diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 00000000..ad93c14a --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,5 @@ +{ + "image": "mcr.microsoft.com/devcontainers/universal:2", + "features": { + } +} diff --git a/new-website/utils/tutorials/__pycache__/utils.cpython-310.pyc b/new-website/utils/tutorials/__pycache__/utils.cpython-310.pyc new file mode 100644 index 00000000..7eb6c2a6 Binary files /dev/null and b/new-website/utils/tutorials/__pycache__/utils.cpython-310.pyc differ diff --git a/new-website/utils/tutorials/acknowledgement.html b/new-website/utils/tutorials/acknowledgement.html index 4c82554a..29c15eaa 100644 --- a/new-website/utils/tutorials/acknowledgement.html +++ b/new-website/utils/tutorials/acknowledgement.html @@ -6,16 +6,43 @@ padding-right: 80px; font-size: 50px; } + h2 { + margin-top: 250px; + padding-right: 80px; + font-size: 20px; + } .general { padding-left: 80px; padding-right: 80px; font-size: 20px; } + .citation { + padding-left: 80px; + padding-right: 80px; + font-size: 15px; + }

Acknowledgement

We acknowledge the DeepChem community for their contributions and support.

+

+

Citing This Book:

+
+ @manual{ +
+ title={The DeepChem Book}, +
+ organization={DeepChem}, +
+ author={Ramsundar, Bharath and DeepChem Community}, +
+ howpublished = {\url{https://deepchem.io/tutorials}}, +
+ year={2024}, +
+ } +

\ No newline at end of file diff --git a/new-website/utils/tutorials/acknowledgement.md b/new-website/utils/tutorials/acknowledgement.md index 448e8843..97b93ee7 100644 --- a/new-website/utils/tutorials/acknowledgement.md +++ b/new-website/utils/tutorials/acknowledgement.md @@ -1,2 +1,13 @@ # Acknowledgement -We acknowledge the DeepChem community for their contributions and support. \ No newline at end of file + +We acknowledge the DeepChem community for their contributions and support. + +Citing This Book: + +@manual{ +title={The DeepChem Book}, +organization={DeepChem}, +author={Ramsundar, Bharath and DeepChem Community}, +howpublished = {\url{https://deepchem.io/tutorials}}, +year={2024}, +} diff --git a/new-website/utils/tutorials/build_pdf_book.py b/new-website/utils/tutorials/build_pdf_book.py index e289939f..9913802d 100644 --- a/new-website/utils/tutorials/build_pdf_book.py +++ b/new-website/utils/tutorials/build_pdf_book.py @@ -25,9 +25,9 @@ from typing import List -INFO_PATH = "/workspaces/deepchem.github.io/new-website/utils/tutorials/website-render-order/" -DATA_PATH = "/workspaces/deepchem.github.io/new-website/utils/tutorials/html-notebooks/" -PDF_PATH = "/workspaces/deepchem.github.io/new-website/utils/tutorials/storage/" +INFO_PATH = "./website-render-order/" +DATA_PATH = "./html-notebooks/" +PDF_PATH = "./storage/" files = os.listdir(INFO_PATH) files = sorted(files) @@ -48,7 +48,10 @@ def html_to_pdf(): chapter = pd.read_csv(INFO_PATH + "-".join(i)) for j in chapter["File Name"]: print(i, j) - pdfkit.from_file(DATA_PATH + j[:-5] + "html", PDF_PATH + j[:-5] + "pdf") + try: + pdfkit.from_file(DATA_PATH + j[:-5] + "html", PDF_PATH + j[:-5] + "pdf") + except: + pass def merge_pdf(): """Merges the compiled PDFs.""" diff --git a/new-website/utils/tutorials/contents.html b/new-website/utils/tutorials/contents.html index ffccb884..fc69a2dd 100644 --- a/new-website/utils/tutorials/contents.html +++ b/new-website/utils/tutorials/contents.html @@ -19,7 +19,7 @@

1. Introduction To Deepchem

  • The Basic Tools of the Deep Life Sciences
  • Working With Datasets
  • An Introduction To MoleculeNet
    • -
  • Molecular Fingerprints
    • +
  • Molecular Fingerprints: Representing Molecules for Deep-Learning
  • Creating Models with TensorFlow and PyTorch
  • Introduction to Graph Convolutions
  • Going Deeper on Molecular Featurizations
    • @@ -33,89 +33,85 @@

    1. Introduction To Deepchem

  • Training a Generative Adversarial Network on MNIST
  • Advanced model training using hyperopt
  • Introduction to Gaussian Processes
    • -
  • PytorchLightning Integration
    • +
  • Pytorch Lightning Integration for DeepChem Models
  • -

    2. Molecular Machine Learning

    +

    2. More Molecular Machine Learning

      -
    1. Molecular Fingerprints -
    2. Going Deeper on Molecular Featurizations -
    3. Learning Unsupervised Embeddings for Molecules -
    4. Atomic Contributions for Molecules -
    5. Interactive Model Evaluation with Trident Chemwidgets -
    6. Transfer Learning With ChemBERTa Transformers -
    7. Training a Normalizing Flow on QM9 -
    8. Large Scale Chemical Screens -
    9. Introduction to Molecular Attention Transformer -
    10. Generating molecules with MolGAN -
    11. Introduction to GROVER +
    12. Going Deeper on Molecular Featurizations
      13. +
    13. Learning Unsupervised Embeddings for Molecules
      14. +
    14. Atomic Contributions for Molecules
      15. +
    15. Interactive Model Evaluation with Trident Chemwidgets
      16. +
    16. Transfer Learning With ChemBERTa Transformers
      17. +
    17. Training a Normalizing Flow on QM9
      18. +
    18. Large Scale Chemical Screens
      19. +
    19. Introduction to Molecular Attention Transformer
      20. +
    20. Generating molecules with MolGAN
      21. +
    21. Introduction to GROVER

  • 3. Modeling Proteins

      -
    1. Protein Deep Learning +
    2. Protein Deep Learning

  • 4. Protein Ligand Modeling

      -
    1. Modeling Protein Ligand Interactions -
    2. Modeling Protein Ligand Interactions With Atomic Convolutions -
    3. DeepChemXAlphafold +
    4. Modeling Protein Ligand Interactions
      5. +
    5. Applications of DeepChem with Alphafold: Docking and protein-ligand interaction from protein sequence

  • 5. Quantum Chemistry

      -
    1. Exploring Quantum Chemistry with GDB1k -
    2. DeepQMC tutorial -
    3. Training an Exchange Correlation Functional using Deepchem +
    4. Exploring Quantum Chemistry with GDB1k
      5. +
    5. DeepQMC integration with DeepChem tutorial
      6. +
    6. Training an Exchange Correlation Functional using Deepchem

  • 6. Bioinformatics

      -
    1. Introduction to Bioinformatics -
    2. Multisequence Alignments -
    3. Deep probabilistic analysis of single-cell omics data +
    4. Introduction to Bioinformatics
      5. +
    5. Multisequence Alignments
      6. +
    6. Deep probabilistic analysis of single-cell omics data

  • 7. Material Sciences

      -
    1. Introduction To Material Science +
    2. Introduction To Material Science

  • 8. Machine Learning Methods

      -
    1. Using Reinforcement Learning to Play Pong -
    2. Introduction to Model Interpretability -
    3. Uncertainty In Deep Learning +
    4. Using Reinforcement Learning to Play Pong
      5. +
    5. Introduction to Model Interpretability
      6. +
    6. Uncertainty In Deep Learning

  • 9. Deep Differential Equations

      -
    1. Physics Informed Neural Networks -
    2. Introducing JaxModel and PINNModel -
    3. About Neural ODE : Using Torchdiffeq with Deepchem +
    4. Physics Informed Neural Networks
      5. +
    5. Introducing JaxModel and PINNModel
      6. +
    6. About Neural ODE : Using Torchdiffeq with Deepchem

  • 10. Equivariance

      -
    1. Introduction to Equivariance -
    2. Modeling Protein Ligand Interactions With Atomic Convolutions -
    3. DeepChemXAlphafold +
    4. Introduction to Equivariance

  • 11. Olfaction

      -
    1. Predict Multi Label Odor Descriptors using OpenPOM +
    2. Predict Multi Label Odor Descriptors using OpenPOM
    • diff --git a/new-website/utils/tutorials/contents.md b/new-website/utils/tutorials/contents.md index 8513475f..6a9f8afd 100644 --- a/new-website/utils/tutorials/contents.md +++ b/new-website/utils/tutorials/contents.md @@ -68,4 +68,4 @@ 1. Introduction to Equivariance ### 11. Olfaction -1. Predict Multi Label Odor Descriptors using OpenPOM \ No newline at end of file +1. Predict Multi Label Odor Descriptors using OpenPOM diff --git a/new-website/utils/tutorials/title.html b/new-website/utils/tutorials/title.html index 74910a53..c0d81af9 100644 --- a/new-website/utils/tutorials/title.html +++ b/new-website/utils/tutorials/title.html @@ -21,7 +21,7 @@

    The DeepChem Book

    - Democratizing Deep-Learning for Drug Discovery Quantum Chemistry, Materials Science and Biology + Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

    Bharath Ramsundar