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MolCraftDiffusion
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Getting Started

  • Installation
  • Model Architectures

Tutorials

  • Tutorials
    • Tutorial 0: Data Preparation & Management
    • Tutorial 1: Training a Diffusion Model
    • Tutorial 2: Training a Regressor Model
    • Tutorial 3: Training a Time-Aware Guidance Model
    • Tutorial 4: Fine-Tuning a Diffusion Model
    • Tutorial 5: Molecule Generation Overview
    • Tutorial 6: Structure-Guided Generation
    • Tutorial 7: Property-Directed Generation
    • Tutorial 8: Prediction and Evaluation Modes
    • Tutorial 9: Analyze Module - 3D Molecular Structure Analysis
    • Tutorial 10: Generation Parameter Sweeps

Applications

  • Applications
    • Application: Local Chemical Space Exploration
    • Application: Library Design with Structure-Directed Generation
    • Application: Inverse Design
  • Application: Local Chemical Space Exploration
  • Application: Library Design with Structure-Directed Generation
  • Application: Inverse Design

Workflows

  • Workflows
    • Workflow Example: Generate and Filter
    • Workflow Example: Transfer Learning and Generate
    • Workflow Example: Conditioned Generation
    • Workflow Example: End-to-End Design Loop
    • Workflow: Visualize the Generated Chemical Space
  • Workflow Example: Generate and Filter
  • Workflow Example: Transfer Learning and Generate
  • Workflow Example: Conditioned Generation
  • Workflow Example: End-to-End Design Loop
  • Workflow: Visualize the Generated Chemical Space

Configuration Templates

  • Configuration Templates

API Reference

  • API Reference
    • MolecularDiffusion
      • MolecularDiffusion.callbacks
        • MolecularDiffusion.callbacks.train_helper
      • MolecularDiffusion.cli
        • MolecularDiffusion.cli.analyze
        • MolecularDiffusion.cli.data
        • MolecularDiffusion.cli.eval_predict
        • MolecularDiffusion.cli.generate
        • MolecularDiffusion.cli.main
        • MolecularDiffusion.cli.predict
        • MolecularDiffusion.cli.train
      • MolecularDiffusion.core
        • MolecularDiffusion.core.core
        • MolecularDiffusion.core.engine
        • MolecularDiffusion.core.engine_lightning
        • MolecularDiffusion.core.lightning_callbacks
          • MolecularDiffusion.core.lightning_callbacks.ema_callback
          • MolecularDiffusion.core.lightning_callbacks.generative_eval_callback
        • MolecularDiffusion.core.logger
        • MolecularDiffusion.core.meter
      • MolecularDiffusion.data
        • MolecularDiffusion.data.component
          • MolecularDiffusion.data.component.dataset
          • MolecularDiffusion.data.component.feature
          • MolecularDiffusion.data.component.pharmacophore
          • MolecularDiffusion.data.component.pointcloud
        • MolecularDiffusion.data.dataloader
        • MolecularDiffusion.data.dataset
        • MolecularDiffusion.data.lightning_data_module
        • MolecularDiffusion.data.valency_tables
      • MolecularDiffusion.molcraftdiff
      • MolecularDiffusion.optional
      • MolecularDiffusion.runmodes
        • MolecularDiffusion.runmodes.analyze
          • MolecularDiffusion.runmodes.analyze.compare_to_optimized
          • MolecularDiffusion.runmodes.analyze.compute_metrics
          • MolecularDiffusion.runmodes.analyze.featurize
          • MolecularDiffusion.runmodes.analyze.ssl3d_embed
          • MolecularDiffusion.runmodes.analyze.uma_embeddings
          • MolecularDiffusion.runmodes.analyze.xtb_electronic
          • MolecularDiffusion.runmodes.analyze.xtb_optimization
          • MolecularDiffusion.runmodes.analyze.xyz2mol
        • MolecularDiffusion.runmodes.generate
          • MolecularDiffusion.runmodes.generate.sweep
          • MolecularDiffusion.runmodes.generate.tasks_generate
        • MolecularDiffusion.runmodes.train
          • MolecularDiffusion.runmodes.train.data
          • MolecularDiffusion.runmodes.train.eval
          • MolecularDiffusion.runmodes.train.logger
          • MolecularDiffusion.runmodes.train.tasks_egcl
          • MolecularDiffusion.runmodes.train.tasks_egt
          • MolecularDiffusion.runmodes.train.tasks_equiformer
          • MolecularDiffusion.runmodes.train.tasks_esen
          • MolecularDiffusion.runmodes.train.tasks_gfmdiff
          • MolecularDiffusion.runmodes.train.trainer
      • MolecularDiffusion.utils
        • MolecularDiffusion.utils.comm
        • MolecularDiffusion.utils.diffusion_utils
        • MolecularDiffusion.utils.file
        • MolecularDiffusion.utils.geom_analyzer
        • MolecularDiffusion.utils.geom_constant
        • MolecularDiffusion.utils.geom_constraint
        • MolecularDiffusion.utils.geom_metrics
        • MolecularDiffusion.utils.geom_stability
        • MolecularDiffusion.utils.geom_utils
        • MolecularDiffusion.utils.io
        • MolecularDiffusion.utils.molgraph_utils
        • MolecularDiffusion.utils.plot_function
        • MolecularDiffusion.utils.pretty
        • MolecularDiffusion.utils.sascore
        • MolecularDiffusion.utils.shepherd_score
          • MolecularDiffusion.utils.shepherd_score.alignment
            • MolecularDiffusion.utils.shepherd_score.alignment.utils
              • MolecularDiffusion.utils.shepherd_score.alignment.utils.pca
              • MolecularDiffusion.utils.shepherd_score.alignment.utils.pca_np
              • MolecularDiffusion.utils.shepherd_score.alignment.utils.se3
              • MolecularDiffusion.utils.shepherd_score.alignment.utils.se3_np
          • MolecularDiffusion.utils.shepherd_score.extract_profiles
          • MolecularDiffusion.utils.shepherd_score.generate_point_cloud
          • MolecularDiffusion.utils.shepherd_score.pharm_utils
            • MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmacophore
            • MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec
          • MolecularDiffusion.utils.shepherd_score.score
            • MolecularDiffusion.utils.shepherd_score.score.analytical_gradients
            • MolecularDiffusion.utils.shepherd_score.score.constants
            • MolecularDiffusion.utils.shepherd_score.score.electrostatic_scoring
            • MolecularDiffusion.utils.shepherd_score.score.electrostatic_scoring_np
            • MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap
            • MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap_np
            • MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring
            • MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring_np
        • MolecularDiffusion.utils.shepherd_utils
        • MolecularDiffusion.utils.smilify
        • MolecularDiffusion.utils.substituent_builder
        • MolecularDiffusion.utils.substituent_geometries
        • MolecularDiffusion.utils.torch
        • MolecularDiffusion.utils.xyz2mol
          • MolecularDiffusion.utils.xyz2mol.converter
          • MolecularDiffusion.utils.xyz2mol.elements
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MolecularDiffusion.modules.models.geoldm¶

GeoLDM model code, ported from the GeoLDM repo (E(n)-equivariant hierarchical-VAE + latent diffusion). See docs/model_integrations/geoldm/INTEGRATION_PLAN.md for the integration plan this package implements.

Submodules¶

  • MolecularDiffusion.modules.models.geoldm.diffusion
  • MolecularDiffusion.modules.models.geoldm.egnn
  • MolecularDiffusion.modules.models.geoldm.networks
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