solvation-analysis 0.3.1__py3-none-any.whl → 0.3.3a0__py3-none-any.whl

solvation_analysis/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2023-04-02T09:17:27-0700",
+ "date": "2023-04-09T10:45:35-0700",
  "dirty": false,
  "error": null,
- "full-revisionid": "c09a1c9f46d8a554e287169d59e0de008b70606b",
- "version": "v0.3.1"
+ "full-revisionid": "7133ecc6ffd3dfca4e85abd2eeb6ec850fabb41d",
+ "version": "v0.3.3-alpha"
 }
 '''  # END VERSION_JSON
 

solvation_analysis/coordination.py

@@ -44,6 +44,10 @@ class Coordination:
         The number of frames in solvation_data.
     n_solutes : int
         The number of solutes in solvation_data.
+    solvent_counts: Dict[str, int]
+        A dictionary of the number of residues for each solvent.
+    atom_group : MDAnalysis.core.groups.AtomGroup
+        The atom group of all atoms in the universe.
 
     Examples
     --------
@@ -58,13 +62,15 @@ class Coordination:
 
     """
 
-    def __init__(self, solvation_data, n_frames, n_solutes, atom_group):
+    def __init__(self, solvation_data, n_frames, n_solutes, solvent_counts, atom_group):
         self.solvation_data = solvation_data
         self.n_frames = n_frames
         self.n_solutes = n_solutes
         self._cn_dict, self._cn_dict_by_frame = self._mean_cn()
         self.atom_group = atom_group
         self._coordinating_atoms = self._calculate_coordinating_atoms()
+        self.solvent_counts = solvent_counts
+        self._coordination_vs_random = self._calculate_coordination_vs_random()
 
     @staticmethod
     def from_solute(solute):
@@ -84,6 +90,7 @@ class Coordination:
             solute.solvation_data,
             solute.n_frames,
             solute.n_solutes,
+            solute.solvent_counts,
             solute.u.atoms,
         )
 
@@ -116,13 +123,32 @@ class Coordination:
         type_fractions = type_counts[SOLVENT_ATOM_IX] / solvent_counts_list
         type_fractions.name = FRACTION
         # change index type
-        type_fractions = (type_fractions
-                         .reset_index(ATOM_TYPE)
-                         .astype({ATOM_TYPE: str})
-                         .set_index(ATOM_TYPE, append=True)
-                         )
+        type_fractions = (
+            type_fractions
+            .reset_index(ATOM_TYPE)
+            .astype({ATOM_TYPE: str})
+            .set_index(ATOM_TYPE, append=True)
+        )
         return type_fractions[type_fractions[FRACTION] > tol]
 
+    def _calculate_coordination_vs_random(self):
+        """
+        Calculate the coordination number relative to random coordination.
+
+        Values higher than 1 imply a higher coordination than expected from
+        random distribution of solvents. Values lower than 1 imply a lower
+        coordination than expected from random distribution of solvents.
+        """
+        average_shell_size = sum(self.coordination_numbers.values())
+        total_solvents = sum(self.solvent_counts.values())
+        coordination_vs_random = {}
+        for solvent, cn in self.coordination_numbers.items():
+            count = self.solvent_counts[solvent]
+            random = count * average_shell_size / total_solvents
+            vs_random = cn / random
+            coordination_vs_random[solvent] = vs_random
+        return coordination_vs_random
+
     @property
     def coordination_numbers(self):
         """
@@ -145,3 +171,13 @@ class Coordination:
         """
         return self._coordinating_atoms
 
+    @property
+    def coordination_vs_random(self):
+        """
+        Coordination number relative to random coordination.
+
+        Values higher than 1 imply a higher coordination than expected from
+        random distribution of solvents. Values lower than 1 imply a lower
+        coordination than expected from random distribution of solvents.
+        """
+        return self._coordination_vs_random

solvation_analysis/plotting.py

@@ -90,6 +90,91 @@ def plot_shell_composition_by_size(speciation):
     return fig
 
 
+def plot_co_occurrence(speciation, colorscale=None):
+    """
+    Plot the co-occurrence matrix of the solute using Plotly.
+
+    Co-occurrence represents the extent to which solvents occur with eachother
+    relative to random. Values higher than 1 mean that solvents occur together
+    more often than random and values lower than 1 mean solvents occur together
+    less often than random. "Random" is calculated based on the total number of
+    solvents participating in solvation, it ignores solvents in the diluent.
+
+    Args
+    ----
+    speciation: Speciation | Solution
+    colorscale : any valid argument to Plotly colorscale.
+
+    Returns
+    -------
+    fig : plotly.graph_objs.Figure
+    """
+    if isinstance(speciation, Solute):
+        if not hasattr(speciation, "speciation"):
+            raise ValueError(f"Solute speciation analysis class must be instantiated.")
+        speciation = speciation.speciation
+
+    solvent_names = speciation.speciation_data.columns.values
+
+    if colorscale:
+        colorscale = colorscale
+    else:
+        min_val = speciation.solvent_co_occurrence.min().min()
+        max_val = speciation.solvent_co_occurrence.max().max()
+        range_val = max_val - min_val
+
+        colorscale = [
+            [0, 'rgb(67,147,195)'],
+            [(1 - min_val) / range_val, "white"],
+            [1, 'rgb(214,96,77)']
+        ]
+
+    # Create a heatmap trace with text annotations
+    trace = go.Heatmap(
+        x=solvent_names,
+        y=solvent_names[::-1],  # Reverse the order of the y-axis labels
+        z=speciation.solvent_co_occurrence.values,  # Keep the data in the original order
+        text=speciation.solvent_co_occurrence.round(2).to_numpy(dtype=str),
+        # Keep the text annotations in the original order
+        hoverinfo="none",
+        colorscale=colorscale
+    )
+
+    # Update layout to display tick labels and text annotations
+    layout = go.Layout(
+        title="Solvent Co-Occurrence Matrix",
+        xaxis=dict(
+            tickmode='array',
+            tickvals=list(range(len(solvent_names))),
+            ticktext=solvent_names,
+            tickangle=-30,
+            side='top'
+        ),
+        yaxis=dict(
+            tickmode='array',
+            tickvals=list(range(len(solvent_names))),
+            ticktext=solvent_names,
+            autorange='reversed'
+        ),
+        margin=dict(l=60, r=60, b=60, t=100, pad=4),
+        annotations=[
+            dict(
+                x=i,
+                y=j,
+                text=str(round(speciation.solvent_co_occurrence.iloc[j, i], 2)),
+                font=dict(size=14, color="black"),
+                showarrow=False
+            )
+            for i in range(len(solvent_names))
+            for j in range(len(solvent_names))
+        ],
+    )
+
+    # Create and return the Figure object
+    fig = go.Figure(data=[trace], layout=layout)
+    return fig
+
+
 def compare_solvent_dicts(
     property_dict,
     rename_solvent_dict,

solvation_analysis/speciation.py

@@ -20,8 +20,6 @@ solvation data a non-issue.
 """
 
 import pandas as pd
-import numpy as np
-import matplotlib.pyplot as plt
 
 from solvation_analysis._column_names import *
 
@@ -193,46 +191,6 @@ class Speciation:
         correlation = actual_df / expected_df
         return correlation
 
-    def plot_co_occurrence(self):
-        """
-        Plot the co-occurrence matrix of the solute.
-
-        Co-occurrence as a heatmap with numerical values in addition to colors.
-
-        Returns
-        -------
-        fig : matplotlib.Figure
-        ax : matplotlib.Axes
-
-        """
-        # TODO: rewrite in plotly and move this to the plotting module
-        solvent_names = self.speciation_data.columns.values
-        fig, ax = plt.subplots()
-        im = ax.imshow(self.solvent_co_occurrence)
-        # We want to show all ticks...
-        ax.set_xticks(np.arange(len(solvent_names)))
-        ax.set_yticks(np.arange(len(solvent_names)))
-        # ... and label them with the respective list entries
-        ax.set_xticklabels(solvent_names, fontsize=14)
-        ax.set_yticklabels(solvent_names, fontsize=14)
-        # Let the horizontal axes labeling appear on top.
-        ax.tick_params(top=True, bottom=False,
-                       labeltop=True, labelbottom=False, )
-        # Rotate the tick labels and set their alignment.
-        plt.setp(ax.get_xticklabels(), rotation=-30, ha="right",
-                 rotation_mode="anchor")
-        # Loop over data dimensions and create text annotations.
-        for i in range(len(solvent_names)):
-            for j in range(len(solvent_names)):
-                ax.text(j, i, round(self.solvent_co_occurrence.iloc[i, j], 2),
-                        horizontalalignment="center",
-                        verticalalignment="center",
-                        color="black",
-                        fontsize=14,
-                        )
-        fig.tight_layout()
-        return fig, ax
-
     @property
     def speciation_data(self):
         """

solvation_analysis/tests/test_coordination.py

@@ -18,8 +18,7 @@ def test_coordination_from_solute(run_solute):
     ],
 )
 def test_coordination(name, cn, solvation_data, run_solute):
-    atoms = run_solute.u.atoms
-    coordination = Coordination(solvation_data, 10, 49, atoms)
+    coordination = Coordination.from_solute(run_solute)
     np.testing.assert_allclose(cn, coordination.coordination_numbers[name], atol=0.05)
     assert len(coordination.coordination_numbers_by_frame) == 3
 
@@ -33,21 +32,21 @@ def test_coordination(name, cn, solvation_data, run_solute):
     ],
 )
 def test_coordinating_atoms(name, atom_type, fraction, solvation_data, run_solute):
-    atoms = run_solute.u.atoms
-    coordination = Coordination(solvation_data, 10, 49, atoms)
+    coordination = Coordination.from_solute(run_solute)
     calculated_fraction = coordination._coordinating_atoms.loc[(name, atom_type)]
     np.testing.assert_allclose(fraction, calculated_fraction, atol=0.05)
 
 
-
-
-
-
-
-
-
-
-
-
-
-
+@pytest.mark.parametrize(
+    "name, coord",
+    [
+        ("fec", 0.15),
+        ("bn", 1.64),
+        ("pf6", 0.38),
+    ],
+)
+def test_coordination_relative_to_random(name, coord, solvation_data, run_solute):
+    atoms = run_solute.u.atoms
+    coordination = Coordination(solvation_data, 10, 49, run_solute.solvent_counts, atoms)
+    np.testing.assert_allclose(coord, coordination.coordination_vs_random[name], atol=0.05)
+    assert len(coordination.coordination_numbers_by_frame) == 3

solvation_analysis/tests/test_plotting.py

@@ -2,6 +2,7 @@ import pytest
 from solvation_analysis.plotting import (
     plot_network_size_histogram,
     plot_shell_composition_by_size,
+    plot_co_occurrence,
     _compare_function_generator,
     compare_free_solvents,
     compare_pairing,
@@ -13,6 +14,7 @@ from solvation_analysis.plotting import (
 
 from solvation_analysis.networking import Networking
 from solvation_analysis.residence import Residence
+from solvation_analysis.speciation import Speciation
 
 
 def test_plot_network_size_histogram(run_solute):
@@ -311,3 +313,10 @@ def test_compare_generic(eax_solutes):
     assert len(fig.data) == 4
     for bar in fig.data:
         assert set(bar.x) == {"pf6", "fec", "EAx"}
+    # fig.show()
+
+
+def test_plot_co_occurrence(solvation_data):
+    speciation = Speciation(solvation_data, 10, 49)
+    fig = plot_co_occurrence(speciation)
+    # fig.show()

solvation_analysis/tests/test_speciation.py

@@ -52,9 +52,3 @@ def test_speciation_correlation(solvent_one, solvent_two, correlation, solvation
     df = speciation.solvent_co_occurrence
     np.testing.assert_allclose(df[solvent_one][solvent_two], correlation, atol=0.05)
 
-
-def test_plot_correlation(solvation_data):
-    speciation = Speciation(solvation_data, 10, 49)
-    fig, ax = speciation.plot_co_occurrence()
-    # fig.show()
-

{solvation_analysis-0.3.1.dist-info → solvation_analysis-0.3.3a0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: solvation-analysis
-Version: 0.3.1
+Version: 0.3.3a0
 Summary: A toolkit to analyze solvation structure in molecular dynamics trajectories.
 Author: Orion Cohen
 Author-email: Orion Cohen <orioncohen@berkeley.edu>
@@ -606,7 +606,6 @@ Requires-Dist: numpy (>=1.20.0)
 Requires-Dist: pandas
 Requires-Dist: mdanalysis (>=2.0.0)
 Requires-Dist: pytest
-Requires-Dist: pathlib
 Requires-Dist: matplotlib
 Requires-Dist: scipy
 Requires-Dist: statsmodels

{solvation_analysis-0.3.1.dist-info → solvation_analysis-0.3.3a0.dist-info}/RECORD

@@ -1,27 +1,27 @@
 solvation_analysis/__init__.py,sha256=nilCtSfGTLm40kUA9syYdl9pGF4XWpNJ2lV3rFyZI2w,335
 solvation_analysis/_column_names.py,sha256=wK9GN1_Pzve4cI3o86R7NQGdSLfhENXct0J036nS2c8,728
 solvation_analysis/_utils.py,sha256=XkdmglL0JjXsyAS-owZU_Vo1rCSdRD0Hz3P8rfWQ3po,8016
-solvation_analysis/_version.py,sha256=rI_DvDURrbONosJPmRe6D_Okkn51y9hPH5XcU99fRnk,498
-solvation_analysis/coordination.py,sha256=md0_XupQ2VPk8Y4n144IflTen2tc9aWX5xBmTcwCMbA,4984
+solvation_analysis/_version.py,sha256=CeTQhwfxdqvxY5Pzehas2dwwJRCXrUik12wq6ckZpSA,504
+solvation_analysis/coordination.py,sha256=AE628q-dsHTzVXnsip953CHf-clqJnHPYQurPhyck3w,6570
 solvation_analysis/networking.py,sha256=PjN_bUGenxYs2dAcjGvnQb4C6dCU2rz4C2AyjhCTtuk,10777
 solvation_analysis/pairing.py,sha256=vAvhj4aPAnDACwEUOi-PS8TC-EiVzeSceOyycpDa7qQ,5709
-solvation_analysis/plotting.py,sha256=hlRg3TMKZSg5XYAz9teCXOuQBx2g3uj1vRjGUcIq76Q,10881
+solvation_analysis/plotting.py,sha256=YtzU3TlQcsOlB0qASUAxviZ4s2g9ZPcP5xml7C9NRiY,13759
 solvation_analysis/rdf_parser.py,sha256=FS8lnoucmngDBgSuakLGiMGb1HDAh1ONvQbTqQRsXWo,11231
 solvation_analysis/residence.py,sha256=VaHAImFwc9tI-9PWLYwmVdeHjzqKEppeUyWpmgFr14Q,10944
 solvation_analysis/solute.py,sha256=-RyExdqJ65GcpOM_kiFqgmFwHWZ026b94gj3fymZU0E,38245
-solvation_analysis/speciation.py,sha256=L8UPeCJfGu1yI5xYG8R0FPSoXDOLYNftgbh0A86hhfA,10663
+solvation_analysis/speciation.py,sha256=rLZCSXGbZ6-P80N-MopLN79_eGnl1feJDFrlv7MxjZk,8970
 solvation_analysis/tests/__init__.py,sha256=tlIleLX_7zJFwQuwnqP9fJ0nQXdD1uA-l8uX8w4KUKM,112
 solvation_analysis/tests/conftest.py,sha256=2cMepIZ0rLza_wnaXpu-mH_Ld2fqxq7tKoQXdm-Cj1Y,9536
 solvation_analysis/tests/datafiles.py,sha256=4vOiZsRWtIpWhq8aEyfMpR8JQWPwkppqNwbTjx2sCVc,2601
-solvation_analysis/tests/test_coordination.py,sha256=zl2FvFnEXmKZnkE8CFBKGipiDXj6yeVq-HY9IQ7nsO0,1196
+solvation_analysis/tests/test_coordination.py,sha256=hrqV5y7yLDi3ysEbL7oNGCDbdVJ26brzDhGAuNAAwO8,1596
 solvation_analysis/tests/test_networking.py,sha256=AcHm1A_ZeIsBSqnl1KV9IzJc3EwkP4pfFRdNyBQnM0k,867
 solvation_analysis/tests/test_pairing.py,sha256=D9haGZGkswmrevOa_GPGXd0KqmusAGjzUcJCYdeKTPY,1516
-solvation_analysis/tests/test_plotting.py,sha256=vui1yoDgDaTcHjaycFyDvol9X85AdQwuzK27l7Z_13k,9786
+solvation_analysis/tests/test_plotting.py,sha256=AshDnsmn3W1Y_AkEnQVGTrNu9oWfWic2k3QxbB4fLqk,10037
 solvation_analysis/tests/test_rdf_parser.py,sha256=2at9a-f43TEWBJKdIR4MCkw6cVt5QEU6kMHx7meDBtE,6317
 solvation_analysis/tests/test_residence.py,sha256=t44krzWcaVhg-uGLmnbFIIZIMSg5INBGd1gk77tSHKI,961
 solvation_analysis/tests/test_selection.py,sha256=VpeRDONNYtVEfcnXGV9UAXnpKSm2XQJoppdP03Dafkc,4012
 solvation_analysis/tests/test_solute.py,sha256=SR2vTc2KdxaP0TF_xVNijl-pcl-LdFlHa6r9wKxrTFM,12563
-solvation_analysis/tests/test_speciation.py,sha256=T7ZmMkprhdgseIwoEaq7i1VB6vlJVc9YXve0td9QkaI,1732
+solvation_analysis/tests/test_speciation.py,sha256=LsY1XlTip_W_yZ6Xh937t-sTPhhuMip2rCftvDa0sQM,1572
 solvation_analysis/tests/data/.DS_Store,sha256=reUv274-_DxmgXdgxkidZh_Eg5vy4GGjtYVNIO9iZIA,8196
 solvation_analysis/tests/data/README.md,sha256=vh4ZQXmH6EsL3sQybINpMXIIL8GqXIN4kk3Dq3AfiUg,2848
 solvation_analysis/tests/data/bn_fec_data/bn_fec.data,sha256=he2A8xzbatbOxbyas_bWaOmE0XJBePKj9HMpOu1wppY,1418421
@@ -109,8 +109,8 @@ solvation_analysis/tests/data/rdf_vs_li_hard/rdf_pf6_all_bins.npz,sha256=Z1knlSh
 solvation_analysis/tests/data/rdf_vs_li_hard/rdf_pf6_all_data.npz,sha256=yKRJ2BGnvWAfRnP9HLdK1USv1RPcwTW54Vk_Z8EqomA,864
 solvation_analysis/tests/data/rdf_vs_li_hard/rdf_universe_all_bins.npz,sha256=Z1knlShdL77EiFMvmh4FXzlkTCM2ziZKUuqYgtg_tZw,864
 solvation_analysis/tests/data/rdf_vs_li_hard/rdf_universe_all_data.npz,sha256=di1BmbLd0oca23XY5sW_M60Xi3Q8leIhHtJ61wDTTGs,864
-solvation_analysis-0.3.1.dist-info/LICENSE,sha256=-mQWu786dxXc5-JBLEYYgWZ2BTFaAueDVwUpzSRfbxI,34684
-solvation_analysis-0.3.1.dist-info/METADATA,sha256=2o_cfq6TDjc-8-J8Fz0AHx6ei65j5_l21uGTRiswWvE,45010
-solvation_analysis-0.3.1.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
-solvation_analysis-0.3.1.dist-info/top_level.txt,sha256=M6YFLMMaJsIEeRqw1v_9jvSq7oXa8GWU5x6nNNc6zbU,19
-solvation_analysis-0.3.1.dist-info/RECORD,,
+solvation_analysis-0.3.3a0.dist-info/LICENSE,sha256=-mQWu786dxXc5-JBLEYYgWZ2BTFaAueDVwUpzSRfbxI,34684
+solvation_analysis-0.3.3a0.dist-info/METADATA,sha256=i5xRZTAAJuAlGJM8o7eFMyqUHwQfUprCYJKN2EoPsok,44989
+solvation_analysis-0.3.3a0.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
+solvation_analysis-0.3.3a0.dist-info/top_level.txt,sha256=M6YFLMMaJsIEeRqw1v_9jvSq7oXa8GWU5x6nNNc6zbU,19
+solvation_analysis-0.3.3a0.dist-info/RECORD,,