue containing this atom.
The atom must be part of a molecular hierarchy.
| 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.
| ValueException | if an invalid character is passed. |
| double IMP::atom::get_resolution | ( | Model * | m, |
| ParticleIndex | pi | ||
| ) |
Estimate the resolution of the hierarchy as used by Representation.
It is currently the inverse average radius of the leaves.
| double IMP::atom::get_resolution | ( | Hierarchy | h | ) |
| double IMP::atom::get_rigid_bodies_drms | ( | const Vector3DsOrXYZs0 & | m1, |
| const Vector3DsOrXYZs1 & | m2, | ||
| const IMP::IntRanges & | ranges | ||
| ) |
DRMS between two sets of rigid bodies.
Points ij belonging to the same rigid body are not evaluated, as they are the same in both sets
| [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 179 of file atom/distance.h.
Here is the call graph for this function:| double IMP::atom::get_rmsd | ( | const core::XYZs & | s0, |
| const core::XYZs & | s1 | ||
| ) |
Get the rmsd between two lists of particles
| double IMP::atom::get_rmsd | ( | const Selection & | s0, |
| const Selection & | s1 | ||
| ) |
RMSD on a pair of Selections.
| double IMP::atom::get_rmsd_transforming_first | ( | const IMP::algebra::Transformation3D & | tr, |
| const core::XYZs & | s0, | ||
| const core::XYZs & | s1 | ||
| ) |
Get the rmsd between two lists of particles
| double IMP::atom::get_rmsd_transforming_first | ( | const algebra::Transformation3D & | tr, |
| const Selection & | s0, | ||
| const Selection & | s1 | ||
| ) |
RMSD on a pair of Selections.
| double IMP::atom::get_rotational_diffusion_coefficient | ( | const algebra::Rotation3Ds & | orientations, |
| double | dt | ||
| ) |
Estimate the rotational diffusion coefficient of a particle in Rad^2/fs from a list of rotational orientations taken at consecutive time steps dt (in fs). It is assumed that the mean angular rotation is zero (as it is otherwise complicated to compute from a list of orientations - may require parameter estimation of the folded-normal distribution)
| Float IMP::atom::get_secondary_structure_match_score | ( | SecondaryStructureResidue | ssr1, |
| SecondaryStructureResidue | ssr2 | ||
| ) |
Compares the secondary structure probabilities of two residues.
| double IMP::atom::get_spring_constant_in_femto_newtons_per_angstrom | ( | double | k_in_kcal_per_mol_per_angstrom_square | ) |
Convert spring constant from kcal/mol/A^2 to femtonewton/A.
| int IMP::atom::get_state_index | ( | Hierarchy | h | ) |
Walk up the hierarchy to find the current state.
| double IMP::atom::get_surface_area | ( | const Selection & | s | ) |
| algebra::Transformation3D IMP::atom::get_transformation_aligning_first_to_second | ( | const Selection & | s1, |
| const Selection & | s2 | ||
| ) |
Get the transformation to align two selections.
| double IMP::atom::get_volume | ( | const Selection & | s | ) |
| double IMP::atom::get_volume_from_mass | ( | double | m, |
| ProteinDensityReference | ref = ALBER |
||
| ) |
Estimate the volume of a protein from its mass.
| [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.
| ValueException | if a non-standard residue type is passed |
| Hierarchy IMP::atom::read_mmcif | ( | TextInput | input, |
| Model * | model, | ||
| PDBSelector * | selector = get_default_pdb_selector() |
||
| ) |
Read all the molecules in the first model of the mmCIF file.
| Hierarchy IMP::atom::read_mol2 | ( | TextInput | mol2_file, |
| Model * | model, | ||
| Mol2Selector * | mol2sel = nullptr |
||
| ) |
Create a hierarchy from a Mol2 file.
| Hierarchies IMP::atom::read_multimodel_mmcif | ( | TextInput | input, |
| Model * | model, | ||
| PDBSelector * | selector = get_default_pdb_selector() |
||
| ) |
Read all models from the mmCIF file.
| Hierarchies IMP::atom::read_multimodel_pdb | ( | TextInput | input, |
| Model * | model, | ||
| PDBSelector * | selector = get_default_pdb_selector() |
||
| ) |
Read all models from the PDB file.
| Hierarchy IMP::atom::read_pdb | ( | TextInput | input, |
| Model * | model, | ||
| PDBSelector * | selector = get_default_pdb_selector(), |
||
| bool | select_first_model = true |
||
| ) |
Read all the molecules in the first model of the PDB file.
| void IMP::atom::read_pdb | ( | 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 | ) |
Remove any atom from the Hierarchy that does not have a CHARMM type.
| void IMP::atom::setup_as_approximation | ( | Particle * | h, |
| const ParticlesTemp & | other | ||
| ) |
Set the mass, radius, residues, and coordinates to approximate the passed particles.
| void IMP::atom::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.
| 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.
| void IMP::atom::show_molecular_hierarchy | ( | Hierarchy | h | ) |
| void IMP::atom::show_with_representations | ( | Hierarchy | h, |
| std::ostream & | out = std::cout |
||
| ) |
Traverse through the tree and show atom info, including representations.
| void IMP::atom::transform | ( | atom::Hierarchy | h, |
| const algebra::Transformation3D & | tr | ||
| ) |
Transform a hierarchy. This is aware of rigid bodies.
Transform a hierarchy, being aware of rigid bodies and intermediate nodes with coordinates. Rigid bodies must either be completely contained within the hierarchy or completely disjoint (no rigid bodies that contain particles in the hierarchy and other particles not in it are allowed).
| void IMP::atom::write_mol2 | ( | Hierarchy | rhd, |
| TextOutput | file_name | ||
| ) |
Write a ligand hierarchy as a mol2 file.
For now, this has to be a hierarchy created by read_mol2()
| void IMP::atom::write_multimodel_pdb | ( | const Hierarchies & | mhd, |
| TextOutput | out | ||
| ) |
Write the hierarchies one per frame.
| void IMP::atom::write_pdb | ( | const Selection & | mhd, |
| TextOutput | out, | ||
| unsigned int | model = 1 |
||
| ) |
Write some atoms to a PDB.
| void IMP::atom::write_pdb_of_c_alphas | ( | const Selection & | mhd, |
| TextOutput | out, | ||
| unsigned int | model = 1 |
||
| ) |
Write a hierarchy to a PDB as C_alpha atoms.
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.
| const AtomType IMP::atom::AT_CA |
| const ChainType IMP::atom::DNA |
Shorthand for IMP::atom::Polydeoxyribonucleotide.
| const ChainType IMP::atom::DPolypeptide |
Polypeptide(D)
| const ChainType IMP::atom::DPolysaccharide |
Polysaccharide(D)
| const ResidueType IMP::atom::GLY |
| const ChainType IMP::atom::LPolypeptide |
Polypeptide(L)
| const ChainType IMP::atom::LPolysaccharide |
Polysaccharide(L)
| const ChainType IMP::atom::Polydeoxyribonucleotide |
DNA.
| const ChainType IMP::atom::Polyribonucleotide |
RNA.
| const ChainType IMP::atom::Protein |
Shorthand for IMP::atom::LPolypeptide.
| const ChainType IMP::atom::RNA |
Shorthand for IMP::atom::Polyribonucleotide.
| const ResidueType IMP::atom::UNK |
Unknown residue.
| const ChainType IMP::atom::UnknownChainType |
Unknown chain type.