This is a Pytorch version of Keras/Tensorflow model training code in https://github.com/SINGROUP/ASD-AFM. The original training procedure is not reproduced exactly, so some differences in the training outcomes may be expected.
Paper: B. Alldritt et. al, Automated structure discovery in atomic force microscopy, Sci. Adv., 2020.
Scripts:
generate_data.py: Download molecule dataset and generate a dataset of AFM images and image descriptors.train.py: Train and test a model using the generated AFM image dataset.run_train.sh: Run the training script with preset parameters.predict_1S-camphor.py: Run prediction for experimental AFM images of 1S-camphor using a pretrained model.
Data:
- https://doi.org/10.5281/zenodo.10562769
afm_camphor.tar.gz: Experimental AFM images of 1S-camphor on Cu(111)molecules.tar.gz: Two datasets of molecules (lightandheavy) with point-charges.
- https://doi.org/10.5281/zenodo.10514470: Pretrained weights for the structure prediction model, one set of weights for each of the molecule datasets (
lightandheavy).