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IMP Reference Guide
develop.63b38c487d,2024/12/21
The Integrative Modeling Platform
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Automatically setup System and Degrees of Freedom with a formatted text file. More...
Automatically setup System 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:
molecule_name: Name of the molecule (chain). Serves as the parent hierarchy for this structure. Multiple copies of the same molecule can be created by appending a copy number after a period; if none is specified, a copy number of 0 is assumed (e.g. Rpb2.1 is the second copy of Rpb2 or Rpb2.0).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. #ff0000).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. The FASTA header may contain multiple fields split by pipe (|) characters. If so, the FASTA sequence name is the first field and the second field (if present) is the UniProt accession. For example, ">cop9|Q13098" yields a FASTA sequence name of "cop9" and UniProt accession of "Q13098". If such an accession is present, it is added to the generated structure (and ultimately recorded in any output RMF file).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 or mmCIF file. This is the "author-provided" chain ID for mmCIF files, not the asym_id.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. For example, an offset of -10 would match the first residue in the FASTA file (which is always numbered sequentially starting from 1) with residue 11 in the PDB file.bead_size: The size (in residues) of beads used to model areas not covered by PDB coordinates. These will be built automatically.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: Add a mover that periodically moves several related domains as if they were a single large rigid body. In between such moves, the domains move independently. This can improve sampling.chain_of_super_rigid_bodies: Do super-rigid-body moves (as above) for all adjacent pairs of domains in the chain.flags additional flags for advanced options Definition at line 1342 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 1412 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 1740 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 1439 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 1724 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 1732 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 1453 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.TopologyReader.set_fasta_dir | ( | self, | |
| fasta_dir | |||
| ) |
Change the FASTA dir.
Definition at line 1710 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.TopologyReader.set_gmm_dir | ( | self, | |
| gmm_dir | |||
| ) |
Change the GMM dir.
Definition at line 1693 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.TopologyReader.set_pdb_dir | ( | self, | |
| pdb_dir | |||
| ) |
Change the PDB dir.
Definition at line 1703 of file pmi/topology/__init__.py.