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|
# get_recent_pdbe.py
# Copyright (C) 2011 Bernhard Lohkamp
# Copyright 2015, 2016 by Medical Research Council
#
# 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/>.
# FIXME: review this initiallisations
import gobject
# some timeout setting (used?)
import socket
# FIXME, depening on what we download!?
socket.setdefaulttimeout(10)
#sys.setcheckinterval(10) # doesnt seem to make much of a difference...
import queue
max_queue = 14
coot_queue = queue.Queue()
import _thread
safe_print = _thread.allocate_lock()
def print_thread(*txt):
safe_print.acquire()
print(" ".join(map(str, txt)))
safe_print.release()
global coot_pdbe_image_cache_dir
coot_pdbe_image_cache_dir = "coot-pdbe-images" # can be shared (dir should
# be writable by sharers)
def coot_pdbe():
pass
#
def get_recent_json(file_name):
import json # maybe should be globally imported
if not os.path.isfile(file_name):
print("file not found", file_name)
return False
else:
fin = open(file_name, 'r')
s = json.load(fin)
fin.close()
return s
# geometry is an improper list of ints.
#
# return the h_box of the buttons.
#
# a button is a list of [label, callback-thunk, text-description]
#
# If check-button-label is False, don't make one, otherwise create with with
# the given label and "on" state.
#
def dialog_box_of_buttons_with_async_ligands(window_name, geometry,
buttons, close_button_label):
"""geometry is an improper list of ints.
return the h_box of the buttons.
a button is a list of [label, callback-thunk, text-description]
If check-button-label is False, don't make one, otherwise create with with
the given label and "on" state.
"""
# the async function is evaluated here
#
def add_button_info_to_box_of_buttons_vbox_for_ligand_images(button_info, vbox):
button_label = button_info[0]
callback = button_info[1]
active_button_label_func = button_info[2] \
if (len(button_info) > 2) \
else False # it doesnt have one
button = gtk.Button()
button_hbox = gtk.HBox(False, 0) # pixmaps and labels get added here.
protein_ribbon_hbox = gtk.HBox(False, 0) # do we need a box here?!
ligands_hbox = gtk.HBox(False, 0)
button_hbox.append(gtk.Label(button_label))
# or just button.set_label?!
button_hbox.append(ligands_hbox)
button_hbox.append(protein_ribbon_hbox)
button.add(button_hbox)
button.connect("clicked", callback)
# this is for function, but thread here!?!
#if callable(active_button_label_func):
# active_button_label_func(button_hbox,
# ligands_hbox,
# protein_ribbon_hbox)
#
# if active_button_label_func:
# ignore nmr for now
if not callable(active_button_label_func):
entry_id = active_button_label_func[0]
ligand_tlc_list = active_button_label_func[1]
make_active_ligand_button(entry_id, ligand_tlc_list,
ligands_hbox, protein_ribbon_hbox)
# we pass the button to update in thread!
vbox.append(button)
button.show()
# the 'new' version, we threaded download and add the
# images to the button's hboxes
def make_active_ligand_button(entry_id, ligand_tlc_list,
ligands_hbox, protein_ribbon_hbox):
global coot_pdbe_image_cache_dir
# main line
image_size = 100
for tlc in ligand_tlc_list:
# image_url = "http://www.ebi.ac.uk/pdbe-srv/pdbechem/image/showNew?code=" + \
# tlc + "&size=" + str(image_size)
image_url = "https://www.ebi.ac.uk/pdbe/static/chem-files/" + \
tlc + "-" + str(image_size) + ".gif"
image_name = os.path.join(coot_pdbe_image_cache_dir,
(tlc + "-" + str(image_size) + ".gif"))
cache_or_net_get_image(image_url, image_name, ligands_hbox)
# now do the protein icon:
image_size = 120
# image_name_stub = entry_id + "_cbc" + str(image_size) + ".png"
image_name_stub = "_deposited_chain_front_image-200x200.png"
# image_url = "http://www.ebi.ac.uk/pdbe/entry-images/" + \
# image_name_stub
image_url = "https://www.ebi.ac.uk/pdbe/static/entry/" + \
entry_id + image_name_stub
entry_image_file_name = os.path.join(coot_pdbe_image_cache_dir,
entry_id + image_name_stub)
cache_or_net_get_image(image_url, entry_image_file_name,
protein_ribbon_hbox)
# main line
window = gtk.Window(gtk.WINDOW_TOPLEVEL)
scrolled_win = gtk.ScrolledWindow()
outside_vbox = gtk.VBox(False, 2)
h_sep = gtk.HSeparator()
inside_vbox = gtk.VBox(False, 0)
window.set_default_size(geometry[0], geometry[1])
window.set_title(window_name)
inside_vbox.set_border_width(2)
window.add(outside_vbox)
outside_vbox.append(scrolled_win)
scrolled_win.add_with_viewport(inside_vbox)
scrolled_win.set_policy(gtk.POLICY_AUTOMATIC,gtk.POLICY_ALWAYS)
if buttons:
list(map(lambda button_info:
coot_gui.add_button_info_to_box_of_buttons_vbox_for_ligand_images(button_info,
inside_vbox),
buttons))
outside_vbox.set_border_width(2)
outside_vbox.append(h_sep)
ok_button = gtk.Button(close_button_label)
outside_vbox.pack_end(ok_button, False, False, 0)
def delete_event(*args):
# global setting of inside vbox (locked?)?
inside_vbox = False
# shall empty the queue
if not coot_queue.empty():
while not coot_queue.empty():
coot_queue.get()
coot_queue.task_done()
window.destroy()
return False
ok_button.connect("clicked", delete_event)
window.connect("destroy", delete_event)
window.show_all()
# make a few downloaders, 14 seems to be a good number according to Paule
for i in range(14):
downloader_thread(i)
return inside_vbox
def is_png_or_gif_qm(file_name):
import imghdr
if not os.path.isfile(file_name):
return False
else:
return imghdr.what(file_name)
# Get image-name (caller doesn't care how) and when it is in place run func.
# This is a generally useful function, so it has been promoted outside of dig-table.
# mMMMmmm not sure if I want to run a lambda function here?! Let's see
# maybe this should be better queued, otherwise we may start lots of
# threads
#
def cache_or_net_get_image(image_url, image_name, hbox):
import _thread # try to get away with the simple ones
import urllib.request, urllib.parse, urllib.error # move to a proper place FIXME
import threading
def show_image_when_ready(image_name, hbox):
if os.path.isfile(image_name):
#apply(func)
# instead of function we put image into vbox here
pixmap = gtk.Image()
if is_png_or_gif_qm(image_name):
pixmap.set_from_file(image_name)
hbox.append(pixmap)
pixmap.show()
return False # stop
else:
return True # continue
def get_image(url, file_name):
try:
file_name, url_info = urllib.request.urlretrieve(url, file_name)
except socket.timeout:
print_thread("BL ERROR:: timout download", url[-50:])
except:
print_thread("BL ERROR:: failed download", url[-50:])
# this takes time!! Use queue instead!
# thread.start_new_thread(get_image, (image_url, image_name))
coot_queue.put((image_url, image_name))
gobject.timeout_add(1000, show_image_when_ready, image_name, hbox)
def downloader_thread(thread_no):
import urllib.request, urllib.parse, urllib.error
def get_image():
while True:
try:
url, file_name = coot_queue.get()
try:
file_name, url_info = urllib.request.urlretrieve(url, file_name)
except socket.timeout:
print_thread("BL ERROR:: timout download", url[-50:])
except:
print_thread("BL ERROR:: failed download", url[-50:])
coot_queue.task_done()
except queue.Empty:
# nothing left to do, die baby
return
_thread.start_new_thread(get_image, ())
# return refmac_result or False
#
def refmac_calc_sfs_make_mtz_with_columns(pdb_in_file_name, mtz_file_name,
mtz_refmaced_file_name,
f_col, sigf_col, r_free_col):
global refmac_extra_params
refmac_stub = os.path.join("coot-refmac",
coot_utils.strip_path(coot_utils.file_name_sans_extension(pdb_in_file_name)))
pdb_out_file_name = refmac_stub + "-refmaced.pdb"
mtz_out_file_name = mtz_refmaced_file_name
extra_cif_lib_filename = ""
imol_refmac_count = 0
swap_map_colours_post_refmac = 0
imol_mtz_molecule = False
show_diff_map_flag = 0
phase_combine_flag = 0
phib_fom_pair = False
force_n_cycles = 0
make_molecules_flag = 0 # ??
save_refmac_extra_params = refmac_extra_params
if isinstance(refmac_extra_params, list):
refmac_extra_params.append("MAKE NEWLIGAND CONTINUE")
else:
refmac_extra_params = ["MAKE NEWLIGAND CONTINUE"]
refmac_result = refmac.run_refmac_by_filename(pdb_in_file_name,
pdb_out_file_name,
mtz_file_name, mtz_out_file_name,
extra_cif_lib_filename,
imol_refmac_count,
swap_map_colours_post_refmac,
imol_mtz_molecule,
show_diff_map_flag,
phase_combine_flag,
phib_fom_pair,
force_n_cycles,
make_molecules_flag,
"", f_col, sigf_col, r_free_col)
# restore refmac-extra-params to what it used to be
#
refmac_extra_params = save_refmac_extra_params
if os.path.isfile(mtz_refmaced_file_name):
return refmac_result
else:
return False
def refmac_calc_sfs_make_mtz(pdb_in_file_name, mtz_file_name,
mtz_refmaced_file_name):
return refmac_calc_sfs_make_mtz_with_columns(pdb_in_file_name, mtz_file_name,
mtz_refmaced_file_name,
"F.F_sigF.F", "F.F_sigF.sigF",
"Rfree.Flag.flag")
# include_get_sfs_flag is either "no-sfs" or "include-sfs"
#
def pdbe_get_pdb_and_sfs_cif(include_get_sfs_flag,
entry_id, method_string=""):
import urllib.request, urllib.parse, urllib.error
import time
global download_thread_status
download_thread_status = None # start
# At the moment PDBe wants lower case entry ids?! So we make them
entry_id = entry_id.lower()
coot_download_dir = coot_utils.get_directory("coot-download")
if (not coot_download_dir):
coot.info_dialog("Failed to make download directory")
else:
# do it!
# just a small bit of abstraction.
#
def make_and_draw_map_local(refmac_out_mtz_file_name):
coot.make_and_draw_map(refmac_out_mtz_file_name, "FWT", "PHWT", "", 0, 0)
coot.make_and_draw_map(refmac_out_mtz_file_name, "DELFWT", "PHDELWT", "", 0, 1)
def get_sfs_run_refmac(sfs_cif_url, sfs_cif_file_name,
sfs_mtz_file_name, pdb_file_name,
refmac_out_mtz_file_name,
cif_progress_bar, window):
global download_thread_status
#
def convert_to_mtz_and_refmac(sfs_cif_file_name,
sfs_mtz_file_name,
pdb_file_name):
global download_thread_status
# OK, let's run convert to mtz and run refmac
#
download_thread_status = "converting-to-mtz"
convert_status = coot.mmcif_sfs_to_mtz(sfs_cif_file_name,
sfs_mtz_file_name)
if not (convert_status == 1):
# why cant we make a dialog?! (if this is threaded)
txt = "WARNING:: Failed to convert " + \
sfs_cif_file_name + " to an mtz file"
print(txt)
#info_dialog(txt)
download_thread_status = "fail"
else:
# first check cancel
if not (download_thread_status == "cancelled"):
# why extra function!?
#refmac_inner(pdb_file_name, sfs_mtz_file_name,
# refmac_out_mtz_file_name)
download_thread_status = "running-refmac-for-phases"
refmac_result = refmac_calc_sfs_make_mtz(pdb_file_name,
sfs_mtz_file_name,
refmac_out_mtz_file_name)
print(" refmac-result: ", refmac_result)
# if refmac_result is good? (is tuple not list)
# good enough if it's not false?!
if not (isinstance(refmac_result, tuple)):
download_thread_status = "fail-refmac"
else:
# make map
# cant do here!! we are in thread!!
#make_and_draw_map_local(refmac_out_mtz_file_name)
download_thread_status = "done" #??
# main line get_sfs_run_refmac
print("in get_sfs_run_refmac", sfs_cif_file_name, end=' ')
sfs_mtz_file_name, pdb_file_name, refmac_out_mtz_file_name
# check for cached results: only run refmac if
# output file does not exist or is empty
if (os.path.isfile(refmac_out_mtz_file_name) and
os.stat(refmac_out_mtz_file_name).st_size > 0):
# using cached result, i.e. skip
download_thread_status = "done"
else:
# the coot refmac interface writes its
# output in coot-refmac directory. If
# that doesn't exist and we can't make
# it, then give up.
#
if (not coot.make_directory_maybe("coot_refmac") == 0):
coot.info_dialog("Can't make output directory coot-refmac")
else:
if (os.path.isfile(sfs_cif_file_name) and
os.stat(sfs_cif_file_name).st_size > 0):
# we have sfs_cif_file_name already
download_thread_status = "done-download" # instruct to?
# needed
else:
# need to get sfs_mtz_file_name
download_thread_status = "downloading-sfs"
cif_thread = _thread.start_new_thread(download_file_and_update_widget,
(sfs_cif_url,
sfs_cif_file_name,
cif_progress_bar,
window))
def check_cif_download_thread():
if download_thread_status == "downloading-sfs":
return True
else:
# done
if (download_thread_status == "done-download"):
convert_to_mtz_and_refmac(sfs_cif_file_name,
sfs_mtz_file_name,
pdb_file_name)
return False
if (download_thread_status == "cancelled"):
return False
else:
return True
gobject.idle_add(check_cif_download_thread)
# return a list of the progress bars and the window
#
# (the pdb-file-name and sfs-cif-file-name are passed so
# that the cancel button knows what transfers to cancel (if
# needed)).
# FIXME:: all needed?!?
def progress_dialog(pdb_file_name, sfs_cif_file_name):
window = gtk.Window(gtk.WINDOW_TOPLEVEL)
dialog_name = "Download and make SFS for " + entry_id
main_vbox = gtk.VBox(False, 6)
cancel_button = gtk.Button(" Cancel ")
buttons_hbox = gtk.HBox(False, 2)
pdb_hbox = gtk.HBox(False, 6)
cif_hbox = gtk.HBox(False, 6)
refmac_hbox = gtk.HBox(False, 6)
pdb_label = gtk.Label("Download PDB: ")
cif_label = gtk.Label("Download SFs cif:")
refmac_label = gtk.Label("Running Refmac:")
# FIXME: shouldnt we rather change the label than making
# or adding a new one?!
refmac_fail_label = gtk.Label("Running Refmac Failed")
fail_label = gtk.Label("Something Went Wrong")
pdb_progress_bar = gtk.ProgressBar()
cif_progress_bar = gtk.ProgressBar()
refmac_progress_bar = gtk.ProgressBar()
pdb_execute_icon = gtk.image_new_from_stock("gtk-execute", 1)
cif_execute_icon = gtk.image_new_from_stock("gtk-execute", 1)
refmac_execute_icon = gtk.image_new_from_stock("gtk-execute", 1)
pdb_good_icon = gtk.image_new_from_stock("gtk-ok", 1)
cif_good_icon = gtk.image_new_from_stock("gtk-ok", 1)
refmac_good_icon = gtk.image_new_from_stock("gtk-ok", 1)
pdb_fail_icon = gtk.image_new_from_stock("gtk-no", 1)
cif_fail_icon = gtk.image_new_from_stock("gtk-no", 1)
refmac_fail_icon = gtk.image_new_from_stock("gtk-no", 1)
h_sep = gtk.HSeparator()
window.set_title(dialog_name)
buttons_hbox.append(cancel_button)
pdb_hbox.append(pdb_label)
pdb_hbox.append(pdb_progress_bar)
# NOTE: shouldnt we rather replace the icons?! Not sure
pdb_hbox.append(pdb_execute_icon)
pdb_hbox.append(pdb_good_icon)
pdb_hbox.append(pdb_fail_icon)
cif_hbox.append(cif_label)
cif_hbox.append(cif_progress_bar)
cif_hbox.append(cif_execute_icon)
cif_hbox.append(cif_good_icon)
cif_hbox.append(cif_fail_icon)
refmac_hbox.append(refmac_label)
refmac_hbox.append(refmac_progress_bar)
refmac_hbox.append(refmac_execute_icon)
refmac_hbox.append(refmac_good_icon)
refmac_hbox.append(refmac_fail_icon)
main_vbox.append(pdb_hbox)
main_vbox.append(cif_hbox)
main_vbox.append(refmac_hbox)
main_vbox.append(refmac_fail_label)
main_vbox.append(fail_label)
main_vbox.append(h_sep)
main_vbox.append(buttons_hbox)
main_vbox.set_border_width(6)
window.add(main_vbox)
window.set_border_width(4)
window.show_all()
# hide the icons
pdb_good_icon.hide()
cif_good_icon.hide()
refmac_good_icon.hide()
pdb_fail_icon.hide()
cif_fail_icon.hide()
refmac_fail_icon.hide()
refmac_fail_label.hide()
fail_label.hide()
pdb_execute_icon.set_sensitive(False)
cif_execute_icon.set_sensitive(False)
refmac_execute_icon.set_sensitive(False)
def cancel_button_cb(*args):
global download_thread_status
window.destroy()
download_thread_status = "cancelled"
cancel_button.connect("clicked", cancel_button_cb)
# return a dictionary (cant we do a lookup directly?!)
return {"window": window,
"pdb_progress_bar": pdb_progress_bar,
"cif_progress_bar": cif_progress_bar,
"refmac_progress_bar": refmac_progress_bar,
"refmac_fail_label": refmac_fail_label,
"fail_label": fail_label,
"pdb_execute_icon": pdb_execute_icon,
"cif_execute_icon": cif_execute_icon,
"refmac_execute_icon": refmac_execute_icon,
"pdb_fail_icon": pdb_fail_icon,
"cif_fail_icon": cif_fail_icon,
"refmac_fail_icon": refmac_fail_icon,
"pdb_good_icon": pdb_good_icon,
"cif_good_icon": cif_good_icon,
"refmac_good_icon": refmac_good_icon}
# main line
coords_type = ".ent" # can/will be ".cif"
# pdb_url = "http://www.ebi.ac.uk/pdbe-srv/view/files/" + \
# entry_id + ".ent"
# sfs_cif_url = "http://www.ebi.ac.uk/pdbe-srv/view/files/r" + \
# entry_id + "sf.ent"
pdb_url = "https://www.ebi.ac.uk/pdbe/entry-files/pdb" + \
entry_id + coords_type
sfs_cif_url = "https://www.ebi.ac.uk/pdbe/entry-files/r" + entry_id + "sf.ent"
pdb_file_name = os.path.join("coot-download", entry_id + coords_type)
sfs_cif_file_name = os.path.join("coot-download", "r" + entry_id + "sf.cif")
sfs_mtz_file_name = os.path.join("coot-download", "r" + entry_id + "sf.mtz")
refmac_out_mtz_file_name = os.path.join("coot-download",
"r" + entry_id + "-refmac.mtz")
refmac_log_file_name = "refmac-from-coot-" + \
str(refmac_count) + ".log" # set in refmac.run_refmac_by_filename
progr_widgets = progress_dialog(pdb_file_name, sfs_cif_file_name)
window = progr_widgets["window"]
pdb_progress_bar = progr_widgets["pdb_progress_bar"]
cif_progress_bar = progr_widgets["cif_progress_bar"]
refmac_progress_bar = progr_widgets["refmac_progress_bar"]
refmac_fail_label = progr_widgets["refmac_fail_label"]
fail_label = progr_widgets["fail_label"]
pdb_execute_icon = progr_widgets["pdb_execute_icon"]
cif_execute_icon = progr_widgets["cif_execute_icon"]
refmac_execute_icon = progr_widgets["refmac_execute_icon"]
pdb_good_icon = progr_widgets["pdb_good_icon"]
cif_good_icon = progr_widgets["cif_good_icon"]
refmac_good_icon = progr_widgets["refmac_good_icon"]
pdb_fail_icon = progr_widgets["pdb_fail_icon"]
cif_fail_icon = progr_widgets["cif_fail_icon"]
refmac_fail_icon = progr_widgets["refmac_fail_icon"]
def download_file_and_update_widget(url, file_name,
progress_bar, window):
global download_thread_status
def update_progressbar_in_download(numblocks, blocksize,
filesize, progress_bar):
global download_thread_status
percent = min((numblocks*blocksize*100)/filesize, 100)
#print "BL DEBUG:: update pg bar" , percent, numblocks, blocksize, filesize, progress_bar
if download_thread_status == "cancelled":
sys.exit()
if (percent > 100):
percent = 100
gobject.idle_add(progress_bar.set_fraction, percent/100.)
# in the end should change icons?!
def sleeper():
global download_thread_status
time.sleep(0.01)
if ("downloading" in download_thread_status):
return True # continue downloading
else:
return False
try:
#print "BL DEBUG:: start download", url
gobject.idle_add(sleeper)
file_name_local, url_info = urllib.request.urlretrieve(url, file_name,
lambda nb, bs, fs, progress_bar=progress_bar:
update_progressbar_in_download(nb, bs, fs, progress_bar))
download_thread_status = "done-download"
except socket.timeout:
print("BL ERROR:: timout download", url[-50:])
download_thread_status = "fail"
except IOError:
print("BL ERROR:: ioerror downloading", url[-50:])
download_thread_status = "fail"
except:
if (not download_thread_status == "cancelled"):
print("BL ERROR:: general problem downloading", url[-50:])
download_thread_status = "fail"
else:
print("BL INFO:: cancelled download")
# or shall this be in the timeout function!?
def update_refmac_progress_bar(refmac_progress_bar, log_file_name):
# refmac puts out 100 lines of text before it starts running.
# Let's not count those as progress of the computation (otherwise
# we jump to 22% after a fraction of a second).
max_lines = 350 # thats 450 - 100
n_lines = coot_utils.file_n_lines(log_file_name)
if n_lines: # check for number?
n_lines_rest = n_lines - 100.
if (n_lines > 0):
f = n_lines_rest / max_lines
if (f <= 1.0 and
f >= 0.):
refmac_progress_bar.set_fraction(f)
def update_dialog_and_check_download(*args):
global download_thread_status
if (download_thread_status == "downloading-pdb"):
pdb_execute_icon.set_sensitive(True)
if (download_thread_status == "downloading-sfs"):
pdb_progress_bar.set_fraction(1.)
pdb_execute_icon.hide()
pdb_good_icon.show()
cif_execute_icon.set_sensitive(True)
if (download_thread_status == "converting-to-mtz"):
pdb_progress_bar.set_fraction(1.)
cif_progress_bar.set_fraction(1.)
if (download_thread_status == "running-refmac-for-phases"):
pdb_progress_bar.set_fraction(1.)
cif_progress_bar.set_fraction(1.)
refmac_execute_icon.set_sensitive(True)
cif_execute_icon.hide()
cif_good_icon.show()
# de-sensitise cancel?!
update_refmac_progress_bar(refmac_progress_bar,
refmac_log_file_name)
if (download_thread_status == "fail-refmac"):
refmac_fail_label.show()
refmac_execute_icon.hide()
refmac_fail_icon.show()
return False # dont continue
# generic fail (don't turn off execute icons because we
# don't know *what* failed. (Not so useful).
if (download_thread_status == "fail"):
fail_label.show()
return False # dont continue
if (download_thread_status == "done"):
make_and_draw_map_local(refmac_out_mtz_file_name)
window.destroy()
return False # we are done!
return True
# could update progressbar here too!?
gobject.timeout_add(200, update_dialog_and_check_download,
window,
pdb_execute_icon, pdb_good_icon, pdb_fail_icon,
cif_execute_icon, cif_good_icon, cif_fail_icon,
pdb_progress_bar, cif_progress_bar,
refmac_progress_bar, refmac_log_file_name,
refmac_fail_label, fail_label)
# Try with individual threads just for downloading, alternative use
# Paul's approach and make functions to be executed in the the idle
# function
def start_cif_download():
global download_thread_status
# read the pdb
imol = coot.read_pdb(pdb_file_name)
if not coot_utils.valid_model_molecule_qm(imol):
s = "Oops - failed to correctly read " + pdb_file_name
coot.info_dialog(s)
download_thread_status = "fail"
if (include_get_sfs_flag != "include-sfs"):
# an NMR structure
#
# FIXME:: better later as timeout_add
# coot.read_pdb(pdb_file_name)
download_thread_status = "done" #?
#print "BL DEBUG:: NMR structure!?"
else:
# An X-ray structure
#
# now read the sfs cif and if that is good then
# convert to mtz and run refmac, but for now, let's
# just show the PDB file.
if not (os.path.isfile(sfs_cif_file_name) and
os.path.isfile(refmac_out_mtz_file_name)):
# download and run refmac
_thread.start_new_thread(get_sfs_run_refmac, (sfs_cif_url, sfs_cif_file_name,
sfs_mtz_file_name, pdb_file_name,
refmac_out_mtz_file_name,
cif_progress_bar, window))
else:
# OK, files are here already.
#
# FIXME:: again for later
# coot.read_pdb(pdb_file_name) # already done above
# coot.auto_read_make_and_draw_maps(refmac_out_mtz_file_name) # done in the updater.
download_thread_status = "done"
def check_pdb_download_thread():
if download_thread_status == "downloading-pdb":
return True
else:
# done
if (download_thread_status == "done-download"):
# really done, now start the cif download
start_cif_download()
return False
else:
if (download_thread_status == "cancelled"):
return False
return True
# Get the PDB file if we don't have it already.
if os.path.isfile(pdb_file_name):
download_thread_status = "done-download"
else:
download_thread_status = "downloading-pdb"
pdb_thread = _thread.start_new_thread(download_file_and_update_widget,
(pdb_url, pdb_file_name, pdb_progress_bar,
window))
gobject.idle_add(check_pdb_download_thread)
#print "BL DEBUG:: done with pdb thread?!"
def recent_structure_browser(t):
import string
import _thread
global refmac_count
global download_thread_status
download_thread_status = None # initiallise
def get_dic_all_entries(js):
# simple minded, we know where the entries are,
# so return the dictionary of these
# print "extract something from ", js
return js["grouped"]["pdb_id"]["groups"]
n_atoms_limit_small_ligands = 6
# truncate (if needed) and newlinify string
#
def pad_and_truncate_name(name):
sl = len(name)
if (sl < 60):
return "\n " + name
else:
return "\n " + name[0:60] + "..."
# as above but no preceeding newline and tab
def truncate_name(name):
sl = len(name)
if (sl < 70):
return name
else:
return name[0:70] + "..."
#
def make_ligands_string(ligand_string_list):
if not ligand_string_list:
return ""
else:
ligand_string = ""
for ligand in ligand_string_list:
ligand_string = ligand_string + " " + ligand + "\n"
if len(ligand_string) > 0:
return "\nLigands:\n" + ligand_string
else:
return ""
# The idea here is that we have a list of ligand tlcs. From that,
# we make a function, which, when passed a button-hbox (you can put
# things into a button) will download images from pdbe and add them
# to the button. We download the images in the background
# (sub-thread) and put them in coot-pdbe-ligand-images directory.
# When/if the tranfer of the file is completed and good, set the
# status to a function.
#
# a timeout function watches the value of the status and when it is
# a function, it runs it. (The function puts the image in the
# button-hbox.)
#
# Also we construct the url of a ribbon picture give the entry id
#
def make_active_ligand_button_func(entry_id, ligand_tlc_list):
# do we need this?!
return
# dic is a dictionary with keys: "Title", "Resolution", "EntryID", etc.
#
def handle_pdb_entry_entity(dic_wrapper):
# return a string. Return "" on failure
def make_authors_string(author_list):
citation = ""
if not author_list:
citation = "No Authors listed"
else:
citation = coot_utils.string_append_with_spaces(author_list)
return citation
global coot_pdbe_image_cache_dir
coot.make_directory_maybe(coot_pdbe_image_cache_dir)
# now make a button list (a label and what to do)
# entry_id = str(dic["EntryID"])
groupValue = dic_wrapper["groupValue"]
if not isinstance(groupValue, str):
print("failed to get groupValue")
else:
dic = dic_wrapper["doclist"]["docs"][0]
entry_id = str(dic["pdb_id"])
entry_label = entry_id if entry_id else "missing entry id" # should not happen, the latter!?
method_item = dic["experimental_method"]
try:
resolution_item = dic["resolution"]
except KeyError:
resolution_item = False
title_item = dic["title"]
try:
authors_string = make_authors_string(dic["pubmed_author_list"])
except KeyError:
authors_string = ""
# method_label = method_item if method_item else "Unknown method"
# should not happen, the latter!?
method_label = method_item[0]
title_label = truncate_name(title_item) if title_item else ""
authors_label = authors_string
try:
ligands = dic["compound_id"]
except KeyError:
ligands = []
ligands_string = make_ligands_string(ligands)
ligand_tlc_list = ligands
resolution_string = (" Resolution: " + str(resolution_item)) \
if resolution_item else ""
if False:
print(" title_label:", title_label)
print(" entry_id:", entry_id)
print(" method_label:", method_label)
print(" resolution_string:", resolution_string)
print(" authors_label:", authors_label)
print(" ligands_string:", ligands_string)
label = entry_id + "\n" + title_label + "\n" + method_label + \
resolution_string + "\n" + authors_label + ligands_string
if (method_label == "X-ray diffraction"):
return[label,
lambda func: pdbe_get_pdb_and_sfs_cif("include-sfs",
entry_id,
method_label),
# we dont do a funtion here, but use the args
# when we construct the button!?
[entry_id, ligand_tlc_list]]
else:
return[label,
lambda func: pdbe_get_pdb_and_sfs_cif("no-sfs",
entry_id,
method_label),
[entry_id, ligand_tlc_list]]
# this one (may) has to be lambda func too
#lambda func2:
#make_active_ligand_button_func(entry_id, ligand_tlc_list)]
# return a list of buttons
#
def handle_pdb_entry_entities(dic):
return list(map(handle_pdb_entry_entity, dic))
# main line!?
aa = get_dic_all_entries(t)
button_list = handle_pdb_entry_entities(aa)
coot_gui.dialog_box_of_buttons_with_async_ligands("Recent Entries", [700, 500],
button_list, " Close ")
def recent_entries_progress_dialog():
window = gtk.Window(gtk.WINDOW_TOPLEVEL)
dialog_name = "Getting recent entries list..."
main_vbox = gtk.VBox(False, 4)
label = gtk.Label("Getting recent entries list...")
progress_bar = gtk.ProgressBar()
window.set_title(dialog_name)
main_vbox.append(label)
main_vbox.append(progress_bar)
window.add(main_vbox)
window.set_border_width(4)
window.show_all()
return (progress_bar, window)
# Sameer Velankar says to get this file for the latest releases
# "http://www.ebi.ac.uk/pdbe-apps/jsonizer/latest/released/" (note the end "/")
#
def pdbe_latest_releases_gui():
import threading
import urllib.request, urllib.parse, urllib.error
url = "https://www.ebi.ac.uk/pdbe/search/latest/select?facet=true&q=*%3A*&group=true&group.field=pdb_id&group.ngroups=true&&json.nl=map&fq=document_type%3Alatest_pdb&fq=entry_type:%28new%20OR%20revised%29&wt=json&fl=pdb_id,release_date,resolution,number_of_bound_molecules,experimental_method,citation_title,citation_doi,pubmed_author_list,journal,title,entry_type&rows=-1"
url = "https://www.ebi.ac.uk/pdbe/search/latest/select?facet=true&q=*%3A*&group=true&group.field=pdb_id&group.ngroups=true&&json.nl=map&fq=document_type%3Alatest_pdb&fq=entry_type:%28new%20OR%20revised%29&wt=json&fl=pdb_id,compound_id,release_date,resolution,number_of_bound_molecules,experimental_method,citation_title,citation_doi,pubmed_author_list,journal,title,entry_type&rows=-1"
# url = "http://www.ebi.ac.uk/pdbe-apps/jsonizer/latest/released/"
json_file_name = "latest-releases.json"
coot.add_status_bar_text("Retrieving list of latest releases...")
# FIXME:: progress bar!?
progress_bars = recent_entries_progress_dialog()
class MyURLopener(urllib.request.FancyURLopener):
def http_error_default(self, url, fp, errcode, errmsg, headers):
# handle errors the way you'd like to
# raise StandardError, ("File not found?")
pass
class GetUrlThread(threading.Thread):
def __init__(self, url, file_name, progressbar, window):
self.url = url
self.file_name = file_name
self.window = window
self.progressbar = progressbar
self.status = None
threading.Thread.__init__(self)
def get_url_status(self):
return self.status
def update_function(self, count, blockSize, totalSize):
# total size is -1! Baeh!!
percent = int(count*blockSize*100/totalSize)
gobject.idle_add(self.update_progressbar, percent)
def update_progressbar(self, count):
self.progressbar.pulse()
return False
def destroy_window(self):
self.window.destroy()
def run(self):
try:
self.file_name = coot_urlretrieve(self.url, self.file_name, self.update_function)
self.status = 0 #?
except socket.timeout:
print("BL ERROR:: timout download", self.url)
except IOError:
print("BL ERROR:: ioerror")
except:
self.status = 1
# FIXME here dies with the thread. need to go to main thread
gobject.idle_add(info_dialog, "Failed to get recent entry list from server.")
gobject.idle_add(self.destroy_window)
thread = GetUrlThread(url, json_file_name,
progress_bars[0], progress_bars[1])
_thread.start()
def start_table():
if _thread.get_url_status() == 0:
recent_structure_browser(get_recent_json(json_file_name))
return False # stop
return True # continue
def run_sleeper():
if _thread.get_url_status() == 0:
return False # stop
time.sleep(0.02)
return True # continue
gobject.idle_add(start_table)
# most likely not needed
# gobject.timeout_add(50, run_sleeper)
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