Adding experimental data
Experimental data is stored in BilayerData/experiments folder. C-H bond order parameters from NMR are in OrderParameters subfolder and X-ray scattering form factors in FormFactors subfolder.
The keys of these dictionaries are summarized in the Experiment metadata description.
Steps to add experimental data
Create and fill the
README.yamlfile of your data.Copy this README file data into a appropriate directory named as described above.
If you have order parameter data, create a file named
{lipidname}_Order_Parameters.datwhere{lipidname}is the universal name of the lipid from which the data is measured from. The first two columns of this file should define the atom pair with universal atom names, third column has the experimental order parameter value, and fourth column has the experimental error. If the experimental error is not known, set it to 0.02. Store the created{lipidname}_Order_Parameters.datfile into the appropriate folder with theREADME.yamlfile. Createjsonversion fromdatfile by runningpython data_to_json.py path-to-dat.dat
in folder experiments/OrderParameters. You can see previously added experiments for examples.
If you have X-ray scattering form factor data, store the form factor into appropriate folders in ASCII format where first column in x-axis values (Å-1), second column is y-axis value, and third is the error. Then create
jsonfile by runnigpython data_to_json.py ascii-file.txt
in folder [experiments/FormFactors](https://github.com/NMRLipids/BilayerData/tree/main/experiments/FormFactors). Please see previously added experiments for examples.
Adding experiments can lead to recalculation of quality of some simulations and rankings. So, after the addition, please run
fmdl_match_experiments fmdl_evaluate_quality fmdl_make_ranking
Submit the files to your branch and make a pull-request.