IMP::sampcon Namespace Reference

Sampling exhaustiveness protocol. More...

Detailed Description

Sampling exhaustiveness protocol.

This module implements the sampling exhaustiveness test described in Viswanath et al, 2017. The protocol is primarily designed to work with models generated by the Integrative Modeling Platform (IMP) (and more specifically the IMP::pmi module), but could probably be adapted for other systems.

Dependencies:

pyRMSD is needed. (This is a fork of the original pyRMSD - which is no longer maintained - to fix bugs and add Python 3 support.)

In the Sali lab, pyRMSD is already built, so can be used with module load python2/pyrmsd or module load python3/pyrmsd.

imp_sampcon: sampling exhaustiveness test

The protocol is typically run using the imp_sampcon command line tool:

• imp_sampcon show_stat to show the available fields (e.g. scoring function terms, restraint satisfaction) in an IMP::pmi stat file.
• imp_sampcon select_good to select a subset of good-scoring models from a set of IMP::pmi trajectories.
• imp_sampcon plot_score to plot the score distributions of the selected models.
• imp_sampcon exhaust to analyze the selected models and determine whether sampling was exhaustive.

For a full demonstration of the protocol, see its usage in IMP's actin modeling tutorial.

Functions
def	get_data_path
	Return the full path to one of this module's data files. More...
def	get_example_path
	Return the full path to one of this module's example files. More...
def	get_module_name
	Return the fully-qualified name of this module. More...
def	get_module_version
	Return the version of this module, as a string. More...

Function Documentation

def IMP.sampcon.get_data_path

(

fname

)

Return the full path to one of this module's data files.

Note

This function is only available in Python.

Definition at line 15 of file sampcon/__init__.py.

def IMP.sampcon.get_example_path

(

fname

)

Return the full path to one of this module's example files.

Note

This function is only available in Python.

Definition at line 20 of file sampcon/__init__.py.

def IMP.sampcon.get_module_name

(

)

Return the fully-qualified name of this module.

Note

This function is only available in Python.

Definition at line 10 of file sampcon/__init__.py.

def IMP.sampcon.get_module_version

(

)

Return the version of this module, as a string.

Note

This function is only available in Python.

Definition at line 5 of file sampcon/__init__.py.