`gradio_molecule3d`

Python library for easily interacting with trained machine learning models

Molecule3D

{}

You can configure the default rendering of the molecule by adding a list of representations

    reps =    [
    {
      "model": 0,
      "style": "cartoon",
      "color": "whiteCarbon",
      "residue_range": "",
      "around": 0,
      "opacity":1
      
    },
    {
      "model": 0,
      "chain": "A",
      "resname": "HIS",
      "style": "stick",
      "color": "red"
    }
  ]

Installation

pip install gradio_molecule3d

Usage


import gradio as gr
from gradio_molecule3d import Molecule3D


example = Molecule3D().example_value()


reps =    [
    {
      "model": 0,
      "chain": "",
      "resname": "",
      "style": "cartoon",
      "color": "hydrophobicity",
      # "residue_range": "",
      "around": 0,
      "byres": False,
      # "visible": False,
      # "opacity": 0.5
    }
  ]



def predict(x):
    print("predict function", x)
    print(x.name)
    return x

# def update_color(mol, color):
#     reps[0]['color'] = color
#     print(reps)
#     return Molecule3D(mol, reps=reps)

with gr.Blocks() as demo:
    gr.Markdown("# Molecule3D")
    # color_choices = ['redCarbon', 'greenCarbon', 'orangeCarbon', 'blackCarbon', 'blueCarbon', 'grayCarbon', 'cyanCarbon']

    inp = Molecule3D(label="Molecule3D", reps=reps)
    # cdr_color = gr.Dropdown(choices=color_choices, label="CDR color", value='redCarbon')
    out = Molecule3D(label="Output", reps=reps)
    # cdr_color.change(update_color, inputs=[inp,cdr_color], outputs=out)
    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,
          "style": "cartoon",
          "color": "whiteCarbon",
          "residue_range": "",
          "around": 0,
          "opacity":1
          
        },
        {
          "model": 0,
          "chain": "A",
          "resname": "HIS",
          "style": "stick",
          "color": "red"
        }
      ]
    </pre>
    """)
    btn.click(predict, inputs=inp, outputs=out)


if __name__ == "__main__":
    demo.launch()

`Molecule3D`

Initialization

value: str | list[str] | Callable | None

default = None

Default file(s) to display, given as a str file path or URL, or a list of str file paths / URLs. If callable, the function will be called whenever the app loads to set the initial value of the component.

reps: Any | None

default = []

config: Any | None

default

= {
    "backgroundColor": "white",
    "orthographic": False,
    "disableFog": False,
}

dictionary of config options

confidenceLabel: str | None

default = "pLDDT"

label for confidence values stored in the bfactor column of a pdb file

file_count: Literal["single", "multiple", "directory"]

default = "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

default = 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: Literal["filepath", "binary"]

default = "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

default = 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: Timer | float | None

default = None

Continously calls `value` to recalculate it if `value` is a function (has no effect otherwise). Can provide a Timer whose tick resets `value`, or a float that provides the regular interval for the reset Timer.

inputs: Component | Sequence[Component] | set[Component] | None

default = None

Components that are used as inputs to calculate `value` if `value` is a function (has no effect otherwise). `value` is recalculated any time the inputs change.

show_label: bool | None

default = None

if True, will display label.

container: bool

default = True

If True, will place the component in a container - providing some extra padding around the border.

scale: int | None

default = None

relative size compared to adjacent Components. For example if Components A and B are in a Row, and A has scale=2, and B has scale=1, A will be twice as wide as B. Should be an integer. scale applies in Rows, and to top-level Components in Blocks where fill_height=True.

min_width: int

default = 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

default = None

The maximum height of the file component, specified in pixels if a number is passed, or in CSS units if a string is passed. If more files are uploaded than can fit in the height, a scrollbar will appear.

interactive: bool | None

default = 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

default = True

If False, component will be hidden.

elem_id: str | None

default = 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

default = 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

default = 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.

key: int | str | None

default = None

if assigned, will be used to assume identity across a re-render. Components that have the same key across a re-render will have their value preserved.

showviewer: bool

default = True

If True, will display the 3Dmol.js viewer. If False, will not display the 3Dmol.js viewer.

Events

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 clear button for the component.

upload

This listener is triggered when the user uploads a file into the Molecule3D.

delete

This listener is triggered when the user deletes and item from the Molecule3D. Uses event data gradio.DeletedFileData to carry `value` referring to the file that was deleted as an instance of FileData. See EventData documentation on how to use this event data

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, passes the file as a str or bytes object, or a list of str or list of bytes objects, depending on type and file_count.
As output: Should return, expects a str filepath or URL, or a list[str] of filepaths/URLs.

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