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Daniel Bauer
981
profiles/pymol/.pymol/startup/dssp_stride.py
Normal file
981
profiles/pymol/.pymol/startup/dssp_stride.py
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@@ -0,0 +1,981 @@
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""" 2011_04_11: Hongbo Zhu
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PyMOL plugin for running DSSP and display SS using different colors.
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The DSSP codes for secondary structure are:
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H - Alpha helix (4-12)
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G - 3-10 helix
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I - pi helix
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E - Strand
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B - Isolated beta-bridge residue
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T - Turn
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S - Bend
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- - None
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2011_04_24: add stride
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STRIDE code (taken from stride.doc) is nearly the same as DSSP
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H Alpha helix
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G 3-10 helix
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I PI-helix
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E Extended conformation
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B or b Isolated bridge
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T Turn
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C Coil (none of the above)
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"""
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# Copyright Notice
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# ================
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#
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# The PyMOL Plugin source code in this file is copyrighted, but you can
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# freely use and copy it as long as you don't change or remove any of
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# the copyright notices.
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#
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# ----------------------------------------------------------------------
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# This PyMOL Plugin is Copyright (C) 2011 by
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# Hongbo Zhu <hongbo.zhu.cn at googlemail dot com>
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#
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# All Rights Reserved
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#
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# Permission to use, copy, modify, distribute, and distribute modified
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# versions of this software and its documentation for any purpose and
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# without fee is hereby granted, provided that the above copyright
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# notice appear in all copies and that both the copyright notice and
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# this permission notice appear in supporting documentation, and that
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# the name(s) of the author(s) not be used in advertising or publicity
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# pertaining to distribution of the software without specific, written
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# prior permission.
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#
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# THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,
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# INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN
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# NO EVENT SHALL THE AUTHOR(S) BE LIABLE FOR ANY SPECIAL, INDIRECT OR
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# CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF
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# USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
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# OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
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# PERFORMANCE OF THIS SOFTWARE.
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# ----------------------------------------------------------------------
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# python lib
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import os
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import sys
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import platform
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if sys.version_info >= (2,4):
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import subprocess # subprocess is introduced in python 2.4
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import math
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import random
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import tempfile
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import tkSimpleDialog
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import tkMessageBox
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import tkFileDialog
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import tkColorChooser
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import Tkinter
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# pymol lib
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try:
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from pymol import cmd
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from pymol.cgo import *
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except ImportError:
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print 'Warning: pymol library cmd not found.'
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sys.exit(1)
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# external lib
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try:
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import Pmw
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except ImportError:
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print 'Warning: failed to import Pmw. Exit ...'
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sys.exit(1)
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VERBOSE = True
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#################
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## here we go
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#################
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def __init__(self):
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""" DSSP and Stride plugin for PyMol
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"""
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self.menuBar.addmenuitem('Plugin', 'command',
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'DSSP & Stride', label = 'DSSP & Stride',
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command = lambda s=self : DSSPPlugin(s))
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#################
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## GUI related
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#################
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class DSSPPlugin:
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def __init__(self, app):
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self.parent = app.root
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self.dialog = Pmw.Dialog(self.parent,
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buttons = ('Run DSSP',
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'Run Stride',
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'Update Color',
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'Update ss',
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'Exit'),
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title = 'DSSP and Stride Plugin for PyMOL',
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command = self.execute)
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Pmw.setbusycursorattributes(self.dialog.component('hull'))
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# parameters used by DSSP
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self.pymol_sel = Tkinter.StringVar()
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self.dssp_bin = Tkinter.StringVar()
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self.stride_bin = Tkinter.StringVar()
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self.dssp_rlt_dict = {}
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self.stride_rlt_dict = {}
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self.ss_asgn_prog = None # which program is used to assign ss
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self.sel_obj_list = [] # there may be more than one seletion or object
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# defined by self.pymol_sel
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# treat each selection and object separately
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if 'DSSP_BIN' not in os.environ and 'PYMOL_GIT_MOD' in os.environ:
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if sys.platform.startswith('linux') and platform.machine() == 'x86_32':
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initialdir_dssp = os.path.join(os.environ['PYMOL_GIT_MOD'],"DSSP","i86Linux2","dssp-2")
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os.environ['DSSP_BIN'] = initialdir_dssp
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elif sys.platform.startswith('linux') and platform.machine() == 'x86_64':
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initialdir_dssp = os.path.join(os.environ['PYMOL_GIT_MOD'],"DSSP","ia64Linux2","dssp-2")
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os.environ['DSSP_BIN'] = initialdir_dssp
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elif sys.platform.startswith('win'):
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initialdir_dssp = os.path.join(os.environ['PYMOL_GIT_MOD'],"DSSP","win32","dssp.exe")
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os.environ['DSSP_BIN'] = initialdir_dssp
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else:
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pass
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if 'DSSP_BIN' in os.environ:
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if VERBOSE: print 'Found DSSP_BIN in environmental variables', os.environ['DSSP_BIN']
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self.dssp_bin.set(os.environ['DSSP_BIN'])
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else:
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if VERBOSE: print 'DSSP_BIN not found in environmental variables.'
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self.dssp_bin.set('')
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if 'STRIDE_BIN' not in os.environ and 'PYMOL_GIT_MOD' in os.environ:
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if sys.platform.startswith('linux') and platform.machine() == 'x86_32':
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initialdir_stride = os.path.join(os.environ['PYMOL_GIT_MOD'],"Stride","i86Linux2","stride")
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os.environ['STRIDE_BIN'] = initialdir_stride
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elif sys.platform.startswith('linux') and platform.machine() == 'x86_64':
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initialdir_stride = os.path.join(os.environ['PYMOL_GIT_MOD'],"Stride","ia64Linux2","stride")
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os.environ['STRIDE_BIN'] = initialdir_stride
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elif sys.platform.startswith('win'):
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initialdir_stride = os.path.join(os.environ['PYMOL_GIT_MOD'],"Stride","win32","stride.exe")
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os.environ['STRIDE_BIN'] = initialdir_stride
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else:
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pass
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if 'STRIDE_BIN' in os.environ:
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if VERBOSE: print 'Found STRIDE_BIN in environmental variables', os.environ['STRIDE_BIN']
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self.stride_bin.set(os.environ['STRIDE_BIN'])
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else:
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if VERBOSE: print 'STRIDE_BIN not found in environmental variables.'
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self.stride_bin.set('')
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# DSSP visualization color
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# - H Alpha helix (4-12)
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# - G 3-10 helix
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# - I pi helix
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#
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# - E Extended strand
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# - B Isolated beta-bridge residue
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#
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# - T Turn
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# - S Bend
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# - - None
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# STRIDE does not have S and None, but it has two more
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# codes: 'b' same as 'B' and 'C' for coil
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self.DSSP_SSE_list = ['H','G','I', 'E','B','T','S','-'] # for the record of the order
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self.STRIDE_SSE_list = ['H','G','I', 'E','B','b','T','C'] # for the record of the order
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self.SSE_map = {'H':'H',
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'G':'H',
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'I':'H',
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'E':'S',
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'B':'S',
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'T':'L',
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'S':'L',
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'-':'L',
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'b':'S',
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'C':'L'
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}
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self.SSE_name = {
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'H' : 'Alpha helix',
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'G' : '3-10 helix',
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'I' : 'Pi helix',
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'E' : 'Extended strand',
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'B' : 'Isolated beta-bridge',
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'T' : 'Turn',
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'S' : 'Bend',
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'-' : 'None',
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'b' : 'Isolated beta-bridge',
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'C' : 'Coil'
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}
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self.SSE_col_RGB = {
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'H':(255, 0, 0),
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'G':(255, 0,128),
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'I':(255,170,170),
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'E':(255,255, 0),
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'B':(153,119, 85),
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'T':( 0,255,255),
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'S':(153,255,119),
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'-':(179,179,179),
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'b':(153,119, 85), # same as 'B'
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'C':( 0, 0,255)
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}
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self.SSE_col = {}
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for sse in self.SSE_col_RGB.keys():
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self.SSE_col[sse] = '#%s%s%s' % (hex(self.SSE_col_RGB[sse][0])[2:].zfill(2),
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hex(self.SSE_col_RGB[sse][1])[2:].zfill(2),
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hex(self.SSE_col_RGB[sse][2])[2:].zfill(2))
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self.SSE_res_dict = {}
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self.SSE_sel_dict = {}
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w = Tkinter.Label(self.dialog.interior(),
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# text = '\nDSSP Plugin for PyMOL\nHongbo Zhu, 2011.\n\nColor proteins according to the secondary structure determined by DSSP.',
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text = '\nDSSP and Stride Plugin for PyMOL\nby Hongbo Zhu, 2011\n',
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background = 'black', foreground = 'green'
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)
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w.pack(expand = 1, fill = 'both', padx = 10, pady = 5)
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# make a few tabs within the dialog
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self.notebook = Pmw.NoteBook(self.dialog.interior())
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self.notebook.pack(fill = 'both', expand=1, padx=10, pady=10)
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######################
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# Tab : Structure Tab
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######################
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page = self.notebook.add('Structure')
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self.notebook.tab('Structure').focus_set()
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group_struc = Tkinter.LabelFrame(page, text = 'Structure')
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group_struc.pack(fill='both', expand=True, padx=10, pady=5)
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pymol_sel_ent = Pmw.EntryField(group_struc,
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label_text='PyMOL selection/object:',
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labelpos='wn',
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entry_textvariable=self.pymol_sel
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)
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dssp_bin_ent = Pmw.EntryField(group_struc,
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label_text='DSSP binary:', labelpos='wn',
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entry_textvariable=self.dssp_bin,
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entry_width=20)
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dssp_bin_but = Tkinter.Button(group_struc, text = 'Browse...',
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command = self.getDSSPBin)
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stride_bin_ent = Pmw.EntryField(group_struc,
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label_text='Stride binary:', labelpos='wn',
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entry_textvariable=self.stride_bin,
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entry_width=20)
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stride_bin_but = Tkinter.Button(group_struc, text = 'Browse...',
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command = self.getStrideBin)
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# arrange widgets using grid
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pymol_sel_ent.grid(sticky='we', row=0, column=0,
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columnspan=2, padx=5, pady=5)
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dssp_bin_ent.grid(sticky='we', row=1, column=0, padx=5, pady=1)
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dssp_bin_but.grid(sticky='we', row=1, column=1, padx=5, pady=1)
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stride_bin_ent.grid(sticky='we', row=2, column=0, padx=5, pady=1)
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stride_bin_but.grid(sticky='we', row=2, column=1, padx=5, pady=1)
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group_struc.columnconfigure(0, weight=9)
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group_struc.columnconfigure(1, weight=1)
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######################
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# Tab : Color Tab
|
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######################
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# H = alpha helix
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# G = 3-helix (3/10 helix)
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# I = 5 helix (pi helix)
|
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|
||||
# E = extended strand, participates in beta ladder
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# B = residue in isolated beta-bridge
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||||
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# T = hydrogen bonded turn
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# S = bend
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#
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# H Alpha helix (4-12)
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# G 3-10 helix
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||||
# I pi helix
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||||
# E Strand
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# B Isolated beta-bridge residue
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# T Turn
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# S Bend
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# - None
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page = self.notebook.add('Color')
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group_sse_color = Tkinter.LabelFrame(page, text = 'Secondary Structure Element Color')
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group_sse_color.grid(sticky='eswn', row=0, column=0, padx=10, pady=5)
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# colors for DSSP surface
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H_col_lab = Tkinter.Label(group_sse_color, text='Alpha helix (H):')
|
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self.H_col_but = Tkinter.Button(group_sse_color,
|
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bg=self.SSE_col['H'],
|
||||
activebackground=self.SSE_col['H'],
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command = self.custermizeHColor)
|
||||
G_col_lab = Tkinter.Label(group_sse_color, text='3-10 helix (G):')
|
||||
self.G_col_but = Tkinter.Button(group_sse_color,
|
||||
bg=self.SSE_col['G'],
|
||||
activebackground=self.SSE_col['G'],
|
||||
command = self.custermizeGColor)
|
||||
I_col_lab = Tkinter.Label(group_sse_color, text='PI helix (I):')
|
||||
self.I_col_but = Tkinter.Button(group_sse_color,
|
||||
bg=self.SSE_col['I'],
|
||||
activebackground=self.SSE_col['G'],
|
||||
command = self.custermizeIColor)
|
||||
|
||||
|
||||
E_col_lab = Tkinter.Label(group_sse_color, text='Extended strand (E):')
|
||||
self.E_col_but = Tkinter.Button(group_sse_color,
|
||||
bg=self.SSE_col['E'],
|
||||
activebackground=self.SSE_col['E'],
|
||||
command = self.custermizeEColor)
|
||||
B_col_lab = Tkinter.Label(group_sse_color, text='Isolated beta-bridge (B):')
|
||||
self.B_col_but = Tkinter.Button(group_sse_color,
|
||||
bg=self.SSE_col['B'],
|
||||
activebackground=self.SSE_col['B'],
|
||||
command = self.custermizeBColor)
|
||||
|
||||
T_col_lab = Tkinter.Label(group_sse_color, text='Turn (T):')
|
||||
self.T_col_but = Tkinter.Button(group_sse_color,
|
||||
bg=self.SSE_col['T'],
|
||||
activebackground=self.SSE_col['T'],
|
||||
command = self.custermizeTColor)
|
||||
S_col_lab = Tkinter.Label(group_sse_color, text='Bend (DSSP S):')
|
||||
self.S_col_but = Tkinter.Button(group_sse_color,
|
||||
bg=self.SSE_col['S'],
|
||||
activebackground=self.SSE_col['S'],
|
||||
command = self.custermizeSColor)
|
||||
N_col_lab = Tkinter.Label(group_sse_color, text='None (DSSP NA):')
|
||||
self.N_col_but = Tkinter.Button(group_sse_color,
|
||||
bg=self.SSE_col['-'],
|
||||
activebackground=self.SSE_col['-'],
|
||||
command = self.custermizeNColor)
|
||||
|
||||
|
||||
b_col_lab = Tkinter.Label(group_sse_color, text='Isolated beta-bridge (Stride b):')
|
||||
self.b_col_but = Tkinter.Button(group_sse_color,
|
||||
bg=self.SSE_col['b'],
|
||||
activebackground=self.SSE_col['b'],
|
||||
command = self.custermizebColor)
|
||||
|
||||
C_col_lab = Tkinter.Label(group_sse_color, text='Coil (Stride C):')
|
||||
self.C_col_but = Tkinter.Button(group_sse_color,
|
||||
bg=self.SSE_col['C'],
|
||||
activebackground=self.SSE_col['C'],
|
||||
command = self.custermizeCColor)
|
||||
|
||||
|
||||
|
||||
H_col_lab.grid(sticky='e', row=0, column=0, padx=5, pady=3)
|
||||
self.H_col_but.grid(sticky='we', row=0, column=1, padx=5, pady=3)
|
||||
G_col_lab.grid(sticky='e', row=1, column=0, padx=5, pady=3)
|
||||
self.G_col_but.grid(sticky='we', row=1, column=1, padx=5, pady=3)
|
||||
I_col_lab.grid(sticky='e', row=2, column=0, padx=5, pady=3)
|
||||
self.I_col_but.grid(sticky='we', row=2, column=1, padx=5, pady=3)
|
||||
|
||||
E_col_lab.grid(sticky='e', row=0, column=2, padx=5, pady=3)
|
||||
self.E_col_but.grid(sticky='we', row=0, column=3, padx=5, pady=3)
|
||||
B_col_lab.grid(sticky='e', row=1, column=2, padx=5, pady=3)
|
||||
self.B_col_but.grid(sticky='we', row=1, column=3, padx=5, pady=3)
|
||||
|
||||
T_col_lab.grid(sticky='e', row=0, column=4, padx=5, pady=3)
|
||||
self.T_col_but.grid(sticky='we', row=0, column=5, padx=5, pady=3)
|
||||
S_col_lab.grid(sticky='e', row=1, column=4, padx=5, pady=3)
|
||||
self.S_col_but.grid(sticky='we', row=1, column=5, padx=5, pady=3)
|
||||
N_col_lab.grid(sticky='e', row=2, column=4, padx=5, pady=3)
|
||||
self.N_col_but.grid(sticky='we', row=2, column=5, padx=5, pady=3)
|
||||
|
||||
b_col_lab.grid(sticky='e', row=2, column=2, padx=5, pady=3)
|
||||
self.b_col_but.grid(sticky='we', row=2, column=3, padx=5, pady=3)
|
||||
|
||||
C_col_lab.grid(sticky='e', row=3, column=4, padx=5, pady=3)
|
||||
self.C_col_but.grid(sticky='we', row=3, column=5, padx=5, pady=3)
|
||||
######################
|
||||
# Tab : About Tab
|
||||
######################
|
||||
page = self.notebook.add('About')
|
||||
group_about = Tkinter.LabelFrame(page, text = 'About DSSP and Stride Plugin for PyMOL')
|
||||
group_about.grid(sticky='we', row=0,column=0,padx=5,pady=3)
|
||||
about_plugin = """ Assign and color secondary structures using DSSP or Stride.
|
||||
by Hongbo Zhu <hongbo.zhu.cn .at. googlemail.com>
|
||||
Please cite this plugin if you use it in a publication.
|
||||
Hongbo Zhu. DSSP and Stride plugin for PyMOL, 2011, BIOTEC, TU Dresden.
|
||||
"""
|
||||
|
||||
label_about = Tkinter.Label(group_about,text=about_plugin)
|
||||
label_about.grid(sticky='we', row=0, column=0, padx=5, pady=10)
|
||||
|
||||
self.notebook.setnaturalsize()
|
||||
|
||||
return
|
||||
|
||||
|
||||
def getDSSPBin(self):
|
||||
dssp_bin_fname = tkFileDialog.askopenfilename(
|
||||
title='DSSP Binary', initialdir='',
|
||||
filetypes=[('all','*')], parent=self.parent)
|
||||
if dssp_bin_fname: # if nonempty
|
||||
self.dssp_bin.set(dssp_bin_fname)
|
||||
return
|
||||
|
||||
def getStrideBin(self):
|
||||
stride_bin_fname = tkFileDialog.askopenfilename(
|
||||
title='Stride Binary', initialdir='',
|
||||
filetypes=[('all','*')], parent=self.parent)
|
||||
if stride_bin_fname: # if nonempty
|
||||
self.stride_bin.set(stride_bin_fname)
|
||||
return
|
||||
|
||||
def runDSSPOneObj(self, one_obj_sel):
|
||||
""" Run DSSP on only one object.
|
||||
|
||||
@param one_obj_sel: the selection/object involving only one object
|
||||
@param type: string
|
||||
"""
|
||||
SSE_res = {
|
||||
'H':{}, 'G':{}, 'I':{},
|
||||
'E':{}, 'B':{},
|
||||
'T':{}, 'S':{}, '-':{}
|
||||
}
|
||||
SSE_sel = {
|
||||
'H':None, 'G':None, 'I':None,
|
||||
'E':None, 'B':None,
|
||||
'T':None, 'S':None, '-':None
|
||||
}
|
||||
|
||||
pdb_fn = None
|
||||
pdb_os_fh, pdb_fn = tempfile.mkstemp(suffix='.pdb') # file os handle, file name
|
||||
os.close(pdb_os_fh)
|
||||
# DSSP 2.0.4 ignores all residues after 1st TER in the same chain
|
||||
v = cmd.get(name='pdb_use_ter_records')
|
||||
if v: cmd.set(name='pdb_use_ter_records', value=0) # do not insert TER into the pdb
|
||||
cmd.save(filename=pdb_fn, selection=one_obj_sel)
|
||||
if v: cmd.set(name='pdb_use_ter_records', value=v) # restore old value
|
||||
|
||||
if VERBOSE:
|
||||
print 'Selection %s saved to %s.' % (one_obj_sel, pdb_fn)
|
||||
|
||||
if pdb_fn is None:
|
||||
print 'WARNING: DSSP has no pdb file to work on!'
|
||||
return None
|
||||
|
||||
print 'Running DSSP for %s ...' % (one_obj_sel,)
|
||||
dssp_sse_dict = {}
|
||||
if sys.version_info >= (2,4):
|
||||
dssp_proc = subprocess.Popen([self.dssp_bin.get(), pdb_fn],
|
||||
stdout=subprocess.PIPE,
|
||||
stderr=subprocess.STDOUT)
|
||||
dssp_stdout, dssp_stderr = dssp_proc.communicate()
|
||||
else: # use os.system + tempfile
|
||||
dssp_tmpout_os_fh, dssp_tmpout_fn = tempfile.mkstemp(suffix='.dssp')
|
||||
os.close(dssp_tmpout_os_fh)
|
||||
dssp_cmd = '%s %s > %s' % (self.dssp_bin.get(), pdb_fn, dssp_tmpout_fn)
|
||||
os.system(dssp_cmd)
|
||||
fh = open(dssp_tmpout_fn)
|
||||
dssp_stdout = ''.join(fh.readlines())
|
||||
fh.close()
|
||||
|
||||
sse_started = False
|
||||
for line in dssp_stdout.splitlines():
|
||||
if line.startswith(' # RESIDUE'):
|
||||
sse_started = True
|
||||
continue
|
||||
elif line.startswith(' !!!'):
|
||||
sse_started = False
|
||||
continue
|
||||
elif sse_started:
|
||||
if len(line) < 10 or line[9] == ' ': continue
|
||||
ch,resname = line[11],line[13]
|
||||
residen,sscode = line[5:11].strip(),line[16] # residen = resnum+icode, col 10 is for icode
|
||||
if sscode == ' ': sscode = '-'
|
||||
k = (ch,resname,residen)
|
||||
dssp_sse_dict[k] = sscode
|
||||
|
||||
self.dssp_rlt_dict[one_obj_sel] = dssp_sse_dict
|
||||
print 'Got SSE for %d residues.' % (len(self.dssp_rlt_dict[one_obj_sel]),)
|
||||
|
||||
# group residues according to their SSE, and chain name
|
||||
for k in self.dssp_rlt_dict[one_obj_sel].keys():
|
||||
#res = '/%s//%s/%d%s/' % (sel,k[0],k[1][1], k[1][2].strip()) # sel name, chain ID, res serial num, icode
|
||||
sse = self.dssp_rlt_dict[one_obj_sel][k]
|
||||
chn = k[0]
|
||||
res = k[2]
|
||||
if VERBOSE: print '(%s) and \"%s\"/%s/ sse=%s' % (str(one_obj_sel),
|
||||
chn.strip(), res, sse)
|
||||
SSE_res[sse].setdefault(chn,[]).append(res)
|
||||
|
||||
self.SSE_res_dict[one_obj_sel] = SSE_res
|
||||
|
||||
for sse in self.DSSP_SSE_list:
|
||||
sse_sel_name = self.selectSSE(one_obj_sel, sse)
|
||||
SSE_sel[sse] = sse_sel_name
|
||||
|
||||
self.SSE_sel_dict[one_obj_sel] = SSE_sel
|
||||
|
||||
print '\nNumber of residues with SSE element:'
|
||||
for sse in self.DSSP_SSE_list:
|
||||
num = sum([len(SSE_res[sse][chn]) for chn in SSE_res[sse]])
|
||||
print '%20s (%s) : %5d' % (self.SSE_name[sse], sse, num)
|
||||
print
|
||||
|
||||
# clean up pdb_fn and dssp_tmpout_fn created by tempfile.mkstemp()
|
||||
if os.path.isfile(pdb_fn):
|
||||
os.remove(pdb_fn)
|
||||
if sys.version_info < (2,4) and os.path.isfile(dssp_tmpout_fn):
|
||||
os.remove(dssp_tmpout_fn)
|
||||
|
||||
return
|
||||
|
||||
|
||||
def runDSSP(self):
|
||||
"""
|
||||
@return: whether DSSP has been executed successfully
|
||||
@rtype: boolean
|
||||
"""
|
||||
# delete old results
|
||||
self.sel_obj_list = []
|
||||
self.dssp_rlt_dict = {}
|
||||
self.SSE_res_dict = {}
|
||||
self.SSE_sel_dict = {}
|
||||
|
||||
pdb_fn = None
|
||||
sel_name= None
|
||||
sel = self.pymol_sel.get()
|
||||
|
||||
if len(sel) > 0: # if any pymol selection/object is specified
|
||||
# save the pymol selection/object in the tmp dir
|
||||
all_sel_names = cmd.get_names('all') # get names of all selections
|
||||
if sel in all_sel_names:
|
||||
if cmd.count_atoms(sel) == 0:
|
||||
err_msg = 'ERROR: The selection %s is empty.' % (sel,)
|
||||
print 'ERROR: %s' % (err_msg,)
|
||||
tkMessageBox.showinfo(title='ERROR', message=err_msg)
|
||||
return False
|
||||
else:
|
||||
sel_name = sel
|
||||
# no selection/object with the input name is found
|
||||
# we assume either a single-word selector or
|
||||
# some other selection-expression is used
|
||||
# NOTE: if more than one selection is selected, they should be
|
||||
# saved separately and SSE should be calculated for each
|
||||
# of the selections.
|
||||
else:
|
||||
print 'The selection/object you specified is not found.'
|
||||
print 'Your input will be interpreted as a selection-expression.'
|
||||
# check whether the selection is empty
|
||||
tmpsel = self.randomSeleName(prefix='your_sele_')
|
||||
cmd.select(tmpsel,sel)
|
||||
if cmd.count_atoms(tmpsel) == 0:
|
||||
cmd.delete(tmpsel)
|
||||
err_msg = 'ERROR: The selection %s is empty.' % (sel,)
|
||||
print 'ERROR: %s' % (err_msg,)
|
||||
tkMessageBox.showinfo(title='ERROR', message=err_msg)
|
||||
return False
|
||||
else:
|
||||
sel_name = tmpsel
|
||||
else: # what structure do you want DSSP to work on?
|
||||
err_msg = 'No PyMOL selection/object specified!'
|
||||
print 'ERROR: %s' % (err_msg,)
|
||||
tkMessageBox.showinfo(title='ERROR', message=err_msg)
|
||||
return False
|
||||
|
||||
# each object in the selection is treated as an independent struc
|
||||
objlist = cmd.get_object_list(sel_name)
|
||||
self.ss_asgn_prog = 'DSSP'
|
||||
print 'Starting %s ...' % (self.ss_asgn_prog, )
|
||||
|
||||
for objname in objlist:
|
||||
self.sel_obj_list.append('%s and %s' % (sel_name, objname))
|
||||
self.runDSSPOneObj(self.sel_obj_list[-1])
|
||||
|
||||
## cmd.delete(tmpsel)
|
||||
|
||||
return True
|
||||
|
||||
|
||||
def runStrideOneObj(self, one_obj_sel):
|
||||
""" Run Stride on only one object.
|
||||
|
||||
@param one_obj_sel: the selection/object involving only one object
|
||||
@param type: string
|
||||
"""
|
||||
SSE_res = {
|
||||
'H':{}, 'G':{}, 'I':{},
|
||||
'E':{}, 'B':{}, 'b':{},
|
||||
'T':{}, 'C':{}
|
||||
}
|
||||
SSE_sel = {
|
||||
'H':None, 'G':None, 'I':None,
|
||||
'E':None, 'B':None, 'b':None,
|
||||
'T':None, 'C':None
|
||||
}
|
||||
|
||||
pdb_fn = None
|
||||
pdb_os_fh, pdb_fn = tempfile.mkstemp(suffix='.pdb') # file os handle, file name
|
||||
os.close(pdb_os_fh)
|
||||
cmd.save(filename=pdb_fn, selection=one_obj_sel)
|
||||
if VERBOSE:
|
||||
print 'Selection %s saved to %s.' % (one_obj_sel, pdb_fn)
|
||||
|
||||
if pdb_fn is None:
|
||||
print 'WARNING: Stride has no pdb file to work on!'
|
||||
return None
|
||||
|
||||
print 'Running Stride for %s ...' % (one_obj_sel,)
|
||||
stride_sse_dict = {}
|
||||
if sys.version_info >= (2,4):
|
||||
stride_proc = subprocess.Popen([self.stride_bin.get(), pdb_fn],
|
||||
stdout=subprocess.PIPE,
|
||||
stderr=subprocess.STDOUT
|
||||
)
|
||||
stride_stdout, stride_stderr = stride_proc.communicate()
|
||||
else: # use os.system + tempfile
|
||||
stride_tmpout_os_fh, stride_tmpout_fn = tempfile.mkstemp(suffix='.stride')
|
||||
os.close(stride_tmpout_os_fh)
|
||||
stride_cmd = '%s %s > %s' % (self.stride_bin.get(), pdb_fn, stride_tmpout_fn)
|
||||
os.system(stride_cmd)
|
||||
fh = open(stride_tmpout_fn)
|
||||
stride_stdout = ''.join(fh.readlines())
|
||||
fh.close()
|
||||
|
||||
for line in stride_stdout.splitlines():
|
||||
if line.startswith('ASG'):
|
||||
resname,ch=line[5:8], line[9]
|
||||
# according to stride doc, col 12-15 are used for residue number
|
||||
# actually, resnum+icode is used in 12-15.
|
||||
# In addition, if residue number is 4-digit or longer,
|
||||
# the field 12-16 or more are used.
|
||||
|
||||
if line[15] == ' ': # col 16 is not occupied
|
||||
residen, sscode = line[11:15].strip(),line[24] # residen = resnum+icode
|
||||
else:
|
||||
shift = line[15:].find(' ') # find where residen stops
|
||||
residen, sscode = line[11:15+shift].strip(),line[24+shift]
|
||||
|
||||
k = (ch,resname,residen)
|
||||
stride_sse_dict[k] = sscode
|
||||
|
||||
self.stride_rlt_dict[one_obj_sel] = stride_sse_dict
|
||||
print 'Got SSE for %d residues.' % (len(self.stride_rlt_dict[one_obj_sel]),)
|
||||
|
||||
# group residues according to their SSE, and chain name
|
||||
for k in self.stride_rlt_dict[one_obj_sel].keys():
|
||||
sse=self.stride_rlt_dict[one_obj_sel][k]
|
||||
chn = k[0] # this can be a space!
|
||||
res = k[2]
|
||||
if VERBOSE: print '(%s) and \"%s\"/%s/ sse=%s' % (str(one_obj_sel),
|
||||
chn.strip(), res, sse)
|
||||
SSE_res[sse].setdefault(chn,[]).append(res)
|
||||
|
||||
self.SSE_res_dict[one_obj_sel] = SSE_res
|
||||
|
||||
for sse in self.STRIDE_SSE_list:
|
||||
sse_sel_name = self.selectSSE(one_obj_sel, sse)
|
||||
SSE_sel[sse] = sse_sel_name
|
||||
self.SSE_sel_dict[one_obj_sel] = SSE_sel
|
||||
|
||||
print '\nNumber of residues with SSE element:'
|
||||
for sse in self.STRIDE_SSE_list:
|
||||
num = sum([len(SSE_res[sse][chn]) for chn in SSE_res[sse]])
|
||||
print '%20s (%s) : %5d' % (self.SSE_name[sse], sse, num)
|
||||
print
|
||||
|
||||
# clean up pdb_fn and dssp_tmpout_fn created by tempfile.mkstemp()
|
||||
if os.path.isfile(pdb_fn):
|
||||
os.remove(pdb_fn)
|
||||
if sys.version_info < (2,4) and os.path.isfile(stride_tmpout_fn):
|
||||
os.remove(stride_tmpout_fn)
|
||||
|
||||
return True
|
||||
|
||||
|
||||
def runStride(self):
|
||||
"""
|
||||
"""
|
||||
# delete old results
|
||||
self.sel_obj_list = []
|
||||
self.stride_rlt_dict = {}
|
||||
self.SSE_res_dict = {}
|
||||
self.SSE_sel_dict = {}
|
||||
|
||||
pdb_fn = None
|
||||
sel_name= None
|
||||
sel = self.pymol_sel.get()
|
||||
|
||||
if len(sel) > 0: # if any pymol selection/object is specified
|
||||
all_sel_names = cmd.get_names('all') # get names of all selections
|
||||
if sel in all_sel_names:
|
||||
if cmd.count_atoms(sel) == 0:
|
||||
err_msg = 'ERROR: The selection %s is empty.' % (sel,)
|
||||
print 'ERROR: %s' % (err_msg,)
|
||||
tkMessageBox.showinfo(title='ERROR', message=err_msg)
|
||||
return False
|
||||
else:
|
||||
sel_name = sel
|
||||
# no selection/object with the input name is found
|
||||
# we assume either a single-word selector or
|
||||
# some other selection-expression is uesd
|
||||
else:
|
||||
print 'The selection/object you specified is not found.'
|
||||
print 'Your input will be interpreted as a selection-expression.'
|
||||
tmpsel = self.randomSeleName(prefix='your_sele_')
|
||||
cmd.select(tmpsel,sel)
|
||||
if cmd.count_atoms(tmpsel) == 0:
|
||||
cmd.delete(tmpsel)
|
||||
err_msg = 'ERROR: The selection %s is empty.' % (sel,)
|
||||
print 'ERROR: %s' % (err_msg,)
|
||||
tkMessageBox.showinfo(title='ERROR', message=err_msg)
|
||||
return False
|
||||
else:
|
||||
sel_name = tmpsel
|
||||
|
||||
else: # what structure do you want Stride to work on?
|
||||
err_msg = 'No PyMOL selection/object specified!'
|
||||
print 'ERROR: %s' % (err_msg,)
|
||||
tkMessageBox.showinfo(title='ERROR', message=err_msg)
|
||||
return False
|
||||
|
||||
# each object in the selection is treated as an independent struc
|
||||
objlist = cmd.get_object_list(sel_name)
|
||||
self.ss_asgn_prog = 'Stride'
|
||||
print 'Starting %s ...' % (self.ss_asgn_prog, )
|
||||
|
||||
for objname in objlist:
|
||||
self.sel_obj_list.append('%s and %s' % (sel_name, objname))
|
||||
self.runStrideOneObj(self.sel_obj_list[-1])
|
||||
|
||||
return True
|
||||
|
||||
|
||||
def randomSeleName(self, prefix='sele',suffix=''):
|
||||
""" generate a random selection name.
|
||||
"""
|
||||
sel_list = cmd.get_names('all')
|
||||
sel_dict = dict(zip(sel_list, range(len(sel_list))))
|
||||
sel_name = '%s%d%s' % (prefix, random.randint(1000,9999), suffix)
|
||||
while(sel_name in sel_dict):
|
||||
sel_name = '%s%d%s' % (prefix, random.randint(1000,9999), suffix)
|
||||
|
||||
return sel_name
|
||||
|
||||
|
||||
def selectSSE(self, sel, sse):
|
||||
""" generate selector for selecting all residues having the given sse.
|
||||
return the selection name.
|
||||
"""
|
||||
#sel = self.pymol_sel.get()
|
||||
sel_list_chn = []
|
||||
|
||||
if VERBOSE: print '\nSelecting SSE %s ... \n' % (sse)
|
||||
|
||||
for chn in self.SSE_res_dict[sel][sse]: # color one chain at a time
|
||||
if chn == ' ': chn_str = '-'
|
||||
else: chn_str = chn
|
||||
if VERBOSE: print 'Selecting SSE %s on chain %s ... \n' % (sse, chn)
|
||||
limit=150 # color every 150 residues
|
||||
sel_name_chn = self.randomSeleName(prefix='%s_%s_%s_' % ('_'.join(sel.split()),chn_str,sse))
|
||||
|
||||
if len(self.SSE_res_dict[sel][sse][chn]) < limit:
|
||||
#sel_expr = '/%s//%s/%s/' % (sel,chn.strip(), '+'.join(self.SSE_res[sse][chn]))
|
||||
# always quote chain name in case it is empty (otherwise sel misinterpreted)
|
||||
sel_expr = '(%s) and \"%s\"/%s/' % (sel,chn.strip(), '+'.join(self.SSE_res_dict[sel][sse][chn]))
|
||||
cmd.select(sel_name_chn, sel_expr)
|
||||
if VERBOSE: print 'select %s, %s' % (sel_name_chn, sel_expr)
|
||||
sel_list_chn.append(sel_name_chn)
|
||||
else:
|
||||
rn = len(self.SSE_res_dict[sel][sse][chn])
|
||||
print 'total number of res with %s = %d' % (sse,rn)
|
||||
sz = int(math.ceil(rn/float(limit)))
|
||||
sel_list_seg = []
|
||||
for i in xrange(sz):
|
||||
s,e = i*limit, min((i+1)*limit, rn)
|
||||
print s,e
|
||||
#sel_expr = '/%s//%s/%s/' % (sel,chn.strip(), '+'.join(self.SSE_res[sse][chn][s:e]))
|
||||
# always quote chain name in case it is empty (otherwise sel misinterpreted)
|
||||
sel_expr = '(%s) and \"%s\"/%s/' % (sel, chn.strip(),
|
||||
'+'.join(self.SSE_res_dict[sel][sse][chn][s:e]))
|
||||
sel_name_seg = self.randomSeleName(prefix='%s_%s_%s_tmp_' % ('_'.join(sel.split()),chn_str,sse))
|
||||
cmd.select(sel_name_seg, sel_expr)
|
||||
if VERBOSE: print 'select %s, %s' % (sel_name_seg, sel_expr)
|
||||
sel_list_seg.append(sel_name_seg)
|
||||
|
||||
sel_expr = ' or '.join(sel_list_seg)
|
||||
cmd.select(sel_name_chn, sel_expr)
|
||||
if VERBOSE: print 'select %s, %s' % (sel_name_chn, sel_expr)
|
||||
[cmd.delete(asel) for asel in sel_list_seg]
|
||||
sel_list_chn.append(sel_name_chn)
|
||||
|
||||
if len(sel_list_chn) > 0:
|
||||
sel_name = self.randomSeleName(prefix='%s_%s_%s_' % ('_'.join(sel.split()), sse, self.ss_asgn_prog))
|
||||
sel_expr = ' or '.join(sel_list_chn)
|
||||
cmd.select(sel_name,sel_expr)
|
||||
[cmd.delete(asel) for asel in sel_list_chn]
|
||||
else:
|
||||
print 'INFO: No residues are assigned to SSE \'%s\'.' % (sse,)
|
||||
sel_name = None
|
||||
|
||||
return sel_name
|
||||
|
||||
|
||||
def updateColor(self):
|
||||
if self.ss_asgn_prog is None:
|
||||
err_msg = 'Run DSSP or Stride to assign secondary structures first!'
|
||||
print 'ERROR: %s' % (err_msg,)
|
||||
tkMessageBox.showinfo(title='ERROR', message=err_msg)
|
||||
else:
|
||||
print 'Update color for %s' % (self.pymol_sel.get()),
|
||||
print 'using secondary structure assignment by %s' % (self.ss_asgn_prog,)
|
||||
|
||||
if self.ss_asgn_prog == 'DSSP': SSE_list = self.DSSP_SSE_list
|
||||
elif self.ss_asgn_prog == 'Stride': SSE_list = self.STRIDE_SSE_list
|
||||
|
||||
for sse in SSE_list: # give color names
|
||||
cmd.set_color('%s_color'%(sse,), self.SSE_col_RGB[sse])
|
||||
for sse in SSE_list: # color each SSE
|
||||
for sel_obj in self.sel_obj_list:
|
||||
if self.SSE_sel_dict[sel_obj][sse] is not None:
|
||||
cmd.color('%s_color'%(sse,), self.SSE_sel_dict[sel_obj][sse])
|
||||
print 'color',self.SSE_sel_dict[sel_obj][sse],',',self.SSE_col_RGB[sse]
|
||||
else:
|
||||
print 'No residues with SSE \'%s\' to color.' % (sse,)
|
||||
|
||||
return
|
||||
|
||||
def updateSS(self):
|
||||
if self.ss_asgn_prog is None:
|
||||
err_msg = 'Run DSSP or Stride to assign secondary structures first!'
|
||||
print 'ERROR: %s' % (err_msg,)
|
||||
tkMessageBox.showinfo(title='ERROR', message=err_msg)
|
||||
else:
|
||||
print 'Update secondary structures for %s' % (self.pymol_sel.get()),
|
||||
print 'using secondary structure assignment by %s' % (self.ss_asgn_prog,)
|
||||
print 'SSE mapping: (H,G,I) ==> H; (E,B,b) ==> S; (T,S,-,C) ==> L'
|
||||
|
||||
if self.ss_asgn_prog == 'DSSP': SSE_list = self.DSSP_SSE_list
|
||||
elif self.ss_asgn_prog == 'Stride': SSE_list = self.STRIDE_SSE_list
|
||||
|
||||
for sse in SSE_list:
|
||||
for sel_obj in self.sel_obj_list:
|
||||
if self.SSE_sel_dict[sel_obj][sse] is not None:
|
||||
cmd.alter(self.SSE_sel_dict[sel_obj][sse], 'ss=\'%s\''% (self.SSE_map[sse],))
|
||||
print 'alter %s, ss=%s' % (self.SSE_sel_dict[sel_obj][sse], self.SSE_map[sse])
|
||||
else:
|
||||
print 'No residue with SSE %s to update ss.' % (sse,)
|
||||
|
||||
# show cartoon for the input selection, and rebuild
|
||||
cmd.show('cartoon',self.pymol_sel.get())
|
||||
cmd.rebuild(self.pymol_sel.get())
|
||||
return
|
||||
|
||||
|
||||
def custermizeHColor(self):
|
||||
self.custermizeSSEColor('H')
|
||||
def custermizeGColor(self):
|
||||
self.custermizeSSEColor('G')
|
||||
def custermizeIColor(self):
|
||||
self.custermizeSSEColor('I')
|
||||
|
||||
def custermizeEColor(self):
|
||||
self.custermizeSSEColor('E')
|
||||
def custermizeBColor(self):
|
||||
self.custermizeSSEColor('B')
|
||||
|
||||
def custermizeTColor(self):
|
||||
self.custermizeSSEColor('T')
|
||||
def custermizeSColor(self):
|
||||
self.custermizeSSEColor('S')
|
||||
def custermizeNColor(self):
|
||||
self.custermizeSSEColor('-')
|
||||
|
||||
def custermizebColor(self):
|
||||
self.custermizeSSEColor('b')
|
||||
def custermizeCColor(self):
|
||||
self.custermizeSSEColor('C')
|
||||
|
||||
def custermizeSSEColor(self,sse):
|
||||
SSE_col_but = {
|
||||
'H':self.H_col_but,
|
||||
'G':self.G_col_but,
|
||||
'I':self.I_col_but,
|
||||
|
||||
'E':self.E_col_but,
|
||||
'B':self.B_col_but,
|
||||
|
||||
'T':self.T_col_but,
|
||||
'S':self.S_col_but,
|
||||
'-':self.N_col_but,
|
||||
|
||||
'b':self.b_col_but,
|
||||
'C':self.C_col_but,
|
||||
}
|
||||
try:
|
||||
color_tuple, color = tkColorChooser.askcolor(color=self.SSE_col[sse])
|
||||
if color_tuple is not None and color is not None:
|
||||
self.SSE_col_RGB[sse] = color_tuple
|
||||
self.SSE_col[sse] = color
|
||||
|
||||
SSE_col_but[sse]['bg']=self.SSE_col[sse]
|
||||
SSE_col_but[sse]['activebackground']=self.SSE_col[sse]
|
||||
SSE_col_but[sse].update()
|
||||
except Tkinter._tkinter.TclError:
|
||||
print 'Old color (%s) will be used.' % (self.mesh_col)
|
||||
|
||||
|
||||
def execute(self, butcmd):
|
||||
""" Run the cmd represented by the botton clicked by user.
|
||||
"""
|
||||
if butcmd == 'OK':
|
||||
print 'is everything OK?'
|
||||
|
||||
elif butcmd == 'Run DSSP':
|
||||
rtn = self.runDSSP()
|
||||
if rtn and VERBOSE: print 'Done with DSSP!'
|
||||
|
||||
elif butcmd == 'Run Stride':
|
||||
rtn = self.runStride()
|
||||
if rtn and VERBOSE: print 'Done with Stride!'
|
||||
|
||||
elif butcmd == 'Update Color':
|
||||
self.updateColor()
|
||||
|
||||
elif butcmd == 'Update ss':
|
||||
self.updateSS()
|
||||
|
||||
elif butcmd == 'Exit':
|
||||
print 'Exiting DSSP and Stride Plugin ...'
|
||||
if __name__ == '__main__':
|
||||
self.parent.destroy()
|
||||
else:
|
||||
self.dialog.withdraw()
|
||||
print 'Done.'
|
||||
else:
|
||||
print 'Exiting DSSP and Stride Plugin because of unknown button click ...'
|
||||
self.dialog.withdraw()
|
||||
print 'Done.'
|
||||
|
||||
|
||||
def quit(self):
|
||||
self.dialog.destroy()
|
||||
|
||||
|
||||
#############################################
|
||||
#
|
||||
#
|
||||
# Create demo in root window for testing.
|
||||
#
|
||||
#
|
||||
##############################################
|
||||
if __name__ == '__main__':
|
||||
|
||||
class App:
|
||||
def my_show(self,*args,**kwargs):
|
||||
pass
|
||||
|
||||
app = App()
|
||||
app.root = Tkinter.Tk()
|
||||
Pmw.initialise(app.root)
|
||||
app.root.title('It seems to work!')
|
||||
|
||||
widget = DSSPPlugin(app)
|
||||
app.root.mainloop()
|
||||
Reference in New Issue
Block a user