/usr/share/pyshared/Bio/FSSP/FSSPTools.py is in python-biopython 1.58-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 | from Bio import FSSP
import copy
from Bio.Align import Generic
from Bio import Alphabet
import time
class FSSPAlign(Generic.Alignment):
def _add_numbering_table(self, new_record):
new_record.annotations['abs2pdb'] = {}
new_record.annotations['pdb2abs'] = {}
class FSSPMultAlign(dict):
def __init__(self):
self.abs_res = []
self.pdb_res = []
self.data = {}
def mult_align(sum_dict,align_dict):
"""Returns a biopython multiple alignment instance (Bio.Align.Generic)"""
mult_align_dict = {}
for j in align_dict.abs(1).pos_align_dict:
mult_align_dict[j] = ''
for i in range(1,len(align_dict)+1):
# loop on positions
for j in align_dict.abs(i).pos_align_dict:
# loop within a position
mult_align_dict[j] += align_dict.abs(i).pos_align_dict[j].aa
seq_order = mult_align_dict.keys()
seq_order.sort()
fssp_align = Generic.Alignment(Alphabet.Gapped(
Alphabet.IUPAC.extended_protein))
for i in seq_order:
fssp_align.add_sequence(sum_dict[i].pdb2+sum_dict[i].chain2,
mult_align_dict[i])
# fssp_align._add_numbering_table()
return fssp_align
# Several routines used to extract information from FSSP sections
# filter:
# filters a passed summary section and alignment section according to a numeric
# attribute in the summary section. Returns new summary and alignment sections
# For example, to filter in only those records which have a zscore greater than
# 4.0 and lesser than 7.5:
# new_sum, new_align = filter(sum, align, 'zscore', 4, 7.5)
#
# Warning: this function really slows down when filtering large FSSP files.
# The reason is the use of copy.deepcopy() to copy align_dict into
# new_align_dict. I have to figure out something better.
# Took me ~160 seconds for the largest FSSP file (1reqA.fssp)
#
def filter(sum_dict,align_dict,filter_attribute,low_bound, high_bound):
"""filters a passed summary section and alignment section according to a numeric
attribute in the summary section. Returns new summary and alignment sections"""
new_sum_dict = FSSP.FSSPSumDict()
new_align_dict = copy.deepcopy(align_dict)
# for i in align_dict:
# new_align_dict[i] = copy.copy(align_dict[i])
# new_align_dict = copy.copy(align_dict)
for prot_num in sum_dict:
attr_value = getattr(sum_dict[prot_num],filter_attribute)
if (attr_value >= low_bound and
attr_value <= high_bound):
new_sum_dict[prot_num] = sum_dict[prot_num]
prot_numbers = new_sum_dict.keys()
prot_numbers.sort()
for pos_num in new_align_dict.abs_res_dict:
new_align_dict.abs(pos_num).pos_align_dict = {}
for prot_num in prot_numbers:
new_align_dict.abs(pos_num).pos_align_dict[prot_num] = \
align_dict.abs(pos_num).pos_align_dict[prot_num]
return new_sum_dict, new_align_dict
def name_filter(sum_dict, align_dict, name_list):
""" Accepts a list of names. Returns a new Summary block and Alignment block which
contain the info only for those names passed."""
new_sum_dict = FSSP.FSSPSumDict()
new_align_dict = copy.deepcopy(align_dict)
for cur_pdb_name in name_list:
for prot_num in sum_dict:
if sum_dict[prot_num].pdb2+sum_dict[prot_num].chain2 == cur_pdb_name:
new_sum_dict[prot_num] = sum_dict[prot_num]
prot_numbers = new_sum_dict.keys()
prot_numbers.sort()
for pos_num in new_align_dict.abs_res_dict:
new_align_dict.abs(pos_num).pos_align_dict = {}
for prot_num in prot_numbers:
new_align_dict.abs(pos_num).pos_align_dict[prot_num] = \
align_dict.abs(pos_num).pos_align_dict[prot_num]
return new_sum_dict, new_align_dict
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