gradio-molecule3d 0.0.5

Molecule3D custom component to visualize pdb or sdf files using 3Dmol.js

gradio_molecule3d

Molecule3D custom component to visualize pdb or sdf files using 3Dmol.js

Installation

pip install gradio_molecule3d

Usage

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:
    gr.Markdown("# Molecule3D")
    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

name	type	default	description
value	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	Any | None	[]	None
config	Any | None	{ "backgroundColor": "white", "orthographic": False, "disableFog": False, }	dictionary of config options
confidenceLabel	str | None	"pLDDT"	label for confidence values stored in the bfactor column of a pdb file
file_count	"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	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	"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	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	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	bool | None	None	if True, will display label.
container	bool	True	If True, will place the component in a container - providing some extra padding around the border.
scale	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	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	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	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	bool	True	If False, component will be hidden.
elem_id	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	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	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	bool	True	If True, will display the 3Dmol.js viewer. If False, will not display the 3Dmol.js viewer.

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.

def predict(
    value: bytes
   | gradio.utils.NamedString
   | list[bytes | gradio.utils.NamedString]
   | None
) -> str | list[str] | None:
    return value