plotprofile

plotProfile

Python code for plotting professional looking reaction profiles with various customisation options available

Installation

From pypi

Simplest installation

pip install plotprofile

Local installation

git clone [e-mail]:aligfellow/plotProfile.git
cd plotProfile
pip install .

[!WARNING] this may not respect the styles.json, if not:

git clone [e-mail]:aligfellow/plotProfile.git
cd plotProfile
python -m build
pip install dist/plotprofile-1.0.1.tar.gz

Python Usage examples

Use case for example:

from plotProfile import ReactionProfilePlotter

energy_sets = {
    "Pathway A": [0.00, -2.0, 10.2, 1.4, -1.5, 2.0, -7.2],
    "Pathway B": [None, -2.0, 6.2, 4.3, 5.8, 2.0],
    "Pathway C": [None, -2.0, -6.8,-6.8],
}

annotations = {
    'Step 1': (0,3),
    'Step 2': (3,5),
    'Step 3': (5,6),
}

plotter = ReactionProfilePlotter(dashed=["Pathway C"])
plotter.plot(energy_sets, annotations=annotations, filename="../images/profile1")

Pass in annotations for labelling of the reaction profile:

• this is done in the plotting function rather than the class
• using dictionary with keys of labels and a tuple of the start and end x-indices
• allowing for multiple plots of the same style with different annotations

A variety of paremters can be tuned for the plotting, including:

• axes="box|y|x|both|None"
• curviness=0.42 - reduce for less curve and vice versa
• colors=["list","of","colors"]|cmap - specify colour list or colour map
• show_legend=Bool
• units="kj|kcal"
• energy="e|electronic|g|gibbs|h|enthalpy|s|entropy|"

For example:

plotter = ReactionProfilePlotter(style="presentation", dashed=["Pathway B"], point_type='bar', desaturate=False, colors='Blues_r', show_legend=False, curviness=0.5)
plotter.plot(energy_sets, filename="../images/profile2")

• Using style="presentation" which sets a larger figsize=(X,X), thicker lines, larger font size:

For example:

plotter = ReactionProfilePlotter(style="straight", figsize=(6,4), dashed=["Pathway C"], point_type='dot', annotation_color='black', axes='y', colors=['darkseagreen', 'slateblue', 'darksalmon'], energy='electronic', units='kj')
plotter.plot(energy_sets,annotations=annotations, filename="../images/profile3")

• Straight lines set in a style, which can also be done by passing in curviness=0:

See examples/example.ipynb for more explicit code

Further details

[!IMPORTANT]

• Secondary curves can begin from after the 1st point, just need to have a None entry in the list of energies e.g. [None, 0.0, 1.0]
• Individual points can be placed if this is a list with only one energy value (e.g. uncluttered diastereomeric TS for example, see examples)
  • labels of theses are not added to the legend
  • these can even be placed as individual points between two indices with [None, 5.0, 5.0]
• Spacing of points on the profile can be altered by:
  • passing the same energy twice in a row, which will place the point halfway between the two x-indices, i.e. Pathway C point in examples, e.g. [0.0, 5.0, 5.0]
  • with an entry like [0.0, None, 1.0] which will have a line connecting indexes 0 and 2 of this list with the correct x-axis alignment
• data types can be:
  • dict, with labels for the legend
  • list of lists (no labelling of different profiles)
  • single list

CLI

[!NOTE] Currently untested - though this won't work for now

python -m plotProfile --input examples/input.json --labels --format png

To Do

[!TIP]

• label placement is primitive and could be improved
  • for now these can be tweaked with postprocessing
• check cli options