Code for Lingo3DMol

Lingo3DMol is a pocket-based 3D molecule generation method that combines the ability of language model with the ability to generate 3D coordinates and geometric deep learning to produce high-quality molecules.System RequirementsHardware requirementsA standard computer with GPU with at least 5GB graphic memory.OS RequirementsThis package is supported for macOS and Linux. The package has been tested on the following systems: Linux: Ubuntu 16.04 macOS: Ventura (13.0)Install via conda yaml fileTypical install time: 40 minutesconda create -n lingo3dmol python=3.8conda activate lingo3dmolconda install pytorch==1.10.1 torchvision==0.11.2 torchaudio==0.10.1 cudatoolkit=11.3 -c pytorch -c conda-forgepip install scipy==1.7.3 pandas==1.5.1 numpy==1.20.3 rdkit==2022.09.1DatasetsWe provide DUD-E pocket files for sampling under \dataset folder. Please Unzipdude_pocket.zip.Model CheckpointsDownload and move these checkpoint to the \checkpoint folder.https://stonewise-lingo3dmol-public.s3.cn-northwest-1.amazonaws.com.cn/contact.pkl md5sum:6a9313726141fcf9201b9b9470dc2a7ehttps://stonewise-lingo3dmol-public.s3.cn-northwest-1.amazonaws.com.cn/gen_mol.pkl md5sum:452bd401667184ae43c9818e5bdb133bSamplingTo inference using the model on DUD-E set, run this code:sh run.shExpected outputThe output should be generated molecules in mol format.Main Parameters Help--coc_dis Define the collision distance with the pocket (A)--nci_thrs Define the threshold of the nci prediction model--topk Select top k nci--max_run_hours Define the max run hours--gennums Define the minimum generation numbers--USE_THRESHOLD Define sampled only categories larger than expectation--isMultiSample Define sampled use multinomial--isGuideSample frag-based sampled use this definition--OnceMolGen no frag-based sample--gen_frag_set Define the number of collections generated, from which the top twenty percent is selected (batch size)--prod_time "go_factory()" func repeat time--tempture "proj1" used Tsoftmax--frag_len_add Defines the minimum length of each generated fragment/ bigger fragments faster generatedLicenseThis program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.</p