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Description:

molviewspec 1.0.0

MolViewSpec
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*.
The Idea behind MolViewSpec
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 MolViewSpec
generic state description as .msvj
open 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 format
open only in Mol*

See the MolViewSpec in Action
Colab Notebook: https://colab.research.google.com/drive/1O2TldXlS01s-YgkD9gy87vWsfCBTYuz9
Access Type Definitions
All type definitions can be found here:

using a dedicated Server endpoint: http://localhost:9000/api/v1/utils/models/openapi.json
in Markdown: https://molstar.org/mol-view-spec-docs/tree-schema/

Description of the MolViewSpec State Tree
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.
The Tree Root
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"
}
}

The root Node
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": []
}

The download Node
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 parse Node
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"
}
}

The structure Node
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"
}
}

The component Node
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 Node
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"
}
}

Expanding the Tree
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.
Development
Install from PyPI
pip install molviewspec

Find the package at: https://pypi.org/project/molviewspec/
Setting up the environment
mamba env create -f ./environment.yaml
conda activate mol-view-spec-dev

Running the server
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

Formatting the Project
make format
make mypy

Publishing the Python Library

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

Mol* Extension
MolViewSpec is supported in Mol* via an official extension.