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# a_rapper_gui.py
# Copyright (C) 2008 Bernhard Lohkamp, The University of York
#
# 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 pygtk, gtk, pango
if (os.name == 'nt'):
home_dir = os.getenv('COOT_HOME')
else:
home_dir = os.getenv('HOME')
rapper_dir = os.path.join(os.path.normpath(home_dir), "rappermc")
rapper_command = "rapper"
def rapper_process():
#needed?
pass
def rename_dir_by_date(dir_name):
import time
date_str = time.strftime("%Y-%m-%d--%H-%M--%S")
new_dir_name = dir_name + date_str
# check if exists?
os.rename(dir_name, new_dir_name)
return new_dir_name
# return a string or False
#
def sequence_string(imol, chain_id, resno_start, resno_end):
def all_chars_qm(ls):
return all(map(lambda x: x.isalpha(), ls))
if (not coot_utils.valid_model_molecule_qm(imol)):
return False
else:
single_letter_code_list = []
for resno in range(resno_start, resno_end + 1):
res_name = coot.residue_name(imol, chain_id, resno, "")
single_letter_code_list.append(mutate.three_letter_code2single_letter(res_name))
if (not all_chars_qm):
print "bad sequence chars ", single_letter_code_list
return False
else:
return "".join(single_letter_code_list)
def rapper_it(imol, chain_id, start_resno, end_resno, sequence, number_of_models):
imol_map = coot.imol_refinement_map()
if (not coot_utils.valid_map_molecule_qm(imol_map)):
print "No valid map molecule given (possibly ambiguous)"
else:
str = "//" + chain_id + "/" + str(start_no) + \
"-" + str(end_resno)
frag_mol = coot.new_molecule_by_atom_selection(imol, str)
fragment_pdb = "coot-rapper-fragment-in.pdb"
rapper_out_pdb = "rapper_out.pdb"
rapper_mode = "model-loops-benchmark" # maybe "ca-trace" perhaps
# rapper_mode = "ca-trace"
length_for_rapper = 3 # test
if (type(sequence) is StringType):
sequence_string = sequence
else:
sequence_string = "AAA"
map_file = "coot-rapper.map"
whole_pdb_file_name = "rapper-all-atoms.pdb"
coot.write_pdb_file(frag_mol, fragment_pdb)
coot.write_pdb_file(imol, whole_pdb_file_name)
coot.close_molecule(frag_mol)
coot.export_map(imol_map, map_file)
print "running rapper: ", imol, chain_id, start_resno, end_resno, \
sequence, number_of_models
if (os.path.isfile("TESTRUNS")):
rename_dir_by_date("TESTRUNS")
rapper_command_line_args = [#"params.xml",
rapper_mode,
"--pdb", fragment_pdb,
# "--framework", whole_pdb_file_name,
"--pdb-out", rapper_out_pdb,
"--map", map_file,
"--models", str(number_of_models),
"--start", str(start_resno),
"--stop", str(end_resno),
# "--length", str(length_for_rapper)
"--seq", sequence_string,
"--mainchain-restraint-threshold", "2.0",
"--sidechain-centroid-restraint-threshold", "2.0",
"--sidechain-mode", "smart",
"--sidechain-radius-reduction", "0.75",
"--enforce-mainchain-restraints", "true",
"--enforce-sidechain-centroid-restraints", "true",
"--edm-fit", "true",
"--rapper-dir", rapper_dir]
rapper_status = coot_utils.popen_command(rapper_command,
rapper_command_line_args,
[],
"rapper.log",
True)
print "rapper_status:", rapper_status
if (os.path.isfile("TESTRUNS")):
new_dir_name = rename_dir_by_date("TESTRUNS")
result_pdb_file_name = os.path.join(new_dir_name, "looptest-best.pdb")
if (os.path.isfile(result_pdb_file_name)):
coot.read_pdb(result_pdb_file_name)
else:
coot.info_dialog("RAPPER failed - no results")
# run rapper, not decided yet how
def stop_rapper():
print "stopping rapper process..."
def cancel_dialog_func(widget, window):
# do something more clever if the rapper process is still running
window.destroy()
# loop_building_tool is either 'rapper' or 'ARP/wARP'
#
def a_rapper_gui(loop_building_tool):
def rapper_go_func(*args):
from types import IntType
imol = coot_gui.get_option_menu_active_molecule(option_menu_pdb, model_mol_list)
if (not (type(imol) is IntType)):
print "bad active model"
else:
chain_text = entry_chain.get_text()
start_resno_text = entry_start_resno.get_text()
end_resno_text = entry_end_resno.get_text()
text_sequence_buffer = text_sequence.get_buffer()
sequence = text_sequence_buffer.get_text()
print "BL DEBUG:: input sequence is", sequence
number_of_models_text = entry_models.get_text()
start_resno = int(start_resno_text)
end_resno = int(end_resno_text)
number_of_models = int(number_of_models_text)
if (not ((type(start_resno) is IntType) and
(type(end_resno) is IntType) and
(type(number_of_models) is IntType))):
print "Something incomprehensible: ", start_resno, end_resno, number_of_models
else:
if (loop_building_tool == 'rapper'):
seq = sequence_string(imol, chain_text, start_resno, end_resno)
rapper_it(imol, chain_text, start_resno, end_resno,
seq, number_of_models)
elif (loop_building_tool == 'ARP/wARP'):
# not supprted yet
new_start = start_resno - 1
new_end = end_resno + 1
seq = sequence_string(imo, chain_text,
new_start, new_end)
arp_warp_it(imol, chain_text,
[start_resno, end_resno],
[new_start, new_end],
seq, number_of_models)
else:
print "INFO:: invalid loop building argument", loop_building_tool
window = gtk.Window(gtk.WINDOW_TOPLEVEL)
vbox = gtk.VBox(False, 2)
pdb_hbox = gtk.HBox(False, 2)
chain_hbox = gtk.HBox(False, 2)
start_resno_hbox = gtk.HBox(False, 2)
end_resno_hbox = gtk.HBox(False, 2)
sequence_vbox = gtk.VBox(False, 2)
models_hbox = gtk.HBox(False, 2)
buttons_hbox = gtk.HBox(False, 2)
h_sep = gtk.HSeparator()
stop_button = gtk.Button(" Stop ")
go_button = gtk.Button(" Go ")
cancel_button = gtk.Button(" Cancel ")
# pdb
label_pdb = gtk.Label("Rebuild fragment of Model: ")
option_menu_pdb = gtk.combo_box_new_text()
# chain
label_chain = gtk.Label("Chain")
entry_chain = gtk.Entry()
# start resno
label_start_resno = gtk.Label("Starting Res Number: ")
entry_start_resno = gtk.Entry()
# end resno
label_end_resno = gtk.Label(" End Res Number: ")
entry_end_resno = gtk.Entry()
# sequence as it currently is:
sequence_as_is_check_button = gtk.CheckButton("As is")
# sequence as text
label_sequence = gtk.Label("Sequence")
text_sequence = gtk.TextView()
# number of rapper models
label_models = gtk.Label("Number of Models: ")
entry_models = gtk.Entry()
#
model_mol_list = coot_gui.fill_option_menu_with_coordinates_mol_options(option_menu_pdb)
#text_sequence.set_usize(-1, 80) # ?? using text view!?
pdb_hbox.pack_start(label_pdb, False, False, 2)
pdb_hbox.pack_start(option_menu_pdb, False, False, 2)
chain_hbox.pack_start(label_chain, False, False, 2)
chain_hbox.pack_start(entry_chain, False, False, 2)
start_resno_hbox.pack_start(label_start_resno, False, False, 2)
start_resno_hbox.pack_start(entry_start_resno, False, False, 2)
end_resno_hbox.pack_start(label_end_resno, False, False, 2)
end_resno_hbox.pack_start(entry_end_resno, False, False, 2)
sequence_vbox.pack_start(label_sequence, False, False, 2)
sequence_vbox.pack_start(sequence_as_is_check_button, False, False, 2)
sequence_vbox.pack_start(text_sequence, False, False, 2)
models_hbox.pack_start(label_models, False, False, 2)
models_hbox.pack_start(entry_models, False, False, 2)
window.set_title("A Rapper GUI")
vbox.pack_start(pdb_hbox, False, False, 2)
vbox.pack_start(chain_hbox, False, False, 2)
vbox.pack_start(start_resno_hbox, False, False, 2)
vbox.pack_start(end_resno_hbox, False, False, 2)
vbox.pack_start(sequence_vbox, False, False, 2)
vbox.pack_start(models_hbox, False, False, 2)
vbox.pack_start(h_sep, False, False, 2)
buttons_hbox.pack_start(go_button, True, False, 6)
buttons_hbox.pack_start(stop_button, True, False, 6)
buttons_hbox.pack_start(cancel_button, True, False, 6)
vbox.pack_start(buttons_hbox, True, False, 2)
window.add(vbox)
entry_models.set_text("2")
sequence_as_is_check_button.set_active(True)
stop_button.connect("clicked", stop_rapper)
cancel_button.connect("clicked", cancel_dialog_func, window)
go_button.connect("clicked", rapper_go_func)
window.show_all()
menu = coot_gui.coot_menubar_menu("Loop")
add_simple_coot_menu_menuitem(menu, "RAPPER...",
lambda func: a_rapper_gui('rapper'))
add_simple_coot_menu_menuitem(menu, "ARP/wARP Loopy...",
lambda func: a_rapper_gui('ARP/wARP'))
a_rapper_gui()
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