# `gradio_molecule3d` Molecule3D custom component to visualize pdb or sdf files using 3Dmol.js ## 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
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, } ]""") btn.click(predict, inputs=inp, outputs=out) if __name__ == '__main__': demo.launch() ``` ## `Molecule3D` ### Initialization
name | type | default | description |
---|---|---|---|
value |
```python str | list[str] | Callable | None ``` | None |
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 |
```python Any | None ``` | [] |
None |
config |
```python Any | None ``` | {
"backgroundColor": "white",
"orthographic": False,
"disableFog": False,
} |
dictionary of config options |
confidenceLabel |
```python str | None ``` | "pLDDT" |
label for confidence values stored in the bfactor column of a pdb file |
file_count |
```python "single" | "multiple" | "directory" ``` | "single" |
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 |
```python list[str] | None ``` | None |
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 |
```python "filepath" | "binary" ``` | "filepath" |
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 |
```python str | None ``` | None |
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 |
```python float | None ``` | None |
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 |
```python bool | None ``` | None |
if True, will display label. |
container |
```python bool ``` | True |
If True, will place the component in a container - providing some extra padding around the border. |
scale |
```python int | None ``` | None |
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 |
```python int ``` | 160 |
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 |
```python int | float | None ``` | None |
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 |
```python bool | None ``` | None |
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 |
```python bool ``` | True |
If False, component will be hidden. |
elem_id |
```python str | None ``` | None |
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 |
```python list[str] | str | None ``` | None |
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 |
```python bool ``` | True |
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 |
```python bool ``` | True |
If True, will display the 3Dmol.js viewer. If False, will not display the 3Dmol.js viewer. |