IMP Reference Guide
2.14.0
The Integrative Modeling Platform
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Class to encode a modeling protocol as mmCIF. More...
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.
See also get_handlers(), get_dumpers().
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 | flush |
Write out all information to the file. More... | |
def | set_ensemble_file |
Point a previously-created ensemble to an 'all-models' file. More... | |
def IMP.pmi.mmcif.ProtocolOutput.create_representation | ( | self, | |
name | |||
) |
def IMP.pmi.mmcif.ProtocolOutput.create_transformed_component | ( | self, | |
state, | |||
name, | |||
original, | |||
transform | |||
) |
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.
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.
def IMP.pmi.mmcif.ProtocolOutput.flush | ( | self, | |
format = 'mmCIF' |
|||
) |
Write out all information to the file.
Information can be written in any format supported by the ihm library (typically this is 'mmCIF' or 'BCIF').
def IMP.pmi.mmcif.ProtocolOutput.set_ensemble_file | ( | self, | |
i, | |||
location | |||
) |