workbench 0.8.174__py3-none-any.whl → 0.8.227__py3-none-any.whl

workbench/themes/dark/plotly.json

@@ -483,11 +483,11 @@
                 [1.0, "rgb(200, 100, 100)"]
             ],
             "sequential": [
-                [0.0, "rgb(100, 100, 200)"],
-                [0.4, "rgb(100, 200, 100)"],
-                [0.65, "rgb(180, 180, 50)"],
-                [0.85, "rgb(200, 100, 100)"],
-                [1.0, "rgb(200, 100, 100)"]
+                [0.0, "rgba(80, 100, 255, 1.0)"],
+                [0.25, "rgba(70, 145, 220, 1.0)"],
+                [0.5, "rgba(70, 220, 100, 1.0)"],
+                [0.75, "rgba(255, 181, 80, 1.0)"],
+                [1.0, "rgba(232, 50, 131, 1.0)"]
             ],
             "sequentialminus": [
                 [0.0, "rgb(255, 100, 100)"],

workbench/themes/light/custom.css

@@ -1,17 +1,66 @@
+/* Light Theme Color Palette - Blue-Purple Blend */
+:root {
+    /* Primary colors - blue to purple blend, low saturation */
+    --wb-lightest: rgb(200, 205, 215);        /* Very light blue-lavender - backgrounds */
+    --wb-light: rgb(195, 205, 225);           /* Light periwinkle - alternate rows */
+    --wb-medium: rgb(175, 185, 215);          /* Medium blue-purple - headers */
+    --wb-accent: rgb(120, 130, 180);          /* Blue-purple accent - borders */
+    --wb-dark: rgb(80, 90, 140);              /* Dark blue-purple - strong accents */
+
+    /* Text colors */
+    --wb-text-primary: rgb(45, 50, 65);       /* Primary text - dark blue-purple */
+    --wb-text-secondary: rgb(70, 75, 95);     /* Secondary text */
+    --wb-text-muted: rgb(95, 100, 120);       /* Muted text */
+
+    /* Semantic colors */
+    --wb-success: rgb(40, 110, 50);
+    --wb-info: rgb(60, 80, 160);
+    --wb-warning: rgb(170, 90, 10);
+    --wb-danger: rgb(180, 50, 80);
+    --wb-pink: rgb(200, 100, 200);
+
+    /* Shadows - purple-tinted */
+    --wb-shadow-light: rgba(80, 90, 140, 0.15);
+    --wb-shadow-medium: rgba(80, 90, 140, 0.25);
+
+    /* Dropdown/form colors */
+    --wb-dropdown-bg: rgb(185, 185, 195);
+    --wb-dropdown-focus: rgb(195, 195, 205);
+    --wb-dropdown-hover: rgb(195, 195, 205);
+
+    /* Container colors (with alpha) */
+    --wb-container-bg: rgba(175, 185, 215, 0.5);
+    --wb-container-bg-light: rgba(175, 185, 215, 0.25);
+    --wb-table-cell-bg: rgba(205, 215, 235, 0.5);
+
+    /* Body gradient colors */
+    --wb-body-gradient-start: rgb(180, 195, 215);
+    --wb-body-gradient-mid: rgb(170, 175, 205);
+    --wb-body-gradient-end: rgb(185, 175, 205);
+
+    /* Table header gradient colors */
+    --wb-header-red-start: rgb(200, 120, 120);
+    --wb-header-red-end: rgb(160, 90, 90);
+    --wb-header-yellow-start: rgb(180, 175, 100);
+    --wb-header-yellow-end: rgb(140, 135, 70);
+    --wb-header-green-start: rgb(110, 170, 110);
+    --wb-header-green-end: rgb(80, 130, 80);
+    --wb-header-purple-start: rgb(160, 120, 180);
+    --wb-header-purple-end: rgb(120, 85, 140);
+}
+
 h1, h2, h3, h4 {
-    color: rgb(80, 80, 80); /* We want the headers dark gray */
+    color: var(--wb-text-primary);
 }
 
 body {
-    color: rgb(80, 80, 80); /* Dark gray text */
-    /* background: linear-gradient(90deg, rgba(240,240,240,1) 0%, rgba(240,240,240,1) 50%, rgba(150,150,195,1) 100%);*/
-    /* background: linear-gradient(90deg, rgba(200,200,220,1) 0%, rgba(150,150,195,1) 100%); */
-    background: linear-gradient(90deg, rgba(200,200,220,1) 0%, rgba(170,170,210,1) 100%);
+    color: var(--wb-text-primary);
+    background: linear-gradient(135deg, var(--wb-body-gradient-start) 0%, var(--wb-body-gradient-mid) 50%, var(--wb-body-gradient-end) 100%);
 }
 
 /* Custom CSS to style bold text */
 b, strong {
-    color: rgb(40, 40, 40);
+    color: var(--wb-text-primary);
 }
 
 /* Reduce spacing around lists */
@@ -27,22 +76,28 @@ ul, ol {
 
 /* Adjust header background color */
 .ag-header {
-    --ag-header-background-color: rgba(150, 150, 195);
+    --ag-header-background-color: var(--wb-medium);
 }
 
-/* Adjust cell background */
+/* Adjust cell background and text color */
 .ag-cell {
-    background-color: rgb(240, 240, 240);
+    background-color: var(--wb-lightest);
+    color: var(--wb-text-primary);
 }
 
 /* Alternate row colors */
 .ag-row:nth-child(even) .ag-cell {
-    background-color: rgb(230, 230, 230);
+    background-color: var(--wb-light);
+}
+
+/* AgGrid header text color */
+.ag-header-cell-text {
+    color: var(--wb-text-primary);
 }
 
 /* Selection color for the entire row */
 .ag-row.ag-row-selected .ag-cell {
-    background-color: rgba(170, 170, 205, 1.0);
+    background-color: var(--wb-medium);
 }
 
 /* There's a one pixel border around the grid that we want to remove */
@@ -53,76 +108,109 @@ ul, ol {
 
 /* Box shadow and rounded corners for all AgGrid themes */
 [class*="ag-theme-"] {
-    box-shadow: 2px 2px 6px 5px rgba(0, 0, 0, 0.2); /* Drop shadow */
-    border-radius: 12px; /* Rounded corners */
-    border: 0.5px solid rgba(0, 0, 205, 0.5);
+    box-shadow: 2px 2px 6px 5px var(--wb-shadow-light);
+    border-radius: 12px;
+    border: 0.5px solid var(--wb-accent);
     margin: 0;
     padding: 0;
 }
 
 /* Apply styling to Workbench containers */
 .workbench-container {
-    background-color: rgba(240, 240, 240, 0.5);
-    box-shadow: 2px 2px 6px 5px rgba(0, 0, 0, 0.2);
-    border-radius: 12px; /* Rounded corners */
+    background-color: var(--wb-container-bg);
+    box-shadow: 2px 2px 6px 5px var(--wb-shadow-light);
+    border-radius: 12px;
 }
 
 /* Apply styling to Workbench Offsets */
 .workbench-offset {
-    background-color: rgba(240, 240, 240, 0.25);
-    box-shadow: 1px 1px 3px 2px rgba(0, 0, 0, 0.2);
-    border-radius: 12px; /* Rounded corners */
+    background-color: var(--wb-container-bg-light);
+    box-shadow: 1px 1px 3px 2px var(--wb-shadow-light);
+    border-radius: 12px;
 }
 
 /* Apply styling to Workbench Highlight */
 .workbench-highlight {
-    background-color: rgba(240, 240, 240, 0.5);
-    box-shadow: 1px 1px 3px 2px rgba(0, 0, 0, 0.2);
-    border-radius: 12px; /* Rounded corners */
+    background-color: var(--wb-container-bg);
+    box-shadow: 1px 1px 3px 2px var(--wb-shadow-light);
+    border-radius: 12px;
 }
 
 /* Apply styling to custom tooltips */
 .custom-tooltip {
-    background-color: rgba(240, 240, 240, 1.0);
-    box-shadow: 2px 2px 6px 5px rgba(0, 0, 0, 0.25);
-    border-radius: 25px; /* Rounded corners */
-    overflow: hidden; /* Ensure contents fit inside the rounded corners */
-    border: 2px solid rgba(128, 128, 128, 1); /* 1-pixel grey */
+    background-color: var(--wb-lightest);
+    box-shadow: 2px 2px 6px 5px var(--wb-shadow-medium);
+    border-radius: 25px;
+    overflow: hidden;
+    border: 2px solid var(--wb-accent);
 }
 
 /* Some of the HTML/Markdown will use color hints like 'green-text' or 'blue-text' */
 .green-text {
-    color: rgb(40, 100, 40);
+    color: var(--wb-success);
 }
 
 .blue-text {
-    color: rgb(70, 70, 160);
+    color: var(--wb-info);
 }
 
 .pink-text {
-    color: rgb(200, 100, 200);
+    color: var(--wb-pink);
 }
 
 .red-text {
-    color: rgb(200, 60, 100);
+    color: var(--wb-danger);
 }
 
 .orange-text {
-    color: rgb(160, 80, 0);
+    color: var(--wb-warning);
 }
 
 .alert {
-    color: rgb(200, 60, 100);
+    color: var(--wb-danger);
 }
 
 .warning {
-    color: rgb(160, 80, 0);
+    color: var(--wb-warning);
 }
 
 .good {
-    color: rgb(40, 100, 40);
+    color: var(--wb-success);
+}
+
+/* Dropdown styling (dcc.Dropdown) - override Bootstrap's variables */
+.dash-dropdown {
+    --bs-body-bg: var(--wb-dropdown-bg);
+    --bs-body-color: var(--wb-text-primary);
+    --bs-border-color: var(--wb-accent);
+}
+
+/* Bootstrap form controls (dbc components) */
+.form-select, .form-control {
+    background-color: var(--wb-dropdown-bg) !important;
+    border: 1px solid var(--wb-accent) !important;
+    color: var(--wb-text-primary) !important;
 }
 
+.form-select:focus, .form-control:focus {
+    background-color: var(--wb-dropdown-focus) !important;
+    border-color: var(--wb-dark) !important;
+    box-shadow: 0 0 0 0.2rem var(--wb-shadow-light) !important;
+}
+
+.dropdown-menu {
+    background-color: var(--wb-dropdown-bg) !important;
+    border: 1px solid var(--wb-accent) !important;
+}
+
+.dropdown-item {
+    color: var(--wb-text-primary) !important;
+}
+
+.dropdown-item:hover, .dropdown-item:focus {
+    background-color: var(--wb-dropdown-hover) !important;
+    color: var(--wb-text-primary) !important;
+}
 
 /* Table styling */
 table {
@@ -131,15 +219,40 @@ table {
 
 th {
     padding: 10px;
-    border: 1px solid rgb(120, 120, 120);
-    background-color: rgba(150, 150, 195);
+    border: 1px solid var(--wb-accent);
+    background-color: var(--wb-medium);
     font-weight: bold;
     text-align: center !important;
 }
 
 td {
     padding: 5px;
-    border: 0.5px solid rgb(120, 120, 120);
-    background-color: rgba(240, 240, 240, 0.5);
+    border: 0.5px solid var(--wb-accent);
+    background-color: var(--wb-table-cell-bg);
     text-align: center !important;
 }
+
+/* AG Grid table header colors - gradient theme */
+/* Data Sources tables - red gradient */
+#main_data_sources .ag-header,
+#data_sources_table .ag-header {
+    background: linear-gradient(180deg, var(--wb-header-red-start) 0%, var(--wb-header-red-end) 100%) !important;
+}
+
+/* Feature Sets tables - yellow/olive gradient */
+#main_feature_sets .ag-header,
+#feature_sets_table .ag-header {
+    background: linear-gradient(180deg, var(--wb-header-yellow-start) 0%, var(--wb-header-yellow-end) 100%) !important;
+}
+
+/* Models tables - green gradient */
+#main_models .ag-header,
+#models_table .ag-header {
+    background: linear-gradient(180deg, var(--wb-header-green-start) 0%, var(--wb-header-green-end) 100%) !important;
+}
+
+/* Endpoints tables - purple gradient */
+#main_endpoints .ag-header,
+#endpoints_table .ag-header {
+    background: linear-gradient(180deg, var(--wb-header-purple-start) 0%, var(--wb-header-purple-end) 100%) !important;
+}

workbench/themes/light/plotly.json

@@ -133,7 +133,7 @@
                     "ticks": ""
                 },
                 "colorscale": [
-                    [0.0, "rgb(100, 100, 200)"],
+                    [0.0, "rgba(100, 100, 200, 0.8)"],
                     [0.4, "rgb(100, 200, 100)"],
                     [0.65, "rgb(170, 170, 50)"],
                     [0.85, "rgb(200, 100, 100)"],
@@ -476,14 +476,14 @@
         },
         "colorscale": {
             "diverging": [
-                [0.0, "rgb(100, 100, 255)"],
+                [0.0, "rgba(100, 100, 255, 0.8)"],
                 [0.4, "rgb(100, 240, 100)"],
                 [0.65, "rgb(200, 200, 50)"],
                 [0.85, "rgb(255, 100, 100)"],
                 [1.0, "rgb(255, 100, 100)"]
             ],
             "sequential": [
-                [0.0, "rgb(100, 100, 200)"],
+                [0.0, "rgba(100, 100, 200, 0.8)"],
                 [0.4, "rgb(100, 200, 100)"],
                 [0.65, "rgb(170, 170, 50)"],
                 [0.85, "rgb(200, 100, 100)"],
@@ -561,8 +561,8 @@
         "mapbox": {
             "style": "light"
         },
-        "paper_bgcolor": "rgba(0, 0, 0, 0.0)",
-        "plot_bgcolor": "rgba(0, 0, 0, 0.0)",
+        "paper_bgcolor": "rgba(255, 255, 255, 0.0)",
+        "plot_bgcolor": "rgba(255, 255, 255, 0.0)",
         "polar": {
             "angularaxis": {
                 "gridcolor": "#EBF0F8",
@@ -633,25 +633,25 @@
         },
         "xaxis": {
             "automargin": true,
-            "gridcolor": "#ffffff",
+            "gridcolor": "rgba(120, 130, 160, 0.3)",
             "linecolor": "#EBF0F8",
             "ticks": "",
             "title": {
                 "standoff": 15
             },
-            "zerolinecolor": "#edeeee",
+            "zerolinecolor": "rgba(120, 130, 160, 0.4)",
             "zerolinewidth": 2,
             "gridwidth": 0.5
         },
         "yaxis": {
             "automargin": true,
-            "gridcolor": "#ffffff",
+            "gridcolor": "rgba(120, 130, 160, 0.3)",
             "linecolor": "#EBF0F8",
             "ticks": "",
             "title": {
                 "standoff": 15
             },
-            "zerolinecolor": "#edeeee",
+            "zerolinecolor": "rgba(120, 130, 160, 0.4)",
             "zerolinewidth": 2,
             "gridwidth": 0.5
         },

workbench/themes/midnight_blue/custom.css

@@ -133,6 +133,40 @@ a:hover {
     color: rgb(100, 255, 100);
 }
 
+/* Dropdown styling (dcc.Dropdown) - override Bootstrap's --bs-body-bg variable */
+.dash-dropdown {
+    --bs-body-bg: rgb(55, 60, 90);
+    --bs-border-color: rgb(80, 85, 115);
+}
+
+
+/* Bootstrap form controls (dbc components) */
+.form-select, .form-control {
+    background-color: rgb(55, 60, 90) !important;
+    border: 1px solid rgb(80, 85, 115) !important;
+    color: rgb(210, 210, 210) !important;
+}
+
+.form-select:focus, .form-control:focus {
+    background-color: rgb(60, 65, 95) !important;
+    border-color: rgb(100, 105, 140) !important;
+    box-shadow: 0 0 0 0.2rem rgba(100, 105, 140, 0.25) !important;
+}
+
+.dropdown-menu {
+    background-color: rgb(55, 60, 90) !important;
+    border: 1px solid rgb(80, 85, 115) !important;
+}
+
+.dropdown-item {
+    color: rgb(210, 210, 210) !important;
+}
+
+.dropdown-item:hover, .dropdown-item:focus {
+    background-color: rgb(70, 75, 110) !important;
+    color: rgb(230, 230, 230) !important;
+}
+
 /* Table styling */
 table {
     width: 100%;
@@ -151,4 +185,29 @@ td {
     padding: 5px;
     border: 0.5px solid #444;
     text-align: center !important;
+}
+
+/* AG Grid table header colors - gradient theme */
+/* Data Sources tables - red gradient */
+#main_data_sources .ag-header,
+#data_sources_table .ag-header {
+    background: linear-gradient(180deg, rgb(130, 55, 55) 0%, rgb(80, 35, 35) 100%) !important;
+}
+
+/* Feature Sets tables - yellow/olive gradient */
+#main_feature_sets .ag-header,
+#feature_sets_table .ag-header {
+    background: linear-gradient(180deg, rgb(110, 105, 50) 0%, rgb(70, 65, 30) 100%) !important;
+}
+
+/* Models tables - green gradient */
+#main_models .ag-header,
+#models_table .ag-header {
+    background: linear-gradient(180deg, rgb(50, 100, 50) 0%, rgb(30, 60, 30) 100%) !important;
+}
+
+/* Endpoints tables - purple gradient */
+#main_endpoints .ag-header,
+#endpoints_table .ag-header {
+    background: linear-gradient(180deg, rgb(90, 55, 110) 0%, rgb(55, 30, 70) 100%) !important;
 }

workbench/utils/aws_utils.py

@@ -17,7 +17,6 @@ from botocore.exceptions import ClientError
 from sagemaker.session import Session as SageSession
 from collections.abc import Mapping, Iterable
 
-
 # Workbench Imports
 from workbench.utils.config_manager import ConfigManager
 from workbench.utils.deprecated_utils import deprecated

workbench/utils/chem_utils/fingerprints.py

@@ -1,31 +1,48 @@
-"""Molecular fingerprint computation utilities"""
+"""Molecular fingerprint computation utilities for ADMET modeling.
+
+This module provides Morgan count fingerprints, the standard for ADMET prediction.
+Count fingerprints outperform binary fingerprints for molecular property prediction.
+
+References:
+    - Count vs Binary: https://pubs.acs.org/doi/10.1021/acs.est.3c02198
+    - ECFP/Morgan: https://pubs.acs.org/doi/10.1021/ci100050t
+"""
 
 import logging
-import pandas as pd
 
-# Molecular Descriptor Imports
-from rdkit import Chem
-from rdkit.Chem import rdFingerprintGenerator
+import numpy as np
+import pandas as pd
+from rdkit import Chem, RDLogger
+from rdkit.Chem import AllChem
 from rdkit.Chem.MolStandardize import rdMolStandardize
 
+# Suppress RDKit warnings (e.g., "not removing hydrogen atom without neighbors")
+# Keep errors enabled so we see actual problems
+RDLogger.DisableLog("rdApp.warning")
+
 # Set up the logger
 log = logging.getLogger("workbench")
 
 
-def compute_morgan_fingerprints(df: pd.DataFrame, radius=2, n_bits=2048, counts=True) -> pd.DataFrame:
-    """Compute and add Morgan fingerprints to the DataFrame.
+def compute_morgan_fingerprints(df: pd.DataFrame, radius: int = 2, n_bits: int = 2048) -> pd.DataFrame:
+    """Compute Morgan count fingerprints for ADMET modeling.
+
+    Generates true count fingerprints where each bit position contains the
+    number of times that substructure appears in the molecule (clamped to 0-255).
+    This is the recommended approach for ADMET prediction per 2025 research.
 
     Args:
-        df (pd.DataFrame): Input DataFrame containing SMILES strings.
-        radius (int): Radius for the Morgan fingerprint.
-        n_bits (int): Number of bits for the fingerprint.
-        counts (bool): Count simulation for the fingerprint.
+        df: Input DataFrame containing SMILES strings.
+        radius: Radius for the Morgan fingerprint (default 2 = ECFP4 equivalent).
+        n_bits: Number of bits for the fingerprint (default 2048).
 
     Returns:
-        pd.DataFrame: The input DataFrame with the Morgan fingerprints added as bit strings.
+        pd.DataFrame: Input DataFrame with 'fingerprint' column added.
+                      Values are comma-separated uint8 counts.
 
     Note:
-        See: https://greglandrum.github.io/rdkit-blog/posts/2021-07-06-simulating-counts.html
+        Count fingerprints outperform binary for ADMET prediction.
+        See: https://pubs.acs.org/doi/10.1021/acs.est.3c02198
     """
     delete_mol_column = False
 
@@ -39,7 +56,7 @@ def compute_morgan_fingerprints(df: pd.DataFrame, radius=2, n_bits=2048, counts=
         log.warning("Detected serialized molecules in 'molecule' column. Removing...")
         del df["molecule"]
 
-    # Convert SMILES to RDKit molecule objects (vectorized)
+    # Convert SMILES to RDKit molecule objects
     if "molecule" not in df.columns:
         log.info("Converting SMILES to RDKit Molecules...")
         delete_mol_column = True
@@ -47,23 +64,32 @@ def compute_morgan_fingerprints(df: pd.DataFrame, radius=2, n_bits=2048, counts=
         # Make sure our molecules are not None
         failed_smiles = df[df["molecule"].isnull()][smiles_column].tolist()
         if failed_smiles:
-            log.error(f"Failed to convert the following SMILES to molecules: {failed_smiles}")
-        df = df.dropna(subset=["molecule"])
+            log.warning(f"Failed to convert {len(failed_smiles)} SMILES to molecules ({failed_smiles})")
+        df = df.dropna(subset=["molecule"]).copy()
 
     # If we have fragments in our compounds, get the largest fragment before computing fingerprints
     largest_frags = df["molecule"].apply(
         lambda mol: rdMolStandardize.LargestFragmentChooser().choose(mol) if mol else None
     )
 
-    # Create a Morgan fingerprint generator
-    if counts:
-        n_bits *= 4  # Multiply by 4 to simulate counts
-    morgan_generator = rdFingerprintGenerator.GetMorganGenerator(radius=radius, fpSize=n_bits, countSimulation=counts)
+    def mol_to_count_string(mol):
+        """Convert molecule to comma-separated count fingerprint string."""
+        if mol is None:
+            return pd.NA
 
-    # Compute Morgan fingerprints (vectorized)
-    fingerprints = largest_frags.apply(
-        lambda mol: (morgan_generator.GetFingerprint(mol).ToBitString() if mol else pd.NA)
-    )
+        # Get hashed Morgan fingerprint with counts
+        fp = AllChem.GetHashedMorganFingerprint(mol, radius, nBits=n_bits)
+
+        # Initialize array and populate with counts (clamped to uint8 range)
+        counts = np.zeros(n_bits, dtype=np.uint8)
+        for idx, count in fp.GetNonzeroElements().items():
+            counts[idx] = min(count, 255)
+
+        # Return as comma-separated string
+        return ",".join(map(str, counts))
+
+    # Compute Morgan count fingerprints
+    fingerprints = largest_frags.apply(mol_to_count_string)
 
     # Add the fingerprints to the DataFrame
     df["fingerprint"] = fingerprints
@@ -71,59 +97,62 @@ def compute_morgan_fingerprints(df: pd.DataFrame, radius=2, n_bits=2048, counts=
     # Drop the intermediate 'molecule' column if it was added
     if delete_mol_column:
         del df["molecule"]
+
     return df
 
 
 if __name__ == "__main__":
-    print("Running molecular fingerprint tests...")
-    print("Note: This requires molecular_screening module to be available")
+    print("Running Morgan count fingerprint tests...")
 
     # Test molecules
     test_molecules = {
         "aspirin": "CC(=O)OC1=CC=CC=C1C(=O)O",
         "caffeine": "CN1C=NC2=C1C(=O)N(C(=O)N2C)C",
         "glucose": "C([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)O)O)O)O",  # With stereochemistry
-        "sodium_acetate": "CC(=O)[O-].[Na+]",  # Salt
+        "sodium_acetate": "CC(=O)[O-].[Na+]",  # Salt (largest fragment used)
         "benzene": "c1ccccc1",
         "butene_e": "C/C=C/C",  # E-butene
         "butene_z": "C/C=C\\C",  # Z-butene
     }
 
-    # Test 1: Morgan Fingerprints
-    print("\n1. Testing Morgan fingerprint generation...")
+    # Test 1: Morgan Count Fingerprints (default parameters)
+    print("\n1. Testing Morgan fingerprint generation (radius=2, n_bits=2048)...")
 
     test_df = pd.DataFrame({"SMILES": list(test_molecules.values()), "name": list(test_molecules.keys())})
-
-    fp_df = compute_morgan_fingerprints(test_df.copy(), radius=2, n_bits=512, counts=False)
+    fp_df = compute_morgan_fingerprints(test_df.copy())
 
     print("   Fingerprint generation results:")
     for _, row in fp_df.iterrows():
         fp = row.get("fingerprint", "N/A")
-        fp_len = len(fp) if fp != "N/A" else 0
-        print(f"   {row['name']:15} → {fp_len} bits")
+        if pd.notna(fp):
+            counts = [int(x) for x in fp.split(",")]
+            non_zero = sum(1 for c in counts if c > 0)
+            max_count = max(counts)
+            print(f"   {row['name']:15} → {len(counts)} features, {non_zero} non-zero, max={max_count}")
+        else:
+            print(f"   {row['name']:15} → N/A")
 
-    # Test 2: Different fingerprint parameters
-    print("\n2. Testing different fingerprint parameters...")
+    # Test 2: Different parameters
+    print("\n2. Testing with different parameters (radius=3, n_bits=1024)...")
 
-    # Test with counts enabled
-    fp_counts_df = compute_morgan_fingerprints(test_df.copy(), radius=3, n_bits=256, counts=True)
+    fp_df_custom = compute_morgan_fingerprints(test_df.copy(), radius=3, n_bits=1024)
 
-    print("   With count simulation (256 bits * 4):")
-    for _, row in fp_counts_df.iterrows():
+    for _, row in fp_df_custom.iterrows():
         fp = row.get("fingerprint", "N/A")
-        fp_len = len(fp) if fp != "N/A" else 0
-        print(f"   {row['name']:15} → {fp_len} bits")
+        if pd.notna(fp):
+            counts = [int(x) for x in fp.split(",")]
+            non_zero = sum(1 for c in counts if c > 0)
+            print(f"   {row['name']:15} → {len(counts)} features, {non_zero} non-zero")
+        else:
+            print(f"   {row['name']:15} → N/A")
 
     # Test 3: Edge cases
     print("\n3. Testing edge cases...")
 
     # Invalid SMILES
     invalid_df = pd.DataFrame({"SMILES": ["INVALID", ""]})
-    try:
-        fp_invalid = compute_morgan_fingerprints(invalid_df.copy())
-        print(f"   ✓ Invalid SMILES handled: {len(fp_invalid)} valid molecules")
-    except Exception as e:
-        print(f"   ✓ Invalid SMILES properly raised error: {type(e).__name__}")
+    fp_invalid = compute_morgan_fingerprints(invalid_df.copy())
+    print(f"   ✓ Invalid SMILES handled: {len(fp_invalid)} rows returned")
 
     # Test with pre-existing molecule column
     mol_df = test_df.copy()
@@ -131,4 +160,16 @@ if __name__ == "__main__":
     fp_with_mol = compute_morgan_fingerprints(mol_df)
     print(f"   ✓ Pre-existing molecule column handled: {len(fp_with_mol)} fingerprints generated")
 
+    # Test 4: Verify count values are reasonable
+    print("\n4. Verifying count distribution...")
+    all_counts = []
+    for _, row in fp_df.iterrows():
+        fp = row.get("fingerprint", "N/A")
+        if pd.notna(fp):
+            counts = [int(x) for x in fp.split(",")]
+            all_counts.extend([c for c in counts if c > 0])
+
+    if all_counts:
+        print(f"   Non-zero counts: min={min(all_counts)}, max={max(all_counts)}, mean={np.mean(all_counts):.2f}")
+
     print("\n✅ All fingerprint tests completed!")