Skip to content

Latest commit

 

History

History
36 lines (25 loc) · 1.89 KB

README.md

File metadata and controls

36 lines (25 loc) · 1.89 KB
Raw

FL_ChemTS

De novo fluorescent molecule generator based on ChemTS (https://github.com/tsudalab/ChemTS) and quantum chemical calculation.
This program includes an extented version of ChemTS that is parallelizaed by MPI and a filter for Gaussian (https://gaussian.com) to compute absorption and fluorescence wavelength of a molecule. The Gaussian filter automatically computes the optimized singlet ground (S0) state, vertical singlet excited (S1) state, and relaxed S1 state of a molecule at the density functional theory level.

Requirements

  1. Gaussian==16
  2. Python>=2.7
  3. Keras (version 2.0.5) If you installed the newest version of keras, some errors will show up. Please change it back to keras 2.0.5 by pip install keras==2.0.5.
  4. RDKit
  5. Intel MPI environment

Usage

The main python script is fl_chemts/mpi_thread_chemts_tree_vl.py.

Paralleled search is performed based on Intel MPI environment using fl_chemts/job_sub.sh.

  1. cd fl_chemts
  2. qsub job_sub

Please setup your MPI and python environment, in fl_chemts/job_sub.sh.

Dataset

We used 153,253 molecules that contain only H, O, N, and C elements obtained from the ZINC database for trainig of the RNN network. The file (250k_rndm_zinc_drugs_clean_std_woSsP+-.smi) is located at FL_ChemTS/data/.

Trained RNN network

We trained a RNN network using the above SMILES dataset. The trained network files are located at FL_ChemTS/RNN_model/.

Generated molecules

The generated 3,643 molecules are listed in the FL_ChemTS/generated_mols/result.csv file. The file contains following information: generated molecules (SMILES), calculated absorption and fluorescence wavelengths and their oscillator strengths, and basic information such as molecular weight.

License

This package is distributed under the MIT License.