IMP  2.4.0
The Integrative Modeling Platform
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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|:

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 490 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 565 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 598 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 575 of file pmi/topology/__init__.py.


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