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IMP Reference Guide
2.5.0
The Integrative Modeling Platform
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This class is constructed from within the State class. More...
Inheritance diagram for IMP.pmi.topology.Molecule:This class is constructed from within the State class.
It wraps an IMP.atom.Molecule and IMP.atom.Copy Structure is read using this class Resolutions and copies can be registered, but are only created when build() is called
Definition at line 197 of file pmi/topology/__init__.py.
Public Member Functions | |
| def | __init__ |
| The user should not call this direclty, instead call State::create_molecule() More... | |
| def | add_representation |
| handles the IMP.atom.Representation decorators, such as multi-scale, density, etc. More... | |
| def | add_structure |
| Read a structure and store the coordinates. More... | |
| def | build |
| Create all parts of the IMP hierarchy including Atoms, Residues, and Fragments/Representations and, finally, Copies /note Any residues assigned a resolution must have an IMP.atom.Residue hierarchy containing at least a CAlpha. More... | |
| def | create_clone |
| Create a Molecule clone (automatically builds same structure and representation) More... | |
| def | create_copy |
| Create a new Molecule with the same name and sequence but a higher copy number. More... | |
| def | get_atomic_residues |
| Return a set of Residues that have associated structure coordinates. More... | |
| def | get_non_atomic_residues |
| Return a set of Residues that don't have associated structure coordinates. More... | |
| def | get_residues |
| Return all Residues as a set. More... | |
| def | residue_range |
| get residue range. More... | |
| Public Member Functions inherited from IMP.pmi.topology.SystemBase | |
| def | build |
| Build the coordinates of the system. More... | |
| def IMP.pmi.topology.Molecule.__init__ | ( | self, | |
| state, | |||
| name, | |||
| sequence, | |||
| chain_id, | |||
| copy_num, | |||
mol_to_clone = None, |
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transformation = None |
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| ) |
The user should not call this direclty, instead call State::create_molecule()
| state | The parent PMI State |
| name | The name of the molecule (string) |
| sequence | Sequence (string) |
| mol_to_clone | The original molecule (for cloning ONLY) |
| transformation | A transform to apply during building (primarily for cloning) |
Definition at line 204 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.Molecule.add_representation | ( | self, | |
res_set = None, |
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representation_type = 'balls', |
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resolutions = [] |
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| ) |
handles the IMP.atom.Representation decorators, such as multi-scale, density, etc.
| res_set | set of PMI residues for adding the representation |
| representation_type | currently supports only balls |
| resolutions | what resolutions to add to the residues (see Resolution in PMI) |
Definition at line 341 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.Molecule.add_structure | ( | self, | |
| pdb_fn, | |||
| chain_id, | |||
res_range = [], |
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offset = 0, |
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model_num = None, |
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ca_only = False, |
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soft_check = False |
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| ) |
Read a structure and store the coordinates.
Returns the atomic residues (as a set)
| pdb_fn | The file to read |
| chain_id | Chain ID to read |
| res_range | Add only a specific set of residues |
| offset | Apply an offset to the residue indexes of the PDB file |
| model_num | Read multi-model PDB and return that model |
| soft_check | If True, it only warns if there are sequence mismatches between the pdb and the Molecules sequence If False (Default), it raises and exit when there are sequence mismatches. |
ote After offset, we expect the PDB residue numbering to match the FASTA file
Definition at line 309 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.Molecule.build | ( | self, | |
merge_type = 'backbone', |
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ca_centers = True, |
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fill_in_missing_residues = True |
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| ) |
Create all parts of the IMP hierarchy including Atoms, Residues, and Fragments/Representations and, finally, Copies /note Any residues assigned a resolution must have an IMP.atom.Residue hierarchy containing at least a CAlpha.
For missing residues, these can be constructed from the PDB file
| merge_type | Principle for grouping into fragments. "backbone": linear sequences along backbone are grouped into fragments if they have identical sets of representations. "volume": at each resolution, groups are made based on spatial distance (not currently implemented) |
| ca_centers | For single-bead-per-residue only. Set the center over the CA position. |
Definition at line 358 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.Molecule.create_clone | ( | self, | |
| chain_id, | |||
transformation = None |
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| ) |
Create a Molecule clone (automatically builds same structure and representation)
| chain_id | If you want to set the chain ID of the copy to something |
| transformation | Apply transformation after building (at the end) |
Definition at line 295 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.Molecule.create_copy | ( | self, | |
| chain_id | |||
| ) |
Create a new Molecule with the same name and sequence but a higher copy number.
Returns the Molecule. No structure or representation will be copied!
| chain_id | Chain ID of the new molecule |
Definition at line 285 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.Molecule.get_atomic_residues | ( | self | ) |
Return a set of Residues that have associated structure coordinates.
Definition at line 269 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.Molecule.get_non_atomic_residues | ( | self | ) |
Return a set of Residues that don't have associated structure coordinates.
Definition at line 277 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.Molecule.get_residues | ( | self | ) |
Return all Residues as a set.
Definition at line 262 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.Molecule.residue_range | ( | self, | |
| a, | |||
| b, | |||
stride = 1 |
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| ) |
get residue range.
Use integers to get 0-indexing, or strings to get PDB-indexing
Definition at line 253 of file pmi/topology/__init__.py.