OpenPharmacophore
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Examples

  • Examples
    • Ligand-receptor pharmacophore
      • Er-alpha
        • Pharmacophore of the protein-ligand complex of estrogen receptor with estradiol.
        • Obtaining the pharmacophore
      • Human Rhinovirus Serotype
        • Load and visualize protein-ligand complexes
        • Extracting ligands
        • Preparing proteins
        • Obtaining binding sites
        • Extracting pharmacophores
        • Finding a common pharmacophore
    • Ligand-based pharmacophore
      • Ligand preparation for pharmacophore extraction
      • Thrombin ligands for pharmacophore extraction
        • Analyizing chem feats
        • Finding common pharmacophores
        • Visualizing the pharmacophores
    • Dynamic pharmacophore
      • Protein-ligand complex pharmacophore
    • Virtual Screening
      • Virtual Screening with a pharmacophore
    • Others
      • Binding site of a protein-ligand complex
        • PDB 3BBH
        • PDB 1M7W
      • Aromatic interactions
      • Hydrogen bonding in protein-ligand complexes
      • Hydrophobic interactions

API Documentation

  • API Documentation
    • Molecular Systems
      • openpharmacophore.Protein
      • openpharmacophore.Ligand
      • openpharmacophore.ComplexBindingSite
    • Pharmacophores
      • openpharmacophore.PharmacophoricPoint
      • openpharmacophore.Pharmacophore
      • openpharmacophore.LigandBasedPharmacophore
      • openpharmacophore.LigandReceptorPharmacophore
    • Visualization
      • openpharmacophore.Viewer
      • openpharmacophore.draw_ligands
      • openpharmacophore.draw_ligands_chem_feats
    • File IO
      • openpharmacophore.io.pharmacophore_reader.read_mol2
      • openpharmacophore.io.pharmacophore_reader.read_ph4
      • openpharmacophore.io.pharmacophore_reader.read_json
      • openpharmacophore.io.pharmacophore_reader.read_ligandscout
      • openpharmacophore.io.pharmacophore_writer.save_mol2
      • openpharmacophore.io.pharmacophore_writer.save_ph4
      • openpharmacophore.io.pharmacophore_writer.save_json
      • openpharmacophore.io.pharmacophore_writer.save_pml
      • openpharmacophore.io.mol_files.read_mol2
      • openpharmacophore.io.mol_files.mol2_supplier
      • openpharmacophore.io.mol_files.read_sdf
    • Virtual Screening
      • openpharmacophore.VirtualScreening
      • openpharmacophore.screening.mol_db.InMemoryMolDB
      • openpharmacophore.screening.mol_db.MolDB
    • Others
      • openpharmacophore.load
      • openpharmacophore.load_ligands
      • openpharmacophore.smiles_from_pdb_id
OpenPharmacophore
  • Overview: module code

All modules for which code is available

  • openpharmacophore.io.mol_files
  • openpharmacophore.io.pharmacophore_reader
  • openpharmacophore.io.pharmacophore_writer
  • openpharmacophore.load
  • openpharmacophore.molecular_systems.binding_site
  • openpharmacophore.molecular_systems.ligand
  • openpharmacophore.molecular_systems.protein
  • openpharmacophore.pharmacophore.ligand_based.ligand_based
  • openpharmacophore.pharmacophore.ligand_receptor.ligand_receptor
  • openpharmacophore.pharmacophore.pharmacophore
  • openpharmacophore.pharmacophore.pharmacophoric_point
  • openpharmacophore.screening.mol_db
  • openpharmacophore.screening.screening
  • openpharmacophore.visualization.draw
  • openpharmacophore.visualization.view
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© Copyright 2021, UIBCDF Lab at the Mexico City Childrens Hospital Federico Gomez and authors. Project structure based on the Computational Molecular Science Python Cookiecutter version 1.5.

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