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IMP Reference Guide  develop.d3e3923077,2019/12/11
The Integrative Modeling Platform
IMP.pmi1.representation.Representation Class Reference

Set up the representation of all proteins and nucleic acid macromolecules. More...

Inherits object.

Detailed Description

Set up the representation of all proteins and nucleic acid macromolecules.

Create the molecular hierarchies, representation, sequence connectivity for the various involved proteins and nucleic acid macromolecules:

Create a protein, DNA or RNA, represent it as a set of connected balls of appropriate radii and number of residues, PDB at given resolution(s), or ideal helices.

How to use the SimplifiedModel class (typical use):

see test/test_hierarchy_contruction.py

examples:

1) Create a chain of helices and flexible parts

c_1_119 =self.add_component_necklace("prot1",1,119,20) c_120_131 =self.add_component_ideal_helix("prot1",resolutions=[1,10],resrange=(120,131)) c_132_138 =self.add_component_beads("prot1",[(132,138)]) c_139_156 =self.add_component_ideal_helix("prot1",resolutions=[1,10],resrange=(139,156)) c_157_174 =self.add_component_beads("prot1",[(157,174)]) c_175_182 =self.add_component_ideal_helix("prot1",resolutions=[1,10],resrange=(175,182)) c_183_194 =self.add_component_beads("prot1",[(183,194)]) c_195_216 =self.add_component_ideal_helix("prot1",resolutions=[1,10],resrange=(195,216)) c_217_250 =self.add_component_beads("prot1",[(217,250)])

self.set_rigid_body_from_hierarchies(c_120_131) self.set_rigid_body_from_hierarchies(c_139_156) self.set_rigid_body_from_hierarchies(c_175_182) self.set_rigid_body_from_hierarchies(c_195_216)

clist=[c_1_119,c_120_131,c_132_138,c_139_156,c_157_174,c_175_182,c_183_194,c_195_216, c_217_250]

self.set_chain_of_super_rigid_bodies(clist,2,3)

self.set_super_rigid_bodies(["prot1"])

Note
This class is only available in Python.

Definition at line 45 of file pmi1/representation.py.

Public Member Functions

def __init__
 Constructor. More...
 
def add_all_atom_densities
 Decorates all specified particles as Gaussians directly. More...
 
def add_component_beads
 add beads to the representation More...
 
def add_component_density
 Sets up a Gaussian Mixture Model for this component. More...
 
def add_component_hierarchy_clone
 Make a copy of a hierarchy and append it to a component. More...
 
def add_component_necklace
 Generates a string of beads with given length. More...
 
def add_component_pdb
 Add a component that has an associated 3D structure in a PDB file. More...
 
def add_component_sequence
 Add the primary sequence for a single component. More...
 
def add_metadata
 Associate some metadata with this modeling. More...
 
def add_protocol_output
 Capture details of the modeling protocol. More...
 
def check_root
 If the root hierarchy does not exist, construct it. More...
 
def coarse_hierarchy
 Generate all needed coarse grained layers. More...
 
def create_components_from_rmf
 still not working. More...
 
def create_non_modeled_component
 Create a component that isn't used in the modeling. More...
 
def create_rotational_symmetry
 The copies must not contain rigid bodies. More...
 
def create_transformed_component
 Create a transformed view of a component. More...
 
def get_file_dataset
 Get the dataset associated with a filename, or None. More...
 
def get_hierarchies_at_given_resolution
 Get the hierarchies at the given resolution. More...
 
def get_particles_from_selection_tuples
 selection tuples must be [(r1,r2,"name1"),(r1,r2,"name2"),.... More...
 
def link_components_to_rmf
 Load coordinates in the current representation. More...
 
def remove_floppy_bodies
 Remove leaves of hierarchies from the floppy bodies list. More...
 
def remove_floppy_bodies_from_component
 Remove leaves of hierarchies from the floppy bodies list based on the component name. More...
 
def set_chain_of_super_rigid_bodies
 Make a chain of super rigid bodies from a list of hierarchies. More...
 
def set_coordinates_from_rmf
 Read and replace coordinates from an RMF file. More...
 
def set_file_dataset
 Associate a dataset with a filename. More...
 
def set_floppy_bodies_as_fixed
 Fix floppy bodies in their actual position. More...
 
def set_rigid_bodies
 Construct a rigid body from a list of subunits. More...
 
def set_rigid_bodies_as_fixed
 Fix rigid bodies in their actual position. More...
 
def set_rigid_body_from_hierarchies
 Construct a rigid body from hierarchies (and optionally particles). More...
 
def setup_component_sequence_connectivity
 Generate restraints between contiguous fragments in the hierarchy. More...
 
def shuffle_configuration
 Shuffle configuration; used to restart the optimization. More...
 

Constructor & Destructor Documentation

def IMP.pmi1.representation.Representation.__init__ (   self,
  model,
  upperharmonic = True,
  disorderedlength = True 
)

Constructor.

Parameters
modelthe model
upperharmonicThis flag uses either harmonic (False) or upperharmonic (True) in the intra-pair connectivity restraint.
disorderedlengthThis flag uses either disordered length calculated for random coil peptides (True) or zero surface-to-surface distance between beads (False) as optimal distance for the sequence connectivity restraint.

Definition at line 85 of file pmi1/representation.py.

Member Function Documentation

def IMP.pmi1.representation.Representation.add_all_atom_densities (   self,
  name,
  hierarchies = None,
  selection_tuples = None,
  particles = None,
  resolution = 0,
  output_map = None,
  voxel_size = 1.0 
)

Decorates all specified particles as Gaussians directly.

Parameters
namecomponent name
hierarchiesset up GMM for some hierarchies
selection_tuples(list of tuples) example (first_residue,last_residue,component_name)
particlesset up GMM for particles directly
resolutionusual PMI resolution for selecting particles from the hierarchies

Definition at line 857 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.add_component_beads (   self,
  name,
  ds,
  colors = None,
  incoord = None 
)

add beads to the representation

Parameters
namethe component name
dsa list of tuples corresponding to the residue ranges of the beads
colorsa list of colors associated to the beads
incoordthe coordinate tuple corresponding to the position of the beads

Definition at line 608 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.add_component_density (   self,
  name,
  hierarchies = None,
  selection_tuples = None,
  particles = None,
  resolution = 0.0,
  num_components = 10,
  inputfile = None,
  outputfile = None,
  outputmap = None,
  kernel_type = None,
  covariance_type = 'full',
  voxel_size = 1.0,
  out_hier_name = '',
  sampled_points = 1000000,
  num_iter = 100,
  simulation_res = 1.0,
  multiply_by_total_mass = True,
  transform = None,
  intermediate_map_fn = None,
  density_ps_to_copy = None,
  use_precomputed_gaussians = False 
)

Sets up a Gaussian Mixture Model for this component.

Can specify input GMM file or it will be computed.

Parameters
namecomponent name
hierarchiesset up GMM for some hierarchies
selection_tuples(list of tuples) example (first_residue,last_residue,component_name)
particlesset up GMM for particles directly
resolutionusual PMI resolution for selecting particles from the hierarchies
inputfileread the GMM from this file
outputfilefit and write the GMM to this file (text)
outputmapafter fitting, create GMM density file (mrc)
kernel_typefor creating the intermediate density (points are sampled to make GMM). Options are IMP.em.GAUSSIAN, IMP.em.SPHERE, and IMP.em.BINARIZED_SPHERE
covariance_typefor fitting the GMM. options are 'full', 'diagonal' and 'spherical'
voxel_sizefor creating the intermediate density map and output map. lower number increases accuracy but also rasterizing time grows
out_hier_namename of the output density hierarchy
sampled_pointsnumber of points to sample. more will increase accuracy and fitting time
num_iternum GMM iterations. more will increase accuracy and fitting time
multiply_by_total_massmultiply the weights of the GMM by this value (only works on creation!)
transformfor input file only, apply a transformation (eg for multiple copies same GMM)
intermediate_map_fnfor debugging, this will write the intermediate (simulated) map
density_ps_to_copyin case you already created the appropriate GMM (eg, for beads)
use_precomputed_gaussiansSet this flag and pass fragments - will use roughly spherical Gaussian setup

Definition at line 730 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.add_component_hierarchy_clone (   self,
  name,
  hierarchy 
)

Make a copy of a hierarchy and append it to a component.

Definition at line 917 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.add_component_necklace (   self,
  name,
  begin,
  end,
  length,
  color = None,
  incoord = None 
)

Generates a string of beads with given length.

Definition at line 706 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.add_component_pdb (   self,
  name,
  pdbname,
  chain,
  resolutions,
  color = None,
  resrange = None,
  offset = 0,
  cacenters = True,
  show = False,
  isnucleicacid = False,
  readnonwateratoms = False,
  read_ca_cb_only = False 
)

Add a component that has an associated 3D structure in a PDB file.

Reads the PDB, and constructs the fragments corresponding to contiguous sequence stretches.

Returns
a list of hierarchies.
Parameters
name(string) the name of the component
pdbname(string) the name of the PDB file
chain(string or integer) can be either a string (eg, "A") or an integer (eg, 0 or 1) in case you want to get the corresponding chain number in the PDB.
resolutions(integers) a list of integers that corresponds to the resolutions that have to be generated
color(float from 0 to 1) the color applied to the hierarchies generated
resrange(tuple of integers): the residue range to extract from the PDB. It is a tuple (beg,end). If not specified, all residues belonging to the specified chain are read.
offset(integer) specifies the residue index offset to be applied when reading the PDB (the FASTA sequence is assumed to start from residue 1, so use this parameter if the PDB file does not start at residue 1)
cacenters(boolean) if True generates resolution=1 beads centered on C-alpha atoms.
show(boolean) print out the molecular hierarchy at the end.
isnucleicacid(boolean) use True if you're reading a PDB with nucleic acids.
readnonwateratoms(boolean) if True fixes some pathological PDB.
read_ca_cb_only(boolean) if True, only reads CA/CB

Definition at line 391 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.add_component_sequence (   self,
  name,
  filename,
  id = None,
  offs = None,
  format = 'FASTA' 
)

Add the primary sequence for a single component.

Parameters
nameHuman-readable name of the component
filenameName of the FASTA file
idIdentifier of the sequence in the FASTA file header (if not provided, use name instead)

Definition at line 267 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.add_metadata (   self,
  m 
)

Associate some metadata with this modeling.

Parameters
man instance of IMP.pmi1.metadata.Metadata or a subclass.

Definition at line 177 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.add_protocol_output (   self,
  p 
)

Capture details of the modeling protocol.

Parameters
pan instance of IMP.pmi1.output.ProtocolOutput or a subclass.

Definition at line 202 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.check_root (   self,
  name,
  protein_h,
  resolution 
)

If the root hierarchy does not exist, construct it.

Definition at line 1228 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.coarse_hierarchy (   self,
  name,
  start,
  end,
  resolutions,
  isnucleicacid,
  input_hierarchy,
  protein_h,
  type,
  color 
)

Generate all needed coarse grained layers.

Parameters
namename of the protein
resolutionslist of resolutions
protein_hroot hierarchy
input_hierarchyhierarchy to coarse grain
typea string, typically "pdb" or "helix"

Definition at line 1239 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.create_components_from_rmf (   self,
  rmfname,
  frameindex 
)

still not working.

create the representation (i.e. hierarchies) from the rmf file. it will be stored in self.prot, which will be overwritten. load the coordinates from the rmf file at frameindex.

Definition at line 1874 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.create_non_modeled_component (   self,
  name 
)

Create a component that isn't used in the modeling.

No coordinates or other structural data for this component will be read or written, but a primary sequence can be assigned. This is useful if the input experimental data is of a system larger than that modeled. Any references to these non-modeled components can then be correctly resolved later.

Definition at line 246 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.create_rotational_symmetry (   self,
  maincopy,
  copies,
  rotational_axis = IMP.algebra.Vector3D(0, 0,
  nSymmetry = None,
  skip_gaussian_in_clones = False 
)

The copies must not contain rigid bodies.

The symmetry restraints are applied at each leaf.

Definition at line 1721 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.create_transformed_component (   self,
  name,
  original,
  transform 
)

Create a transformed view of a component.

This does not copy the coordinates or representation of the component, and the transformed component is not visible to IMP, but when the model is written to a ProtocolOutput, the transformed component is added. This can be used to easily add symmetry-related 'copies' of a component without copying the underlying IMP objects.

Definition at line 235 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.get_file_dataset (   self,
  fname 
)

Get the dataset associated with a filename, or None.

Parameters
fnamefilename
Returns
an ihm.dataset.Dataset, or None.

Definition at line 195 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.get_hierarchies_at_given_resolution (   self,
  resolution 
)

Get the hierarchies at the given resolution.

The map between resolution and hierarchies is cached to accelerate the selection algorithm. The cache is invalidated when the representation was changed by any add_component_xxx.

Definition at line 1380 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.get_particles_from_selection_tuples (   self,
  selection_tuples,
  resolution = None 
)

selection tuples must be [(r1,r2,"name1"),(r1,r2,"name2"),....

]

Returns
the particles

Definition at line 2121 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.link_components_to_rmf (   self,
  rmfname,
  frameindex 
)

Load coordinates in the current representation.

This should be done only if the hierarchy self.prot is identical to the one as stored in the rmf i.e. all components were added.

Definition at line 1860 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.remove_floppy_bodies (   self,
  hierarchies 
)

Remove leaves of hierarchies from the floppy bodies list.

Given a list of hierarchies, get the leaves and remove the corresponding particles from the floppy bodies list. We need this function because sometimes we want to constrain the floppy bodies in a rigid body - for instance when you want to associate a bead with a density particle.

Definition at line 2082 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.remove_floppy_bodies_from_component (   self,
  component_name 
)

Remove leaves of hierarchies from the floppy bodies list based on the component name.

Definition at line 2067 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.set_chain_of_super_rigid_bodies (   self,
  hiers,
  min_length = None,
  max_length = None,
  axis = None 
)

Make a chain of super rigid bodies from a list of hierarchies.

Takes a linear list of hierarchies (they are supposed to be sequence-contiguous) and produces a chain of super rigid bodies with given length range, specified by min_length and max_length.

Definition at line 2019 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.set_coordinates_from_rmf (   self,
  component_name,
  rmf_file_name,
  rmf_frame_number,
  rmf_component_name = None,
  check_number_particles = True,
  representation_name_to_rmf_name_map = None,
  state_number = 0,
  skip_gaussian_in_rmf = False,
  skip_gaussian_in_representation = False,
  save_file = False,
  force_rigid_update = False 
)

Read and replace coordinates from an RMF file.

Replace the coordinates of particles with the same name. It assumes that the RMF and the representation have the particles in the same order.

Parameters
component_nameComponent name
rmf_component_nameName of the component in the RMF file (if not specified, use component_name)
representation_name_to_rmf_name_mapa dictionary that map the original rmf particle name to the recipient particle component name
save_filesave a file with the names of particles of the component
force_rigid_updateupdate the coordinates of rigid bodies (normally this should be called before rigid bodies are set up)

Definition at line 1084 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.set_file_dataset (   self,
  fname,
  dataset 
)

Associate a dataset with a filename.

This can be used to identify how the file was produced (in many cases IMP can determine this automatically from a file header or other metadata, but not always). For example, a manually-produced PDB file (not from the PDB database or Modeller) can be identified this way.

Parameters
fnamefilename the ihm.dataset.Dataset object to associate.

Definition at line 187 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.set_floppy_bodies_as_fixed (   self,
  floppybodiesarefixed = True 
)

Fix floppy bodies in their actual position.

The get_particles_to_sample() function will return just the rigid bodies (if they are not fixed).

Definition at line 2164 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.set_rigid_bodies (   self,
  subunits 
)

Construct a rigid body from a list of subunits.

Each subunit is a tuple that identifies the residue ranges and the component name (as used in create_component()).

subunits: [(name_1,(first_residue_1,last_residue_1)),(name_2,(first_residue_2,last_residue_2)),.....] or [name_1,name_2,(name_3,(first_residue_3,last_residue_3)),.....]

example: ["prot1","prot2",("prot3",(1,10))]

sometimes, we know about structure of an interaction and here we make such PPIs rigid

Definition at line 1933 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.set_rigid_bodies_as_fixed (   self,
  rigidbodiesarefixed = True 
)

Fix rigid bodies in their actual position.

The get_particles_to_sample() function will return just the floppy bodies (if they are not fixed).

Definition at line 2156 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.set_rigid_body_from_hierarchies (   self,
  hiers,
  particles = None 
)

Construct a rigid body from hierarchies (and optionally particles).

Parameters
hierslist of hierarchies to make rigid
particleslist of particles to add to the rigid body

Definition at line 1896 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.setup_component_sequence_connectivity (   self,
  name,
  resolution = 10,
  scale = 1.0 
)

Generate restraints between contiguous fragments in the hierarchy.

The linkers are generated at resolution 10 by default.

Definition at line 1629 of file pmi1/representation.py.

def IMP.pmi1.representation.Representation.shuffle_configuration (   self,
  max_translation = 300.0,
  max_rotation = 2.0 * pi,
  avoidcollision = True,
  cutoff = 10.0,
  niterations = 100,
  bounding_box = None,
  excluded_rigid_bodies = None,
  ignore_initial_coordinates = False,
  hierarchies_excluded_from_collision = None 
)

Shuffle configuration; used to restart the optimization.

The configuration of the system is initialized by placing each rigid body and each bead randomly in a box with a side of max_translation angstroms, and far enough from each other to prevent any steric clashes. The rigid bodies are also randomly rotated.

Parameters
avoidcollisioncheck if the particle/rigid body was placed close to another particle; uses the optional arguments cutoff and niterations
bounding_boxdefined by ((x1,y1,z1),(x2,y2,z2))

Definition at line 1404 of file pmi1/representation.py.


The documentation for this class was generated from the following file: