add ppix folding data example

Author: Jhsmit

templates/01a_load_ppix_data.py

@@ -0,0 +1,40 @@
+"""Load a HDX-MS dataset with both a FD and ND control"""
+
+from pathlib import Path
+
+import numpy as np
+
+from pyhdx import read_dynamx
+from pyhdx.process import apply_control, filter_peptides
+
+# %%
+
+root_dir = Path(__file__).parent.parent
+np.random.seed(43)
+
+fpath = root_dir / "tests" / "test_data" / "input" / "PpiA_folding.csv"
+
+# Load the full .csv file
+df = read_dynamx(fpath)
+df
+# %%
+
+fd_spec = {"state": "Native", "exposure": {"value": 86400, "unit": "s"}}
+nd_spec = {"state": "FD", "exposure": {"value": 0.6, "unit": "s"}}
+
+# Filter out peptides for the full deuteration control
+fd_df = filter_peptides(df, **fd_spec)
+
+# Filter out peptides for the non-deuterated control
+nd_df = filter_peptides(df, **nd_spec)
+
+# Filter out peptides for the experiment with state "Folding"
+peptides = filter_peptides(df, state="Folding")
+
+# %%
+# Apply the FD and ND controls. This adds the columns 'rfu' and 'rfu_sd' (Relative Fractional Uptake)
+# as well as 'fd_uptake' and 'nd_uptake', and their standard deviations.
+peptides_control = apply_control(peptides, fd_control=fd_df, nd_control=nd_df)
+peptides_control.columns
+
+# %%