schrodinger.application.bioluminate.nucleic.mutator module¶

class schrodinger.application.bioluminate.nucleic.mutator.NucleobaseMutator(mutations, concurrent)¶

Bases: schrodinger.application.bioluminate.mutation.MacromoleculeMutator

Mutates a set of residues in a DNA or RNA structure allowing concurrent mutations as well as the option to limit concurrent mutations to sequential residues only.

MUTS_FILE_REGEX = re.compile('(?P<chain>[a-zA-Z0-9_]{1})\n :\n (?P<resnum>-?\\d+)\n (?P<inscode>[a-zA-Z]{1})? # optional\n ->\n (?P<new_resname>(A|C|T|G|U))\n ', re.VERBOSE)¶

RES_FILE_REGEX = re.compile('(?P<chain>[a-zA-Z0-9_]{1})\n :\n (?P<resnum>-?\\d+)\n (?P<inscode>[a-zA-Z]{1})? # optional\n \\s? # optional\n (?P<mutations>(A|C|T|G|U)(,A|,C|,T|,G|,U)*)? # op, re.VERBOSE)¶

SUPPORTED_BUILD_RESIDUES = ['A', 'C', 'T', 'G', 'U']¶

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

calculateMutationsList()¶

Calculate all combintations of mutations.

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

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)

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 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

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

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

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

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.

class schrodinger.application.bioluminate.nucleic.mutator.NucleobaseMutation(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: schrodinger.application.bioluminate.mutation.Mutation

property mut_frag_name¶

__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¶

from_res_3l: str = None¶

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

res_asl()¶

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

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

property res_id¶

property resnum_with_inscode¶

chain: str¶

res_num: int¶

inscode: str¶

to_res_3l: str¶

polymer_type: str¶