def loadScop(self, cla_path=None, des_path=None, hie_path=None):
if cla_path is None:
self.cla_file = file(parms.get('scopClassification'), 'r')
self.des_file = file(parms.get('scopDescription'), 'r')
self.hie_file = file(parms.get('scopHierarchy'), 'r')
elif cla_path is not None and hie_path is not None and des_path is not None:
self.cla_file = file(cla_path, 'r')
self.des_file = file(des_path, 'r')
self.hie_file = file(hie_path, 'r')
else:
print "Error in arguments"
return
self.ScopStructure = SCOP.Scop(self.cla_file, self.des_file,
self.hie_file)
self.ScopDomains = self.ScopStructure.getDomains()
cla_file_name = self.cla_file.name
if self.isAprofile == 1:
self.profileName = cla_file_name[
cla_file_name[:cla_file_name.rindex('\\')].rindex('\\') +
1:cla_file_name.rindex('\\')]
self.profileSunid = cla_file_name[cla_file_name.rindex('\\') +
1:cla_file_name.rindex('\\') + 6]
print "Profile Name: " + self.profileName
def copyPDBs(self, savePath):
cla = file(self.saveResultsin+str(self.currentSelection.thisNode.sunid)+"_cla.txt", 'r')
hie = file(self.saveResultsin+str(self.currentSelection.thisNode.sunid)+"_hie.txt", 'r')
des = file(self.saveResultsin+str(self.currentSelection.thisNode.sunid)+"_des.txt", 'r')
scopStruct = SCOP.Scop(cla, des, hie)
domsStruct = scopStruct.getDomains()
for eachItem in domsStruct:
hierarchy = []
curItem = eachItem
"""
This loop creates a list of directories need to save the domain
Eg: If the node hierarchy is of the form
Globin->Globin_child->Globin_child_child->Globin_child_child_child
and 'Globin_child_child_child' is selected
then the list hierarchy will contain
[Globin, Globin_child, Globin_child_child, Globin_child_child_child]
"""
while curItem is not None:
name = self.filterFoldername(curItem.description)
#If the length of the node.description is > 20, the pad the end of it
#with its sunid
if len(name)>20:
name = name[:20]+'_'+curItem.sunid
hierarchy.append(name.strip())
if self.currentSelection.thisNode.sunid.find(curItem.sunid) == 0:
curItem = None
else:
curItem = curItem.parent
curPath = savePath
#From the 'hierarchy' list, from top down, each item is checked to see if the
#folder exists by that name. If it doesnot exist, the folder structure is created.
#If the folder by that name exists, then the next item in the 'heirarchy' list is checked
while len(hierarchy) > 0:
foldr = hierarchy.pop()
curPath = curPath+'\\'+foldr
if not path.isdir(curPath):
mkdir(curPath)
while len(hierarchy) > 0:
curPath = curPath + '\\' + hierarchy.pop()
mkdir(curPath)
scopPdbsLoc = parms.get('scopPDBsLocation')
#Copy the .ent file from the SCOP Database to the current profile location
if path.isdir(scopPdbsLoc+eachItem.sid[2:4]) and path.isfile(scopPdbsLoc+eachItem.sid[2:4]+'\\'+eachItem.sid+'.ent'):
copy(scopPdbsLoc+eachItem.sid[2:4]+'\\'+eachItem.sid+'.ent', curPath+'\\'+eachItem.sid+'.ent')
else:
print "Protein Domain: "+eachItem.sid+" doesnot exist!"
def getAllNodes(self):
files = listdir(self.dirpath)
for item in files:
if re.compile('\d\d\d\d\d_hie.txt').match(item):
if path.isfile(self.dirpath+item[:5]+'_des.txt') and path.isfile(self.dirpath+item[:5]+'_cla.txt'):
self.nodesNames.append(item[:5])
clasi = file(self.dirpath+item[:5]+'_cla.txt', 'r')
descr = file(self.dirpath+item[:5]+'_des.txt', 'r')
hiera = file(self.dirpath+item[:5]+'_hie.txt', 'r')
self.nodesScop.append(SCOP.Scop(clasi, descr, hiera))
self.domainsScop.append(self.nodesScop[len(self.nodesScop)-1].getDomains())
descr.seek(0)
self.nodesScop[len(self.nodesScop)-1].root.description = descr.readline().split('\t').pop().strip()+'_'+item[:5]
hiera.seek(0)
line = hiera.readline()
lineage = []
while line[0] == '#':
lineage.append(line[1:].strip())
line = hiera.readline()
lineage.reverse()
self.nodesLineage.append(lineage)
def test_search(self):
"""Bio.SCOP.search(...)"""
handle = SCOP.search("1JOY")
def test_search(self):
"""Test search."""
handle = SCOP.search("1JOY")
def updateClaList(self, nde, cla):
if len(nde.children) == 0:
if self.currentNodeClaList.count(nde.sunid) == 0:
self.currentNodeClaList.append(nde.sunid)
cla.write(self.entireClaList[nde.sunid])
#Builds a hashed list with the sunids as keys from the classification file
def buildClaList(self):
fullFile = file(parms.get('scopClassification'), 'r').readlines()
rex = re.compile('\t\d\d\d\d\d\t')
for line in fullFile:
a = rex.search(line)
if a:
self.entireClaList[a.group().strip()] = line
#else:
# print "Unable to index the line: "+line
if __name__ == '__main__':
main_window = Tk()
clasi = file(parms.get('scopClassification'), 'r')
descr = file(parms.get('scopDescription'), 'r')
heira = file(parms.get('scopHierarchy'), 'r')
scopStruct = SCOP.Scop(clasi, descr, heira)
a = SearchFrame(main_window, scopStruct.root)
a.mainloop()
def __init__(self, parent, viewer, menSystem):
Frame.__init__(self, parent.pane('top'), bg='white')
self.focus()
self.nodesList = [
] #List of all the nodes in the treeWinText textbox. (has ScopNode objects)
self.currentNodeClaList = [
] #Temp. variable used in UpdateCla funciton
self.entireClaList = {
} #Classification file is parsed and all domains are hashed by their sids
#The bottom pane in the viewer represents the Molecular Viewer
self.molnir_level = parent.pane('bottom')
self.viewer_window = viewer
self.topMenuSystem = menSystem
self.saveResultsin = "" #directory path set by the user to save the profile
self.currentProfileName = ""
self.profilesPath = parms.get('profilesPath')
self.type = parms.get('classifications_fullname')
#Open the SCOP Parseable Text files
clasi = file(parms.get('scopClassification'), 'r')
descr = file(parms.get('scopDescription'), 'r')
heira = file(parms.get('scopHierarchy'), 'r')
#Load SCOP Structure and SCOP Domains
self.scopDataStruct = SCOP.Scop(clasi, descr, heira)
self.domains = self.scopDataStruct.getDomains()
self.nameHierarchy = parms.get('nameHierarchy')
self.pdbPath = ""
self.balloon = Pmw.Balloon(self)
self.menuBar = Pmw.MenuBar(self,
hull_relief=RAISED,
hull_borderwidth=1,
balloon=self.balloon)
self.menuBar.pack(fill=X, expand=NO, anchor=N)
self.menuBar.addmenu('Profiles', 'Search Profiles')
self.menuBar.addmenuitem('Profiles',
'command',
command=self.loadProfile,
label='Load Profile')
self.menuBar.addmenuitem('Profiles',
'command',
command=self.editProfile,
label='Edit Profile(s)')
self.menuBar.addmenu('Save', 'Create a local DB Structure')
self.menuBar.addmenuitem('Save',
'command',
command=self.saveSelectedNode,
label='Save selected Node as a Profile')
self.menuBar.addmenu('Search', 'Search Entire SCOP Database')
self.menuBar.addmenuitem('Search',
'command',
command=self.loadSCOPSearch,
label='Search SCOP')
self.treeWinText = Pmw.ScrolledText(self,
labelpos='n',
usehullsize=1,
label_text='SCOP Domain Viewer',
hull_width=100,
hull_height=20,
text_padx=1,
text_pady=1,
text_wrap='none',
text_cursor='arrow')
self.treeWinText.pack(side=LEFT, expand=YES, fill=BOTH)
self.pack(expand=YES, fill=BOTH)
self.lineageBox = Text(self, relief=FLAT, cursor="arrow")
self.lineageBox.pack(side=TOP, anchor=N)
self.lineageBox.config(height=12, width=38, state=DISABLED)
self.viewButton = Button(self,
text="View",
state=DISABLED,
height=1,
command=self.displaySelected,
width=5)
self.viewButton.pack(side=LEFT, anchor=S, padx=10)
self.lines = 1
#Load all the toplevel nodes (all of type 'Class') into the textbox
for item in self.scopDataStruct.root.children:
self.nodesList.append(ScopNode(item, self))
indx = "%0.1f" % (self.lines)
self.treeWinText.window_create(
indx, window=self.nodesList[len(self.nodesList) - 1])
indx = "%0.1f" % (self.lines + 0.1)
self.treeWinText.insert(indx, '\n')
self.lines = self.lines + 1
#self.currentSelection is updated everytime when a user clicks on a Node in the treeWinText text box
self.currentSelection = self.nodesList[0]
self.treeWinText.pack()
self.treeWinText.configure(text_state='disabled')
self.pack()
def test_search(self):
"""Bio.SCOP.search(...)"""
handle = SCOP.search("1JOY")
def test_search(self):
"""Test search."""
handle = SCOP.search("1JOY")