bindtools 0.1.2__tar.gz → 0.1.3__tar.gz

{bindtools-0.1.2 → bindtools-0.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bindtools
-Version: 0.1.2
+Version: 0.1.3
 Keywords: chemistry,analytical chemistry,binding constants,supramolecular
 Author: Martin Peeks
 Author-email: Martin Peeks <martinp23@googlemail.com>, m.peeks@unsw.edu.au
@@ -14,7 +14,7 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Requires-Dist: arviz==0.21.0
 Requires-Dist: corner==2.2.3
 Requires-Dist: emcee==3.1.6
-Requires-Dist: h5py==3.13.0
+Requires-Dist: h5py>=3.14.0
 Requires-Dist: lmfit==1.3.3
 Requires-Dist: matplotlib==3.10.7
 Requires-Dist: numba>=0.65.1

{bindtools-0.1.2 → bindtools-0.1.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "bindtools"
-version = "0.1.2"
+version = "0.1.3"
 readme = "README.md"
 classifiers = [
   # How mature is this project? Common values are
@@ -30,7 +30,7 @@ dependencies = [
     "arviz==0.21.0",
     "corner==2.2.3",
     "emcee==3.1.6",
-    "h5py==3.13.0",
+    "h5py>=3.14.0",
     "lmfit==1.3.3",
     "matplotlib==3.10.7",
     "numba>=0.65.1",

{bindtools-0.1.2 → bindtools-0.1.3}/src/bindtools/binding.py

@@ -97,9 +97,9 @@ def getConcsScipy(eqMat, initComponentConc, logK, alg="L-BFGS-B"):
     eqMat = eqMat.astype("float64")
     K = 10.0**logK
     guessCompConc = np.zeros(len(initComponentConc)) + np.mean(initComponentConc)
-    guessLogCompConc = np.log(guessCompConc)
+    guessLogCompConc = np.log10(guessCompConc)
 
-    bds = [(None, np.log(np.max(initComponentConc))) for _ in range(len(guessLogCompConc))]
+    bds = [(None, np.log10(np.max(initComponentConc))) for _ in range(len(guessLogCompConc))]
     # jac=True says that specObj returns float,arr(n) where arr(n) is the Jacobian
     res = sp.optimize.minimize(
         specObj,
@@ -112,7 +112,7 @@ def getConcsScipy(eqMat, initComponentConc, logK, alg="L-BFGS-B"):
         options={"gtol": 1e-20},
     )
 
-    compTotCalc, specConc = specCalc(np.exp(res.x), len(K), eqMat, K)
+    compTotCalc, specConc = specCalc(10**(res.x), len(K), eqMat, K)
     return specConc
 
 
@@ -150,7 +150,7 @@ def _specJac(ncomp, eqMat, speciesConc):  # this function calculates the Jacobia
 
 
 def specObj(logConc, initComponentConc, eqMat, K):
-    conc = np.exp(logConc)
+    conc = 10**(logConc)
     nspecies = len(K)
     compTotCalc, specConc = specCalc(conc, nspecies, eqMat, K)
 
@@ -567,15 +567,29 @@ def fitfun(params, fcn_opts):  # ,eqMat,specConcs,startShifts=None,sigma=1,ret='
 
     bindingParams = np.array([*parvals][: fcn_opts["nK"]], dtype=np.float64)
     error = False
-    specCalc = []
-    for row in fcn_opts["compConcs"]:
-        try:
-            yEq = getConcs(fcn_opts["eqMat"], row, bindingParams)
-        except EquilibriumError as e:
-            yEq = e.val
-            error = True
-        specCalc.append(yEq)  # yEq[4:])
-    specCalc = np.array(specCalc)
+
+    analytical_topology = fcn_opts.get("analytical_topology")
+    if analytical_topology in ("1:1", "1:2", "2:1"):
+        comp_concs = np.array(fcn_opts["compConcs"], dtype=float)
+        complex_indices = [int(x) for x in fcn_opts.get("analytical_complex_indices", [])]
+        specCalc, error = calc_analytical_speciation(
+            comp_concs=comp_concs,
+            eq_mat=np.array(fcn_opts["eqMat"], dtype=float),
+            binding_params=bindingParams,
+            topology=str(analytical_topology),
+            n_comp=int(comp_concs.shape[1]),
+            complex_indices=complex_indices,
+        )
+    else:
+        specCalc = []
+        for row in fcn_opts["compConcs"]:
+            try:
+                yEq = getConcs(fcn_opts["eqMat"], row, bindingParams)
+            except EquilibriumError as e:
+                yEq = e.val
+                error = True
+            specCalc.append(yEq)  # yEq[4:])
+        specCalc = np.array(specCalc)
     # except EquilibriumError as e:
     #     if fcn_opts['ret'] == 'residual':
     #         return 1000