IMP.pmi.mmcif.ProtocolOutput Class Reference

Class to encode a modeling protocol as mmCIF. More...

Inheritance diagram for IMP.pmi.mmcif.ProtocolOutput:

Detailed Description

Class to encode a modeling protocol as mmCIF.

IMP has basic support for writing out files in mmCIF format, for deposition in PDB-Dev. After creating an instance of this class, attach it to an IMP.pmi.topology.System object. After this, any generated models and metadata are automatically collected in the system attribute, which is an ihm.System object. Once the protocol is complete, call finalize() to make sure system contains everything, then use the python-ihm API to write out files in mmCIF or BinaryCIF format.

Each PMI subunit will be mapped to an IHM AsymUnit class which contains the subset of the sequence that was represented. Use the asym_units dict to get this object given a PMI subunit name. Each unique sequence will be mapped to an IHM Entity class (for example when modeling a homodimer there will be two AsymUnits which both point to the same Entity). Use the entities dict to get this object from a PMI subunit name.

See also Entity, AsymUnit, get_handlers(), get_dumpers().

Note

This class is only available in Python.

Definition at line 1270 of file mmcif.py.

Public Member Functions
def	create_representation
	Create a new Representation and return it. More...
def	create_transformed_component
	Make a new component that's a transformed copy of another. More...
def	exclude_coordinates
	Don't record coordinates for the given domain. More...
def	finalize
	Do any final processing on the class hierarchy. More...
def	finalize_build
	Called immediately after the PMI system is built. More...
def	set_ensemble_file
	Point a previously-created ensemble to an 'all-models' file. More...

Member Function Documentation

def IMP.pmi.mmcif.ProtocolOutput.create_representation	(		self,
			name
	)

Create a new Representation and return it.

This can be passed to add_model(), add_bead_element() or add_pdb_element().

Definition at line 1319 of file mmcif.py.

def IMP.pmi.mmcif.ProtocolOutput.create_transformed_component	(		self,
			state,
			name,
			original,
			transform
	)

Make a new component that's a transformed copy of another.

All representation for the existing component is copied to the new one.

Definition at line 1370 of file mmcif.py.

def IMP.pmi.mmcif.ProtocolOutput.exclude_coordinates	(		self,
			component,
			seqrange
	)

Don't record coordinates for the given domain.

Coordinates for the given domain (specified by a component name and a 2-element tuple giving the start and end residue numbers) will be excluded from the mmCIF file. This can be used to exclude parts of the structure that weren't well resolved in modeling. Any bead or residue that lies wholly within this range will be excluded. Multiple ranges for a given component can be excluded by calling this method multiple times.

Definition at line 1329 of file mmcif.py.

def IMP.pmi.mmcif.ProtocolOutput.finalize

(

self

)

Do any final processing on the class hierarchy.

After calling this method, the system member (an instance of ihm.System) completely reproduces the PMI modeling, and can be written out to an mmCIF file with ihm.dumper.write, and/or modified using the ihm API.

Definition at line 1436 of file mmcif.py.

def IMP.pmi.mmcif.ProtocolOutput.finalize_build

(

self

)

Called immediately after the PMI system is built.

Definition at line 1422 of file mmcif.py.

def IMP.pmi.mmcif.ProtocolOutput.set_ensemble_file	(		self,
			i,
			location
	)

Point a previously-created ensemble to an 'all-models' file.

This could be a trajectory such as DCD, an RMF, or a multimodel PDB file.

Definition at line 1565 of file mmcif.py.

---

The documentation for this class was generated from the following file:

• mmcif.py