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# shelx_extensions.py
# Copyright 2007, 2008 by The University of York
# Copyright 2008 by Bernhard Lohkamp
# Copyright 2007 by Paul Emsley
# Copyright 2007 by The University of Oxford
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or (at
# your option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import numbers
import coot
import coot_utils
import coot_gui
def add_module_shelx():
# we only have the menu if shelxl is in PATH (and if we have the
# python menubar)
if not coot_utils.find_exe("shelxl", "PATH"):
coot.info_dialog("WARNING:: Cannot find shelxl.\n\nSome SHELX plugin functions may not be working")
if have_coot_python:
menu = coot_gui.coot_menubar_menu("SHELX")
def combobox_to_molecule_number(combobox):
imol = -1
tree_iter = combobox.get_active_iter()
if tree_iter is not None:
model = combobox.get_model()
it = model[tree_iter]
imol = it[0]
return imol
def shelx_refine_func():
window = Gtk.Window()
vbox = Gtk.Box(orientation=Gtk.Orientation.VERTICAL)
hbox = Gtk.Box(orientation=Gtk.Orientation.HORIZONTAL)
go_button = Gtk.Button(" Refine ")
cancel_button = Gtk.Button(" Cancel ")
entry_hint_text = "HKL data filename \n(leave blank for default)"
chooser_hint_text = " Choose molecule for SHELX refinement "
h_sep = Gtk.HSeparator()
window.add(vbox)
# option_menu_mol_list_pair = coot_gui.generic_molecule_chooser(vbox, chooser_hint_text)
combobox_items = make_store_for_molecule_combobox(molecule_filter_function)
combobox = Gtk.ComboBox.new_with_model(combobox_items)
renderer_text = Gtk.CellRendererText()
if len(combobox_items) > 0:
combobox.set_active(0)
combobox.set_entry_text_column(1) # Sets the model column which combo_box
# should use to get strings from to be text_column
combobox.pack_start(renderer_text, True)
combobox.add_attribute(renderer_text, "text", 1)
entry = coot_gui.file_selector_entry(vbox, entry_hint_text)
def shelx_delete_event(*args):
window.destroy()
return False
def shelx_refine_go_funcn_event(*args):
import operator
txt = entry.get_text()
imol = combobox_to_molecule_number(combobox)
if (isinstance(imol, numbers.Number)):
editable_shelx_gui(imol, txt)
window.destroy()
return False
go_button.connect("clicked", shelx_refine_go_funcn_event)
cancel_button.connect("clicked", shelx_delete_event)
vbox.append(h_sep)
vbox.append(hbox)
hbox.append(go_button)
hbox.append(cancel_button)
window.show_all()
coot_gui.add_simple_coot_menu_menuitem(
menu, "SHELXL Refine...",
lambda func: shelx_refine_func())
def shelx_read_project_func(*args):
def shelx_delete_event(*args):
window.destroy()
return False
def shelx_read_go_funcn_event(*args):
file_name = entry.get_text()
shelx.read_shelx_project(file_name)
window.destroy()
return False
window = Gtk.Window(Gtk.WINDOW_TOPLEVEL)
hbox = Gtk.Box(orientation=Gtk.Orientation.HORIZONTAL)
vbox = Gtk.Box(orientation=Gtk.Orientation.VERTICAL)
h_sep = Gtk.HSeparator()
go_button = Gtk.Button(" Read Project ")
cancel_button = Gtk.Button(" Cancel ")
entry = coot_gui.file_selector_entry(vbox, " Project Name: ")
cancel_button.connect("clicked", shelx_delete_event)
go_button.connect("clicked", shelx_read_go_funcn_event)
window.add(vbox)
hbox.append(go_button)
hbox.append(cancel_button)
vbox.append(h_sep)
vbox.append(hbox)
window.show_all()
coot_gui.add_simple_coot_menu_menuitem(
menu, "Read SHELX Project...",
lambda func: shelx_read_project_func())
coot_gui.add_simple_coot_menu_menuitem(
menu, "Read LST file...",
lambda func: coot_gui.generic_chooser_and_file_selector("Model Corresponding to LST file: ",
coot_utils.valid_model_molecule_qm,
"LST file",
"",
lambda imol, lst_file_name: shelx.read_shelx_lst_file(lst_file_name, imol)))
coot_gui.add_simple_coot_menu_menuitem(
menu, "Add SHELXL instruction...",
lambda func: coot_gui.generic_chooser_and_entry("Add new SHELXL command to model:",
"SHELX instruction:",
"",
lambda imol, text: coot.add_shelx_string_to_molecule(imol, text)))
def shelx_ins_strings(imol):
ins_tmp_file = "coot-tmp.ins"
coot.write_shelx_ins_file(imol, ins_tmp_file)
lines = []
try:
fin = open(ins_tmp_file, 'r')
lines = fin.readlines()
fin.close()
except:
print("INFO:: problems reading file", ins_tmp_file)
return lines
def shelxl_refine_gui(imol, hkl_file_name_maybe=False):
def shelx_delete_event(*args):
window.destroy()
return False
def shelx_refine_go_funcn_event(*args):
import operator
start, end = textbuffer.get_bounds()
txt = textbuffer.get_text(start, end)
shelx.shelxl_refine_primitive(imol, txt, hkl_file_name_maybe)
window.destroy()
return False
window = Gtk.Window()
window.set_size_request(500, 500)
vbox = Gtk.Box(orientation=Gtk.Orientation.VERTICAL)
buttons_hbox = Gtk.Box(orientation=Gtk.Orientation.HORIZONTAL)
scrolled_win = Gtk.ScrolledWindow()
text = Gtk.TextView()
textbuffer = text.get_buffer()
text.set_editable(True)
refine_button = Gtk.Button(" Refine ")
cancel_button = Gtk.Button(" Cancel ")
window.add(vbox)
scrolled_win.add(text)
buttons_hbox.append(refine_button)
buttons_hbox.append(cancel_button)
scrolled_win.set_policy(Gtk.POLICY_AUTOMATIC, Gtk.POLICY_ALWAYS)
vbox.append(buttons_hbox)
vbox.pack_start(scrolled_win)
text_strings = shelx_ins_strings(imol)
bg_col = "#c0e6c0"
text.modify_base(Gtk.STATE_NORMAL, Gtk.gdk.color_parse(bg_col))
text.modify_text(Gtk.STATE_NORMAL, Gtk.gdk.color_parse("black"))
for string in text_strings:
end = textbuffer.get_end_iter()
textbuffer.insert(end, string)
refine_button.connect("clicked", shelx_refine_go_funcn_event)
cancel_button.connect("clicked", shelx_delete_event)
window.show_all()
def editable_shelx_gui(imol, hklin_file_name):
def shelx_delete_event(*args):
window.destroy()
return False
def shelx_refine_go_funcn_event(*args):
from types import StringType
start, end = textbuffer.get_bounds()
txt = textbuffer.get_text(start, end)
if (type(txt) == StringType):
hklin_file_info = False
if (len(hklin_file_name) > 0):
hklin_file_info = hklin_file_name
shelx.shelxl_refine_primitive(imol, txt, hklin_file_info)
window.destroy()
return False
window = Gtk.Window(Gtk.WINDOW_TOPLEVEL)
text = Gtk.TextView()
textbuffer = text.get_buffer()
scrolled_win = Gtk.ScrolledWindow()
cancel_button = Gtk.Button(" Cancel ")
run_button = Gtk.Button(" Run ")
vbox = Gtk.Box(orientation=Gtk.Orientation.VERTICAL)
buttons_hbox = Gtk.Box(orientation=Gtk.Orientation.HORIZONTAL)
window.set_size_request(450, 400)
window.add(vbox)
scrolled_win.add(text)
vbox.set_border_width(5)
buttons_hbox.append(run_button)
buttons_hbox.append(cancel_button)
vbox.append(buttons_hbox)
vbox.append(scrolled_win)
scrolled_win.set_policy(Gtk.POLICY_AUTOMATIC, Gtk.POLICY_ALWAYS)
text.set_editable(True)
shelx_ins_list = get_shelx_ins_list(imol)
bg_col = "white"
text.modify_base(Gtk.STATE_NORMAL, Gtk.gdk.color_parse(bg_col))
text.modify_text(Gtk.STATE_NORMAL, Gtk.gdk.color_parse("black"))
for string in shelx_ins_list:
end = textbuffer.get_end_iter()
textbuffer.insert(end, string)
run_button.connect("clicked", shelx_refine_go_funcn_event)
cancel_button.connect("clicked", shelx_delete_event)
window.show_all()
# seems to be the same...
get_shelx_ins_list = shelx_ins_strings
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