cgexplore.utilities

utilities package.

Classes

AtomliteDatabase	Holds an atomlite database with some useful methods.
Pymol	Pymol visualiser.

Functions

add_structure_to_ax	Add an image to an axis.
add_text_to_ax	Add a string to an axis.
check_directory	Check if a directory exists, make if not.
convert_pyramid_angle	Some basic trig on square-pyramids.
draw_pie	Draw a pie chart at a specific point on ax.
extract_property	Extract property from nested dict.
get_energy_per_bb	Get the energy per building blocks used in most papers.
get_supramolecule
get_unforced_supramolecule
optimise_ligand	Optimise a building block.
rattle	Randomly displace atoms.
rmsd_checker	Check if an un-optimised molecule has a low RMSD to another one.
run_constrained_optimisation	Run optimisation with constraints and softened potentials.
run_optimisation	Run optimisation.
run_soft_md_cycle	Run MD exploration with soft potentials.
shift_beads	Shift beads away from cage centroid.
soften_forcefield	Soften force field by scaling parameters and turning off torsions.
write_chemiscope_json	Write the chemiscope json.
yield_near_models	Yield structures of models with neighbouring force field parameters.
yield_shifted_models	Yield conformers with atom positions of particular beads shifted.

Exceptions

ForceFieldUnavailableError	Error found assigning forcefield term.
ForceFieldUnitError	Error found in units of forcefield term.