schrodinger.protein.nonstandard_residues module¶

class schrodinger.protein.nonstandard_residues.StructureSource¶

Bases: str, Enum

Standard = 'standard built-in'¶

Nonstandard = 'nonstandard built-in'¶

Custom = 'nonstandard provided'¶

schrodinger.protein.nonstandard_residues.get_residue_database()¶

schrodinger.protein.nonstandard_residues.get_default_user_dbfile() → str | None¶

Return the path to the user’s DB file, if one was saved into the user’s .schrodinger directory in release 24-3 or prior. Returns None if file was not saved.

Returns:: Default path to user DB file.

schrodinger.protein.nonstandard_residues.get_enamine_dbfile()¶

schrodinger.protein.nonstandard_residues.get_nucleotides_collection_dbfile()¶

schrodinger.protein.nonstandard_residues.get_mutate_to_filename(db_file: str) → str¶

get the path to the “.mutateto” file which lists the nonstandard residues from the database file that are enabled for mutation

Parameters:: db_file – the path to the database file
Returns:: the path to the “.mutateto” file

schrodinger.protein.nonstandard_residues.strip_capping_groups(st, oxt_charge=-1)¶: Strip any ACE & NMA caps, and add an OXT cap.

schrodinger.protein.nonstandard_residues.add_oxt_cap(st, formal_charge=-1)¶

schrodinger.protein.nonstandard_residues.find_atom(st, name)¶: Find the atom with the given PDB name. None is returned if no such atom is present.

schrodinger.protein.nonstandard_residues.flip_isomer(st)¶: Invert the isomerism of the alpha carbon. So D residue gets converted to L and vice versa.

schrodinger.protein.nonstandard_residues.get_db_amino_acids(source: StructureSource)¶: Return a list of AminoAcid objects from the specified built-in database file. :param source: the source database type

schrodinger.protein.nonstandard_residues.get_db_nucleotides()¶: Return a list of AminoAcid objects from the built-in nucleotides database files.

schrodinger.protein.nonstandard_residues.is_excluded_amino_acid(st)¶

class schrodinger.protein.nonstandard_residues.AminoAcidDatabase(db_file=None)¶

Bases: _ResidueDatabase

classmethod get_built_in_residues()¶: Return a list of built-in residues AminoAcid objects from the installation.

classmethod get_saved_db_file()¶

Return the path to the global/current database, as selected in the GUI. First use the database file that is saved in Maestro’s prefs. If not DB is safed in the preferences, and a custom DB was saved by a prior release (25-3 or earlier), return that path. Otherwise return None.

Returns:: Saved DB filepath to be used or None
Return type:: str or None

class schrodinger.protein.nonstandard_residues.NucleotideDatabase(db_file=None)¶

Bases: _ResidueDatabase

classmethod get_built_in_residues()¶

class schrodinger.protein.nonstandard_residues.AminoAcid(st, source=StructureSource.Custom)¶

Bases: object

Class representing an amino acid (residue) row in the table.

__init__(st, source=StructureSource.Custom)¶

property name¶: AminoAcid.name will return the PDB residue name for this AA.

property code¶: AminoAcid.code will return the 1-letter code for this residue.

property built_in¶: AminoAcid.built_in will return whether this is a built-in residue.

property standard¶: AminoAcid.standard will return whether this is a standard residue.

property aligns_with¶

property description¶: AminoAcid.description will return the title of the CT.

property locked¶: AminoAcid.code will return whether the residue is locked from editing.

property natural_analog_similarity: float | None¶: Get the similarity score for this residue relative to its natural analog.

st_changed()¶: Must be called every time the structure is modified. Will update the SMILES string and the .isomer property.

property identifier¶: Return an ID string for this residue, which includes the residue name, isomer, and description.

is_editable()¶

schrodinger.protein.nonstandard_residues.filter_residues_mutating_to_custom(residues)¶

Parameters:: residues (list[AminoAcid]) – a list of residues
Returns:: the elements of residues that are non-standard and for which “mutate to” has been enabled
Return type:: list[AminoAcid]

schrodinger.protein.nonstandard_residues.get_db_residues()¶

Returns:: a list of residues from the non-standard protein residue database
Return type:: list[AminoAcid]

schrodinger.protein.nonstandard_residues.prepare_res_st_for_prime(st)¶

Create a copy of the specified residue structure that has been prepared for use in Prime.

This includes removing the OXT group (-OH), and setting the title of the CT to the 3-letter residue name.

Parameters:: st (Structure) – a residue structure
Returns:: a copy of st that has been prepared for use in Prime
Return type:: Structure

schrodinger.protein.nonstandard_residues.generate_custom_res_names()¶: Generate three-letter residue names starting with a letter and ending with a two-digit number from 01 to 99

schrodinger.protein.nonstandard_residues.get_unique_res_name(used_names)¶: Return a unique residue name, one that doesn’t exist in the input list.

schrodinger.protein.nonstandard_residues.validate_alpha_aa(st: Structure) → None¶

Validate that a structure is an alpha amino acid. Requires that the atom names be assigned.

Raises:: ValueError – if the structure has any unexpected bonds for an alpha amino acid