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IMP Reference Guide
2.6.0
The Integrative Modeling Platform
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Automatically setup Sytem and Degrees of Freedom with a formatted text file. More...
Inherits object.
Automatically setup Sytem and Degrees of Freedom with a formatted text file.
The topology file should be in a simple pipe-delimited format:
All filenames are relative to the paths specified in the constructor. These are the fields you can enter:
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). 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.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: Number corresponding to the rigid body containing this object. The number itself is used for grouping things.super_rigid_body: Like a rigid_body, except things are only occasionally rigidchain_of_super_rigid_bodies For a polymer, create SRBs from groups.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 787 of file pmi/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_component_topologies |
| 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 | import_topology_file |
| Read system components from topology file. More... | |
| def | set_dir |
| DEPRECATED: This old function sets things relative to 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... | |
| def IMP.pmi.topology.TopologyReader.__init__ | ( | self, | |
| topology_file, | |||
resolutions = [1, |
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pdb_dir = './', |
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fasta_dir = './', |
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gmm_dir = './' |
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| ) |
Constructor.
| topology_file | Pipe-delimited file specifying the topology |
| resolutions | What resolutions to build for ALL structured components |
| 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 830 of file pmi/topology/__init__.py.
| 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 1104 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.TopologyReader.get_component_topologies | ( | self, | |
topology_list = 'all' |
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| ) |
Return list of ComponentTopologies for selected components.
| topology_list | List of indices to return |
Definition at line 860 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.TopologyReader.get_rigid_bodies | ( | self | ) |
Return list of lists of rigid bodies (as domain name)
Definition at line 1088 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.TopologyReader.get_super_rigid_bodies | ( | self | ) |
Return list of lists of super rigid bodies (as domain name)
Definition at line 1096 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.TopologyReader.import_topology_file | ( | self, | |
| topology_file, | |||
append = False |
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| ) |
Read system components from topology file.
append=False will erase current topology and overwrite with new
Definition at line 874 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.TopologyReader.set_dir | ( | self, | |
| default_dir, | |||
| new_dir | |||
| ) |
DEPRECATED: This old function sets things relative to topology file.
Definition at line 1066 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.TopologyReader.set_fasta_dir | ( | self, | |
| fasta_dir | |||
| ) |
Change the FASTA dir.
Definition at line 1060 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.TopologyReader.set_gmm_dir | ( | self, | |
| gmm_dir | |||
| ) |
Change the GMM dir.
Definition at line 1045 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.TopologyReader.set_pdb_dir | ( | self, | |
| pdb_dir | |||
| ) |
Change the PDB dir.
Definition at line 1053 of file pmi/topology/__init__.py.