schrodinger.protein.nonstandard_residues module¶

class schrodinger.protein.nonstandard_residues.StructureSource¶

Bases: str, enum.Enum

Standard = 'standard built-in'¶

Nonstandard = 'nonstandard built-in'¶

Custom = 'nonstandard provided'¶

schrodinger.protein.nonstandard_residues.get_residue_database(*, load_saved=True)¶

Get the global nonstandard residue database.

If there is an error loading the saved database file, an empty (default) database will be returned.

schrodinger.protein.nonstandard_residues.get_default_user_dbfile()¶

Return the path to the default user DB file.

Returns: Default path to user DB file.
Return type: str

schrodinger.protein.nonstandard_residues.get_enamine_dbfile()¶

schrodinger.protein.nonstandard_residues.get_saved_db_file()¶

Return the path to the database file that is saved in Maestro’s prefs or, if no preference is specified, a default location in the user’s userdata directory.,

Returns: Saved DB filepath to be used
Return type: str

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(db_type)¶: Return a list of AminoAcid objects from the specified built-in database file. :param db_type: the source database type

schrodinger.protein.nonstandard_residues.is_excluded_amino_acid(st)¶

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

Bases: PyQt6.QtCore.QObject

A collection of AminoAcid objects. Included built-in residues. For now, just a collection of database-related functions.

residuesChanged¶: A pyqtSignal emitted by instances of the class.

__init__(db_file=None)¶

getAminoAcid(name)¶

Retrieve an amino acid by PDB residue name

Parameters: name (str) – PDB residue name
Returns: Amino acid object
Return type: Optional[AminoAcid]

property amino_acids¶

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

readDatabaseFile(db_file)¶: Read the specified database file, and return a ResidueDatabase (which is basically a list of AminoAcid objects, including built-in residues). Raises RuntimeError on failure.

reset()¶

saveDatabase(amino_acids, db_file=None)¶

static exportDatabase(amino_acids, db_file)¶

Export the amino acids database.

Parameters

amino_acids (list[AminoAcid]) – Amino acids to export.
db_file (str) – Database file path.

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[non_standard_residues.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[non_standard_residues.AminoAcid]

schrodinger.protein.nonstandard_residues.get_db_residues()¶

Returns: a list of residues from the non-standard residue database
Return type: list[non_standard_residues.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.Structure) – a residue structure
Returns: a copy of st that has been prepared for use in Prime
Return type: _structure.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.fix_and_validate_res_structure(st: schrodinger.structure._structure.Structure, skip_minimization=False) → schrodinger.structure._structure.Structure¶

Modify the CT: Add hydrogens, assign PDB names, and minimize.
Validate to ensure #atoms < 300, backbone PDB atoms are present, minimization succeeded (valences are proper), and structure is not one of the 20 standard AAs.

Raises: ValueError – if it is not possible to validate the structure as a non-standard amino acid

schrodinger.protein.nonstandard_residues.validate_alpha_aa(st: schrodinger.structure._structure.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