[FEATURE] Merge pull request #16 from menoliu/update-syntax

Fixes bug for reading `pre` and `noe` data files

Author: menoliu

CHANGELOG.rst

@@ -2,6 +2,8 @@
 Changelog
 =========
 
+* Update syntax for NOE and PRE experimental values from ``value`` to ``dist_value``
+
 v0.1.5 (2024-11-19)
 ------------------------------------------------------------
 

src/xeisd/components/__init__.py

@@ -9,6 +9,7 @@
 exp_idx = 'index'
 exp_resnum = 'resnum'
 exp_val = 'value'
+exp_dist_val = 'dist_value'
 exp_max = 'upper'
 exp_atmID = 'atomname'
 exp_min = 'lower'
@@ -80,9 +81,9 @@
 
 XEISD_TITLE = (
     "\n _  _     ____  ____  ___  ____  \n"  # noqa: W605
-    "( \/ )___( ___)(_  _)/ __)(  _ \ \n"  # noqa: W605
-    " )  ((___))__)  _)(_ \__ \ )(_) )\n"  # noqa: W605
-    "(_/\_)   (____)(____)(___/(____/ \n"  # noqa: W605
+    "( \\/ )___( ___)(_  _)/ __)(  _ \\ \n"  # noqa: W605
+    " )  ((___))__)  _)(_ \\__ \\ )(_) )\n"  # noqa: W605
+    "(_/\\_)   (____)(____)(___/(____/ \n"  # noqa: W605
     "================================="
     )
 

src/xeisd/components/parser.py

@@ -78,6 +78,7 @@
     cs_name,
     default_bc_errors,
     exp_atmID,
+    exp_dist_val,
     exp_err,
     exp_idx,
     exp_max,
@@ -218,7 +219,7 @@ def parse_nmrstar_data(fpath, type=None):
                 lower.append(float(min))
 
     if type == noe_name or type == pre_name:
-        return pd.DataFrame({exp_idx: index, exp_val: values, exp_max: upper, exp_min: lower, exp_err: errors})  # noqa: E501
+        return pd.DataFrame({exp_idx: index, exp_dist_val: values, exp_max: upper, exp_min: lower, exp_err: errors})  # noqa: E501
     return pd.DataFrame({exp_idx: index, exp_val: values, exp_err: errors})
 
 
@@ -317,6 +318,8 @@ def parse_data(filenames, mode, bc_errors=default_bc_errors):
             try:
                 with open(filenames[module], 'r') as f:
                     raw = json.load(f)
+                if module == pre_name or module == noe_name:
+                    del raw['format']
                 if isinstance(list(raw.items())[0][1], float):
                     data = pd.DataFrame(raw, index=[0]).T
                 else:

src/xeisd/components/scorers.py

@@ -10,6 +10,7 @@
 from xeisd.components import (
     cs_name,
     exp_atmID,
+    exp_dist_val,
     exp_err,
     exp_idx,
     exp_max,
@@ -332,7 +333,7 @@ def noe_optimization_ensemble(
         new_index=None,
         ):
     """Logic for NOE scoring."""
-    exp_distance = exp_data[noe_name].data[exp_val].values
+    exp_distance = exp_data[noe_name].data[exp_dist_val].values
 
     # Either `upper,lower` or `error` is required for exp_sigma
     try:
@@ -380,7 +381,7 @@ def pre_optimization_ensemble(
         ):
     """Logic for PRE scoring function."""
     # prepare data
-    exp_distance = exp_data[pre_name].data[exp_val].values
+    exp_distance = exp_data[pre_name].data[exp_dist_val].values
     # Either `upper,lower` or `error` is required for exp_sigma
     try:
         upper_bound_value = exp_data[pre_name].data[exp_max].values