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# This happens when user clicks on the "Launch JLigand" button.
# It starts a jligand and puts it in the background.
#
def launch_jligand_function():
global jligand_jar
global jligand_home_env
global java_command
jligand.start_jligand_listener()
# maybe this should rather check PATH or similar!? FIXME
if not os.path.isfile(jligand_jar):
# Boo. Give us a warning dialog
#
s = "jligand java jar file: " + jligand_jar + " not found"
# make an extra message telling us that JLIGAND_HOME is
# not set if it is not set.
env_message = "Environment variable JLIGAND_HOME not set\n\n" \
if not jligand_home_env else ""
coot.info_dialog(env_message + s)
else:
# OK, it does exist - run it!
#
java_exe = coot_utils.find_exe(java_command)
if not java_exe:
print("BL INFO:: no java found")
else:
# first check if we can run it with coot, i.e. is '-version'
# a valid command line arg
jligand_version = ["-jar", jligand_jar, "-version"]
cmd = java_exe + " " + \
coot_utils.string_append_with_spaces(jligand_version)
res = coot_utils.shell_command_to_string(cmd)
if (not res):
message = "Sorry, your JLigand:\n\n " + jligand_jar + "\n\n" + \
"is not new enough to work with Coot!\n" + \
"Please download a new one!"
coot.info_dialog(message)
else:
coot_utils.run_concurrently(java_exe, jligand_args)
# beam in a new menu to the menu bar:
if True:
if coot_gui_api.main_menubar():
jligand_menu = coot_gui.coot_menubar_menu("JLigand")
coot_gui.add_simple_coot_menu_menuitem(
jligand_menu, "Send Link to JLigand (click 2 monomers)",
lambda func: click_select_residues_for_jligand()
)
# This happens when user clicks on the "Select Residues for JLigand"
# (or some such) button. It expects the user to click on atoms of
# the two residues involved in the link.
#
def click_select_residues_for_jligand():
global imol_jligand_link
def link_em(*args):
print("we received these clicks", args)
if (len(args) == 2):
click_1 = args[0]
click_2 = args[1]
print("click_1:", click_1)
print("click_2:", click_2)
if ((len(click_1) == 7)
and (len(click_2) ==7)):
resname_1 = coot.residue_name(click_1[1],
click_1[2],
click_1[3],
click_1[4])
resname_2 = coot.residue_name(click_2[1],
click_2[2],
click_2[3],
click_2[4])
imol_click_1 = click_1[1]
imol_click_2 = click_2[1]
chain_click_1 = click_1[2]
chain_click_2 = click_2[2]
resno_click_1 = click_1[3]
resno_click_2 = click_2[3]
if not (isinstance(resname_1, str) and
isinstance(resname_2, str)):
print("Bad resnames: %s and %s" %(resname_1, resname_2))
else:
if not (imol_click_1 == imol_click_2):
msg = "Two different molecules %s and %s selected.\n" \
%(imol_click_1, imol_click_2) + \
"Make sure to select residues in the same molecule."
coot.info_dialog(msg)
imol_jligand_link = False
elif (chain_click_1 == chain_click_2 and
resno_click_1 == resno_click_2):
msg = "Same residue %s %s selected.\n" \
%(chain_click_1, resno_click_1) + \
"Make sure to select different residues."
coot.info_dialog(msg)
imol_jligand_link = False
else:
# happy path
imol_jligand_link = imol_click_1
jligand.write_file_for_jligand(jligand.click2res_spec(click_1), resname_1,
jligand.click2res_spec(click_2), resname_2)
user_defined_click(2, link_em)
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