IMP.pmi1.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::pmi1::macros::BuildSystem. The topology file should be in a simple pipe-delimited format:

|molecule_name|color|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|flags|
|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:

• component_name: Name of the component (chain). Serves as the parent hierarchy for this structure.
• color: The color used in the output RMF file. Uses chimera names or R,G,B values
• 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 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.
• 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: 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: Like a rigid_body, except things are only occasionally rigid
• chain_of_super_rigid_bodies For a polymer, create SRBs from groups.
• flags additional flags for advanced options

ote All filenames are relative to the paths specified in the constructor.

Note

This class is only available in Python.

Definition at line 130 of file pmi1/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_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.pmi1.topology.TopologyReader.__init__	(		self,
			topology_file,
			pdb_dir = './',
			fasta_dir = './',
			gmm_dir = './'
	)

Constructor.

Parameters

topology_file	Pipe-delimited file specifying the topology
pdb_dir	Relative path to the pdb directory
fasta_dir	Relative path to the fasta directory
gmm_dir	Relative path to the GMM directory

Definition at line 177 of file pmi1/topology/__init__.py.

Member Function Documentation

def IMP.pmi1.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 488 of file pmi1/topology/__init__.py.

def IMP.pmi1.topology.TopologyReader.get_components	(		self,
			topology_list = 'all'
	)

Return list of ComponentTopologies for selected components.

Parameters

topology_list

List of indices to return

Definition at line 211 of file pmi1/topology/__init__.py.

def IMP.pmi1.topology.TopologyReader.get_rigid_bodies

(

self

)

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

Definition at line 472 of file pmi1/topology/__init__.py.

def IMP.pmi1.topology.TopologyReader.get_super_rigid_bodies

(

self

)

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

Definition at line 480 of file pmi1/topology/__init__.py.

def IMP.pmi1.topology.TopologyReader.read	(		self,
			topology_file,
			append = False
	)

Read system components from topology file.

append=False will erase current topology and overwrite with new

Definition at line 225 of file pmi1/topology/__init__.py.

def IMP.pmi1.topology.TopologyReader.set_fasta_dir	(		self,
			fasta_dir
	)

Change the FASTA dir.

Definition at line 458 of file pmi1/topology/__init__.py.

def IMP.pmi1.topology.TopologyReader.set_gmm_dir	(		self,
			gmm_dir
	)

Change the GMM dir.

Definition at line 443 of file pmi1/topology/__init__.py.

def IMP.pmi1.topology.TopologyReader.set_pdb_dir	(		self,
			pdb_dir
	)

Change the PDB dir.

Definition at line 451 of file pmi1/topology/__init__.py.

---

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

• pmi1/topology/__init__.py