added user defined solute functionality

data/soluteData.xlsx

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:4fcdcf105050265e26b8a02ea38ae6ce9a8d1618f9a29fd0282579b026fc4478
-size 9612
+oid sha256:7fda2bcddef252ad66a0529ca9e1f600f0ff2527cfaca8655e7d674d4e7e9e5d
+size 9715

instructions.py

@@ -41,6 +41,19 @@ def build_instructions_layout() -> html.Div:
         "fontSize": "13.5px",
     }
 
+    table_header_style = {
+        "border": "1px solid #ccc",
+        "padding": "5px 8px",
+        "textAlign": "left",
+        "backgroundColor": "#f2f2f2",
+    }
+
+    table_cell_style = {
+        "border": "1px solid #ccc",
+        "padding": "5px 8px",
+        "textAlign": "left",
+    }
+
     return html.Div(
         style=page_style,
         children=[
@@ -112,11 +125,115 @@ def build_instructions_layout() -> html.Div:
                         ],
                     ),
 
+                    # ---------------------------------------------------------
+                    # 2. Solutes
+                    # ---------------------------------------------------------
+                    html.H2("2) Choose solutes", style=h2_style),
+
+                    html.P(
+                        "Select the set of chemicals to evaluate in the “Solutes” section. "
+                        "You can use the default representative boundary chemicals or upload "
+                        "a user-defined Excel file.",
+                        style=p_style,
+                    ),
+
+                    html.Ul(
+                        style=ul_style,
+                        children=[
+                            html.Li(
+                                [
+                                    html.B("Default boundary chemicals: "),
+                                    "Uses the predefined set of representative chemicals included "
+                                    "with the tool.",
+                                ],
+                                style=li_style,
+                            ),
+
+                            html.Li(
+                                [
+                                    html.B("User-defined chemicals: "),
+                                    "Upload an Excel file containing the chemicals you want to evaluate.",
+                                ],
+                                style=li_style,
+                            ),
+                        ],
+                    ),
+
+                    html.Div(
+                        style=callout_style,
+                        children=[
+                            html.B("Required Excel columns"),
+                            html.Br(),
+                            "A user-defined Excel file must contain the following four columns, "
+                            "with the column names written exactly as shown:",
+                            html.Br(),
+                            html.Br(),
+
+                            html.Table(
+                                [
+                                    html.Thead(
+                                        html.Tr(
+                                            [
+                                                html.Th("CASRN", style=table_header_style),
+                                                html.Th("MW", style=table_header_style),
+                                                html.Th("LogP", style=table_header_style),
+                                                html.Th("Vabc", style=table_header_style),
+                                            ]
+                                        )
+                                    ),
+
+                                    html.Tbody(
+                                        [
+                                            html.Tr(
+                                                [
+                                                    html.Td(
+                                                        "Chemical Abstracts Service Registry Number",
+                                                        style=table_cell_style,
+                                                    ),
+                                                    html.Td(
+                                                        "Molecular weight",
+                                                        style=table_cell_style,
+                                                    ),
+                                                    html.Td(
+                                                        "Octanol/water partition coefficient (log10)",
+                                                        style=table_cell_style,
+                                                    ),
+                                                    html.Td(
+                                                        "Molecular volume",
+                                                        style=table_cell_style,
+                                                    ),
+                                                ]
+                                            )
+                                        ]
+                                    ),
+                                ],
+                                style={
+                                    "borderCollapse": "collapse",
+                                    "width": "100%",
+                                    "marginTop": "6px",
+                                    "marginBottom": "6px",
+                                },
+                            ),
+
+                            html.Br(),
+
+                            "The MW, LogP, and Vabc columns must contain numeric values. "
+                            "LogP values greater than 10 are limited to 10 for use in the model.",
+                        ],
+                    ),
+
+                    html.P(
+                        "After a valid file is uploaded, the tool will use the uploaded chemical "
+                        "properties in place of the default boundary-chemical set when Calculate "
+                        "is selected.",
+                        style=small_style,
+                    ),
+
                     # ---------------------------------------------------------
                     # 2. Conditions
                     # ---------------------------------------------------------
                     html.H2(
-                        "2) Define Condition #1 and Condition #2",
+                        "3) Define Condition #1 and Condition #2",
                         style=h2_style,
                     ),
 
@@ -185,7 +302,7 @@ def build_instructions_layout() -> html.Div:
                     # ---------------------------------------------------------
                     # 3. Monte Carlo
                     # ---------------------------------------------------------
-                    html.H2("3) Monte Carlo settings", style=h2_style),
+                    html.H2("4) Monte Carlo settings", style=h2_style),
 
                     html.P(
                         "Set the number of samples under “Monte Carlo → Samples” and "
@@ -238,7 +355,7 @@ def build_instructions_layout() -> html.Div:
                     # ---------------------------------------------------------
                     # 4. Results
                     # ---------------------------------------------------------
-                    html.H2("4) Run and interpret results", style=h2_style),
+                    html.H2("5) Run and interpret results", style=h2_style),
 
                     html.P(
                         [

main.py

@@ -11,6 +11,8 @@ from main_layout import build_main_layout
 from instructions import build_instructions_layout
 from rst_info import build_rst_layout
 from dash import html, dcc
+import base64
+import io
 
 app = Dash(
     __name__,
@@ -47,8 +49,85 @@ def route(pathname):
         return build_main_layout()
 
 # --------------------------------------------------------------------
-# Main callback
+# Callbacks
 # --------------------------------------------------------------------
+
+@app.callback(
+    Output("solute_upload_container", "style"),
+    Input("solute_source", "value"),
+)
+def show_solute_upload(solute_source):
+
+    if solute_source == "upload":
+        return {"display": "block"}
+
+    return {"display": "none"}
+
+@app.callback(
+    Output("uploaded_solute_data", "data"),
+    Output("solute_upload_status", "children"),
+    Input("solute_upload", "contents"),
+    State("solute_upload", "filename"),
+    prevent_initial_call=True,
+)
+def load_solute_file(contents, filename):
+
+    if contents is None:
+        return None, ""
+
+    try:
+        content_type, content_string = contents.split(",")
+
+        decoded = base64.b64decode(content_string)
+
+        uploaded_df = pd.read_excel(
+            io.BytesIO(decoded)
+        )
+
+        required_columns = [
+            "CASRN",
+            "MW",
+            "LogP",
+            "Vabc",
+        ]
+
+        missing = [
+            col for col in required_columns
+            if col not in uploaded_df.columns
+        ]
+
+        if missing:
+            return (
+                None,
+                f"Missing required columns: {', '.join(missing)}"
+            )
+
+        numeric_columns = [
+            "MW",
+            "LogP",
+            "Vabc",
+        ]
+
+        for col in numeric_columns:
+            uploaded_df[col] = pd.to_numeric(
+                uploaded_df[col],
+                errors="coerce"
+            )
+
+        if uploaded_df[numeric_columns].isna().any().any():
+            return (
+                None,
+                "One or more required numeric values are missing or invalid."
+            )
+
+        return (
+            uploaded_df.to_dict("records"),
+            f"Loaded {len(uploaded_df)} solutes from {filename}"
+        )
+
+    except Exception as e:
+        return None, f"Could not read file: {e}"
+
 @app.callback(
     Output("c1_solvent", "disabled"),
     Output("c1_volume", "disabled"),
@@ -86,6 +165,7 @@ def toggle_condition2_inputs(mode, current_value):
     State("density", "value"),
     State("polymer_volume", "value"),
     State("surface_area", "value"),
+
     # Condition 1
     State("condition1_mode", "value"),
     State("c1_solvent", "value"),
@@ -105,6 +185,9 @@ def toggle_condition2_inputs(mode, current_value):
     # MC
     State("samples", "value"),
     State("mc_option", "value"),
+    # Solutes
+    State("solute_source", "value"),
+    State("uploaded_solute_data", "data"),
     prevent_initial_call=True,
 )
 
@@ -113,13 +196,25 @@ def update_chart(n_clicks,
                  c1_mode, c1_solvent, c1_volume, c1_swelling,
                  c1_temp, c1_time, c1_iter,
                  c2_mode, c2_solvent, c2_volume,
-                 c2_swelling, c2_temp, c2_time, c2_iter,samples,mc_option):
+                 c2_swelling, c2_temp, c2_time, c2_iter,samples,mc_option,solute_source,uploaded_solute_data):
+
+    if solute_source == "default":
+
+        current_soluteData = soluteData.copy()
+
+    else:
+
+        if uploaded_solute_data is None:
+            raise PreventUpdate
 
-    # TODO: replace with logic that uses the form inputs
-    # For now, simply return the same figure when "Calculate" is clicked.
+        current_soluteData = pd.DataFrame(
+            uploaded_solute_data
+        )
 
     df = pd.DataFrame()
-    df['CASRN'] = soluteData['CASRN'].to_numpy()
+    df['CASRN'] = current_soluteData['CASRN'].to_numpy()
+
+    current_soluteData["LogP"] = current_soluteData["LogP"].clip(upper=10)
 
     N = int(samples)
     pindex = np.where(polymers == matrix)[0][0]
@@ -133,10 +228,10 @@ def update_chart(n_clicks,
     # Condition 1
     ExtractionTime = float(c1_time) * 3600.
     if c1_mode == 'in_vivo_conservative':
-        c1_dist = ConservativeMonteCarlo(soluteData, CHRIS_category, L, ExtractionTime, N)
+        c1_dist = ConservativeMonteCarlo(current_soluteData, CHRIS_category, L, ExtractionTime, N)
 
     elif c1_mode == 'in_vivo_tissue':
-        c1_dist = TissueMonteCarlo(soluteData, CHRIS_category, L, ExtractionTime, N)
+        c1_dist = TissueMonteCarlo(current_soluteData, CHRIS_category, L, ExtractionTime, N)
 
     else:
         Solvent_Name = c1_solvent
@@ -150,16 +245,16 @@ def update_chart(n_clicks,
         Iterations = float(c1_iter)
         Lbath = float(c1_volume) / float(surface_area)
 
-        c1_dist = ExtractMonteCarlo(soluteData, Solvent_PI, w, ExtractionT, Polymer_Tg, Solvent_Name, Solvent_MW,
+        c1_dist = ExtractMonteCarlo(current_soluteData, Solvent_PI, w, ExtractionT, Polymer_Tg, Solvent_Name, Solvent_MW,
                                                     ExtractionTime, Swell, Iterations, CHRIS_category, L, Lbath, N)
 
     # Condition 2
     ExtractionTime = float(c2_time) * 3600.
     if c2_mode == 'in_vivo_conservative':
-        c2_dist = ConservativeMonteCarlo(soluteData, CHRIS_category, L, ExtractionTime, N)
+        c2_dist = ConservativeMonteCarlo(current_soluteData, CHRIS_category, L, ExtractionTime, N)
 
     elif c2_mode == 'in_vivo_tissue':
-        c2_dist = TissueMonteCarlo(soluteData, CHRIS_category, L, ExtractionTime, N)
+        c2_dist = TissueMonteCarlo(current_soluteData, CHRIS_category, L, ExtractionTime, N)
 
     else:
         Solvent_Name = c2_solvent
@@ -173,7 +268,7 @@ def update_chart(n_clicks,
         Iterations = float(c2_iter)
         Lbath = float(c2_volume) / float(surface_area)
 
-        c2_dist = ExtractMonteCarlo(soluteData, Solvent_PI, w, ExtractionT, Polymer_Tg, Solvent_Name, Solvent_MW,
+        c2_dist = ExtractMonteCarlo(current_soluteData, Solvent_PI, w, ExtractionT, Polymer_Tg, Solvent_Name, Solvent_MW,
                                                     ExtractionTime, Swell, Iterations, CHRIS_category, L, Lbath, N)
 
     if mc_option == "absolute":
@@ -227,7 +322,7 @@ def ConservativeMonteCarlo(soluteData, CHRIS_category, L, time, N):
 
     for iSolute in range(nSolutes):
 
-        Solute_MW = soluteData['MW_new'].iloc[iSolute]
+        Solute_MW = soluteData['MW'].iloc[iSolute]
 
         D_CHRIS = get_D_CHRIS(
             Solute_MW,
@@ -249,8 +344,8 @@ def TissueMonteCarlo(soluteData, CHRIS_category, L, time, N):
 
     for iSolute in range(nSolutes):
 
-        Solute_MW = soluteData['MW_new'].iloc[iSolute]
-        Solute_logP = soluteData['LogP_new'].iloc[iSolute]
+        Solute_MW = soluteData['MW'].iloc[iSolute]
+        Solute_logP = soluteData['LogP'].iloc[iSolute]
 
         D_CHRIS = get_D_CHRIS(
             Solute_MW,
@@ -282,8 +377,8 @@ def ExtractMonteCarlo(
 
     for iSolute in range(nSolutes):
 
-        Solute_MW = soluteData['MW_new'].iloc[iSolute]
-        Solute_logP = soluteData['LogP_new'].iloc[iSolute]
+        Solute_MW = soluteData['MW'].iloc[iSolute]
+        Solute_logP = soluteData['LogP'].iloc[iSolute]
         Solute_Vabc = soluteData['Vabc'].iloc[iSolute]
 
         if Solvent_Name == 'blood':
@@ -334,4 +429,4 @@ def ExtractMonteCarlo(
 
 
 if __name__ == "__main__":
-    app.run(debug=False)
+    app.run(debug=True)

main_layout.py

@@ -145,6 +145,63 @@ def build_main_layout() -> html.Div:
                             ],
                         ),
 
+                        # Solutes row
+                        html.H3(
+                            "Solutes",
+                            style={
+                                "textDecoration": "underline",
+                                "fontSize": "18px",
+                                "marginBottom": "10px",
+                            },
+                        ),
+
+                        dcc.RadioItems(
+                            id="solute_source",
+                            options=[
+                                {"label": "Default boundary chemicals", "value": "default"},
+                                {"label": "User-defined chemicals", "value": "upload"},
+                            ],
+                            value="default",
+                            inline=True,
+                            labelStyle={"marginRight": "15px"},
+                        ),
+
+                        html.Div(
+                            id="solute_upload_container",
+                            children=[
+                                dcc.Upload(
+                                    id="solute_upload",
+                                    children=html.Div([
+                                        "Drag and drop or ",
+                                        html.A("select an Excel file"),
+                                    ]),
+                                    accept=".xlsx,.xls",
+                                    multiple=False,
+                                    style={
+                                        "width": "100%",
+                                        "height": "55px",
+                                        "lineHeight": "55px",
+                                        "borderWidth": "1px",
+                                        "borderStyle": "dashed",
+                                        "borderRadius": "4px",
+                                        "textAlign": "center",
+                                        "marginTop": "10px",
+                                    },
+                                ),
+
+                                html.Div(
+                                    id="solute_upload_status",
+                                    style={
+                                        "marginTop": "5px",
+                                        "fontSize": "13px",
+                                    },
+                                ),
+                            ],
+                            style={"display": "none"},
+                        ),
+
+                        dcc.Store(id="uploaded_solute_data"),
+
                         # Conditions row
                         html.Div(
                             style={