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IMP Reference Guide  develop.cc86c9801d,2022/11/22
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 file is read in and each part of the topology is stored as a ComponentTopology object for input into IMP::pmi::macros::BuildSystem. The topology file should be in a simple pipe-delimited format:

|Rpb1 |blue |1WCM.fasta|1WCM:A|1WCM.pdb|A|1,1140 |0|10|0|1|1,3|1||
|Rpb1 |blue |1WCM.fasta|1WCM:A|1WCM.pdb|A|1141,1274|0|10|0|2|1,3|1||
|Rpb1 |blue |1WCM.fasta|1WCM:A|1WCM.pdb|A|1275,END |0|10|0|3|1,3|1||
|Rpb2 |red |1WCM.fasta|1WCM:B|1WCM.pdb|B|all |0|10|0|4|2,3|2||
|Rpb2.1 |green |1WCM.fasta|1WCM:B|1WCM.pdb|B|all |0|10|0|4|2,3|2||

These are the fields you can enter:

  • molecule_name: Name of the molecule (chain). Serves as the parent hierarchy for this structure. Multiple copies of the same molecule can be created by appending a copy number after a period; if none is specified, a copy number of 0 is assumed (e.g. Rpb2.1 is the second copy of Rpb2 or Rpb2.0).
  • color: The color used in the output RMF file. Uses Chimera names, (e.g. "red"), or R,G,B values as three comma-separated floating point numbers from 0 to 1 (e.g. "1.0, 0.0, 0.0") or a 6-digit hex string starting with '#' (e.g. #ff0000).
  • fasta_fn: Name of FASTA file containing this component.
  • fasta_id: String found in FASTA sequence header line. The sequence read from the file is assumed to be a protein sequence. If it should instead be treated as RNA or DNA, add an ',RNA' or ',DNA' suffix. For example, a fasta_id of 'myseq,RNA' will read the sequence 'myseq' from the FASTA file and treat it as RNA.
  • pdb_fn: Name of PDB or mmCIF 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. The second item in the pair can be END to select the last residue in the PDB chain.
  • pdb_offset: Offset to sync PDB residue numbering with FASTA numbering. For example, an offset of -10 would match the first residue in the FASTA file (which is always numbered sequentially starting from 1) with residue 11 in the PDB file.
  • bead_size: The size (in residues) of beads used to model areas not covered by PDB coordinates. These will be built automatically.
  • 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: Leave empty if this object is not in a rigid body. Otherwise, this is a number corresponding to the rigid body containing this object. The number itself is just used for grouping things.
  • super_rigid_body: Add a mover that periodically moves several related domains as if they were a single large rigid body. In between such moves, the domains move independently. This can improve sampling.
  • chain_of_super_rigid_bodies: Do super-rigid-body moves (as above) for all adjacent pairs of domains in the chain.
  • flags additional flags for advanced options
    All filenames are relative to the paths specified in the constructor.
    This class is only available in Python.

Definition at line 1272 of file pmi/topology/

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_components
 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 read
 Read system components from 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,
  pdb_dir = './',
  fasta_dir = './',
  gmm_dir = './' 


topology_filePipe-delimited file specifying the topology
pdb_dirRelative path to the pdb directory
fasta_dirRelative path to the fasta directory
gmm_dirRelative path to the GMM directory

Definition at line 1335 of file pmi/topology/

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 1663 of file pmi/topology/

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

Return list of ComponentTopologies for selected components.

topology_listList of indices to return

Definition at line 1362 of file pmi/topology/

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

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

Definition at line 1647 of file pmi/topology/

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

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

Definition at line 1655 of file pmi/topology/

def (   self,
  append = False 

Read system components from topology file.

append=False will erase current topology and overwrite with new

Definition at line 1376 of file pmi/topology/

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

Change the FASTA dir.

Definition at line 1633 of file pmi/topology/

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

Change the GMM dir.

Definition at line 1616 of file pmi/topology/

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

Change the PDB dir.

Definition at line 1626 of file pmi/topology/

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