#!/usr/bin/env python
# coding: utf-8

# # Test tube design example
# 
# Design a test tube ensemble intended to contain a 4-stranded stick figure at 1 M. 
# 
# Material: RNA    
# Temperature: 23 C

# In[1]:


# Import Python NUPACK module
from nupack import *


# In[2]:


# Define physical model
my_model = Model(material='rna', celsius=23)

# Define sequence domains
da = Domain('N27', name='da')
db = Domain('N29', name='db')
dc = Domain('N25', name='dc')
dd = Domain('N18', name='dd')

# Define strands containing these domains
sa = TargetStrand([da], name='sa')
sb = TargetStrand([db], name='sb')
sc = TargetStrand([dc], name='sc')
sd = TargetStrand([dd], name='sd')

# Define a target complex
cstickfigure = TargetComplex([sa, sb, sc, sd], '..((((((((..((((((((((((...+))))))(((.........)))((((((..+.))))))))))))..((((((((..+.)))))))))))))))).', name='cstickfigure')

#Define a target test tube containing all off-target complexes of up to 4 strands
tstickfigure = TargetTube(on_targets={cstickfigure: 1e-06}, off_targets=SetSpec(max_size=4), name='tfigure')

# Set a stop condition of 1% and a seed for random number generation to get a reproducible result for this demo
my_options = DesignOptions(f_stop=0.01, seed=93)

# Define and run the test tube design job
my_design = tube_design(tubes=[tstickfigure], model=my_model, options=my_options)
my_results = my_design.run(trials=1)[0]

# Display the design results
my_results


# In[3]:


# For more detail, display the analysis results performed on the designed tube ensemble
my_results.analysis_result