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IMP Reference Guide  2.19.0
The Integrative Modeling Platform
IMP.pmi.output.Output Class Reference

Class for easy writing of PDBs, RMFs, and stat files. More...

Inherits object.

Detailed Description

Class for easy writing of PDBs, RMFs, and stat files.

Note
Model should be updated prior to writing outputs.
This class is only available in Python.

Definition at line 203 of file output.py.

Public Member Functions

def get_pdb_names
 Get a list of all PDB files being output by this instance. More...
 
def get_prot_name_from_particle
 Get the protein name from the particle. More...
 
def init_pdb
 Init PDB Writing. More...
 
def init_pdb_best_scoring
 Prepare for writing best-scoring PDBs (or mmCIFs) for a sampling run. More...
 
def init_rmf
 Initialize an RMF file. More...
 

Member Function Documentation

def IMP.pmi.output.Output.get_pdb_names (   self)

Get a list of all PDB files being output by this instance.

Definition at line 231 of file output.py.

def IMP.pmi.output.Output.get_prot_name_from_particle (   self,
  name,
  p 
)

Get the protein name from the particle.

This is done by traversing the hierarchy.

Definition at line 356 of file output.py.

def IMP.pmi.output.Output.init_pdb (   self,
  name,
  prot,
  mmcif = False 
)

Init PDB Writing.

Parameters
nameThe PDB filename
protThe hierarchy to write to this pdb file
mmcifIf True, write PDBs in mmCIF format
Note
if the PDB name is 'System' then will use Selection to get molecules

Definition at line 270 of file output.py.

def IMP.pmi.output.Output.init_pdb_best_scoring (   self,
  prefix,
  prot,
  nbestscoring,
  replica_exchange = False,
  mmcif = False,
  best_score_file = 'best.scores.rex.py' 
)

Prepare for writing best-scoring PDBs (or mmCIFs) for a sampling run.

Parameters
prefixInitial part of each PDB filename (e.g. 'model').
protThe top-level Hierarchy to output.
nbestscoringThe number of best-scoring files to output.
replica_exchangeWhether to combine best scores from a replica exchange run.
mmcifIf True, output models in mmCIF format. If False (the default) output in legacy PDB format.
best_score_fileThe filename to use for replica exchange scores.

Definition at line 480 of file output.py.

def IMP.pmi.output.Output.init_rmf (   self,
  name,
  hierarchies,
  rs = None,
  geometries = None,
  listofobjects = None 
)

Initialize an RMF file.

Parameters
namethe name of the RMF file
hierarchiesthe hierarchies to be included (it is a list)
rsoptional, the restraint sets (it is a list)
geometriesoptional, the geometries (it is a list)
listofobjectsoptional, the list of objects for the stat (it is a list)

Definition at line 577 of file output.py.


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