__doc__ = """ Written in 2013 by Robert Pantazes of the Costas Maranas Lab in the Chemical Engineering Department of the Pennsylvania State University This program creates an Experiment class object, which asks the user for all information needed to run an experiment. Once that has been gathered, it goes to the Experiment's folder, puts the proper program there, and optionally starts the Experiment.""" # Include PYTHON information import os import sys sys.path.append(InstallFolder + "modules/") # Include the EXPERIMENT module import EXPERIMENT # The STANDARDS module is needed for answering questions from STANDARDS import * # The source of the functions that can generate scripts to run the experiment import SUBMITTER # Make the experiment, using user input experiment = EXPERIMENT.Experiment(False) # Move to the experiment's folder and output it's information os.chdir(experiment["Folder"]) experiment.output() # Copy the appropriate program to this folder command = "cp " + InstallFolder + "programs/" + experiment["Type"] + ".py ." i = os.system(command) # Generate scripts to run this experiment and possibly submit them dummy = SUBMITTER.script_generator(experiment)
Written in 2013 by Robert Pantazes of the Costas Maranas Lab in the Chemical
Engineering Department of the Pennsylvania State University.
This program runs IPRO to design proteins to have modified binding behaviors
(typically improved) to target molecules."""
# Load the needed PYTHON Modules
import os
import sys
sys.path.append(InstallFolder + "modules/")
import EXPERIMENT
import IPRO_FUNCTIONS
import REFINEMENT
# Start by loading an Experiment
experiment = EXPERIMENT.Experiment()
# Initialize the Experiment so that it can run calculations
dummy = IPRO_FUNCTIONS.INITIALIZE(experiment)
# initialize the antigen position
# Pick the antibody parts combination for each position
# Refine the antigen position and antibody parts combination
# IPRO to redesign the selected antibody parts against antigen
# Declare an iteration variable and set it to 0
iteration = 0
# Do the appropriate number of iterations
while iteration <= experiment["IPRO Iterations"]:
# If appropriate, do a refinement
REFINEMENT.DO(experiment)