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updated dssp_stride.py so it works with dssp-2.0.4 #38

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merged 6 commits into from
Oct 22, 2012
Merged

updated dssp_stride.py so it works with dssp-2.0.4 #38

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dd9ff64
Update plugins/dssp_stride.py
hongbo-zhu-cn Apr 10, 2012
2bcc741
Update plugins/dssp_stride.py
hongbo-zhu-cn Apr 12, 2012
25ba60f
Update plugins/dssp_stride.py
hongbo-zhu-cn Apr 12, 2012
80e7ae5
Update plugins/dssp_stride.py
hongbo-zhu-cn Apr 19, 2012
12b44b9
Update plugins/dssp_stride.py
hongbo-zhu-cn Apr 19, 2012
ba6619b
Update plugins/dssp_stride.py
hongbo-zhu-cn Oct 22, 2012
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182 changes: 54 additions & 128 deletions plugins/dssp_stride.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,13 +16,13 @@

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)
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)

"""

Expand Down Expand Up @@ -61,7 +61,8 @@
import os
import sys
import platform
import subprocess
if sys.version_info >= (2,4):
import subprocess # subprocess is introduced in python 2.4
import math
import random
import tempfile
Expand Down Expand Up @@ -165,7 +166,6 @@ def __init__(self, app):
else:
if VERBOSE: print 'STRIDE_BIN not found in environmental variables.'
self.stride_bin.set('')


# DSSP visualization color
# - H Alpha helix (4-12)
Expand Down Expand Up @@ -230,18 +230,6 @@ def __init__(self, app):
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 = {
## 'H':{}, 'G':{}, 'I':{},
## 'E':{}, 'B':{},
## 'T':{}, 'S':{}, '-':{},
## 'b':{}, 'C':{}
## }
## self.SSE_sel = {
## 'H':None, 'G':None, 'I':None,
## 'E':None, 'B':None,
## 'T':None, 'S':None, '-':None,
## 'b':None, 'C':None
## }

self.SSE_res_dict = {}
self.SSE_sel_dict = {}
Expand Down Expand Up @@ -462,7 +450,12 @@ def runDSSPOneObj(self, one_obj_sel):
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)

Expand All @@ -472,30 +465,30 @@ def runDSSPOneObj(self, one_obj_sel):

print 'Running DSSP for %s ...' % (one_obj_sel,)
dssp_sse_dict = {}
# To make the plugin work in windows, I have to use
# tempfile.makestemp() instead of
# tempfile.NamedTemporaryFile()
# Therefore, remember to clean up the mess later!
#dssp_tmpout = tempfile.NamedTemporaryFile(suffix='.dssp')
#dssp_cmd = '%s %s > %s' % (self.dssp_bin.get(), pdb_fn, dssp_tmpout.name)
## 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)
## fd = fh.readlines()
## fh.close()
dssp_proc = subprocess.Popen([self.dssp_bin.get(), pdb_fn],
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
dssp_stdout, dssp_stderr = dssp_proc.communicate()
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 line[9] == ' ': continue
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 = '-'
Expand Down Expand Up @@ -532,8 +525,8 @@ def runDSSPOneObj(self, one_obj_sel):
# clean up pdb_fn and dssp_tmpout_fn created by tempfile.mkstemp()
if os.path.isfile(pdb_fn):
os.remove(pdb_fn)
## if os.path.isfile(dssp_tmpout_fn):
## os.remove(dssp_tmpout_fn)
if sys.version_info < (2,4) and os.path.isfile(dssp_tmpout_fn):
os.remove(dssp_tmpout_fn)

return

Expand All @@ -548,16 +541,6 @@ def runDSSP(self):
self.dssp_rlt_dict = {}
self.SSE_res_dict = {}
self.SSE_sel_dict = {}
## self.SSE_res = {
## 'H':{}, 'G':{}, 'I':{},
## 'E':{}, 'B':{},
## 'T':{}, 'S':{}, '-':{}
## }
## self.SSE_sel = {
## 'H':None, 'G':None, 'I':None,
## 'E':None, 'B':None,
## 'T':None, 'S':None, '-':None
## }

pdb_fn = None
sel_name= None
Expand All @@ -574,18 +557,6 @@ def runDSSP(self):
return False
else:
sel_name = sel
## # To make the plugin work in windows, I have to use
## # tempfile.makestemp() instead of
## # tempfile.NamedTemporaryFile()
## # Therefore, remember to clean up the mess later!
## #tmpf = tempfile.NamedTemporaryFile(suffix='.pdb')
## #pdb_fn = tmpf.name
## tmpf = tempfile.mkstemp(suffix='.pdb')
## pdb_os_fh, pdb_fn = tmpf # file os handle, file name
## os.close(pdb_os_fh)
## cmd.save(filename=pdb_fn,selection=sel)
## if VERBOSE:
## print 'Selection/object %s saved to tmp file %s.' % (sel, pdb_fn)
# no selection/object with the input name is found
# we assume either a single-word selector or
# some other selection-expression is used
Expand All @@ -606,15 +577,6 @@ def runDSSP(self):
return False
else:
sel_name = tmpsel
## #tmpf = tempfile.NamedTemporaryFile(suffix='.pdb')
## #pdb_fn = tmpf.name
## tmpf = tempfile.mkstemp(suffix='.pdb')
## pdb_os_fh, pdb_fn = tmpf # file os handle, file name
## os.close(pdb_os_fh)
## cmd.save(filename=pdb_fn,selection=sel)
## cmd.delete(tmpsel)
## if VERBOSE:
## print 'Selection %s saved to %s.' % (sel, pdb_fn)
else: # what structure do you want DSSP to work on?
err_msg = 'No PyMOL selection/object specified!'
print 'ERROR: %s' % (err_msg,)
Expand All @@ -624,7 +586,7 @@ def runDSSP(self):
# each object in the selection is treated as an independent struc
objlist = cmd.get_object_list(sel_name)
self.ss_asgn_prog = 'DSSP'
print 'Running %s ...' % (self.ss_asgn_prog, )
print 'Starting %s ...' % (self.ss_asgn_prog, )

for objname in objlist:
self.sel_obj_list.append('%s and %s' % (sel_name, objname))
Expand Down Expand Up @@ -660,26 +622,26 @@ def runStrideOneObj(self, one_obj_sel):
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!'
print 'WARNING: Stride has no pdb file to work on!'
return None

print 'Running Stride for %s ...' % (one_obj_sel,)
stride_sse_dict = {}
#stride_tmpout = tempfile.NamedTemporaryFile(suffix='.stride')
#stride_cmd = '%s %s > %s' % (self.stride_bin.get(), pdb_fn, stride_tmpout.name)
## 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)
## fd = fh.readlines()
## fh.close()
stride_proc = subprocess.Popen([self.stride_bin.get(), pdb_fn],
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT
)
stride_stdout, stride_stderr = stride_proc.communicate()
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]
Expand Down Expand Up @@ -725,8 +687,8 @@ def runStrideOneObj(self, one_obj_sel):
# clean up pdb_fn and dssp_tmpout_fn created by tempfile.mkstemp()
if os.path.isfile(pdb_fn):
os.remove(pdb_fn)
## if os.path.isfile(stride_tmpout_fn):
## os.remove(stride_tmpout_fn)
if sys.version_info < (2,4) and os.path.isfile(stride_tmpout_fn):
os.remove(stride_tmpout_fn)

return True

Expand All @@ -739,16 +701,6 @@ def runStride(self):
self.stride_rlt_dict = {}
self.SSE_res_dict = {}
self.SSE_sel_dict = {}
## self.SSE_res = {
## 'H':{}, 'G':{}, 'I':{},
## 'E':{}, 'B':{}, 'b':{},
## 'T':{}, 'C':{}
## }
## self.SSE_sel = {
## 'H':None, 'G':None, 'I':None,
## 'E':None, 'B':None, 'b':None,
## 'T':None, 'C':None
## }

pdb_fn = None
sel_name= None
Expand All @@ -764,18 +716,6 @@ def runStride(self):
return False
else:
sel_name = sel
## # To make the plugin work in windows, I have to use
## # tempfile.makestemp() instead of
## # tempfile.NamedTemporaryFile()
## # Therefore, remember to clean up the mess later!
## #tmpf = tempfile.NamedTemporaryFile(suffix='.pdb')
## #pdb_fn = tmpf.name
## tmpf = tempfile.mkstemp(suffix='.pdb')
## pdb_os_fh, pdb_fn = tmpf # file os handle, file name
## os.close(pdb_os_fh)
## cmd.save(filename=pdb_fn,selection=sel)
## if VERBOSE:
## print 'Selection/object %s saved to tmp file %s.' % (sel, pdb_fn)
# no selection/object with the input name is found
# we assume either a single-word selector or
# some other selection-expression is uesd
Expand All @@ -792,19 +732,6 @@ def runStride(self):
return False
else:
sel_name = tmpsel
## # To make the plugin work in windows, I have to use
## # tempfile.makestemp() instead of
## # tempfile.NamedTemporaryFile()
## # Therefore, remember to clean up the mess later!
## #tmpf = tempfile.NamedTemporaryFile(suffix='.pdb')
## #pdb_fn = tmpf.name
## tmpf = tempfile.mkstemp(suffix='.pdb')
## pdb_os_fh, pdb_fn = tmpf # file os handle, file name
## os.close(pdb_os_fh)
## cmd.save(filename=pdb_fn,selection=sel)
## cmd.delete(tmpsel)
## if VERBOSE:
## print 'Selection %s saved to %s.' % (sel, pdb_fn)

else: # what structure do you want Stride to work on?
err_msg = 'No PyMOL selection/object specified!'
Expand All @@ -815,7 +742,7 @@ def runStride(self):
# each object in the selection is treated as an independent struc
objlist = cmd.get_object_list(sel_name)
self.ss_asgn_prog = 'Stride'
print 'Running %s ...' % (self.ss_asgn_prog, )
print 'Starting %s ...' % (self.ss_asgn_prog, )

for objname in objlist:
self.sel_obj_list.append('%s and %s' % (sel_name, objname))
Expand Down Expand Up @@ -1053,4 +980,3 @@ def my_show(self,*args,**kwargs):

widget = DSSPPlugin(app)
app.root.mainloop()