molecular_simulations.build package

molecular_simulations.build.add_chains(pdb, first_res=1, last_res=-1)

Helper function to add chain IDs to a model.

Return type:

Union[Path, str]

Parameters:

• pdb (Path | str)

• first_res (int)

• last_res (int)

molecular_simulations.build.convert_cif_with_biopython(cif)

Helper function to convert a cif file to a pdb file using biopython.

Return type:

Union[Path, str]

Parameters:

cif (Path | str)

molecular_simulations.build.convert_cif_with_gemmi(cif)

Return type:

Union[Path, str]

Parameters:

cif (Path | str)

Submodules

• molecular_simulations.build.build_amber module
  • ExplicitSolvent
    • ExplicitSolvent.assemble_system()
    • ExplicitSolvent.build()
    • ExplicitSolvent.clean_up_directory()
    • ExplicitSolvent.get_ion_numbers()
    • ExplicitSolvent.get_pdb_extent()
    • ExplicitSolvent.prep_pdb()
  • ImplicitSolvent
    • ImplicitSolvent.build()
    • ImplicitSolvent.pdbfix_it()
    • ImplicitSolvent.temp_tleap()
    • ImplicitSolvent.tleap_it()
    • ImplicitSolvent.write_leap()
• molecular_simulations.build.build_interface module
  • InterfaceBuilder
    • InterfaceBuilder.build_all()
    • InterfaceBuilder.merge_proteins()
    • InterfaceBuilder.parse_interface()
    • InterfaceBuilder.place_binder()
    • InterfaceBuilder.write_cvae_yaml()
    • InterfaceBuilder.write_ddmd_yaml()
• molecular_simulations.build.build_ligand module
  • ComplexBuilder
    • ComplexBuilder.add_ion_to_pdb()
    • ComplexBuilder.assemble_system()
    • ComplexBuilder.build()
    • ComplexBuilder.process_ligand()
  • LigandBuilder
    • LigandBuilder.check_sqm()
    • LigandBuilder.convert_to_mol2()
    • LigandBuilder.move_antechamber_outputs()
    • LigandBuilder.parameterize_ligand()
    • LigandBuilder.process_pdb()
    • LigandBuilder.process_sdf()
    • LigandBuilder.write_leap()
  • LigandError
  • PLINDERBuilder
    • PLINDERBuilder.anion_list
    • PLINDERBuilder.assemble_system()
    • PLINDERBuilder.build()
    • PLINDERBuilder.cation_list
    • PLINDERBuilder.check_ligand()
    • PLINDERBuilder.check_ptms()
    • PLINDERBuilder.inject_fasta()
    • PLINDERBuilder.ligand_handler()
    • PLINDERBuilder.migrate_files()
    • PLINDERBuilder.place_ions()
    • PLINDERBuilder.prep_protein()
    • PLINDERBuilder.triage_pdb()