/usr/lib/pyrite-publisher/PyritePublisher/plugin_pdboutput.py is in pyrite-publisher 2.1.1-11.
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 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 | #
# $Id: plugin_pdboutput.py,v 1.4 2002/07/15 21:40:28 rob Exp $
#
# Copyright 2001 Rob Tillotson <rob@pyrite.org>
# All Rights Reserved
#
# Permission to use, copy, modify, and distribute this software and
# its documentation for any purpose and without fee or royalty is
# hereby granted, provided that the above copyright notice appear in
# all copies and that both the copyright notice and this permission
# notice appear in supporting documentation or portions thereof,
# including modifications, that you you make.
#
# THE AUTHOR ROB TILLOTSON DISCLAIMS ALL WARRANTIES WITH REGARD TO
# THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY
# AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
# SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER
# RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF
# CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN
# CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE!
#
"""Generic Palm database output plugin.
This simple plugin allows the previous plugin in the chain to
write a pdb/prc file in whatever arbitrary manner it wants.
The value passed to the previous plugin is simply a prc.File
instance.
"""
__version__ = '$Id: plugin_pdboutput.py,v 1.4 2002/07/15 21:40:28 rob Exp $'
__author__ = 'Rob Tillotson <rob@pyrite.org>'
__copyright__ = 'Copyright 2001 Rob Tillotson <rob@pyrite.org>'
import os, time
from dtkplugins import OutputPlugin
import prc
# from the python cookbook
_num_rep = {}
for x in 'abcdefghijklmnopqrstuvwxyz':
_num_rep[ord(x)-ord('a')+10] = x
def decimalToN(num,n):
new_num_string=''
current=num
while current!=0:
remainder=current%n
if 36>remainder>9:
remainder_string=_num_rep[remainder]
elif remainder>=36:
remainder_string='('+str(remainder)+')'
else:
remainder_string=str(remainder)
new_num_string=remainder_string+new_num_string
current=current/n
return new_num_string
_id_begin = 1017175873
def gen_id():
s = decimalToN(long((time.time()-1015000000)*10), 36)
if len(s) < 6: return ('000000'+s)[-6:]
class Plugin(OutputPlugin):
name = 'PDBOutput'
description = 'Generic Palm database output'
installable = 1
links = [ (0, "pdb-output", None) ]
def __init__(self, *a, **kw):
apply(OutputPlugin.__init__, (self,)+a, kw)
self._add_property('output_dir', 'Output directory')
self._add_cli_option('output_dir', 'd', 'output-directory',
'Set the output directory',
vtype="STR")
self.output_dir = '.'
self._add_property('output_filename', 'Output filename')
self._add_cli_option('output_filename', 'o', None,
'Set the output filename',
vtype="STR")
self.output_filename = ''
self._add_property('unique_names', 'Guarantee unique DB names')
self._add_cli_option('unique_names', None, 'unique-names',
'Guarantee unique DB names', boolean=1)
self.unique_names = 0
def open(self, chain, next, protocol, basename, *a, **kw):
if self.output_filename: fn = self.output_filename
else: fn = os.path.join(self.output_dir, basename+'.pdb')
self.filename = fn
self.pdb = prc.File(fn, read=0, write=1, info={'name': basename})
return self.pdb
def close(self):
if self.unique_names:
id = gen_id()
oldname = self.pdb.getDBInfo().get('name','')
newname = (oldname + ' '*31)[:31-len(id)]+id
self.pdb.updateDBInfo({'name': newname})
self.pdb.close()
self.pdb = None
if self.install:
self.do_install(self.filename)
|