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# Define an environment variable for the place where jligand.jar
# resides in a canonical distribution
#
# should be global?
to_jligand_secret_file_name = ".coot-to-jligand-8lcs"
global from_jligand_secret_file_name
from_jligand_secret_file_name = ".jligand-to-coot"
jligand_home = os.getenv("JLIGAND_HOME") if os.getenv("JLIGAND_HOME") else "."
java_command = "java" # may have to absolute FIXME
jligand_jar = os.path.join(os.path.normpath(jligand_home), "jligand.jar")
jligand_args = ["-jar", jligand_jar, "-coot"]
def write_file_for_jligand(resname_1, resname_2):
fin = open(to_jligand_secret_file_name, 'w')
int_time = time.time()
fin.write("CODE " + resname_1 + "\n")
fin.write("CODE " + resname_2 + "\n")
fin.write("TIME " + str(int_time) + "\n")
fin.close()
if True:
if coot_gui_api.main_menubar():
menu = coot_gui.coot_menubar_menu("JLigand")
def launch_jligand():
if not os.path.isfile(jligand_jar):
s = "jligand java jar file: " + jligand_jar + " not found"
coot.info_dialog(s)
else:
java_exe = coot_utils.find_exe(java_command)
if java_exe:
coot_utils.run_concurrently(java_exe, jligand_args)
else:
print "BL INFO:: no java found"
coot_gui.add_simple_coot_menu_menuitem(
menu, "Launch Jligand",
lambda func: launch_jligand()
)
def make_jligand_link():
def link_em(*args):
print "we received these clicks", args
if (len(args) == 2):
click_1 = args[0]
click_2 = args[1]
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])
if not (isinstance(resname_1, str) and
isinstance(resname_2, str)):
print "Bad resnames: %s and %s" %(resname_1, resname_2)
else:
write_file_for_jligand(resname_1, resname_2)
user_defined_click(2, link_em)
coot_gui.add_simple_coot_menu_menuitem(
menu, "Send Link to JLigand (click 2 monomers)",
lambda func: make_jligand_link()
)
def handle_read_from_jligand_file():
global from_jligand_secret_file_name
if (os.path.isfile(from_jligand_secret_file_name)):
coot.read_cif_dictionary(from_jligand_secret_file_name)
global startup_mtime
startup_mtime = prodrg_import.get_file_latest_time(from_jligand_secret_file_name)
def jligand_timeout_func():
global startup_mtime
global from_jligand_secret_file_name
import operator
now_time = prodrg_import.get_file_latest_time(from_jligand_secret_file_name)
#print "startup-mtime: %s now-time: %s" %(startup_mtime, now_time)
if operator.isNumberType(now_time):
if not operator.isNumberType(startup_mtime):
startup_mtime = now_time
print "just set startup-mtime to (first)", startup_mtime
handle_read_from_jligand_file()
else:
if (now_time > startup_mtime):
startup_mtime = now_time
print "just set startup-mtime to", startup_mtime
handle_read_from_jligand_file()
return True # we never expire...
gobject.timeout_add(500, jligand_timeout_func)
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