bindtools 0.3.1__tar.gz → 0.3.3__tar.gz

{bindtools-0.3.1 → bindtools-0.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bindtools
-Version: 0.3.1
+Version: 0.3.3
 Keywords: chemistry,analytical chemistry,binding constants,supramolecular
 Author: Martin Peeks
 Author-email: Martin Peeks <martinp23@googlemail.com>, m.peeks@unsw.edu.au
@@ -11,18 +11,18 @@ Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Scientific/Engineering :: Chemistry
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Dist: corner==2.2.3
+Requires-Dist: corner==2.3.0
 Requires-Dist: emcee==3.1.6
 Requires-Dist: h5py>=3.14.0
 Requires-Dist: latex2mathml>=3.81.0
 Requires-Dist: lmfit==1.3.4
-Requires-Dist: matplotlib==3.11.0
+Requires-Dist: matplotlib==3.11.2
 Requires-Dist: numba>=0.66
 Requires-Dist: numpy>=2.3.4
 Requires-Dist: openpyxl>=3.1.5
 Requires-Dist: pandas>=2.3.3
-Requires-Dist: scipy==1.18.0
-Requires-Dist: tqdm==4.68.3
+Requires-Dist: scipy==1.18.1
+Requires-Dist: tqdm==4.70.1
 Requires-Dist: uncertainties==3.2.3
 Requires-Python: >=3.12
 Project-URL: Homepage, https://github.com/martinp23/bindtools

{bindtools-0.3.1 → bindtools-0.3.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "bindtools"
-version = "0.3.1"
+version = "0.3.3"
 readme = "README.md"
 classifiers = [
     "Development Status :: 3 - Alpha",
@@ -23,18 +23,18 @@ keywords = [
     "supramolecular",
 ]
 dependencies = [
-    "corner==2.2.3",
+    "corner==2.3.0",
     "emcee==3.1.6",
     "h5py>=3.14.0",
     "latex2mathml>=3.81.0",
     "lmfit==1.3.4",
-    "matplotlib==3.11.0",
+    "matplotlib==3.11.2",
     "numba>=0.66",
     "numpy>=2.3.4",
     "openpyxl>=3.1.5",
     "pandas>=2.3.3",
-    "scipy==1.18.0",
-    "tqdm==4.68.3",
+    "scipy==1.18.1",
+    "tqdm==4.70.1",
     "uncertainties==3.2.3",
 ]
 

{bindtools-0.3.1 → bindtools-0.3.3}/pyproject.toml.orig

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "bindtools"
-version = "0.3.1"
+version = "0.3.3"
 readme = "README.md"
 classifiers = [
   # How mature is this project? Common values are
@@ -27,18 +27,18 @@ classifiers = [
 requires-python = ">=3.12"
 keywords = ["chemistry", "analytical chemistry", "binding constants", "supramolecular"]
 dependencies = [
-    "corner==2.2.3",
+    "corner==2.3.0",
     "emcee==3.1.6",
     "h5py>=3.14.0",
     "latex2mathml>=3.81.0",
     "lmfit==1.3.4",
-    "matplotlib==3.11.0",
+    "matplotlib==3.11.2",
     "numba>=0.66",
     "numpy>=2.3.4",
     "openpyxl>=3.1.5",
     "pandas>=2.3.3",
-    "scipy==1.18.0",
-    "tqdm==4.68.3",
+    "scipy==1.18.1",
+    "tqdm==4.70.1",
     "uncertainties==3.2.3",
 ]
 authors = [

{bindtools-0.3.1 → bindtools-0.3.3}/src/bindtools/models/binding_model.py

@@ -10,11 +10,12 @@ from bindtools.models.objective import fitfun
 class bindingModel:
     def __init__(
         self,
-        eqMat,
-        compNames,
-        speciesList,
-        specToInteg=None,
-        specToDd=None,
+        eqMat: np.ndarray,
+        compNames: List[str],
+        speciesList: List[str],
+        specToInteg: Optional[np.ndarray|List]=None,
+        specToDd: Optional[List|np.ndarray]=None,
+        specToLinear: Optional[List|np.ndarray]=None,
         colToComp=None,
         obsList=None,
         rawData=None,
@@ -47,8 +48,8 @@ class bindingModel:
             self.nConcs = np.shape(compConcs)[0]
 
         self.concUnits = None  # mM #TODO
-        self.specToDd = specToDd
-        self.specToLinear: Optional[np.ndarray] = None  # (n_species, n_obs) object array for UV-vis / fluorescence
+        self.specToDd = specToDd  # (n_species, n_obs) object array for NMR chemical shifts
+        self.specToLinear: Optional[List] = specToLinear  # (n_species, n_obs) object array for UV-vis / fluorescence
         self.analytical_fast_exchange: bool = False
         self.analytical_topology: Optional[str] = None
         self.analytical_complex_indices: list[int] = []
@@ -142,18 +143,58 @@ class bindingModel:
 
         # Register UV-vis / fluorescence parameters from specToLinear (object array).
         if self.specToLinear is not None:
-            for _, x in np.ndenumerate(self.specToLinear):
-                if isinstance(x, lmfit.Parameter):
+            # Coerce list or 1D array to 2D object array safely
+            if not isinstance(self.specToLinear, np.ndarray) or self.specToLinear.dtype != object:
+                raw_list = list(self.specToLinear)
+                if len(raw_list) > 0 and isinstance(raw_list[0], (list, tuple, np.ndarray)):
+                    # Already 2D-like
+                    rows, cols = len(raw_list), len(raw_list[0])
+                    arr = np.empty((rows, cols), dtype=object)
+                    for r in range(rows):
+                        for c in range(cols):
+                            arr[r, c] = raw_list[r][c]
+                else:
+                    # 1D-like -> reshape to (n_species, 1)
+                    arr = np.empty((len(raw_list), 1), dtype=object)
+                    for r, val in enumerate(raw_list):
+                        arr[r, 0] = val
+                self.specToLinear = arr
+            elif self.specToLinear.ndim == 1:
+                self.specToLinear = self.specToLinear[:, None]
+            # Register parameters (supporting both lmfit.Parameter and (min, init, max[, name]) tuples)
+            for ii, x in np.ndenumerate(self.specToLinear):
+                if isinstance(x, tuple):
+                    param_name = x[3] if len(x) > 3 else f"lin_{ii[0]}_{ii[1]}"
+                    self._addParam(param_name, x[1], min=x[0], max=x[2])
+                elif isinstance(x, lmfit.Parameter):
                     self._addExistingParam(x)
 
-        # add chemical shift fitting params
         if self.specToDd is not None:
+            if not isinstance(self.specToDd, np.ndarray) or self.specToDd.dtype != object:
+                raw_list = list(self.specToDd)
+                if len(raw_list) > 0 and isinstance(raw_list[0], (list, tuple, np.ndarray)):
+                    # Already 2D-like
+                    rows, cols = len(raw_list), len(raw_list[0])
+                    arr = np.empty((rows, cols), dtype=object)
+                    for r in range(rows):
+                        for c in range(cols):
+                            arr[r, c] = raw_list[r][c]
+                else:
+                    # 1D-like -> reshape to (n_species, 1)
+                    arr = np.empty((len(raw_list), 1), dtype=object)
+                    for r, val in enumerate(raw_list):
+                        arr[r, 0] = val
+                self.specToDd = arr
+            elif self.specToDd.ndim == 1:
+                self.specToDd = self.specToDd[:, None]
+
+
             for ii, x in np.ndenumerate(self.specToDd):
                 if isinstance(x, tuple):
                     self._addParam("shift_{}_{}".format(ii[0], ii[1]), x[1], min=x[0], max=x[2])
                 elif isinstance(x, lmfit.Parameter):
                     self._addExistingParam(x)
-
+                
     def runModel(self, sigma=1, skip_col=1, method="least_squares", ret=False, kwargs={}) -> Optional["bindingModel"]:
         exptData = np.copy(self.rawData)
         spec_to_integ = None

{bindtools-0.3.1 → bindtools-0.3.3}/src/bindtools/observables/transforms.py

@@ -46,6 +46,10 @@ def concToLinearObs(
 
     Returns an ndarray of shape (n_pts, n_obs).
     """
+
+    if hasattr(specToLinear, "ndim") and specToLinear.ndim == 1:
+        specToLinear = specToLinear[:, None]
+
     mlen, nlen = np.shape(specToLinear)  # (n_species, n_obs)
     specToLinearTrial = np.copy(specToLinear)
 

{bindtools-0.3.1 → bindtools-0.3.3}/src/bindtools/observables/types.py

@@ -43,6 +43,8 @@ class ObsType:
             self.param = lmfit.Parameter("lnsigmaFluorescence", value=-4, vary=True, min=-8, max=0)
 
         else:
+            print("Unknown observable type. Using default units and parameter name.")
+
             self.units = units
             self.param = lmfit.Parameter("lnsigma" + name)