NASequence#

class pyopenms.NASequence#

Bases: object

OpenMS class NASequence

__init__() → None#
__init__(arg: pyopenms.NASequence, /) → None

Methods

`__init__`()
`empty`()	Check if empty
`fromString`(s)	Create NASequence from string
`get`(index)	Returns a copy of the ribonucleotide at the given index
`getAverageWeight`()	Overloaded function.
`getFivePrimeMod`()	Returns a copy of the 5' modification, or None if not set
`getFormula`()	Overloaded function.
`getMonoWeight`()	Overloaded function.
`getPrefix`(length)	Returns the prefix of the given length
`getSequence`()	Returns a copy of the sequence of ribonucleotides
`getSubsequence`(start, length)	Returns a subsequence starting at start with the given length
`getSuffix`(length)	Returns the suffix of the given length
`getThreePrimeMod`()	Returns a copy of the 3' modification, or None if not set
`hasFivePrimeMod`()	Returns true if the sequence has a 5' modification
`hasThreePrimeMod`()	Returns true if the sequence has a 3' modification
`set`(index, ribonucleotide)	Sets the ribonucleotide at the given index, resolved by its code against RibonucleotideDB (NASequence stores the database entry)
`setFivePrimeMod`(mod)	Sets the 5' modification, resolved by its code against RibonucleotideDB (NASequence stores the database entry).
`setSequence`(seq)	Sets the sequence of ribonucleotides, each resolved by its code against RibonucleotideDB (NASequence stores the database entries)
`setThreePrimeMod`(mod)	Sets the 3' modification, resolved by its code against RibonucleotideDB (NASequence stores the database entry).
`size`()	Get number of residues
`toString`()	Get string representation

class NASFragmentType(*values)#

Bases: IntEnum

AIon = 4#

AminusB = 18#

BIon = 5#

BIonMinusH20 = 11#

BIonMinusNH3 = 13#

CIon = 6#

DIon = 19#

FivePrime = 2#

Full = 0#

Internal = 1#

NonIdentified = 15#

Precursor = 10#

SizeOfNASFragmentType = 20#

ThreePrime = 3#

Unannotated = 16#

WIon = 17#

XIon = 7#

YIon = 8#

YIonMinusH20 = 12#

YIonMinusNH3 = 14#

ZIon = 9#

as_integer_ratio()#

Return a pair of integers, whose ratio is equal to the original int.

The ratio is in lowest terms and has a positive denominator.

>>> (10).as_integer_ratio()
(10, 1)
>>> (-10).as_integer_ratio()
(-10, 1)
>>> (0).as_integer_ratio()
(0, 1)

bit_count()#

Number of ones in the binary representation of the absolute value of self.

Also known as the population count.

>>> bin(13)
'0b1101'
>>> (13).bit_count()
3

bit_length()#

Number of bits necessary to represent self in binary.

>>> bin(37)
'0b100101'
>>> (37).bit_length()
6

conjugate()#: Returns self, the complex conjugate of any int.

denominator#: the denominator of a rational number in lowest terms

classmethod from_bytes(bytes, byteorder='big', *, signed=False)#

Return the integer represented by the given array of bytes.

bytes: Holds the array of bytes to convert. The argument must either support the buffer protocol or be an iterable object producing bytes. Bytes and bytearray are examples of built-in objects that support the buffer protocol.
byteorder: The byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use sys.byteorder as the byte order value. Default is to use ‘big’.
signed: Indicates whether two’s complement is used to represent the integer.

getMapping()#: Returns a dict mapping int values to enum member name strings.

imag#: the imaginary part of a complex number

is_integer()#: Returns True. Exists for duck type compatibility with float.is_integer.

numerator#: the numerator of a rational number in lowest terms

real#: the real part of a complex number

to_bytes(length=1, byteorder='big', *, signed=False)#

Return an array of bytes representing an integer.

length: Length of bytes object to use. An OverflowError is raised if the integer is not representable with the given number of bytes. Default is length 1.
byteorder: The byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use sys.byteorder as the byte order value. Default is to use ‘big’.
signed: Determines whether two’s complement is used to represent the integer. If signed is False and a negative integer is given, an OverflowError is raised.

empty() → bool#: Check if empty

static fromString(s: str) → pyopenms.NASequence#: Create NASequence from string

get(index: int) → pyopenms.Ribonucleotide#: Returns a copy of the ribonucleotide at the given index

getAverageWeight() → float#

getAverageWeight(type: pyopenms.NASequence.NASFragmentType, charge: int = 0) → float

Overloaded function.

getAverageWeight() -> float

Get average weight

getAverageWeight(type: pyopenms.NASequence.NASFragmentType, charge: int = 0) -> float

Get average weight for a fragment type

getFivePrimeMod() → pyopenms.Ribonucleotide | None#: Returns a copy of the 5’ modification, or None if not set

getFormula() → pyopenms.EmpiricalFormula#

getFormula(type: pyopenms.NASequence.NASFragmentType, charge: int = 0) → pyopenms.EmpiricalFormula

Overloaded function.

getFormula() -> pyopenms.EmpiricalFormula

Get empirical formula

getFormula(type: pyopenms.NASequence.NASFragmentType, charge: int = 0) -> pyopenms.EmpiricalFormula

Get empirical formula for a fragment type

getMonoWeight() → float#

getMonoWeight(type: pyopenms.NASequence.NASFragmentType, charge: int = 0) → float

Overloaded function.

getMonoWeight() -> float

Get monoisotopic weight

getMonoWeight(type: pyopenms.NASequence.NASFragmentType, charge: int = 0) -> float

Get monoisotopic weight for a fragment type

getPrefix(length: int) → pyopenms.NASequence#: Returns the prefix of the given length

getSequence() → list[pyopenms.Ribonucleotide]#: Returns a copy of the sequence of ribonucleotides

getSubsequence(start: int, length: int) → pyopenms.NASequence#: Returns a subsequence starting at start with the given length

getSuffix(length: int) → pyopenms.NASequence#: Returns the suffix of the given length

getThreePrimeMod() → pyopenms.Ribonucleotide | None#: Returns a copy of the 3’ modification, or None if not set

hasFivePrimeMod() → bool#: Returns true if the sequence has a 5’ modification

hasThreePrimeMod() → bool#: Returns true if the sequence has a 3’ modification

set(index: int, ribonucleotide: pyopenms.Ribonucleotide) → None#: Sets the ribonucleotide at the given index, resolved by its code against RibonucleotideDB (NASequence stores the database entry)

setFivePrimeMod(mod: pyopenms.Ribonucleotide | None) → None#: Sets the 5’ modification, resolved by its code against RibonucleotideDB (NASequence stores the database entry). Pass None to clear it

setSequence(seq: collections.abc.Sequence[pyopenms.Ribonucleotide]) → None#: Sets the sequence of ribonucleotides, each resolved by its code against RibonucleotideDB (NASequence stores the database entries)

setThreePrimeMod(mod: pyopenms.Ribonucleotide | None) → None#: Sets the 3’ modification, resolved by its code against RibonucleotideDB (NASequence stores the database entry). Pass None to clear it

size() → int#: Get number of residues

toString() → str#: Get string representation