def get_current_domain_location(self):
if self.currentDomain == -1:
print "Load the first domain first before accessing this funciton"
if self.isAprofile == 1:
profilePath = parms.get('profilesPath') + self.profileName
tmpPath = ""
#parse the domain's parent structure to get the path
curDomain = self.currentDomainNode()
hierarchy = []
while curDomain is not None:
name = self.filterFoldername(curDomain.description)
hierarchy.append(name)
if self.profileSunid.find(curDomain.sunid) == 0:
curDomain = None
else:
curDomain = curDomain.parent
while len(hierarchy) > 0:
foldr = hierarchy.pop()
profilePath = profilePath +'\\'+foldr
if not path.isfile(profilePath+'\\'+self.currentDomainNode().sid+'.ent'):
print "Cannot find File!"
return ""
return profilePath+'\\'+self.currentDomainNode().sid+'.ent'
else:
pdb_path = parms.get('scopPDBsLocation') + self.currentDomainNode().sid[2:4] + '\\' + self.currentDomainNode().sid + '.ent'
if path.isfile(pdb_path):
return pdb_path
def getPDBLocation(self):
#check if the path includes the profiles directory path
pdb_path=""
pos = 0
while pos < len(self.domainsScop[self.currentSelection.id-1]) and self.currentSelection.thisNode.sunid != self.domainsScop[self.currentSelection.id-1][pos].sunid:
pos = pos + 1
if self.dirpath.find(parms.get('saveResultsin')) >= 0: #if the domain is to be viewed from a profile
pdb_path = parms.get('scopPDBsLocation') + self.domainsScop[self.currentSelection.id-1][pos].sid[2:4] + '\\' + self.domainsScop[self.currentSelection.id-1][pos].sid + '.ent'
if path.isfile(pdb_path):
return pdb_path
print "Selected Domain doesnot exist in the SCOP Database"
elif self.dirpath.find(parms.get('profilesPath')) >= 0: #if the domain is to be viewed from the ScopDatabase
curItem = self.domainsScop[self.currentSelection.id-1][pos]
tmpPath = ""
while curItem is not None:
name = self.filterFoldername(curItem.description)
if len(name) > 20:
name = name[:20]+'_'+curItem.sunid
tmpPath = name.strip() + '\\' + tmpPath
curItem = curItem.parent
tmpPath = tmpPath[tmpPath.index('\\')+1:]
print "TmpPath: "+tmpPath
pdb_path = parms.get('profilesPath')+ self.currentProfileName + '\\' + tmpPath + self.domainsScop[self.currentSelection.id-1][pos].sid + '.ent'
print "PDB PATH: "+pdb_path
if path.isfile(pdb_path):
return pdb_path
print "Selected Domain doesnot exist in the profile"
return ""
def loadProfile(self):
files = listdir(parms.get('profilesPath'))
profiles = []
for item in files:
direc = parms.get('profilesPath')+item
if path.isdir(direc):
profiles.append(item)
self.neww = Toplevel()
dropdown = Pmw.ComboBox(self.neww, label_text = 'Select a Profile:', labelpos = 'nw', selectioncommand=self.loadSelectedProfile,
scrolledlist_items = profiles)
dropdown.pack(side = LEFT, anchor = N, fill = X, expand = 1, padx = 8, pady = 8)
def get_chain_color_word(self): # returns the word color
if parms.get('colorblind'):
colormap = parms.get('colorblind_colormap')
else:
colormap = parms.get('colormap')
index = 0
for pchain in self.parent.ProteinList:
if self.chain_name == pchain.chain_name:
return 'chain%s'%(index%12+1)
index = index + 1
for nchain in self.parent.NucleotideChainList:
if self.chain_name == nchain.chain_name:
return 'chain%s'%(index%12+1)
index = index + 1
def __init__(self, obj, id, parent=None, toplevel=None):
Frame.__init__(self, parent, bg='white')
self.pack()
self.toplevel = toplevel
self.thisNode = Node()
self.thisNode = obj
self.isDisplayed = 1
self.isExpanded = 0
self.isALeaf = 0
self.id = id #### EACH SCOP Struct. in the profile is assigned an ID
self.gifs_dir = parms.get('gifs_dir')
self.pdb_dir = parms.get('pdb_dir')
self.createButton()
self.createLabel()
def loadSelectedProfile(self, selection):
self.neww.destroy()
new_window=Toplevel()
pw = Pmw.PanedWidget(new_window)
pw.add('top', min=10)
pw.add('bottom', min = 10)
new_window.title("SCOP Profile")
new_window.config(bg='white')
geometry_string = "%dx%d%+d%+d" %(700,800,50,30) # width,height,x-offset,y-offset
new_window.geometry(geometry_string)
pw.pane('top').configure(background='white')
a = ResultsFrame(parms.get('profilesPath')+selection+'\\', pw, new_window, self.scopViewer).pack(side=TOP)
pw.pack(expand=1, fill=BOTH)
bottomPane = pw.pane('bottom')
bottomPane.system = MolecularSystem.System(self, bottomPane)
bottomPane.system.load_pdb("")
bottomPane.system.color_ribbon_by_chain()
bottomPane.viewer = MolnirMolecularViewer(bottomPane, bottomPane.system)
bottomPane.viewer.loadSystem(bottomPane.system)
bottomPane.cardframe = CardFrame(bottomPane, bottomPane.system)
bottomPane.cardframe.pack(expand=NO, fill=X)
self.scopViewer.topMenuSystem.parent.scopViewer_windows.append(new_window)
self.topFrame.config(bg='white')
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
def get_chain_color(self): # returns three doubles
if parms.get('colorblind'):
colormap = parms.get('colorblind_colormap')
colormap_count = len(colormap)
else:
colormap = parms.get('colormap')
colormap_count = len(colormap)
index = 0
for pchain in self.parent.ProteinList:
if self.chain_name == pchain.chain_name:
color_name = 'chain%s'%(index%12+1)
return colormap[color_name]
index = index + 1
for nchain in self.parent.NucleotideChainList:
if self.chain_name == nchain.chain_name:
color_name = 'chain%s'%(index%12+1)
return colormap[color_name]
index = index + 1
def loadKeywords(self):
if path.isfile(parms.get('keywordsFile')):
wordsFile = file(parms.get('keywordsFile'), 'r')
strg = wordsFile.readline()
while strg.find('#keywords') == -1:
strg = wordsFile.readline()
strg = wordsFile.readline()
while strg.find('#removed keywords') == -1:
for words in strg.split(','):
if len(words.strip()) > 0:
self.keywords.append(words.strip())
strg = wordsFile.readline()
strg = wordsFile.readline()
while strg:
for words in strg.split(','):
if len(words.strip()) > 0:
self.removedKwds.append(words.strip())
strg = wordsFile.readline()
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 updateKeywords(self):
wordsFile = file(parms.get('keywordsFile'), 'w')
wordsFile.write('#keywords\n')
for word in self.keywords:
if self.keywords.index(word) < (len(self.keywords) - 1):
wordsFile.write(word+', ')
else:
wordsFile.write(word)
wordsFile.write('\n#removed keywords\n')
for word in self.removedKwds:
if self.removedKwds.index(word) < (len(self.removedKwds) - 1):
wordsFile.write(word+', ')
else:
wordsFile.write(word)
def copyPDBs(self, savePath):
#dirNamesDonotIncludelist = ['(', ')', ':', '-', '.', ',', ';']
for ScopItem in self.nodesScop:
indx = self.nodesNames.index(ScopItem.root.description[len(ScopItem.root.description)-5:])+1
if self.removedNames.count(indx) == 0:
pos = 0
#parse the scop structure
for eachItem in self.domainsScop[indx-1]:
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())
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
hierarchy.pop()
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 validateName(self, result):
if result is None or result == 'Cancel':
self.nameProfileDlg.withdraw()
elif result == 'OK':
self.currentProfileName = self.nameProfileDlg.get()
self.nameProfileDlg.withdraw()
print self.currentProfileName+' IN get'
if path.isdir(parms.get('profilesPath')+self.currentProfileName):
dialog = Pmw.MessageDialog(self, title = 'Profile Name Rejected',
defaultbutton = 0,
buttons = ('OK', ),
message_text = 'A Profile with name \''+self.currentProfileName+'\' already exists!')
dialog.activate()
self.currentProfileName = ""
self.saveCurrentProfile()
else:
self.finishOffSaving()
def getCurrentDomainLineage(self):
type = parms.get('classifications_fullname')
lineage = []
currentNode = self.currentDomainNode()
while currentNode is not None and len(currentNode.type) > 0:
lineage.insert(0, type[currentNode.type]+": "+currentNode.description+'\n')
currentNode = currentNode.parent
if self.isAprofile == 1:
self.hie_file.seek(0)
line = self.hie_file.readline()
while line[0] == '#':
lineage.insert(0,line[1:].strip()+'\n')
line = self.hie_file.readline()
return lineage
def getCurrentDomainLineage(self):
type = parms.get('classifications_fullname')
lineage = []
currentNode = self.currentDomainNode()
while currentNode is not None and len(currentNode.type) > 0:
lineage.insert(
0, type[currentNode.type] + ": " + currentNode.description +
'\n')
currentNode = currentNode.parent
if self.isAprofile == 1:
self.hie_file.seek(0)
line = self.hie_file.readline()
while line[0] == '#':
lineage.insert(0, line[1:].strip() + '\n')
line = self.hie_file.readline()
return lineage
def finishOffSaving(self):
print 'In save: '+self.currentProfileName
if len(self.currentProfileName) > 0:
#Create a profile directory,
try:
mkdir(parms.get('profilesPath')+self.currentProfileName)
except OSError:
dialog = Pmw.MessageDialog(self, title = 'Unable to Create Directory',
defaultbutton = 0,
buttons = ('OK', ),
message_text = 'Unable to create the directory: '+parms.get('profilesPath')+self.currentProfileName)
dialog.activate()
dialog = Pmw.MessageDialog(self, title = 'Profile Not Saved',
defaultbutton = 0,
buttons = ('OK', ),
message_text = 'Unable to Save Profile')
dialog.activate()
return
#Copy all the results from the temperory directory to the actual profile directory
files = listdir(parms.get('saveResultsin'))
for name in self.nodesNames:
if self.removedNames.count(self.nodesNames.index(name)+1) == 0 and files.count(name+'_hie.txt') > 0 and files.count(name+'_cla.txt') > 0 and files.count(name+'_des.txt') > 0:
copy(parms.get('saveResultsin')+name+'_hie.txt', parms.get('profilesPath')+self.currentProfileName+'\\'+name+'_hie.txt')
copy(parms.get('saveResultsin')+name+'_des.txt', parms.get('profilesPath')+self.currentProfileName+'\\'+name+'_des.txt')
copy(parms.get('saveResultsin')+name+'_cla.txt', parms.get('profilesPath')+self.currentProfileName+'\\'+name+'_cla.txt')
remove(parms.get('saveResultsin')+name+'_hie.txt')
remove(parms.get('saveResultsin')+name+'_des.txt')
remove(parms.get('saveResultsin')+name+'_cla.txt')
else:
print "Unable to save: "+name+" under the profile name: "+self.currentProfileName
self.copyPDBs(parms.get('profilesPath')+self.currentProfileName)
self.isCurrentProfileSaved = 1
self.treeWinText.configure(label_text = 'Current Profile: '+self.currentProfileName)
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from Tkinter import *
import urllib
import re
import parms
import Pmw
import string
import MolecularSystem
from GUICards import *
import MolecularViewer
from os import *
#location of image: plusImage, minusImage
pdb_dir = parms.get('pdb_dir')
gifs_dir = path.abspath('./Tools/DatabaseManager') + path.normpath('/')
class DirNode(Frame):
""" This class represents each Directory/File item in the treeWinText textbox.
Creates a frame with:
1.path to the item (path)
2.actual item (name)
3.Pointer to the actual Node in SCOP Data structure
"""
def __init__(self, pth, obj, parent=None):
Frame.__init__(self, parent, bg='white')
self.pack()
self.toplevel = parent
self.thisNode = obj
def filterFoldername(self, name):
dirNamesDonotIncludelist = parms.get('dirNamesDonotIncludelist')
for itm in dirNamesDonotIncludelist:
name = name.replace(itm, '')
return name.strip()
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from Tkinter import *
import urllib
import re
import parms
import Pmw
import string
import MolecularSystem
from GUICards import *
import MolecularViewer
from os import *
#location of image: plusImage, minusImage
pdb_dir = parms.get('pdb_dir')
gifs_dir = path.abspath('./Tools/DatabaseManager') + path.normpath('/')
class DirNode(Frame):
""" This class represents each Directory/File item in the treeWinText textbox.
Creates a frame with:
1.path to the item (path)
2.actual item (name)
3.Pointer to the actual Node in SCOP Data structure
"""
def __init__(self, pth, obj, parent=None):
Frame.__init__(self, parent, bg='white')
self.pack()
self.toplevel= parent
self.thisNode = obj
self.thisPath = pth
def filterFoldername(self, name):
dirNamesDonotIncludelist = parms.get('dirNamesDonotIncludelist')
for itm in dirNamesDonotIncludelist:
name = name.replace(itm, '')
return name.strip()
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 __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 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 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 okbutton(self):
if len(self.keywords) > 0:
self.types_state = []
#Get the state of Check Boxes
for var in self.chk_vars:
self.types_state.append(var.get())
#Delete the previous search results
tempFiles = listdir(self.saveResultsin)
if len(tempFiles) > 0:
dialog = Pmw.MessageDialog(self, title = 'Temp Results Directory',
defaultbutton = 0,
buttons = ('OK', ),
message_text = 'Deleting Results of previous Search!')
dialog.activate()
for rfile in tempFiles:
os.remove(self.saveResultsin+rfile)
#Parse the comments file and build a hash
allComms = file(parms.get('scopComments'), 'r').readlines()
for line in allComms:
self.commsList[line[:5]] = line[8:]
#Build lists of regular expressions
for item in self.keywords:
if item.find('(+)') == 0:
self.includeRegex.append(re.compile(item[3:], re.IGNORECASE))
elif item.find('(-)') == 0:
self.excludeRegex.append(re.compile(item[3:], re.IGNORECASE))
for kwrd in self.keywords:
self.currentNodeClaList = []
self.findKeyword(self.scopStruct.root)
self.updateKeywords()
print "KEY WORDS ARE:"
print self.keywords
if len(self.listOfresultsSunid) > 0:
#If there are any search results, display them in ResultsFrame
self.destroy()
self.toplevel.title("SCOP Search Results")
self.toplevel.config(bg='white')
pw = Pmw.PanedWidget(self.toplevel)
pw.add('top', min=10)
pw.add('bottom', min = 10)
geometry_string = "%dx%d%+d%+d" %(700,800,50,30) # width,height,x-offset,y-offset
self.toplevel.geometry(geometry_string)
pw.pane('top').configure(background='white')
a = ResultsFrame(self.saveResultsin, pw, self.toplevel, self.scopViewer).pack(side=TOP)
pw.pack(expand=1, fill=BOTH)
bottomPane = pw.pane('bottom')
bottomPane.system = MolecularSystem.System(self, bottomPane)
bottomPane.system.load_pdb("")
bottomPane.system.color_ribbon_by_chain()
bottomPane.viewer = MolnirMolecularViewer(bottomPane, bottomPane.system)
bottomPane.viewer.loadSystem(bottomPane.system)
bottomPane.cardframe = CardFrame(bottomPane, bottomPane.system)
bottomPane.cardframe.pack(expand=NO, fill=X)
self.scopViewer.topMenuSystem.parent.scopViewer_windows.append(self.toplevel)
else:
dialog = Pmw.MessageDialog(self, title = 'Search Results',
defaultbutton = 0,
buttons = ('OK', ), command='self.destroy()',
message_text = 'Search returned 0 results!')
dialog.activate()
else:
print "No Keywords Entered"
def okbutton(self):
if len(self.keywords) > 0:
self.types_state = []
#Get the state of Check Boxes
for var in self.chk_vars:
self.types_state.append(var.get())
#Delete the previous search results
tempFiles = listdir(self.saveResultsin)
if len(tempFiles) > 0:
dialog = Pmw.MessageDialog(self, title = 'Temp Results Directory',
defaultbutton = 0,
buttons = ('OK', ),
message_text = 'Deleting Results of previous Search!')
dialog.activate()
for rfile in tempFiles:
os.remove(self.saveResultsin+rfile)
#Parse the comments file and build a hash
allComms = file(parms.get('scopComments'), 'r').readlines()
for line in allComms:
self.commsList[line[:5]] = line[8:]
#Build lists of regular expressions
for item in self.keywords:
if item.find('(+)') == 0:
self.includeRegex.append(re.compile(item[3:], re.IGNORECASE))
elif item.find('(-)') == 0:
self.excludeRegex.append(re.compile(item[3:], re.IGNORECASE))
for kwrd in self.keywords:
self.currentNodeClaList = []
self.findKeyword(self.scopStruct.root)
self.updateKeywords()
print "KEY WORDS ARE:"
print self.keywords
if len(self.listOfresultsSunid) > 0:
#If there are any search results, display them in ResultsFrame
self.destroy()
self.toplevel.title("SCOP Search Results")
self.toplevel.config(bg='white')
pw = Pmw.PanedWidget(self.toplevel)
pw.add('top', min=10)
pw.add('bottom', min = 10)
geometry_string = "%dx%d%+d%+d" %(700,800,50,30) # width,height,x-offset,y-offset
self.toplevel.geometry(geometry_string)
pw.pane('top').configure(background='white')
a = ResultsFrame(self.saveResultsin, pw, self.toplevel, self.scopViewer).pack(side=TOP)
pw.pack(expand=1, fill=BOTH)
bottomPane = pw.pane('bottom')
bottomPane.system = MolecularSystem.System(self, bottomPane)
bottomPane.system.load_pdb("")
bottomPane.system.color_ribbon_by_chain()
bottomPane.viewer = MolnirMolecularViewer(bottomPane, bottomPane.system)
bottomPane.viewer.loadSystem(bottomPane.system)
bottomPane.cardframe = CardFrame(bottomPane, bottomPane.system)
bottomPane.cardframe.pack(expand=NO, fill=X)
self.scopViewer.topMenuSystem.parent.scopViewer_windows.append(self.toplevel)
else:
dialog = Pmw.MessageDialog(self, title = 'Search Results',
defaultbutton = 0,
buttons = ('OK', ), command='self.destroy()',
message_text = 'Search returned 0 results!')
dialog.activate()
else:
print "No Keywords Entered"
def __init__(self, parent, viewer):
Frame.__init__(self, parent, bg='white')
self.pack(expand=YES, fill=BOTH)
self.scopViewer = viewer
self.scopStruct = viewer.scopDataStruct
self.tier1_frame = Frame(self, bg='white')
self.currentExpr = re.compile('')
self.toplevel = parent
geometry_string = "%dx%d%+d%+d" %(700,500,150,150) # width,height,x-offset,y-offset
self.toplevel.geometry(geometry_string)
self.toplevel.title('SCOP Search')
self.keywords=[]
self.removedKwds=[]
self.includeRegex = []
self.excludeRegex = []
self.entireClaList = {}
self.commsList = {}
self.buildClaList() #Build a hash table with sunids as kes from the classification.txt file
self.currentNodeClaList = []
self.loadKeywords()
self.types_state = []
self.listOfresultsSunid = []
self.saveResultsin = parms.get('saveResultsin')
#########
self.add_txt_frame = Frame(self.tier1_frame, bg='white')
self.enter_txt_label = Label(self.add_txt_frame, bg='white', text='Enter Keyword:', justify=LEFT)
self.enter_txt_label.pack(anchor=W, pady=5)
self.kwd_entry = Entry(self.add_txt_frame, width=15)
self.kwd_entry.pack()
self.kwd_entry.focus()
self.kwd_entry.bind('<Return>', (lambda event: self.addKeywordToList()))
self.add_kwd_button = Button(self.add_txt_frame, text='Add Keyword', command=self.addKeywordToList)
self.add_kwd_button.pack(pady=5)
self.exclude_txt_label = Label(self.add_txt_frame, bg='white', text='Exclude Keyword:', justify=LEFT)
self.exclude_txt_label.pack(anchor=W, pady=5)
self.exclude_kwd_entry = Entry(self.add_txt_frame, width=15)
self.exclude_kwd_entry.pack()
self.exclude_kwd_entry.bind('<Return>', (lambda event: self.addExcludeKeywordToList()))
self.exclude_kwd_button = Button(self.add_txt_frame, text='Add Keyword', command=self.addExcludeKeywordToList)
self.exclude_kwd_button.pack(pady=5)
self.add_txt_frame.pack(side=LEFT, anchor=N, padx = 25, pady=75)
##########
self.keyword_lstbox_frame = Frame(self.tier1_frame, bg='white')
self.kwd_listbox_label = Label(self.keyword_lstbox_frame, text='Keywords List', bg='white')
self.kwd_listbox_label.pack(pady=5)
self.kwd_listbox = Pmw.ScrolledListBox(self.keyword_lstbox_frame, listbox_selectmode=SINGLE, items=self.keywords,
listbox_height=15, vscrollmode='static', usehullsize=1, hull_width=200, hull_height=250)
self.kwd_listbox.config(background='white')
self.kwd_listbox.pack(side=LEFT)
self.keyword_lstbox_frame.pack(side=LEFT, anchor=N)
##########
self.add_remove_frame = Frame(self.tier1_frame, bg='white')
self.add_from_remove = Button(self.add_remove_frame, text='<-- Add', width=10, command=self.addFromRemoveList)
self.add_from_remove.pack(padx=15, pady=15)
self.remove_from_keyword = Button(self.add_remove_frame, text='Remove -->', width=10, command=self.removeFromKeywordList)
self.remove_from_keyword.pack(padx=15)
self.add_remove_frame.pack(side=LEFT, anchor=N, pady=75)
##########
self.remove_lstbox_frame = Frame(self.tier1_frame, bg='white')
self.rm_listbox_label = Label(self.remove_lstbox_frame, text='Removed Keywords List', bg='white')
self.rm_listbox_label.pack(pady=5)
self.rm_listbox = Pmw.ScrolledListBox(self.remove_lstbox_frame, listbox_selectmode=SINGLE, items = self.removedKwds,
listbox_height=15, vscrollmode='static', usehullsize=1, hull_width=200, hull_height=250)
self.rm_listbox.config(background='white')
self.rm_listbox.pack(side=LEFT)
self.remove_lstbox_frame.pack(side=LEFT, anchor=N)
self.tier1_frame.pack()
self.type = parms.get('classifications_fullname')
self.indx = parms.get('classifications')
self.classi_index = parms.get('nameHierarchy')
self.tier2_frame = Frame(self, bg='white')
self.toInlcludeSublevels = IntVar(self)
self.include_sublevels_checkbox = Checkbutton(self.tier2_frame, text='Search sublevels of Hits', bg='white', variable=self.toInlcludeSublevels)
self.include_sublevels_checkbox.pack(side=LEFT)
self.searchComments = IntVar(self)
self.searchComments_checkbox = Checkbutton(self.tier2_frame, text='Search Comments', bg='white', variable=self.searchComments)
self.searchComments_checkbox.pack(side=LEFT)
self.tier2_frame.pack()
self.tier3_frame = Frame(self, bg='white')
self.chkBox_frame_label = Label(self.tier3_frame, text='Refine Search by selecting the TYPES', bg='white', justify=LEFT)
self.chkBox_frame_label.pack(side=TOP, anchor=W, fill=X)
self.chk_vars=[]
for sel in self.indx:
var = IntVar(self)
chk = Checkbutton(self.tier3_frame, text=self.type[sel], bg='white', variable=var)
chk.pack(side=LEFT, anchor=W)
if sel == 'cl': #Donot search the Class Level of the hierarchy, because of a BUG while
#displaying the corresponding hit in SearchResults
chk.forget()
else:
chk.select()
self.chk_vars.append(var)
self.tier3_frame.pack(pady=30)
self.tier4_frame = Frame(self, bg='white')
self.ok_button = Button(self.tier4_frame, text='OK', command=self.okbutton)
self.ok_button.pack(side=LEFT, padx=100)
self.cancel_button = Button(self.tier4_frame, text='Cancel', command=self.cancelbutton)
self.cancel_button.pack(side=LEFT, padx=100)
self.tier4_frame.pack()
from Tkinter import *
from Bio.SCOP import Node
from Bio import SCOP
import urllib
import MolecularSystem
from GUICards import *
from BlissMolecularViewer import *
from ScopSearch import *
from ScopResults import *
import parms
import Pmw
import re
#location of plusImage, minusImage
gifs_dir = parms.get('gifs_dir')
pdb_dir = parms.get('pdb_dir')
"""
This class represents each SCOP Node item in the treeWinText textbox.
Creates a frame with:
1.+/-button,
2.Empty Label for padding, and
3.Pointer to the actual Node in SCOP Data structure
"""
class ScopNode(Frame):
def __init__(self, obj, parent=None):
Frame.__init__(self, parent, bg='white')
self.pack()
def load_pdb(self, filename):
print "Opening pdb file %s\n"%(os.path.split(filename)[1])
""" parse a pdb file and load it as a system object."""
self.filename = filename
self.selected = 1
self.ProteinList = []
self.NucleotideChainList = []
self.LigandList = []
self.WaterList = []
self.HeaderLines = []
self.HBonds = []
self.header = ''
# open the file
if len(filename) == 0:
return
PDBfile = open(filename, 'r')
# separate atoms, HETATMS, and other
ATOMlines = []
HETATMlines = []
ANISlines = [] # anisotropy cards are ignored
otherlines = []
while 1:
line = PDBfile.readline()
# should be able to tell from the first 4 characters of each line
if line[0:4] == 'ATOM':
ATOMlines.append(line)
elif line[0:4] == 'HETA':
HETATMlines.append(line)
elif line[0:4] == 'ANIS':
ANISlines.append(line)
elif line[0:4] in ['TER ','MAST','CONE','END ']:
pass
else:
self.HeaderLines.append(line)
if not line: break
for line in self.HeaderLines:
if line[0:4] == 'HEAD':
self.header = string.strip(line[6:])
if verbose:
print "%d atoms" % len(ATOMlines)
print "%d hetero atoms" % len(HETATMlines)
print "%d header lines" % len(otherlines)
# next make a list of lines for the amino acids and nucleotides
AATypes = parms.get('AATypes')
NUCTypes = parms.get('NUCTypes')
WATTypes = parms.get('WATTypes')
AAlines = []
NUClines = []
WATlines = []
OTHlines = []
for line in ATOMlines:
if line[17:20] in AATypes:
AAlines.append(line)
elif line[17:20] in NUCTypes:
NUClines.append(line)
elif line[17:20] in WATTypes:
WATlines.append(line)
else:
OTHlines.append(line)
for line in HETATMlines:
if line[17:20] in WATTypes:
WATlines.append(line)
else:
OTHlines.append(line)
# now separate the chains
# first collect the chain names for AAlines
if len(AAlines) > 0:
proteinchainlist = []
for line in AAlines:
if line[21:22] in proteinchainlist:
pass
else:
proteinchainlist.append(line[21:22])
# and create a list for each
separatedlists = []
for chainname in proteinchainlist:
newlist = []
for line in AAlines:
if chainname == line[21:22]:
newlist.append(line)
separatedlists.append(newlist)
# now create all of the Protein objects
for slist in separatedlists:
newprotein = Protein(slist, self)
self.ProteinList.append(newprotein)
# next make a list of all nucleotide lines
# and create all of the NucleotideChain objects
if len(NUClines) > 0:
NUCchainlist = []
for line in NUClines:
if line[21:22]in NUCchainlist:
pass
else:
NUCchainlist.append(line[21:22])
if verbose:
if len(NUCchainlist) == 1:
print "1 nucleotide chain loading"
else:
print "%d nucleotide chains loading" % len(NUCchainlist)
# and create a list for each
separatedlists = []
for chainname in NUCchainlist:
newlist = []
for line in NUClines:
if chainname == line[21:22]:
newlist.append(line)
separatedlists.append(newlist)
# now create all of the Nucleotide chain objects
for slist in separatedlists:
newnucchain = NucleotideChain(slist, self)
self.NucleotideChainList.append(newnucchain)
# now make a list of all other molecule types
# and create all of the ligand Molecule objects
# pass through the list, collecting by residue number
if len(OTHlines) > 0:
last_rez_num = None
current_molecule = []
for line in OTHlines:
current_rez_num = string.atoi(line[23:26])
if current_rez_num == last_rez_num:
current_molecule.append(line)
else:
if len(current_molecule)>0:
new_molecule = Ligand(current_molecule, self)
self.LigandList.append(new_molecule)
current_molecule = []
current_molecule.append(line)
last_rez_num = current_rez_num
new_molecule = Ligand(current_molecule, self)
self.LigandList.append(new_molecule)
mol_names = []
for mol in self.LigandList:
mol_names.append(mol.res_type)
if verbose:
if len(self.LigandList) == 1:
print "1 ligand molecule %s" % (mol_names)
else:
print "%d ligand molecules %s" % (len(self.LigandList), mol_names)
# once ligands have been read in, then process the water list
# so that they can be numbered sequentially
if len(WATlines) > 0:
last_rez_num = None
current_molecule = []
for line in WATlines:
current_rez_num = line[23:26]
if current_rez_num == last_rez_num:
current_molecule.append(line)
else:
if len(current_molecule)>0:
new_molecule = Water(current_molecule,self)
self.WaterList.append(new_molecule)
current_molecule = []
current_molecule.append(line)
last_rez_num = current_rez_num
if len(current_molecule) > 0:
new_molecule = Water(current_molecule,self)
self.WaterList.append(new_molecule)
if verbose:
if len(self.WaterList) == 1:
print "1 water molecule"
else:
print "%d water molecules" % (len(self.WaterList))
PDBfile.close()
self._supplementary_initialization()
def __init__(self, parent, viewer):
Frame.__init__(self, parent, bg='white')
self.pack(expand=YES, fill=BOTH)
self.scopViewer = viewer
self.scopStruct = viewer.scopDataStruct
self.tier1_frame = Frame(self, bg='white')
self.currentExpr = re.compile('')
self.toplevel = parent
geometry_string = "%dx%d%+d%+d" %(700,500,150,150) # width,height,x-offset,y-offset
self.toplevel.geometry(geometry_string)
self.toplevel.title('SCOP Search')
self.keywords=[]
self.removedKwds=[]
self.includeRegex = []
self.excludeRegex = []
self.entireClaList = {}
self.commsList = {}
self.buildClaList() #Build a hash table with sunids as kes from the classification.txt file
self.currentNodeClaList = []
self.loadKeywords()
self.types_state = []
self.listOfresultsSunid = []
self.saveResultsin = parms.get('saveResultsin')
#########
self.add_txt_frame = Frame(self.tier1_frame, bg='white')
self.enter_txt_label = Label(self.add_txt_frame, bg='white', text='Enter Keyword:', justify=LEFT)
self.enter_txt_label.pack(anchor=W, pady=5)
self.kwd_entry = Entry(self.add_txt_frame, width=15)
self.kwd_entry.pack()
self.kwd_entry.focus()
self.kwd_entry.bind('<Return>', (lambda event: self.addKeywordToList()))
self.add_kwd_button = Button(self.add_txt_frame, text='Add Keyword', command=self.addKeywordToList)
self.add_kwd_button.pack(pady=5)
self.exclude_txt_label = Label(self.add_txt_frame, bg='white', text='Exclude Keyword:', justify=LEFT)
self.exclude_txt_label.pack(anchor=W, pady=5)
self.exclude_kwd_entry = Entry(self.add_txt_frame, width=15)
self.exclude_kwd_entry.pack()
self.exclude_kwd_entry.bind('<Return>', (lambda event: self.addExcludeKeywordToList()))
self.exclude_kwd_button = Button(self.add_txt_frame, text='Add Keyword', command=self.addExcludeKeywordToList)
self.exclude_kwd_button.pack(pady=5)
self.add_txt_frame.pack(side=LEFT, anchor=N, padx = 25, pady=75)
##########
self.keyword_lstbox_frame = Frame(self.tier1_frame, bg='white')
self.kwd_listbox_label = Label(self.keyword_lstbox_frame, text='Keywords List', bg='white')
self.kwd_listbox_label.pack(pady=5)
self.kwd_listbox = Pmw.ScrolledListBox(self.keyword_lstbox_frame, listbox_selectmode=SINGLE, items=self.keywords,
listbox_height=15, vscrollmode='static', usehullsize=1, hull_width=200, hull_height=250)
self.kwd_listbox.config(background='white')
self.kwd_listbox.pack(side=LEFT)
self.keyword_lstbox_frame.pack(side=LEFT, anchor=N)
##########
self.add_remove_frame = Frame(self.tier1_frame, bg='white')
self.add_from_remove = Button(self.add_remove_frame, text='<-- Add', width=10, command=self.addFromRemoveList)
self.add_from_remove.pack(padx=15, pady=15)
self.remove_from_keyword = Button(self.add_remove_frame, text='Remove -->', width=10, command=self.removeFromKeywordList)
self.remove_from_keyword.pack(padx=15)
self.add_remove_frame.pack(side=LEFT, anchor=N, pady=75)
##########
self.remove_lstbox_frame = Frame(self.tier1_frame, bg='white')
self.rm_listbox_label = Label(self.remove_lstbox_frame, text='Removed Keywords List', bg='white')
self.rm_listbox_label.pack(pady=5)
self.rm_listbox = Pmw.ScrolledListBox(self.remove_lstbox_frame, listbox_selectmode=SINGLE, items = self.removedKwds,
listbox_height=15, vscrollmode='static', usehullsize=1, hull_width=200, hull_height=250)
self.rm_listbox.config(background='white')
self.rm_listbox.pack(side=LEFT)
self.remove_lstbox_frame.pack(side=LEFT, anchor=N)
self.tier1_frame.pack()
self.type = parms.get('classifications_fullname')
self.indx = parms.get('classifications')
self.classi_index = parms.get('nameHierarchy')
self.tier2_frame = Frame(self, bg='white')
self.toInlcludeSublevels = IntVar(self)
self.include_sublevels_checkbox = Checkbutton(self.tier2_frame, text='Search sublevels of Hits', bg='white', variable=self.toInlcludeSublevels)
self.include_sublevels_checkbox.pack(side=LEFT)
self.searchComments = IntVar(self)
self.searchComments_checkbox = Checkbutton(self.tier2_frame, text='Search Comments', bg='white', variable=self.searchComments)
self.searchComments_checkbox.pack(side=LEFT)
self.tier2_frame.pack()
self.tier3_frame = Frame(self, bg='white')
self.chkBox_frame_label = Label(self.tier3_frame, text='Refine Search by selecting the TYPES', bg='white', justify=LEFT)
self.chkBox_frame_label.pack(side=TOP, anchor=W, fill=X)
self.chk_vars=[]
for sel in self.indx:
var = IntVar(self)
chk = Checkbutton(self.tier3_frame, text=self.type[sel], bg='white', variable=var)
chk.pack(side=LEFT, anchor=W)
if sel == 'cl': #Donot search the Class Level of the hierarchy, because of a BUG while
#displaying the corresponding hit in SearchResults
chk.forget()
else:
chk.select()
self.chk_vars.append(var)
self.tier3_frame.pack(pady=30)
self.tier4_frame = Frame(self, bg='white')
self.ok_button = Button(self.tier4_frame, text='OK', command=self.okbutton)
self.ok_button.pack(side=LEFT, padx=100)
self.cancel_button = Button(self.tier4_frame, text='Cancel', command=self.cancelbutton)
self.cancel_button.pack(side=LEFT, padx=100)
self.tier4_frame.pack()
def load_pdb(self, filename):
print "Opening pdb file %s\n" % (os.path.split(filename)[1])
""" parse a pdb file and load it as a system object."""
self.filename = filename
self.selected = 1
self.ProteinList = []
self.NucleotideChainList = []
self.LigandList = []
self.WaterList = []
self.HeaderLines = []
self.HBonds = []
self.header = ''
# open the file
if len(filename) == 0:
return
PDBfile = open(filename, 'r')
# separate atoms, HETATMS, and other
ATOMlines = []
HETATMlines = []
ANISlines = [] # anisotropy cards are ignored
otherlines = []
while 1:
line = PDBfile.readline()
# should be able to tell from the first 4 characters of each line
if line[0:4] == 'ATOM':
ATOMlines.append(line)
elif line[0:4] == 'HETA':
HETATMlines.append(line)
elif line[0:4] == 'ANIS':
ANISlines.append(line)
elif line[0:4] in ['TER ', 'MAST', 'CONE', 'END ']:
pass
else:
self.HeaderLines.append(line)
if not line: break
for line in self.HeaderLines:
if line[0:4] == 'HEAD':
self.header = string.strip(line[6:])
if verbose:
print "%d atoms" % len(ATOMlines)
print "%d hetero atoms" % len(HETATMlines)
print "%d header lines" % len(otherlines)
# next make a list of lines for the amino acids and nucleotides
AATypes = parms.get('AATypes')
NUCTypes = parms.get('NUCTypes')
WATTypes = parms.get('WATTypes')
AAlines = []
NUClines = []
WATlines = []
OTHlines = []
for line in ATOMlines:
if line[17:20] in AATypes:
AAlines.append(line)
elif line[17:20] in NUCTypes:
NUClines.append(line)
elif line[17:20] in WATTypes:
WATlines.append(line)
else:
OTHlines.append(line)
for line in HETATMlines:
if line[17:20] in WATTypes:
WATlines.append(line)
else:
OTHlines.append(line)
# now separate the chains
# first collect the chain names for AAlines
if len(AAlines) > 0:
proteinchainlist = []
for line in AAlines:
if line[21:22] in proteinchainlist:
pass
else:
proteinchainlist.append(line[21:22])
# and create a list for each
separatedlists = []
for chainname in proteinchainlist:
newlist = []
for line in AAlines:
if chainname == line[21:22]:
newlist.append(line)
separatedlists.append(newlist)
# now create all of the Protein objects
for slist in separatedlists:
newprotein = Protein(slist, self)
self.ProteinList.append(newprotein)
# next make a list of all nucleotide lines
# and create all of the NucleotideChain objects
if len(NUClines) > 0:
NUCchainlist = []
for line in NUClines:
if line[21:22] in NUCchainlist:
pass
else:
NUCchainlist.append(line[21:22])
if verbose:
if len(NUCchainlist) == 1:
print "1 nucleotide chain loading"
else:
print "%d nucleotide chains loading" % len(NUCchainlist)
# and create a list for each
separatedlists = []
for chainname in NUCchainlist:
newlist = []
for line in NUClines:
if chainname == line[21:22]:
newlist.append(line)
separatedlists.append(newlist)
# now create all of the Nucleotide chain objects
for slist in separatedlists:
newnucchain = NucleotideChain(slist, self)
self.NucleotideChainList.append(newnucchain)
# now make a list of all other molecule types
# and create all of the ligand Molecule objects
# pass through the list, collecting by residue number
if len(OTHlines) > 0:
last_rez_num = None
current_molecule = []
for line in OTHlines:
current_rez_num = string.atoi(line[23:26])
if current_rez_num == last_rez_num:
current_molecule.append(line)
else:
if len(current_molecule) > 0:
new_molecule = Ligand(current_molecule, self)
self.LigandList.append(new_molecule)
current_molecule = []
current_molecule.append(line)
last_rez_num = current_rez_num
new_molecule = Ligand(current_molecule, self)
self.LigandList.append(new_molecule)
mol_names = []
for mol in self.LigandList:
mol_names.append(mol.res_type)
if verbose:
if len(self.LigandList) == 1:
print "1 ligand molecule %s" % (mol_names)
else:
print "%d ligand molecules %s" % (len(
self.LigandList), mol_names)
# once ligands have been read in, then process the water list
# so that they can be numbered sequentially
if len(WATlines) > 0:
last_rez_num = None
current_molecule = []
for line in WATlines:
current_rez_num = line[23:26]
if current_rez_num == last_rez_num:
current_molecule.append(line)
else:
if len(current_molecule) > 0:
new_molecule = Water(current_molecule, self)
self.WaterList.append(new_molecule)
current_molecule = []
current_molecule.append(line)
last_rez_num = current_rez_num
if len(current_molecule) > 0:
new_molecule = Water(current_molecule, self)
self.WaterList.append(new_molecule)
if verbose:
if len(self.WaterList) == 1:
print "1 water molecule"
else:
print "%d water molecules" % (len(self.WaterList))
PDBfile.close()
self._supplementary_initialization()
def __init__(self, pth, parent=None, toplevel=None, viewer=None):
Frame.__init__(self, bg='white')
self.focus()
self.scopViewer = viewer
#The top pane in the viewer represents the SCOP Browser frame
self.topFrame = parent.pane('top')
#The bottom pane in the viewer represents the Molecular Viewer
self.toplevel = parent.pane('bottom')
self.viewer_window = toplevel
self.dirpath = pth
self.isCurrentProfileSaved = 0
self.currentProfileName = ""
if self.dirpath.find(parms.get('profilesPath')) == 0 and self.dirpath.find(parms.get('saveResultsin')) != 0:
pt = self.dirpath
if pt[len(pt)-1] == '\\':
self.currentProfileName = self.dirpath[self.dirpath[:-1].rindex('\\')+1:-1]
else:
self.currentProfileName = self.dirpath[self.dirpath.rindex('\\')+1:]
self.isCurrentProfileSaved = 1
print "HERE++++++++++++"+self.currentProfileName+" -- "+self.dirpath
self.nodesList = []
self.nodesNames = []
self.removedNames = []
self.nodesLineage = []
self.nodesScop = []
self.domainsScop = []
self.nameHierarchy = parms.get('nameHierarchy')
if self.dirpath[len(self.dirpath)-1] != '\\':
self.dirpath = self.dirpath + '\\'
#Loads the profile/search results from the path given
self.getAllNodes()
print "Nodes SCOP: "+str(len(self.nodesScop))
self.balloon = Pmw.Balloon(self.topFrame)
self.menuBar = Pmw.MenuBar(self.topFrame, 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.saveCurrentProfile, label='Save Profile')
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('Edit', 'Edit Results')
self.menuBar.addmenuitem('Edit', 'command', command=self.removeSelectedNode, label='Remove Node')
self.menuBar.addmenu('SCOP', 'Search Entire SCOP Database')
self.menuBar.addmenuitem('SCOP', 'command', label='View Selected Node in SCOP Domain Viewer', command=self.dispInScopDomViewer)
self.treeWinText = Pmw.ScrolledText(self.topFrame, labelpos = 'n', usehullsize = 1, label_text='SCOP Search Results',
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.topFrame, relief=FLAT, cursor = "arrow")
self.lineageBox.pack(side=TOP, anchor=N)
self.lineageBox.config(height=12, width=38, state=DISABLED)
self.viewButton = Button(self.topFrame, text="View", state=DISABLED, height=1, command=self.displaySelected, width=5)
self.viewButton.pack(side=LEFT, anchor=S, padx=10)
self.scopNodeId = 0
self.lines = 1
#Load all the toplevel nodes (all of type 'Class') into the textbox
for item in self.nodesScop:
self.scopNodeId = self.scopNodeId + 1
self.nodesList.append(ResultsScopNode(item.root, self.scopNodeId, self.topFrame, 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')
