mythos.input.topology

Topological information for DNA/RNA.

Attributes

`N_1ST_LINE_OXDNA_CLASSIC`
`N_1ST_LINE_OXDNA_NEW`
`VALID_NEIGHBOR_SECOND_DIM`
`ERR_TOPOLOGY_INVALID_NUMBER_NUCLEOTIDES`
`ERR_TOPOLOGY_INVALID_STRAND_COUNTS`
`ERR_TOPOLOGY_SEQ_NOT_MATCH_NUCLEOTIDES`
`ERR_TOPOLOGY_STRAND_COUNTS_NOT_MATCH`
`ERR_TOPOLOGY_BONDED_NEIGHBORS_INVALID_SHAPE`
`ERR_TOPOLOGY_UNBONDED_NEIGHBORS_INVALID_SHAPE`
`ERR_TOPOLOGY_INVALID_SEQUENCE_LENGTH`
`ERR_TOPOLOGY_INVALID_SEQUENCE_NUCLEOTIDES`
`ERR_TOPOLOGY_INVALID_DISCRETE_SEQUENCE_SHAPE`
`ERR_TOPOLOGY_INVALID_UNPAIRED_PSEQ_SHAPE`
`ERR_TOPOLOGY_MISMATCH_PSEQ_SHAPE_NUM_NUCLEOTIDES`
`ERR_TOPOLOGY_INVALID_BP_PSEQ_SHAPE`
`ERR_TOPOLOGY_INVALID_PROBABILITIES`
`ERR_TOPOLOGY_PSEQ_NOT_NORMALIZED`
`ERR_INVALID_OXDNA_FORMAT`
`ERR_STRAND_COUNTS_CIRCULAR_MISMATCH`
`ERR_FILE_NOT_FOUND`
`ERR_TOPOLOGY_INVALID_SEQUENCE_TYPE`
`WARN_CLASSIC_UNSPECIFIED_NT_TYPE`
`WARN_NEW_UNSPECIFIED_NT_TYPE`

Classes

`NucleotideType`	Defines nucleotide types as integer enumerations.
`Topology`	Topology information for a RNA/DNA strand.

Functions

`check_valid_seq`(→ None)	Checks if a sequence is well-formed.
`from_oxdna_file`(→ Topology \| tuple[Topology, ...)	Read topology information from an oxDNA file.
`_determine_oxdna_format`(...)	Determine the format of an oxDNA file from the first line of the file.
`_get_bonded_neighbors`(→ list[tuple[int, int]])	Convert 5' neighbors to bonded neighbors by index.
`_get_unbonded_neighbors`(→ list[tuple[int, int]])	Get unbonded neighbors.
`_from_file_oxdna_classic`(→ Topology)	Read topology information from a file in the classix oxDNA format.
`_from_file_oxdna_new`(→ Topology)

Module Contents

mythos.input.topology.N_1ST_LINE_OXDNA_CLASSIC = 2

mythos.input.topology.N_1ST_LINE_OXDNA_NEW = 3

mythos.input.topology.VALID_NEIGHBOR_SECOND_DIM = 2

mythos.input.topology.ERR_TOPOLOGY_INVALID_NUMBER_NUCLEOTIDES = 'Invalid number of nucleotides'

mythos.input.topology.ERR_TOPOLOGY_INVALID_STRAND_COUNTS = 'Invalid strand counts'

mythos.input.topology.ERR_TOPOLOGY_SEQ_NOT_MATCH_NUCLEOTIDES = 'Sequence does not match number of nucleotides'

mythos.input.topology.ERR_TOPOLOGY_STRAND_COUNTS_NOT_MATCH = 'Strand counts do not match number of nucleotides'

mythos.input.topology.ERR_TOPOLOGY_BONDED_NEIGHBORS_INVALID_SHAPE = 'Invalid bonded neighbors shape'

mythos.input.topology.ERR_TOPOLOGY_UNBONDED_NEIGHBORS_INVALID_SHAPE = 'Invalid unbonded neighbors shape'

mythos.input.topology.ERR_TOPOLOGY_INVALID_SEQUENCE_LENGTH = 'Invalid sequence length'

mythos.input.topology.ERR_TOPOLOGY_INVALID_SEQUENCE_NUCLEOTIDES = 'Invalid sequence nucleotides'

mythos.input.topology.ERR_TOPOLOGY_INVALID_DISCRETE_SEQUENCE_SHAPE = 'Invalid discrete sequence shape'

mythos.input.topology.ERR_TOPOLOGY_INVALID_UNPAIRED_PSEQ_SHAPE = 'Invalid unpaired probabilistic sequence shape'

mythos.input.topology.ERR_TOPOLOGY_MISMATCH_PSEQ_SHAPE_NUM_NUCLEOTIDES = 'Pseq shape does not match number of nucleotides'

mythos.input.topology.ERR_TOPOLOGY_INVALID_BP_PSEQ_SHAPE = 'Invalid base-paired probabilistic sequence shape'

mythos.input.topology.ERR_TOPOLOGY_INVALID_PROBABILITIES = 'Probabilities must be > 0'

mythos.input.topology.ERR_TOPOLOGY_PSEQ_NOT_NORMALIZED = 'Probabilities must be normalized'

mythos.input.topology.ERR_INVALID_OXDNA_FORMAT = 'Invalid oxDNA topology format. See...

mythos.input.topology.ERR_STRAND_COUNTS_CIRCULAR_MISMATCH = 'Strand counts and cicularity do not match'

mythos.input.topology.ERR_FILE_NOT_FOUND = 'Topology file not found'

mythos.input.topology.ERR_TOPOLOGY_INVALID_SEQUENCE_TYPE = 'Invalid sequence type. Must be discrete or probabilistic'

mythos.input.topology.WARN_CLASSIC_UNSPECIFIED_NT_TYPE = 'Type of strand {strand_idx} not specified, and did not find T/U for autodetect'

mythos.input.topology.WARN_NEW_UNSPECIFIED_NT_TYPE = 'Type of strand {strand_idx} not specified'

class mythos.input.topology.NucleotideType[source]

Bases: enum.IntEnum

Defines nucleotide types as integer enumerations.

UNSPECIFIED = 0

DNA = 1

RNA = 2

mythos.input.topology.check_valid_seq(seq: mythos.utils.types.Sequence, n_nucleotides: int) → None[source]: Checks if a sequence is well-formed.

class mythos.input.topology.Topology[source]

Topology information for a RNA/DNA strand.

n_nucleotides: int

strand_counts: numpy.ndarray

bonded_neighbors: numpy.ndarray

unbonded_neighbors: numpy.ndarray

seq: mythos.utils.types.Sequence

is_end: numpy.ndarray

nt_type: numpy.ndarray

__post_init__() → None[source]: Check that the topology is valid.

mythos.input.topology.from_oxdna_file(path: mythos.utils.types.PathOrStr, *, return_format: bool = False) → Topology | tuple[Topology, mythos.utils.types.oxDNAFormat][source]

Read topology information from an oxDNA file.

Parameters:

path (typ.PathOrStr) – Path to the oxDNA topology file.
return_format (bool, optional) – Whether to return the oxDNA format along with the topology as a tuple (top, fmt). Defaults to False.

Returns:

The parsed topology, and: optionally the format.

Return type:

Topology or tuple[Topology, typ.oxDNAFormat]

mythos.input.topology._determine_oxdna_format(first_line: str) → tuple[mythos.utils.types.oxDNAFormat, collections.abc.Callable[[list[str]], Topology]][source]: Determine the format of an oxDNA file from the first line of the file.

mythos.input.topology._get_bonded_neighbors(strand_lengths: list[int], is_circular: list[bool]) → list[tuple[int, int]][source]: Convert 5’ neighbors to bonded neighbors by index.

mythos.input.topology._get_unbonded_neighbors(n_nucleotides: int, bonded_neighbors: list[tuple[int, int]]) → list[tuple[int, int]][source]: Get unbonded neighbors.

mythos.input.topology._from_file_oxdna_classic(lines: list[str]) → Topology[source]

Read topology information from a file in the classix oxDNA format.

See https://lorenzo-rovigatti.github.io/oxDNA/configurations.html#topology-file for more information.

Parameters:: lines (List[str]) – lines from topology file
Returns:: Topology object
Return type:: Topology

mythos.input.topology._from_file_oxdna_new(lines: list[str]) → Topology[source]