gtsr 0.0.1

Graph neural network tool for solvent removal from MOF structures

GTsR

GTsR (GNN Tool for Solvent Removal) is a tool for solvent identification, solvent removal, and activation-stability prediction in metal-organic frameworks (MOFs).

GTsR uses graph neural networks to classify atoms in CIF structures and generate solvent-free framework CIF files. It also provides a random forest model that predicts the activation stability of cleaned MOFs using structural, pore, and RAC descriptors.

Models

checkpoint	Model file	Purpose
free (default)	ckpt/free_best.pth	Remove free solvent
all	ckpt/all_best.pth	Remove all solvent
stability	ckpt/stability_best.pkl	Predict activation stability

The free and all checkpoints are atom-level GNN classifiers. The stability checkpoint is a random forest model bundled with its missing-value imputer.

Installation

git clone https://github.com/coollkr/GTsR.git
cd GTsR
pip install -e .

Usage

Solvent Removal

from gtsr import GTsRunner

runner = GTsRunner(checkpoint="free") ### for free solvent removal
runner = GTsRunner(checkpoint="all") ### for all solvent removal
runner = GTsRunner(checkpoint="path/to/ckpt.pth", device="cpu") #### use your model
result = runner.clean(
    cif="input.cif",
    output="prediction",
    threshold=0.5,
)

clean() Result

clean() returns a dictionary containing the following fields:

Field	Description
input	Absolute path to the input CIF
output	Output directory
framework	Path to the cleaned framework CIF
solvent	Path to the solvent CIF, or None if no file was generated
checkpoint	Path to the checkpoint used for prediction
task	Task name stored in the checkpoint
threshold	Atom-classification threshold
num_atoms	Total number of atoms
num_framework_atoms	Number of framework atoms
num_solvent_atoms	Number of solvent atoms
probabilities	Solvent probability for each atom
labels	Predicted class label for each atom
solvent_smiles	SMILES strings of identified solvents

Predict Activation Stability

from gtsr import GTsRunner

runner = GTsRunner(checkpoint="stability")
score = runner.stability(cif="cleaned_framework.cif")

if score == 1:
    print("The cleaned structure is stable.")
else:
    print("The cleaned structure is not stable.")

Web Interface

Host on Streamlit or in your location

streamlit run webapp/Home.py

Citation

Update the following entry when the associated publication becomes available:

@article{gtsr-xyl-group,
  title   = {GTSR: A GNN Based Tool for Solvent Removal from MOF with Stability Check},
  author  = {Liang, Kairui and Zhao, Guobin and Li, Xiao-Yan},
  year    = {2026}
}

License

The repository's LICENSE file currently uses the MIT License.