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IMP Reference Guide
2.12.0
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 file is read in and each part of the topology is stored as a ComponentTopology object for input into IMP::pmi::macros::BuildSystem. The topology file should be in a simple pipe-delimited format:
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, (e.g. "red"), or R,G,B values as three comma-separated floating point numbers from 0 to 1 (e.g. "1.0, 0.0, 0.0") or a 6-digit hex string starting with '#' (e.g. 0xff0000).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 or mmCIF 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 rigidchain_of_super_rigid_bodies For a polymer, create SRBs from groups.flags additional flags for advanced options Definition at line 1118 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_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... | |
| def IMP.pmi.topology.TopologyReader.__init__ | ( | self, | |
| topology_file, | |||
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 |
| 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 1170 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 1475 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.TopologyReader.get_components | ( | 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 1198 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 1459 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 1467 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.TopologyReader.read | ( | 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 1212 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.TopologyReader.set_fasta_dir | ( | self, | |
| fasta_dir | |||
| ) |
Change the FASTA dir.
Definition at line 1445 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.TopologyReader.set_gmm_dir | ( | self, | |
| gmm_dir | |||
| ) |
Change the GMM dir.
Definition at line 1430 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.TopologyReader.set_pdb_dir | ( | self, | |
| pdb_dir | |||
| ) |
Change the PDB dir.
Definition at line 1438 of file pmi/topology/__init__.py.