schrodinger.protein.process_enamine_db module

schrodinger.protein.process_enamine_db.parse_args()

schrodinger.protein.process_enamine_db.main(options)

schrodinger.protein.process_enamine_db.process_enamine_db(enamine_db, output_file, skip_minimization=False, allow_non_alpha_aa=False)

Process Enamine database to extract only the amino acids that are compatible with mmshare workflows

Parameters

• enamine_db – path to Enamine database

• output_file – path to output file

• skip_minimization – if True, skip minimization step

• allow_non_alpha_aa – if True, allow non-alpha amino acids to be processed

schrodinger.protein.process_enamine_db.get_built_in_aa_names() → set[str]

Get the names of all built-in standard and non-standard amino acids

Returns

a set of built-in amino acid names

schrodinger.protein.process_enamine_db.get_reserved_aa_names() → set[str]

Get amino acid names that are reserved for built-in amino acids or custom amino acids from the nonstandard amino acid panel residue sketcher

Returns

a set of reserved amino acid names

schrodinger.protein.process_enamine_db.contains_built_in_aa(st) → bool

Check if an enamine residue structure contains any built-in amino acids

schrodinger.protein.process_enamine_db.get_unique_aa_names(reserved)

Generate unique amino acid names

Parameters

reserved – a set of reserved amino acid names that should not be generated

schrodinger.protein.process_enamine_db.get_standardized_aa_structure(st, skip_minimization=False, allow_non_alpha_aa=False)

Standardize an amino acid structure by removing any solvent molecules, applying pdb atom names, and minimizing. Confirm the structure is a valid alpha amino acid and not a built-in amino acid.

Parameters

• st – a structure containing a single amino acid

• skip_minimization – if True, skip minimization step

• allow_non_alpha_aa – if True, allow non-alpha amino acids to be processed

Raises

ValueError – if the structure is not a valid alpha amino acid for any reason

schrodinger.protein.process_enamine_db.process_one_aa(mol_st, id='', skip_minimization=False, allow_non_alpha_aa=False)

Process a structure containing one molecule is a valid amio acid

Parameters

• mol_st – a structure containing one molecule

• id – the identifier for the molecule, for logging purposes only

• skip_minimization – if True, skip minimization step

• allow_non_alpha_aa – if True, allow non-alpha amino acids to be processed

Raises

ValueError – if the molecule is not a valid amino acid for any reason

schrodinger.protein.process_enamine_db.attempt_tripeptide_mutation(mol_st: schrodinger.structure._structure.Structure) → schrodinger.structure._structure.Structure

Attempt to mutate the middle residue of a tripeptide to the residue in the provided structure. The final test to see if a residue is valid is to confirm that we can perform a mutation with it

Parameters

mol_st – a structure containing a single molecule

Returns

the tripeptide structure with the middle residue mutated, for debugging purposes

schrodinger.protein.process_enamine_db.set_res_name(st, name)

Set residue name for a structure