Welcome to rdkit_to_params’s documentation!

Contents:

• RDKit-to-Params overview
  • Installation
  • Rationale
  • Website
  • Roundtrip
  • From mol object
    • Requirements
  • From SMILES string
  • From SMILES string and PDB for names
  • Rename
    • DIY
  • Constraints
  • Bond order
  • Amino acids
    • Greek
  • Optionals
  • Terminal caps
  • Caveat: I do not know many things!
    • Chemical
    • Generic
    • Rings and cis-trans
    • Notes
  • To Do
  • Footnote
  • Legal Disclaimer
• Atom Types
• AtomType options
• Database entries
• rdkit_to_params package
  • Subpackages
    • rdkit_to_params.cli package
      • Module contents
    • rdkit_to_params.rdkitside package
      • Submodules
      • rdkit_to_params.rdkitside.utilities module
      • Module contents
  • Module contents
    • Params
      • Params.NAME
      • Params._Measure
      • Params.__init__()
      • Params._add_genrtypes()
      • Params._add_icoor()
      • Params._add_partial_charges()
      • Params._add_partial_charges_OLD()
      • Params._add_rtypes()
      • Params._aminoacid_override()
      • Params._change_conn_for_terminal()
      • Params._find_centroid()
      • Params._fix_atom_names()
      • Params._from_smiles_w_pdb()
      • Params._get_PDBInfo_atomname()
      • Params._get_atom_descriptors()
      • Params._get_measurements()
      • Params._get_nondummy_neighbors()
      • Params._get_resn_from_PDBInfo()
      • Params._get_unseen_neighbors()
      • Params._parse_atom()
      • Params._parse_atoms()
      • Params._parse_bond()
      • Params._parse_bonds()
      • Params._parse_icoors()
      • Params._parse_line()
      • Params._parse_rotatables()
      • Params._parse_w_virtuals()
      • Params._prep_dump_pdb()
      • Params._prep_for_terminal()
      • Params._prevent_overcycling()
      • Params._relax()
      • Params._rename_atom_in_entries()
      • Params._repr_html_()
      • Params._set_PDBInfo_atomname()
      • Params.add_Hs()
      • Params.add_conformer()
      • Params.add_names()
      • Params.add_residuetype()
      • Params.convert_mol()
      • Params.dummyless
      • Params.dump()
      • Params.dump_pdb()
      • Params.dump_pdb_conf()
      • Params.dumps()
      • Params.dumps_pdb()
      • Params.fields
      • Params.fix_mol()
      • Params.from_mol()
      • Params.from_smiles()
      • Params.from_smiles_w_pdbblock()
      • Params.from_smiles_w_pdbfile()
      • Params.get_atom_by_name()
      • Params.get_correct_atomname()
      • Params.greekification
      • Params.greekify()
      • Params.is_aminoacid()
      • Params.load()
      • Params.load_mol()
      • Params.load_smiles()
      • Params.loads()
      • Params.log
      • Params.make_C_terminal_cap()
      • Params.make_N_terminal_cap()
      • Params.move_aside()
      • Params.move_back()
      • Params.nbr
      • Params.ordering
      • Params.pad_name()
      • Params.params_to_pose()
      • Params.polish_mol()
      • Params.rename()
      • Params.rename_atom()
      • Params.rename_atom_by_name()
      • Params.rename_by_substructure()
      • Params.rename_from_dict()
      • Params.rename_from_list()
      • Params.rename_from_str()
      • Params.rename_from_template()
      • Params.rename_repeated_atoms()
      • Params.retype_by_name()
      • Params.split_stereoisomers()
      • Params.test()
      • Params.to_polymeric_pose()
      • Params.to_pose()
      • Params.validate()
  • Submodules
  • rdkit_to_params.constraint module
    • Constraints
      • Constraints.__init__()
      • Constraints._get_conformer()
      • Constraints._get_new_index()
      • Constraints._repr_html_()
      • Constraints.angle_covalent
      • Constraints.angle_target
      • Constraints.assign_names()
      • Constraints.conformer
      • Constraints.dihedral
      • Constraints.distance
      • Constraints.dump()
      • Constraints.dumps()
      • Constraints.get_atom()
      • Constraints.get_conn()
      • Constraints.join_by_dummy()
      • Constraints.make_coordinate_constraints()
      • Constraints.make_inverse_coordinate_constraints_by_neighbours()
      • Constraints.mock()
      • Constraints.nominalise()
      • Constraints.nominalize()
  • rdkit_to_params.entries module
    • AAEntry
      • AAEntry.__init__()
      • AAEntry._repr_html_()
      • AAEntry.from_str()
      • AAEntry.log
    • ACT_COORD_ATOMSEntry
      • ACT_COORD_ATOMSEntry.__init__()
      • ACT_COORD_ATOMSEntry._repr_html_()
      • ACT_COORD_ATOMSEntry.from_str()
    • ADD_RINGEntry
      • ADD_RINGEntry.__init__()
      • ADD_RINGEntry._repr_html_()
      • ADD_RINGEntry.from_str()
      • ADD_RINGEntry.log
    • ATOMEntry
      • ATOMEntry.__init__()
      • ATOMEntry._repr_html_()
      • ATOMEntry.from_str()
      • ATOMEntry.mtype
      • ATOMEntry.name
      • ATOMEntry.partial
      • ATOMEntry.rtype
    • ATOM_ALIASEntry
      • ATOM_ALIASEntry.__init__()
      • ATOM_ALIASEntry._repr_html_()
      • ATOM_ALIASEntry.from_str()
      • ATOM_ALIASEntry.log
    • BACKBONE_AAEntry
      • BACKBONE_AAEntry.__init__()
      • BACKBONE_AAEntry._repr_html_()
      • BACKBONE_AAEntry.from_str()
      • BACKBONE_AAEntry.log
    • BONDEntry
      • BONDEntry.__init__()
      • BONDEntry._repr_html_()
      • BONDEntry.first
      • BONDEntry.from_str()
      • BONDEntry.order
      • BONDEntry.second
    • CHARGEEntry
      • CHARGEEntry.__init__()
      • CHARGEEntry._repr_html_()
      • CHARGEEntry.atom
      • CHARGEEntry.charge
      • CHARGEEntry.from_str()
    • CHIEntry
      • CHIEntry.__init__()
      • CHIEntry._repr_html_()
      • CHIEntry.first
      • CHIEntry.fourth
      • CHIEntry.from_str()
      • CHIEntry.index
      • CHIEntry.second
      • CHIEntry.third
    • CONNECTEntry
      • CONNECTEntry.__init__()
      • CONNECTEntry._repr_html_()
      • CONNECTEntry.atom_name
      • CONNECTEntry.connect_name
      • CONNECTEntry.connect_type
      • CONNECTEntry.from_str()
      • CONNECTEntry.index
    • CUT_BONDEntry
      • CUT_BONDEntry.__init__()
      • CUT_BONDEntry._repr_html_()
      • CUT_BONDEntry.first
      • CUT_BONDEntry.from_str()
      • CUT_BONDEntry.second
    • CommentEntry
      • CommentEntry.__init__()
      • CommentEntry._repr_html_()
      • CommentEntry.from_str()
      • CommentEntry.log
    • Entries
      • Entries.__init__()
      • Entries._abc_impl
      • Entries._assign_value()
      • Entries._repr_html_()
      • Entries.append()
      • Entries.choices
      • Entries.clear()
      • Entries.count()
      • Entries.extend()
      • Entries.from_name()
      • Entries.index()
      • Entries.insert()
      • Entries.pop()
      • Entries.remove()
      • Entries.reverse()
    • FIRST_SIDECHAIN_ATOMEntry
      • FIRST_SIDECHAIN_ATOMEntry.__init__()
      • FIRST_SIDECHAIN_ATOMEntry._repr_html_()
      • FIRST_SIDECHAIN_ATOMEntry.from_str()
      • FIRST_SIDECHAIN_ATOMEntry.log
    • GenericEntry
      • GenericEntry.__init__()
      • GenericEntry._repr_html_()
      • GenericEntry.from_str()
      • GenericEntry.log
    • GenericListEntry
      • GenericListEntry.__init__()
      • GenericListEntry._repr_html_()
      • GenericListEntry.from_str()
    • ICOOR_INTERNALEntry
      • ICOOR_INTERNALEntry.__init__()
      • ICOOR_INTERNALEntry._repr_html_()
      • ICOOR_INTERNALEntry.child
      • ICOOR_INTERNALEntry.distance
      • ICOOR_INTERNALEntry.from_str()
      • ICOOR_INTERNALEntry.parent
      • ICOOR_INTERNALEntry.phi
      • ICOOR_INTERNALEntry.second_parent
      • ICOOR_INTERNALEntry.theta
      • ICOOR_INTERNALEntry.third_parent
    • IO_STRINGEntry
      • IO_STRINGEntry.__init__()
      • IO_STRINGEntry._repr_html_()
      • IO_STRINGEntry.from_str()
      • IO_STRINGEntry.name1
      • IO_STRINGEntry.name3
    • MAINCHAIN_ATOMS
      • MAINCHAIN_ATOMS.__init__()
      • MAINCHAIN_ATOMS._repr_html_()
      • MAINCHAIN_ATOMS.from_str()
    • METAL_BINDING_ATOMSEntry
      • METAL_BINDING_ATOMSEntry.__init__()
      • METAL_BINDING_ATOMSEntry._repr_html_()
      • METAL_BINDING_ATOMSEntry.from_str()
    • NBR_ATOMEntry
      • NBR_ATOMEntry.__init__()
      • NBR_ATOMEntry._repr_html_()
      • NBR_ATOMEntry.from_str()
      • NBR_ATOMEntry.log
    • NBR_RADIUSEntry
      • NBR_RADIUSEntry.__init__()
      • NBR_RADIUSEntry._repr_html_()
      • NBR_RADIUSEntry.from_str()
      • NBR_RADIUSEntry.log
    • PDB_ROTAMERSEntry
      • PDB_ROTAMERSEntry.__init__()
      • PDB_ROTAMERSEntry._repr_html_()
      • PDB_ROTAMERSEntry.from_str()
      • PDB_ROTAMERSEntry.log
    • PROPERTIESEntry
      • PROPERTIESEntry.__init__()
      • PROPERTIESEntry._repr_html_()
      • PROPERTIESEntry.from_str()
    • RAMA_PREPRO_FILENAMEEntry
      • RAMA_PREPRO_FILENAMEEntry.__init__()
      • RAMA_PREPRO_FILENAMEEntry._repr_html_()
      • RAMA_PREPRO_FILENAMEEntry.from_str()
      • RAMA_PREPRO_FILENAMEEntry.log
    • ROTAMER_AAEntry
      • ROTAMER_AAEntry.__init__()
      • ROTAMER_AAEntry._repr_html_()
      • ROTAMER_AAEntry.from_str()
      • ROTAMER_AAEntry.log
    • Singletony
      • Singletony.list_singleton
      • Singletony.multiton
      • Singletony.singleton
    • TYPEEntry
      • TYPEEntry.__init__()
      • TYPEEntry._repr_html_()
      • TYPEEntry.from_str()
      • TYPEEntry.log
    • UNKNOWNEntry
      • UNKNOWNEntry.__init__()
      • UNKNOWNEntry._repr_html_()
      • UNKNOWNEntry.from_str()
      • UNKNOWNEntry.log
    • VARIANTEntry
      • VARIANTEntry.__init__()
      • VARIANTEntry._repr_html_()
      • VARIANTEntry.from_str()
    • html_span()

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• Module Index

• Search Page