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
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
|
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2018 João Pedro Rodrigues
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""
Assigns the elements in the PDB file from atom names.
Usage:
python pdb_element.py <pdb file>
Example:
python pdb_element.py 1CTF.pdb
This program is part of the `pdb-tools` suite of utilities and should not be
distributed isolatedly. The `pdb-tools` were created to quickly manipulate PDB
files using the terminal, and can be used sequentially, with one tool streaming
data to another. They are based on old FORTRAN77 code that was taking too much
effort to maintain and compile. RIP.
"""
import os
import sys
__author__ = "Joao Rodrigues"
__email__ = "j.p.g.l.m.rodrigues@gmail.com"
def check_input(args):
"""Checks whether to read from stdin/file and validates user input/options.
"""
# Defaults
fh = sys.stdin # file handle
if not len(args):
# Reading from pipe with default option
if sys.stdin.isatty():
sys.stderr.write(__doc__)
sys.exit(1)
elif len(args) == 1:
if not os.path.isfile(args[0]):
emsg = 'ERROR!! File not found or not readable: \'{}\'\n'
sys.stderr.write(emsg.format(args[0]))
sys.stderr.write(__doc__)
sys.exit(1)
fh = open(args[0], 'r')
else: # Whatever ...
emsg = 'ERROR!! Script takes 1 argument, not \'{}\'\n'
sys.stderr.write(emsg.format(len(args)))
sys.stderr.write(__doc__)
sys.exit(1)
return fh
def pad_line(line):
"""Helper function to pad line to 80 characters in case it is shorter"""
size_of_line = len(line)
if size_of_line < 80:
padding = 80 - size_of_line + 1
line = line.strip('\n') + ' ' * padding + '\n'
return line[:81] # 80 + newline character
def run(fhandle):
"""
Assign each atom's element based on the atom name field.
Rules specified in the format specification:
- Alignment of one-letter atom name such as C starts at column 14,
while two-letter atom name such as FE starts at column 13.
- Atom nomenclature begins with atom type.
This function is a generator.
Parameters
----------
fhandle : a line-by-line iterator of the original PDB file.
Yields
------
str (line-by-line)
The modified (or not) PDB line.
"""
_pad_line = pad_line
elements = set(('H', 'D', 'HE', 'LI', 'BE', 'B', 'C', 'N', 'O', 'F', 'NE',
'NA', 'MG', 'AL', 'SI', 'P', 'S', 'CL', 'AR', 'K', 'CA',
'SC', 'TI', 'V', 'CR', 'MN', 'FE', 'CO', 'NI', 'CU', 'ZN',
'GA', 'GE', 'AS', 'SE', 'BR', 'KR', 'RB', 'SR', 'Y', 'ZR',
'NB', 'MO', 'TC', 'RU', 'RH', 'PD', 'AG', 'CD', 'IN', 'SN',
'SB', 'TE', 'I', 'XE', 'CS', 'BA', 'LA', 'CE', 'PR', 'ND',
'PM', 'SM', 'EU', 'GD', 'TB', 'DY', 'HO', 'ER', 'TM', 'YB',
'LU', 'HF', 'TA', 'W', 'RE', 'OS', 'IR', 'PT', 'AU', 'HG',
'TL', 'PB', 'BI', 'PO', 'AT', 'RN', 'FR', 'RA', 'AC', 'TH',
'PA', 'U', 'NP', 'PU', 'AM', 'CM', 'BK', 'CF', 'ES', 'FM',
'MD', 'NO', 'LR', 'RF', 'DB', 'SG', 'BH', 'HS', 'MT'))
records = ('ATOM', 'HETATM', 'ANISOU')
for line in fhandle:
if line.startswith(records):
line = _pad_line(line)
atom_name = line[12:16]
if atom_name[0].isalpha() and not atom_name[2:].isdigit():
element = atom_name.strip()
else:
atom_name = atom_name.strip()
if atom_name[0].isdigit():
element = atom_name[1]
else:
element = atom_name[0]
if element not in elements:
element = ' ' # empty element in case we cannot assign
line = line[:76] + element.rjust(2) + line[78:]
yield line
assign_element = run
def main():
# Check Input
pdbfh = check_input(sys.argv[1:])
# Do the job
new_pdb = run(pdbfh)
try:
_buffer = []
_buffer_size = 5000 # write N lines at a time
for lineno, line in enumerate(new_pdb):
if not (lineno % _buffer_size):
sys.stdout.write(''.join(_buffer))
_buffer = []
_buffer.append(line)
sys.stdout.write(''.join(_buffer))
sys.stdout.flush()
except IOError:
# This is here to catch Broken Pipes
# for example to use 'head' or 'tail' without
# the error message showing up
pass
# last line of the script
# We can close it even if it is sys.stdin
pdbfh.close()
sys.exit(0)
if __name__ == '__main__':
main()
|
