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# 18/3/2018 version 2.3 (acedrg?)
import gi
gi.require_version('Gtk', '4.0')
from gi.repository import Gtk
import coot
import coot_utils
import coot_gui
#this could be in coot_gui.coot_gui.py
def old_function_fill_option_menu_with_string_options(menu, string_list, default_option_value):
for item in string_list:
menu.append_text(item)
if (default_option_value == item):
count = string_list.index(item)
menu.set_active(count)
print("setting menu active ", default_option_value, count)
def fill_combobox_with_string_options(combobox, string_list, default_string):
model = coot_gui.make_store_for_string_list_combobox(combobox, string_list, default_string)
combobox.set_model(model)
for i in range(len(string_list)):
if (string_list[i] == default_string):
combobox.set_active(i)
return model
def acedrg_link_generation_control_window():
def delete_event(*args):
window.destroy()
return False
# main body
window = Gtk.Window()
vbox = Gtk.Box(orientation=Gtk.Orientation.VERTICAL,spacing=10)
vbox.set_margin_top(10)
vbox.set_margin_bottom(10)
vbox.set_margin_start(10)
vbox.set_margin_end(10)
inside_hbox_1 = Gtk.Box(orientation=Gtk.Orientation.HORIZONTAL, spacing=5)
inside_hbox_2 = Gtk.Box(orientation=Gtk.Orientation.HORIZONTAL, spacing=5)
inside_hbox_3 = Gtk.Box(orientation=Gtk.Orientation.HORIZONTAL, spacing=5)
inside_hbox_4 = Gtk.Box(orientation=Gtk.Orientation.HORIZONTAL, spacing=5)
cancel_hbox = Gtk.Box(orientation=Gtk.Orientation.HORIZONTAL, spacing=5)
cancel_hbox.set_homogeneous(True)
cancel_hbox.set_halign(Gtk.Align.END)
cancel_hbox.set_valign(Gtk.Align.END)
order_label = Gtk.Label(label="Order:")
delete_atom_label = Gtk.Label(label="Delete Atom:")
change_bond_order_label = Gtk.Label(label="Change Bond Order of the Bond between Atoms")
delete_bond_label = Gtk.Label(label="Delete Bond:")
other_label = Gtk.Label(label="from First Residue ")
to_order_label = Gtk.Label(label="to order")
right_space_label = Gtk.Label(label=" ") # PE hackey
# option_menu_bond_order = Gtk.combo_box_new_text()
# option_menu_change_bond_order = Gtk.combo_box_new_text() # for a bond already in the ligand
bond_list = ["Single", "Double"]
# fill_option_menu_with_string_options(option_menu_bond_order, bond_list, "Single")
# fill_option_menu_with_string_options(option_menu_change_bond_order, bond_list, "Single")
combobox_bond_order = Gtk.ComboBox()
combobox_change_bond_order = Gtk.ComboBox()
combobox_bond_order_model = fill_combobox_with_string_options(combobox_bond_order, bond_list, "Single")
# maybe the default change bond order should be ""?
combobox_change_bond_order_model = fill_combobox_with_string_options(combobox_change_bond_order, bond_list, "Single")
combobox_bond_order.set_model(combobox_bond_order_model)
combobox_change_bond_order.set_model(combobox_change_bond_order_model)
renderer_text = Gtk.CellRendererText()
combobox_bond_order.set_entry_text_column(0)
combobox_bond_order.pack_start(renderer_text, True)
combobox_bond_order.add_attribute(renderer_text, "text", 0)
renderer_text = Gtk.CellRendererText()
combobox_change_bond_order.set_entry_text_column(0)
combobox_change_bond_order.pack_start(renderer_text, True)
combobox_change_bond_order.add_attribute(renderer_text, "text", 0)
# tt = Gtk.Tooltips()
delete_atom_entry = Gtk.Entry()
delete_bond_entry = Gtk.Entry()
change_bond_order_entry = Gtk.Entry()
h_sep = Gtk.Separator(orientation=Gtk.Orientation.HORIZONTAL)
h_sep.set_valign(Gtk.Align.END)
h_sep.set_vexpand(True)
cancel_button = Gtk.Button(label="Cancel")
pick_button = Gtk.Button(label="Start (Pick 2 Atoms)...")
advanced_section = Gtk.Expander(label="Advanced")
adv_vbox = Gtk.Box(orientation=Gtk.Orientation.VERTICAL,spacing=10)
adv_vbox.set_margin_top(10)
adv_vbox.set_margin_bottom(10)
adv_vbox.set_margin_start(10)
adv_vbox.set_margin_end(10)
advanced_section.set_child(adv_vbox)
adv_vbox.append(inside_hbox_2)
adv_vbox.append(inside_hbox_3)
adv_vbox.append(inside_hbox_4)
window.set_title("Make a Link using Acedrg and Atom Click Click")
vbox.append(inside_hbox_1)
vbox.append(advanced_section)
inside_hbox_1.append(order_label)
inside_hbox_1.append(combobox_bond_order)
inside_hbox_2.append(delete_atom_label)
inside_hbox_2.append(delete_atom_entry)
inside_hbox_2.append(other_label)
inside_hbox_3.append(change_bond_order_label)
inside_hbox_3.append(change_bond_order_entry)
inside_hbox_3.append(to_order_label)
inside_hbox_3.append(combobox_change_bond_order)
inside_hbox_3.append(right_space_label)
inside_hbox_4.append(delete_bond_label)
inside_hbox_4.append(delete_bond_entry)
vbox.append(h_sep)
vbox.append(cancel_hbox)
cancel_hbox.append(cancel_button)
cancel_hbox.append(pick_button)
delete_atom_entry.set_size_request(80, -1)
delete_bond_entry.set_size_request(80, -1)
change_bond_order_entry.set_size_request(80, -1)
# restore the tooltips one day
cancel_button.connect("clicked", delete_event)
pick_button.connect("clicked", lambda func:
click_select_residues_for_acedrg(window,
combobox_bond_order,
delete_atom_entry,
delete_bond_entry,
change_bond_order_entry,
combobox_change_bond_order))
window.set_child(vbox)
window.show()
# hack link cif file so that it works in coot 0.8.9 (:-/)
#
# return the new file name
def hack_link(fn):
import os
stub = coot_utils.file_name_sans_extension(fn)
new_file_name = fn + "-hack.cif"
with open(fn, "rt") as fin:
with open(new_file_name, "wt") as fout:
for line in fin:
fout.write(line.replace("L-PEPTIDE", "L-peptide"))
return new_file_name
def click_select_residues_for_acedrg(window, combobox_bond_order, delete_atom_entry,
delete_bond_entry, change_bond_order_entry,
combobox_change_bond_order):
# return a 3-member list: is-correct atom-name-1 atom-name-2)
# is-correct can either be
# True or False or None
# False means that there was a blank or empty string
# True mean we found 2 atom names
# None means that we found 1 or 3 or more atom names
# Typicall this will return [False, "", ""]
def extract_atom_names_from_string(str_in):
atom_name_1 = ""
atom_name_2 = ""
is_correct = False
sl = len(str_in)
if (sl == 0):
return [is_correct, atom_name_1, atom_name_2]
else:
parts = str_in.split("")
if (not len(parts) == 2):
return [None, atom_name_1, atom_name_2] #
else:
return [True] + parts
def make_acedrg_bond(*clicks):
print("DEBUG:: make_acedrg_bond(): we received these clicks:", clicks)
bond_list = ['single', 'double']
bond_order = combobox_bond_order.get_active()
change_bond_order = combobox_change_bond_order.get_active()
print("debug:: make_acedrg_bond(): bond_order", bond_order)
print("debug:: make_acedrg_bond(): change_bond_order", change_bond_order)
if len(clicks) == 2:
click_1 = clicks[0]
click_2 = clicks[1]
print("DEBUG:: make_acedrg_bond(): click_1", click_1)
print("DEBUG:: make_acedrg_bond(): click_2", click_2)
if len(click_1) == 7 and len(click_2) == 7:
print("DEBUG:: length of clicks was correct")
resname_1 = coot.residue_name(*click_1[1:5])
resname_2 = coot.residue_name(*click_2[1:5])
at_name_1 = click_1[5]
at_name_2 = click_2[5]
spec_1 = click_1[1:]
spec_2 = click_2[1:]
imol_click_1 = click_1[1]
imol_click_2 = click_2[1]
delete_atom_text = delete_atom_entry.get_text()
delete_bond_entry_text = delete_bond_entry.get_text()
change_bond_order_entry_text = change_bond_order_entry.get_text()
print("DEBUG:: make_acedrg_bond() resname_1", resname_1)
print("DEBUG:: make_acedrg_bond() resname_2", resname_2)
if not (isinstance(resname_1, str) and
isinstance(resname_2, str)):
print("Bad resnames: %s and %s " %(resname_1, resname_2))
return False # just in case
else:
if not imol_click_1 == imol_click_2:
coot.add_status_bar_text("These residues are not in the same molecule")
return False
else:
print("got here A")
imol = imol_click_1
delete_stripped_1 = delete_atom_text.replace(" ", "")
delete_atom_txt = " DELETE ATOM " + delete_stripped_1 + " 1 " \
if len(delete_stripped_1) > 0 else \
""
print("got here B1")
delete_bond_info = extract_atom_names_from_string(delete_bond_entry_text)
print("got here B2")
change_bond_order_info = extract_atom_names_from_string(change_bond_order_entry_text)
s = "LINK:" + \
" RES-NAME-1 " + resname_1 + " ATOM-NAME-1 " + at_name_1 + \
" RES-NAME-2 " + resname_2 + " ATOM-NAME-2 " + at_name_2
print("got here B3")
# I need to check here if resname_1 or resname_2 came from a file that
# was read into Coot from somewhere other than the refmac monomer library
# (that acedrg knows about).
print("got here C")
cif_fn_1 = coot.cif_file_for_comp_id_py(resname_1)
cif_fn_2 = coot.cif_file_for_comp_id_py(resname_2)
print("got here D1")
ns = coot.non_standard_residue_names_py(imol)
print("got here D2")
# if the resnames are not non-standard-residue-names
# then we don't need to specify the file - if they
# are not, then use cif_fn_1 (or cif_fn_2)
print("DEBUG:: cif_fn_1:", cif_fn_1)
print("DEBUG:: cif_fn_2:", cif_fn_2)
print("DEBUG:: ns: ", ns)
if (bond_order == 'double'):
s += " BOND-TYPE DOUBLE"
if (resname_1 in ns):
s += " FILE-1 " + cif_fn_1
if (resname_2 in ns):
s += " FILE-2 " + cif_fn_2
# delete atom?
s += delete_atom_txt
# change bond order?
if change_bond_order_info[0]:
ss = " CHANGE BOND " + \
change_bond_order_info[1] + \
" " + \
change_bond_order_info[2] + \
" " + \
("DOUBLE" if change_bond_order == 'double' else "SINGLE") + \
" 1 "
s += ss
# delete bond?
if delete_bond_info[0]:
ss = " DELETE BOND " + \
delete_bond_info[1] + \
" " + \
delete_bond_info[2] + \
" 1 "
s += ss
print("BL DEBUG:: LINK string:", s)
st_1 = "acedrg-link-from-coot-" + \
resname_1 + "-" + \
resname_2
st = st_1 + "-link-instructions"
log_file_name = st + ".log"
ins_file_name = st + ".txt"
# maybe can make a function for call_with_output_file
fin = open(ins_file_name, "w")
fin.write(s)
fin.close()
status = coot_utils.popen_command("acedrg",
["-L", ins_file_name, "-o", st_1],
[],
log_file_name,
False,
local_env=acedrg_env())
if not status == 0:
m = "WARNING:: acedrg failed.\nSee " + log_file_name
coot.info_dialog(m)
else:
# happy path
link_file_name = st_1 + "_link.cif" # acedrg name
hack_link_file_name = hack_link(link_file_name)
dict_read_status = coot.read_cif_dictionary(hack_link_file_name)
# dict_read_status is the number of bonds read
if (dict_read_status > -2):
coot.make_link_py(imol_click_1, spec_1, spec_2, "dummy-name", 1.0)
window.destroy() # when?
coot.user_defined_click_py(2, make_acedrg_bond)
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