Bio.SeqUtils.IsoelectricPoint模块

使用Bestival qvist的方法计算肽的等份点。

pK值和方法取自：

* Bjellqvist, B.,Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F.,
Sanchez, J.-Ch., Frutiger, S. & Hochstrasser, D.F.
The focusing positions of polypeptides in immobilized pH gradients can be
predicted from their amino acid sequences. Electrophoresis 1993, 14,
1023-1031.

* Bjellqvist, B., Basse, B., Olsen, E. and Celis, J.E.
Reference points for comparisons of two-dimensional maps of proteins from
different human cell types defined in a pH scale where isoelectric points
correlate with polypeptide compositions. Electrophoresis 1994, 15, 529-539.

我根据David L的注释设计了算法。Tabb，网址：http://fields.scripps.edu/DTASelect/20010710-pI-Algorithm.pdf

class Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint(protein_sequence, aa_content=None)

基类：object

用于计算蛋白质给定pH值下的IEP或电荷的类。

参数:

:protein_sequence: A ``Bio.Seq`` or string object containing a protein

顺序

:aa_content: A dictionary with amino acid letters as keys and its

出现的情况为整体，例如 {"A": 3, "C": 0, ...} .默认： None .如果 None 将从给定序列计算DIC。

方法

:charge_at_pH(pH): Calculates the charge of the protein for a given pH
:pi(): Calculates the isoelectric point

示例

此类的方法可以从类本身或 ProtParam.ProteinAnalysis 对象（部分名称不同）：

>>> from Bio.SeqUtils.IsoelectricPoint import IsoelectricPoint as IP
>>> protein = IP("INGAR")
>>> print(f"IEP of peptide {protein.sequence} is {protein.pi():.2f}")
IEP of peptide INGAR is 9.75
>>> print(f"Its charge at pH 7 is {protein.charge_at_pH(7.0):.2f}")
Its charge at pH 7 is 0.76

>>> from Bio.SeqUtils.ProtParam import ProteinAnalysis as PA
>>> protein = PA("PETER")
>>> print(f"IEP of {protein.sequence}: {protein.isoelectric_point():.2f}")
IEP of PETER: 4.53
>>> print(f"Charge at pH 4.53: {protein.charge_at_pH(4.53):.2f}")
Charge at pH 4.53: 0.00

__init__(protein_sequence, aa_content=None)

初始化课程。

charge_at_pH(pH)

计算给定pH值下蛋白质的电荷。

pi(pH=7.775, min_=4.05, max_=12)

计算并返回等距点为浮点。

这是一个使用二分法的递归函数。关于二分法的Wiki：https://en.wikipedia.org/wiki/Bisection_method

论点：

• pH：计算蛋白质当前电荷的pH值。该pH值位于区间的中心（平均值 min_ 和 max_ ).

• min_：最小间隔。当蛋白质仅由麸质组成时，初始值默认为4.05，低于理论最小值。

• max_：间隔的最大值。当蛋白质仅由Argine组成时，初始值默认为12，高于理论最大值。

__firstlineno__ = 41

__static_attributes__ = ('charged_aas_content', 'neg_pKs', 'pos_pKs', 'sequence')