st-oxview 1.0.0

A Streamlit component for coarse-grained DNA/RNA visualization with OxView

Streamlit Oxview Component

A Streamlit component for the display of coarse-grained DNA/RNA 3D models. It is a wrapper around the oxdna-viewer. The colormap is always disabled.

Installation

This component requires access to write files to the temporary directory.

pip install st_oxview

Example

Look at the example for a streamlit Web App:

Usage

Display with drag and drop

You can make a empty oxview fram and drag and drop the files to the frame.

import streamlit as st
from st_oxview import oxview_from_file

success = oxview_from_file()

Just drag and drop the files to the frame.

Display from file paths

import streamlit as st
from st_oxview import oxview_from_file

success = oxview_from_file(configuration=path_to_conf, # path to the configuration file
                           topology=path_to_topo,      # path to the topology file
                           forces=None,                # path to the forces file
                           pdb=None,                   # path to the pdb file
                           js_script=None,             # path to the javascript script file
                           colormap=None,              # name of the Matplotlib colormap
                           index_colors=None,          # A color for each index according to the colormap (list of values between 0 and 1)
                           frame_id=None,                 # ID of the oxView frame: if a frame ID is set, it will be reused instead of creating a new frame
                           width='99%',                # width of the viewer frame
                           height='500',               # height of the viewer frame
                           key=None)                   # streamlit component key

Display from text

import streamlit as st
from st_oxview import oxview_from_text

with open("configuration.dat", "r") as f:
    conf_text = f.read()

with open("topology.top", "r") as f:
    topo_text = f.read()

success = oxview_from_file(configuration=conf_text, # text of the configuration file
                           topology=topo_text,      # text of the topology file
                           forces=None,             # text of the forces file
                           pdb=None,                # text of the pdb file
                           js_script=None,          # text of the javascript script file
                           colormap=None,           # name of the Matplotlib colormap
                           index_colors=None,       # A color for each index according to the colormap (list of values between 0 and 1)
                           width='99%',             # width of the viewer frame
                           height='500',            # height of the viewer frame
                           key=None)                # streamlit component key

The functions return a boolean value indicating if the program was able to write and read the files.

Display from an OxView JSON file

You can load a saved OxView scene directly from a .oxview file with oxview_from_json.

From a local .oxview file

import streamlit as st
from st_oxview import oxview_from_json

with open("scene.oxview", "r", encoding="utf-8") as f:
    scene_text = f.read()

success = oxview_from_json(scene_data=scene_text,  # text content of the .oxview file
                           frame_id=None,          # if None, the component creates a new frame
                           width='99%',            # width of the viewer frame
                           height=500,             # height of the viewer frame
                           key='oxview_json')      # streamlit component key

From a Streamlit file uploader

import streamlit as st
from st_oxview import oxview_from_json

json_file = st.file_uploader("Upload an OxView file", type=["oxview"])

if json_file is not None:
    success = oxview_from_json(scene_data=json_file.getvalue(),  # uploaded file content
                               frame_id=None,
                               width='99%',
                               height=500,
                               key='oxview_json_upload')

Scene_data can be provided as:

• a Python dict
• a JSON str
• the bytes returned by st.file_uploader(...).getvalue()

The function returns a boolean value indicating whether the scene was successfully processed and displayed.

How to cite:

Please include this citation if the OxView Component is used in an academic study:

Lucandia. Lucandia/st_oxview; Zenodo, 2024. https://zenodo.org/doi/10.5281/zenodo.12515559.

License

Code is licensed under the GNU General Public License v3.0 (GPL-3.0)