analysis

analysis

Analysis tools for KIMMDY runs. For command line usage, run kimmdy-analysis -h.

Functions

Name Description
concat_traj Find and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory.
entry_point_analysis Analyse existing KIMMDY runs.
get_analysis_cmdline_args Parse command line arguments.
get_analysis_dir Get analysis directory for a KIMMDY run.
plot_energy Plot GROMACS energy for a KIMMDY run.
plot_rates Plot rates of all possible reactions for each ‘decide_recipe’ step.
radical_migration Plot population of radicals for a KIMMDY run.
radical_population Plot population of radicals for a KIMMDY run.
reaction_participation Plot which atoms participate in reactions.
runtime_analysis Plot which atoms participate in reactions.

concat_traj

analysis.concat_traj(dir, filetype, steps, open_vmd=False, output_group=None)

Find and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory. The concatenated trajectory is centered and pbc corrected.

Parameters

Name Type Description Default
dir str Directory to search for subdirectories required
steps Union[list[str], str] List of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories required
open_vmd bool Open concatenated trajectory in VMD False
output_group Optional[str] index group for output. Default is “Protein” for xtc and “System” for trr. None

entry_point_analysis

analysis.entry_point_analysis()

Analyse existing KIMMDY runs.

get_analysis_cmdline_args

analysis.get_analysis_cmdline_args()

Parse command line arguments.

Returns

Type Description
Parsed command line arguments

get_analysis_dir

analysis.get_analysis_dir(dir)

Get analysis directory for a KIMMDY run.

Creates the directory if it does not exist.

Parameters

Name Type Description Default
dir Path Directory of KIMMDY run required

Returns

Type Description
Path to analysis directory

plot_energy

analysis.plot_energy(dir, steps, terms, open_plot=False)

Plot GROMACS energy for a KIMMDY run.

Parameters

Name Type Description Default
dir str Directory to search for subdirectories required
steps Union[list[str], str] List of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories. Default is “all”. required
terms list[str] Terms from gmx energy that will be plotted. Uses ‘Potential’ by default. required
open_plot bool Open plot in default system viewer. False

plot_rates

analysis.plot_rates(dir)

Plot rates of all possible reactions for each ‘decide_recipe’ step.

Parameters

Name Type Description Default
dir str Directory of KIMMDY run required

radical_migration

analysis.radical_migration(dirs, type='qualitative', cutoff=1)

Plot population of radicals for a KIMMDY run.

Parameters

Name Type Description Default
dirs list[str] KIMMDY run directories to be analysed. required
type str How to analyse radical migration. Available are ‘qualitative’,‘occurence’ and ‘min_rate’“, 'qualitative'
cutoff int Ignore migration between two atoms if it happened less often than the specified value. 1

radical_population

analysis.radical_population(dir, population_type='frequency', steps='all', select_atoms='protein', open_plot=False, open_vmd=False)

Plot population of radicals for a KIMMDY run.

Parameters

Name Type Description Default
dir str KIMMDY run directory to be analysed. required
population_type str How to calculate the fractional radical occupancy. Available are ‘frequency’ and ‘time’ 'frequency'
steps Union[list[str], str] List of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories. Default is “all”. 'all'
select_atoms str Atoms chosen for radical population analysis, default is protein (uses MDAnalysis selection syntax) 'protein'
open_plot bool Open plot in default system viewer. False
open_vmd bool Open a pdb in VMD with the radical occupation as B-factors. False

reaction_participation

analysis.reaction_participation(dir, open_plot=False)

Plot which atoms participate in reactions.

Parameters

Name Type Description Default
dir str Directory of KIMMDY run required
open_plot bool Open plot in default system viewer. False

runtime_analysis

analysis.runtime_analysis(dir, open_plot=False)

Plot which atoms participate in reactions.

Parameters

Name Type Description Default
dir str Directory of KIMMDY run required
open_plot bool Open plot in default system viewer. False
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