cpt_helical_wheel: plotWheels/descriptors.py annotate

annotate plotWheels/descriptors.py @ 2:e9fb56f44c35 draft default tip

planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc

author	cpt
date	Fri, 05 Jan 2024 05:52:58 +0000
parents	9b276485c94a
children

rev	line source
1 9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1 # -- coding: utf-8 --
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	2 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	3 .. currentmodule:: modlamp.descriptors
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	4
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	5 .. moduleauthor:: modlab Alex Mueller ETH Zurich <alex.mueller@pharma.ethz.ch>
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	6
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	7 This module incorporates different classes to calculate peptide descriptor values. The following classes are available:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	8
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	9 ============================= ============================================================================
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	10 Class Characteristics
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	11 ============================= ============================================================================
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	12 :py:class:`GlobalDescriptor` Global one-dimensional peptide descriptors calculated from the AA sequence.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	13 :py:class:`PeptideDescriptor` AA scale based global or convoluted descriptors (auto-/cross-correlated).
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	14 ============================= ============================================================================
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	15
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	16 .. seealso:: :class:`modlamp.core.BaseDescriptor` from which the classes in :mod:`modlamp.descriptors` inherit.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	17 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	18
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	19 import sys
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	20
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	21 import numpy as np
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	22 from scipy import stats
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	23 from sklearn.externals.joblib import Parallel, delayed
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	24
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	25 from plotWheels.core import (
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	26 BaseDescriptor,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	27 load_scale,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	28 count_aas,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	29 aa_weights,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	30 aa_energies,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	31 aa_formulas,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	32 )
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	33
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	34 __author__ = "Alex Müller, Gisela Gabernet"
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	35 __docformat__ = "restructuredtext en"
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	36
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	37
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	38 def _one_autocorr(seq, window, scale):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	39 """Private function used for calculating auto-correlated descriptors for 1 given sequence, window and an AA scale.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	40 This function is used by the :py:func:`calculate_autocorr` method of :py:class:`PeptideDescriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	41
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	42 :param seq: {str} amino acid sequence to calculate descriptor for
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	43 :param window: {int} correlation-window size
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	44 :param scale: {str} amino acid scale to be used to calculate descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	45 :return: {numpy.array} calculated descriptor data
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	46 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	47 try:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	48 m = list() # list of lists to store translated sequence values
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	49 for l in range(len(seq)): # translate AA sequence into values
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	50 m.append(scale[str(seq[l])])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	51 # auto-correlation in defined sequence window
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	52 seqdesc = list()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	53 for dist in range(window): # for all correlation distances
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	54 for val in range(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	55 len(scale["A"])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	56 ): # for all features of the descriptor scale
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	57 valsum = list()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	58 cntr = 0.0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	59 for pos in range(len(seq)): # for every position in the sequence
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	60 if (pos + dist) < len(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	61 seq
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	62 ): # check if corr distance is possible at that sequence position
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	63 cntr += 1 # counter to scale sum
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	64 valsum.append(m[pos][val] * m[pos + dist][val])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	65 seqdesc.append(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	66 sum(valsum) / cntr
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	67 ) # append scaled correlation distance values
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	68 return seqdesc
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	69 except ZeroDivisionError:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	70 print(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	71 "ERROR!\nThe chosen correlation window % i is larger than the sequence %s !"
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	72 % (window, seq)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	73 )
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	74
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	75
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	76 def _one_crosscorr(seq, window, scale):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	77 """Private function used for calculating cross-correlated descriptors for 1 given sequence, window and an AA scale.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	78 This function is used by the :py:func:`calculate_crosscorr` method of :py:class:`PeptideDescriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	79
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	80 :param seq: {str} amino acid sequence to calculate descriptor for
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	81 :param window: {int} correlation-window size
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	82 :param scale: {str} amino acid scale to be used to calculate descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	83 :return: {numpy.array} calculated descriptor data
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	84 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	85 try:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	86 m = list() # list of lists to store translated sequence values
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	87 for l in range(len(seq)): # translate AA sequence into values
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	88 m.append(scale[str(seq[l])])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	89 # auto-correlation in defined sequence window
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	90 seqdesc = list()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	91 for val in range(len(scale["A"])): # for all features of the descriptor scale
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	92 for cc in range(len(scale["A"])): # for every feature cross correlation
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	93 if (val + cc) < len(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	94 scale["A"]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	95 ): # check if corr distance is in range of the num of features
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	96 for dist in range(window): # for all correlation distances
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	97 cntr = float()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	98 valsum = list()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	99 for pos in range(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	100 len(seq)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	101 ): # for every position in the sequence
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	102 if (pos + dist) < len(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	103 seq
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	104 ): # check if corr distance is possible at that sequence pos
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	105 cntr += 1 # counter to scale sum
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	106 valsum.append(m[pos][val] * m[pos + dist][val + cc])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	107 seqdesc.append(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	108 sum(valsum) / cntr
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	109 ) # append scaled correlation distance values
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	110 return seqdesc
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	111 except ZeroDivisionError:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	112 print(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	113 "ERROR!\nThe chosen correlation window % i is larger than the sequence %s !"
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	114 % (window, seq)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	115 )
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	116
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	117
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	118 def _one_arc(seq, modality, scale):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	119 """Privat function used for calculating arc descriptors for one sequence and AA scale. This function is used by
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	120 :py:func:`calculate_arc` method method of :py:class:`PeptideDescriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	121
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	122 :param seq: {str} amino acid sequence to calculate descriptor for
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	123 :param scale: {str} amino acid scale to be used to calculate descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	124 :return: {numpy.array} calculated descriptor data
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	125 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	126 desc_mat = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	127 for aa in seq:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	128 desc_mat.append(scale[aa])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	129 desc_mat = np.asarray(desc_mat)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	130
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	131 # Check descriptor dimension
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	132 desc_dim = desc_mat.shape[1]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	133
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	134 # list to store descriptor values for all windows
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	135 allwindows_arc = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	136
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	137 if len(seq) > 18:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	138 window = 18
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	139 # calculates number of windows in sequence
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	140 num_windows = len(seq) - window
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	141 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	142 window = len(seq)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	143 num_windows = 1
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	144
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	145 # loop through all windows
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	146 for j in range(num_windows):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	147 # slices descriptor matrix into current window
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	148 window_mat = desc_mat[j : j + window, :]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	149
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	150 # defines order of amino acids in helical projection
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	151 order = [0, 11, 4, 15, 8, 1, 12, 5, 16, 9, 2, 13, 6, 17, 10, 3, 14, 7]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	152
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	153 # orders window descriptor matrix into helical projection order
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	154 ordered = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	155 for pos in order:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	156 try:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	157 ordered.append(window_mat[pos, :])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	158 except:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	159 # for sequences of len < 18 adding dummy vector with 2s, length of descriptor dimensions
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	160 ordered.append([2] * desc_dim)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	161 ordered = np.asarray(ordered)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	162
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	163 window_arc = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	164
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	165 # loop through pharmacophoric features
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	166 for m in range(desc_dim):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	167 all_arcs = (
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	168 []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	169 ) # stores all arcs that can be found of a pharmacophoric feature
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	170 arc = 0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	171
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	172 for n in range(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	173 18
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	174 ): # for all positions in helix, regardless of sequence length
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	175 if (
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	176 ordered[n, m] == 0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	177 ): # if position does not contain pharmacophoric feature
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	178 all_arcs.append(arc) # append previous arc to all arcs list
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	179 arc = 0 # arc is initialized
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	180 elif (
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	181 ordered[n, m] == 1
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	182 ): # if position contains pharmacophoric feature(PF), elongate arc by 20°
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	183 arc += 20
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	184 elif ordered[n, m] == 2: # if position doesn't contain amino acid:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	185 if (
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	186 ordered[n - 1, m] == 1
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	187 ): # if previous position contained PF add 10°
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	188 arc += 10
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	189 elif (
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	190 ordered[n - 1, m] == 0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	191 ): # if previous position didn't contain PF don't add anything
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	192 arc += 0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	193 elif (
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	194 ordered[n - 2, m] == 1
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	195 ): # if previous position is empty then check second previous for PF
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	196 arc += 10
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	197 if (
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	198 n == 17
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	199 ): # if we are at the last position check for position n=0 instead of next position.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	200 if ordered[0, m] == 1: # if it contains PF add 10° extra
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	201 arc += 10
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	202 else: # if next position contains PF add 10° extra
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	203 if ordered[n + 1, m] == 1:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	204 arc += 10
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	205 elif ordered[n + 1, m] == 0:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	206 arc += 0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	207 else: # if next position is empty check for 2nd next position
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	208 if n == 16:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	209 if ordered[0, m] == 1:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	210 arc += 10
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	211 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	212 if ordered[n + 2, m] == 1:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	213 arc += 10
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	214
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	215 all_arcs.append(arc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	216 if not arc == 360:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	217 arc0 = all_arcs.pop() + all_arcs[0] # join first and last arc together
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	218 all_arcs = [arc0] + all_arcs[1:]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	219
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	220 window_arc.append(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	221 np.max(all_arcs)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	222 ) # append to window arcs the maximum arc of this PF
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	223 allwindows_arc.append(window_arc) # append all PF arcs of this window
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	224
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	225 allwindows_arc = np.asarray(allwindows_arc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	226
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	227 if modality == "max":
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	228 final_arc = np.max(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	229 allwindows_arc, axis=0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	230 ) # calculate maximum / mean arc along all windows
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	231 elif modality == "mean":
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	232 final_arc = np.mean(allwindows_arc, axis=0)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	233 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	234 print('modality is unknown, please choose between "max" and "mean"\n.')
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	235 sys.exit()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	236 return final_arc
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	237
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	238
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	239 def _charge(seq, ph=7.0, amide=False):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	240 """Calculates charge of a single sequence. The method used is first described by Bjellqvist. In the case of
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	241 amidation, the value for the 'Cterm' pKa is 15 (and Cterm is added to the pos_pks dictionary.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	242 The pKa scale is extracted from: http://www.hbcpnetbase.com/ (CRC Handbook of Chemistry and Physics, 96th ed).
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	243
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	244 pos_pks = {'Nterm': 9.38, 'K': 10.67, 'R': 12.10, 'H': 6.04}
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	245
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	246 neg_pks = {'Cterm': 2.15, 'D': 3.71, 'E': 4.15, 'C': 8.14, 'Y': 10.10}
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	247
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	248 :param ph: {float} pH at which to calculate peptide charge.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	249 :param amide: {boolean} whether the sequences have an amidated C-terminus.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	250 :return: {array} descriptor values in the attribute :py:attr:`descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	251 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	252
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	253 if amide:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	254 pos_pks = {"Nterm": 9.38, "K": 10.67, "R": 12.10, "H": 6.04}
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	255 neg_pks = {"Cterm": 15.0, "D": 3.71, "E": 4.15, "C": 8.14, "Y": 10.10}
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	256 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	257 pos_pks = {"Nterm": 9.38, "K": 10.67, "R": 12.10, "H": 6.04}
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	258 neg_pks = {"Cterm": 2.15, "D": 3.71, "E": 4.15, "C": 8.14, "Y": 10.10}
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	259
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	260 aa_content = count_aas(seq, scale="absolute")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	261 aa_content["Nterm"] = 1.0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	262 aa_content["Cterm"] = 1.0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	263 pos_charge = 0.0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	264 for aa, pK in pos_pks.items():
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	265 c_r = 10 ** (pK - ph)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	266 partial_charge = c_r / (c_r + 1.0)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	267 pos_charge += aa_content[aa] * partial_charge
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	268 neg_charge = 0.0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	269 for aa, pK in neg_pks.items():
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	270 c_r = 10 ** (ph - pK)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	271 partial_charge = c_r / (c_r + 1.0)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	272 neg_charge += aa_content[aa] * partial_charge
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	273 return round(pos_charge - neg_charge, 3)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	274
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	275
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	276 class GlobalDescriptor(BaseDescriptor):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	277 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	278 Base class for global, non-amino acid scale dependant descriptors. The following descriptors can be calculated by
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	279 the methods linked below:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	280
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	281 - `Sequence Length <modlamp.html#modlamp.descriptors.GlobalDescriptor.length>`_
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	282 - `Molecular Formula <modlamp.html#modlamp.descriptors.GlobalDescriptor.formula>`_
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	283 - `Molecular Weight <modlamp.html#modlamp.descriptors.GlobalDescriptor.calculate_MW>`_
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	284 - `Sequence Charge <modlamp.html#modlamp.descriptors.GlobalDescriptor.calculate_charge>`_
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	285 - `Charge Density <modlamp.html#modlamp.descriptors.GlobalDescriptor.charge_density>`_
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	286 - `Isoelectric Point <modlamp.html#modlamp.descriptors.GlobalDescriptor.isoelectric_point>`_
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	287 - `Instability Index <modlamp.html#modlamp.descriptors.GlobalDescriptor.instability_index>`_
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	288 - `Aromaticity <modlamp.html#modlamp.descriptors.GlobalDescriptor.aromaticity>`_
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	289 - `Aliphatic Index <modlamp.html#modlamp.descriptors.GlobalDescriptor.aliphatic_index>`_
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	290 - `Boman Index <modlamp.html#modlamp.descriptors.GlobalDescriptor.boman_index>`_
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	291 - `Hydrophobic Ratio <modlamp.html#modlamp.descriptors.GlobalDescriptor.hydrophobic_ratio>`_
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	292 - `all of the above <modlamp.html#modlamp.descriptors.GlobalDescriptor.calculate_all>`_
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	293 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	294
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	295 def length(self, append=False):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	296 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	297 Method to calculate the length (total AA count) of every sequence in the attribute :py:attr:`sequences`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	298
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	299 :param append: {boolean} whether the produced descriptor values should be appended to the existing ones in the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	300 attribute :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	301 :return: array of sequence lengths in the attribute :py:attr:`descriptor`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	302 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	303
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	304 >>> desc = GlobalDescriptor(['AFDGHLKI','KKLQRSDLLRTK','KKLASCNNIPPR'])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	305 >>> desc.length()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	306 >>> desc.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	307 array([[ 8.], [12.], [12.]])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	308 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	309 desc = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	310 for seq in self.sequences:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	311 desc.append(float(len(seq.strip())))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	312 desc = np.asarray(desc).reshape(len(desc), 1)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	313 if append:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	314 self.descriptor = np.hstack((self.descriptor, np.array(desc)))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	315 self.featurenames.append("Length")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	316 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	317 self.descriptor = np.array(desc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	318 self.featurenames = ["Length"]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	319
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	320 def formula(self, amide=False, append=False):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	321 """Method to calculate the molecular formula of every sequence in the attribute :py:attr:`sequences`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	322
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	323 :param amide: {boolean} whether the sequences are C-terminally amidated.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	324 :param append: {boolean} whether the produced descriptor values should be appended to the existing ones in the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	325 attribute :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	326 :return: array of molecular formulas {str} in the attribute :py:attr:`descriptor`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	327 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	328
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	329 >>> desc = GlobalDescriptor(['KADSFLSADGHSADFSLDKKLKERL', 'ERTILSDFPQWWFASLDFLNC', 'ACDEFGHIKLMNPQRSTVWY'])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	330 >>> desc.formula(amide=True)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	331 >>> for v in desc.descriptor:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	332 ... print(v[0])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	333 C122 H197 N35 O39
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	334 C121 H168 N28 O33 S
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	335 C106 H157 N29 O30 S2
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	336
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	337 .. seealso:: :py:func:`modlamp.core.aa_formulas()`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	338
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	339 .. versionadded:: v2.7.6
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	340 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	341 desc = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	342 formulas = aa_formulas()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	343 for seq in self.sequences:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	344 f = {"C": 0, "H": 0, "N": 0, "O": 0, "S": 0}
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	345 for aa in seq: # loop over all AAs
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	346 for k in f.keys():
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	347 f[k] += formulas[aa][k]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	348
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	349 # substract H2O for every peptide bond
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	350 f["H"] -= 2 * (len(seq) - 1)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	351 f["O"] -= len(seq) - 1
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	352
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	353 if amide: # add C-terminal amide --> replace OH with NH2
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	354 f["O"] -= 1
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	355 f["H"] += 1
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	356 f["N"] += 1
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	357
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	358 if f["S"] != 0:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	359 val = "C%s H%s N%s O%s %s%s" % (
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	360 f["C"],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	361 f["H"],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	362 f["N"],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	363 f["O"],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	364 "S",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	365 f["S"],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	366 )
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	367 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	368 val = "C%s H%s N%s O%s" % (f["C"], f["H"], f["N"], f["O"])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	369
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	370 desc.append([val])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	371
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	372 if append:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	373 self.descriptor = np.hstack((self.descriptor, np.array(desc)))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	374 self.featurenames.append("Formula")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	375 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	376 self.descriptor = np.array(desc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	377 self.featurenames = ["Formula"]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	378
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	379 def calculate_MW(self, amide=False, append=False):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	380 """Method to calculate the molecular weight [g/mol] of every sequence in the attribute :py:attr:`sequences`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	381
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	382 :param amide: {boolean} whether the sequences are C-terminally amidated (subtracts 0.95 from the MW).
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	383 :param append: {boolean} whether the produced descriptor values should be appended to the existing ones in the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	384 attribute :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	385 :return: array of descriptor values in the attribute :py:attr:`descriptor`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	386 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	387
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	388 >>> desc = GlobalDescriptor('IAESFKGHIPL')
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	389 >>> desc.calculate_MW(amide=True)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	390 >>> desc.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	391 array([[ 1210.43]])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	392
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	393 .. seealso:: :py:func:`modlamp.core.aa_weights()`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	394
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	395 .. versionchanged:: v2.1.5 amide option added
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	396 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	397 desc = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	398 weights = aa_weights()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	399 for seq in self.sequences:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	400 mw = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	401 for aa in seq: # sum over aa weights
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	402 mw.append(weights[aa])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	403 desc.append(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	404 round(sum(mw) - 18.015 * (len(seq) - 1), 2)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	405 ) # sum over AA MW and subtract H20 MW for every
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	406 # peptide bond
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	407 desc = np.asarray(desc).reshape(len(desc), 1)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	408 if (
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	409 amide
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	410 ): # if sequences are amidated, subtract 0.98 from calculated MW (OH - NH2)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	411 desc = [d - 0.98 for d in desc]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	412 if append:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	413 self.descriptor = np.hstack((self.descriptor, np.array(desc)))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	414 self.featurenames.append("MW")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	415 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	416 self.descriptor = np.array(desc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	417 self.featurenames = ["MW"]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	418
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	419 def calculate_charge(self, ph=7.0, amide=False, append=False):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	420 """Method to overall charge of every sequence in the attribute :py:attr:`sequences`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	421
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	422 The method used is first described by Bjellqvist. In the case of amidation, the value for the 'Cterm' pKa is 15
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	423 (and Cterm is added to the pos_pKs dictionary.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	424 The pKa scale is extracted from: http://www.hbcpnetbase.com/ (CRC Handbook of Chemistry and Physics, 96th ed).
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	425
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	426 pos_pKs = {'Nterm': 9.38, 'K': 10.67, 'R': 12.10, 'H': 6.04}
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	427
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	428 neg_pKs = {'Cterm': 2.15, 'D': 3.71, 'E': 4.15, 'C': 8.14, 'Y': 10.10}
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	429
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	430 :param ph: {float} ph at which to calculate peptide charge.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	431 :param amide: {boolean} whether the sequences have an amidated C-terminus.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	432 :param append: {boolean} whether the produced descriptor values should be appended to the existing ones in the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	433 attribute :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	434 :return: array of descriptor values in the attribute :py:attr:`descriptor`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	435 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	436
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	437 >>> desc = GlobalDescriptor('KLAKFGKRSELVALSG')
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	438 >>> desc.calculate_charge(ph=7.4, amide=True)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	439 >>> desc.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	440 array([[ 3.989]])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	441 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	442
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	443 desc = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	444 for seq in self.sequences:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	445 desc.append(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	446 _charge(seq, ph, amide)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	447 ) # calculate charge with helper function
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	448 desc = np.asarray(desc).reshape(len(desc), 1)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	449 if append:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	450 self.descriptor = np.hstack((self.descriptor, np.array(desc)))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	451 self.featurenames.append("Charge")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	452 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	453 self.descriptor = np.array(desc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	454 self.featurenames = ["Charge"]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	455
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	456 def charge_density(self, ph=7.0, amide=False, append=False):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	457 """Method to calculate the charge density (charge / MW) of every sequences in the attributes :py:attr:`sequences`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	458
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	459 :param ph: {float} pH at which to calculate peptide charge.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	460 :param amide: {boolean} whether the sequences have an amidated C-terminus.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	461 :param append: {boolean} whether the produced descriptor values should be appended to the existing ones in the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	462 attribute :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	463 :return: array of descriptor values in the attribute :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	464 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	465
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	466 >>> desc = GlobalDescriptor('GNSDLLIEQRTLLASDEF')
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	467 >>> desc.charge_density(ph=6, amide=True)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	468 >>> desc.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	469 array([[-0.00097119]])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	470 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	471 self.calculate_charge(ph, amide)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	472 charges = self.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	473 self.calculate_MW(amide)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	474 masses = self.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	475 desc = charges / masses
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	476 desc = np.asarray(desc).reshape(len(desc), 1)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	477 if append:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	478 self.descriptor = np.hstack((self.descriptor, np.array(desc)))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	479 self.featurenames.append("ChargeDensity")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	480 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	481 self.descriptor = np.array(desc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	482 self.featurenames = ["ChargeDensity"]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	483
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	484 def isoelectric_point(self, amide=False, append=False):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	485 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	486 Method to calculate the isoelectric point of every sequence in the attribute :py:attr:`sequences`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	487 The pK scale is extracted from: http://www.hbcpnetbase.com/ (CRC Handbook of Chemistry and Physics, 96th ed).
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	488
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	489 pos_pKs = {'Nterm': 9.38, 'K': 10.67, 'R': 12.10, 'H': 6.04}
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	490
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	491 neg_pKs = {'Cterm': 2.15, 'D': 3.71, 'E': 4.15, 'C': 8.14, 'Y': 10.10}
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	492
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	493 :param amide: {boolean} whether the sequences have an amidated C-terminus.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	494 :param append: {boolean} whether the produced descriptor values should be appended to the existing ones in the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	495 attribute :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	496 :return: array of descriptor values in the attribute :py:attr:`descriptor`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	497 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	498
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	499 >>> desc = GlobalDescriptor('KLFDIKFGHIPQRST')
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	500 >>> desc.isoelectric_point()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	501 >>> desc.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	502 array([[ 10.6796875]])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	503 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	504 ph, ph1, ph2 = float(), float(), float()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	505 desc = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	506 for seq in self.sequences:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	507
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	508 # Bracket between ph1 and ph2
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	509 ph = 7.0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	510 charge = _charge(seq, ph, amide)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	511 if charge > 0.0:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	512 ph1 = ph
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	513 charge1 = charge
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	514 while charge1 > 0.0:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	515 ph = ph1 + 1.0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	516 charge = _charge(seq, ph, amide)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	517 if charge > 0.0:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	518 ph1 = ph
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	519 charge1 = charge
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	520 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	521 ph2 = ph
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	522 break
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	523 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	524 ph2 = ph
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	525 charge2 = charge
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	526 while charge2 < 0.0:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	527 ph = ph2 - 1.0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	528 charge = _charge(seq, ph, amide)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	529 if charge < 0.0:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	530 ph2 = ph
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	531 charge2 = charge
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	532 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	533 ph1 = ph
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	534 break
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	535 # Bisection
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	536 while ph2 - ph1 > 0.0001 and charge != 0.0:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	537 ph = (ph1 + ph2) / 2.0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	538 charge = _charge(seq, ph, amide)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	539 if charge > 0.0:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	540 ph1 = ph
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	541 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	542 ph2 = ph
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	543 desc.append(ph)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	544 desc = np.asarray(desc).reshape(len(desc), 1)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	545 if append:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	546 self.descriptor = np.hstack((self.descriptor, np.array(desc)))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	547 self.featurenames.append("pI")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	548 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	549 self.descriptor = np.array(desc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	550 self.featurenames = ["pI"]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	551
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	552 def instability_index(self, append=False):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	553 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	554 Method to calculate the instability of every sequence in the attribute :py:attr:`sequences`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	555 The instability index is a prediction of protein stability based on the amino acid composition.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	556 ([1] K. Guruprasad, B. V Reddy, M. W. Pandit, Protein Eng. 1990, 4, 155–161.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	557
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	558 :param append: {boolean} whether the produced descriptor values should be appended to the existing ones in the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	559 attribute :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	560 :return: array of descriptor values in the attribute :py:attr:`descriptor`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	561 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	562
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	563 >>> desc = GlobalDescriptor('LLASMNDLLAKRST')
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	564 >>> desc.instability_index()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	565 >>> desc.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	566 array([[ 63.95714286]])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	567 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	568
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	569 desc = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	570 dimv = load_scale("instability")[1]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	571 for seq in self.sequences:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	572 stabindex = float()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	573 for i in range(len(seq) - 1):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	574 stabindex += dimv[seq[i]][seq[i + 1]]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	575 desc.append((10.0 / len(seq)) * stabindex)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	576 desc = np.asarray(desc).reshape(len(desc), 1)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	577 if append:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	578 self.descriptor = np.hstack((self.descriptor, np.array(desc)))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	579 self.featurenames.append("InstabilityInd")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	580 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	581 self.descriptor = np.array(desc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	582 self.featurenames = ["InstabilityInd"]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	583
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	584 def aromaticity(self, append=False):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	585 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	586 Method to calculate the aromaticity of every sequence in the attribute :py:attr:`sequences`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	587 According to Lobry, 1994, it is simply the relative frequency of Phe+Trp+Tyr.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	588
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	589 :param append: {boolean} whether the produced descriptor values should be appended to the existing ones in the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	590 attribute :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	591 :return: array of descriptor values in the attribute :py:attr:`descriptor`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	592 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	593
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	594 >>> desc = GlobalDescriptor('GLFYWRFFLQRRFLYWW')
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	595 >>> desc.aromaticity()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	596 >>> desc.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	597 array([[ 0.52941176]])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	598 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	599 desc = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	600 for seq in self.sequences:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	601 f = seq.count("F")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	602 w = seq.count("W")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	603 y = seq.count("Y")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	604 desc.append(float(f + w + y) / len(seq))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	605 desc = np.asarray(desc).reshape(len(desc), 1)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	606 if append:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	607 self.descriptor = np.hstack((self.descriptor, np.array(desc)))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	608 self.featurenames.append("Aromaticity")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	609 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	610 self.descriptor = np.array(desc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	611 self.featurenames = ["Aromaticity"]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	612
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	613 def aliphatic_index(self, append=False):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	614 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	615 Method to calculate the aliphatic index of every sequence in the attribute :py:attr:`sequences`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	616 According to Ikai, 1980, the aliphatic index is a measure of thermal stability of proteins and is dependant
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	617 on the relative volume occupied by aliphatic amino acids (A,I,L & V).
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	618 ([1] A. Ikai, J. Biochem. 1980, 88, 1895–1898.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	619
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	620 :param append: {boolean} whether the produced descriptor values should be appended to the existing ones in the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	621 attribute :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	622 :return: array of descriptor values in the attribute :py:attr:`descriptor`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	623 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	624
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	625 >>> desc = GlobalDescriptor('KWLKYLKKLAKLVK')
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	626 >>> desc.aliphatic_index()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	627 >>> desc.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	628 array([[ 139.28571429]])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	629 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	630 desc = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	631 aa_dict = aa_weights()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	632 for seq in self.sequences:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	633 d = {aa: seq.count(aa) for aa in aa_dict.keys()} # count aa
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	634 d = {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	635 k: (float(d[k]) / len(seq)) * 100 for k in d.keys()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	636 } # get mole percent of all AA
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	637 desc.append(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	638 d["A"] + 2.9 * d["V"] + 3.9 * (d["I"] + d["L"])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	639 ) # formula for calculating the AI (Ikai, 1980)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	640 desc = np.asarray(desc).reshape(len(desc), 1)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	641 if append:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	642 self.descriptor = np.hstack((self.descriptor, np.array(desc)))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	643 self.featurenames.append("AliphaticInd")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	644 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	645 self.descriptor = np.array(desc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	646 self.featurenames = ["AliphaticInd"]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	647
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	648 def boman_index(self, append=False):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	649 """Method to calculate the boman index of every sequence in the attribute :py:attr:`sequences`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	650 According to Boman, 2003, the boman index is a measure for protein-protein interactions and is calculated by
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	651 summing over all amino acid free energy of transfer [kcal/mol] between water and cyclohexane,[2] followed by
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	652 dividing by sequence length.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	653 ([1] H. G. Boman, D. Wade, I. a Boman, B. Wåhlin, R. B. Merrifield, FEBS Lett. 1989, 259, 103–106.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	654 [2] A. Radzick, R. Wolfenden, Biochemistry 1988, 27, 1664–1670.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	655
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	656 .. seealso:: :py:func:`modlamp.core.aa_energies()`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	657
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	658 :param append: {boolean} whether the produced descriptor values should be appended to the existing ones in the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	659 attribute :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	660 :return: array of descriptor values in the attribute :py:attr:`descriptor`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	661 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	662
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	663 >>> desc = GlobalDescriptor('GLFDIVKKVVGALGSL')
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	664 >>> desc.boman_index()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	665 >>> desc.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	666 array([[-1.011875]])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	667 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	668 d = aa_energies()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	669 desc = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	670 for seq in self.sequences:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	671 val = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	672 for a in seq:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	673 val.append(d[a])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	674 desc.append(sum(val) / len(val))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	675 desc = np.asarray(desc).reshape(len(desc), 1)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	676 if append:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	677 self.descriptor = np.hstack((self.descriptor, np.array(desc)))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	678 self.featurenames.append("BomanInd")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	679 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	680 self.descriptor = np.array(desc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	681 self.featurenames = ["BomanInd"]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	682
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	683 def hydrophobic_ratio(self, append=False):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	684 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	685 Method to calculate the hydrophobic ratio of every sequence in the attribute :py:attr:`sequences`, which is the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	686 relative frequency of the amino acids A,C,F,I,L,M & V.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	687
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	688 :param append: {boolean} whether the produced descriptor values should be appended to the existing ones in the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	689 attribute :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	690 :return: array of descriptor values in the attribute :py:attr:`descriptor`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	691 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	692
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	693 >>> desc = GlobalDescriptor('VALLYWRTVLLAIII')
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	694 >>> desc.hydrophobic_ratio()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	695 >>> desc.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	696 array([[ 0.73333333]])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	697 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	698 desc = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	699 aa_dict = aa_weights()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	700 for seq in self.sequences:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	701 pa = {aa: seq.count(aa) for aa in aa_dict.keys()} # count aa
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	702 # formula for calculating the AI (Ikai, 1980):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	703 desc.append(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	704 (pa["A"] + pa["C"] + pa["F"] + pa["I"] + pa["L"] + pa["M"] + pa["V"])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	705 / float(len(seq))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	706 )
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	707 desc = np.asarray(desc).reshape(len(desc), 1)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	708 if append:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	709 self.descriptor = np.hstack((self.descriptor, np.array(desc)))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	710 self.featurenames.append("HydrophRatio")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	711 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	712 self.descriptor = np.array(desc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	713 self.featurenames = ["HydrophRatio"]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	714
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	715 def calculate_all(self, ph=7.4, amide=True):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	716 """Method combining all global descriptors and appending them into the feature matrix in the attribute
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	717 :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	718
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	719 :param ph: {float} pH at which to calculate peptide charge
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	720 :param amide: {boolean} whether the sequences have an amidated C-terminus.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	721 :return: array of descriptor values in the attribute :py:attr:`descriptor`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	722 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	723
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	724 >>> desc = GlobalDescriptor('AFGHFKLKKLFIFGHERT')
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	725 >>> desc.calculate_all(amide=True)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	726 >>> desc.featurenames
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	727 ['Length', 'MW', 'ChargeDensity', 'pI', 'InstabilityInd', 'Aromaticity', 'AliphaticInd', 'BomanInd', 'HydRatio']
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	728 >>> desc.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	729 array([[ 18., 2.17559000e+03, 1.87167619e-03, 1.16757812e+01, ... 1.10555556e+00, 4.44444444e-01]])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	730 >>> desc.save_descriptor('/path/to/outputfile.csv') # save the descriptor data (with feature names header)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	731 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	732
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	733 # This is a strange way of doing it. However, the append=True option excludes length and charge, no idea why!
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	734 fn = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	735 self.length() # sequence length
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	736 l = self.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	737 fn.extend(self.featurenames)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	738 self.calculate_MW(amide=amide) # molecular weight
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	739 mw = self.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	740 fn.extend(self.featurenames)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	741 self.calculate_charge(ph=ph, amide=amide) # net charge
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	742 c = self.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	743 fn.extend(self.featurenames)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	744 self.charge_density(ph=ph, amide=amide) # charge density
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	745 cd = self.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	746 fn.extend(self.featurenames)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	747 self.isoelectric_point(amide=amide) # pI
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	748 pi = self.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	749 fn.extend(self.featurenames)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	750 self.instability_index() # instability index
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	751 si = self.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	752 fn.extend(self.featurenames)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	753 self.aromaticity() # global aromaticity
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	754 ar = self.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	755 fn.extend(self.featurenames)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	756 self.aliphatic_index() # aliphatic index
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	757 ai = self.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	758 fn.extend(self.featurenames)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	759 self.boman_index() # Boman index
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	760 bi = self.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	761 fn.extend(self.featurenames)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	762 self.hydrophobic_ratio() # Hydrophobic ratio
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	763 hr = self.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	764 fn.extend(self.featurenames)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	765
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	766 self.descriptor = np.concatenate((l, mw, c, cd, pi, si, ar, ai, bi, hr), axis=1)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	767 self.featurenames = fn
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	768
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	769
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	770 class PeptideDescriptor(BaseDescriptor):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	771 """Base class for peptide descriptors. The following amino acid descriptor scales are available for descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	772 calculation:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	773
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	774 - AASI (An amino acid selectivity index scale for helical antimicrobial peptides, [1] D. Juretić, D. Vukicević, N. Ilić, N. Antcheva, A. Tossi, J. Chem. Inf. Model. 2009, 49, 2873–2882.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	775 - ABHPRK (modlabs inhouse physicochemical feature scale (Acidic, Basic, Hydrophobic, Polar, aRomatic, Kink-inducer)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	776 - argos (Argos hydrophobicity amino acid scale, [2] Argos, P., Rao, J. K. M. & Hargrave, P. A., Eur. J. Biochem. 2005, 128, 565–575.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	777 - bulkiness (Amino acid side chain bulkiness scale, [3] J. M. Zimmerman, N. Eliezer, R. Simha, J. Theor. Biol. 1968, 21, 170–201.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	778 - charge_phys (Amino acid charge at pH 7.0 - Hystidine charge +0.1.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	779 - charge_acid (Amino acid charge at acidic pH - Hystidine charge +1.0.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	780 - cougar (modlabs inhouse selection of global peptide descriptors)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	781 - eisenberg (the Eisenberg hydrophobicity consensus amino acid scale, [4] D. Eisenberg, R. M. Weiss, T. C. Terwilliger, W. Wilcox, Faraday Symp. Chem. Soc. 1982, 17, 109.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	782 - Ez (potential that assesses energies of insertion of amino acid side chains into lipid bilayers, [5] A. Senes, D. C. Chadi, P. B. Law, R. F. S. Walters, V. Nanda, W. F. DeGrado, J. Mol. Biol. 2007, 366, 436–448.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	783 - flexibility (amino acid side chain flexibilitiy scale, [6] R. Bhaskaran, P. K. Ponnuswamy, Int. J. Pept. Protein Res. 1988, 32, 241–255.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	784 - grantham (amino acid side chain composition, polarity and molecular volume, [8] Grantham, R. Science. 185, 862–864 (1974).)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	785 - gravy (GRAVY hydrophobicity amino acid scale, [9] J. Kyte, R. F. Doolittle, J. Mol. Biol. 1982, 157, 105–132.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	786 - hopp-woods (Hopp-Woods amino acid hydrophobicity scale,[10] T. P. Hopp, K. R. Woods, Proc. Natl. Acad. Sci. 1981, 78, 3824–3828.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	787 - ISAECI (Isotropic Surface Area (ISA) and Electronic Charge Index (ECI) of amino acid side chains, [11] E. R. Collantes, W. J. Dunn, J. Med. Chem. 1995, 38, 2705–2713.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	788 - janin (Janin hydrophobicity amino acid scale, [12] J. L. Cornette, K. B. Cease, H. Margalit, J. L. Spouge, J. A. Berzofsky, C. DeLisi, J. Mol. Biol. 1987, 195, 659–685.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	789 - kytedoolittle (Kyte & Doolittle hydrophobicity amino acid scale, [13] J. Kyte, R. F. Doolittle, J. Mol. Biol. 1982, 157, 105–132.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	790 - levitt_alpha (Levitt amino acid alpha-helix propensity scale, extracted from http://web.expasy.org/protscale. [14] M. Levitt, Biochemistry 1978, 17, 4277-4285.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	791 - MSS (A graph-theoretical index that reflects topological shape and size of amino acid side chains, [15] C. Raychaudhury, A. Banerjee, P. Bag, S. Roy, J. Chem. Inf. Comput. Sci. 1999, 39, 248–254.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	792 - MSW (Amino acid scale based on a PCA of the molecular surface based WHIM descriptor (MS-WHIM), extended to natural amino acids, [16] A. Zaliani, E. Gancia, J. Chem. Inf. Comput. Sci 1999, 39, 525–533.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	793 - pepArc (modlabs pharmacophoric feature scale, dimensions are: hydrophobicity, polarity, positive charge, negative charge, proline.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	794 - pepcats (modlabs pharmacophoric feature based PEPCATS scale, [17] C. P. Koch, A. M. Perna, M. Pillong, N. K. Todoroff, P. Wrede, G. Folkers, J. A. Hiss, G. Schneider, PLoS Comput. Biol. 2013, 9, e1003088.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	795 - polarity (Amino acid polarity scale, [18] J. M. Zimmerman, N. Eliezer, R. Simha, J. Theor. Biol. 1968, 21, 170–201.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	796 - PPCALI (modlabs inhouse scale derived from a PCA of 143 amino acid property scales, [19] C. P. Koch, A. M. Perna, M. Pillong, N. K. Todoroff, P. Wrede, G. Folkers, J. A. Hiss, G. Schneider, PLoS Comput. Biol. 2013, 9, e1003088.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	797 - refractivity (Relative amino acid refractivity values, [20] T. L. McMeekin, M. Wilensky, M. L. Groves, Biochem. Biophys. Res. Commun. 1962, 7, 151–156.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	798 - t_scale (A PCA derived scale based on amino acid side chain properties calculated with 6 different probes of the GRID program, [21] M. Cocchi, E. Johansson, Quant. Struct. Act. Relationships 1993, 12, 1–8.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	799 - TM_tend (Amino acid transmembrane propensity scale, extracted from http://web.expasy.org/protscale, [22] Zhao, G., London E. Protein Sci. 2006, 15, 1987-2001.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	800 - z3 (The original three dimensional Z-scale, [23] S. Hellberg, M. Sjöström, B. Skagerberg, S. Wold, J. Med. Chem. 1987, 30, 1126–1135.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	801 - z5 (The extended five dimensional Z-scale, [24] M. Sandberg, L. Eriksson, J. Jonsson, M. Sjöström, S. Wold, J. Med. Chem. 1998, 41, 2481–2491.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	802
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	803 Further, amino acid scale independent methods can be calculated with help of the :class:`GlobalDescriptor` class.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	804
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	805 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	806
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	807 def __init__(self, seqs, scalename="Eisenberg"):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	808 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	809 :param seqs: a .fasta file with sequences, a list of sequences or a single sequence as string to calculate the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	810 descriptor values for.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	811 :param scalename: {str} name of the amino acid scale (one of the given list above) used to calculate the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	812 descriptor values
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	813 :return: initialized attributes :py:attr:`sequences`, :py:attr:`names` and dictionary :py:attr:`scale` with
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	814 amino acid scale values of the scale name in :py:attr:`scalename`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	815 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	816
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	817 >>> AMP = PeptideDescriptor('KLLKLLKKLLKLLK','pepcats')
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	818 >>> AMP.sequences
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	819 ['KLLKLLKKLLKLLK']
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	820 >>> seqs = PeptideDescriptor('/Path/to/file.fasta', 'eisenberg') # load sequences from .fasta file
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	821 >>> seqs.sequences
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	822 ['AFDGHLKI','KKLQRSDLLRTK','KKLASCNNIPPR'...]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	823 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	824 super(PeptideDescriptor, self).__init__(seqs)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	825 self.scalename, self.scale = load_scale(scalename.lower())
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	826 self.all_moms = list() # for passing hydrophobic moments to calculate_profile
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	827 self.all_globs = list() # for passing global to calculate_profile
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	828
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	829 def load_scale(self, scalename):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	830 """Method to load amino acid values from a given scale
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	831
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	832 :param scalename: {str} name of the amino acid scale to be loaded.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	833 :return: loaded amino acid scale values in a dictionary in the attribute :py:attr:`scale`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	834
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	835 .. seealso:: :func:`modlamp.core.load_scale()`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	836 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	837 self.scalename, self.scale = load_scale(scalename.lower())
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	838
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	839 def calculate_autocorr(self, window, append=False):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	840 """Method for auto-correlating the amino acid values for a given descriptor scale
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	841
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	842 :param window: {int} correlation window for descriptor calculation in a sliding window approach
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	843 :param append: {boolean} whether the produced descriptor values should be appended to the existing ones in the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	844 attribute :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	845 :return: calculated descriptor numpy.array in the attribute :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	846 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	847
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	848 >>> AMP = PeptideDescriptor('GLFDIVKKVVGALGSL','PPCALI')
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	849 >>> AMP.calculate_autocorr(7)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	850 >>> AMP.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	851 array([[ 1.28442339e+00, 1.29025116e+00, 1.03240901e+00, .... ]])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	852 >>> AMP.descriptor.shape
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	853 (1, 133)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	854
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	855 .. versionchanged:: v.2.3.0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	856 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	857 desc = Parallel(n_jobs=-1)(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	858 delayed(_one_autocorr)(seq, window, self.scale) for seq in self.sequences
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	859 )
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	860
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	861 if append:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	862 self.descriptor = np.hstack((self.descriptor, np.array(desc)))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	863 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	864 self.descriptor = np.array(desc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	865
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	866 def calculate_crosscorr(self, window, append=False):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	867 """Method for cross-correlating the amino acid values for a given descriptor scale
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	868
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	869 :param window: {int} correlation window for descriptor calculation in a sliding window approach
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	870 :param append: {boolean} whether the produced descriptor values should be appended to the existing ones in the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	871 attribute :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	872 :return: calculated descriptor numpy.array in the attribute :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	873 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	874
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	875 >>> AMP = PeptideDescriptor('GLFDIVKKVVGALGSL','pepcats')
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	876 >>> AMP.calculate_crosscorr(7)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	877 >>> AMP.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	878 array([[ 0.6875 , 0.46666667, 0.42857143, 0.61538462, 0.58333333, ... ]])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	879 >>> AMP.descriptor.shape
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	880 (1, 147)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	881 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	882 desc = Parallel(n_jobs=-1)(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	883 delayed(_one_crosscorr)(seq, window, self.scale) for seq in self.sequences
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	884 )
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	885
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	886 if append:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	887 self.descriptor = np.hstack((self.descriptor, np.array(desc)))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	888 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	889 self.descriptor = np.array(desc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	890
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	891 def calculate_moment(self, window=1000, angle=100, modality="max", append=False):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	892 """Method for calculating the maximum or mean moment of the amino acid values for a given descriptor scale and
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	893 window.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	894
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	895 :param window: {int} amino acid window in which to calculate the moment. If the sequence is shorter than the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	896 window, the length of the sequence is taken. So if the default window of 1000 is chosen, for all sequences
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	897 shorter than 1000, the global hydrophobic moment will be calculated. Otherwise, the maximal
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	898 hydrophiobic moment for the chosen window size found in the sequence will be returned.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	899 :param angle: {int} angle in which to calculate the moment. 100 for alpha helices, 180 for beta sheets.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	900 :param modality: {'all', 'max' or 'mean'} Calculate respectively maximum or mean hydrophobic moment. If all,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	901 moments for all windows are returned.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	902 :param append: {boolean} whether the produced descriptor values should be appended to the existing ones in the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	903 attribute :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	904 :return: Calculated descriptor as a numpy.array in the attribute :py:attr:`descriptor` and all possible global
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	905 values in :py:attr:`all_moms` (needed for the :py:func:`calculate_profile` method)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	906 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	907
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	908 >>> AMP = PeptideDescriptor('GLFDIVKKVVGALGSL', 'eisenberg')
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	909 >>> AMP.calculate_moment()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	910 >>> AMP.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	911 array([[ 0.48790226]])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	912 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	913 if self.scale["A"] == list:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	914 print(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	915 "\n Descriptor moment calculation is only possible for one dimensional descriptors.\n"
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	916 )
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	917
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	918 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	919 desc = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	920 for seq in self.sequences:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	921 wdw = min(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	922 window, len(seq)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	923 ) # if sequence is shorter than window, take the whole sequence instead
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	924 mtrx = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	925 mwdw = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	926
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	927 for aa in range(len(seq)):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	928 mtrx.append(self.scale[str(seq[aa])])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	929
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	930 for i in range(len(mtrx) - wdw + 1):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	931 mwdw.append(sum(mtrx[i : i + wdw], []))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	932
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	933 mwdw = np.asarray(mwdw)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	934 rads = (
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	935 angle * (np.pi / 180) * np.asarray(range(wdw))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	936 ) # calculate actual moment (radial)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	937 vcos = (mwdw * np.cos(rads)).sum(axis=1)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	938 vsin = (mwdw * np.sin(rads)).sum(axis=1)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	939 moms = np.sqrt(vsin2 + vcos2) / wdw
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	940
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	941 if modality == "max": # take window with maximal value
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	942 moment = np.max(moms)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	943 elif modality == "mean": # take average value over all windows
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	944 moment = np.mean(moms)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	945 elif modality == "all":
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	946 moment = moms
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	947 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	948 print(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	949 '\nERROR!\nModality parameter is wrong, please choose between "all", "max" and "mean".\n'
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	950 )
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	951 return
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	952 desc.append(moment)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	953 self.all_moms.append(moms)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	954
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	955 desc = np.asarray(desc).reshape(len(desc), 1) # final descriptor array
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	956
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	957 if append:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	958 self.descriptor = np.hstack((self.descriptor, np.array(desc)))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	959 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	960 self.descriptor = np.array(desc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	961
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	962 def calculate_global(self, window=1000, modality="max", append=False):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	963 """Method for calculating a global / window averaging descriptor value of a given AA scale
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	964
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	965 :param window: {int} amino acid window in which to calculate the moment. If the sequence is shorter than the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	966 window, the length of the sequence is taken.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	967 :param modality: {'max' or 'mean'} Calculate respectively maximum or mean hydrophobic moment.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	968 :param append: {boolean} whether the produced descriptor values should be appended to the existing ones in the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	969 attribute :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	970 :return: Calculated descriptor as a numpy.array in the attribute :py:attr:`descriptor` and all possible global
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	971 values in :py:attr:`all_globs` (needed for the :py:func:`calculate_profile` method)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	972 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	973
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	974 >>> AMP = PeptideDescriptor('GLFDIVKKVVGALGSL','eisenberg')
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	975 >>> AMP.calculate_global(window=1000, modality='max')
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	976 >>> AMP.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	977 array([[ 0.44875]])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	978 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	979 desc = list()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	980 for n, seq in enumerate(self.sequences):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	981 wdw = min(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	982 window, len(seq)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	983 ) # if sequence is shorter than window, take the whole sequence instead
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	984 mtrx = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	985 mwdw = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	986
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	987 for l in range(len(seq)): # translate AA sequence into values
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	988 mtrx.append(self.scale[str(seq[l])])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	989
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	990 for i in range(len(mtrx) - wdw + 1):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	991 mwdw.append(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	992 sum(mtrx[i : i + wdw], [])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	993 ) # list of all the values for the different windows
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	994
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	995 mwdw = np.asarray(mwdw)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	996 glob = np.sum(mwdw, axis=1) / float(wdw)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	997 outglob = float()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	998
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	999 if modality in ["max", "mean"]:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1000 if modality == "max":
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1001 outglob = np.max(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1002 glob
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1003 ) # returned moment will be the maximum of all windows
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1004 elif modality == "mean":
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1005 outglob = np.mean(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1006 glob
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1007 ) # returned moment will be the mean of all windows
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1008 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1009 print(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1010 'Modality parameter is wrong, please choose between "max" and "mean"\n.'
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1011 )
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1012 return
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1013 desc.append(outglob)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1014 self.all_globs.append(glob)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1015
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1016 desc = np.asarray(desc).reshape(len(desc), 1)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1017 if append:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1018 self.descriptor = np.hstack((self.descriptor, np.array(desc)))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1019 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1020 self.descriptor = np.array(desc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1021
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1022 def calculate_profile(self, prof_type="uH", window=7, append=False):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1023 """Method for calculating hydrophobicity or hydrophobic moment profiles for given sequences and fitting for
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1024 slope and intercept. The hydrophobicity scale used is "eisenberg"
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1025
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1026 :param prof_type: prof_type of profile, available: 'H' for hydrophobicity or 'uH' for hydrophobic moment
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1027 :param window: {int} size of sliding window used (odd-numbered).
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1028 :param append: {boolean} whether the produced descriptor values should be appended to the existing ones in the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1029 attribute :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1030 :return: Fitted slope and intercept of calculated profile for every given sequence in the attribute
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1031 :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1032 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1033
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1034 >>> AMP = PeptideDescriptor('KLLKLLKKVVGALG','kytedoolittle')
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1035 >>> AMP.calculate_profile(prof_type='H')
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1036 >>> AMP.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1037 array([[ 0.03731293, 0.19246599]])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1038 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1039 if prof_type == "uH":
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1040 self.calculate_moment(window=window)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1041 y_vals = self.all_moms
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1042 elif prof_type == "H":
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1043 self.calculate_global(window=window)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1044 y_vals = self.all_globs
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1045 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1046 print(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1047 'prof_type parameter is unknown, choose "uH" for hydrophobic moment or "H" for hydrophobicity\n.'
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1048 )
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1049 sys.exit()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1050
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1051 desc = list()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1052 for n, seq in enumerate(self.sequences):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1053 x_vals = range(len(seq))[int((window - 1) / 2) : -int((window - 1) / 2)]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1054 if len(seq) <= window:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1055 slope, intercept, r_value, p_value, std_err = [0, 0, 0, 0, 0]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1056 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1057 slope, intercept, r_value, p_value, std_err = stats.linregress(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1058 x_vals, y_vals[n]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1059 )
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1060 desc.append([slope, intercept])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1061
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1062 if append:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1063 self.descriptor = np.hstack((self.descriptor, np.array(desc)))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1064 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1065 self.descriptor = np.array(desc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1066
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1067 def calculate_arc(self, modality="max", append=False):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1068 """Method for calculating property arcs as seen in the helical wheel plot. Use for binary amino acid scales only.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1069
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1070 :param modality: modality of the arc to calculate, to choose between "max" and "mean".
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1071 :param append: if true, append to current descriptor stored in the descriptor attribute.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1072 :return: calculated descriptor as numpy.array in the descriptor attribute.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1073
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1074 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1075
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1076 >>> arc = PeptideDescriptor("KLLKLLKKLLKLLK", scalename="peparc")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1077 >>> arc.calculate_arc(modality="max", append=False)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1078 >>> arc.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1079 array([[200, 160, 160, 0, 0]])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1080 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1081 desc = Parallel(n_jobs=-1)(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1082 delayed(_one_arc)(seq, modality, self.scale) for seq in self.sequences
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1083 )
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1084
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1085 # Converts each of the amino acids to descriptor vector
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1086 for seq in self.sequences:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1087
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1088 # desc_mat = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1089 # for aa in seq:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1090 # desc_mat.append(self.scale[aa])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1091 # desc_mat = np.asarray(desc_mat)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1092 #
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1093 # # Check descriptor dimension
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1094 # desc_dim = desc_mat.shape[1]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1095 #
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1096 # # list to store descriptor values for all windows
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1097 # allwindows_arc = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1098 #
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1099 # if len(seq) > 18:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1100 # window = 18
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1101 # # calculates number of windows in sequence
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1102 # num_windows = len(seq) - window
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1103 # else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1104 # window = len(seq)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1105 # num_windows = 1
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1106 #
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1107 # # loop through all windows
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1108 # for j in range(num_windows):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1109 # # slices descriptor matrix into current window
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1110 # window_mat = desc_mat[j:j + window, :]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1111 #
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1112 # # defines order of amino acids in helical projection
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1113 # order = [0, 11, 4, 15, 8, 1, 12, 5, 16, 9, 2, 13, 6, 17, 10, 3, 14, 7]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1114 #
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1115 # # orders window descriptor matrix into helical projection order
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1116 # ordered = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1117 # for pos in order:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1118 # try:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1119 # ordered.append(window_mat[pos, :])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1120 # except:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1121 # # for sequences of len < 18 adding dummy vector with 2s, length of descriptor dimensions
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1122 # ordered.append([2] * desc_dim)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1123 # ordered = np.asarray(ordered)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1124 #
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1125 # window_arc = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1126 #
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1127 # # loop through pharmacophoric features
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1128 # for m in range(desc_dim):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1129 # all_arcs = [] # stores all arcs that can be found of a pharmacophoric feature
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1130 # arc = 0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1131 #
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1132 # for n in range(18): # for all positions in helix, regardless of sequence length
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1133 # if ordered[n, m] == 0: # if position does not contain pharmacophoric feature
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1134 # all_arcs.append(arc) # append previous arc to all arcs list
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1135 # arc = 0 # arc is initialized
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1136 # elif ordered[n, m] == 1: # if position contains pharmacophoric feature(PF), elongate arc by 20°
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1137 # arc += 20
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1138 # elif ordered[n, m] == 2: # if position doesn't contain amino acid:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1139 # if ordered[n - 1, m] == 1: # if previous position contained PF add 10°
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1140 # arc += 10
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1141 # elif ordered[n - 1, m] == 0: # if previous position didn't contain PF don't add anything
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1142 # arc += 0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1143 # elif ordered[
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1144 # n - 2, m] == 1: # if previous position is empty then check second previous for PF
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1145 # arc += 10
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1146 # if n == 17: # if we are at the last position check for position n=0 instead of next position.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1147 # if ordered[0, m] == 1: # if it contains PF add 10° extra
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1148 # arc += 10
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1149 # else: # if next position contains PF add 10° extra
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1150 # if ordered[n + 1, m] == 1:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1151 # arc += 10
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1152 # elif ordered[n + 1, m] == 0:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1153 # arc += 0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1154 # else: # if next position is empty check for 2nd next position
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1155 # if n == 16:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1156 # if ordered[0, m] == 1:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1157 # arc += 10
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1158 # else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1159 # if ordered[n + 2, m] == 1:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1160 # arc += 10
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1161 #
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1162 # all_arcs.append(arc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1163 # if not arc == 360:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1164 # arc0 = all_arcs.pop() + all_arcs[0] # join first and last arc together
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1165 # all_arcs = [arc0] + all_arcs[1:]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1166 #
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1167 # window_arc.append(np.max(all_arcs)) # append to window arcs the maximum arc of this PF
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1168 # allwindows_arc.append(window_arc) # append all PF arcs of this window
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1169 #
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1170 # allwindows_arc = np.asarray(allwindows_arc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1171 #
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1172 # if modality == 'max':
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1173 # final_arc = np.max(allwindows_arc, axis=0) # calculate maximum / mean arc along all windows
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1174 # elif modality == 'mean':
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1175 # final_arc = np.mean(allwindows_arc, axis=0)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1176 # else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1177 # print('modality is unknown, please choose between "max" and "mean"\n.')
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1178 # sys.exit()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1179
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1180 if append:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1181 self.descriptor = np.hstack((self.descriptor, np.array(desc)))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1182 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c cpt parents: diff changeset	1183 self.descriptor = np.array(desc)

Mercurial > repos > cpt > cpt_helical_wheel

annotate plotWheels/descriptors.py @ 2:e9fb56f44c35 draft default tip