IMP
2.4.0
The Integrative Modeling Platform
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Read a pipe-delimited PMI topology file. More...
Inherits object.
Read a pipe-delimited PMI topology file.
The topology file should be in a simple pipe-delimited format, such as
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.
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... | |
def IMP.pmi.topology.TopologyReader.get_component_topologies | ( | self, | |
topology_list = 'all' |
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) |
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 |
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) |
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.