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,
    center_group=None,
    use_last_names=False,
)

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
output_group Optional[str] index group for centering. None
use_last_names bool Use the tpr/topology of the last trajectory for the output, default is the first. This influences the names and types of the atoms in the output, which can be useful for VMD. False

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

Name 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

Name Type Description
Path to analysis directory

plot_energy

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

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
truncate bool Truncate energy files to the reaction time marker. True

plot_rates

analysis.plot_rates(dir, open=False)

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

Parameters

Name Type Description Default
dir str Directory of KIMMDY run required
open bool open plots in default system viewer False

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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