Upload folder using huggingface_hub

Dockerfile

@@ -7,10 +7,10 @@ COPY --link --chown=1000 . .
 
 RUN mkdir -p /tmp/cache/
 RUN chmod a+rwx -R /tmp/cache/
-ENV TRANSFORMERS_CACHE=/tmp/cache/ 
+ENV TRANSFORMERS_CACHE=/tmp/cache/
 
 RUN pip install --no-cache-dir -r requirements.txt
 
 ENV PYTHONUNBUFFERED=1 	GRADIO_ALLOW_FLAGGING=never 	GRADIO_NUM_PORTS=1 	GRADIO_SERVER_NAME=0.0.0.0     GRADIO_SERVER_PORT=7860 	SYSTEM=spaces
 
-CMD ["python", "app.py"]
+CMD ["python", "space.py"]

README.md

@@ -2,8 +2,8 @@
 ---
 tags: [gradio-custom-component,machine learning,reproducibility,visualization,gradio,gradio-template-File,protein]
 title: gradio_molecule3d V0.0.3
-colorFrom: gray
-colorTo: gray
+colorFrom: yellow
+colorTo: pink
 sdk: docker
 pinned: false
 license: apache-2.0
@@ -12,6 +12,6 @@ license: apache-2.0
 
 # Name: gradio_molecule3d
 
-Description: Molecule3D custom component to visualize pdb or sdf files
+Description: Molecule3D custom component to visualize pdb or sdf files using 3Dmol.js
 
 Install with: pip install gradio_molecule3d

app.py

@@ -12,37 +12,30 @@ reps =    [
       "model": 0,
       "chain": "",
       "resname": "",
-      "style": "cartoon",
+      "style": "stick",
       "color": "whiteCarbon",
       "residue_range": "",
       "around": 0,
       "byres": False,
-      "visible": False,
-    },
+      "visible": False
+    }
   ]
 
+
+
 def predict(x):
     print("predict function", x)
+    print(x.name)
     return x
 
-#doesn't work
-#demo = gr.Interface(
-#     predict,
-#     Molecule3D(label="Molecule3D", reps=reps),  # interactive version of your component
-#     Molecule3D(),  # static version of your component
-#     examples=[[example]],  # uncomment this line to view the "example version" of your component
-# )
-
-#works
 with gr.Blocks() as demo:
-    #gr.Markdown("# 3dmol.js Molecule Viewer")
-    #inp = Molecule3D(label="Molecule3D", reps=reps)
-    #gr.Markdown("Viewer disabled")
-    inp = Molecule3D(label="Molecule3D", reps=reps, showviewer=False)
-    out = Molecule3D(label="Molecule3D", reps=reps)
+    inp = Molecule3D(label="Molecule3D", reps=reps)
+    out = Molecule3D(label="Output", reps=reps)
+
+    btn = gr.Button("Predict")
     gr.Markdown(""" 
     You can configure the default rendering of the molecule by adding a list of representations
-    <code>
+    <pre>
         reps =    [
         {
           "model": 0,
@@ -55,11 +48,22 @@ with gr.Blocks() as demo:
           "byres": False,
           "visible": False,
         },
+        {
+          "model": 0,
+          "chain": "A",
+          "resname": "HIS",
+          "style": "stick",
+          "color": "red",
+          "residue_range": "",
+          "around": 0,
+          "byres": False,
+          "visible": False,
+        }
       ]
-    </code>
+    </pre>
     """)
-    btn = gr.Button("Predict")
     btn.click(predict, inputs=inp, outputs=out)
 
-demo.launch()
-# blocks.launch()
+
+if __name__ == '__main__':
+  demo.launch()

css.css

@@ -0,0 +1,157 @@
+html {
+	font-family: Inter;
+	font-size: 16px;
+	font-weight: 400;
+	line-height: 1.5;
+	-webkit-text-size-adjust: 100%;
+	background: #fff;
+	color: #323232;
+	-webkit-font-smoothing: antialiased;
+	-moz-osx-font-smoothing: grayscale;
+	text-rendering: optimizeLegibility;
+}
+
+:root {
+	--space: 1;
+	--vspace: calc(var(--space) * 1rem);
+	--vspace-0: calc(3 * var(--space) * 1rem);
+	--vspace-1: calc(2 * var(--space) * 1rem);
+	--vspace-2: calc(1.5 * var(--space) * 1rem);
+	--vspace-3: calc(0.5 * var(--space) * 1rem);
+}
+
+.app {
+	max-width: 748px !important;
+}
+
+.prose p {
+	margin: var(--vspace) 0;
+	line-height: var(--vspace * 2);
+	font-size: 1rem;
+}
+
+code {
+	font-family: "Inconsolata", sans-serif;
+	font-size: 16px;
+}
+
+h1,
+h1 code {
+	font-weight: 400;
+	line-height: calc(2.5 / var(--space) * var(--vspace));
+}
+
+h1 code {
+	background: none;
+	border: none;
+	letter-spacing: 0.05em;
+	padding-bottom: 5px;
+	position: relative;
+	padding: 0;
+}
+
+h2 {
+	margin: var(--vspace-1) 0 var(--vspace-2) 0;
+	line-height: 1em;
+}
+
+h3,
+h3 code {
+	margin: var(--vspace-1) 0 var(--vspace-2) 0;
+	line-height: 1em;
+}
+
+h4,
+h5,
+h6 {
+	margin: var(--vspace-3) 0 var(--vspace-3) 0;
+	line-height: var(--vspace);
+}
+
+.bigtitle,
+h1,
+h1 code {
+	font-size: calc(8px * 4.5);
+	word-break: break-word;
+}
+
+.title,
+h2,
+h2 code {
+	font-size: calc(8px * 3.375);
+	font-weight: lighter;
+	word-break: break-word;
+	border: none;
+	background: none;
+}
+
+.subheading1,
+h3,
+h3 code {
+	font-size: calc(8px * 1.8);
+	font-weight: 600;
+	border: none;
+	background: none;
+	letter-spacing: 0.1em;
+	text-transform: uppercase;
+}
+
+h2 code {
+	padding: 0;
+	position: relative;
+	letter-spacing: 0.05em;
+}
+
+blockquote {
+	font-size: calc(8px * 1.1667);
+	font-style: italic;
+	line-height: calc(1.1667 * var(--vspace));
+	margin: var(--vspace-2) var(--vspace-2);
+}
+
+.subheading2,
+h4 {
+	font-size: calc(8px * 1.4292);
+	text-transform: uppercase;
+	font-weight: 600;
+}
+
+.subheading3,
+h5 {
+	font-size: calc(8px * 1.2917);
+	line-height: calc(1.2917 * var(--vspace));
+
+	font-weight: lighter;
+	text-transform: uppercase;
+	letter-spacing: 0.15em;
+}
+
+h6 {
+	font-size: calc(8px * 1.1667);
+	font-size: 1.1667em;
+	font-weight: normal;
+	font-style: italic;
+	font-family: "le-monde-livre-classic-byol", serif !important;
+	letter-spacing: 0px !important;
+}
+
+#start .md > *:first-child {
+	margin-top: 0;
+}
+
+h2 + h3 {
+	margin-top: 0;
+}
+
+.md hr {
+	border: none;
+	border-top: 1px solid var(--block-border-color);
+	margin: var(--vspace-2) 0 var(--vspace-2) 0;
+}
+.prose ul {
+	margin: var(--vspace-2) 0 var(--vspace-1) 0;
+}
+
+.gap {
+	gap: 0;
+}

requirements.txt

@@ -1,2 +1 @@
-gradio_molecule3d-0.0.3-py3-none-any.whl
-gradio>=4.21.0
+gradio_molecule3d==0.0.3

space.py

@@ -0,0 +1,191 @@
+
+import gradio as gr
+from app import demo as app
+import os
+
+_docs = {'Molecule3D': {'description': 'Creates a file component that allows uploading generic file (when used as an input) and or displaying generic files (output).', 'members': {'__init__': {'value': {'type': 'str | list[str] | Callable | None', 'default': 'None', 'description': 'Default file to display, given as str file path. If callable, the function will be called whenever the app loads to set the initial value of the component.'}, 'reps': {'type': 'Any | None', 'default': '[]', 'description': None}, 'config': {'type': 'Any | None', 'default': '{\n    "backgroundColor": "white",\n    "orthographic": False,\n    "disableFog": False,\n}', 'description': 'dictionary of config options'}, 'confidenceLabel': {'type': 'str | None', 'default': '"pLDDT"', 'description': 'label for confidence values stored in the bfactor column of a pdb file'}, 'file_count': {'type': 'Literal["single", "multiple", "directory"]', 'default': '"single"', 'description': 'if single, allows user to upload one file. If "multiple", user uploads multiple files. If "directory", user uploads all files in selected directory. Return type will be list for each file in case of "multiple" or "directory".'}, 'file_types': {'type': 'list[str] | None', 'default': 'None', 'description': 'List of file extensions or types of files to be uploaded (e.g. [\'image\', \'.json\', \'.mp4\']). "file" allows any file to be uploaded, "image" allows only image files to be uploaded, "audio" allows only audio files to be uploaded, "video" allows only video files to be uploaded, "text" allows only text files to be uploaded.'}, 'type': {'type': 'Literal["filepath", "binary"]', 'default': '"filepath"', 'description': 'Type of value to be returned by component. "file" returns a temporary file object with the same base name as the uploaded file, whose full path can be retrieved by file_obj.name, "binary" returns an bytes object.'}, 'label': {'type': 'str | None', 'default': 'None', 'description': 'The label for this component. Appears above the component and is also used as the header if there are a table of examples for this component. If None and used in a `gr.Interface`, the label will be the name of the parameter this component is assigned to.'}, 'every': {'type': 'float | None', 'default': 'None', 'description': "If `value` is a callable, run the function 'every' number of seconds while the client connection is open. Has no effect otherwise. Queue must be enabled. The event can be accessed (e.g. to cancel it) via this component's .load_event attribute."}, 'show_label': {'type': 'bool | None', 'default': 'None', 'description': 'if True, will display label.'}, 'container': {'type': 'bool', 'default': 'True', 'description': 'If True, will place the component in a container - providing some extra padding around the border.'}, 'scale': {'type': 'int | None', 'default': 'None', 'description': 'relative width compared to adjacent Components in a Row. For example, if Component A has scale=2, and Component B has scale=1, A will be twice as wide as B. Should be an integer.'}, 'min_width': {'type': 'int', 'default': '160', 'description': 'minimum pixel width, will wrap if not sufficient screen space to satisfy this value. If a certain scale value results in this Component being narrower than min_width, the min_width parameter will be respected first.'}, 'height': {'type': 'int | float | None', 'default': 'None', 'description': 'The maximum height of the file component, in pixels. If more files are uploaded than can fit in the height, a scrollbar will appear.'}, 'interactive': {'type': 'bool | None', 'default': 'None', 'description': 'if True, will allow users to upload a file; if False, can only be used to display files. If not provided, this is inferred based on whether the component is used as an input or output.'}, 'visible': {'type': 'bool', 'default': 'True', 'description': 'If False, component will be hidden.'}, 'elem_id': {'type': 'str | None', 'default': 'None', 'description': 'An optional string that is assigned as the id of this component in the HTML DOM. Can be used for targeting CSS styles.'}, 'elem_classes': {'type': 'list[str] | str | None', 'default': 'None', 'description': 'An optional list of strings that are assigned as the classes of this component in the HTML DOM. Can be used for targeting CSS styles.'}, 'render': {'type': 'bool', 'default': 'True', 'description': 'If False, component will not render be rendered in the Blocks context. Should be used if the intention is to assign event listeners now but render the component later.'}, 'showviewer': {'type': 'bool', 'default': 'True', 'description': 'If True, will display the 3Dmol.js viewer. If False, will not display the 3Dmol.js viewer.'}}, 'postprocess': {'value': {'type': 'str | list[str] | None', 'description': "The output data received by the component from the user's function in the backend."}}, 'preprocess': {'return': {'type': 'bytes | NamedString | list[bytes | NamedString] | None', 'description': "The preprocessed input data sent to the user's function in the backend."}, 'value': None}}, 'events': {'change': {'type': None, 'default': None, 'description': 'Triggered when the value of the Molecule3D changes either because of user input (e.g. a user types in a textbox) OR because of a function update (e.g. an image receives a value from the output of an event trigger). See `.input()` for a listener that is only triggered by user input.'}, 'select': {'type': None, 'default': None, 'description': 'Event listener for when the user selects or deselects the Molecule3D. Uses event data gradio.SelectData to carry `value` referring to the label of the Molecule3D, and `selected` to refer to state of the Molecule3D. See EventData documentation on how to use this event data'}, 'clear': {'type': None, 'default': None, 'description': 'This listener is triggered when the user clears the Molecule3D using the X button for the component.'}, 'upload': {'type': None, 'default': None, 'description': 'This listener is triggered when the user uploads a file into the Molecule3D.'}}}, '__meta__': {'additional_interfaces': {}, 'user_fn_refs': {'Molecule3D': []}}}
+
+abs_path = os.path.join(os.path.dirname(__file__), "css.css")
+
+with gr.Blocks(
+    css=abs_path,
+    theme=gr.themes.Default(
+        font_mono=[
+            gr.themes.GoogleFont("Inconsolata"),
+            "monospace",
+        ],
+    ),
+) as demo:
+    gr.Markdown(
+"""
+# `gradio_molecule3d`
+
+<div style="display: flex; gap: 7px;">
+<a href="https://pypi.org/project/gradio_molecule3d/" target="_blank"><img alt="PyPI - Version" src="https://img.shields.io/pypi/v/gradio_molecule3d"></a>  
+</div>
+
+Molecule3D custom component to visualize pdb or sdf files using 3Dmol.js
+""", elem_classes=["md-custom"], header_links=True)
+    app.render()
+    gr.Markdown(
+"""
+## Installation
+
+```bash
+pip install gradio_molecule3d
+```
+
+## Usage
+
+```python
+
+import gradio as gr
+from gradio_molecule3d import Molecule3D
+
+import os
+
+example = Molecule3D().example_inputs()
+
+
+reps =    [
+    {
+      "model": 0,
+      "chain": "",
+      "resname": "",
+      "style": "stick",
+      "color": "whiteCarbon",
+      "residue_range": "",
+      "around": 0,
+      "byres": False,
+      "visible": False
+    }
+  ]
+
+
+
+def predict(x):
+    print("predict function", x)
+    print(x.name)
+    return x
+
+with gr.Blocks() as demo:
+    inp = Molecule3D(label="Molecule3D", reps=reps)
+    out = Molecule3D(label="Output", reps=reps)
+
+    btn = gr.Button("Predict")
+    gr.Markdown(\"\"\" 
+    You can configure the default rendering of the molecule by adding a list of representations
+    <pre>
+        reps =    [
+        {
+          "model": 0,
+          "chain": "",
+          "resname": "",
+          "style": "cartoon",
+          "color": "whiteCarbon",
+          "residue_range": "",
+          "around": 0,
+          "byres": False,
+          "visible": False,
+        },
+        {
+          "model": 0,
+          "chain": "A",
+          "resname": "HIS",
+          "style": "stick",
+          "color": "red",
+          "residue_range": "",
+          "around": 0,
+          "byres": False,
+          "visible": False,
+        }
+      ]
+    </pre>
+    \"\"\")
+    btn.click(predict, inputs=inp, outputs=out)
+
+
+if __name__ == '__main__':
+  demo.launch()
+
+```
+""", elem_classes=["md-custom"], header_links=True)
+
+
+    gr.Markdown("""
+## `Molecule3D`
+
+### Initialization
+""", elem_classes=["md-custom"], header_links=True)
+
+    gr.ParamViewer(value=_docs["Molecule3D"]["members"]["__init__"], linkify=[])
+
+
+    gr.Markdown("### Events")
+    gr.ParamViewer(value=_docs["Molecule3D"]["events"], linkify=['Event'])
+
+
+
+
+    gr.Markdown("""
+
+### User function
+
+The impact on the users predict function varies depending on whether the component is used as an input or output for an event (or both).
+
+- When used as an Input, the component only impacts the input signature of the user function.
+- When used as an output, the component only impacts the return signature of the user function.
+
+The code snippet below is accurate in cases where the component is used as both an input and an output.
+
+- **As input:** Is passed, the preprocessed input data sent to the user's function in the backend.
+- **As output:** Should return, the output data received by the component from the user's function in the backend.
+
+ ```python
+def predict(
+    value: bytes | NamedString | list[bytes | NamedString] | None
+) -> str | list[str] | None:
+    return value
+```
+""", elem_classes=["md-custom", "Molecule3D-user-fn"], header_links=True)
+
+
+
+
+    demo.load(None, js=r"""function() {
+    const refs = {};
+    const user_fn_refs = {
+          Molecule3D: [], };
+    requestAnimationFrame(() => {
+
+        Object.entries(user_fn_refs).forEach(([key, refs]) => {
+            if (refs.length > 0) {
+                const el = document.querySelector(`.${key}-user-fn`);
+                if (!el) return;
+                refs.forEach(ref => {
+                    el.innerHTML = el.innerHTML.replace(
+                        new RegExp("\\b"+ref+"\\b", "g"),
+                        `<a href="#h-${ref.toLowerCase()}">${ref}</a>`
+                    );
+                })
+            }
+        })
+
+        Object.entries(refs).forEach(([key, refs]) => {
+            if (refs.length > 0) {
+                const el = document.querySelector(`.${key}`);
+                if (!el) return;
+                refs.forEach(ref => {
+                    el.innerHTML = el.innerHTML.replace(
+                        new RegExp("\\b"+ref+"\\b", "g"),
+                        `<a href="#h-${ref.toLowerCase()}">${ref}</a>`
+                    );
+                })
+            }
+        })
+    })
+}
+
+""")
+
+demo.launch()

src/README.md

@@ -1,16 +1,397 @@
 
-# gradio_molecule3d
-A Custom Gradio component to visualize molecules in pdb, sdf or mol2 format.
+# `gradio_molecule3d`
+<a href="https://pypi.org/project/gradio_molecule3d/" target="_blank"><img alt="PyPI - Version" src="https://img.shields.io/pypi/v/gradio_molecule3d"></a>  
 
+Molecule3D custom component to visualize pdb or sdf files using 3Dmol.js
 
-Developed by Simon Dürr. 
+## Installation
 
-If you use this component for academic work please cite:
-3Dmol.js: molecular visualization with WebGL , Nicholas Rego, David Koes, Bioinformatics, Volume 31, Issue 8, April 2015, Pages 1322–1324, https://doi.org/10.1093/bioinformatics/btu829
+```bash
+pip install gradio_molecule3d
+```
 
-## How to use
+## Usage
 
 ```python
+
 import gradio as gr
 from gradio_molecule3d import Molecule3D
+
+import os
+
+example = Molecule3D().example_inputs()
+
+
+reps =    [
+    {
+      "model": 0,
+      "chain": "",
+      "resname": "",
+      "style": "stick",
+      "color": "whiteCarbon",
+      "residue_range": "",
+      "around": 0,
+      "byres": False,
+      "visible": False
+    }
+  ]
+
+
+
+def predict(x):
+    print("predict function", x)
+    print(x.name)
+    return x
+
+with gr.Blocks() as demo:
+    inp = Molecule3D(label="Molecule3D", reps=reps)
+    out = Molecule3D(label="Output", reps=reps)
+
+    btn = gr.Button("Predict")
+    gr.Markdown(""" 
+    You can configure the default rendering of the molecule by adding a list of representations
+    <pre>
+        reps =    [
+        {
+          "model": 0,
+          "chain": "",
+          "resname": "",
+          "style": "cartoon",
+          "color": "whiteCarbon",
+          "residue_range": "",
+          "around": 0,
+          "byres": False,
+          "visible": False,
+        },
+        {
+          "model": 0,
+          "chain": "A",
+          "resname": "HIS",
+          "style": "stick",
+          "color": "red",
+          "residue_range": "",
+          "around": 0,
+          "byres": False,
+          "visible": False,
+        }
+      ]
+    </pre>
+    """)
+    btn.click(predict, inputs=inp, outputs=out)
+
+
+if __name__ == '__main__':
+  demo.launch()
+
+```
+
+## `Molecule3D`
+
+### Initialization
+
+<table>
+<thead>
+<tr>
+<th align="left">name</th>
+<th align="left" style="width: 25%;">type</th>
+<th align="left">default</th>
+<th align="left">description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td align="left"><code>value</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+str | list[str] | Callable | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">Default file to display, given as str file path. If callable, the function will be called whenever the app loads to set the initial value of the component.</td>
+</tr>
+
+<tr>
+<td align="left"><code>reps</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+Any | None
+```
+
+</td>
+<td align="left"><code>[]</code></td>
+<td align="left">None</td>
+</tr>
+
+<tr>
+<td align="left"><code>config</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+Any | None
+```
+
+</td>
+<td align="left"><code>{
+    "backgroundColor": "white",
+    "orthographic": False,
+    "disableFog": False,
+}</code></td>
+<td align="left">dictionary of config options</td>
+</tr>
+
+<tr>
+<td align="left"><code>confidenceLabel</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+str | None
+```
+
+</td>
+<td align="left"><code>"pLDDT"</code></td>
+<td align="left">label for confidence values stored in the bfactor column of a pdb file</td>
+</tr>
+
+<tr>
+<td align="left"><code>file_count</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+Literal["single", "multiple", "directory"]
+```
+
+</td>
+<td align="left"><code>"single"</code></td>
+<td align="left">if single, allows user to upload one file. If "multiple", user uploads multiple files. If "directory", user uploads all files in selected directory. Return type will be list for each file in case of "multiple" or "directory".</td>
+</tr>
+
+<tr>
+<td align="left"><code>file_types</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+list[str] | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">List of file extensions or types of files to be uploaded (e.g. ['image', '.json', '.mp4']). "file" allows any file to be uploaded, "image" allows only image files to be uploaded, "audio" allows only audio files to be uploaded, "video" allows only video files to be uploaded, "text" allows only text files to be uploaded.</td>
+</tr>
+
+<tr>
+<td align="left"><code>type</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+Literal["filepath", "binary"]
+```
+
+</td>
+<td align="left"><code>"filepath"</code></td>
+<td align="left">Type of value to be returned by component. "file" returns a temporary file object with the same base name as the uploaded file, whose full path can be retrieved by file_obj.name, "binary" returns an bytes object.</td>
+</tr>
+
+<tr>
+<td align="left"><code>label</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+str | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">The label for this component. Appears above the component and is also used as the header if there are a table of examples for this component. If None and used in a `gr.Interface`, the label will be the name of the parameter this component is assigned to.</td>
+</tr>
+
+<tr>
+<td align="left"><code>every</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+float | None
 ```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">If `value` is a callable, run the function 'every' number of seconds while the client connection is open. Has no effect otherwise. Queue must be enabled. The event can be accessed (e.g. to cancel it) via this component's .load_event attribute.</td>
+</tr>
+
+<tr>
+<td align="left"><code>show_label</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+bool | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">if True, will display label.</td>
+</tr>
+
+<tr>
+<td align="left"><code>container</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+bool
+```
+
+</td>
+<td align="left"><code>True</code></td>
+<td align="left">If True, will place the component in a container - providing some extra padding around the border.</td>
+</tr>
+
+<tr>
+<td align="left"><code>scale</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+int | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">relative width compared to adjacent Components in a Row. For example, if Component A has scale=2, and Component B has scale=1, A will be twice as wide as B. Should be an integer.</td>
+</tr>
+
+<tr>
+<td align="left"><code>min_width</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+int
+```
+
+</td>
+<td align="left"><code>160</code></td>
+<td align="left">minimum pixel width, will wrap if not sufficient screen space to satisfy this value. If a certain scale value results in this Component being narrower than min_width, the min_width parameter will be respected first.</td>
+</tr>
+
+<tr>
+<td align="left"><code>height</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+int | float | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">The maximum height of the file component, in pixels. If more files are uploaded than can fit in the height, a scrollbar will appear.</td>
+</tr>
+
+<tr>
+<td align="left"><code>interactive</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+bool | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">if True, will allow users to upload a file; if False, can only be used to display files. If not provided, this is inferred based on whether the component is used as an input or output.</td>
+</tr>
+
+<tr>
+<td align="left"><code>visible</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+bool
+```
+
+</td>
+<td align="left"><code>True</code></td>
+<td align="left">If False, component will be hidden.</td>
+</tr>
+
+<tr>
+<td align="left"><code>elem_id</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+str | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">An optional string that is assigned as the id of this component in the HTML DOM. Can be used for targeting CSS styles.</td>
+</tr>
+
+<tr>
+<td align="left"><code>elem_classes</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+list[str] | str | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">An optional list of strings that are assigned as the classes of this component in the HTML DOM. Can be used for targeting CSS styles.</td>
+</tr>
+
+<tr>
+<td align="left"><code>render</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+bool
+```
+
+</td>
+<td align="left"><code>True</code></td>
+<td align="left">If False, component will not render be rendered in the Blocks context. Should be used if the intention is to assign event listeners now but render the component later.</td>
+</tr>
+
+<tr>
+<td align="left"><code>showviewer</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+bool
+```
+
+</td>
+<td align="left"><code>True</code></td>
+<td align="left">If True, will display the 3Dmol.js viewer. If False, will not display the 3Dmol.js viewer.</td>
+</tr>
+</tbody></table>
+
+
+### Events
+
+| name | description |
+|:-----|:------------|
+| `change` | Triggered when the value of the Molecule3D changes either because of user input (e.g. a user types in a textbox) OR because of a function update (e.g. an image receives a value from the output of an event trigger). See `.input()` for a listener that is only triggered by user input. |
+| `select` | Event listener for when the user selects or deselects the Molecule3D. Uses event data gradio.SelectData to carry `value` referring to the label of the Molecule3D, and `selected` to refer to state of the Molecule3D. See EventData documentation on how to use this event data |
+| `clear` | This listener is triggered when the user clears the Molecule3D using the X button for the component. |
+| `upload` | This listener is triggered when the user uploads a file into the Molecule3D. |
+
+
+
+### User function
+
+The impact on the users predict function varies depending on whether the component is used as an input or output for an event (or both).
+
+- When used as an Input, the component only impacts the input signature of the user function.
+- When used as an output, the component only impacts the return signature of the user function.
+
+The code snippet below is accurate in cases where the component is used as both an input and an output.
+
+- **As output:** Is passed, the preprocessed input data sent to the user's function in the backend.
+- **As input:** Should return, the output data received by the component from the user's function in the backend.
+
+ ```python
+ def predict(
+     value: bytes | NamedString | list[bytes | NamedString] | None
+ ) -> str | list[str] | None:
+     return value
+ ```
+ 

src/backend/gradio_molecule3d/molecule3d.py

@@ -153,7 +153,6 @@ class Molecule3D(Component):
     def preprocess(
         self, payload: ListFiles | FileData | None
     ) -> bytes | NamedString | list[bytes | NamedString] | None:
-        print("preprocess", payload)
         if payload is None:
             return None
         if self.file_count == "single":
@@ -168,7 +167,6 @@ class Molecule3D(Component):
                 return [self._process_single_file(payload)]
 
     def postprocess(self, value: str | list[str] | None) -> ListFiles | FileData | None:
-        print("postprocess",value)
         if value is None:
             return None
         

src/backend/gradio_molecule3d/molecule3d.pyi

@@ -154,7 +154,6 @@ class Molecule3D(Component):
     def preprocess(
         self, payload: ListFiles | FileData | None
     ) -> bytes | NamedString | list[bytes | NamedString] | None:
-        print("preprocess", payload)
         if payload is None:
             return None
         if self.file_count == "single":
@@ -169,7 +168,6 @@ class Molecule3D(Component):
                 return [self._process_single_file(payload)]
 
     def postprocess(self, value: str | list[str] | None) -> ListFiles | FileData | None:
-        print("postprocess",value)
         if value is None:
             return None
         

src/backend/gradio_molecule3d/templates/component/index.js

@@ -25018,7 +25018,7 @@ const _3Dmol = /* @__PURE__ */ getDefaultExportFromCjs(_3DmolExports), Molecular
   text: text$3,
   toggle_class: toggle_class$5,
   transition_in: transition_in$7
-} = window.__gradio__svelte__internal, { onMount: onMount$1 } = window.__gradio__svelte__internal;
+} = window.__gradio__svelte__internal, { onMount: onMount$1, onDestroy: onDestroy$1 } = window.__gradio__svelte__internal;
 function get_each_context$2(t, e, r) {
   const n = t.slice();
   return n[53] = e[r], n[54] = e, n[55] = r, n;
@@ -26251,12 +26251,13 @@ function instance$9(t, e, r) {
     }), a.render());
   }
   onMount$1(() => {
+    console.log("MolecularViewer Mounted");
     let pe = { ..._, cartoonQuality: 7 };
     r(20, a = n.createViewer(f, pe));
     let de = [];
     y.forEach((ce) => {
       de.some((Ae) => Ae.model === ce.model && Ae.chain === ce.chain && Ae.resname === ce.resname && Ae.style === ce.style && Ae.color === ce.color && Ae.residue_range === ce.residue_range && Ae.around === ce.around && Ae.byres === ce.byres && Ae.sidechain === ce.sidechain) || de.push(ce);
-    }), r(1, y = de), b.length > 0 && b.forEach((ce) => {
+    }), r(1, y = de), console.log(b), b.length > 0 && b.forEach((ce) => {
       ce.asFrames ? a.addModelsAsFrames(ce.data, ce.format) : a.addModel(ce.data, ce.format);
     }), g(y), a.zoomTo(), a.render(), a.zoom(0.8, 2e3), y.forEach((ce) => {
       ce.color === "alphafold" && r(11, T = !0);
@@ -32692,7 +32693,7 @@ function create_fragment$5(t) {
         "placeholder",
         /*placeholder*/
         t[2]
-      ), attr$4(n, "class", "wfull inp svelte-18kpwjt"), b.__value = "pdb_assym", set_input_value(b, b.__value), h.__value = "pdb_bioass", set_input_value(h, h.__value), _.__value = "af", set_input_value(_, _.__value), E.__value = "esm", set_input_value(E, E.__value), attr$4(u, "name", ""), attr$4(u, "id", ""), attr$4(u, "class", "select svelte-18kpwjt"), attr$4(r, "class", "flex input wfull svelte-18kpwjt"), attr$4(S, "class", "btn text-center svelte-18kpwjt"), attr$4(e, "class", "flex mt-2 svelte-18kpwjt"), attr$4(s, "class", "or py svelte-18kpwjt");
+      ), attr$4(n, "class", "wfull inp svelte-1nnwgsd"), b.__value = "pdb_assym", set_input_value(b, b.__value), h.__value = "pdb_bioass", set_input_value(h, h.__value), _.__value = "af", set_input_value(_, _.__value), E.__value = "esm", set_input_value(E, E.__value), attr$4(u, "name", ""), attr$4(u, "id", ""), attr$4(u, "class", "select svelte-1nnwgsd"), attr$4(r, "class", "flex input wfull svelte-1nnwgsd"), attr$4(S, "class", "btn text-center svelte-1nnwgsd"), attr$4(e, "class", "flex mt-2 svelte-1nnwgsd"), attr$4(s, "class", "or py svelte-1nnwgsd");
     },
     m(g, M) {
       insert$5(g, e, M), append$4(e, r), append$4(r, n), set_input_value(
@@ -32763,7 +32764,7 @@ function instance$5(t, e, r) {
   async function h(p) {
     await tick$2();
     const v = Math.random().toString(36).substring(2, 15);
-    console.log("file to upload", p), n = await upload([p], b, v, u), console.log("uploaded files", n[0]), f("load", n[0]);
+    n = await upload([p], b, v, u), f("load", n[0]);
   }
   let _ = !1;
   async function E(p, v) {
@@ -32792,7 +32793,7 @@ function instance$5(t, e, r) {
         if (r(1, _ = !1), T.status == 200)
           return T.blob();
         f("notfound");
-      }).then((T) => new File([T], p + g, { type: "text/plain" }));
+      }).then((T) => new File([T], p + ".pdb", { type: "text/plain" }));
     } catch {
       r(1, _ = !1), f("notfound");
     }
@@ -32817,7 +32818,7 @@ function instance$5(t, e, r) {
     esm: "Enter MGnify protein identifier"
   };
   function s(p) {
-    p.key === "Enter" && (console.log("Enter pressed"), console.log(y), console.log(c), E(y, c));
+    p.key === "Enter" && E(y, c);
   }
   function o() {
     y = this.value, r(3, y);
@@ -32874,7 +32875,7 @@ function create_else_block$2(t) {
   let e, r, n, f, u;
   e = new FileRetrieval({ props: { root: (
     /*root*/
-    t[5]
+    t[6]
   ) } }), e.$on(
     "load",
     /*handle_upload*/
@@ -32894,11 +32895,11 @@ function create_else_block$2(t) {
     ),
     file_count: (
       /*file_count*/
-      t[3]
+      t[4]
     ),
     root: (
       /*root*/
-      t[5]
+      t[6]
     ),
     $$slots: { default: [create_default_slot$1] },
     $$scope: { ctx: t }
@@ -32920,16 +32921,16 @@ function create_else_block$2(t) {
       p(_, E) {
         const c = {};
         E & /*root*/
-        32 && (c.root = /*root*/
-        _[5]), e.$set(c);
+        64 && (c.root = /*root*/
+        _[6]), e.$set(c);
         const S = {};
         E & /*accept_file_types*/
         16384 && (S.filetype = /*accept_file_types*/
         _[14]), E & /*file_count*/
-        8 && (S.file_count = /*file_count*/
-        _[3]), E & /*root*/
-        32 && (S.root = /*root*/
-        _[5]), E & /*$$scope*/
+        16 && (S.file_count = /*file_count*/
+        _[4]), E & /*root*/
+        64 && (S.root = /*root*/
+        _[6]), E & /*$$scope*/
         8388608 && (S.$$scope = { dirty: E, ctx: _ }), !f && E & /*dragging*/
         8192 && (f = !0, S.dragging = /*dragging*/
         _[13], add_flush_callback(() => f = !1)), n.$set(S);
@@ -32951,7 +32952,7 @@ function create_if_block$2(t) {
   e = new ModifyUpload({
     props: { i18n: (
       /*i18n*/
-      t[7]
+      t[8]
     ), absolute: !0 }
   }), e.$on(
     "clear",
@@ -32961,11 +32962,11 @@ function create_if_block$2(t) {
     props: {
       i18n: (
         /*i18n*/
-        t[7]
+        t[8]
       ),
       selectable: (
         /*selectable*/
-        t[4]
+        t[5]
       ),
       value: (
         /*value*/
@@ -32973,7 +32974,7 @@ function create_if_block$2(t) {
       ),
       height: (
         /*height*/
-        t[6]
+        t[7]
       )
     }
   }), n.$on(
@@ -32983,7 +32984,7 @@ function create_if_block$2(t) {
   );
   let h = (
     /*moldata*/
-    t[11] != null && /*molviewer*/
+    t[1] != null && /*molviewer*/
     t[12] && create_if_block_1$2(t)
   );
   return {
@@ -32996,21 +32997,21 @@ function create_if_block$2(t) {
     p(_, E) {
       const c = {};
       E & /*i18n*/
-      128 && (c.i18n = /*i18n*/
-      _[7]), e.$set(c);
+      256 && (c.i18n = /*i18n*/
+      _[8]), e.$set(c);
       const S = {};
       E & /*i18n*/
-      128 && (S.i18n = /*i18n*/
-      _[7]), E & /*selectable*/
-      16 && (S.selectable = /*selectable*/
-      _[4]), E & /*value*/
+      256 && (S.i18n = /*i18n*/
+      _[8]), E & /*selectable*/
+      32 && (S.selectable = /*selectable*/
+      _[5]), E & /*value*/
       1 && (S.value = /*value*/
       _[0]), E & /*height*/
-      64 && (S.height = /*height*/
-      _[6]), n.$set(S), /*moldata*/
-      _[11] != null && /*molviewer*/
+      128 && (S.height = /*height*/
+      _[7]), n.$set(S), /*moldata*/
+      _[1] != null && /*molviewer*/
       _[12] ? h ? (h.p(_, E), E & /*moldata, molviewer*/
-      6144 && transition_in$2(h, 1)) : (h = create_if_block_1$2(_), h.c(), transition_in$2(h, 1), h.m(u.parentNode, u)) : h && (group_outros$2(), transition_out$2(h, 1, 1, () => {
+      4098 && transition_in$2(h, 1)) : (h = create_if_block_1$2(_), h.c(), transition_in$2(h, 1), h.m(u.parentNode, u)) : h && (group_outros$2(), transition_out$2(h, 1, 1, () => {
         h = null;
       }), check_outros$2());
     },
@@ -33082,19 +33083,19 @@ function create_if_block_1$2(t) {
     props: {
       moldata: (
         /*moldata*/
-        t[11]
+        t[1]
       ),
       config: (
         /*config*/
-        t[8]
+        t[9]
       ),
       confidenceLabel: (
         /*confidenceLabel*/
-        t[9]
+        t[10]
       ),
       representations: (
         /*representations*/
-        t[10]
+        t[11]
       )
     }
   }), {
@@ -33107,14 +33108,14 @@ function create_if_block_1$2(t) {
     p(n, f) {
       const u = {};
       f & /*moldata*/
-      2048 && (u.moldata = /*moldata*/
-      n[11]), f & /*config*/
-      256 && (u.config = /*config*/
-      n[8]), f & /*confidenceLabel*/
-      512 && (u.confidenceLabel = /*confidenceLabel*/
-      n[9]), f & /*representations*/
-      1024 && (u.representations = /*representations*/
-      n[10]), e.$set(u);
+      2 && (u.moldata = /*moldata*/
+      n[1]), f & /*config*/
+      512 && (u.config = /*config*/
+      n[9]), f & /*confidenceLabel*/
+      1024 && (u.confidenceLabel = /*confidenceLabel*/
+      n[10]), f & /*representations*/
+      2048 && (u.representations = /*representations*/
+      n[11]), e.$set(u);
     },
     i(n) {
       r || (transition_in$2(e.$$.fragment, n), r = !0);
@@ -33133,7 +33134,7 @@ function create_fragment$4(t) {
     props: {
       show_label: (
         /*show_label*/
-        t[2]
+        t[3]
       ),
       Icon: File$1,
       float: (
@@ -33142,7 +33143,7 @@ function create_fragment$4(t) {
       ),
       label: (
         /*label*/
-        t[1] || "File"
+        t[2] || "File"
       )
     }
   });
@@ -33163,12 +33164,12 @@ function create_fragment$4(t) {
     p(c, [S]) {
       const y = {};
       S & /*show_label*/
-      4 && (y.show_label = /*show_label*/
-      c[2]), S & /*value*/
+      8 && (y.show_label = /*show_label*/
+      c[3]), S & /*value*/
       1 && (y.float = /*value*/
       c[0] === null), S & /*label*/
-      2 && (y.label = /*label*/
-      c[1] || "File"), e.$set(y);
+      4 && (y.label = /*label*/
+      c[2] || "File"), e.$set(y);
       let w = n;
       n = E(c), n === w ? _[n].p(c, S) : (group_outros$2(), transition_out$2(_[w], 1, 1, () => {
         _[w] = null;
@@ -33188,10 +33189,10 @@ function create_fragment$4(t) {
 function instance$4(t, e, r) {
   let { $$slots: n = {}, $$scope: f } = e, { value: u } = e, { label: b } = e, { show_label: h = !0 } = e, { file_count: _ = "single" } = e, { file_types: E = null } = e, { selectable: c = !1 } = e, { root: S } = e, { height: y = void 0 } = e, { i18n: w } = e, { config: L = {} } = e, { confidenceLabel: s = "" } = e, { representations: o = [] } = e, { moldata: A = null } = e, { molviewer: p = !1 } = e;
   async function v({ detail: I }) {
-    r(0, u = I), await tick$1(), l("change", u), l("upload", I);
+    r(0, u = I), await tick$1(), l("change", u), l("upload", I), console.log("upload", I);
   }
   function a() {
-    r(0, u = null), l("change", null), l("clear");
+    r(0, u = null), r(1, A = null), l("change", null), l("clear");
   }
   const l = createEventDispatcher();
   let g;
@@ -33205,12 +33206,13 @@ function instance$4(t, e, r) {
     M = I, r(13, M);
   }
   return t.$$set = (I) => {
-    "value" in I && r(0, u = I.value), "label" in I && r(1, b = I.label), "show_label" in I && r(2, h = I.show_label), "file_count" in I && r(3, _ = I.file_count), "file_types" in I && r(18, E = I.file_types), "selectable" in I && r(4, c = I.selectable), "root" in I && r(5, S = I.root), "height" in I && r(6, y = I.height), "i18n" in I && r(7, w = I.i18n), "config" in I && r(8, L = I.config), "confidenceLabel" in I && r(9, s = I.confidenceLabel), "representations" in I && r(10, o = I.representations), "moldata" in I && r(11, A = I.moldata), "molviewer" in I && r(12, p = I.molviewer), "$$scope" in I && r(23, f = I.$$scope);
+    "value" in I && r(0, u = I.value), "label" in I && r(2, b = I.label), "show_label" in I && r(3, h = I.show_label), "file_count" in I && r(4, _ = I.file_count), "file_types" in I && r(18, E = I.file_types), "selectable" in I && r(5, c = I.selectable), "root" in I && r(6, S = I.root), "height" in I && r(7, y = I.height), "i18n" in I && r(8, w = I.i18n), "config" in I && r(9, L = I.config), "confidenceLabel" in I && r(10, s = I.confidenceLabel), "representations" in I && r(11, o = I.representations), "moldata" in I && r(1, A = I.moldata), "molviewer" in I && r(12, p = I.molviewer), "$$scope" in I && r(23, f = I.$$scope);
   }, t.$$.update = () => {
     t.$$.dirty & /*dragging*/
     8192 && l("drag", M);
   }, [
     u,
+    A,
     b,
     h,
     _,
@@ -33221,7 +33223,6 @@ function instance$4(t, e, r) {
     L,
     s,
     o,
-    A,
     p,
     M,
     g,
@@ -33240,18 +33241,18 @@ class FileUpload extends SvelteComponent$4 {
   constructor(e) {
     super(), init$4(this, e, instance$4, create_fragment$4, safe_not_equal$4, {
       value: 0,
-      label: 1,
-      show_label: 2,
-      file_count: 3,
+      label: 2,
+      show_label: 3,
+      file_count: 4,
       file_types: 18,
-      selectable: 4,
-      root: 5,
-      height: 6,
-      i18n: 7,
-      config: 8,
-      confidenceLabel: 9,
-      representations: 10,
-      moldata: 11,
+      selectable: 5,
+      root: 6,
+      height: 7,
+      i18n: 8,
+      config: 9,
+      confidenceLabel: 10,
+      representations: 11,
+      moldata: 1,
       molviewer: 12
     });
   }
@@ -34697,7 +34698,7 @@ function create_if_block(t) {
       e = element("div"), r = svg_element("svg"), n = svg_element("path"), f = space(), u = element("span"), u.textContent = "Error in the representations", b = space(), h = element("div"), _ = element("span"), _.textContent = "Couldn't display Molecule. Fix the following problems:", E = space(), c = element("ul");
       for (let w = 0; w < y.length; w += 1)
         y[w].c();
-      attr(n, "stroke-linecap", "round"), attr(n, "stroke-linejoin", "round"), attr(n, "d", "M12 9v3.75m-9.303 3.376c-.866 1.5.217 3.374 1.948 3.374h14.71c1.73 0 2.813-1.874 1.948-3.374L13.949 3.378c-.866-1.5-3.032-1.5-3.898 0L2.697 16.126zM12 15.75h.007v.008H12v-.008z"), attr(r, "class", "flex-shrink-0 inline w-4 h-4 mr-3 mt-[2px] svelte-1j3z0by"), attr(r, "xmlns", "http://www.w3.org/2000/svg"), attr(r, "fill", "none"), attr(r, "viewBox", "0 0 24 24"), attr(r, "stroke-width", "1.5"), attr(r, "stroke", "currentColor"), attr(u, "class", "sr-only svelte-1j3z0by"), attr(_, "class", "font-medium svelte-1j3z0by"), attr(c, "class", "mt-1.5 ml-4 list-disc list-inside svelte-1j3z0by"), attr(e, "class", "flex m-2 p-4 mb-4 text-sm text-red-800 rounded-lg bg-red-50 dark:bg-gray-800 dark:text-red-400 svelte-1j3z0by"), attr(e, "role", "alert");
+      attr(n, "stroke-linecap", "round"), attr(n, "stroke-linejoin", "round"), attr(n, "d", "M12 9v3.75m-9.303 3.376c-.866 1.5.217 3.374 1.948 3.374h14.71c1.73 0 2.813-1.874 1.948-3.374L13.949 3.378c-.866-1.5-3.032-1.5-3.898 0L2.697 16.126zM12 15.75h.007v.008H12v-.008z"), attr(r, "class", "flex-shrink-0 inline w-4 h-4 mr-3 mt-[2px] svelte-1xezsv6"), attr(r, "xmlns", "http://www.w3.org/2000/svg"), attr(r, "fill", "none"), attr(r, "viewBox", "0 0 24 24"), attr(r, "stroke-width", "1.5"), attr(r, "stroke", "currentColor"), attr(u, "class", "sr-only svelte-1xezsv6"), attr(_, "class", "font-medium svelte-1xezsv6"), attr(c, "class", "mt-1.5 ml-4 list-disc list-inside svelte-1xezsv6"), attr(e, "class", "flex m-2 p-4 mb-4 text-sm text-red-800 rounded-lg bg-red-50 dark:bg-gray-800 dark:text-red-400 svelte-1xezsv6"), attr(e, "role", "alert");
     },
     m(w, L) {
       insert(w, e, L), append(e, r), append(r, n), append(e, f), append(e, u), append(e, b), append(e, h), append(h, _), append(h, E), append(h, c);
@@ -34960,7 +34961,7 @@ function instance(t, e, r) {
     around: { type: Number, default: 0 },
     byres: { type: Boolean, default: !1 },
     visible: { type: Boolean, default: !0 }
-  }, I = null, B = ["pdb", "sdf", "mol2"], P = [];
+  }, I = null, B = ["pdb", "sdf", "mol2", "pdb1"], P = [];
   async function z(X) {
     if (X == null)
       return [];
@@ -34985,12 +34986,12 @@ function instance(t, e, r) {
       if (!B.includes(oe))
         P.push(`Invalid file extension for ${X.orig_name}. Expected one of ${B.join(", ")}, got ${oe}`), r(20, I = null);
       else {
-        let te = await fetchFileContent(X.url);
-        console.log("t", te), r(20, I = [
+        let te = await fetchFileContent(X.url), ve = X.orig_name.split(".").pop();
+        ve === "pdb1" && (ve = "pdb"), r(20, I = [
           {
             data: te,
             name: X.orig_name,
-            format: "pdb",
+            format: ve,
             asFrames: !1
           }
         ]);
@@ -35006,7 +35007,7 @@ function instance(t, e, r) {
     "elem_id" in X && r(1, n = X.elem_id), "elem_classes" in X && r(2, f = X.elem_classes), "visible" in X && r(3, u = X.visible), "value" in X && r(0, b = X.value), "interactive" in X && r(4, h = X.interactive), "root" in X && r(5, _ = X.root), "label" in X && r(6, E = X.label), "show_label" in X && r(7, c = X.show_label), "height" in X && r(8, S = X.height), "reps" in X && r(24, y = X.reps), "config" in X && r(9, w = X.config), "confidenceLabel" in X && r(10, L = X.confidenceLabel), "showviewer" in X && r(11, s = X.showviewer), "_selectable" in X && r(12, o = X._selectable), "loading_status" in X && r(13, A = X.loading_status), "container" in X && r(14, p = X.container), "scale" in X && r(15, v = X.scale), "min_width" in X && r(16, a = X.min_width), "gradio" in X && r(17, l = X.gradio), "file_count" in X && r(18, g = X.file_count), "file_types" in X && r(19, M = X.file_types);
   }, t.$$.update = () => {
     t.$$.dirty[0] & /*old_value, value, gradio*/
-    33685505 && JSON.stringify(C) !== JSON.stringify(b) && (l.dispatch("change"), r(25, C = b), console.log("value change", b)), t.$$.dirty[0] & /*moldata*/
+    33685505 && JSON.stringify(C) !== JSON.stringify(b) && (l.dispatch("change"), r(25, C = b), console.log("value change", b), r(20, I = null), z(b)), t.$$.dirty[0] & /*moldata*/
     1048576 && r(26, k = I ? I.length : 0), t.$$.dirty[0] & /*reps, errors, lenMoldata*/
     85983232 && (y.forEach((X) => {
       for (const [oe, te] of Object.entries(D))

src/backend/gradio_molecule3d/templates/component/style.css

@@ -1 +1 @@
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var(--block-title-border-color);border-radius:var(--block-title-radius);background:var(--block-title-background-fill);padding:var(--block-title-padding);color:var(--block-title-text-color);font-weight:var(--block-title-text-weight);font-size:var(--block-title-text-size);line-height:var(--line-sm)}.hide.svelte-22c38v{margin:0;height:0}label.svelte-9gxdi0{display:inline-flex;align-items:center;z-index:var(--layer-2);box-shadow:var(--block-label-shadow);border:var(--block-label-border-width) solid var(--border-color-primary);border-top:none;border-left:none;border-radius:var(--block-label-radius);background:var(--block-label-background-fill);padding:var(--block-label-padding);pointer-events:none;color:var(--block-label-text-color);font-weight:var(--block-label-text-weight);font-size:var(--block-label-text-size);line-height:var(--line-sm)}.gr-group 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var(--size-10))}}div.svelte-1hgn91n{overflow:hidden;text-overflow:ellipsis;white-space:nowrap}.gallery.svelte-1hgn91n{display:flex;align-items:center;cursor:pointer;padding:var(--size-1) var(--size-2);text-align:left}.sr-only.svelte-1xezsv6{position:absolute;width:1px;height:1px;padding:0;margin:-1px;overflow:hidden;clip:rect(0,0,0,0);white-space:nowrap;border-width:0}.mb-4.svelte-1xezsv6{margin-bottom:1rem}.ml-4.svelte-1xezsv6{margin-left:1rem}.mr-3.svelte-1xezsv6{margin-right:.75rem}.mt-1\.5.svelte-1xezsv6{margin-top:.375rem}.mt-\[2px\].svelte-1xezsv6{margin-top:2px}.inline.svelte-1xezsv6{display:inline}.flex.svelte-1xezsv6{display:flex}.h-4.svelte-1xezsv6{height:1rem}.w-4.svelte-1xezsv6{width:1rem}.flex-shrink-0.svelte-1xezsv6{flex-shrink:0}.list-inside.svelte-1xezsv6{list-style-position:inside}.list-disc.svelte-1xezsv6{list-style-type:disc}.rounded-lg.svelte-1xezsv6{border-radius:.5rem}.bg-red-50.svelte-1xezsv6{--tw-bg-opacity:1;background-color:rgb(254 242 242 / var(--tw-bg-opacity))}.m-2.svelte-1xezsv6{margin:.5rem}.p-4.svelte-1xezsv6{padding:1rem}.text-sm.svelte-1xezsv6{font-size:.875rem;line-height:1.25rem}.font-medium.svelte-1xezsv6{font-weight:500}.text-red-800.svelte-1xezsv6{--tw-text-opacity:1;color:rgb(153 27 27 / var(--tw-text-opacity))}@media (prefers-color-scheme: dark){.dark\:bg-gray-800.svelte-1xezsv6{--tw-bg-opacity:1;background-color:rgb(31 41 55 / var(--tw-bg-opacity))}.dark\:text-red-400.svelte-1xezsv6{--tw-text-opacity:1;color:rgb(248 113 113 / var(--tw-text-opacity))}}

src/demo/app.py

@@ -12,34 +12,58 @@ reps =    [
       "model": 0,
       "chain": "",
       "resname": "",
-      "style": "cartoon",
+      "style": "stick",
       "color": "whiteCarbon",
       "residue_range": "",
       "around": 0,
       "byres": False,
-      "visible": False,
-    },
+      "visible": False
+    }
   ]
 
+
+
 def predict(x):
     print("predict function", x)
+    print(x.name)
     return x
 
-#doesn't work
-demo = gr.Interface(
-    predict,
-    Molecule3D(label="Molecule3D", reps=reps),  # interactive version of your component
-    Molecule3D(reps=reps),  # static version of your component
-    #examples=[[example]],  # uncomment this line to view the "example version" of your component
-)
-
-#works
-# with gr.Blocks() as demo:
-#     inp = Molecule3D("demo/1pga.pdb",label="Molecule3D", reps=reps)
-#     inp = Molecule3D("demo/1pga.pdb",label="Molecule3D", reps=reps, showviewer=False)
-#     out = Molecule3D(label="Molecule3D", reps=reps)
-#     btn = gr.Button("Predict")
-#     btn.click(predict, inputs=inp, outputs=out)
-
-if __name__ == "__main__":
-    demo.launch()
+with gr.Blocks() as demo:
+    inp = Molecule3D(label="Molecule3D", reps=reps)
+    out = Molecule3D(label="Output", reps=reps)
+
+    btn = gr.Button("Predict")
+    gr.Markdown(""" 
+    You can configure the default rendering of the molecule by adding a list of representations
+    <pre>
+        reps =    [
+        {
+          "model": 0,
+          "chain": "",
+          "resname": "",
+          "style": "cartoon",
+          "color": "whiteCarbon",
+          "residue_range": "",
+          "around": 0,
+          "byres": False,
+          "visible": False,
+        },
+        {
+          "model": 0,
+          "chain": "A",
+          "resname": "HIS",
+          "style": "stick",
+          "color": "red",
+          "residue_range": "",
+          "around": 0,
+          "byres": False,
+          "visible": False,
+        }
+      ]
+    </pre>
+    """)
+    btn.click(predict, inputs=inp, outputs=out)
+
+
+if __name__ == '__main__':
+  demo.launch()

src/demo/css.css

@@ -0,0 +1,157 @@
+html {
+	font-family: Inter;
+	font-size: 16px;
+	font-weight: 400;
+	line-height: 1.5;
+	-webkit-text-size-adjust: 100%;
+	background: #fff;
+	color: #323232;
+	-webkit-font-smoothing: antialiased;
+	-moz-osx-font-smoothing: grayscale;
+	text-rendering: optimizeLegibility;
+}
+
+:root {
+	--space: 1;
+	--vspace: calc(var(--space) * 1rem);
+	--vspace-0: calc(3 * var(--space) * 1rem);
+	--vspace-1: calc(2 * var(--space) * 1rem);
+	--vspace-2: calc(1.5 * var(--space) * 1rem);
+	--vspace-3: calc(0.5 * var(--space) * 1rem);
+}
+
+.app {
+	max-width: 748px !important;
+}
+
+.prose p {
+	margin: var(--vspace) 0;
+	line-height: var(--vspace * 2);
+	font-size: 1rem;
+}
+
+code {
+	font-family: "Inconsolata", sans-serif;
+	font-size: 16px;
+}
+
+h1,
+h1 code {
+	font-weight: 400;
+	line-height: calc(2.5 / var(--space) * var(--vspace));
+}
+
+h1 code {
+	background: none;
+	border: none;
+	letter-spacing: 0.05em;
+	padding-bottom: 5px;
+	position: relative;
+	padding: 0;
+}
+
+h2 {
+	margin: var(--vspace-1) 0 var(--vspace-2) 0;
+	line-height: 1em;
+}
+
+h3,
+h3 code {
+	margin: var(--vspace-1) 0 var(--vspace-2) 0;
+	line-height: 1em;
+}
+
+h4,
+h5,
+h6 {
+	margin: var(--vspace-3) 0 var(--vspace-3) 0;
+	line-height: var(--vspace);
+}
+
+.bigtitle,
+h1,
+h1 code {
+	font-size: calc(8px * 4.5);
+	word-break: break-word;
+}
+
+.title,
+h2,
+h2 code {
+	font-size: calc(8px * 3.375);
+	font-weight: lighter;
+	word-break: break-word;
+	border: none;
+	background: none;
+}
+
+.subheading1,
+h3,
+h3 code {
+	font-size: calc(8px * 1.8);
+	font-weight: 600;
+	border: none;
+	background: none;
+	letter-spacing: 0.1em;
+	text-transform: uppercase;
+}
+
+h2 code {
+	padding: 0;
+	position: relative;
+	letter-spacing: 0.05em;
+}
+
+blockquote {
+	font-size: calc(8px * 1.1667);
+	font-style: italic;
+	line-height: calc(1.1667 * var(--vspace));
+	margin: var(--vspace-2) var(--vspace-2);
+}
+
+.subheading2,
+h4 {
+	font-size: calc(8px * 1.4292);
+	text-transform: uppercase;
+	font-weight: 600;
+}
+
+.subheading3,
+h5 {
+	font-size: calc(8px * 1.2917);
+	line-height: calc(1.2917 * var(--vspace));
+
+	font-weight: lighter;
+	text-transform: uppercase;
+	letter-spacing: 0.15em;
+}
+
+h6 {
+	font-size: calc(8px * 1.1667);
+	font-size: 1.1667em;
+	font-weight: normal;
+	font-style: italic;
+	font-family: "le-monde-livre-classic-byol", serif !important;
+	letter-spacing: 0px !important;
+}
+
+#start .md > *:first-child {
+	margin-top: 0;
+}
+
+h2 + h3 {
+	margin-top: 0;
+}
+
+.md hr {
+	border: none;
+	border-top: 1px solid var(--block-border-color);
+	margin: var(--vspace-2) 0 var(--vspace-2) 0;
+}
+.prose ul {
+	margin: var(--vspace-2) 0 var(--vspace-1) 0;
+}
+
+.gap {
+	gap: 0;
+}

src/demo/space.py

@@ -0,0 +1,191 @@
+
+import gradio as gr
+from app import demo as app
+import os
+
+_docs = {'Molecule3D': {'description': 'Creates a file component that allows uploading generic file (when used as an input) and or displaying generic files (output).', 'members': {'__init__': {'value': {'type': 'str | list[str] | Callable | None', 'default': 'None', 'description': 'Default file to display, given as str file path. If callable, the function will be called whenever the app loads to set the initial value of the component.'}, 'reps': {'type': 'Any | None', 'default': '[]', 'description': None}, 'config': {'type': 'Any | None', 'default': '{\n    "backgroundColor": "white",\n    "orthographic": False,\n    "disableFog": False,\n}', 'description': 'dictionary of config options'}, 'confidenceLabel': {'type': 'str | None', 'default': '"pLDDT"', 'description': 'label for confidence values stored in the bfactor column of a pdb file'}, 'file_count': {'type': 'Literal["single", "multiple", "directory"]', 'default': '"single"', 'description': 'if single, allows user to upload one file. If "multiple", user uploads multiple files. If "directory", user uploads all files in selected directory. Return type will be list for each file in case of "multiple" or "directory".'}, 'file_types': {'type': 'list[str] | None', 'default': 'None', 'description': 'List of file extensions or types of files to be uploaded (e.g. [\'image\', \'.json\', \'.mp4\']). "file" allows any file to be uploaded, "image" allows only image files to be uploaded, "audio" allows only audio files to be uploaded, "video" allows only video files to be uploaded, "text" allows only text files to be uploaded.'}, 'type': {'type': 'Literal["filepath", "binary"]', 'default': '"filepath"', 'description': 'Type of value to be returned by component. "file" returns a temporary file object with the same base name as the uploaded file, whose full path can be retrieved by file_obj.name, "binary" returns an bytes object.'}, 'label': {'type': 'str | None', 'default': 'None', 'description': 'The label for this component. Appears above the component and is also used as the header if there are a table of examples for this component. If None and used in a `gr.Interface`, the label will be the name of the parameter this component is assigned to.'}, 'every': {'type': 'float | None', 'default': 'None', 'description': "If `value` is a callable, run the function 'every' number of seconds while the client connection is open. Has no effect otherwise. Queue must be enabled. The event can be accessed (e.g. to cancel it) via this component's .load_event attribute."}, 'show_label': {'type': 'bool | None', 'default': 'None', 'description': 'if True, will display label.'}, 'container': {'type': 'bool', 'default': 'True', 'description': 'If True, will place the component in a container - providing some extra padding around the border.'}, 'scale': {'type': 'int | None', 'default': 'None', 'description': 'relative width compared to adjacent Components in a Row. For example, if Component A has scale=2, and Component B has scale=1, A will be twice as wide as B. Should be an integer.'}, 'min_width': {'type': 'int', 'default': '160', 'description': 'minimum pixel width, will wrap if not sufficient screen space to satisfy this value. If a certain scale value results in this Component being narrower than min_width, the min_width parameter will be respected first.'}, 'height': {'type': 'int | float | None', 'default': 'None', 'description': 'The maximum height of the file component, in pixels. If more files are uploaded than can fit in the height, a scrollbar will appear.'}, 'interactive': {'type': 'bool | None', 'default': 'None', 'description': 'if True, will allow users to upload a file; if False, can only be used to display files. If not provided, this is inferred based on whether the component is used as an input or output.'}, 'visible': {'type': 'bool', 'default': 'True', 'description': 'If False, component will be hidden.'}, 'elem_id': {'type': 'str | None', 'default': 'None', 'description': 'An optional string that is assigned as the id of this component in the HTML DOM. Can be used for targeting CSS styles.'}, 'elem_classes': {'type': 'list[str] | str | None', 'default': 'None', 'description': 'An optional list of strings that are assigned as the classes of this component in the HTML DOM. Can be used for targeting CSS styles.'}, 'render': {'type': 'bool', 'default': 'True', 'description': 'If False, component will not render be rendered in the Blocks context. Should be used if the intention is to assign event listeners now but render the component later.'}, 'showviewer': {'type': 'bool', 'default': 'True', 'description': 'If True, will display the 3Dmol.js viewer. If False, will not display the 3Dmol.js viewer.'}}, 'postprocess': {'value': {'type': 'str | list[str] | None', 'description': "The output data received by the component from the user's function in the backend."}}, 'preprocess': {'return': {'type': 'bytes | NamedString | list[bytes | NamedString] | None', 'description': "The preprocessed input data sent to the user's function in the backend."}, 'value': None}}, 'events': {'change': {'type': None, 'default': None, 'description': 'Triggered when the value of the Molecule3D changes either because of user input (e.g. a user types in a textbox) OR because of a function update (e.g. an image receives a value from the output of an event trigger). See `.input()` for a listener that is only triggered by user input.'}, 'select': {'type': None, 'default': None, 'description': 'Event listener for when the user selects or deselects the Molecule3D. Uses event data gradio.SelectData to carry `value` referring to the label of the Molecule3D, and `selected` to refer to state of the Molecule3D. See EventData documentation on how to use this event data'}, 'clear': {'type': None, 'default': None, 'description': 'This listener is triggered when the user clears the Molecule3D using the X button for the component.'}, 'upload': {'type': None, 'default': None, 'description': 'This listener is triggered when the user uploads a file into the Molecule3D.'}}}, '__meta__': {'additional_interfaces': {}, 'user_fn_refs': {'Molecule3D': []}}}
+
+abs_path = os.path.join(os.path.dirname(__file__), "css.css")
+
+with gr.Blocks(
+    css=abs_path,
+    theme=gr.themes.Default(
+        font_mono=[
+            gr.themes.GoogleFont("Inconsolata"),
+            "monospace",
+        ],
+    ),
+) as demo:
+    gr.Markdown(
+"""
+# `gradio_molecule3d`
+
+<div style="display: flex; gap: 7px;">
+<a href="https://pypi.org/project/gradio_molecule3d/" target="_blank"><img alt="PyPI - Version" src="https://img.shields.io/pypi/v/gradio_molecule3d"></a>  
+</div>
+
+Molecule3D custom component to visualize pdb or sdf files using 3Dmol.js
+""", elem_classes=["md-custom"], header_links=True)
+    app.render()
+    gr.Markdown(
+"""
+## Installation
+
+```bash
+pip install gradio_molecule3d
+```
+
+## Usage
+
+```python
+
+import gradio as gr
+from gradio_molecule3d import Molecule3D
+
+import os
+
+example = Molecule3D().example_inputs()
+
+
+reps =    [
+    {
+      "model": 0,
+      "chain": "",
+      "resname": "",
+      "style": "stick",
+      "color": "whiteCarbon",
+      "residue_range": "",
+      "around": 0,
+      "byres": False,
+      "visible": False
+    }
+  ]
+
+
+
+def predict(x):
+    print("predict function", x)
+    print(x.name)
+    return x
+
+with gr.Blocks() as demo:
+    inp = Molecule3D(label="Molecule3D", reps=reps)
+    out = Molecule3D(label="Output", reps=reps)
+
+    btn = gr.Button("Predict")
+    gr.Markdown(\"\"\" 
+    You can configure the default rendering of the molecule by adding a list of representations
+    <pre>
+        reps =    [
+        {
+          "model": 0,
+          "chain": "",
+          "resname": "",
+          "style": "cartoon",
+          "color": "whiteCarbon",
+          "residue_range": "",
+          "around": 0,
+          "byres": False,
+          "visible": False,
+        },
+        {
+          "model": 0,
+          "chain": "A",
+          "resname": "HIS",
+          "style": "stick",
+          "color": "red",
+          "residue_range": "",
+          "around": 0,
+          "byres": False,
+          "visible": False,
+        }
+      ]
+    </pre>
+    \"\"\")
+    btn.click(predict, inputs=inp, outputs=out)
+
+
+if __name__ == '__main__':
+  demo.launch()
+
+```
+""", elem_classes=["md-custom"], header_links=True)
+
+
+    gr.Markdown("""
+## `Molecule3D`
+
+### Initialization
+""", elem_classes=["md-custom"], header_links=True)
+
+    gr.ParamViewer(value=_docs["Molecule3D"]["members"]["__init__"], linkify=[])
+
+
+    gr.Markdown("### Events")
+    gr.ParamViewer(value=_docs["Molecule3D"]["events"], linkify=['Event'])
+
+
+
+
+    gr.Markdown("""
+
+### User function
+
+The impact on the users predict function varies depending on whether the component is used as an input or output for an event (or both).
+
+- When used as an Input, the component only impacts the input signature of the user function.
+- When used as an output, the component only impacts the return signature of the user function.
+
+The code snippet below is accurate in cases where the component is used as both an input and an output.
+
+- **As input:** Is passed, the preprocessed input data sent to the user's function in the backend.
+- **As output:** Should return, the output data received by the component from the user's function in the backend.
+
+ ```python
+def predict(
+    value: bytes | NamedString | list[bytes | NamedString] | None
+) -> str | list[str] | None:
+    return value
+```
+""", elem_classes=["md-custom", "Molecule3D-user-fn"], header_links=True)
+
+
+
+
+    demo.load(None, js=r"""function() {
+    const refs = {};
+    const user_fn_refs = {
+          Molecule3D: [], };
+    requestAnimationFrame(() => {
+
+        Object.entries(user_fn_refs).forEach(([key, refs]) => {
+            if (refs.length > 0) {
+                const el = document.querySelector(`.${key}-user-fn`);
+                if (!el) return;
+                refs.forEach(ref => {
+                    el.innerHTML = el.innerHTML.replace(
+                        new RegExp("\\b"+ref+"\\b", "g"),
+                        `<a href="#h-${ref.toLowerCase()}">${ref}</a>`
+                    );
+                })
+            }
+        })
+
+        Object.entries(refs).forEach(([key, refs]) => {
+            if (refs.length > 0) {
+                const el = document.querySelector(`.${key}`);
+                if (!el) return;
+                refs.forEach(ref => {
+                    el.innerHTML = el.innerHTML.replace(
+                        new RegExp("\\b"+ref+"\\b", "g"),
+                        `<a href="#h-${ref.toLowerCase()}">${ref}</a>`
+                    );
+                })
+            }
+        })
+    })
+}
+
+""")
+
+demo.launch()

src/frontend/Index.svelte

@@ -11,30 +11,24 @@
   import type { Gradio, SelectData } from "@gradio/utils";
   import File from "./shared/File.svelte";
   import FileUpload from "./shared/FileUpload.svelte";
-
   import { type FileData } from "@gradio/client";
   import { Block, UploadText } from "@gradio/atoms";
-
   import { StatusTracker } from "@gradio/statustracker";
   import type { LoadingStatus } from "@gradio/statustracker";
-
   export let elem_id = "";
   export let elem_classes: string[] = [];
   export let visible = true;
   export let value: null | FileData | FileData[];
-
   export let interactive: boolean;
   export let root: string;
   export let label: string;
   export let show_label: boolean;
   export let height: number | undefined = undefined;
-
   //Molecule3D specific arguments
   export let reps: any = [];
   export let config: any = {};
   export let confidenceLabel: string = "";
   export let showviewer: boolean = true;
-
   export let _selectable = false;
   export let loading_status: LoadingStatus;
   export let container = true;
@@ -49,17 +43,16 @@
   }>;
   export let file_count: string;
   export let file_types: string[] = ["file"];
-
   let old_value = value;
   $: if (JSON.stringify(old_value) !== JSON.stringify(value)) {
     gradio.dispatch("change");
     old_value = value;
     console.log("value change", value);
+    moldata = null;
+    retrieveContent(value);
   }
-
   let dragging = false;
   let pending_upload = false;
-
   //check for missing keys in reps
   let keys_for_reps = {
     model: {
@@ -115,10 +108,8 @@
       default: true,
     },
   };
-
   let moldata = null;
-
-  let allowed_extensions = ["pdb", "sdf", "mol2"];
+  let allowed_extensions = ["pdb", "sdf", "mol2", "pdb1"];
   async function fetchFileContent(url) {
     const response = await fetch(url);
     const content = await response.text();
@@ -126,14 +117,12 @@
   }
   let promise = null;
   let errors = [];
-
   async function retrieveContent(value) {
     if (value == null) {
       return [];
     } else if (Array.isArray(value)) {
       let tempMoldata = [];
       // get file extension
-
       for (const element of value) {
         let ext = element.orig_name.split(".").pop();
         if (!allowed_extensions.includes(ext)) {
@@ -164,9 +153,12 @@
         moldata = null;
       } else {
         let t = await fetchFileContent(value.url);
-        console.log("t", t);
+        let ext = value.orig_name.split(".").pop();
+        if (ext === "pdb1") {
+          ext = "pdb";
+        }
         moldata = [
-          { data: t, name: value.orig_name, format: "pdb", asFrames: false },
+          { data: t, name: value.orig_name, format: ext, asFrames: false },
         ];
       }
     } else {
@@ -175,10 +167,8 @@
     // value is object
   }
   // go through each rep, do a type check and add missing keys to the rep
-
   let lenMoldata = 0;
   $: lenMoldata = moldata ? moldata.length : 0;
-
   let representations = [];
   //first add all missing keys
   $: {
@@ -203,7 +193,6 @@
       }
     });
   }
-
   $: promise = retrieveContent(value);
 </script>
 
@@ -232,7 +221,7 @@
     <File
       on:select={({ detail }) => gradio.dispatch("select", detail)}
       selectable={_selectable}
-      value={value}
+      {value}
       {label}
       {show_label}
       {height}
@@ -248,7 +237,7 @@
     <FileUpload
       {label}
       {show_label}
-      value={value}
+      {value}
       {file_count}
       {file_types}
       selectable={_selectable}
@@ -325,63 +314,48 @@
     white-space: nowrap;
     border-width: 0;
   }
-
   .mb-4 {
     margin-bottom: 1rem;
   }
-
   .ml-4 {
     margin-left: 1rem;
   }
-
   .mr-3 {
     margin-right: 0.75rem;
   }
-
   .mt-1 {
     margin-top: 0.25rem;
   }
-
   .mt-1\.5 {
     margin-top: 0.375rem;
   }
-
   .mt-\[2px\] {
     margin-top: 2px;
   }
-
   .inline {
     display: inline;
   }
-
   .flex {
     display: flex;
   }
-
   .h-4 {
     height: 1rem;
   }
-
   .w-4 {
     width: 1rem;
   }
-
   .flex-shrink-0 {
     flex-shrink: 0;
   }
-
   .list-inside {
     list-style-position: inside;
   }
-
   .list-disc {
     list-style-type: disc;
   }
-
   .rounded-lg {
     border-radius: 0.5rem;
   }
-
   .bg-red-50 {
     --tw-bg-opacity: 1;
     background-color: rgb(254 242 242 / var(--tw-bg-opacity));
@@ -392,31 +366,25 @@
   .p-4 {
     padding: 1rem;
   }
-
   .text-sm {
     font-size: 0.875rem;
     line-height: 1.25rem;
   }
-
   .font-medium {
     font-weight: 500;
   }
-
   .lowercase {
     text-transform: lowercase;
   }
-
   .text-red-800 {
     --tw-text-opacity: 1;
     color: rgb(153 27 27 / var(--tw-text-opacity));
   }
-
   @media (prefers-color-scheme: dark) {
     .dark\:bg-gray-800 {
       --tw-bg-opacity: 1;
       background-color: rgb(31 41 55 / var(--tw-bg-opacity));
     }
-
     .dark\:text-red-400 {
       --tw-text-opacity: 1;
       color: rgb(248 113 113 / var(--tw-text-opacity));

src/frontend/package.json

@@ -22,4 +22,4 @@
     "./example": "./Example.svelte",
     "./package.json": "./package.json"
   }
-}
+}

src/frontend/shared/FileRetrieval.svelte

@@ -1,33 +1,19 @@
 <script lang="ts">
   import { createEventDispatcher, tick, getContext } from "svelte";
 
-  // import { upload_files as default_upload_files } from "@gradio/client";
-
-  // import { blobToBase64, normalise_file } from "@gradio/upload";
-  import {
-    upload_files,
-    upload,
-    FileData,
-  } from "@gradio/client";
-
+  import { upload_files, upload, FileData } from "@gradio/client";
   import LoadingSpinner from "./loading_spinner.svelte";
   let uploaded_files;
-
   const dispatch = createEventDispatcher();
-
   const upload_fn = getContext<typeof upload_files>("upload_files");
-
   export let root: string;
-
   async function handle_upload(file_data: FileData): Promise<void> {
     await tick();
     const upload_id = Math.random().toString(36).substring(2, 15);
     uploaded_files = await upload([file_data], root, upload_id, upload_fn);
     dispatch("load", uploaded_files[0]);
   }
-
   let loading = false;
-
   async function fetchFromDB(identifier, database): Promise<void> {
     let dbs = {
       pdb_assym: {
@@ -52,39 +38,37 @@
     let url = dbs[database]["url"];
     let ext = dbs[database]["ext"];
     // load the file and save blob
-
     // emulate file upload by fetching from the db and triggering upload
     // check if response status is 200, then return blob
-
     loading = true;
     let file = null;
     try {
-      file = await fetch(url + identifier + ext).then((r) => {
-        loading = false;
-        if (r.status == 200) {
-          return r.blob();
-        } else {
-          dispatch("notfound");
-        }
-      }).then((blob) => {
-        return new File([blob], identifier + ext, { type: "text/plain" });
-      })} catch (error) {
+      file = await fetch(url + identifier + ext)
+        .then((r) => {
+          loading = false;
+          if (r.status == 200) {
+            return r.blob();
+          } else {
+            dispatch("notfound");
+          }
+        })
+        .then((blob) => {
+          return new File([blob], identifier + ".pdb", { type: "text/plain" });
+        });
+    } catch (error) {
       loading = false;
       dispatch("notfound");
     }
-
     let file_data = new FileData({
-				path: identifier + ".pdb",
-				orig_name: identifier + ".pdb",
-				blob: file,
-				size: file.size,
-				mime_type: file.type,
-				is_stream: false,
-			});
-
+      path: identifier + ".pdb",
+      orig_name: identifier + ".pdb",
+      blob: file,
+      size: file.size,
+      mime_type: file.type,
+      is_stream: false,
+    });
     await handle_upload(file_data);
   }
-
   let selectedValue = "pdb_assym";
   let placeholder = "";
   let textInput = "";
@@ -100,7 +84,6 @@
     // text: "Enter molecule in PDB or mol2 format",
   };
   $: placeholder = placeholders[selectedValue];
-
   function isEnterPressed(event) {
     if (event.key === "Enter") {
       fetchFromDB(textInput, selectedValue);
@@ -173,7 +156,6 @@
   .mt-2 {
     margin-top: 2rem;
   }
-
   .input {
     box-shadow: var(--input-shadow);
     background: var(--input-background-fill);

src/frontend/shared/FileUpload.svelte

@@ -34,10 +34,12 @@
     await tick();
     dispatch("change", value);
     dispatch("upload", detail);
+    console.log("upload", detail);
   }
 
   function handle_clear(): void {
     value = null;
+    moldata = null;
     dispatch("change", null);
     dispatch("clear");
   }

src/frontend/shared/MolecularViewer.svelte

@@ -2,7 +2,7 @@
   import * as mol from "3dmol/build/3Dmol.js";
   let TDmol = mol.default;
 
-  import { onMount } from "svelte";
+  import { onMount, onDestroy } from "svelte";
 
   // import RepresentationsIcon from "../static/RepresentationsIcon.svelte";
   // import JSZip from "jszip";
@@ -179,17 +179,8 @@
     }
   }
 
-  // function downloadFiles() {
-  //   var zip = new JSZip();
-  //   moldata.forEach((element, i) => {
-  //     zip.file(element.name + "_" + i + "." + element.format, element.data);
-  //   });
-  //   zip.generateAsync({ type: "blob" }).then(function (content) {
-  //     saveAs(content, "files.zip");
-  //   });
-  // }
-
   onMount(() => {
+    console.log("MolecularViewer Mounted");
     let startingConfig = { ...config, cartoonQuality: 7 };
 
     view = TDmol.createViewer(viewer, startingConfig);
@@ -215,7 +206,7 @@
       }
     });
     representations = uniqueReps;
-
+    console.log(moldata);
     if (moldata.length > 0) {
       moldata.forEach((element) => {
         if (element.asFrames) {
@@ -313,29 +304,6 @@
 <div class="bg-white w-full minh">
   <div class="overflow-hidden flex gap-px w-full h-full flex-wrap">
     <div class="gr-block gr-box relative w-full overflow-hidden">
-      <!-- <div
-        style="  "
-        class="absolute z-50 top-0 left-0 bg-white rounded-br border-b border-r border-gray-200 p-1"
-      >
-        <span class=" flex items-center space-x-1 text-xs text-gray-500"
-          ><svg
-            xmlns="http://www.w3.org/2000/svg"
-            width="100%"
-            height="100%"
-            viewBox="0 0 24 24"
-            fill="none"
-            stroke="currentColor"
-            stroke-width="1.5"
-            stroke-linecap="round"
-            stroke-linejoin="round"
-            class="feather feather-file h-3 w-3"
-            ><path
-              d="M13 2H6a2 2 0 0 0-2 2v16a2 2 0 0 0 2 2h12a2 2 0 0 0 2-2V9z"
-            /><polyline points="13 2 13 9 20 9" /></svg
-          > <span>Molecule3D</span>
-        </span>
-      </div> -->
-
       <div
         class="absolute z-50 top-0 right-0 mr-2 flex flex-col divide-y border border-gray-200 mt-2 rounded items-center justify-center bg-white dark:bg-gray-800"
       >

src/pyproject.toml

@@ -9,7 +9,7 @@ build-backend = "hatchling.build"
 [project]
 name = "gradio_molecule3d"
 version = "0.0.3"
-description = "Molecule3D custom component to visualize pdb or sdf files"
+description = "Molecule3D custom component to visualize pdb or sdf files using 3Dmol.js"
 readme = "README.md"
 license = "MIT"
 requires-python = ">=3.8"
@@ -24,7 +24,7 @@ keywords = [
   "protein"
 ]
 # Add dependencies here
-dependencies = ["gradio>=4.21.0,<5.0"]
+dependencies = ["gradio>=4.0,<5.0"]
 classifiers = [
   'Development Status :: 3 - Alpha',
   'License :: OSI Approved :: Apache Software License',
@@ -44,7 +44,7 @@ classifiers = [
 dev = ["build", "twine"]
 
 [tool.hatch.build]
-artifacts = ["/backend/gradio_molecule3d/templates", "*.pyi", "backend/gradio_molecule3d/templates", "backend/gradio_molecule3d/templates", "backend/gradio_molecule3d/templates", "backend/gradio_molecule3d/templates"]
+artifacts = ["/backend/gradio_molecule3d/templates", "*.pyi", "backend/gradio_molecule3d/templates", "backend/gradio_molecule3d/templates", "backend/gradio_molecule3d/templates", "backend/gradio_molecule3d/templates", "backend/gradio_molecule3d/templates"]
 
 [tool.hatch.build.targets.wheel]
 packages = ["/backend/gradio_molecule3d"]