class TrajectoryDialog():
def on_TrajectoryDialog_button_load_clicked(self, button):
""" Function doc """
self.project = self.EasyHybridSession.project
first = int(
self.builder.get_object('TrajectoryDialog_first').get_text())
last = int(self.builder.get_object('TrajectoryDialog_last').get_text())
stride = int(
self.builder.get_object('TrajectoryDialog_stride').get_text())
#traj_name = self.builder.get_object('filechooserbutton1').get_text()
#traj_name2 = self.builder.get_object('filechooserbutton2').get_text()
new_pymol_object = self.builder.get_object('entry1').get_text()
_type = self.builder.get_object('combobox1').get_active_text()
""" Function doc """
if _type == 'folder - pDynamo':
traj_name = self.builder.get_object(
'filechooserbutton1').get_filename()
else:
traj_name = self.builder.get_object(
'filechooserbutton2').get_filename()
print(first, last, stride, traj_name, new_pymol_object, _type)
frames = self.project.load_trajectory_to_system(
first, last, stride, traj_name, new_pymol_object, _type)
self.EasyHybridSession.builder.get_object(
'trajectory_max_entrey').set_text(str(frames))
self.EasyHybridSession.on_TrajectoryTool_HSCALE_update()
def on_combobox1_changed(self, button):
_type = self.builder.get_object('combobox1').get_active_text()
""" Function doc """
if _type == 'folder - pDynamo':
self.builder.get_object('filechooserbutton2').hide()
self.builder.get_object('filechooserbutton1').show()
else:
self.builder.get_object('filechooserbutton2').show()
self.builder.get_object('filechooserbutton1').hide()
def __init__(self, EasyHybridSession):
""" Class initialiser """
self.EasyHybridSession = EasyHybridSession
self.project = EasyHybridSession.project
self.main_builder = EasyHybridSession.builder
self.builder = gtk.Builder()
self.builder.add_from_file(
os.path.join(EasyHybrid_GUI, 'DialogLoadTrajectory',
'TrajectoryDialog.glade'))
self.builder.connect_signals(self)
self.dialog = self.builder.get_object('TrajectoryDialog')
'''
--------------------------------------------------
- -
- WindowControl -
- -
--------------------------------------------------
'''
self.window_control = WindowControl(self.builder)
self.builder.get_object('filechooserbutton2').hide()
#----------------- Setup ComboBoxes -------------------------#
combobox = 'combobox1' #
combolist = [
"folder - pDynamo", "trj - AMBER", "dcd - CHARMM", 'xtc - GROMACS'
]
self.window_control.SETUP_COMBOBOXES(combobox, combolist, 0)
class NonBondDialog():
""" Class doc """
def on_button1_apply_NBModel_clicked(self, button):
""" Function doc """
self.project = self.EasyHybridSession.project
nbModel = self.builder.get_object(
'combobox1_nb_types').get_active_text()
innercutoff = float(self.builder.get_object('entry1').get_text())
outercutoff = float(self.builder.get_object('entry2').get_text())
listcutoff = float(self.builder.get_object('entry3').get_text())
kappa = float(self.builder.get_object('entry4').get_text())
if self.project == None:
print(nbModel, innercutoff, outercutoff, listcutoff, kappa)
else:
self.project.ABFS_options = {
"innerCutoff": innercutoff,
"outerCutoff": outercutoff,
"listCutoff": listcutoff
}
self.project.settings['nbModel_type'] = nbModel
self.project.set_nbModel_to_system()
def QCcomboxChange(self, combobox):
""" Function doc """
mode = self.builder.get_object('combobox1_nb_types').get_active_text()
if mode == 'NBModelFull':
self.builder.get_object('entry1').set_sensitive(False)
self.builder.get_object('entry2').set_sensitive(False)
self.builder.get_object('entry3').set_sensitive(False)
self.builder.get_object('entry4').set_sensitive(False)
if mode == 'NBModelABFS':
self.builder.get_object('entry1').set_sensitive(True)
self.builder.get_object('entry2').set_sensitive(True)
self.builder.get_object('entry3').set_sensitive(True)
self.builder.get_object('entry4').set_sensitive(True)
if mode == 'NBModelGABFS':
self.builder.get_object('entry1').set_sensitive(True)
self.builder.get_object('entry2').set_sensitive(True)
self.builder.get_object('entry3').set_sensitive(True)
self.builder.get_object('entry4').set_sensitive(True)
if mode == 'NBModelSSBP':
self.builder.get_object('entry1').set_sensitive(False)
self.builder.get_object('entry2').set_sensitive(False)
self.builder.get_object('entry3').set_sensitive(False)
self.builder.get_object('entry4').set_sensitive(False)
if mode == 'No NB model':
self.builder.get_object('entry1').set_sensitive(False)
self.builder.get_object('entry2').set_sensitive(False)
self.builder.get_object('entry3').set_sensitive(False)
self.builder.get_object('entry4').set_sensitive(False)
def __init__(self, EasyHybridSession=None):
""" Class initialiser """
self.builder = gtk.Builder()
if EasyHybridSession != None:
self.project = EasyHybridSession.project
self.main_builder = EasyHybridSession.builder
self.EasyHybridSession = EasyHybridSession
self.window_control = EasyHybridSession.window_control
#self.project = project
#self.window_control = window_control
#self.builder = gtk.Builder()
#self.main_builder = main_builder
self.builder.add_from_file(
os.path.join(EasyHybrid_GUI, 'DialogNonBond',
'NonBondDialog.glade'))
self.builder.connect_signals(self)
self.dialog = self.builder.get_object('dialog1')
'''
--------------------------------------------------
- -
- WindowControl -
- -
--------------------------------------------------
'''
self.window_control = WindowControl(self.builder)
#----------------- Setup ComboBoxes -------------------------#
combobox = 'combobox1_nb_types' #
combolist = nbList
self.window_control.SETUP_COMBOBOXES(combobox, combolist, 0)
class ScanWindow2D():
""" Class doc """
def on_ScanWindow_destroy(self, widget):
""" Function doc """
self.Visible = False
def RunScan(self, button):
#---------------------------------------------------#
# #
# Reaction COORD-1 #
# #
#---------------------------------------------------#
#---------------------------------- importing parameters COORD-1 ---------------------------#
DINCREMENT = float(
self.builder.get_object('entry_STEP_size1').get_text()) #
NWINDOWS = int(
self.builder.get_object('entry_NWINDOWS1').get_text()) #
DMINIMUM = float(
self.builder.get_object('entry_param_DMINIMUM1').get_text()) #
FORCECONSTANT = float(
self.builder.get_object('entry_FORCE1').get_text()) #
#-------------------------------------------------------------------------------------------#
mode = self.builder.get_object(
'combobox_SCAN_reaction_coordiante_type').get_active_text()
print "\n\n"
print mode
self.EasyHybridSession.project.ActiveModeCheck()
#-------------------------------------------------------------------------------------------------#
# simple-distance #
#-------------------------------------------------------------------------------------------------#
if mode == "simple-distance": #
ATOM1 = int(
self.builder.get_object("entry_coord1_ATOM1").get_text()) #
ATOM1_name = self.builder.get_object(
"entry_coord1_ATOM1_name").get_text() #
ATOM2 = int(
self.builder.get_object("entry_coord1_ATOM2").get_text()) #
ATOM2_name = self.builder.get_object(
"entry_coord1_ATOM2_name").get_text() #
#
REACTION_COORD1 = {
'MODE': mode, #
'ATOM1': ATOM1, #
'ATOM1_name': ATOM1_name, #
'ATOM2': ATOM2, #
'ATOM2_name': ATOM2_name, #
'DINCREMENT': DINCREMENT, #
'NWINDOWS': NWINDOWS, #
'FORCECONSTANT': FORCECONSTANT, #
'DMINIMUM': DMINIMUM
} #
#-------------------------------------------------------------------------------------------------#
#-------------------------------------------------------------------------------------------------#
# multiple-distance #
#-------------------------------------------------------------------------------------------------#
if mode == "multiple-distance": #
ATOM1 = int(
self.builder.get_object("entry_coord1_ATOM1").get_text()) #
ATOM1_name = self.builder.get_object(
"entry_coord1_ATOM1_name").get_text() #
ATOM2 = int(
self.builder.get_object("entry_coord1_ATOM2").get_text()) #
ATOM2_name = self.builder.get_object(
"entry_coord1_ATOM2_name").get_text() #
ATOM3 = int(
self.builder.get_object("entry_coord1_ATOM3").get_text()) #
ATOM3_name = self.builder.get_object(
"entry_coord1_ATOM3_name").get_text() #
#
print " " + ATOM1_name + " ->- " + ATOM2_name + " -->-- " + ATOM3_name + " " #
print " pk1 --- pk2 ---- pk3 \n" #
print "DMINIMUM : ", DMINIMUM #
print "\n\n" #
print #
#sigma_pk1_pk3 = self.coord1_sigma_pk1_pk3 #
#sigma_pk3_pk1 = self.coord1_sigma_pk3_pk1 #
#print sigma_pk3_pk1 #
#print sigma_pk1_pk3 #
#
REACTION_COORD1 = {
'MODE': mode, #
'ATOM1': ATOM1, #
'ATOM1_name': ATOM1_name, #
'ATOM2': ATOM2, #
'ATOM2_name': ATOM2_name, #
'ATOM3': ATOM3, #
'ATOM3_name': ATOM3_name, #
'DINCREMENT': DINCREMENT, #
'NWINDOWS': NWINDOWS, #
'FORCECONSTANT': FORCECONSTANT, #
'DMINIMUM': DMINIMUM, #
'sigma_pk1_pk3': self.coord1_sigma_pk1_pk3, #
'sigma_pk3_pk1': self.coord1_sigma_pk3_pk1
} #
#-------------------------------------------------------------------------------------------------#
#---------------------------------------------------#
# #
# Reaction COORD-2 #
# #
#---------------------------------------------------#
#---------------------------------- importing parameters COORD-2 ---------------------------#
DINCREMENT = float(
self.builder.get_object('entry_STEP_size2').get_text()) #
NWINDOWS = int(
self.builder.get_object('entry_NWINDOWS2').get_text()) #
DMINIMUM = float(
self.builder.get_object('entry_param_DMINIMUM2').get_text()) #
FORCECONSTANT = float(
self.builder.get_object('entry_FORCE2').get_text()) #
#-------------------------------------------------------------------------------------------#
mode = self.builder.get_object(
'combobox_SCAN_reaction_coordiante2_type').get_active_text()
print "\n\n"
print mode
self.EasyHybridSession.project.ActiveModeCheck()
#-------------------------------------------------------------------------------------------------#
# simple-distance #
#-------------------------------------------------------------------------------------------------#
if mode == "simple-distance": #
ATOM1 = int(
self.builder.get_object("entry_coord2_ATOM1").get_text()) #
ATOM1_name = self.builder.get_object(
"entry_coord2_ATOM1_name").get_text() #
ATOM2 = int(
self.builder.get_object("entry_coord2_ATOM2").get_text()) #
ATOM2_name = self.builder.get_object(
"entry_coord2_ATOM2_name").get_text() #
#
REACTION_COORD2 = {
'MODE': mode, #
'ATOM1': ATOM1, #
'ATOM1_name': ATOM1_name, #
'ATOM2': ATOM2, #
'ATOM2_name': ATOM2_name, #
'DINCREMENT': DINCREMENT, #
'NWINDOWS': NWINDOWS, #
'FORCECONSTANT': FORCECONSTANT, #
'DMINIMUM': DMINIMUM
} #
#-------------------------------------------------------------------------------------------------#
#-------------------------------------------------------------------------------------------------#
# multiple-distance #
#-------------------------------------------------------------------------------------------------#
if mode == "multiple-distance": #
ATOM1 = int(
self.builder.get_object("entry_coord2_ATOM1").get_text()) #
ATOM1_name = self.builder.get_object(
"entry_coord2_ATOM1_name").get_text() #
ATOM2 = int(
self.builder.get_object("entry_coord2_ATOM2").get_text()) #
ATOM2_name = self.builder.get_object(
"entry_coord2_ATOM2_name").get_text() #
ATOM3 = int(
self.builder.get_object("entry_coord2_ATOM3").get_text()) #
ATOM3_name = self.builder.get_object(
"entry_coord2_ATOM3_name").get_text() #
#
print " " + ATOM1_name + " ->- " + ATOM2_name + " -->-- " + ATOM3_name + " " #
print " pk1 --- pk2 ---- pk3 \n" #
print "DMINIMUM : ", DMINIMUM #
print "\n\n" #
print #
#sigma_pk1_pk3 = self.sigma_pk1_pk3 #
#sigma_pk3_pk1 = self.sigma_pk3_pk1 #
#print sigma_pk3_pk1 #
#print sigma_pk1_pk3 #
#
REACTION_COORD2 = {
'MODE': mode, #
'ATOM1': ATOM1, #
'ATOM1_name': ATOM1_name, #
'ATOM2': ATOM2, #
'ATOM2_name': ATOM2_name, #
'ATOM3': ATOM3, #
'ATOM3_name': ATOM3_name, #
'DINCREMENT': DINCREMENT, #
'NWINDOWS': NWINDOWS, #
'FORCECONSTANT': FORCECONSTANT, #
'DMINIMUM': DMINIMUM, #
'sigma_pk1_pk3': self.coord2_sigma_pk1_pk3, #
'sigma_pk3_pk1': self.coord2_sigma_pk3_pk1,
} #
#-------------------------------------------------------------------------------------------------#
#-----------------------------------import trajectory parameters--------------------------------#
max_int = int(
self.builder.get_object("SCAN_MIN_entry_max_int").get_text()) #
rms_grad = float(
self.builder.get_object("SCAN_MIN_entry_rmsd_grad").get_text()) #
mim_method = self.builder.get_object(
'combobox_optimization_method').get_active_text() #
log_freq = None #
#-----------------------------------------------------------------------------------------------#
#-----------------------------------------------------------------------------------------------#
data_path = self.EasyHybridSession.project.settings['data_path'] #
traj = self.builder.get_object(
'SCAN_entry_trajectory_name').get_text() #
if not os.path.exists(os.path.join(data_path, traj)):
os.mkdir(os.path.join(data_path, traj)) #
outpath = os.path.join(data_path, traj) #
#-----------------------------------------------------------------------------------------------#
PARAMETERS = {
'max_int': max_int,
'log_freq': log_freq,
'rms_grad': rms_grad,
'mim_method': mim_method,
'outpath': outpath
}
pprint(REACTION_COORD1)
pprint(REACTION_COORD2)
pprint(PARAMETERS)
X, X_norm, logFile = Scan2D(outpath, REACTION_COORD1, REACTION_COORD2,
PARAMETERS, self.EasyHybridSession.project)
self.EasyHybridSession.project.From_PDYNAMO_to_EasyHybrid(type_='scn',
log=logFile)
self.Visible = False
self.window.destroy()
#return x, y,
def Button_import_PyMOL_index(self, button):
'''
----------------------------------------------------self.coord1_sigma_pk1_pk3
REACTION COORDINATE 1 self.coord1_sigma_pk3_pk1
----------------------------------------------------
'''
if button == self.builder.get_object('Button_import_PyMOL_index1'):
mode = self.builder.get_object(
'combobox_SCAN_reaction_coordiante_type').get_active_text()
if mode == "simple-distance":
try:
name1, atom1_index, name2, atom2_index, distance_a1_a2 = import_ATOM1_ATOM2(
"pk1", "pk2")
distance_a1_a2 = str(distance_a1_a2)
self.builder.get_object('entry_param_DMINIMUM1').set_text(
distance_a1_a2)
self.builder.get_object("entry_coord1_ATOM1").set_text(
str(atom1_index))
self.builder.get_object(
"entry_coord1_ATOM1_name").set_text(name1)
self.builder.get_object("entry_coord1_ATOM2").set_text(
str(atom2_index))
self.builder.get_object(
"entry_coord1_ATOM2_name").set_text(name2)
except:
cmd.edit_mode()
print "pk1, pk2 selection not found"
print texto_d1
return
if mode == "multiple-distance":
try:
name1, atom1_index, name2, atom2_index, distance_a1_a2 = import_ATOM1_ATOM2(
"pk1", "pk2")
name2, atom2_index, name3, atom3_index, distance_a2_a3 = import_ATOM1_ATOM2(
"pk2", "pk3")
print "distance between atom 1 and atom 2: ", distance_a1_a2
print "distance between atom 2 and atom 3: ", distance_a2_a3
if self.builder.get_object(
"checkbutton_mass_weight1").get_active():
self.coord1_sigma_pk1_pk3, self.coord1_sigma_pk3_pk1 = compute_sigma_a1_a3(
name1, name3)
"""
R R
\ /
A1--A2 . . . . A3
/ \
R R
^ ^ ^
| | |
pk1-pk2 . . . . pk3
d1 d2
q1 = 1 / (mpk1 + mpk3) = [ mpk1 * r (pk3_pk2) - mpk3 * r (pk1_pk2) ]
"""
DMINIMUM = (self.coord1_sigma_pk1_pk3 * distance_a1_a2
) - (self.coord1_sigma_pk3_pk1 *
distance_a2_a3 * -1)
self.builder.get_object(
'entry_param_DMINIMUM1').set_text(str(DMINIMUM))
print "\n\nUsing mass weighted restraints"
print "Sigma pk1_pk3", self.coord1_sigma_pk1_pk3
print "Sigma pk3_pk1", self.coord1_sigma_pk3_pk1
print "Estimated minimum distance", DMINIMUM
else:
self.coord1_sigma_pk1_pk3 = 1.0
self.coord1_sigma_pk3_pk1 = -1.0
DMINIMUM = distance_a1_a2 - distance_a2_a3
self.builder.get_object(
'entry_param_DMINIMUM1').set_text(str(DMINIMUM))
print "\n\nSigma pk1_pk3 ", self.coord1_sigma_pk1_pk3
print "Sigma pk3_pk1", self.coord1_sigma_pk3_pk1
print "Estimated minimum distance", DMINIMUM
except:
cmd.edit_mode()
print "pk1, pk2 and pk3 selections not found"
print texto_d2d1
return
print name3, name2, name1
self.builder.get_object("entry_coord1_ATOM1").set_text(
str(atom1_index))
self.builder.get_object("entry_coord1_ATOM1_name").set_text(
name1)
self.builder.get_object("entry_coord1_ATOM2").set_text(
str(atom2_index))
self.builder.get_object("entry_coord1_ATOM2_name").set_text(
name2)
self.builder.get_object("entry_coord1_ATOM3").set_text(
str(atom3_index))
self.builder.get_object("entry_coord1_ATOM3_name").set_text(
name3)
'''
----------------------------------------------------
REACTION COORDINATE 2
----------------------------------------------------
'''
if button == self.builder.get_object('Button_import_PyMOL_index2'):
mode = self.builder.get_object(
'combobox_SCAN_reaction_coordiante2_type').get_active_text()
if mode == "simple-distance":
try:
name1, atom1_index, name2, atom2_index, distance_a1_a2 = import_ATOM1_ATOM2(
"pk1", "pk2")
distance_a1_a2 = str(distance_a1_a2)
self.builder.get_object('entry_param_DMINIMUM2').set_text(
distance_a1_a2)
self.builder.get_object("entry_coord2_ATOM1").set_text(
str(atom1_index))
self.builder.get_object(
"entry_coord2_ATOM1_name").set_text(name1)
self.builder.get_object("entry_coord2_ATOM2").set_text(
str(atom2_index))
self.builder.get_object(
"entry_coord2_ATOM2_name").set_text(name2)
except:
cmd.edit_mode()
print "pk1, pk2 selection not found"
print texto_d1
return
if mode == "multiple-distance":
try:
name1, atom1_index, name2, atom2_index, distance_a1_a2 = import_ATOM1_ATOM2(
"pk1", "pk2")
name2, atom2_index, name3, atom3_index, distance_a2_a3 = import_ATOM1_ATOM2(
"pk2", "pk3")
print "distance between atom 1 and atom 2: ", distance_a1_a2
print "distance between atom 2 and atom 3: ", distance_a2_a3
if self.builder.get_object(
"checkbutton_mass_weight2").get_active():
self.coord2_sigma_pk1_pk3, self.coord2_sigma_pk3_pk1 = compute_sigma_a1_a3(
name1, name3)
"""
R R
\ /
A1--A2 . . . . A3
/ \
R R
^ ^ ^
| | |
pk1-pk2 . . . . pk3
d1 d2
q1 = 1 / (mpk1 + mpk3) = [ mpk1 * r (pk3_pk2) - mpk3 * r (pk1_pk2) ]
"""
DMINIMUM = (self.coord2_sigma_pk1_pk3 * distance_a1_a2
) - (self.coord2_sigma_pk3_pk1 *
distance_a2_a3 * -1)
self.builder.get_object(
'entry_param_DMINIMUM2').set_text(str(DMINIMUM))
print "\n\nUsing mass weighted restraints"
print "Sigma pk1_pk3", self.coord2_sigma_pk1_pk3
print "Sigma pk3_pk1", self.coord2_sigma_pk3_pk1
print "Estimated minimum distance", DMINIMUM
else:
self.coord2_sigma_pk1_pk3 = 1.0
self.coord2_sigma_pk3_pk1 = -1.0
DMINIMUM = distance_a1_a2 - distance_a2_a3
self.builder.get_object(
'entry_param_DMINIMUM2').set_text(str(DMINIMUM))
print "\n\nSigma pk1_pk3 ", self.coord2_sigma_pk1_pk3
print "Sigma pk3_pk1", self.coord2_sigma_pk3_pk1
print "Estimated minimum distance", DMINIMUM
except:
cmd.edit_mode()
print "pk1, pk2 and pk3 selections not found"
print texto_d2d1
return
print name3, name2, name1
self.builder.get_object("entry_coord2_ATOM1").set_text(
str(atom1_index))
self.builder.get_object("entry_coord2_ATOM1_name").set_text(
name1)
self.builder.get_object("entry_coord2_ATOM2").set_text(
str(atom2_index))
self.builder.get_object("entry_coord2_ATOM2_name").set_text(
name2)
self.builder.get_object("entry_coord2_ATOM3").set_text(
str(atom3_index))
self.builder.get_object("entry_coord2_ATOM3_name").set_text(
name3)
def Mass_weight_check(self, checkbutton):
'''
----------------------------------------------------
REACTION COORDINATE 1
----------------------------------------------------
'''
if checkbutton == self.builder.get_object('checkbutton_mass_weight1'):
try:
name1, atom1_index, name2, atom2_index, distance_a1_a2 = import_ATOM1_ATOM2(
"pk1", "pk2")
name2, atom2_index, name3, atom3_index, distance_a2_a3 = import_ATOM1_ATOM2(
"pk2", "pk3")
except:
print texto_d2d1
return
if self.builder.get_object(
"checkbutton_mass_weight1").get_active():
self.coord1_sigma_pk1_pk3, self.coord1_sigma_pk3_pk1 = compute_sigma_a1_a3(
name1, name3)
"""
R R
\ /
A1--A2 . . . . A3
/ \
R R
^ ^ ^
| | |
pk1-pk2 . . . . pk3
d1 d2
q1 = 1 / (mpk1 + mpk3) = [ mpk1 * r (pk3_pk2) - mpk3 * r (pk1_pk2) ]
"""
DMINIMUM = (self.coord1_sigma_pk1_pk3 * distance_a1_a2) - (
self.coord1_sigma_pk3_pk1 * distance_a2_a3 * -1)
self.builder.get_object('entry_param_DMINIMUM1').set_text(
str(DMINIMUM))
print "\n\nUsing mass weighted restraints"
print "Sigma pk1_pk3", self.coord1_sigma_pk1_pk3
print "Sigma pk3_pk1", self.coord1_sigma_pk3_pk1
print "Estimated minimum distance", DMINIMUM
else:
self.coord1_sigma_pk1_pk3 = 1.0
self.coord1_sigma_pk3_pk1 = -1.0
DMINIMUM = distance_a1_a2 - distance_a2_a3
self.builder.get_object('entry_param_DMINIMUM1').set_text(
str(DMINIMUM))
print "\n\nSigma pk1_pk3 ", self.coord1_sigma_pk1_pk3
print "Sigma pk3_pk1", selfcoord1_sigma_pk3_pk1
print "Estimated minimum distance", DMINIMUM
'''
----------------------------------------------------
REACTION COORDINATE 2
----------------------------------------------------
'''
if checkbutton == self.builder.get_object('checkbutton_mass_weight2'):
try:
name1, atom1_index, name2, atom2_index, distance_a1_a2 = import_ATOM1_ATOM2(
"pk1", "pk2")
name2, atom2_index, name3, atom3_index, distance_a2_a3 = import_ATOM1_ATOM2(
"pk2", "pk3")
except:
print texto_d2d1
return
if self.builder.get_object(
"checkbutton_mass_weight2").get_active():
self.coord2_sigma_pk1_pk3, self.coord2_sigma_pk3_pk1 = compute_sigma_a1_a3(
name1, name3)
"""
R R
\ /
A1--A2 . . . . A3
/ \
R R
^ ^ ^
| | |
pk1-pk2 . . . . pk3
d1 d2
q1 = 1 / (mpk1 + mpk3) = [ mpk1 * r (pk3_pk2) - mpk3 * r (pk1_pk2) ]
"""
DMINIMUM = (self.coord2_sigma_pk1_pk3 * distance_a1_a2) - (
self.coord2_sigma_pk3_pk1 * distance_a2_a3 * -1)
self.builder.get_object('entry_param_DMINIMUM2').set_text(
str(DMINIMUM))
print "\n\nUsing mass weighted restraints"
print "Sigma pk1_pk3", self.coord2_sigma_pk1_pk3
print "Sigma pk3_pk1", self.coord2_sigma_pk3_pk1
print "Estimated minimum distance", DMINIMUM
else:
self.coord2_sigma_pk1_pk3 = 1.0
self.coord2_sigma_pk3_pk1 = -1.0
DMINIMUM = distance_a1_a2 - distance_a2_a3
self.builder.get_object('entry_param_DMINIMUM2').set_text(
str(DMINIMUM))
print "\n\nSigma pk1_pk3 ", self.coord2_sigma_pk1_pk3
print "Sigma pk3_pk1", self.coord2_sigma_pk3_pk1
print "Estimated minimum distance", DMINIMUM
def checkbutton_MassWeight(self, checkbutton):
""" Function doc """
print 'checkbutton_MassWeight'
self.Mass_weight_check(checkbutton)
def Scan2DComboxChange(self, combobox):
""" Function doc """
if combobox == self.builder.get_object(
'combobox_SCAN_reaction_coordiante_type'):
mode = self.builder.get_object(
'combobox_SCAN_reaction_coordiante_type').get_active_text()
if mode == 'simple-distance':
self.builder.get_object('label_coord1_atom3').set_sensitive(
False)
self.builder.get_object('entry_coord1_ATOM3').set_sensitive(
False)
self.builder.get_object(
'label_coord1_ATOM3_name').set_sensitive(False)
self.builder.get_object(
'entry_coord1_ATOM3_name').set_sensitive(False)
self.builder.get_object(
'checkbutton_mass_weight1').set_sensitive(False)
if mode == 'multiple-distance':
self.builder.get_object('label_coord1_atom3').set_sensitive(
True)
self.builder.get_object('entry_coord1_ATOM3').set_sensitive(
True)
self.builder.get_object(
'label_coord1_ATOM3_name').set_sensitive(True)
self.builder.get_object(
'entry_coord1_ATOM3_name').set_sensitive(True)
self.builder.get_object(
'checkbutton_mass_weight1').set_sensitive(True)
if combobox == self.builder.get_object(
'combobox_SCAN_reaction_coordiante2_type'):
mode = self.builder.get_object(
'combobox_SCAN_reaction_coordiante2_type').get_active_text()
if mode == 'simple-distance':
self.builder.get_object('label_coord2_atom3').set_sensitive(
False)
self.builder.get_object('entry_coord2_ATOM3').set_sensitive(
False)
self.builder.get_object(
'label_coord2_ATOM3_name').set_sensitive(False)
self.builder.get_object(
'entry_coord2_ATOM3_name').set_sensitive(False)
self.builder.get_object(
'checkbutton_mass_weight2').set_sensitive(False)
if mode == 'multiple-distance':
self.builder.get_object('label_coord2_atom3').set_sensitive(
True)
self.builder.get_object('entry_coord2_ATOM3').set_sensitive(
True)
self.builder.get_object(
'label_coord2_ATOM3_name').set_sensitive(True)
self.builder.get_object(
'entry_coord2_ATOM3_name').set_sensitive(True)
self.builder.get_object(
'checkbutton_mass_weight2').set_sensitive(True)
def OpenWindow(self, text):
""" Function doc """
if self.Visible == False:
self.builder = gtk.Builder()
self.builder.add_from_file(
os.path.join(self.EasyHybrid_GUI, 'WindowScan2D',
'ScanWindow2D.glade'))
self.builder.connect_signals(self)
self.window = self.builder.get_object('ScanWindow')
self.coord2_sigma_pk1_pk3 = None
self.coord2_sigma_pk3_pk1 = None
self.coord1_sigma_pk1_pk3 = None
self.coord1_sigma_pk3_pk1 = None
self.builder.get_object("SCAN_entry_trajectory_name").set_text(
text)
'''
--------------------------------------------------
- -
- WindowControl -
- -
--------------------------------------------------
'''
self.window_control = WindowControl(self.builder)
#--------------------- Setup ComboBoxes -------------------------
combobox = 'combobox_SCAN_reaction_coordiante_type'
combolist = ['simple-distance', 'multiple-distance']
self.window_control.SETUP_COMBOBOXES(combobox, combolist, 0)
combobox = 'combobox_SCAN_reaction_coordiante2_type'
combolist = ['simple-distance', 'multiple-distance']
self.window_control.SETUP_COMBOBOXES(combobox, combolist, 0)
combobox = 'combobox_optimization_method'
combolist = ['Conjugate Gradient', 'Steepest Descent', 'LBFGS']
self.window_control.SETUP_COMBOBOXES(combobox, combolist, 0)
self.window.show()
#
self.builder.connect_signals(self)
self.Visible = True
gtk.main()
#----------------------------------------------------------------
def CloseWindow(self, button):
""" Function doc """
#print "Bacheguissimo"
self.window.destroy()
def __init__(self, EasyHybridSession=None):
""" Class initialiser """
self.Visible = False
if EasyHybridSession != None:
self.project = EasyHybridSession.project
self.main_builder = EasyHybridSession.builder
self.EasyHybridSession = EasyHybridSession
self.window_control = EasyHybridSession.window_control
self.EasyHybrid_ROOT = EasyHybridSession.EasyHybrid_ROOT
self.EasyHybrid_GUI = EasyHybridSession.EasyHybrid_GUI
else:
self.EasyHybrid_ROOT = ''
self.EasyHybrid_GUI = ''
self.project = None
#self.window_control = window_control
#self.builder = gtk.Builder()
#self.main_builder = main_builder
#self.builder.add_from_file(
# os.path.join(EasyHybrid_GUI, 'ScanWindow.glade'))
#
#self.builder.connect_signals(self)
#self.window = self.builder.get_object('ScanWindow')
#
#self.sigma_pk1_pk3 = None
#self.sigma_pk3_pk1 = None
'''
class NewProjectDialog():
""" Class doc """
def on_new_project_entry_changed (self, entry):
""" Function doc """
text = self.builder.get_object("new_project_entry").get_text()
WorkSpace = self.EasyHybridSession.EasyHybridConfig['WorkSpace']
try:
path = os.path.join(WorkSpace, text)
self.builder.get_object("ProjectDirectory").set_text(path)
except:
pass
def on_combobox1_changed(self, combobox):
""" Function doc """
fftype = self.builder.get_object("combobox1").get_active_text()
if fftype == "AMBER":
#print fftype
self.builder.get_object("amber_prmtop_label"). show()
self.builder.get_object("amber_prmtop_chooser").show()
self.builder.get_object("charmm_topologies_label").hide()
self.builder.get_object("charmm_topologies_chooser").hide()
self.builder.get_object("opls_prmtop_label").hide()
self.builder.get_object("opls_prmtop_chooser").hide()
if fftype == "CHARMM":
#print fftype
self.builder.get_object("opls_prmtop_label").hide()
self.builder.get_object("opls_prmtop_chooser").hide()
self.builder.get_object("amber_prmtop_label"). show()
self.builder.get_object("amber_prmtop_chooser").show()
self.builder.get_object("charmm_topologies_label").show()
self.builder.get_object("charmm_topologies_chooser").show()
if fftype == "GROMACS":
#print fftype
self.builder.get_object("amber_prmtop_label"). show()
self.builder.get_object("amber_prmtop_chooser").show()
self.builder.get_object("charmm_topologies_label").hide()
self.builder.get_object("charmm_topologies_chooser").hide()
self.builder.get_object("opls_prmtop_label").hide()
self.builder.get_object("opls_prmtop_chooser").hide()
if fftype == "OPLS":
#print fftype
self.builder.get_object("amber_prmtop_label"). hide()
self.builder.get_object("amber_prmtop_chooser").hide()
self.builder.get_object("opls_prmtop_label").show()
self.builder.get_object("opls_prmtop_chooser").show()
self.builder.get_object("charmm_topologies_label"). hide()
self.builder.get_object("charmm_topologies_chooser").hide()
if fftype == "pDynamo files(*.pkl,*.yaml)":
self.builder.get_object("opls_prmtop_label").hide()
self.builder.get_object("opls_prmtop_chooser").hide()
self.builder.get_object("amber_prmtop_label"). hide()
self.builder.get_object("amber_prmtop_chooser").hide()
self.builder.get_object("charmm_topologies_label"). hide()
self.builder.get_object("charmm_topologies_chooser").hide()
if fftype == "Other(*.pdb,*.xyz,*.mol2...)":
self.builder.get_object("opls_prmtop_label").hide()
self.builder.get_object("opls_prmtop_chooser").hide()
self.builder.get_object("amber_prmtop_label"). hide()
self.builder.get_object("amber_prmtop_chooser").hide()
self.builder.get_object("charmm_topologies_label"). hide()
self.builder.get_object("charmm_topologies_chooser").hide()
# "old import_molmec_system(*args): "
def on_button1_clicked_create_new_project(self, button):
BufferText = self.builder.get_object('textview1').get_buffer() #
BufferText = BufferText.get_text(*BufferText.get_bounds(), include_hidden_chars=False)
#print BufferText
#print '\n\n\n' + BufferText + '\n\n\n' + 'teste aqui'
project = self.project
name = self.builder.get_object("new_project_entry").get_text()
ProjectDirectory = self.builder.get_object("ProjectDirectory").get_text()
ProjectDirectory = ProjectDirectory.split('/')
path = '/'
for i in ProjectDirectory:
path = os.path.join(path, i)
if not os.path.exists (path):
os.mkdir (path)
#data_path = self.builder.get_object("filechooserbutton1").get_filename()
data_path = self.builder.get_object("ProjectDirectory").get_text()
FileType = self.builder.get_object("combobox1").get_active_text() # combo box combox_model
filename = os.path.join(data_path,name)
filesin = {}
try:
import shutil
except:
print "shutil module is no available"
if FileType == "AMBER":
filesin['amber_params'] = self.builder.get_object(
"amber_prmtop_chooser").get_filename()
filesin['amber_coords'] = self.builder.get_object(
"amber_inpcrd_chooser").get_filename()
elif FileType == "CHARMM":
filesin['charmm_params'] = self.builder.get_object(
"amber_prmtop_chooser").get_filename()
filesin['charmm_topologies'] = self.builder.get_object(
"charmm_topologies_chooser").get_filename()
filesin['charmm_coords'] = self.builder.get_object(
"amber_inpcrd_chooser").get_filename()
elif FileType == "GROMACS":
filesin['gromacs_params'] = self.builder.get_object(
"amber_prmtop_chooser").get_filename() #
filesin['gromacs_coords'] = self.builder.get_object(
"amber_inpcrd_chooser").get_filename()
elif FileType == "OPLS":
filesin['opls_params'] = self.builder.get_object(
"opls_prmtop_chooser").get_filename()
filesin['opls_coords'] = self.builder.get_object(
"amber_inpcrd_chooser").get_filename()
elif FileType == "pDynamo files(*.pkl,*.yaml)":
filesin['pDynamoFile'] = self.builder.get_object(
"amber_inpcrd_chooser").get_filename() #
elif FileType == "Other(*.pdb,*.xyz,*.mol2...)":
filesin['coordinates'] = self.builder.get_object(
"amber_inpcrd_chooser").get_filename() #
self.project = self.EasyHybridSession.project
#self.project.DeleteActualProject()
self.project.Create_New_Project(
name, data_path, FileType, filesin, BufferText)
self.project.Save_Project_To_File (filename = filename, type_ = 'pkl')
# self.project.From_PDYNAMO_to_EasyHybrid()
self.project.system.Summary()
self.project.settings['add_info'] = BufferText
#
def __init__(self, EasyHybridSession = None):
""" Class initialiser """
self.builder = gtk.Builder()
if EasyHybridSession != None:
self.project = EasyHybridSession.project
self.main_builder = EasyHybridSession.builder
self.EasyHybridSession = EasyHybridSession
self.builder.add_from_file(
os.path.join(EasyHybrid_GUI,'DialogNewProject', 'NewProjectDialog.glade'))
self.builder.connect_signals(self)
self.dialog = self.builder.get_object('dialog1')
self.dualLog = None
#self.scrath = os.environ.get('PDYNAMO_SCRATCH')
#
#self.builder.get_object('ProjectDirectory').set_text(self.scrath )
'''
--------------------------------------------------
- -
- WindowControl -
- -
--------------------------------------------------
'''
self.window_control = WindowControl(self.builder)
#----------------- Setup ComboBoxes -------------------------#
combobox = 'combobox1' #
combolist = ["AMBER", #
"CHARMM", #
#
#"GROMACS",
#
"OPLS",
#
"pDynamo files(*.pkl,*.yaml)",
"Other(*.pdb,*.xyz,*.mol2...)"] #
#
self.window_control.SETUP_COMBOBOXES(combobox, combolist, 0)
#------------------------------------------------------------#
localtime = time.asctime(time.localtime(time.time()))
print "Local current time :", localtime
localtime = localtime.split()
# 0 1 2 3 4
#[Sun] [Sep] [28] [02:32:04] [2014]
text = 'NewProject_' + localtime[1] + \
'_' + localtime[2] + '_' + localtime[4]
self.builder.get_object("new_project_entry").set_text(text)
class TrajectoryEnergyRefineDialog():
def runTrajectoryEnergyRefine (self, button):
""" Function doc """
trajectory = self.builder.get_object('filechooserbutton1').get_filename()
data_path = self.project.settings['data_path']
logfile = self.builder.get_object('filechooserbutton4').get_filename()
input_type = self.builder.get_object('combobox4').get_active_text()
nCPUs = self.builder.get_object('spinbutton2').get_value_as_int()
#nCPUs = 8
REACTION_COORD1 = None
REACTION_COORD2 = None
set_MM_chrgs_to_zero = False
exclude_MM_atoms = False
system = Clone(self.project.system)
if self.builder.get_object("checkbutton_set_MM_charges_to_zero").get_active():
charges = system.energyModel.mmAtoms.AtomicCharges()
natoms = len(charges)
ZeroCharges = [0.0] * natoms
system.energyModel.mmAtoms.SetAtomicCharges(ZeroCharges)
#if self.builder.get_object("checkbutton_exclude_MM_atoms").get_active():
# exclude_MM_atoms = True
#_type = None
#-------------------------------------------------------------------------------------------------#
# Coordinate 1
#-------------------------------------------------------------------------------------------------#
mode = self.builder.get_object('combobox_reaction_coordiante_type1').get_active_text()
if mode == "simple-distance":
REACTION_COORD1 = {'MODE' : mode,
'ATOM1' : int(self.builder.get_object("entry_coord1_ATOM1" ).get_text()) ,
'ATOM1_name' : self.builder.get_object ("entry_coord1_ATOM1_name").get_text() ,
'ATOM2' : int(self.builder.get_object("entry_coord1_ATOM2" ).get_text()) ,
'ATOM2_name' : self.builder.get_object ("entry_coord1_ATOM2_name").get_text() ,
}
if mode == "multiple-distance":
REACTION_COORD1 = {'MODE' : mode,
'ATOM1' : int(self.builder.get_object("entry_coord1_ATOM1" ).get_text()),
'ATOM1_name' : self.builder.get_object ("entry_coord1_ATOM1_name").get_text() ,
'ATOM2' : int(self.builder.get_object("entry_coord1_ATOM2" ).get_text()),
'ATOM2_name' : self.builder.get_object ("entry_coord1_ATOM2_name").get_text() ,
'ATOM3' : int(self.builder.get_object("entry_coord1_ATOM3" ).get_text()),
'ATOM3_name' : self.builder.get_object ("entry_coord1_ATOM3_name").get_text() ,
}
#-------------------------------------------------------------------------------------------------#
#-------------------------------------------------------------------------------------------------#
# Coordinate 2
#-------------------------------------------------------------------------------------------------#
if self.refine_type == '2D':
mode = self.builder.get_object('combobox_reaction_coordiante_type2').get_active_text()
if mode == "simple-distance":
REACTION_COORD2 = {'MODE' : mode,
'ATOM1' : int(self.builder.get_object("entry_coord2_ATOM1" ).get_text()),
'ATOM1_name' : self.builder.get_object ("entry_coord2_ATOM1_name").get_text() ,
'ATOM2' : int(self.builder.get_object("entry_coord2_ATOM2" ).get_text()),
'ATOM2_name' : self.builder.get_object ("entry_coord2_ATOM2_name").get_text() ,
}
if mode == "multiple-distance":
REACTION_COORD2 = {'MODE' : mode,
'ATOM1' : int(self.builder.get_object("entry_coord2_ATOM1" ).get_text()),
'ATOM1_name' : self.builder.get_object ("entry_coord2_ATOM1_name").get_text() ,
'ATOM2' : int(self.builder.get_object("entry_coord2_ATOM2" ).get_text()),
'ATOM2_name' : self.builder.get_object ("entry_coord2_ATOM2_name").get_text() ,
'ATOM3' : int(self.builder.get_object("entry_coord2_ATOM3" ).get_text()),
'ATOM3_name' : self.builder.get_object ("entry_coord2_ATOM3_name").get_text() ,
}
#-------------------------------------------------------------------------------------------------#
'''
if self.builder.get_object('checkbutton_minimization').get_active() :
#---------------------------------- importing parameters COORD-1 ---------------------------#
FORCECONSTANT = float(self.builder.get_object('entry_FORCE1').get_text()) #
#-------------------------------------------------------------------------------------------#
self.EasyHybridSession.project.ActiveModeCheck()
MINIMIZATION_PARAMETERS = None
if self.builder.get_object("checkbutton_minimization").get_active():
#---------------------------------------------------------------------------------------------------------#
mim_method = self.builder.get_object('combobox_optimization_method').get_active_text() # #
max_int = self.builder.get_object("entry_max_interactions") .get_text() #
rms_grad = self.builder.get_object("entry_rmsd_grad") .get_text() #
log_freq = 1
#---------------------------------------------------------------------------------------------------------#
MINIMIZATION_PARAMETERS={
'do_minimizaton': True ,
'max_int' : max_int ,
'log_freq' : log_freq ,
'rms_grad' : rms_grad ,
'mim_method' : mim_method}
pprint(REACTION_COORD1)
pprint(MINIMIZATION_PARAMETERS)
else:
pass
'''
_type = 'energy'
outputLogFile = self.builder.get_object("output_entry").get_text()
pDynamoTrajectoryEnergyRefine (system = system ,
data_path = outputLogFile ,
trajectory = trajectory ,
REACTION_COORD1 = REACTION_COORD1 ,
REACTION_COORD2 = REACTION_COORD2 ,
input_type = input_type ,
_type = self.refine_type ,
nCPUs = nCPUs ,
set_MM_chrgs_to_zero = set_MM_chrgs_to_zero,
exclude_MM_atoms = exclude_MM_atoms )
#if self.builder.get_object("checkbutton_set_MM_charges_to_zero").get_active():
# self.project.system.energyModel.mmAtoms.SetAtomicCharges(charges)
#
def fileChooser_logFile (self, widget):
""" Function doc
parameters = {
1: {
'type' : 'line' , # line / matrix
'title' : '' , #
'X' : [] , # X
'Y' : [] , # Y
'xlabel' : 'x label' , # xlabel,
'ylabel' : 'y label' , # ylabel,
'energy_model' : 'UNK' ,
'c1_ATOM1_id' : None ,
'c1_ATOM2_id' : None ,
'c1_ATOM3_id' : None ,
'c1_ATOM1_name' : None ,
'c1_ATOM2_name' : None ,
'c1_ATOM3_name' : None ,
'c2_ATOM1_id' : None ,
'c2_ATOM2_id' : None ,
'c2_ATOM3_id' : None ,
'c2_ATOM1_name' : None ,
'c2_ATOM2_name' : None ,
'c2_ATOM3_name' : None ,
}
REACTION_COORD1 = {'MODE' : mode,
'ATOM1' : int(self.builder.get_object("entry_coord1_ATOM1" ).get_text()),
'ATOM1_name' : self.builder.get_object ("entry_coord1_ATOM1_name").get_text() ,
'ATOM2' : int(self.builder.get_object("entry_coord1_ATOM2" ).get_text()),
'ATOM2_name' : self.builder.get_object ("entry_coord1_ATOM2_name").get_text() ,
'ATOM3' : int(self.builder.get_object("entry_coord1_ATOM3" ).get_text()),
'ATOM3_name' : self.builder.get_object ("entry_coord1_ATOM3_name").get_text() ,
"""
FileName = self.builder.get_object("filechooserbutton4").get_filename()
parameters = ParseProcessLogFile(FileName)
#print parameters
if parameters[1]['c1_ATOM1_id']:
self.builder.get_object("entry_coord1_ATOM1").set_text(parameters[1]['c1_ATOM1_id'])
self.builder.get_object ("entry_coord1_ATOM1_name").set_text(parameters[1]['c1_ATOM1_name'])
if parameters[1]['c1_ATOM2_id']:
self.builder.get_object("entry_coord1_ATOM2").set_text(parameters[1]['c1_ATOM2_id'])
self.builder.get_object ("entry_coord1_ATOM2_name").set_text(parameters[1]['c1_ATOM2_name'])
if parameters[1]['c1_ATOM3_id']:
self.builder.get_object("entry_coord1_ATOM3").set_text(parameters[1]['c1_ATOM3_id'])
self.builder.get_object ("entry_coord1_ATOM3_name").set_text(parameters[1]['c1_ATOM3_name'])
self.builder.get_object('combobox_reaction_coordiante_type1').set_active(1)
else:
self.builder.get_object('combobox_reaction_coordiante_type1').set_active(0)
if parameters[1]['c2_ATOM1_id']:
self.builder.get_object("entry_coord2_ATOM1").set_text(parameters[1]['c2_ATOM1_id'])
self.builder.get_object ("entry_coord2_ATOM1_name").set_text(parameters[1]['c2_ATOM1_name'])
if parameters[1]['c2_ATOM2_id']:
self.builder.get_object("entry_coord2_ATOM2").set_text(parameters[1]['c2_ATOM2_id'])
self.builder.get_object ("entry_coord2_ATOM2_name").set_text(parameters[1]['c2_ATOM2_name'])
if parameters[1]['c2_ATOM3_id']:
self.builder.get_object("entry_coord2_ATOM3").set_text(parameters[1]['c2_ATOM3_id'])
self.builder.get_object ("entry_coord2_ATOM3_name").set_text(parameters[1]['c2_ATOM3_name'])
self.builder.get_object('combobox_reaction_coordiante_type2').set_active(1)
else:
self.builder.get_object('combobox_reaction_coordiante_type2').set_active(0)
def Button_import_PyMOL_index(self, button):
'''
----------------------------------------------------
REACTION COORDINATE 1
----------------------------------------------------
'''
if button == self.builder.get_object('import_indexes_from_PyMOL1'):
mode = self.builder.get_object('combobox_reaction_coordiante_type1').get_active_text()
if mode == "simple-distance":
try:
name1, atom1_index, name2, atom2_index, distance_a1_a2 = import_ATOM1_ATOM2("pk1", "pk2")
distance_a1_a2 = str(distance_a1_a2)
#self.builder.get_object('entry_param_DMINIMUM1' ).set_text(distance_a1_a2)
self.builder.get_object("entry_coord1_ATOM1" ).set_text(str(atom1_index))
self.builder.get_object("entry_coord1_ATOM1_name").set_text(name1)
self.builder.get_object("entry_coord1_ATOM2" ).set_text(str(atom2_index))
self.builder.get_object("entry_coord1_ATOM2_name").set_text(name2)
except:
cmd.edit_mode()
print "pk1, pk2 selection not found"
print texto_d1
return
if mode == "multiple-distance":
try:
name1, atom1_index, name2, atom2_index, distance_a1_a2 = import_ATOM1_ATOM2("pk1", "pk2")
name2, atom2_index, name3, atom3_index, distance_a2_a3 = import_ATOM1_ATOM2("pk2", "pk3")
#print "distance between atom 1 and atom 2: ",distance_a1_a2
#print "distance between atom 2 and atom 3: ",distance_a2_a3
'''
if self.builder.get_object("checkbutton_mass_weight").get_active():
self.sigma_pk1_pk3, self.sigma_pk3_pk1 = compute_sigma_a1_a3 (name1, name3)
"""
R R
\ /
A1--A2 . . . . A3
/ \
R R
^ ^ ^
| | |
pk1-pk2 . . . . pk3
d1 d2
q1 = 1 / (mpk1 + mpk3) = [ mpk1 * r (pk3_pk2) - mpk3 * r (pk1_pk2) ]
"""
#DMINIMUM = (self.sigma_pk1_pk3 * distance_a1_a2) -(self.sigma_pk3_pk1 * distance_a2_a3*-1)
#self.builder.get_object('entry_param_DMINIMUM1').set_text(str(DMINIMUM))
print "\n\nUsing mass weighted restraints"
print "Sigma pk1_pk3", self.sigma_pk1_pk3
print "Sigma pk3_pk1", self.sigma_pk3_pk1
#print "Estimated minimum distance", DMINIMUM
else:
self.sigma_pk1_pk3 = 1.0
self.sigma_pk3_pk1 = -1.0
#DMINIMUM = distance_a1_a2 - distance_a2_a3
#self.builder.get_object('entry_param_DMINIMUM1').set_text(str(DMINIMUM))
print "\n\nSigma pk1_pk3 ", self.sigma_pk1_pk3
print "Sigma pk3_pk1", self.sigma_pk3_pk1
#print "Estimated minimum distance", DMINIMUM
'''
except:
cmd.edit_mode()
print "pk1, pk2 and pk3 selections not found"
return
print name3, name2, name1
self.builder.get_object("entry_coord1_ATOM1" ).set_text(str(atom1_index))
self.builder.get_object("entry_coord1_ATOM1_name").set_text(name1)
self.builder.get_object("entry_coord1_ATOM2" ).set_text(str(atom2_index))
self.builder.get_object("entry_coord1_ATOM2_name").set_text(name2)
self.builder.get_object("entry_coord1_ATOM3" ).set_text(str(atom3_index))
self.builder.get_object("entry_coord1_ATOM3_name").set_text(name3)
if button == self.builder.get_object('import_indexes_from_PyMOL2'):
mode = self.builder.get_object('combobox_reaction_coordiante_type2').get_active_text()
if mode == "simple-distance":
try:
name1, atom1_index, name2, atom2_index, distance_a1_a2 = import_ATOM1_ATOM2("pk1", "pk2")
distance_a1_a2 = str(distance_a1_a2)
#self.builder.get_object('entry_param_DMINIMUM1' ).set_text(distance_a1_a2)
self.builder.get_object("entry_coord2_ATOM1" ).set_text(str(atom1_index))
self.builder.get_object("entry_coord2_ATOM1_name").set_text(name1)
self.builder.get_object("entry_coord2_ATOM2" ).set_text(str(atom2_index))
self.builder.get_object("entry_coord2_ATOM2_name").set_text(name2)
except:
cmd.edit_mode()
print "pk1, pk2 selection not found"
print texto_d1
return
if mode == "multiple-distance":
try:
name1, atom1_index, name2, atom2_index, distance_a1_a2 = import_ATOM1_ATOM2("pk1", "pk2")
name2, atom2_index, name3, atom3_index, distance_a2_a3 = import_ATOM1_ATOM2("pk2", "pk3")
#print "distance between atom 1 and atom 2: ",distance_a1_a2
#print "distance between atom 2 and atom 3: ",distance_a2_a3
'''
if self.builder.get_object("checkbutton_mass_weight").get_active():
self.sigma_pk1_pk3, self.sigma_pk3_pk1 = compute_sigma_a1_a3 (name1, name3)
"""
R R
\ /
A1--A2 . . . . A3
/ \
R R
^ ^ ^
| | |
pk1-pk2 . . . . pk3
d1 d2
q1 = 1 / (mpk1 + mpk3) = [ mpk1 * r (pk3_pk2) - mpk3 * r (pk1_pk2) ]
"""
#DMINIMUM = (self.sigma_pk1_pk3 * distance_a1_a2) -(self.sigma_pk3_pk1 * distance_a2_a3*-1)
#self.builder.get_object('entry_param_DMINIMUM1').set_text(str(DMINIMUM))
print "\n\nUsing mass weighted restraints"
print "Sigma pk1_pk3", self.sigma_pk1_pk3
print "Sigma pk3_pk1", self.sigma_pk3_pk1
#print "Estimated minimum distance", DMINIMUM
else:
self.sigma_pk1_pk3 = 1.0
self.sigma_pk3_pk1 = -1.0
#DMINIMUM = distance_a1_a2 - distance_a2_a3
#self.builder.get_object('entry_param_DMINIMUM1').set_text(str(DMINIMUM))
print "\n\nSigma pk1_pk3 ", self.sigma_pk1_pk3
print "Sigma pk3_pk1", self.sigma_pk3_pk1
#print "Estimated minimum distance", DMINIMUM
'''
except:
cmd.edit_mode()
print "pk1, pk2 and pk3 selections not found"
#print texto_d2d1
return
print name3, name2, name1
self.builder.get_object("entry_coord2_ATOM1" ).set_text(str(atom1_index))
self.builder.get_object("entry_coord2_ATOM1_name").set_text(name1)
self.builder.get_object("entry_coord2_ATOM2" ).set_text(str(atom2_index))
self.builder.get_object("entry_coord2_ATOM2_name").set_text(name2)
self.builder.get_object("entry_coord2_ATOM3" ).set_text(str(atom3_index))
self.builder.get_object("entry_coord2_ATOM3_name").set_text(name3)
def ComboxChange(self, combobox):
""" Function doc """
#print combobox, combobox.get_active_text()
if combobox == self.builder.get_object('combobox_reaction_coordiante_type1'):
mode = self.builder.get_object('combobox_reaction_coordiante_type1').get_active_text()
if mode == 'simple-distance':
self.builder.get_object('label_coord1_atom3' ).set_sensitive(False)
self.builder.get_object('entry_coord1_ATOM3' ).set_sensitive(False)
self.builder.get_object('label_coord1_ATOM3_name' ).set_sensitive(False)
self.builder.get_object('entry_coord1_ATOM3_name' ).set_sensitive(False)
if mode == 'multiple-distance':
self.builder.get_object('label_coord1_atom3' ).set_sensitive(True)
self.builder.get_object('entry_coord1_ATOM3' ).set_sensitive(True)
self.builder.get_object('label_coord1_ATOM3_name' ).set_sensitive(True)
self.builder.get_object('entry_coord1_ATOM3_name' ).set_sensitive(True)
if combobox == self.builder.get_object('combobox_reaction_coordiante_type2'):
mode = self.builder.get_object('combobox_reaction_coordiante_type2').get_active_text()
if mode == 'simple-distance':
self.builder.get_object('label_coord2_atom3' ).set_sensitive(False)
self.builder.get_object('entry_coord2_ATOM3' ).set_sensitive(False)
self.builder.get_object('label_coord2_ATOM3_name' ).set_sensitive(False)
self.builder.get_object('entry_coord2_ATOM3_name' ).set_sensitive(False)
if mode == 'multiple-distance':
self.builder.get_object('label_coord2_atom3' ).set_sensitive(True)
self.builder.get_object('entry_coord2_ATOM3' ).set_sensitive(True)
self.builder.get_object('label_coord2_ATOM3_name' ).set_sensitive(True)
self.builder.get_object('entry_coord2_ATOM3_name' ).set_sensitive(True)
if combobox == self.builder.get_object('combobox1'):
mode = combobox.get_active_text()
if mode == 'Scan 1D':
self.builder.get_object('vseparator1').hide()
self.builder.get_object('vbox4').hide()
self.refine_type = "1D"
if mode == 'Scan 2D':
self.builder.get_object('vseparator1').show()
self.builder.get_object('vbox4').show()
self.refine_type = '2D'
def on_combobox1_changed(self, button):
_type = self.builder.get_object('combobox1').get_active_text()
""" Function doc """
if _type == 'folder - pDynamo':
self.builder.get_object('filechooserbutton2').hide()
self.builder.get_object('filechooserbutton1').show()
else:
self.builder.get_object('filechooserbutton2').show()
self.builder.get_object('filechooserbutton1').hide()
def geo_opt_change(self, widget):
if self.builder.get_object('checkbutton_minimization').get_active():
self.builder.get_object('vbox3').set_sensitive(True)
else:
self.builder.get_object('vbox3').set_sensitive(False)
def __init__(self, EasyHybridSession = None):
self.builder = gtk.Builder()
if EasyHybridSession != None:
self.project = EasyHybridSession.project
self.main_builder = EasyHybridSession.builder
self.window_control = EasyHybridSession.window_control
self.EasyHybridSession = EasyHybridSession
self.EasyHybrid_ROOT = EasyHybridSession.EasyHybrid_ROOT
self.EasyHybrid_GUI = EasyHybridSession.EasyHybrid_GUI
# - - - importing ORCA PATH from EasyHybridConfig file. - - -
#-----------------------------------------------------------------------#
try: #
ORCA = EasyHybridSession.EasyHybridConfig['ORCAPATH']#
except: #
ORCA = '' #
#-----------------------------------------------------------------------#
self.builder.add_from_file(
os.path.join(self.EasyHybrid_GUI, 'DialogTrajectoryEnergyRefine','TrajectoryEnergyRefine.glade'))
self.builder.connect_signals(self)
self.dialog = self.builder.get_object('dialog1')
self.window_control = WindowControl(self.builder)
self.builder.get_object('filechooserbutton2').hide()
self.builder.get_object('vseparator1').hide()
self.builder.get_object('vbox4').hide()
self.builder.get_object('Optimize_Geometry_frame').hide()
self.builder.get_object('checkbutton_exclude_MM_atoms').hide()
#----------------- Setup ComboBoxes -------------------------#
combobox = 'combobox1' #
combolist = ["Scan 1D", "Scan 2D"]#, "trj - AMBER", "dcd - CHARMM", 'xtc - GROMACS']
self.window_control.SETUP_COMBOBOXES(combobox, combolist, 0)
combobox = 'combobox4' #
combolist = ["pkl", "xyz", 'pdb']#, "trj - AMBER", "dcd - CHARMM", 'xtc - GROMACS']
self.window_control.SETUP_COMBOBOXES(combobox, combolist, 0)
combobox = 'combobox_optimization_method' #
combolist = ['Conjugate Gradient', 'Steepest Descent','LBFGS']
self.window_control.SETUP_COMBOBOXES(combobox, combolist,0)
combobox = 'combobox_reaction_coordiante_type1'
combolist = ['simple-distance', 'multiple-distance']
self.window_control.SETUP_COMBOBOXES(combobox, combolist,0)
combobox = 'combobox_reaction_coordiante_type2'
combolist = ['simple-distance', 'multiple-distance']
self.window_control.SETUP_COMBOBOXES(combobox, combolist,0)
self.refine_type = '1D'
# QC SPIN MULTIPLICITY
self.spinbutton = 'spinbutton2'
config = [0.0, 1.0, 500.0, 1.0, 0.0, 0.0]
self.window_control.SETUP_SPINBUTTON(self.spinbutton, config)
#if self.builder.get_object('check_opt_geometry'):
self.builder.get_object('vbox3').set_sensitive(False)
self.sigma_pk1_pk3 = None
self.sigma_pk3_pk1 = None
def Mass_weight_check(self, checkbutton):
'''
----------------------------------------------------
REACTION COORDINATE 1
----------------------------------------------------
'''
if checkbutton == self.builder.get_object('checkbutton_mass_weight'):
try:
name1, atom1_index, name2, atom2_index, distance_a1_a2 = import_ATOM1_ATOM2("pk1", "pk2")
name2, atom2_index, name3, atom3_index, distance_a2_a3 = import_ATOM1_ATOM2("pk2", "pk3")
except:
print texto_d2d1
return
if self.builder.get_object("checkbutton_mass_weight").get_active():
self.sigma_pk1_pk3, self.sigma_pk3_pk1 = compute_sigma_a1_a3 (name1, name3)
"""
R R
\ /
A1--A2 . . . . A3
/ \
R R
^ ^ ^
| | |
pk1-pk2 . . . . pk3
d1 d2
q1 = 1 / (mpk1 + mpk3) = [ mpk1 * r (pk3_pk2) - mpk3 * r (pk1_pk2) ]
"""
#DMINIMUM = (self.sigma_pk1_pk3 * distance_a1_a2) -(self.sigma_pk3_pk1 * distance_a2_a3*-1)
#self.builder.get_object('entry_param_DMINIMUM1').set_text(str(DMINIMUM))
print "\n\nUsing mass weighted restraints"
print "Sigma pk1_pk3", self.sigma_pk1_pk3
print "Sigma pk3_pk1", self.sigma_pk3_pk1
#print "Estimated minimum distance", DMINIMUM
else:
self.sigma_pk1_pk3 = 1.0
self.sigma_pk3_pk1 = -1.0
#DMINIMUM = distance_a1_a2 - distance_a2_a3
#self.builder.get_object('entry_param_DMINIMUM1').set_text(str(DMINIMUM))
print "\n\nSigma pk1_pk3 ", self.sigma_pk1_pk3
print "Sigma pk3_pk1", self.sigma_pk3_pk1
class PreferencesDialog():
""" Class doc """
def SavePreferences(self, button):
""" Function doc """
atom_color = self.builder.get_object('combobox1').get_active_text()
fixed_atom_color = self.builder.get_object(
'combobox2').get_active_text()
bq_color = self.builder.get_object('combobox3').get_active_text()
QC_representations = {
'lines': self.builder.get_object('QC_lines').get_active(),
'sticks': self.builder.get_object('QC_sticks').get_active(),
'spheres': self.builder.get_object('QC_spheres').get_active(),
'dots': self.builder.get_object('QC_dots').get_active(),
}
FIX_representations = {
'lines': self.builder.get_object('FIX_lines').get_active(),
'sticks': self.builder.get_object('FIX_sticks').get_active(),
'spheres': self.builder.get_object('FIX_spheres').get_active(),
'dots': self.builder.get_object('FIX_dots').get_active(),
}
#FIX_representations = {'lines' : self.builder.get_object('FIX_lines').get_active()
# }
#
self.EasyHybridSession.EasyHybridConfig['bg_color'] = bq_color
self.EasyHybridSession.EasyHybridConfig['fixed'] = fixed_atom_color
self.EasyHybridSession.EasyHybridConfig['color'] = atom_color
self.EasyHybridSession.EasyHybridConfig['QC'] = QC_representations
self.EasyHybridSession.EasyHybridConfig['FIX'] = FIX_representations
self.EasyHybridSession.Save_EasyHybrid_ConfigFile()
self.EasyHybridSession.project.SystemCheck(status=True,
PyMOL=True,
_color=True,
_cell=True,
treeview_selections=True,
ORCA_backup=False)
def __init__(self, EasyHybridSession=None):
""" Class initialiser """
self.builder = gtk.Builder()
if EasyHybridSession != None:
self.project = EasyHybridSession.project
self.main_builder = EasyHybridSession.builder
self.EasyHybridSession = EasyHybridSession
self.window_control = EasyHybridSession.window_control
self.builder.add_from_file(
os.path.join(EasyHybrid_GUI, 'DialogPreferences',
'Preferences.glade'))
self.builder.connect_signals(self)
self.dialog = self.builder.get_object('dialog_preferences')
'''
--------------------------------------------------
- -
- WindowControl -
- -
--------------------------------------------------
'''
self.window_control = WindowControl(self.builder)
#colors = [ ]
#colors = [
#'actinium','darksalmon','iodine','palecyan','sodium',
#'aluminum','dash','iridium','palegreen','splitpea',
#'americium','deepblue','iron','paleyellow','strontium',
#'antimony','deepolive','krypton','palladium','sulfur',
#'aquamarine','deeppurple','lanthanum','phosphorus','tantalum',
#'argon','deepsalmon','lawrencium','pink','teal',
#'arsenic','deepsalmon','lead','platinum','technetium',
#'astatine','deepteal','lightblue','plutonium','tellurium',
#'atomic','default','lightmagenta','polonium','terbium',
#'auto','density','lightorange','potassium','thallium',
#'barium','deuterium','lightpink','praseodymium','thorium',
#'berkelium','dirtyviolet','lightteal','promethium','thulium',
#'beryllium','dubnium','lime','protactinium','tin',
#'bismuth','dysprosium','limegreen','pseudoatom','titanium',
#'black','einsteinium','limon','purple','tungsten',
#'blue','erbium','lithium','purpleblue','tv_blue',
#'bluewhite','europium','lonepair','radium','tv_green',
#'bohrium','fermium','lutetium','radon','tv_orange',
#'boron','firebrick','magenta','raspberry','tv_red',
#'brightorange','fluorine','magnesium','red','tv_yellow',
#'bromine','forest','manganese','rhenium','uranium',
#'brown','francium','marine','rhodium','vanadium',
#'cadmium','gadolinium','meitnerium','rubidium','violet',
#'calcium','gallium','mendelevium','ruby','violetpurple',
#'californium','germanium','mercury','ruthenium','warmpink',
#'carbon','gold','molybdenum','rutherfordium','wheat',
#'cerium','gray','neodymium','salmon','white',
#'cesium','green','neon','samarium','xenon',
#'chartreuse','greencyan','neptunium','sand','yellow',
#'chlorine','grey','nickel','scandium','yelloworange',
#'chocolate','hafnium','niobium','seaborgium','ytterbium',
#'chromium','hassium','nitrogen','selenium','yttrium',
#'cobalt','helium','nobelium','silicon','zinc',
#'copper','holmium','olive','silver','zirconium',
#'curium','hotpink','orange','skyblue'
#'current','hydrogen','osmium','slate'
#'cyan','indium','oxygen','smudg'
#]
colors = [
'darksalmon', 'palecyan', 'palegreen', 'deepblue', 'deeppurple',
'deepsalmon', 'deepsalmon', 'lightblue', 'lightorange',
'lightpink', 'dirtyviolet', 'lime', 'tin', 'limegreen', 'black',
'limon', 'purple', 'blue', 'purpleblue', 'tv_blue', 'bluewhite',
'tv_green', 'radon', 'tv_orange', 'firebrick', 'magenta',
'raspberry', 'tv_red', 'brightorange', 'red', 'tv_yellow',
'forest', 'brown', 'marine', 'violet', 'ruby', 'violetpurple',
'warmpink', 'wheat', 'gray', 'salmon', 'white', 'green',
'greencyan', 'sand', 'yellow', 'yelloworange', 'chocolate',
'olive', 'hotpink', 'orange', 'skyblue', 'slate', 'cyan', 'smudg'
]
fixed_colors = [
'black', 'grey10', 'grey20', 'grey30', 'grey40', 'grey50',
'grey60', 'grey70', 'grey80', 'grey90', 'white'
]
bg_color = ['white', 'grey', 'black']
#----------------- Setup ComboBoxes -------------------------#
combobox = 'combobox1' #
self.window_control.SETUP_COMBOBOXES(combobox, colors, 0)
#------------------------------------------------------------#
#----------------- Setup ComboBoxes -------------------------#
combobox = 'combobox2' #
self.window_control.SETUP_COMBOBOXES(combobox, fixed_colors, 0)
#------------------------------------------------------------#
#----------------- Setup ComboBoxes -------------------------#
combobox = 'combobox3' #
self.window_control.SETUP_COMBOBOXES(combobox, bg_color, 0)
class MOPACSEnergyDialog():
def runMOPACEnergy(self, button):
""" Function doc """
parameters = {}
parameters['methods'] = None
parameters['overwrite_files'] = True #AUX = True ,
parameters['trajectory'] = None
parameters['charge'] = 0 #charge = charge ,
parameters['multiplicity'] = 1 #multiplicity = multiplicity,
parameters['mopac_AUX'] = True #AUX = True ,
parameters['mopac_1SCF'] = True #single_point = True ,
parameters['mopac_MOZYME'] = True #MOZYME = MOZYME ,
parameters['mopac_BONDS'] = False #BONDS = False ,
parameters['mopac_LARGE'] = True #PDBOUT = False ,
parameters['mopac_PDBOUT'] = True #PDBOUT = False ,
parameters['mopac_SOLV'] = False #SOLV = SOLV ,
parameters['mopac_ESP'] = None #ESP = ESP ,
parameters['mopac_RSOLV'] = None #RSOLV = RSOLV ,
parameters['mopac_QMMM'] = False #QMMM = QMMM )
parameters['tmpfile_outpath'] = None
parameters['logfile_outpath'] = None
parameters['log_file_name'] = None
parameters['trajectory_type'] = "SCAN"
parameters['mopac_path'] = '/opt/mopac/MOPAC2016.exe'
#---------------------------------------------------------------------------------------------------------------#
# Time and log file #
#---------------------------------------------------------------------------------------------------------------#
localtime = time.asctime(time.localtime(time.time())) #
localtime = localtime.split() #
# 0 1 2 3 4 #
#[Sun] [Sep] [28] [02:32:04] [2014] #
log_file_name = 'MOPAC_Energy_' + localtime[1] + '_' + localtime[
2] + '_' + localtime[3] + '_' + localtime[4] + '.log' #
parameters['log_file_name'] = log_file_name #
#---------------------------------------------------------------------------------------------------------------#
#-----------------------------------------------------------------------------------------------#
# folder and datapath #
#-----------------------------------------------------------------------------------------------#
data_path = self.EasyHybridSession.project.settings['data_path'] #
#
#traj = self.builder.get_object('umbrella_entry_TRAJECTORY').get_text() #
if not os.path.exists(os.path.join(data_path, 'MOPAC_files')): #
os.mkdir(os.path.join(data_path, 'MOPAC_files')) #
logfile_outpath = os.path.join(data_path, 'MOPAC_files') #
#
#
if not os.path.exists(os.path.join(logfile_outpath, 'tmp')): #
os.mkdir(os.path.join(logfile_outpath, 'tmp')) #
tmpfile_outpath = os.path.join(logfile_outpath, 'tmp') #
parameters['tmpfile_outpath'] = tmpfile_outpath #
parameters['logfile_outpath'] = logfile_outpath #
#-----------------------------------------------------------------------------------------------#
#-----------------------------------------------------------------------------------------------#
# LOG file - optional #
#-----------------------------------------------------------------------------------------------#
scanLogFile = self.builder.get_object(
'filechooserbutton3').get_filename() #
#
if scanLogFile == None: #
#parameters = False #
#summary = False #
parameters['original_system_summary'] = False #
parameters['original_scan_log'] = False #
else: #
parameters['original_scan_log'] = ParseProcessLogFile(
scanLogFile) #
parameters['original_system_summary'] = ParseSummaryLogFile(
scanLogFile) #
#-----------------------------------------------------------------------------------------------#
#-----------------------------------------------------------------------------------------------#
if self.builder.get_object('checkbutton4').get_active() == True:
parameters['overwrite_files'] = False #
else: #
parameters['overwrite_files'] = True #
#-----------------------------------------------------------------------------------------------#
#-----------------------------------------------------------------------------------------------#
charge = self.builder.get_object(
'spinbutton_charge').get_value_as_int() #
charge = str(charge) #
multiplicity = self.builder.get_object(
'spinbutton_multiplicity').get_value_as_int() #
multiplicity = 'Singlet' #
#
parameters['charge'] = charge #
parameters['multiplicity'] = multiplicity #
#-----------------------------------------------------------------------------------------------#
#-----------------------------------------------------------------------------------------------#
# mopac path #
#-----------------------------------------------------------------------------------------------#
parameters['mopac_path'] = self.builder.get_object(
'mopac_path').get_text() #
print parameters['mopac_path']
#-----------------------------------------------------------------------------------------------#
if self.builder.get_object('checkbutton1').get_active() == True:
SOLV = True
ESP = self.builder.get_object('entry2').get_text()
RSOLV = self.builder.get_object('entry3').get_text()
parameters['mopac_SOLV'] = True
parameters['mopac_ESP'] = ESP
parameters['mopac_RSOLV'] = RSOLV
else:
parameters['mopac_SOLV'] = False
parameters['mopac_ESP'] = None
parameters['mopac_RSOLV'] = None
if self.builder.get_object('checkbutton2').get_active() == True:
MOZYME = True
parameters['mopac_MOZYME'] = MOZYME
else:
MOZYME = False
parameters['mopac_MOZYME'] = MOZYME
if self.builder.get_object('checkbutton3').get_active() == True:
QMMM = True
parameters['mopac_QMMM'] = QMMM
else:
QMMM = False
parameters['mopac_QMMM'] = QMMM
#-----------------------------------------------------------------------------------------------
trajectory_type = self.builder.get_object(
'combobox2').get_active_text()
# SCAN
# SCAN-2D
parameters['trajectory_type'] = trajectory_type
#---------------------------------------------------------------------------#
system = self.project.system #
parameters['system'] = system #
trajectory = self.builder.get_object(
'filechooserbutton1').get_filename() #
parameters['trajectory'] = trajectory #
#
methods = self.builder.get_object('entry1').get_text() #
methods = methods.split() #
parameters['methods'] = methods #
system.Summary() #
#---------------------------------------------------------------------------#
print charge, multiplicity, methods #, trajectory
if trajectory_type == 'SCAN':
self.run_MOPAC_SCAN_refine(parameters=parameters)
if trajectory_type == 'SCAN-2D':
self.run_MOPAC_SCAN2D_refine(parameters=parameters)
def run_MOPAC_SCAN_refine(self, parameters=None):
""" Function doc """
'''
parameters['methods']
parameters['trajectory']
parameters['charge' ]
parameters['multiplicity']
parameters['mopac_AUX' ]
parameters['mopac_1SCF' ]
parameters['mopac_MOZYME']
parameters['mopac_BONDS' ]
parameters['mopac_PDBOUT']
parameters['mopac_SOLV' ]
parameters['mopac_ESP' ]
parameters['mopac_RSOLV' ]
parameters['mopac_QMMM' ]
parameters['tmpfile_outpath']
parameters['logfile_outpath']
parameters['log_file_name']
'''
logs = {}
for method in parameters['methods']:
logs[method] = {
'energy': [],
'energyNorm': [],
}
trajectory = SystemGeometryTrajectory(parameters['trajectory'],
parameters['system'],
mode="r")
n = 0
while trajectory.RestoreOwnerData():
MOPAC_system = pDynamoToMOPAC(system=parameters['system'])
keywords = MOPAC_system.DefineMopacKeys(
methods=method,
charge=parameters['charge'],
multiplicity=parameters['multiplicity'],
AUX=parameters['mopac_AUX'],
single_point=parameters['mopac_1SCF'],
MOZYME=parameters['mopac_MOZYME'],
BONDS=parameters[
'mopac_BONDS'], # False
PDBOUT=parameters[
'mopac_PDBOUT'], # False
SOLV=parameters['mopac_SOLV'],
ESP=parameters['mopac_ESP'],
RSOLV=parameters['mopac_RSOLV'],
QMMM=parameters['mopac_QMMM'])
energy = MOPAC_system.Energy(
fileout=os.path.join(parameters['tmpfile_outpath'],
'system' + str(n) + '.mop'),
mopac_path=parameters['mopac_path'],
overwrite_files=parameters['overwrite_files'])
logs[method]['energy'].append(float(energy))
logs[method]['energyNorm'].append(
float(energy) - logs[method]['energy'][0])
n += 1
#-------------------------------------------------------#
# LOG FILE SUMMARY #
#-------------------------------------------------------#
header = '----------------------------- EasyHybrid - MOPAC Energy Refine ---------------------------------'
#header += "\nMETHOD =%20s " % (parameters['actual_method'] )
header += "\nTOTAL CHARGE =%20s " % (str(
parameters['charge']))
header += "\nMULTIPLICITYE =%20s " % (str(
parameters['multiplicity']))
if parameters['mopac_MOZYME']:
header += "\nMOZYME =%20s " % ("True")
else:
header += "\nMOZYME =%20s " % ("False")
if parameters['mopac_SOLV']:
header += "\nSOLV =%20s " % ('True') #
header += "\nmopac_ESP =%20s " % (str(
parameters['mopac_ESP']))
header += "\nmopac_RSOLV =%20s " % (str(
parameters['mopac_RSOLV']))
else:
header += "\nSOLV =%20s " % ('False') #
header += "\n------------------------------------------------------------------------------------------------"
header += "\nTRAJECTORY =%20s " % (
parameters['trajectory'])
#header += "\nORIGINAL LOG =%20s " % ("True")
header += "\n------------------------------------------------------------------------------------------------"
#trajetoryFile = parameters['trajectory']
string = header
#string += 'trajectoy: ' + trajetoryFile + '\n'
#string += 'keywords: ' + keywords + '\n'
string += '\n'
for method in logs:
string += " %15s " % (method)
string += '\n'
for i in range(0, n): #len(logs['AM1']['energyNorm'])):
for method in logs:
string += " %15.5f " % (logs[method]['energyNorm'][i])
string += '\n'
print string
arq = open(
os.path.join(parameters['logfile_outpath'],
parameters['log_file_name']), 'w')
arq.writelines(string)
arq.close()
def run_MOPAC_SCAN2D_refine(self, parameters):
""" Function doc """
#--------------------------------------------------------------#
pass #
trajectory_files = os.listdir(parameters['trajectory']) #
trajectory_files2 = [] #
#--------------------------------------------------------------#
for File in trajectory_files: #
File2 = File.split('.') #
#
if File2[-1] == 'pkl': #
trajectory_files2.append(File) #
#--------------------------------------------------------------#
for method in parameters['methods']:
i_table = []
j_table = []
n = 1
energy_table = {(0, 0): 0.0}
print method
#--------------------------------------------------------------------------------------------------------------------------------#
for File in trajectory_files2: #
File2 = File.split('.') #
File2 = File2[0].split('_') #
i = int(File2[1]) #
j = int(File2[2]) #
#
system = parameters['system'] #
system.coordinates3 = Unpickle(
os.path.join(parameters['trajectory'], File)) #
MOPAC_system = pDynamoToMOPAC(system=system) #
#
keywords = MOPAC_system.DefineMopacKeys(
methods=method, #
charge=parameters['charge'], #
multiplicity=parameters['multiplicity'], #
AUX=parameters['mopac_AUX'], #
single_point=parameters['mopac_1SCF'], #
MOZYME=parameters['mopac_MOZYME'], #
BONDS=parameters[
'mopac_BONDS'], # False #
PDBOUT=parameters[
'mopac_PDBOUT'], # False #
SOLV=parameters['mopac_SOLV'], #
ESP=parameters['mopac_ESP'], #
RSOLV=parameters['mopac_RSOLV'], #
QMMM=parameters['mopac_QMMM']) #
#
#
energy = MOPAC_system.Energy(
fileout=os.path.join(
parameters['tmpfile_outpath'],
'system_' + method + '_' + str(i) + '_' + str(j) +
'.mop',
),
mopac_path=parameters['mopac_path'],
overwrite_files=parameters['overwrite_files']) #
energy_table[(i, j)] = float(energy) #
i_table.append(i) #
j_table.append(j) #
print n, i, j, energy #
n = n + 1 #
#--------------------------------------------------------------------------------------------------------------------------------#
#---------------------------------------------------------#
import numpy as np #
i_table = np.array(i_table)
j_table = np.array(j_table)
i_max = i_table.max()
j_max = j_table.max()
X = 0 * np.random.rand(i_max + 1, j_max + 1)
#---------------------------------------------------------#
#print X
text = ''
for i in range(0, i_max + 1):
text = text + "\nMATRIX1 "
for j in range(0, j_max + 1):
X[i][j] = energy_table[(i, j)]
#text = text + "%18.8f " % (X[i][j])
X_norm = X - np.min(X)
parameters['energy_matrix'] = X
parameters['energy_matrix_norm'] = X_norm
parameters['actual_method'] = method
parameters['matrix_i'] = i_max
parameters['matrix_j'] = j_max
self.build_SCAN2D_log(parameters)
def build_SCAN2D_log(self, parameters):
""" Function doc """
header = '----------------------------- EasyHybrid - MOPAC Energy Refine ---------------------------------'
header += "\nMETHOD =%20s " % (
parameters['actual_method'])
header += "\nTOTAL CHARGE =%20s " % (str(
parameters['charge']))
header += "\nMULTIPLICITYE =%20s " % (str(
parameters['multiplicity']))
if parameters['mopac_MOZYME']:
header += "\nMOZYME =%20s " % ("True")
else:
header += "\nMOZYME =%20s " % ("False")
if parameters['mopac_SOLV']:
header += "\nSOLV =%20s " % ('True') #
header += "\nmopac_ESP =%20s " % (str(
parameters['mopac_ESP']))
header += "\nmopac_RSOLV =%20s " % (str(
parameters['mopac_RSOLV']))
else:
header += "\nSOLV =%20s " % ('False') #
header += "\n------------------------------------------------------------------------------------------------"
header += "\nRCOORD1 size =%20s " % (str(
parameters['matrix_i']))
header += "\nRCOORD2 size =%20s " % (str(
parameters['matrix_j']))
if parameters['original_scan_log']:
header += "\nRCOORD1 =%20s " % (
parameters['original_scan_log'][1]['xlabel'])
header += "\nRCOORD2 =%20s " % (
parameters['original_scan_log'][1]['ylabel'])
header += "\nTRAJECTORY =%20s " % (
parameters['trajectory'])
#header += "\nORIGINAL LOG =%20s " % ("True")
header += "\n------------------------------------------------------------------------------------------------"
text_matrix1 = '\n\n'
for i in range(0, parameters['matrix_i'] + 1):
text_matrix1 += "\nMATRIX1 "
for j in range(0, parameters['matrix_j'] + 1):
text_matrix1 += "%18.8f " % (
parameters['energy_matrix'][i][j])
text_matrix1 += '\n\n'
for i in range(0, parameters['matrix_i'] + 1):
text_matrix1 += "\nMATRIX2 "
for j in range(0, parameters['matrix_j'] + 1):
text_matrix1 += "%18.8f " % (
parameters['energy_matrix_norm'][i][j])
#print parameters['original_scan_log']
#print parameters['original_scan_log'][1]
#print parameters['original_scan_log'][1]['R1' ]
if parameters['original_scan_log']:
print parameters['original_scan_log'][1]['R1']
#parameters['original_scan_log']
if parameters['original_scan_log']:
R1 = parameters['original_scan_log'][1]['R1']
R2 = parameters['original_scan_log'][1]['R2']
try:
text_matrix1 += '\n\n'
for i in range(0, parameters['matrix_i'] + 1):
text_matrix1 += "\nRCOORD1 "
for j in range(0, parameters['matrix_j'] + 1):
print i, j
text_matrix1 += "%18.8f " % (R1[i][j])
text_matrix1 += '\n\n'
for i in range(0, parameters['matrix_i'] + 1):
text_matrix1 += "\nRCOORD2 "
for j in range(0, parameters['matrix_j'] + 1):
text_matrix1 += "%18.8f " % (R2[i][j])
except:
pass
#---------------------------------------------------------------------------------------------------------------
# Time and log file
#---------------------------------------------------------------------------------------------------------------
localtime = time.asctime(time.localtime(time.time()))
localtime = localtime.split()
# 0 1 2 3 4
#[Sun] [Sep] [28] [02:32:04] [2014]
log_file_name = "Scan2D_" + parameters[
'actual_method'] + '_' + localtime[1] + '_' + localtime[
2] + '_' + localtime[3] + '_' + localtime[4] + '.log' #
#--------------------------------------------------------------------------------------------------------------
arq = open(os.path.join(parameters['trajectory'], log_file_name), 'w')
arq.writelines(header)
arq.writelines(text_matrix1)
arq.close()
#---------------------------------------------------------------------------------------------------------------
def on_checkbutton_continue_an_incomplete_scan_toggled(self, button):
""" Function doc """
if self.builder.get_object('checkbutton4').get_active():
pass
#print 'and here'
#self.builder.get_object('entry2').set_sensitive(True)
#self.builder.get_object('entry3').set_sensitive(True)
else:
pass
#self.builder.get_object('entry2').set_sensitive(False)
#self.builder.get_object('entry3').set_sensitive(False)
def on_checkbutton1_toggled(self, button):
""" Function doc """
if self.builder.get_object('checkbutton1').get_active():
self.builder.get_object('entry2').set_sensitive(True)
self.builder.get_object('entry3').set_sensitive(True)
else:
self.builder.get_object('entry2').set_sensitive(False)
self.builder.get_object('entry3').set_sensitive(False)
def on_combobox1_changed(self, button):
_type = self.builder.get_object('combobox1').get_active_text()
""" Function doc """
if _type == 'folder - pDynamo':
self.builder.get_object('filechooserbutton2').hide()
self.builder.get_object('filechooserbutton1').show()
else:
self.builder.get_object('filechooserbutton2').show()
self.builder.get_object('filechooserbutton1').hide()
def __init__(self, EasyHybridSession=None):
self.builder = gtk.Builder()
if EasyHybridSession != None:
self.project = EasyHybridSession.project
self.main_builder = EasyHybridSession.builder
self.window_control = EasyHybridSession.window_control
self.EasyHybridSession = EasyHybridSession
self.EasyHybrid_ROOT = EasyHybridSession.EasyHybrid_ROOT
self.EasyHybrid_GUI = EasyHybridSession.EasyHybrid_GUI
# - - - importing ORCA PATH from EasyHybridConfig file. - - -
#-----------------------------------------------------------------------#
try: #
ORCA = EasyHybridSession.EasyHybridConfig['ORCAPATH'] #
except: #
ORCA = '' #
#-----------------------------------------------------------------------#
self.builder.add_from_file(
os.path.join(self.EasyHybrid_GUI, 'MOPACEnergy',
'MOPACEnergy.glade'))
self.builder.connect_signals(self)
self.dialog = self.builder.get_object('dialog1')
self.window_control = WindowControl(self.builder)
# QC SPIN CHARGE
spinbutton = 'spinbutton_charge'
config = [0.0, -500.0, 500.0, 1.0, 0.0, 0.0]
self.window_control.SETUP_SPINBUTTON(spinbutton, config)
# QC SPIN MULTIPLICITY
spinbutton = 'spinbutton_multiplicity'
config = [0.0, 1.0, 500.0, 1.0, 0.0, 0.0]
self.window_control.SETUP_SPINBUTTON(spinbutton, config)
self.builder.get_object('filechooserbutton2').hide()
#----------------- Setup ComboBoxes ----------------------------------------------#
combobox = 'combobox1' # #
combolist = ["folder - pDynamo"
] #, "trj - AMBER", "dcd - CHARMM", 'xtc - GROMACS']#
self.window_control.SETUP_COMBOBOXES(combobox, combolist, 0) #
combobox = 'combobox2' # #
combolist = ["SCAN", 'SCAN-2D'
] #, "trj - AMBER", "dcd - CHARMM", 'xtc - GROMACS']#
#---------------------------------------------------------------------------------#
self.window_control.SETUP_COMBOBOXES(combobox, combolist, 0)
# Hide unfinished widgets
self.builder.get_object('checkbutton3').set_sensitive(False)
