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# gui_prosmart.py
# 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 os
import gi
gi.require_version("Gtk", "4.0")
from gi.repository import Gtk, GObject
from gi.repository import Gio
from gi.repository import GLib
import coot
import coot_gui_api
import coot_utils
import coot_gui
from coot_gui import add_simple_action_to_menu, attach_module_menu_button
# target is my molecule, ref is the homologous (high-res) model
#
# extra arg: include_side_chains=False
#
def run_prosmart(imol_target, imol_ref, include_side_chains=False):
"""
target is my molecule, ref is the homologous (high-res) model
extra arg: include_side_chains=False
"""
dir_stub = "coot-ccp4"
coot.make_directory_maybe(dir_stub)
r_t_name = coot.molecule_name_stub_py(imol_target, 0).replace(" ", "_");
r_r_name = coot.molecule_name_stub_py(imol_ref, 0).replace(" ", "_");
target_pdb_file_name = os.path.join(dir_stub, r_t_name + "-prosmart.pdb")
reference_pdb_file_name = os.path.join(dir_stub, r_r_name + "-prosmart-ref.pdb")
prosmart_out = os.path.join("ProSMART_Output", r_t_name + "-prosmart.txt")
coot.write_pdb_file(imol_target, target_pdb_file_name)
coot.write_pdb_file(imol_ref, reference_pdb_file_name)
prosmart_exe = coot_utils.find_exe("prosmart")
if prosmart_exe:
l = ["-p1", target_pdb_file_name,
"-p2", reference_pdb_file_name,
"-restrain_seqid", "30"]
if include_side_chains:
l += ["-side"]
coot_utils.popen_command(prosmart_exe,
l,
[],
os.path.join(dir_stub, "prosmart.log"),
False)
if (not os.path.isfile(prosmart_out)):
print("file not found", prosmart_out)
else:
print("Reading ProSMART restraints from", prosmart_out)
coot.add_refmac_extra_restraints(imol_target, prosmart_out)
else:
coot.info_dialog("No prosmart")
# this should not be in gui_prosmart. Put it in restraints_gui.py
#
def add_module_restraints():
menu = attach_module_menu_button("Restraints")
def generate_all_molecule_self_restraints(val):
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]:
coot.generate_self_restraints(aa_imol, val)
def generate_self_restraint_func(sig):
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]:
print("in generate_self_restraint_func()", aa_imol, aa_chain_id, sig)
coot.generate_local_self_restraints(aa_imol, aa_chain_id, sig)
# Generate self restraints for residues around sphere
def generate_self_restraint_in_sphere_func():
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]:
centred_residue = [aa_chain_id, aa_res_no, aa_ins_code]
radius = 10
local_dist_max = 4.2
other_residues = coot.residues_near_residue_py(aa_imol, centred_residue, radius)
residue_specs = (centred_residue + other_residues) if isinstance(other_residues, list) else centred_residue
coot.generate_local_self_restraints_by_residues_py(aa_imol, residue_specs, local_dist_max)
def display_extra_restraints_func(state):
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
aa_ins_code, aa_atom_name, aa_alt_conf]:
# this is a bit confusing
coot.set_show_extra_restraints(aa_imol, state)
coot.set_show_extra_distance_restraints(state)
def delete_all_extra_restraints_func():
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
aa_ins_code, aa_atom_name, aa_alt_conf]:
coot.delete_all_extra_restraints(aa_imol)
add_simple_action_to_menu(
menu, "Generate Self Restraints 3.7 for Chain", "generate_self_restraint_37",
lambda _simple_action, _arg: generate_self_restraint_func(3.7))
add_simple_action_to_menu(
menu, "Generate Chain Self Restraints 4.3 for Chain", "generate_self_restraint_43",
lambda _simple_action, _arg: generate_self_restraint_func(4.3))
add_simple_action_to_menu(
menu, "Generate Chain Self Restraints 5.0 for Chain", "generate_self_restraint_50",
lambda _simple_action, _arg: generate_self_restraint_func(5.0))
add_simple_action_to_menu(
menu, "Generate Chain Self Restraints 6.0 for Chain", "generate_self_restraint_60",
lambda _simple_action, _arg: generate_self_restraint_func(6))
add_simple_action_to_menu(
menu, "Generate Local Self Restraints 6", "generate_self_restraint_in_sphere",
lambda _simple_action, _arg: generate_self_restraint_in_sphere_func())
add_simple_action_to_menu(menu, "Generate All-molecule Self Restraints 4.3",
"generate_all_molecule_self_restraints_43",
lambda _simple_action, _arg: generate_all_molecule_self_restraints(4.3))
add_simple_action_to_menu(menu, "Generate All-molecule Self Restraints 5.0",
"generate_all_molecule_self_restraints_50",
lambda _simple_action, _arg: generate_all_molecule_self_restraints(5.0))
add_simple_action_to_menu(menu, "Generate All-molecule Self Restraints 6.0",
"generate_all_molecule_self_restraints_60",
lambda _simple_action, _arg: generate_all_molecule_self_restraints(6.0))
add_simple_action_to_menu(menu, "Delete All Extra Restraints", "delete_all_extra_restraints",
lambda _simple_action, _arg: delete_all_extra_restraints_func())
# todo: Move it under R/RC and make it a single toggle
# add_simple_action_to_menu(
# menu, "Undisplay Extra Restraints","undisplay_extra_restraints",
# lambda _simple_action, _arg: display_extra_restraints_func(0))
# add_simple_action_to_menu(
# menu, "Display Extra Restraints","display_extra_restraints",
# lambda _simple_action, _arg: display_extra_restraints_func(1))
def add_module_prosmart():
menu = attach_module_menu_button("ProSMART")
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 launch_prosmart_gui():
def go_button_cb(*args):
imol_tar = combobox_to_molecule_number(combobox_tar)
imol_ref = combobox_to_molecule_number(combobox_ref)
do_side_chains = check_button.get_active()
run_prosmart(imol_tar, imol_ref, do_side_chains)
window.destroy()
window = Gtk.Window()
window.set_size_request(240,180)
hbox = Gtk.Box(orientation=Gtk.Orientation.HORIZONTAL,spacing=5)
hbox.set_homogeneous(True)
hbox.set_halign(Gtk.Align.END)
vbox = Gtk.Box(orientation=Gtk.Orientation.VERTICAL,spacing=10)
vbox.set_margin_start(10)
vbox.set_margin_end(10)
vbox.set_margin_top(10)
vbox.set_margin_bottom(10)
h_sep = Gtk.Separator(orientation=Gtk.Orientation.HORIZONTAL)
chooser_hint_text_1 = "Target molecule"
chooser_hint_text_2 = "Reference (high-res) molecule"
go_button = Gtk.Button(label="ProSMART")
cancel_button = Gtk.Button(label="Cancel")
check_button = Gtk.CheckButton(label="Include Side-chains")
combobox_tar = coot_gui.generic_molecule_chooser(vbox, chooser_hint_text_1)
combobox_ref = coot_gui.generic_molecule_chooser(vbox, chooser_hint_text_2)
vbox.append(check_button)
vbox.append(h_sep)
vbox.append(hbox)
hbox.append(cancel_button)
hbox.append(go_button)
window.set_child(vbox)
cancel_button.connect("clicked", lambda _w: window.close())
go_button.connect("clicked", go_button_cb)
window.show()
def generate_self_restraint_func(sig):
# is this used?
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]:
generate_local_self_restraints(aa_imol, aa_chain_id, sig)
def prosmart_cut_to_func(sig_low, sig_high):
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]:
coot.set_extra_restraints_prosmart_sigma_limits(aa_imol, sig_low, sig_high)
add_simple_action_to_menu(
menu, "Show Only Deviant Distances Beyond 6","prosmart_cut_to_6",
lambda _simple_action, _arg: prosmart_cut_to_func(-6, 6))
add_simple_action_to_menu(
menu, "Show Only Deviant Distances Beyond 4","prosmart_cut_to_4",
lambda _simple_action, _arg: prosmart_cut_to_func(-4, 4))
add_simple_action_to_menu(
menu, "Show Only Deviant Distances Beyond 2.0","prosmart_cut_to_2",
lambda _simple_action, _arg: prosmart_cut_to_func(-2, 2))
add_simple_action_to_menu(
menu, "Show Only Deviant Distances Beyond 1.0","prosmart_cut_to_1",
lambda _simple_action, _arg: prosmart_cut_to_func(-1, 1))
add_simple_action_to_menu(
menu, "Undisplay All Extra Distance Restraints","prosmart_cut_to_0",
lambda _simple_action, _arg: prosmart_cut_to_func(0, 0))
def restraint_to_ca_func(state):
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
aa_ins_code, aa_atom_name, aa_alt_conf]:
coot.set_extra_restraints_representation_for_bonds_go_to_CA(aa_imol, state)
# # clutter
# coot_gui.add_simple_coot_menu_menuitem(
# menu, "Restraint Representation To CA",
# lambda func: restraint_to_ca_func(1))
# coot_gui.add_simple_coot_menu_menuitem(
# menu, "Restraint Representation To Home Atom",
# lambda func: restraint_to_ca_func(0))
add_simple_action_to_menu(
menu, "Run ProSMART...","run_prosmart_gui", lambda _simple_action, _arg: launch_prosmart_gui())
## extra
# def delete_all_extra_restraints_func():
# with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
# aa_ins_code, aa_atom_name, aa_alt_conf]:
# coot.delete_all_extra_restraints(aa_imol)
# coot_gui.add_simple_coot_menu_menuitem(
# menu, "Delete All Extra Restraints",
# lambda func: delete_all_extra_restraints_func())
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