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IMP Reference Guide
2.8.0
The Integrative Modeling Platform
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Stores a named protein chain. More...
Inherits _SystemBase.
Stores a named protein chain.
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 226 of file pmi/topology/__init__.py.
Public Member Functions | |
| def | __init__ |
| The user should not call this directly; instead call State::create_molecule() More... | |
| def | add_representation |
| Set the representation for some residues. 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 Will only build requested representations. 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 TempResidues that have associated structure coordinates. More... | |
| def | get_hierarchy |
| Return the IMP Hierarchy corresponding to this Molecule. More... | |
| def | get_ideal_helices |
| Returns list of OrderedSets with requested ideal helices. More... | |
| def | get_name |
| Return this Molecule name. More... | |
| def | get_non_atomic_residues |
| Return a set of TempResidues that don't have associated structure coordinates. More... | |
| def | get_particles_at_all_resolutions |
| Helpful utility for getting particles at all resolutions from this molecule. More... | |
| def | get_represented |
| Return set of TempResidues that have representation. More... | |
| def | get_residues |
| Return all modeled TempResidues as a set. More... | |
| def | get_state |
| Return the State containing this Molecule. More... | |
| def | residue_range |
| get residue range from a to b, inclusive. More... | |
| def IMP.pmi.topology.Molecule.__init__ | ( | self, | |
| state, | |||
| name, | |||
| sequence, | |||
| chain_id, | |||
| copy_num, | |||
mol_to_clone = None, |
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is_nucleic = None |
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| ) |
The user should not call this directly; instead call State::create_molecule()
| state | The parent PMI State |
| name | The name of the molecule (string) |
| sequence | Sequence (string) |
| chain_id | The chain of this molecule |
| copy_num | Store the copy number |
| mol_to_clone | The original molecule (for cloning ONLY) |
ote It's expected that you will not use this constructor directly, but rather create a Molecule with pmi::State::create_molecule()
Definition at line 238 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.Molecule.add_representation | ( | self, | |
residues = None, |
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resolutions = [], |
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bead_extra_breaks = [], |
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bead_ca_centers = True, |
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bead_default_coord = [0, |
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density_residues_per_component = None, |
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density_prefix = None, |
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density_force_compute = False, |
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density_voxel_size = 1.0, |
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setup_particles_as_densities = False, |
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ideal_helix = False, |
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color = None |
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| ) |
Set the representation for some residues.
Some options (beads, ideal helix) operate along the backbone. Others (density options) are volumetric. Some of these you can combine e.g., beads+densities or helix+densities See Resolution in PMI
| residues | Set of PMI TempResidues for adding the representation. Can use Molecule slicing to get these, e.g. mol[a:b]+mol[c:d] If None, will select all residues for this Molecule. |
| resolutions | Resolutions for beads representations. If structured, will average along backbone, breaking at sequence breaks. If unstructured, will just create beads. Pass an integer or list of integers |
| bead_extra_breaks | Additional breakpoints for splitting beads. The value can be the 0-ordered position, after which it'll insert the break. Alternatively pass PDB-style (1-ordered) indices as a string. I.e., bead_extra_breaks=[5,25] is the same as ['6','26'] |
| bead_ca_centers | Set to True if you want the resolution=1 beads to be at CA centers (otherwise will average atoms to get center). Defaults to True. |
| bead_default_coord | Advanced feature. Normally beads are placed at the nearest structure. If no structure provided (like an all bead molecule), the beads go here. |
| density_residues_per_component | Create density (Gaussian Mixture Model) for these residues. Must also supply density_prefix |
| density_prefix | Prefix (assuming '.txt') to read components from or write to. If exists, will read unless you set density_force_compute=True. Will also write map (prefix+'.mrc'). Must also supply density_residues_per_component. |
| density_force_compute | Set true to force overwrite density file. |
| density_voxel_size | Advanced feature. Set larger if densities taking too long to rasterize. Set to 0 if you don't want to create the MRC file |
| setup_particles_as_densities | Set to True if you want each particle to be its own density. Useful for all-atom models or flexible beads. Mutually exclusive with density_ options |
| ideal_helix | Create idealized helix structures for these residues at resolution 1. Any other resolutions passed will be coarsened from there. Resolution 0 will not work, you may have to use MODELLER to do that (for now). |
| color | the color applied to the hierarchies generated. Format options: tuple (r,g,b) with values 0 to 1 or float (from 0 to 1, a map from Blue to Green to Red) or IMP.display.Color object |
ote You cannot call add_representation multiple times for the same residues.
Definition at line 405 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 from the PDB file. res_range[0] is the starting and res_range[1] is the ending residue index. |
| offset | Apply an offset to the residue indexes of the PDB file. This number is added to the PDB sequence. |
| model_num | Read multi-model PDB and return that model |
| ca_only | Only read the CA positions from the PDB file |
| soft_check | If True, it only warns if there are sequence mismatches between the pdb and the Molecules sequence. Actually replaces the fasta values. If False (Default), it raises and exit when there are sequence mismatches. |
ote If you are adding structure without a FASTA file, set soft_check to True
Definition at line 361 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.Molecule.build | ( | self | ) |
Create all parts of the IMP hierarchy including Atoms, Residues, and Fragments/Representations and, finally, Copies Will only build requested representations.
/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
Definition at line 552 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.Molecule.create_clone | ( | self, | |
| chain_id | |||
| ) |
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 |
ote You cannot add structure or representations to a clone!
Definition at line 343 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 333 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.Molecule.get_atomic_residues | ( | self | ) |
Return a set of TempResidues that have associated structure coordinates.
Definition at line 317 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.Molecule.get_hierarchy | ( | self | ) |
Return the IMP Hierarchy corresponding to this Molecule.
Definition at line 282 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.Molecule.get_ideal_helices | ( | self | ) |
Returns list of OrderedSets with requested ideal helices.
Definition at line 294 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.Molecule.get_name | ( | self | ) |
Return this Molecule name.
Definition at line 286 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.Molecule.get_non_atomic_residues | ( | self | ) |
Return a set of TempResidues that don't have associated structure coordinates.
Definition at line 325 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.Molecule.get_particles_at_all_resolutions | ( | self, | |
residue_indexes = None |
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| ) |
Helpful utility for getting particles at all resolutions from this molecule.
Can optionally pass a set of residue indexes
Definition at line 634 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.Molecule.get_represented | ( | self | ) |
Return set of TempResidues that have representation.
Definition at line 313 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.Molecule.get_residues | ( | self | ) |
Return all modeled TempResidues as a set.
Definition at line 308 of file pmi/topology/__init__.py.
| def IMP.pmi.topology.Molecule.get_state | ( | self | ) |
Return the State containing this Molecule.
Definition at line 290 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 from a to b, inclusive.
Use integers to get 0-indexing, or strings to get PDB-indexing
Definition at line 298 of file pmi/topology/__init__.py.
