Restoring OP quality functionality (still not working)

Author: comcon1

src/fairmd/lipids/bin/evaluate_quality.py

@@ -65,18 +65,18 @@ def _evaluate_op_qualities(simulations) -> int:
             fragment_qual_dict = {}
             data_dict = {}
 
-            for expid in simulation["EXPERIMENT"]["ORDERPARAMETER"][lipid1]:
+            for expid in simulation["EXPERIMENT"]["ORDERPARAMETER"].get(lipid1, []):
                 print(
                     f"Evaluating {lipid1} lipid using experimental data from {expid}",
                 )
                 OP_qual_data = {}
-                exp_lipid_ops = opexps.loc(expid)
+                exp_lipid_ops = opexps.loc(expid).data[lipid1]
                 exp_error = 0.02
 
                 for key, op_array_ in md_lipid_ops.items():
                     OP_array = op_array_.copy()
-                    try:
-                        OP_exp = exp_lipid_ops[key][0][0]
+                    try:  # TODO: very bad! must remove TRY-EXCEPT BLOCK
+                        OP_exp = exp_lipid_ops[key][0]
                     except KeyError:
                         continue
                     else:
@@ -144,7 +144,7 @@ def _evaluate_op_qualities(simulations) -> int:
             _round_quality_values(system_qual_output)
             with open(outfile2, "w") as f:
                 json.dump(system_qual_output, f)
-            print("Order parameter quality evaluated for " + simulation.idx_path)
+            print("Order parameter quality evaluated for " + simulation["path"])
             counter += 1
             print()
     return counter
@@ -195,10 +195,10 @@ def _evaluate_ff_qualities(simulations) -> int:
 def evaluate_quality():
     simulations = qq.QualSimulation.load_all_paired()
 
-    # evaluated_op_counter = _evaluate_op_qualities(simulations)
+    evaluated_op_counter = _evaluate_op_qualities(simulations)
     evaluated_ff_counter = _evaluate_ff_qualities(simulations)
 
-    # print("The number of systems with evaluated order parameters:", evaluated_op_counter)
+    print("The number of systems with evaluated order parameters:", evaluated_op_counter)
     print("The number of systems with evaluated form factors:", evaluated_ff_counter)
 
 

src/fairmd/lipids/quality.py

@@ -4,7 +4,6 @@
 TODO: remove code duplication and commented code
 """
 
-import decimal as dc
 import re
 import warnings
 
@@ -84,7 +83,7 @@ def prob_op_within_trustinterval(
 
 
 # quality of molecule fragments
-def get_fragments(mapping_dict: dict):
+def get_fragments(mapping_dict: dict) -> dict:
     fragments = {}
 
     for key_m, value in mapping_dict.items():
@@ -124,7 +123,7 @@ def evaluated_percentage(fragments, exp_op_data):
         for key, value in exp_op_data.items():
             if key.split(" ")[0] in fragments[fragment_key]:  # check if atom belongs to the fragment
                 fragment_size += 1
-                if not np.isnan(value[0][0]):
+                if not np.isnan(value[0]):
                     count_value += 1
         if fragment_size != 0:
             frag_percentage[fragment_key] = count_value / fragment_size
@@ -137,7 +136,7 @@ def evaluated_percentage(fragments, exp_op_data):
     return frag_percentage
 
 
-def fragmentQuality(fragments, exp_op_data, sim_op_data):
+def fragmentQuality(fragments: dict, exp_op_data: dict, sim_op_data: dict):
     # depends on the experiment file what fragments are in this dictionary
     p_F = evaluated_percentage(fragments, exp_op_data)
     exp_error = 0.02
@@ -156,8 +155,8 @@ def fragmentQuality(fragments, exp_op_data, sim_op_data):
         else:
             if p_F[fragment_key] != 0:
                 for key_exp, value_exp in exp_op_data.items():
-                    if key_exp.split()[0] in fragments[fragment_key] and not np.isnan(value_exp[0][0]):
-                        OP_exp = value_exp[0][0]
+                    if key_exp.split()[0] in fragments[fragment_key] and not np.isnan(value_exp[0]):
+                        OP_exp = value_exp[0]
                         try:
                             OP_sim = sim_op_data[key_exp][0]
                         except (KeyError, TypeError):
@@ -242,7 +241,7 @@ def fragmentQualityAvg(
 
 
 # fragments is different for each lipid ---> need to make individual dictionaries
-def systemQuality(system_fragment_qualities, simulation):
+def systemQuality(system_fragment_qualities, simulation: QualSimulation):
     system_dict = {}
     lipid_dict = {}
     w_nan = []
@@ -251,7 +250,7 @@ def systemQuality(system_fragment_qualities, simulation):
         # copy keys to new dictionary
         lipid_dict = dict.fromkeys(system_fragment_qualities[lipid].keys(), 0)
 
-        w = simulation.molar_fraction(lipid)
+        w = simulation.membrane_composition(basis="molar")[lipid]
 
         for key, value in system_fragment_qualities[lipid].items():
             if not np.isnan(value):

tests/test_quality.py

@@ -19,6 +19,7 @@
 # run only on sim2 mocking data
 pytestmark = [pytest.mark.nodata, pytest.mark.min]
 
+
 def test_prob_op_within_trustinterval():
     from fairmd.lipids.quality import prob_op_within_trustinterval
 
@@ -47,4 +48,3 @@ def test_prob_op_within_trustinterval():
 
     p2 = prob_op_within_trustinterval(op_exp, exp_error, op_sim, op_sim_sd)
     npt.assert_allclose(p2, [0.505148, np.nan, 0.526465], atol=1e-6)
-