def map_datatab2structure(self):
"""If the PEATDB record has a structure, then we allow the user to map each datatab
to a specific part of the protein.
One can map a datatab to an atom, a residue, a chain, or define a structural group and map to it"""
if not self.parent:
import tkMessageBox
tkMessageBox.showinfo(
"No PEAT",
"This option is only available when Ekin is started from PEAT",
parent=self.ekin_win)
return
#
# Do we have a record name
#
if not self.protein:
import tkMessageBox
tkMessageBox.showinfo(
"No PEAT record",
"This option is only available when Ekin has been started by clicking a PEAT record",
parent=self.ekin_win)
return
#
# Is there a structure?
#
error = None
if not self.parent.data.has_key('DBinstance'):
error = 1
else:
DB = self.parent.data['DBinstance'].DB
if not DB[self.protein].has_key('Structure'):
error = 1
else:
print 'Trying to get PDB'
self.pdblines, X = self.parent.get_structure(
self.protein, 'Structure')
if not self.pdblines:
error = 1
if error:
import tkMessageBox
tkMessageBox.showinfo(
"No Structure in PEAT",
"This option is only available when the PEAT record has a structure",
parent=self.ekin_win)
return
#
# Open the mapping window
#
mapper_win = Toplevel()
mapper_win.title('Map datatab to structure. %s - %s' %
(self.protein, self.field))
self.set_geometry(self.ekin_win, mapper_win)
#
# Mapping Manager
#
row = 0
Label(mapper_win, text='Mapping Manager',
bg='lightblue').grid(row=row,
column=0,
columnspan=3,
sticky='news')
row = row + 1
Label(mapper_win,
textvariable=self.currentdataset.get()).grid(row=row,
column=0,
columnspan=3,
sticky='news')
#
# Headers
#
#row=row+1
#Label(mapper_win,text='Structural group type').grid(row=row,column=0,sticky='news')
#Label(mapper_win,text='Structural element').grid(row=row,column=1,sticky='news')
#Label(mapper_win,text='Datatab property').grid(row=row,column=2,sticky='news')
#
# Structural groupings for this protein
#
#if not DB[self.protein].has_key('structgroups'):
# DB[self.protein]['structgroups']={}
#structgroups=DB[self.protein]['structgroups'].keys()
#
# Load the residue definitions
#
import Protool.mutate
self.M_instance = Protool.mutate.Mutate(onlydefs=1)
self.AAdefs = self.M_instance.aadefs
#
# Struct group types
#
row = row + 1
listbox_height = 5
self.group_type_box = Pmw.ScrolledListBox(
mapper_win,
items=['Residues', 'Atoms', 'Titratable groups'],
labelpos='nw',
label_text='Group type',
listbox_height=listbox_height,
usehullsize=1,
hull_width=200,
hull_height=100,
selectioncommand=self.update_elements)
self.group_type_box.grid(row=row,
column=0,
columnspan=1,
sticky='news')
self.group_type_box.configure(listbox_bg='white')
self.group_type_box.configure(listbox_selectmode='single')
self.group_type_box.configure(listbox_exportselection=0)
#
#
# Dropdown list of elements of each structgroup type
#
self.group_elements_box = Pmw.ScrolledListBox(
mapper_win,
items=[],
labelpos='nw',
label_text='Group Elements',
listbox_height=listbox_height,
usehullsize=1,
hull_width=200,
hull_height=100)
self.group_elements_box.grid(row=row,
column=1,
columnspan=1,
sticky='news')
self.group_elements_box.configure(listbox_bg='white')
self.group_elements_box.configure(listbox_selectmode='extended')
self.group_elements_box.configure(listbox_exportselection=0)
# Parameters that we can map to structgroups
import Fitter
self.FIT = Fitter.FITTER('1 pKa 2 Chemical shifts', self)
self.dataprops = ['Data source'] + self.FIT.parameter_names
self.data_prop_box = Pmw.ScrolledListBox(mapper_win,
items=self.dataprops,
labelpos='nw',
label_text='Data properties',
listbox_height=listbox_height,
usehullsize=1,
hull_width=200,
hull_height=100)
self.data_prop_box.grid(row=row, column=2, columnspan=1, sticky='news')
self.data_prop_box.configure(listbox_bg='white')
self.data_prop_box.configure(listbox_selectmode='extended')
self.data_prop_box.configure(listbox_exportselection=0)
#
# List of existing mappings
#
row = row + 1
datatab = self.currentdataset.get()
print 'Loading this datatab in mapper', datatab
mappings = self.get_structmappings(datatab)
self.mapping_box = Pmw.ScrolledListBox(mapper_win,
items=mappings,
labelpos='nw',
label_text='Existing mappings',
listbox_height=6,
usehullsize=1,
hull_width=200,
hull_height=200)
self.mapping_box.grid(row=row, column=0, columnspan=3, sticky='news')
self.mapping_box.configure(listbox_selectmode='single')
self.mapping_box.configure(listbox_bg='white')
#
# Buttons
#
row = row + 1
Button(mapper_win,
text='Create mapping',
bg='lightgreen',
borderwidth=2,
relief=GROOVE,
command=self.create_mapping).grid(row=row,
column=0,
sticky='news',
padx=2,
pady=2)
Button(mapper_win,
text='Delete mapping',
bg='yellow',
borderwidth=2,
relief=GROOVE,
command=self.delete_mapping).grid(row=row,
column=1,
sticky='news',
padx=2,
pady=2)
Button(mapper_win,
text='Export',
bg='#CFECEC',
borderwidth=2,
relief=GROOVE,
command=self.export_dialog).grid(row=row,
column=2,
sticky='news',
padx=2,
pady=2)
row = row + 1
Button(mapper_win,
text='Close',
borderwidth=2,
relief=GROOVE,
command=self.close_mapper_window).grid(row=row,
column=1,
columnspan=2,
sticky='news',
padx=2,
pady=2)
#
# Structural group manager
#
#row=row+1
#Label(mapper_win,text='Structural Group Manager',bg='lightblue').grid(row=row,column=0,columnspan=3,sticky='news')
#import os, sys
#PEAT_dir=os.path.split(__file__)[0]
#sys.path.append(PEAT_dir)
#import protein_selector
#row=row+1
#SEL=protein_selector.select_residue(mapper_win,self.pdblines)
#SEL.box.grid(row=row,column=0)
##
#row=row+1
#Label(mapper_win,text='Atoms').grid(row=row,column=1)
#row=row+1
#Button(mapper_win,text='Create new structural grouping',command=self.create_new_structgroup).grid(row=row,column=0)
#Button(mapper_win,text='Add to structural grouping',command=self.add_to_structgroup).grid(row=row,column=1)
#Button(mapper_win,text='Close',command=mapper_win.destroy).grid(row=row,column=2,sticky='news')
mapper_win.rowconfigure(2, weight=1)
self.mapper_win = mapper_win
self.mapper_win.transient(master=self.ekin_win)
return
