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IMP Reference Guide  develop.eba5f5c79c,2020/07/08
The Integrative Modeling Platform
IMP.pmi.mmcif Namespace Reference

Support for the mmCIF file format. More...

Detailed Description

Support for the mmCIF file format.

IMP has basic support for writing out files in mmCIF format, for deposition in PDB-Dev. mmCIF files are currently generated by creating an IMP.pmi.mmcif.ProtocolOutput class, and attaching it to an IMP.pmi.representation.Representation object, after which any generated models and metadata are collected and output as mmCIF.

Classes

class  AsymUnit
 A single asymmetric unit in the system. More...
 
class  Entity
 A single entity in the system. More...
 
class  GMMParser
 Extract metadata from an EM density GMM file. More...
 
class  ProtocolOutput
 Class to encode a modeling protocol as mmCIF. More...
 

Functions

def get_dumpers
 Get custom python-ihm dumpers for writing PMI to from mmCIF. More...
 
def get_handlers
 Get custom python-ihm handlers for reading PMI data from mmCIF. More...
 
def read
 Read data from the mmCIF file handle fh. More...
 

Function Documentation

def IMP.pmi.mmcif.get_dumpers ( )

Get custom python-ihm dumpers for writing PMI to from mmCIF.

This returns a list of custom dumpers that can be passed as all or part of the dumpers argument to ihm.dumper.write(). They add PMI-specific information to mmCIF or BinaryCIF files written out by python-ihm.

Note
This function is only available in Python.

Definition at line 1643 of file mmcif.py.

def IMP.pmi.mmcif.get_handlers ( )

Get custom python-ihm handlers for reading PMI data from mmCIF.

This returns a list of custom handlers that can be passed as all or part of the handlers argument to ihm.reader.read(). They read PMI-specific information from mmCIF or BinaryCIF files read in by python-ihm.

Note
This function is only available in Python.

Definition at line 1652 of file mmcif.py.

def IMP.pmi.mmcif.read (   fh,
  model_class = ihm.model.Model,
  format = 'mmCIF',
  handlers = [] 
)

Read data from the mmCIF file handle fh.

This is a simple wrapper around ihm.reader.read(), which also reads PMI-specific information from the mmCIF or BinaryCIF file.

Deprecated:
As of IMP release 2.13. See the IMP Deprecation Policy for more information about deprecation in IMP. Use ihm.reader.read() instead with handlers=get_handlers()
Note
This function is only available in Python.

Definition at line 1661 of file mmcif.py.