API Examples

An example of a script to run a SEEKR2 calculation can be found in Listing 1. This script defines a “model input” object, loads its parameters from an XML file, generates the full model, checks the model for potential problems, runs any and all of the MD and BD simulations, and analyzes the results.

Listing 1: a sample Python script using the SEEKR2 API to perform a full SEEKR calculation. NOTE: this script should be run from the seekr2/seekr2/ directory to work as-is.:

import seekr2
model_input_filename = “data/sample_input_mmvt_openmm.xml"
model_input = seekr2.prepare.common_prepare.Model_input()
model_input.deserialize(model_input_filename, user_input=True)
model, xml_path = seekr2.prepare.prepare(model_input)
model.anchor_rootdir = os.path.dirname(xml_path)
seekr2.modules.check.check_pre_simulation_all(model)
seekr2.run.run(model, "any")
analysis = seekr2.analyze.analyze(model)
analysis.print_results()

The objects can be accessed/modified from the Python API at any step in the process. For instance, if one wishes to add or move milestones, one could add the lines shown in Listing 2 before the model is prepared. Or say that one wants to access the milestoning matrix directly, one could add the lines in listing 3 after analysis object is generated.

Listing 2: a an additional snippet of sample Python code to use the SEEKR2 API for first add an anchor to the calculation and generate the model. Then, to demonstrate that the radius can be changed after the model is generated, the anchor’s radius is changed and the model is regenerated.:

from openmm import unit
new_input_anchor = seekr2.modules.common_cv.Spherical_cv_anchor()
new_input_anchor.radius = 0.1 * unit.nanometer
model_input.cv_inputs[0].input_anchors.insert(1, new_input_anchor)
model, xml_path = seekr2.prepare.prepare(model_input, force_overwrite=True)
model_input.cv_inputs[0].input_anchors[1].radius = 0.11 * unit.nanometers
model, xml_path = seekr2.prepare.prepare(model_input, force_overwrite=True)

Listing 3: The milestoning rate matrix “Q” or free energy profile are just two examples of many quantities that may be accessed directly from the Python analysis object.:

print(analysis.main_data_sample.Q)
print(analysis.free_energy_profile)

This script is just intended to give developers a glimpse of what is possible when using the API. Please consult the documentation within the code itself for details about the arguments to each of these functions.