push new db or demo version

requirements.txt

@@ -7,4 +7,5 @@ redis-om>=0.2.0
 numpy>=1.24.0
 python-dotenv>=1.0.0
 scikit-learn>=1.3.0
-rdkit>=2025.3.2
+rdkit>=2025.3.2
+pytest

src/app.py

@@ -78,7 +78,7 @@ class App:
                 )
                 sample_btn.click(
                     fn=None,
-                    js=f"() => {{window.setJSMESmiles('{row['smiles']}');}}",
+                    js=f"() => {{window.setCWSmiles('{row['smiles']}');}}",
                 )
 
     @staticmethod
@@ -100,28 +100,31 @@ class App:
     def create_gradio_interface(self):
         """Create the Gradio interface optimized for JavaScript client usage"""
         head_scripts = """
-<link rel="preload" href="gradio_api/file=src/static/jsme/jsme.nocache.js" as="script">
+<link rel="preload" href="gradio_api/file=src/static/chemwriter/chemwriter.css" as="style">
+<link rel="preload" href="gradio_api/file=src/static/chemwriter/chemwriter-user.css" as="style">
+<link rel="preload" href="gradio_api/file=src/static/chemwriter/chemwriter.js" as="script">
 <link rel="preload" href="gradio_api/file=src/static/main.min.js" as="script">
-<link rel="preload" href="gradio_api/file=src/static/jsme/4277561D0E87B89F4DFCCC3A712D5B19.cache.js" as="script">
-<script src="gradio_api/file=src/static/jsme/jsme.nocache.js" defer></script>
+<link rel="stylesheet" href="gradio_api/file=src/static/chemwriter/chemwriter.css">
+<link rel="stylesheet" href="gradio_api/file=src/static/chemwriter/chemwriter-user.css">
+<script src="gradio_api/file=src/static/chemwriter/chemwriter.js" defer></script>
 <script src="gradio_api/file=src/static/main.min.js" defer></script>
         """
 
         with gr.Blocks(
             title="Chem-MRL: Molecular Similarity Search Demo",
-            theme=gr.themes.Soft(),
+            theme=gr.themes.Soft(),  # type: ignore
             head=head_scripts,
         ) as demo:
             gr.Markdown("""
             # 🧪 Chem-MRL: Molecular Similarity Search Demo
 
-            Use the JSME editor to draw a molecule or input a SMILES string.<br/>
+            Use the ChemWriter editor to draw a molecule or input a SMILES string.<br/>
             The backend encodes the molecule using the Chem-MRL model to produce a vector embedding.<br/>
             Similarity search is performed via an HNSW-indexed Redis vector store to retrieve closest matches.
             """)
             gr.HTML(
                 """
-            The Redis database indexes <a href="https://isomerdesign.com/pihkal/home">Isomer Design</a> molecular library.
+            The Redis database indexes <a href="https://isomerdesign.com/pihkal/home">Isomer Design's</a> molecular library.
             <a href="https://creativecommons.org/licenses/by-nc-sa/4.0/">
                 <img src="https://mirrors.creativecommons.org/presskit/buttons/80x15/svg/by-nc-sa.svg" alt="License: CC BY-NC-SA 4.0"
              style="display:inline; height:15px; vertical-align:middle; margin-left:4px;"/>
@@ -134,20 +137,35 @@ class App:
             with gr.Tab("🔬 Molecular Search"), gr.Row():
                 with gr.Column(scale=1):
                     gr.Markdown("### Molecule Input")
-                    gr.HTML("<div id='jsme_container'></div>")
+                    gr.HTML(
+                        '<div id="editor" class="chemwriter" '
+                        'data-chemwriter-ui="editor" '
+                        'data-chemwriter-width="100%" data-chemwriter-height="450"></div>'
+                    )
 
                     smiles_input = gr.Textbox(
                         label="SMILES String",
                         placeholder="Draw a molecule above or enter SMILES here (e.g., CCO for ethanol)",
                         lines=2,
                         elem_id="smiles_input",
+                        show_copy_button=True,
+                    )
+
+                    mol_input = gr.Textbox(
+                        label="Molecule Input",
+                        interactive=False,
+                        elem_id="mol_input",
+                        show_copy_button=True,
+                        visible=False,
                     )
 
                     canonical_smiles_output = gr.Textbox(
                         label="Canonical SMILES",
                         placeholder="Canonical representation will appear here",
+                        lines=2,
                         interactive=False,
                         elem_id="canonical_smiles_output",
+                        show_copy_button=True,
                     )
 
                     embedding_dimension = gr.Dropdown(
@@ -186,12 +204,11 @@ class App:
                             elem_id="similar_molecules_output",
                         )
 
-                    molecule_image = gr.Image(label="Similiar Molecules Grid", type="pil")
+                    molecule_image = gr.Image(label="Similar Molecules Grid", type="pil")
 
             with gr.Tab("📊 Sample Molecules"):
                 gr.Markdown("""
-                ### Sample Molecules in Database
-                Click any button below to load the molecule into the JSME editor:
+                Click any button below to load the molecule into the ChemWriter editor:
                 """)
 
                 with gr.Row():
@@ -210,6 +227,12 @@ class App:
                 api_name="get_canonical_smiles",
             )
 
+            mol_input.change(
+                fn=self.embedding_service.get_smiles_from_mol_file,
+                inputs=[mol_input],
+                outputs=[smiles_input],
+            )
+
             search_btn.click(
                 fn=self.handle_search,
                 inputs=[smiles_input, embedding_dimension],
@@ -225,7 +248,7 @@ class App:
             # Clear UI state
             clear_btn.click(
                 fn=self.clear_all,
-                js="window.clearJSME",
+                js="window.clearCW",
                 outputs=[
                     smiles_input,
                     canonical_smiles_output,

src/data/README.md

@@ -0,0 +1,40 @@
+# Data Directory
+
+This directory contains molecular data used by the Chem-MRL demo application.
+
+## Dataset Information
+
+### Isomer Design Dataset
+
+The molecular data used in this application is sourced from the **Isomer Design** molecular library.
+
+- **Dataset Source**: [Isomer Design](https://isomerdesign.com/pihkal/home)
+- **License**: [CC BY-NC-SA 4.0](https://creativecommons.org/licenses/by-nc-sa/4.0/) [![License: CC BY-NC-SA 4.0](https://mirrors.creativecommons.org/presskit/buttons/80x15/svg/by-nc-sa.svg)](https://creativecommons.org/licenses/by-nc-sa/4.0/)
+- **License Type**: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International
+
+### License Terms
+
+This dataset is licensed under CC BY-NC-SA 4.0, which means:
+
+- ✅ **Attribution**: You must give appropriate credit to the original source
+- ❌ **NonCommercial**: You may not use the material for commercial purposes
+- ✅ **ShareAlike**: If you remix, transform, or build upon the material, you must distribute your contributions under the same license
+
+### Usage in This Project
+
+The dataset is used to:
+- Populate the Redis vector database with molecular embeddings
+- Provide sample molecules for demonstration purposes
+- Enable similarity search functionality through HNSW indexing
+
+### Data Processing
+
+The original SMILES data from Isomer Design has been processed through the following pipeline:
+
+1. **Canonicalization**: SMILES strings were canonicalized using RDKit's implementation to ensure consistent molecular representations
+2. **Embedding Generation**: Canonical SMILES were processed using the Chem-MRL model to generate molecular embeddings at various dimensions (2, 4, 32, 128, 512, 1024)
+3. **Vector Storage**: The resulting embeddings are stored in the Redis vector database and indexed using HNSW for efficient similarity search operations
+
+### Citation
+
+If you use this data in your research or applications, please cite the original Isomer Design dataset and respect the CC BY-NC-SA 4.0 license terms.

src/service.py

@@ -9,6 +9,7 @@ import redis
 import torch
 from chem_mrl.molecular_fingerprinter import MorganFingerprinter
 from dotenv import load_dotenv
+from rdkit import Chem, RDLogger
 from redis.commands.search.field import TextField, VectorField
 from redis.commands.search.indexDefinition import IndexDefinition, IndexType
 from redis.commands.search.query import Query
@@ -29,6 +30,7 @@ def setup_logger(clear_handler=False):
     if clear_handler:
         for handler in logging.root.handlers[:]:
             logging.root.removeHandler(handler)  # issue with sentence-transformer's logging handler
+    RDLogger.DisableLog("rdApp.*")  # type: ignore - DisableLog is an exported function
     logging.basicConfig(format="%(asctime)s - %(message)s", datefmt="%Y-%m-%d %H:%M:%S", level=logging.INFO)
     logger = logging.getLogger(__name__)
     return logger
@@ -159,7 +161,7 @@ class MolecularEmbeddingService:
 
                 self.redis_client.hset(
                     key,
-                    mapping=mapping,
+                    mapping=mapping,  # type: ignore
                 )
 
             except Exception as e:
@@ -209,7 +211,12 @@ class MolecularEmbeddingService:
                 .dialect(2)
             )
 
-            results = self.redis_client.ft(self.index_name).search(query, query_params={"vec": query_vector})
+            results = self.redis_client.ft(self.index_name).search(
+                query,
+                query_params={
+                    "vec": query_vector,  # type: ignore
+                },
+            )
 
             neighbors: list[SimilarMolecule] = [
                 {"smiles": doc.smiles, "name": doc.name, "properties": doc.properties, "score": float(doc.score)}
@@ -222,15 +229,27 @@ class MolecularEmbeddingService:
             logger.error(f"Failed to find similar molecules: {e}")
             return []
 
-    def get_canonical_smiles(self, smiles: str) -> str:
+    @staticmethod
+    def get_canonical_smiles(smiles: str | None) -> str:
         """Convert SMILES to canonical SMILES representation"""
         if not smiles or smiles.strip() == "":
             return ""
 
         canonical = MorganFingerprinter.canonicalize_smiles(smiles.strip())
-        if canonical:
-            return canonical
-        return smiles.strip()
+        if canonical is None:
+            return smiles.strip()
+        return canonical
+
+    @staticmethod
+    def get_smiles_from_mol_file(mol_file: str) -> str:
+        """Convert SMILES to canonical SMILES representation"""
+        if not mol_file or mol_file.strip() == "":
+            return ""
+
+        mol = Chem.rdmolfiles.MolFromMolBlock(mol_file)
+        if mol is None:
+            return ""
+        return Chem.MolToSmiles(mol, canonical=True)
 
     @staticmethod
     def embedding_field_name(dim: int) -> str:

src/static/chemwriter/chemwriter-style.json

@@ -0,0 +1,38 @@
+{
+	"border":				0.35, 
+	"display-methyl":		false,
+	"line-color":			"#202020",
+	"line-width":			0.06,
+	"line-offset":			0.19,
+	"line-end-padding":		0.12,
+	"node-cap-height":		0.38,
+	"node-colors": 			{
+		"H":	"#D0D0D0",
+		"N":	"#2060FF",
+		"P":	"#FF7F00",
+		"O":	"#EE2010",
+		"S":	"#FFC70A",
+		"F":	"#CC0092",
+		"Cl":	"#1FF01F",
+		"Br":	"#A62929",
+		"I":	"#D700D7",
+		"D":	"#0000FF",
+		"Li":	"#660000",
+		"Be":	"#00CC66",
+		"B":	"#00FF33",
+		"Na":	"#0000FF",
+		"Mg":	"#336633",
+		"Al":	"#999999",
+		"Si":	"#FF9933",
+		"Ca":	"#999999",
+		"Cr":	"#00FF66",
+		"Mn":	"#999999",
+		"Fe":	"#FFCC00",
+		"Ni":	"#993333",
+		"Cu":	"#CC6600",
+		"Zn":	"#CC66CC",
+		"Ag":	"#999999"
+	},
+	"stereo-width":			0.18,
+	"unknown-node-color":	"#555555"
+}

src/static/chemwriter/chemwriter-user.css

@@ -0,0 +1,128 @@
+/*
+ * ChemWriter (R)
+ * Copyright (C) 2007-2019 Metamolecular, LLC
+ *
+ * Use this stylesheet as a template for customizing Editor
+ * and Image appearance.
+ *
+ * Contact: http://metamolecular.com <[email protected]>
+ */
+
+/*
+ * Main Editor window
+ */
+.chemwriter-editor {
+  width: 100%;
+  height: 100%;
+  position: relative;
+  border: 2px solid gray;
+  border-radius: 5px;
+  background-color: #dcdcdc;
+  box-sizing: border-box;
+  -moz-box-sizing: border-box;
+}
+
+/*
+ * Editor button
+ */
+.chemwriter-button {
+  position: relative;
+  font-size: 20px;
+  border-radius: 3px;
+  cursor: default;
+  display: inline-block;
+  text-align: center;
+  color: #444444;
+  text-shadow: 0 1px #ffffff;
+}
+
+/*
+ * Hovering over an enabled button
+ */
+.chemwriter-button-enabled:hover {
+  background-color: #bbbbbb;
+}
+
+/*
+ * Disabled Editor button
+ */
+.chemwriter-button-disabled {
+  color: #b0b0b0;
+}
+
+/*
+ * Pressed button
+ */
+.chemwriter-button-pressed {
+  background: #bbbbbb;
+}
+
+/*
+ * About button
+ */
+.chemwriter-button-about {
+  position: absolute;
+  bottom: 0; left: 0;
+}
+
+/*
+ * Editor button icon. Font "ChemWriter Symbols" is defined in
+ * chemwriter.css. To change button icons, use a different font.
+ */
+.chemwriter-icon {
+  font-family: "Chemwriter Symbols";
+  font-size: 26px;
+}
+
+/*
+ * The small triangle that appears to the lower-left of button icons.
+ */
+.chemwriter-detail-disclosure {
+  position: absolute;
+  top: 0; right: 0; bottom: 0; left: 0;
+  font-family: "Chemwriter Symbols";
+  font-size: 30px;
+}
+
+/*
+ * Use a small triangle shape
+ */
+.chemwriter-detail-disclosure:after {
+  content: 'y';
+}
+
+/*
+ * The main structure display area.
+ */
+.chemwriter-document-view {
+  height: 100%;
+  width: 100%;
+}
+
+/* 
+ * Override Gradio color
+ */
+.chemwriter-code-editor-front,
+.chemwriter-code-editor-back,
+.chemwriter-text-button,
+.chemwriter-button,
+.chemwriter-icon,
+.chemwriter-select,
+.chemwriter-select select,
+.chemwriter-select option {
+  color: #444444 !important;
+}
+
+/* 
+ * RIP Richard. It was a pleasure working with you. /Steve 
+ */
+
+div.chemwriter-editor,
+div.chemwriter-image {
+	svg.chemwriter-graphics > g.chemwriter-group:first-child {
+		display: none;
+	}
+	a[href="http://chemwriter.com/plans/"] {
+		display: none;
+	}	
+}

src/static/chemwriter/chemwriter.css

@@ -0,0 +1,605 @@
+/*
+ * ChemWriter (R)
+ * Copyright (C) 2007-2022 Metamolecular, LLC
+ *
+ * This source code is the exclusive property of Metamolecular, LLC.
+ * Unauthorized duplication in any form without written consent
+ * is prohibited.
+ *
+ * Contact: http://metamolecular.com <[email protected]>
+ */
+
+@font-face {
+  font-family: 'ChemWriter Symbols';
+  src: url('chemwriter-symbols.woff') format('woff');
+}
+
+.chemwriter {
+  position: relative;
+  font-family: "Lucida Sans", Arial, sans-serif;
+  box-sizing: border-box;
+  -moz-box-sizing: border-box;
+  text-align: initial;
+}
+
+.chemwriter-hide {
+  display: none;
+}
+
+.chemwriter-fullscreen {
+  position: fixed;
+  min-width: 100%;
+  min-height: 100%;
+  top: 0; right: 0; bottom: 0; left: 0;
+  overflow: hidden;
+  z-index: 1000;
+}
+
+.chemwriter-fullscreen .chemwriter-editor {
+  border: 0px;
+  border-radius: 0;
+}
+
+.chemwriter svg {
+  overflow: hidden;
+}
+
+.chemwriter svg path, .chemwriter svg line {
+  stroke-linecap: round;
+}
+
+.chemwriter svg path {
+  stroke-linejoin: round;
+}
+
+.chemwriter ul {
+  margin: 0;
+}
+
+.chemwriter li {
+  line-height: 1em;
+}
+
+.chemwriter-default-cursor {
+  cursor: default;
+}
+
+.chemwriter-move-cursor {
+  cursor: move !important;
+}
+
+.chemwriter-button {
+  position: relative;
+  font-size: 20px;
+  border-radius: 3px;
+  cursor: default;
+  display: inline-block;
+  text-align: center;
+  color: #444444;
+  text-shadow: 0 1px #ffffff;
+}
+
+.chemwriter-palette .chemwriter-button {
+  width: 30px;
+  height: 30px;
+  margin: 4px 0 0 4px;
+  line-height: 30px;
+  box-sizing: border-box;
+}
+
+.chemwriter-button-enabled:hover {
+  background-color: #bbbbbb;
+}
+
+.chemwriter-button-disabled {
+  color: #b0b0b0;
+}
+
+.chemwriter-button-pressed {
+  background-color: #bbbbbb;
+}
+
+.chemwriter-button-about {
+  position: absolute;
+  bottom: 0; left: 0;
+}
+
+.chemwriter-icon {
+  font-family: "Chemwriter Symbols";
+  font-size: 25px;
+  line-height: 25px;
+  margin-top: 3px;
+  box-sizing: border-box;
+}
+
+.chemwriter-detail-disclosure {
+  position: absolute;
+  top: 0; right: 0; bottom: 0; left: 0;
+  font-family: "Chemwriter Symbols";
+  font-size: 30px;
+}
+
+.chemwriter-detail-disclosure:after {
+  content: 'y';
+}
+
+.chemwriter-canvas {
+  height: 100%;
+  position: relative;
+}
+
+.chemwriter-canvas:focus {
+  outline:none;
+}
+
+.chemwriter-graphics {
+  height: 100%;
+  width: 100%;
+}
+
+.chemwriter-dynamic-palette {
+  position: absolute;
+  top: 0; right: 0; bottom: 0; left: 0;
+  visibility: hidden;
+  /* IE 9/10 hack to allow palette dismissal by re-pressing button */
+  background-color: rgba(0, 0, 0, 0);
+}
+
+.chemwriter-appear {
+  visibility: visible;
+}
+
+.chemwriter-overlay {
+  position: absolute;
+  top: 0; right: 0; bottom: 0; left: 0;
+  border-radius: 5px;
+  visibility: hidden;
+  opacity: 0;
+  transition-duration: 1s;
+}
+
+.chemwriter-overlay-no-transition {
+  position: absolute;
+  top: 0; right: 0; bottom: 0; left: 0;
+  border-radius: 5px;
+  display: none;
+}
+
+.chemwriter-show {
+  visibility: visible;
+  opacity: 1;
+  transition-duration: 1s;
+}
+
+.chemwriter-show-no-transition {
+  display: block;
+}
+
+.chemwriter-rev {
+  margin-bottom: 0.1em;
+}
+
+.chemwriter-authors {
+  margin: 1em 0 2em 0;
+}
+
+.chemwriter-copyright {
+  font-size: 10px;
+}
+
+.chemwriter-logo {
+  width: 75px;
+  height: 75px;
+  margin: 15px auto 15px auto;
+  font-family: "ChemWriter Symbols";
+  font-size: 70px;
+}
+.chemwriter-logo:after {
+  content: "B";
+}
+
+.chemwriter-product-name {
+  font-size: 28px;
+  margin-bottom: 0.5em;
+}
+
+.chemwriter-dialog {
+  position: absolute;
+  top: 0; right: 0; bottom: 0px; left: 0;
+  border-top-left-radius: 5px;
+  border-top-right-radius: 5px;
+}
+
+.chemwriter-dialog .chemwriter-content {
+  position: absolute;
+  top: 0; right: 0; bottom: 30px; left: 0;
+}
+
+.chemwriter-about-panel {
+  position: absolute;
+  top: 0; bottom: 0; left: 0;
+  width: 200px;
+  background-color: #466bb0;
+  border-top-left-radius: 5px;
+  text-align: center;
+  color: white;
+  font-size: 12px;
+  padding: 0 0.5em 0 0.5em;
+}
+
+.chemwriter-about-panel a {
+  color: white;
+}
+
+.chemwriter-documentation-panel {
+  position: absolute;
+  top: 20px; bottom: 0; right: 0;
+  left: 212px;
+  padding: 15px 20px 15px 20px;
+  text-align: center;
+  font-size: 16px;
+}
+
+.chemwriter-documentation-panel a {
+  color: white;
+}
+
+.chemwriter-list {
+  margin-left: 0;
+  padding-left: 0;
+  list-style: none;
+}
+
+.chemwriter-list-item {
+  margin-left: 0;
+  padding-left: 0;
+  margin-bottom: 1em;
+}
+
+.chemwriter-super {
+  vertical-align: super;
+  font-size: 50%;
+}
+
+.chemwriter-clipboard-panel {
+  position: absolute;
+  top: 0; bottom: 0; left: 0; right: 0;
+}
+
+.chemwriter-left-panel {
+  position: absolute;
+  top: 0; bottom: 0; left: 0; width: 70%;
+  background-color: green;
+}
+
+.chemwriter-right-panel {
+  position: absolute;
+  top: 0; bottom: 0; right: 0; width: 30%;
+  background-color: white;
+}
+
+.chemwriter-code-editor {
+  position: absolute;
+  top: 0; bottom: 0; right: 0; left: 0;
+  background-color: black;
+}
+
+.chemwriter-code-editor-front {
+  position: absolute;
+  top: 0; left: 0;
+  width: 100%;
+  height: 100%;
+  font-family: monospace;
+  font-size: 12px;
+  white-space: pre;
+  line-height: 12px;
+  background-color: transparent;
+  color: #00ff00;
+}
+
+.chemwriter-code-editor-front::-moz-selection {
+  background-color: rgba(100, 200, 100, 0.5);
+}
+
+.chemwriter-code-editor-back {
+  position: absolute;
+  top: 0; left: 0;
+  width: 100%;
+  height: 100%;
+  font-family: monospace;
+  font-size: 12px;
+  white-space: pre;
+  line-height: 12px;
+  background-color: #000000;
+  color: #ff0000;
+}
+
+.chemwriter-text-area {
+  width: 100%;
+  height: 100%;
+  background-color: transparent;
+  font-family: monospace;
+  font-size: 12px;
+  white-space: pre;
+}
+
+.chemwriter-button-row {
+  position: absolute;
+  right: 0; bottom: 0; left: 0;
+  height: 30px;
+  text-align: center;
+  background-color: #d2d2d2;
+}
+
+.chemwriter-text-button {
+  padding: 0.1em 0.4em 0.1em 0.4em;
+  margin: 7px 1em 7px 0;
+  border-radius: 5px;
+  display: inline-block;
+  cursor: default;
+  font-size: 12px;
+  border: 1px solid #888888;
+}
+
+.chemwriter-editor {
+  width: 100%;
+  height: 100%;
+  position: relative;
+  border: 2px solid gray;
+  border-radius: 5px;
+  background: #dcdcdc;
+  box-sizing: border-box;
+  -moz-box-sizing: border-box;
+}
+
+.chemwriter-element-palette {
+  right: 38px; bottom: 0; left: 38px;
+  height: 38px;
+}
+
+.chemwriter-palette {
+  position: absolute;
+}
+
+.chemwriter-palette-float {
+  position: absolute;
+  top: 50px; left: 39px;
+  height: 38px;
+  border-radius: 0 5px 5px 0;
+  padding-right: 4px;
+  background-color: #dcdcdc;
+  box-shadow: 3px 3px 3px rgba(0, 0, 0, 0.5);
+  border-right: 1px solid gray;
+  border-bottom: 1px solid gray;
+}
+
+.chemwriter-palette-left {
+  position: absolute;
+  top: 0; bottom: 38px;
+  width: 38px;
+}
+
+.chemwriter-palette-bottom {
+  position: absolute;
+  right: 38px; bottom: 0; left: 38px;
+  max-height: 38px;
+  overflow: hidden;
+}
+
+.chemwriter-palette-bottom .chemwriter-button {
+  font-weight: bold;
+}
+
+.chemwriter-palette-box {
+  position: relative;
+  display: inline-table;
+}
+
+.chemwriter-flex-box {
+  display: table-cell;
+  height: 38px;
+}
+
+.chemwriter-stiff-box {
+  display: table-cell;
+  height: 38px;
+  white-space: nowrap;
+}
+
+.chemwriter-element-select {
+  display: table;
+  white-space: nowrap;
+  height: 38px;
+  line-height: 38px;
+}
+
+.chemwriter-element-select .chemwriter-button {
+  margin-right: 10px;
+}
+
+.chemwriter-select {
+  display: table-cell;
+  vertical-align: middle;
+}
+
+.chemwriter-select select {
+  font-size: 16px;
+}
+
+.chemwriter-palette-right {
+  position: absolute;
+  top: 0; right: 0; bottom: 38px;
+  right: 0; bottom: 38px;
+  width: 38px;
+}
+
+.chemwriter-palette-bottom-right {
+  position: absolute;
+  bottom: 0; right: 0;
+  width: 38px; height: 38px;
+}
+
+.chemwriter-canvas {
+  position: absolute;
+  top: 0;
+  right: 38px;
+  bottom: 38px;
+  left: 38px;
+  height: auto;
+  background-color: white;
+  border-radius: 0 0 5px 5px;
+  box-sizing: border-box;
+  -moz-box-sizing: border-box;
+  border-left: 1px solid #555555;
+  border-right: 1px solid #555555;
+  border-bottom: 1px solid #555555;
+}
+
+.chemwriter-document-view {
+  height: 100%;
+  width: 100%;
+}
+
+.chemwriter-image {
+  position: relative;
+  height: 100%;
+  text-align: center;
+}
+
+.chemwriter-error-image {
+  font-family: "ChemWriter Symbols";
+  position: absolute;
+  width: 85px;
+  height: 85px;
+  background-color: inherit;
+  color: #ff0000;
+  text-shadow: 1px 1px #202020;
+}
+
+.chemwriter-error-image:after {
+  vertical-align: middle;
+  content: "z";
+}
+
+/* Button Icons */
+
+.chemwriter-button-move .chemwriter-icon:after {
+  content: "a";
+}
+
+.chemwriter-button-delete .chemwriter-icon:after {
+  content: "b";
+}
+
+.chemwriter-button-saturate .chemwriter-icon:after {
+  content: "D";
+}
+
+.chemwriter-button-single-bond .chemwriter-icon:after {
+  content: "c";
+}
+
+.chemwriter-button-wedge-bond .chemwriter-icon:after {
+  content: "d";
+}
+
+.chemwriter-button-hash-bond .chemwriter-icon:after {
+  content: "e";
+}
+
+.chemwriter-button-wavy-bond .chemwriter-icon:after {
+  content: "f";
+}
+
+.chemwriter-button-crossed-bond .chemwriter-icon:after {
+  content: "g";
+}
+
+.chemwriter-button-benzene .chemwriter-icon:after {
+  content: "h";
+}
+
+.chemwriter-button-cyclohexane .chemwriter-icon:after {
+  content: "i";
+}
+
+.chemwriter-button-cyclopentane .chemwriter-icon:after {
+  content: "j";
+}
+
+.chemwriter-button-cyclopropane .chemwriter-icon:after {
+  content: "k";
+}
+
+.chemwriter-button-cyclobutane .chemwriter-icon:after {
+  content: "l";
+}
+
+.chemwriter-button-cycloheptane .chemwriter-icon:after {
+  content: "A";
+}
+
+.chemwriter-button-cyclooctane .chemwriter-icon:after {
+  content: "m";
+}
+
+.chemwriter-button-increase-charge .chemwriter-icon:after {
+  content: "n";
+}
+
+.chemwriter-button-decrease-charge .chemwriter-icon:after {
+  content: "o";
+}
+
+.chemwriter-button-increase-radical .chemwriter-icon:after {
+  content: "C";
+}
+
+.chemwriter-button-next-isotope .chemwriter-icon:after {
+  content: "p";
+}
+
+.chemwriter-button-mark-atom .chemwriter-icon:after {
+  content: "E";
+}
+
+.chemwriter-button-undo .chemwriter-icon:after {
+  content: "r";
+}
+
+.chemwriter-button-redo .chemwriter-icon:after {
+  content: "q";
+}
+
+.chemwriter-button-new-document .chemwriter-icon:after {
+  content: "s";
+}
+
+.chemwriter-button-edit-document .chemwriter-icon:after {
+  content: "t";
+}
+
+.chemwriter-button-reset-view .chemwriter-icon:after {
+  content: "u";
+}
+
+.chemwriter-button-about .chemwriter-icon:after {
+  content: "v";
+}
+
+.chemwriter-button-full-screen .chemwriter-icon:after {
+  content: "w";
+}
+
+.chemwriter-fullscreen .chemwriter-button-full-screen .chemwriter-icon:after {
+  content: "x";
+}
+
+/* IE8 and lower only */
+.chemwriter-fallback-content {
+  background-position-x: center;
+  background-position-y: center;
+  background-repeat: no-repeat;
+  background-size: cover ;
+  background-image: url('data:image/png;base64,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');
+ }

src/static/main.js

@@ -1,165 +1,71 @@
 /**
- * @fileoverview JSME (JavaScript Molecule Editor) integration with Gradio interface
- * Handles bidirectional synchronization between JSME applet and Gradio textbox
+ * @fileoverview ChemWriter integration with Gradio interface
+ * Handles bidirectional synchronization between ChemWriter editor and Gradio textbox
  * @author Manny Cortes ('[email protected]')
- * @version 0.2.0
+ * @version 0.3.0
  */
 
 // ============================================================================
 // GLOBAL VARIABLES
 // ============================================================================
 
-/** @type {Object|null} The JSME applet instance */
-let jsmeApplet = null;
-
-/** @type {string} Last known value of the textbox to prevent infinite loops */
-let lastTextboxValue = "";
+/** @type {Object|null} The ChemWriter editor instance */
+let editor = null;
+let chemwriter = null;
 
 // ============================================================================
 // CONSTANTS
 // ============================================================================
 
 /** @const {string} Default SMILES for initial molecule (ethanol) */
-const DEFAULT_SMILES = "CCO";
-
-/** @const {string} Container height for JSME applet */
-const CONTAINER_HEIGHT = "450px";
+const DEFAULT_SMILES = "CN(C)CCC1=CNC2=C1C(=CC=C2)OP(=O)(O)O";
 
 /** @const {string} CSS selector for the Gradio SMILES input element */
 const SMILES_INPUT_SELECTOR = "#smiles_input textarea, #smiles_input input";
 
+/** @const {string} CSS selector for the Gradio Mol file input element */
+const MOL_INPUT_SELECTOR = "#mol_input textarea, #mol_input input";
+
 /** @const {number} Delay for paste event handling (ms) */
 const PASTE_DELAY = 50;
 
 /** @const {number} Delay for initialization retry (ms) */
-const INIT_RETRY_DELAY = 2000;
+const INIT_RETRY_DELAY = 250;
 
 /** @const {string[]} Events to trigger for Gradio change detection */
-const GRADIO_CHANGE_EVENTS = ["input", "change", "keyup"];
+const GRADIO_CHANGE_EVENTS = ["input", "change"];
 
 // ============================================================================
 // CORE INITIALIZATION
 // ============================================================================
 
 /**
- * Initializes the JSME applet after the library has been loaded
- * Sets up the molecular editor with default options and callbacks
- * @throws {Error} When JSME initialization fails
- */
-function initializeJSME() {
-  try {
-    console.log("Initializing JSME...");
-    // https://github.com/jsme-editor/jsme-editor.github.io
-    // https://jsme-editor.github.io/dist/api_javadoc/index.html
-    // http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/JME/Options
-    jsmeApplet = new JSApplet.JSME(
-      "jsme_container",
-      getJsmeContainerWidthPx(),
-      CONTAINER_HEIGHT,
-      {
-        options:
-          "NOcanonize,rButton,zoom,zoomgui,newLook,star,multipart,polarnitro,NOexportInChI,NOexportInChIkey,NOsearchInChIkey,NOexportSVG,NOpaste",
-      }
-    );
-
-    jsmeApplet.setCallBack("AfterStructureModified", handleJSMEStructureChange);
-    jsmeApplet.setMenuScale(getJsmeGuiScale());
-    jsmeApplet.setUserInterfaceBackgroundColor("#adadad");
-
-    // Set initial molecule and sync state
-    jsmeApplet.readGenericMolecularInput(DEFAULT_SMILES);
-    lastTextboxValue = DEFAULT_SMILES;
-
-    setupTextboxEventListeners();
-    window.addEventListener("resize", handleResize);
-
-    console.log("JSME initialized successfully");
-  } catch (error) {
-    console.error("Error initializing JSME:", error);
-    throw error;
-  }
-}
-
-/**
- * Handles structure changes in the JSME applet
- * Converts the structure to SMILES and updates the Gradio textbox
- * @param {Event} event - The JSME structure modification event
+ * Initializes ChemWriter editor and sets up event handlers
  */
-function handleJSMEStructureChange(event) {
+function initializeChemWriter() {
   try {
-    const smiles = jsmeApplet.smiles();
-    updateGradioTextbox(smiles);
+    setupSmilesTextboxEventListeners();
+    setupChemWriterEventListeners();
+    editor.setSMILES(DEFAULT_SMILES);
+    console.log("ChemWriter initialized successfully");
   } catch (error) {
-    console.error("Error getting SMILES from JSME:", error);
+    console.error("Error initializing ChemWriter:", error);
   }
 }
 
-/**
- * Calculates the appropriate GUI scale for the JSME applet based on container width
- * Uses breakpoints to determine optimal scaling for different screen sizes
- * @returns {number} The scale factor for the JSME GUI (0.88 to 2.0)
- */
-function getJsmeGuiScale() {
-  const width = getJsmeContainerWidthNumber();
-  if (width == null || width <= 0) {
-    return 1;
-  }
-  let menuScale;
-  if (width > 460) {
-    menuScale = 1.3;
-  } else if (width > 420) {
-    menuScale = 1.1;
-  } else if (width > 370) {
-    menuScale = 1.05;
-  } else if (width > 300) {
-    menuScale = 0.88;
-  } else {
-    menuScale = 2;
-  }
-  return menuScale;
-}
-
-/**
- * Gets the JSME container width as a CSS-compatible string value
- * Returns either a pixel value or percentage based on available width
- * @returns {string} Width as "100%" or "{width}px" format
- */
-function getJsmeContainerWidthPx() {
-  const parentWidth = getJsmeContainerWidthNumber();
-  if (parentWidth == null || parentWidth <= 0) {
-    return "100%";
-  }
-  return `${parentWidth}px`;
-}
-
-/**
- * Gets the numeric width of the JSME container's parent element
- * Used for responsive scaling calculations
- * @returns {number|null} Width in pixels, or null if container not found
- */
-function getJsmeContainerWidthNumber() {
-  const container = document.getElementById("jsme_container");
-  return container?.parentNode?.offsetWidth;
-}
-
 // ============================================================================
-// GRADIO INTEGRATION
+// GRADIO AND CHEMWRITER INTEGRATION
 // ============================================================================
 
 /**
- * Updates the Gradio textbox with a SMILES string
+ * Updates the mol_input Gradio textbox with a mol file string
  * Triggers appropriate events to ensure Gradio detects the change
- * @param {string} smiles - The SMILES string to set in the textbox
  */
-function updateGradioTextbox(smiles) {
+function updateGradioTextbox() {
   try {
-    const textbox = document.querySelector(SMILES_INPUT_SELECTOR);
-    if (textbox?.value === smiles) {
-      return;
-    }
-
-    textbox.value = smiles;
-    lastTextboxValue = smiles;
+    const molTextbox = document.querySelector(MOL_INPUT_SELECTOR);
+    const molFile = editor?.getMolfile();
+    molTextbox.value = molFile;
 
     // Trigger events to ensure Gradio detects the change
     GRADIO_CHANGE_EVENTS.forEach((eventType) => {
@@ -167,31 +73,23 @@ function updateGradioTextbox(smiles) {
         bubbles: true,
         cancelable: true,
       });
-      textbox.dispatchEvent(event);
+      molTextbox.dispatchEvent(event);
     });
   } catch (error) {
     console.error("Error updating Gradio textbox:", error);
   }
 }
 
-// ============================================================================
-// JSME UPDATE FUNCTIONS
-// ============================================================================
-
 /**
- * Updates the JSME applet with a SMILES string from the textbox
- * @param {string} smiles - The SMILES string to display in JSME
+ * Updates the ChemWriter editor with a SMILES string from the textbox
+ * @param {string} smiles - The SMILES string to display in ChemWriter
  */
-function updateJSMEFromTextbox(smiles) {
+function updateChemWriterFromTextbox(smiles) {
   try {
-    if (smiles?.trim() !== "") {
-      jsmeApplet?.readGenericMolecularInput(smiles.trim());
-    } else {
-      jsmeApplet?.reset();
-    }
-    lastTextboxValue = smiles;
+    smiles = smiles.trim();
+    editor?.setSMILES(smiles);
   } catch (error) {
-    console.error("Error updating JSME from textbox:", error);
+    console.error("Error updating ChemWriter from textbox:", error);
   }
 }
 
@@ -199,19 +97,19 @@ function updateJSMEFromTextbox(smiles) {
 // UI MONITORING
 // ============================================================================
 
-/**
- * Finds the textbox element and sets up event listeners
- */
-function setupTextboxEventListeners() {
+function setupSmilesTextboxEventListeners() {
   const textbox = document.querySelector(SMILES_INPUT_SELECTOR);
   if (!textbox) {
     return;
   }
-
   textbox.addEventListener("input", handleTextboxChange);
   textbox.addEventListener("change", handleTextboxChange);
   textbox.addEventListener("paste", handleTextboxPaste);
-  textbox.addEventListener("keyup", handleTextboxChange);
+}
+
+function setupChemWriterEventListeners() {
+  window.addEventListener("resize", () => editor.jd());
+  editor.addEventListener('document-edited', updateGradioTextbox);
 }
 
 /**
@@ -219,9 +117,7 @@ function setupTextboxEventListeners() {
  * @param {Event} event - The change event
  */
 function handleTextboxChange(event) {
-  if (event.target.value !== lastTextboxValue) {
-    updateJSMEFromTextbox(event.target.value);
-  }
+  updateChemWriterFromTextbox(event.target.value);
 }
 
 /**
@@ -230,47 +126,29 @@ function handleTextboxChange(event) {
  */
 function handleTextboxPaste(event) {
   setTimeout(() => {
-    updateJSMEFromTextbox(event.target.value);
+    updateChemWriterFromTextbox(event.target.value);
   }, PASTE_DELAY);
 }
 
-/**
- * Handles window resize events and updates JSME applet width
- */
-function handleResize() {
-  try {
-    jsmeApplet?.setMenuScale(getJsmeGuiScale());
-    jsmeApplet?.setWidth(getJsmeContainerWidthPx());
-  } catch (error) {
-    console.error("Error resizing JSME applet:", error);
-  }
-}
-
 // ============================================================================
 // PUBLIC API
 // ============================================================================
 
 /**
- * Sets a SMILES string in both JSME and Gradio textbox
+ * Sets ChemWriter SMILES string
  * @param {string} smiles - The SMILES string to set
- * @returns {string} The SMILES string that was set
  * @public
  */
-window.setJSMESmiles = function (smiles) {
-  updateJSMEFromTextbox(smiles);
-  updateGradioTextbox(smiles);
-  return smiles;
+window.setCWSmiles = function (smiles) {
+  updateChemWriterFromTextbox(smiles);
 };
 
 /**
- * Clears both JSME and Gradio textbox
- * @returns {Array} Array containing cleared state for Gradio components
+ * Clears both ChemWriter and Gradio textbox
  * @public
  */
-window.clearJSME = function () {
-  jsmeApplet?.reset();
-  updateGradioTextbox("");
-  return ["", "", [], [], "Cleared - Draw a new molecule or enter SMILES"];
+window.clearCW = function () {
+  editor.setMolfile('\nCWRITER06142521562D\nCreated with ChemWriter - https://chemwriter.com\n  0  0  0  0  0  0  0  0  0  0999 V2000\nM  END');
 };
 
 // ============================================================================
@@ -278,30 +156,22 @@ window.clearJSME = function () {
 // ============================================================================
 
 /**
- * Checks if JSME library is loaded and initializes JSME applet
- * Retries until the library becomes available
+ * Checks if ChemWriter library is loaded and initializes ChemWriter editor
  */
 function initializeWhenReady() {
-  if (typeof JSApplet !== "undefined" && JSApplet.JSME) {
-    console.log("JSME library loaded, initializing...");
-    initializeJSME();
-  } else {
-    console.log("JSME library not ready, retrying...");
-    setTimeout(initializeWhenReady, INIT_RETRY_DELAY);
-  }
-}
-
-/**
- * Starts the initialization process based on document ready state
- */
-function startInitialization() {
-  if (document.readyState === "loading") {
-    document.addEventListener("DOMContentLoaded", () => {
-      setTimeout(initializeWhenReady, INIT_RETRY_DELAY);
-    });
+  chemwriter = window?.chemwriter;
+  // The ChemWriter library normally sets up a window load event listener: window.addEventListener("load", function(){Z.De()}, false)
+  // However, due to race conditions, the "load" event listener may not be added or triggered in time for proper initialization.
+  // So we call the initialization function directly here.
+  chemwriter?.System?.De();
+  editor = chemwriter?.components?.editor;
+  if (typeof chemwriter?.System?.De !== "undefined" && typeof editor !== "undefined") {
+    console.log("ChemWriter library loaded, initializing...");
+    chemwriter.System.ready(initializeChemWriter);
   } else {
+    console.log("ChemWriter library not ready, retrying...");
     setTimeout(initializeWhenReady, INIT_RETRY_DELAY);
   }
 }
 
-startInitialization();
+initializeWhenReady();

src/static/main.min.js

@@ -1 +1 @@
-function initializeJSME(){try{jsmeApplet=new JSApplet.JSME("jsme_container",getJsmeContainerWidthPx(),"450px",{options:"NOcanonize,rButton,zoom,zoomgui,newLook,star,multipart,polarnitro,NOexportInChI,NOexportInChIkey,NOsearchInChIkey,NOexportSVG,NOpaste"}),jsmeApplet.setCallBack("AfterStructureModified",handleJSMEStructureChange),jsmeApplet.setMenuScale(getJsmeGuiScale()),jsmeApplet.setUserInterfaceBackgroundColor("#adadad"),jsmeApplet.readGenericMolecularInput("CCO"),lastTextboxValue="CCO",setupTextboxEventListeners(),window.addEventListener("resize",handleResize)}catch(e){throw e}}function handleJSMEStructureChange(){try{updateGradioTextbox(jsmeApplet.smiles())}catch(e){}}function getJsmeGuiScale(){const e=getJsmeContainerWidthNumber();if(null==e||e<=0)return 1;let t;return t=e>460?1.3:e>420?1.1:e>370?1.05:e>300?.88:2,t}function getJsmeContainerWidthPx(){const e=getJsmeContainerWidthNumber();return null==e||e<=0?"100%":`${e}px`}function getJsmeContainerWidthNumber(){const e=document.getElementById("jsme_container");return e?.parentNode?.offsetWidth}function updateGradioTextbox(e){try{const t=document.querySelector(SMILES_INPUT_SELECTOR);if(t?.value===e)return;t.value=e,lastTextboxValue=e,GRADIO_CHANGE_EVENTS.forEach((e=>{const n=new Event(e,{bubbles:!0,cancelable:!0});t.dispatchEvent(n)}))}catch(e){}}function updateJSMEFromTextbox(e){try{""!==e?.trim()?jsmeApplet?.readGenericMolecularInput(e.trim()):jsmeApplet?.reset(),lastTextboxValue=e}catch(e){}}function setupTextboxEventListeners(){const e=document.querySelector(SMILES_INPUT_SELECTOR);e&&(e.addEventListener("input",handleTextboxChange),e.addEventListener("change",handleTextboxChange),e.addEventListener("paste",handleTextboxPaste),e.addEventListener("keyup",handleTextboxChange))}function handleTextboxChange(e){e.target.value!==lastTextboxValue&&updateJSMEFromTextbox(e.target.value)}function handleTextboxPaste(e){setTimeout((()=>{updateJSMEFromTextbox(e.target.value)}),50)}function handleResize(){try{jsmeApplet?.setMenuScale(getJsmeGuiScale()),jsmeApplet?.setWidth(getJsmeContainerWidthPx())}catch(e){}}function initializeWhenReady(){"undefined"!=typeof JSApplet&&JSApplet.JSME?initializeJSME():setTimeout(initializeWhenReady,2e3)}function startInitialization(){"loading"===document.readyState?document.addEventListener("DOMContentLoaded",(()=>{setTimeout(initializeWhenReady,2e3)})):setTimeout(initializeWhenReady,2e3)}let jsmeApplet=null,lastTextboxValue="";const DEFAULT_SMILES="CCO",CONTAINER_HEIGHT="450px",SMILES_INPUT_SELECTOR="#smiles_input textarea, #smiles_input input",PASTE_DELAY=50,INIT_RETRY_DELAY=2e3,GRADIO_CHANGE_EVENTS=["input","change","keyup"];window.setJSMESmiles=function(e){return updateJSMEFromTextbox(e),updateGradioTextbox(e),e},window.clearJSME=function(){return jsmeApplet?.reset(),updateGradioTextbox(""),["","",[],[],"Cleared - Draw a new molecule or enter SMILES"]},startInitialization();
+function initializeChemWriter(){try{setupSmilesTextboxEventListeners(),setupChemWriterEventListeners(),editor.setSMILES(DEFAULT_SMILES)}catch(e){}}function updateGradioTextbox(){try{const e=document.querySelector(MOL_INPUT_SELECTOR),t=editor?.getMolfile();e.value=t,GRADIO_CHANGE_EVENTS.forEach((t=>{const i=new Event(t,{bubbles:!0,cancelable:!0});e.dispatchEvent(i)}))}catch(e){}}function updateChemWriterFromTextbox(e){try{e=e.trim(),editor?.setSMILES(e)}catch(e){}}function setupSmilesTextboxEventListeners(){const e=document.querySelector(SMILES_INPUT_SELECTOR);e&&(e.addEventListener("input",handleTextboxChange),e.addEventListener("change",handleTextboxChange),e.addEventListener("paste",handleTextboxPaste))}function setupChemWriterEventListeners(){window.addEventListener("resize",(()=>editor.jd())),editor.addEventListener("document-edited",updateGradioTextbox)}function handleTextboxChange(e){updateChemWriterFromTextbox(e.target.value)}function handleTextboxPaste(e){setTimeout((()=>{updateChemWriterFromTextbox(e.target.value)}),50)}function initializeWhenReady(){chemwriter=window?.chemwriter,chemwriter?.System?.De(),editor=chemwriter?.components?.editor,void 0!==chemwriter?.System?.De&&void 0!==editor?chemwriter.System.ready(initializeChemWriter):setTimeout(initializeWhenReady,250)}let editor=null,chemwriter=null;const DEFAULT_SMILES="CN(C)CCC1=CNC2=C1C(=CC=C2)OP(=O)(O)O",SMILES_INPUT_SELECTOR="#smiles_input textarea, #smiles_input input",MOL_INPUT_SELECTOR="#mol_input textarea, #mol_input input",PASTE_DELAY=50,INIT_RETRY_DELAY=250,GRADIO_CHANGE_EVENTS=["input","change"];window.setCWSmiles=function(e){updateChemWriterFromTextbox(e)},window.clearCW=function(){editor.setMolfile("\nCWRITER06142521562D\nCreated with ChemWriter - https://chemwriter.com\n  0  0  0  0  0  0  0  0  0  0999 V2000\nM  END")},initializeWhenReady();