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IMP Reference Guide  2.6.1
The Integrative Modeling Platform
IMP.pmi.topology.TopologyReader Class Reference

Automatically setup Sytem and Degrees of Freedom with a formatted text file. More...

Inherits object.

Detailed Description

Automatically setup Sytem and Degrees of Freedom with a formatted text file.

The topology file should be in a simple pipe-delimited format:

|component_name|domain_name|fasta_fn|fasta_id|pdb_fn|chain|residue_range|pdb_offset|bead_size|em_residues_per_gaussian|rigid_body|super_rigid_body|chain_of_super_rigid_bodies|
|Rpb1 |Rpb1_1|1WCM.fasta|1WCM:A|1WCM.pdb|A|1,1140 |0|10|0|1|1,3|1|
|Rpb1 |Rpb1_2|1WCM.fasta|1WCM:A|1WCM.pdb|A|1141,1274|0|10|0|2|1,3|1|
|Rpb1 |Rpb1_3|1WCM.fasta|1WCM:A|1WCM.pdb|A|1275,-1 |0|10|0|3|1,3|1|
|Rpb2 |Rpb2 |1WCM.fasta|1WCM:B|1WCM.pdb|B|all |0|10|0|4|2,3|2|

All filenames are relative to the paths specified in the constructor. These are the fields you can enter:

  • component_name: Name of the component (chain). Serves as the parent hierarchy for this structure.
  • domain_name: Allows subdivision of chains into individual domains. A model consists of a number of individual units, referred to as domains. Each domain can be an individual chain, or a subset of a chain, and these domains are used to set rigid body movers. A chain may be separated into multiple domains if the user wishes different sections to move independently, and/or analyze the portions separately.
  • fasta_fn: Name of FASTA file containing this component.
  • fasta_id: String found in FASTA sequence header line.
  • pdb_fn: Name of PDB file with coordinates (if available). If left empty, will set up as BEADS (you can also specify "BEADS") Can also write "IDEAL_HELIX".
  • chain: Chain ID of this domain in the PDB file.
  • residue_range: Comma delimited pair defining range. Can leave empty or use 'all' for entire sequence from PDB file.
  • pdb_offset: Offset to sync PDB residue numbering with FASTA numbering.
  • bead_size: The size (in residues) of beads used to model areas not covered by PDB coordinates. These will be automatically built.
  • em_residues: The number of Gaussians used to model the electron density of this domain. Set to zero if no EM fitting will be done. The GMM files will be written to <gmm_dir>/<component_name>_<em_res>.txt (and .mrc)
  • rigid_body: Number corresponding to the rigid body containing this object. The number itself is used for grouping things.
  • super_rigid_body: Like a rigid_body, except things are only occasionally rigid
  • chain_of_super_rigid_bodies For a polymer, create SRBs from groups.

The file is read in and each part of the topology is stored as a ComponentTopology object for input into IMP::pmi::macros::BuildModel.

Note
This class is only available in Python.

Definition at line 787 of file pmi/topology/__init__.py.

Public Member Functions

def __init__
 Constructor. More...
 
def get_chains_of_super_rigid_bodies
 Return list of lists of chains of super rigid bodies (as domain name) More...
 
def get_component_topologies
 Return list of ComponentTopologies for selected components. More...
 
def get_rigid_bodies
 Return list of lists of rigid bodies (as domain name) More...
 
def get_super_rigid_bodies
 Return list of lists of super rigid bodies (as domain name) More...
 
def import_topology_file
 Read system components from topology file. More...
 
def set_dir
 DEPRECATED: This old function sets things relative to topology file. More...
 
def set_fasta_dir
 Change the FASTA dir. More...
 
def set_gmm_dir
 Change the GMM dir. More...
 
def set_pdb_dir
 Change the PDB dir. More...
 

Constructor & Destructor Documentation

def IMP.pmi.topology.TopologyReader.__init__ (   self,
  topology_file,
  resolutions = [1,
  pdb_dir = './',
  fasta_dir = './',
  gmm_dir = './' 
)

Constructor.

Parameters
topology_filePipe-delimited file specifying the topology
resolutionsWhat resolutions to build for ALL structured components
pdb_dirRelative path to the pdb directory
fasta_dirRelative path to the fasta directory
gmm_dirRelative path to the GMM directory

Definition at line 830 of file pmi/topology/__init__.py.

Member Function Documentation

def IMP.pmi.topology.TopologyReader.get_chains_of_super_rigid_bodies (   self)

Return list of lists of chains of super rigid bodies (as domain name)

Definition at line 1104 of file pmi/topology/__init__.py.

def IMP.pmi.topology.TopologyReader.get_component_topologies (   self,
  topology_list = 'all' 
)

Return list of ComponentTopologies for selected components.

Parameters
topology_listList of indices to return

Definition at line 860 of file pmi/topology/__init__.py.

def IMP.pmi.topology.TopologyReader.get_rigid_bodies (   self)

Return list of lists of rigid bodies (as domain name)

Definition at line 1088 of file pmi/topology/__init__.py.

def IMP.pmi.topology.TopologyReader.get_super_rigid_bodies (   self)

Return list of lists of super rigid bodies (as domain name)

Definition at line 1096 of file pmi/topology/__init__.py.

def IMP.pmi.topology.TopologyReader.import_topology_file (   self,
  topology_file,
  append = False 
)

Read system components from topology file.

append=False will erase current topology and overwrite with new

Definition at line 874 of file pmi/topology/__init__.py.

def IMP.pmi.topology.TopologyReader.set_dir (   self,
  default_dir,
  new_dir 
)

DEPRECATED: This old function sets things relative to topology file.

Definition at line 1066 of file pmi/topology/__init__.py.

def IMP.pmi.topology.TopologyReader.set_fasta_dir (   self,
  fasta_dir 
)

Change the FASTA dir.

Definition at line 1060 of file pmi/topology/__init__.py.

def IMP.pmi.topology.TopologyReader.set_gmm_dir (   self,
  gmm_dir 
)

Change the GMM dir.

Definition at line 1045 of file pmi/topology/__init__.py.

def IMP.pmi.topology.TopologyReader.set_pdb_dir (   self,
  pdb_dir 
)

Change the PDB dir.

Definition at line 1053 of file pmi/topology/__init__.py.


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