schrodinger.application.bioluminate.mutation module¶

class schrodinger.application.bioluminate.mutation.PolymerType(value)¶

Bases: enum.Enum

An enumeration.

PEPTIDE = 'peptide'¶

RNA = 'rna'¶

DNA = 'dna'¶

class schrodinger.application.bioluminate.mutation.MutationStructureMap(ref_struct, struct, residue_map)¶

Bases: object

Helper class for Mutator. This will store a mutated structure and the resides that were mutated.

__init__(ref_struct, struct, residue_map)¶

Parameters

ref_struct (schrodinger.structure.Structure) – Reference structure (potentially “idealized”)
struct (schrodinger.structure.Structure) – Mutated structure
residue_map (dict instance of reference and mutated residues) – The mapping of reference residues to their mutated residues

class schrodinger.application.bioluminate.mutation.Mutation(chain: str, res_num: int, inscode: str, to_res_3l: str, polymer_type: str, from_res_3l: Optional[str] = None, _resnum_with_inscode: Optional[str] = None)¶

Bases: object

Container for a single mutation

chain: str¶

res_num: int¶

inscode: str¶

to_res_3l: str¶

polymer_type: str¶

from_res_3l: str = None¶

property resnum_with_inscode¶

property mut_frag_name¶

property res_id¶

res_asl()¶

Return atom selection language (asl) of the mutating residue.

Returns: asl for selecting the mutating residue of this mutation
Return type: str

make_reverse_mutation()¶

Return a new Mutation object that mutates the same residue from self.to_res_3l to self.from_res_3l.

Returns: reversed mutation
Return type: Mutation

__init__(chain: str, res_num: int, inscode: str, to_res_3l: str, polymer_type: str, from_res_3l: Optional[str] = None, _resnum_with_inscode: Optional[str] = None) → None¶

class schrodinger.application.bioluminate.mutation.MacromoleculeMutator(mutations, concurrent)¶

Bases: object

__init__(mutations, concurrent)¶

Parameters

mutations – A list of the mutations to carry out on the ref_struct. Each element of the list is a tuple of (“res num.”, [“pdbnames”]) where “res num.” is the residue number being altered and “pdbnames” is a list of the standard PDB residue names to mutate it to.
concurrent – Maximum concurrent mutations

Raises

RuntimeError – If concurrent is less than 1.

property mutations¶: The list of mutations that will be carried out

property total_mutations¶: Total number of mutations that will be generated

static makeMutation(mutation_tuple, polymer_type)¶: Convert a mutation tuple into a Mutation object.

static validateMutatedResidues(cls, residues)¶

Method for validating the residues used in mutations passed in to the MutateProtein class.

Raises: ValueError – If the 1-letter residue name is not supported by the build.mutate method.

static validateMutations(mutations)¶

Private method for validating the mutations passed in to the MutateProtein class.

Raises: ValueError – If the mutations passed in is not a list, if each item in the list is not a tuple, if the tuple is not of length 4 (chain, resnum idx, inscode, mutation resnames), if the resnum is not an integer, or any of the 3-letter residue names in “mutation resnames” is not supported by the build,mutate method.

classmethod convertResFile(filename, regex=None)¶

Converts lines in filename into a list of mutations to use. Returns a list of tuples where each tuple is (“chain”, “resnum”, “inscode”, “three-letter resnames for mutation”).

Each line could be multiple mutations (one residue to multiple mutation states)

Parameters

filename (str) – Name of file containing the list of mutations.
regex (regular expression object) – Regular expression for matching residues

Raises

RuntimeError – If any of chain, resnum or mutation is missing

Returns

List of mutations with valid syntax for the class

Return type

list of tuples

classmethod convertResList(reslist, regex=None, validate=True)¶

Converts list of residues into a list of mutations to use. Returns a list of tuples where each tuple is (“chain”, “resnum”, “inscode”, “three-letter resnames for mutation”).

Each residue string could be multiple mutations (one residue to multiple mutation states)

Parameters

reslist (list of str) – List of residues to convert to mutations
regex (regular expression object) – Regular expression for matching residues
validate (bool) – Whether to validate the potential mutations

Returns

List of mutations with valid syntax for the class or None if any item in the list is not valid

Return type

list of tuples or None

classmethod convertResidueList(residues, mutations, regex=None)¶

Convert a list of residues and mutations to a standard list of mutations. Returns a list of tuples where each tuple is (“chain”, “resnum”, “inscode”, “one-letter resnames for mutation”).

Parameters

residues (list of strings (Syntax: <chain>:<resnum> if no chain use "_")) – Residues that will be mutated.
mutations – The one-letter names for the residues that will be used in mutation.

Raises

RuntimeError – If any of chain, resnum or mutation is missing or if there is an invalid residue name

Returns

List of mutations with valid syntax for the class

Return type

list of tuples

classmethod convertMutsFile(muts_file, regex=None)¶

Converts lines in filename into a list of mutations to use. Returns a list of tuples where each tuple is (“chain”, “resnum”, “inscode”, “one-letter nucleobase for mutation”).

Each line is one mutation (could be multiple residues)

calculateMutationsList()¶

Calculate all combintations of mutations.

Returns: list of list of mutations
Return type: List[List[Tuple]]

classmethod convertResToMuts(res_str, regex=None, validate=True)¶

Converts a residue string into a list of mutations to use. Returns a list of tuples of (“chain”, “resnum”, “inscode”, “one-letter resnames for mutation”). Will return None if any item in the list is not a valid residue string.

A residue string could be multiple mutations (one residue to multiple mutation states)

Parameters

res_str (str) – Residue string to convert to mutations
regex (regular expression object) – Regular expression for matching residues
validate (bool) – Whether to run validation on the mutation

Returns

List of mutations with valid syntax for the class or None if the res_str is not valid.

Return type

list tuples or None

schrodinger.application.bioluminate.mutation.generate_mutant_combinations(mutations, max_concurrent)¶

Given a tuple of allowed mutations and the number of allowed concurrent mutations, return a list of all possible mutation combinations.

Parameters

mutations (Tuple[Tuple[str, int, str, str]]) – a tuple of mutation tuples
max_concurrent (int) – the max number of allowed simultaneous mutations, e.g. concurrent = 2 for all single and double mutants

Returns

list of all possible mutation combinations

Return type

List[Tuple[Tuple[str, int, str, str]]]

schrodinger.application.bioluminate.mutation.convert_res_file(filename, regex)¶

Converts lines in filename into a list of mutations to use. Returns a list of tuples where each tuple is (“chain”, “resnum”, “inscode”, “three-letter resnames for mutation”).

Each line could be multiple mutations (one residue to multiple mutation states)

Parameters

filename (str) – Name of file containing the list of mutations.
regex (regular expression object) – Regular expression for matching residues

Raises

RuntimeError – If any of chain, resnum or mutation is missing

Returns

List of mutations with valid syntax for the class

Return type

list of tuples

schrodinger.application.bioluminate.mutation.convert_res_to_muts(res_str, regex)¶

Converts a residue string into a list of mutations to use. Returns a list of tuples of (“chain”, “resnum”, “inscode”, “three-letter resnames for mutation”). Will return None if any item in the list is not a valid residue string.

A residue string could be multiple mutations (one residue to multiple mutation states)

Parameters

res_str (str) – Residue string to convert to mutations
regex (regular expression object) – Regular expression for matching residues
validate (bool) – Whether to run validation on the mutation

Returns

List of mutations with valid syntax for the class or None if the res_str is not valid.

Return type

list tuples or None

schrodinger.application.bioluminate.mutation.convert_muts_file(muts_file, regex)¶

Converts lines in filename into a list of mutations to use. Returns a list of tuples where each tuple is (“chain”, “resnum”, “inscode”, “three-letter resnames for mutation”).

Also supports loop insertion and deletion.

Each line is one mutation (could be multiple residues)

schrodinger.application.bioluminate.mutation.convert_residue_list(residues, mutations, regex)¶

Convert a list of residues and mutations to a standard list of mutations. Returns a list of tuples where each tuple is (“chain”, “resnum”, “inscode”, “three-letter resnames for mutation”).

Parameters

residues (list of strings (Syntax: <chain>:<resnum> if no chain use "_")) – Residues that will be mutated.
mutations – The three-letter names for the residues that will be used in mutation.

Raises

RuntimeError – If any of chain, resnum or mutation is missing or if there is an invalid residue name

Returns

List of mutations with valid syntax for the class

Return type

list of tuples