README

Notebook to test the Complex class



In [5]:

    
monomer_example1 = {'ident': 'CARNRACE-MONOMER', 
                    'subunit_stoich': {'b0036': 1.0}}
# monomer_example2 = {'ident': '', 
#                     'subunit_stoich': }
homomer_example1 = {'ident': 'ANSB-CPLX', 
                    'subunit_stoich': {'b2957': 4.0}}
# homomer_example2 = {'ident': '', 
#                     'subunit_stoich': }
heteromer_example1 = {'ident': 'CPLX0-1762', 
                      'subunit_stoich': {'b1388': 1.0,
                                         'b1389': 1.0,
                                         'b1390': 1.0,
                                         'b1392': 1.0}}
heteromer_example2 = {'ident': 'SULFITE-REDUCT-CPLX', 
                      'subunit_stoich': {'b2763': 4.0, 
                                         'b2764': 8.0}}



In [6]:

    
from ssbio.core.complex import Complex



In [17]:

    
import tempfile



In [22]:

    
# Makes a new Complex object
# root_dir is where a folder named after the identifier will be created 
monomer = Complex(ident=monomer_example1['ident'], 
                  subunits=monomer_example1['subunit_stoich'], 
                  root_dir=tempfile.gettempdir())


print('id:', monomer.id)

print('complex_dir:', monomer.complex_dir)

print('subunit_dict:', monomer.subunit_dict)

# Should print "monomer" 
print('oligomeric_state:', monomer.oligomeric_state)









    



id: CARNRACE-MONOMER
complex_dir: /tmp/CARNRACE-MONOMER
subunit_dict: {'b0036': 1.0}
oligomeric_state: None



In [16]:

    
!ls









    



Complex - Testing.ipynb
Complex - Testing (undergrads).ipynb
FATCAT - Structure Similarity.ipynb
GEM-PRO - Calculating Protein Properties.ipynb
GEM-PRO - Genes & Sequences.ipynb
GEM-PRO - List of Gene IDs.ipynb
GEM-PRO - SBML Model.ipynb
I-TASSER and TMHMM Install Guide.ipynb
PDBProp - Working With a Single PDB Structure.ipynb
Protein - Structure Mapping, Alignments, and Visualization.ipynb
SeqProp - Protein Sequence Properties.ipynb
Software Installation Tester.ipynb
SWISS-MODEL - Downloading homology models.ipynb



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