Bio.SeqUtils.IsoElectricPoint模块

用Bjellqvist方法计算多肽的等电点。

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.

我根据大卫·L·塔布(David L.Tabb)的一篇笔记设计了算法，这篇笔记可以在http://fields.scripps.edu/DTASelect/20010710-pI-Algorithm.pdf上找到

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

基类：object

在给定的pH下计算蛋白质等电点或电荷的一类。

参数:

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

序列。

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

以整数形式出现，例如 {{"A": 3, "C": 0, ...}} 。默认值： None 。如果 None 则将根据给定的序列计算DIC。

示例

此类的方法可以从类本身访问，也可以从 ProtParam.ProteinAnalysis 对象(名称部分不同)：

>>> 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

方法：

:charge_at_pH(pH): Calculates the charge of the protein for a given pH
：pi()：计算等电点

__init__(protein_sequence, aa_content=None)

初始化类。

charge_at_pH(pH)

计算蛋白质在给定pH下的电荷。

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

计算等电点并将其作为浮点返回。

这是一个使用二分法的递归函数。一分为二的维基：https://en.wikipedia.org/wiki/Bisection_method

参数：

• pH：计算蛋白质电流电荷的pH值。此pH值位于区间的中心(平均值 min_ 和 max_ )。

• MIN_：间隔的最小值。当蛋白质完全由天冬氨酸组成时，初始值默认为4.05，低于理论最小值。

• MAX_：间隔的最大值。当蛋白质完全由精氨酸组成时，初始值默认为12，高于理论最大值。