IMP.pmi.topology.TopologyReader Class Reference

Read a pipe-delimited PMI topology file. More...

Inherits object.

Detailed Description

Read a pipe-delimited PMI topology file.

The topology file should be in a simple pipe-delimited format, such as

|directories|
|pdb_dir|./|
|fasta_dir|./|
|gmm_dir|./|

|topology_dictionary|
|component_name|domain_name|fasta_fn|fasta_id|pdb_fn|chain|residue_range|pdb_offset|bead_size|em_residues_per_gaussian|rmf_file|rmf_frame_number|
|Rpb1 |Rpb1_1|1WCM.fasta|1WCM:A|1WCM.pdb|A|1,1140   |0|10|0 |None   | None|
|Rpb1 |Rpb1_2|1WCM.fasta|1WCM:A|1WCM.pdb|A|1141,1274|0|10|0 |0.rmf3 | 0   |
|Rpb1 |Rpb1_3|1WCM.fasta|1WCM:A|1WCM.pdb|A|1275,-1  |0|10|0 |None   | None|
|Rpb2 |Rpb2  |1WCM.fasta|1WCM:B|1WCM.pdb|B|all      |0|10|0 |None   | None|

The |directories| section lists paths (relative to the topology file) where various inputs can be found.

The columns under |topology_dictionary|:

• 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).
• chain: Chain ID of this domain in the PDB file.
• residue_range: Comma delimited pair defining range. -1 = last residue. all = [1,-1]
• 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.
• 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.
• rmf_file: File path of rmf file with coordinates (if available).
• rmf_frame_number: File path of rmf file.

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 494 of file pmi/topology/__init__.py.

Public Member Functions
def	get_component_topologies
	Return list of ComponentTopologies for selected components given a list of indices. More...
def	import_topology_file
	Import system components from topology file. More...
def	set_dir
	Changes the default directories and renames the files for each ComponentTopology object. More...

Member Function Documentation

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

Return list of ComponentTopologies for selected components given a list of indices.

Definition at line 569 of file pmi/topology/__init__.py.

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

Import system components from topology file.

append=False will erase current topology and overwrite with new

Definition at line 602 of file pmi/topology/__init__.py.

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

Changes the default directories and renames the files for each ComponentTopology object.

Definition at line 579 of file pmi/topology/__init__.py.

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

• pmi/topology/__init__.py