Oligomer

Modules and libraries

The code in analysis.py depends on well-known Python libraries NumPy and scikit-learn. Both are installable through tools such as pip or conda.

The code in oligomer.py is written in Python with references to the SageMath library. SageMath is documented at https://www.sagemath.org/.

Executing code

analysis.py and hotspots.py

The code in these files can be run by the standard Python 3 interpreter though it requires installing some third-party packages.

oligomer.py and SageMath

1. For the time being, the recommended method for using oligomer.py is to paste its contents into the cell at https://sagecell.sagemath.org/, then add the commands you want to be executed below.
2. Alternative method:
   1. Install SageMath as a standalone software.
   2. Write SageMath code (in particular, almost any Python code is valid SageMath code) in a file, say main.sage, containing the line import oligomer.
   3. Place oligomer.py in the same directory.
   4. Run sage main.sage.
3. Finally one could get SageMath as a Python package via some package manager and try to import oligomer in standard Python code. This is not tested yet.

simulation.py and Chimera

The code in simulation.py must be run from inside the UCSF Chimera software (https://www.cgl.ucsf.edu/chimera/). From the command line, this is done by:

chimera --nogui simulation.py

It is also possible to open simulation.py inside Chimera's graphical interface via its File > Open menu.

Example commands for oligomer.py

For each of the unique colourings with 6 blue dimers, up to rotations, display it as a net, as a graph, as a polyhedron, then print the corresponding Chimera code.

for c in unique_colorings(6):
    c.show('net')
    c.show('graph')
    c.show('polyhedron')
    c.print_Chimera_commands()

For each of the unique colourings with 7 blue dimers, up to rotations, display information about its junctions, but only if it has 8 blue -> red junctions.

for c in unique_colorings(7):
    if c.adjacencies.BR == 8:
        print(c)

Print the Chimera commands that describe all unique colourings with 6 blue dimers, up to rotations, in a file tmp.txt.

with open('tmp.txt', 'a') as file:
    print('Arrangements with 6 blue dimers up to rotation:\n', file=file)
    for c in unique_colorings(6):
        c.print_Chimera_commands(file=file)

Print each unique 6:6 colouring with its rotation class.

from collections import defaultdict
dictionary = defaultdict(list)
for c in unique_colorings(6, isomorphism=False):
    dictionary[c].append(c)
# dictionary has 48 entries, each being a list of isomorphic colourings
for c, l in dictionary.items():
    print('Canonical representation:')
    c.show('net')
    c.print_Chimera_commands()
    print('Alternate representations:')
    for alternate_colouring in l:
        alternate_colouring.show('net')
        alternate_colouring.print_Chimera_commands()