MolViewSpec (*.msvj) is a JSON-based file format that is used to describe visual scenes or views used in molecular visualization. It adopts declarative data-driven approach to describe, load, render, and visually deliver molecular structures, along with 3D representations, coloring schemes, and associated structural, biological, or functional annotations. This Python toolkit allows for describing the information required for representing a molecular view state as data in a nested tree format that can be consumed by visualization software tools such as Mol*.
When using MolViewSpec, please cite:
Sebastian Bittrich, Adam Midlik, Mihaly Varadi, Sameer Velankar, Stephen K. Burley, Jasmine Y. Young, David Sehnal, Brinda Vallat: Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit, Current Protocols, 2024; https://doi.org/10.1002/cpz1.1099.
In the long run, MolViewSpec aims to re-imagine how users define molecular scenes by detaching this process from any concrete 3D viewer.
MolViewSpec's workflow is:
define scene using MolViewSpecgeneric state description as .msvjopen in any MolViewSpec-compatible 3D viewer
Opposed to the traditional workflow that locks users into using a specific 3D viewer, such as:
define scene in Mol*Mol*-specific state formatopen only in Mol*
Colab Notebook: https://colab.research.google.com/drive/1O2TldXlS01s-YgkD9gy87vWsfCBTYuz9
All type definitions can be found here:
- using a dedicated Server endpoint: http://localhost:9000/api/v1/utils/models/openapi.json
- same content as static file: https://molstar.org/mol-view-spec-docs/files/molviewspec-v1-openapi-schema.json
- in Markdown: https://molstar.org/mol-view-spec-docs/tree-schema/
MolViewSpec provides a generic description of typical visual scenes that may occur as part of molecular visualizations. A tree format allows the composition of complex scene descriptors by combining reoccurring nodes that serve as building blocks.
Nodes can be nested to allow chaining of operations as child nodes will be applied to the result of the operation described by its parent node.
The corresponding MolViewSpec tree is provided in JSON and may look like this:
{
"root": {
"kind": "root",
"children": [
{
"kind": "download",
"params": {
"url": "https://files.wwpdb.org/download/1cbs.cif"
},
"children": [
{
"kind": "parse",
"params": {
"format": "mmcif"
},
"children": [
{
"kind": "structure",
"params": {
"type": "model"
},
"children": [
{
"kind": "component",
"params": {
"selector": "all"
},
"children": [
{
"kind": "representation",
"params": {
"type": "cartoon"
}
}
]
}
]
}
]
}
]
}
]
},
"metadata": {
"version": "0.1",
"timestamp": "2023-11-16T11:41:07.421220"
}
}Mol* is the reference implementation for reading MolViewSpec files.
Every tree starts with a single root node, which contains all nodes in a structure fashion, and a metadata node,
which can hold additional information such as a version tag as well as the timestamp when a view was created.
{
"root": {},
"metadata": {
"version": "0.1",
"timestamp": "2023-11-16T11:41:07.421220"
}
}All nodes of the tree must define their kind and may have 0 or more child nodes (children).
The root is a special node with a kind of root that contains a collection of children.
{
"kind": "root",
"children": []
}Node types other than the root may contain an optional params property. A common action is loading of 3D structure
data. This is done using a node of kind download. In this context, params can for example provide the url from
which data will be loaded from.
{
"kind": "download",
"children": [],
"params": {
"url": "https://files.wwpdb.org/download/1cbs.cif"
}
}The previous download operation merely obtains the resources from the specified URL. To make it available to the
viewer, the data must be parsed. This operation expects that the format is defined (in this case mmCIF is parsed).
{
"kind": "parse",
"children": [],
"params": {
"format": "mmcif"
}
}There are different ways to load the content of a mmCIF file. Common actions are loading the 1st biological assembly or
loading the deposited coordinates (also called "asymmetric unit" or "model coordinates").
The action is defined as kind. In this example, the model coordinates are loaded.
{
"kind": "structure",
"children": [],
"params": {
"kind": "model"
}
}At this point, the loaded file is available in the viewer but nothing is visualized yet. Several selection (called
"components") can be created. The example creates a component that includes everything using a selector set to all.
Other options could be a selection for protein chains, nucleic acids, ligands etc.
Components are reusable groups of atoms, residues, or chains, which can be interacted with programmatically.
{
"kind": "component",
"children": [],
"params": {
"selector": "all"
}
}The representation nodes applies to previously created components, which is provided by the parent node of a
representation node. Representations are dedicated visuals that constitute a component. In this example, the selection
from above -- which selects the entire structure -- and depicts it as cartoon by specifying cartoon as type.
{
"kind": "representation",
"params": {
"type": "cartoon"
}
}Nodes can have 0 or more nodes as children. It is, for example, possible to create multiple component nodes based on a
particular structure node to create different representations for different types of molecules.
pip install molviewspecFind the package at: https://pypi.org/project/molviewspec/
micromamba env create -f ./environment.yaml
micromamba activate mol-view-spec-dev
cd molviewspec
python serve.py # or make serve
will run the server on localhost:9000 with reload mode on.
- API Docs:
http://localhost:9000/docs - Example:
http://localhost:9000/api/v1/examples/load?id=1tqn
cd molviewspec
make format
make mypy
- Set version (in https://github.com/molstar/mol-view-spec/blob/master/molviewspec/molviewspec/__init__.py)
- Create a GitHub release
- Tag will automatically publish to PyPI
MolViewSpec is supported in Mol* via an official extension.