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dotfiles/profiles/pymol/.pymol/startup/dssp_stride.py
Daniel Bauer 30779f0939 reorganize dotfiles
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""" 2011_04_11: Hongbo Zhu
PyMOL plugin for running DSSP and display SS using different colors.
The DSSP codes for secondary structure are:
H - Alpha helix (4-12)
G - 3-10 helix
I - pi helix
E - Strand
B - Isolated beta-bridge residue
T - Turn
S - Bend
- - None
2011_04_24: add stride
STRIDE code (taken from stride.doc) is nearly the same as DSSP
H Alpha helix
G 3-10 helix
I PI-helix
E Extended conformation
B or b Isolated bridge
T Turn
C Coil (none of the above)
"""
# Copyright Notice
# ================
#
# The PyMOL Plugin source code in this file is copyrighted, but you can
# freely use and copy it as long as you don't change or remove any of
# the copyright notices.
#
# ----------------------------------------------------------------------
# This PyMOL Plugin is Copyright (C) 2011 by
# Hongbo Zhu <hongbo.zhu.cn at googlemail dot com>
#
# All Rights Reserved
#
# Permission to use, copy, modify, distribute, and distribute modified
# versions of this software and its documentation for any purpose and
# without fee 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, and that
# the name(s) of the author(s) not be used in advertising or publicity
# pertaining to distribution of the software without specific, written
# prior permission.
#
# THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,
# INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN
# NO EVENT SHALL THE AUTHOR(S) 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.
# ----------------------------------------------------------------------
# python lib
import os
import sys
import platform
if sys.version_info >= (2,4):
import subprocess # subprocess is introduced in python 2.4
import math
import random
import tempfile
import tkSimpleDialog
import tkMessageBox
import tkFileDialog
import tkColorChooser
import Tkinter
# pymol lib
try:
from pymol import cmd
from pymol.cgo import *
except ImportError:
print 'Warning: pymol library cmd not found.'
sys.exit(1)
# external lib
try:
import Pmw
except ImportError:
print 'Warning: failed to import Pmw. Exit ...'
sys.exit(1)
VERBOSE = True
#################
## here we go
#################
def __init__(self):
""" DSSP and Stride plugin for PyMol
"""
self.menuBar.addmenuitem('Plugin', 'command',
'DSSP & Stride', label = 'DSSP & Stride',
command = lambda s=self : DSSPPlugin(s))
#################
## GUI related
#################
class DSSPPlugin:
def __init__(self, app):
self.parent = app.root
self.dialog = Pmw.Dialog(self.parent,
buttons = ('Run DSSP',
'Run Stride',
'Update Color',
'Update ss',
'Exit'),
title = 'DSSP and Stride Plugin for PyMOL',
command = self.execute)
Pmw.setbusycursorattributes(self.dialog.component('hull'))
# parameters used by DSSP
self.pymol_sel = Tkinter.StringVar()
self.dssp_bin = Tkinter.StringVar()
self.stride_bin = Tkinter.StringVar()
self.dssp_rlt_dict = {}
self.stride_rlt_dict = {}
self.ss_asgn_prog = None # which program is used to assign ss
self.sel_obj_list = [] # there may be more than one seletion or object
# defined by self.pymol_sel
# treat each selection and object separately
if 'DSSP_BIN' not in os.environ and 'PYMOL_GIT_MOD' in os.environ:
if sys.platform.startswith('linux') and platform.machine() == 'x86_32':
initialdir_dssp = os.path.join(os.environ['PYMOL_GIT_MOD'],"DSSP","i86Linux2","dssp-2")
os.environ['DSSP_BIN'] = initialdir_dssp
elif sys.platform.startswith('linux') and platform.machine() == 'x86_64':
initialdir_dssp = os.path.join(os.environ['PYMOL_GIT_MOD'],"DSSP","ia64Linux2","dssp-2")
os.environ['DSSP_BIN'] = initialdir_dssp
elif sys.platform.startswith('win'):
initialdir_dssp = os.path.join(os.environ['PYMOL_GIT_MOD'],"DSSP","win32","dssp.exe")
os.environ['DSSP_BIN'] = initialdir_dssp
else:
pass
if 'DSSP_BIN' in os.environ:
if VERBOSE: print 'Found DSSP_BIN in environmental variables', os.environ['DSSP_BIN']
self.dssp_bin.set(os.environ['DSSP_BIN'])
else:
if VERBOSE: print 'DSSP_BIN not found in environmental variables.'
self.dssp_bin.set('')
if 'STRIDE_BIN' not in os.environ and 'PYMOL_GIT_MOD' in os.environ:
if sys.platform.startswith('linux') and platform.machine() == 'x86_32':
initialdir_stride = os.path.join(os.environ['PYMOL_GIT_MOD'],"Stride","i86Linux2","stride")
os.environ['STRIDE_BIN'] = initialdir_stride
elif sys.platform.startswith('linux') and platform.machine() == 'x86_64':
initialdir_stride = os.path.join(os.environ['PYMOL_GIT_MOD'],"Stride","ia64Linux2","stride")
os.environ['STRIDE_BIN'] = initialdir_stride
elif sys.platform.startswith('win'):
initialdir_stride = os.path.join(os.environ['PYMOL_GIT_MOD'],"Stride","win32","stride.exe")
os.environ['STRIDE_BIN'] = initialdir_stride
else:
pass
if 'STRIDE_BIN' in os.environ:
if VERBOSE: print 'Found STRIDE_BIN in environmental variables', os.environ['STRIDE_BIN']
self.stride_bin.set(os.environ['STRIDE_BIN'])
else:
if VERBOSE: print 'STRIDE_BIN not found in environmental variables.'
self.stride_bin.set('')
# DSSP visualization color
# - H Alpha helix (4-12)
# - G 3-10 helix
# - I pi helix
#
# - E Extended strand
# - B Isolated beta-bridge residue
#
# - T Turn
# - S Bend
# - - None
# STRIDE does not have S and None, but it has two more
# codes: 'b' same as 'B' and 'C' for coil
self.DSSP_SSE_list = ['H','G','I', 'E','B','T','S','-'] # for the record of the order
self.STRIDE_SSE_list = ['H','G','I', 'E','B','b','T','C'] # for the record of the order
self.SSE_map = {'H':'H',
'G':'H',
'I':'H',
'E':'S',
'B':'S',
'T':'L',
'S':'L',
'-':'L',
'b':'S',
'C':'L'
}
self.SSE_name = {
'H' : 'Alpha helix',
'G' : '3-10 helix',
'I' : 'Pi helix',
'E' : 'Extended strand',
'B' : 'Isolated beta-bridge',
'T' : 'Turn',
'S' : 'Bend',
'-' : 'None',
'b' : 'Isolated beta-bridge',
'C' : 'Coil'
}
self.SSE_col_RGB = {
'H':(255, 0, 0),
'G':(255, 0,128),
'I':(255,170,170),
'E':(255,255, 0),
'B':(153,119, 85),
'T':( 0,255,255),
'S':(153,255,119),
'-':(179,179,179),
'b':(153,119, 85), # same as 'B'
'C':( 0, 0,255)
}
self.SSE_col = {}
for sse in self.SSE_col_RGB.keys():
self.SSE_col[sse] = '#%s%s%s' % (hex(self.SSE_col_RGB[sse][0])[2:].zfill(2),
hex(self.SSE_col_RGB[sse][1])[2:].zfill(2),
hex(self.SSE_col_RGB[sse][2])[2:].zfill(2))
self.SSE_res_dict = {}
self.SSE_sel_dict = {}
w = Tkinter.Label(self.dialog.interior(),
# text = '\nDSSP Plugin for PyMOL\nHongbo Zhu, 2011.\n\nColor proteins according to the secondary structure determined by DSSP.',
text = '\nDSSP and Stride Plugin for PyMOL\nby Hongbo Zhu, 2011\n',
background = 'black', foreground = 'green'
)
w.pack(expand = 1, fill = 'both', padx = 10, pady = 5)
# make a few tabs within the dialog
self.notebook = Pmw.NoteBook(self.dialog.interior())
self.notebook.pack(fill = 'both', expand=1, padx=10, pady=10)
######################
# Tab : Structure Tab
######################
page = self.notebook.add('Structure')
self.notebook.tab('Structure').focus_set()
group_struc = Tkinter.LabelFrame(page, text = 'Structure')
group_struc.pack(fill='both', expand=True, padx=10, pady=5)
pymol_sel_ent = Pmw.EntryField(group_struc,
label_text='PyMOL selection/object:',
labelpos='wn',
entry_textvariable=self.pymol_sel
)
dssp_bin_ent = Pmw.EntryField(group_struc,
label_text='DSSP binary:', labelpos='wn',
entry_textvariable=self.dssp_bin,
entry_width=20)
dssp_bin_but = Tkinter.Button(group_struc, text = 'Browse...',
command = self.getDSSPBin)
stride_bin_ent = Pmw.EntryField(group_struc,
label_text='Stride binary:', labelpos='wn',
entry_textvariable=self.stride_bin,
entry_width=20)
stride_bin_but = Tkinter.Button(group_struc, text = 'Browse...',
command = self.getStrideBin)
# arrange widgets using grid
pymol_sel_ent.grid(sticky='we', row=0, column=0,
columnspan=2, padx=5, pady=5)
dssp_bin_ent.grid(sticky='we', row=1, column=0, padx=5, pady=1)
dssp_bin_but.grid(sticky='we', row=1, column=1, padx=5, pady=1)
stride_bin_ent.grid(sticky='we', row=2, column=0, padx=5, pady=1)
stride_bin_but.grid(sticky='we', row=2, column=1, padx=5, pady=1)
group_struc.columnconfigure(0, weight=9)
group_struc.columnconfigure(1, weight=1)
######################
# Tab : Color Tab
######################
# H = alpha helix
# G = 3-helix (3/10 helix)
# I = 5 helix (pi helix)
# E = extended strand, participates in beta ladder
# B = residue in isolated beta-bridge
# T = hydrogen bonded turn
# S = bend
#
# H Alpha helix (4-12)
# G 3-10 helix
# I pi helix
# E Strand
# B Isolated beta-bridge residue
# T Turn
# S Bend
# - None
page = self.notebook.add('Color')
group_sse_color = Tkinter.LabelFrame(page, text = 'Secondary Structure Element Color')
group_sse_color.grid(sticky='eswn', row=0, column=0, padx=10, pady=5)
# colors for DSSP surface
H_col_lab = Tkinter.Label(group_sse_color, text='Alpha helix (H):')
self.H_col_but = Tkinter.Button(group_sse_color,
bg=self.SSE_col['H'],
activebackground=self.SSE_col['H'],
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()
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