def scale(root, amber_prmtop, messages):
""" Allows us to scale every value in a particular prmtop section """
# The spinbox is sent with the Spinbox, label, and then a list of all of the
# values to give to it
changeable_properties = ['Spinbox', 'Property to scale']
for flag in amber_prmtop.parm.flag_list:
if amber_prmtop.parm.formats[flag].type is float:
changeable_properties.append(flag)
widget_list = [changeable_properties, ('Entry', 'Value to scale by')]
# We need 2 string variables, then get the description
var_list = [StringVar(), StringVar()]
description = 'Scales all values in a given prmtop section by a given value'
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('scale', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# See if we got any variables back
vars_found = var_list[0].get() or var_list[1].get()
if not vars_found: return
# If we did, store them and pass it to the class
var_list = [v.get() for v in var_list]
try:
action = actions.scale(amber_prmtop, ArgumentList(var_list))
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
action.execute()
messages.write('%s\n' % action)
def changeljsingletype(root, amber_prmtop, messages):
""" Changes radius/well depth of a single LJ type given by the mask """
# We need a mask, radius, and well depth
widget_list = [('MaskEntry', 'Mask to change LJ Type'),
('Entry', 'New LJ Radius'), ('Entry', 'New LJ Depth')]
var_list = [StringVar(), StringVar(), StringVar()]
description = "Change a given atom type's LJ radius and well depth"
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('changeLJSingleType', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# See if we got any variables back
vars_found = True in [bool(v.get()) for v in var_list]
if not vars_found: return
# addljtype expects any _non_specified variables to be None
var_list = [v.get() for v in var_list]
for i, v in enumerate(var_list):
if not v: var_list[i] = None
# If we did, store them and pass it to the class
try:
action = actions.changeLJSingleType(amber_prmtop,
ArgumentList(var_list))
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
messages.write('%s\n' % action)
action.execute()
def excepthook(exception_type, exception_value, tb):
""" Default exception handler """
import traceback
if debug: traceback.print_tb(tb)
showerror('Fatal Error','%s: %s' % (exception_type.__name__,
exception_value))
sys.exit(1)
def excepthook(exception_type, exception_value, tb):
""" Default exception handler """
import traceback
if debug: traceback.print_tb(tb)
showerror('Fatal Error',
'%s: %s' % (exception_type.__name__, exception_value))
sys.exit(1)
def strip(root, amber_prmtop, messages):
""" Strips a mask from the topology file """
# We need a mask, new radius, new epsilon, and for chamber topologies,
# a new radius-1-4 and epsilon-1-4. Don't add the latter ones until we
# know if we have a chamber prmtop or not.
widget_list = [('MaskEntry', 'Atoms to strip from topology')]
# We need 5 string variables, then get the description.
var_list = [StringVar()]
description=('Strips the selected atoms from the topology file. All\n'
'remaining atoms and parameters remain unchanged. Any\n'
'parameters associated with stripped atoms are removed.')
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('strip', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# See if we got any variables back
var = var_list[0]
if not var.get(): return
try:
action = actions.strip(amber_prmtop, ArgumentList(var.get()))
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
messages.write('%s\n' % action)
action.execute()
def printinfo(root, amber_prmtop, messages):
""" Prints all of the info in a given FLAG """
# Set up the window
# variables we need for printInfo
widget_list = [('Entry', '%FLAG you want info from')]
# Variable list -- we need a single string
var_list = [StringVar()]
# description
description = ' '.join(actions.printInfo.__doc__.split())
cmd_window = _guiwidgets.ActionWindow('printInfo', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# Make sure we didn't cancel (or just press OK with no input), or just leave
var = var_list[0].get()
if not var: return
# Now that we did something, do it
action = actions.printInfo(amber_prmtop, ArgumentList(var))
if not action.found:
showerror('Not Found!', '%%FLAG %s not found!' % var.upper())
return
window = Toplevel(root)
window.resizable(True, True)
window.title('%%FLAG %s Info in %s' % (var.upper(), amber_prmtop))
text = _guiwidgets.ExitingScrollText(window, None, spacing3=5, padx=5,
pady=5, width=82, height=20)
text.write(action)
text.pack(fill=BOTH, expand=1)
window.wait_window()
messages.write('Wrote info for flag %s\n' % var.upper())
def change(root, amber_prmtop, messages):
""" Allows us to change a specific atomic property """
# The spinbox is sent with the Spinbox, label, and then a list of all of the
# values to give to it
widget_list = [('Spinbox', 'Property to change', 'CHARGE', 'MASS',
'RADII', 'SCREEN', 'ATOM_NAME', 'AMBER_ATOM_TYPE',
'ATOM_TYPE_INDEX', 'ATOMIC_NUMBER'),
('MaskEntry', 'Atoms to change'),
('Entry', 'New Value for Property')]
# We need 3 string variables, then get the description
var_list = [StringVar(), StringVar(), StringVar()]
description = 'Changes the property of given atoms to a new value'
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('change', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# See if we got any variables back
vars_found = True in [bool(v.get()) for v in var_list]
if not vars_found: return
# If we did, store them and pass it to the class
var_list = [v.get() for v in var_list]
try:
action = actions.change(amber_prmtop, ArgumentList(var_list))
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
action.execute()
messages.write('%s\n' % action)
def changelj14pair(root, amber_prmtop, messages):
""" Changes specific 1-4 Lennard Jones pairs """
# Only good for chamber topologies
if not amber_prmtop.parm.chamber:
showerror('Incompatible',
'changeLJ14Pair is only valid for chamber topologies!')
return
# variables we need for changelj14pair
widget_list = [('MaskEntry', 'Atom(s) Type 1 Mask'),
('MaskEntry', 'Atom(s) Type 2 Mask'),
('Entry', 'Combined Radius'),
('Entry', 'Combined Well Depth')]
# Variable list -- we need 2 masks and 2 floats
var_list = [StringVar(), StringVar(), StringVar(), StringVar()]
# description
description = ' '.join(actions.changeLJ14Pair.__doc__.split())
cmd_window = _guiwidgets.ActionWindow('changeLJ14Pair', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# Make sure we didn't cancel (or just press OK with no input), or just leave
vars_exist = True in [bool(v.get()) for v in var_list]
if not vars_exist: return
# Now that we did something, do it
var_list = [v.get() for v in var_list]
try:
action=actions.changeLJ14Pair(amber_prmtop,ArgumentList(var_list))
messages.write('%s\n' % action)
action.execute()
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
def addexclusions(root, amber_prmtop, messages):
""" Adds atoms to other atoms' exclusion list """
# We need 2 masks
widget_list = [('MaskEntry', 'Atoms to add excluded atoms to'),
('MaskEntry', 'Atoms to exclude from other mask')]
# We have 2 mask variables
var_list = [StringVar(), StringVar()]
# Description
description = ('Allows you to add arbitrary excluded atoms to exclusion\n'
'lists. This omits all non-bonded interactions in the '
'direct-space\ncalculation, but does not omit interactions '
'from adjacent cells in\nperiodic simulations')
cmd_window = _guiwidgets.ActionWindow('addExclusions', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# Bail out if we didn't get any variables
if not True in [bool(v.get()) for v in var_list]: return
var_list = [v.get() for v in var_list]
try:
act = actions.addExclusions(amber_prmtop, ArgumentList(var_list))
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
act.execute()
messages.write('%s\n' % act)
def addpdb(root, amber_prmtop, messages):
""" Adds PDB information to a topology file """
# Get the name of the file
type_list = [('PDB', '*.pdb'), ('All Files', '*')]
fname = file_chooser('PDB File', type_list)
if not fname: return
widget_list = [('Checkbutton', 'Require all residue names be consistent.'),
('Checkbutton', 'Print element names in %FLAG ELEMENT'),
('Checkbutton', 'Print all insertion codes, even if all are '
'blank.')]
var_list = [StringVar(value='no') for i in range(3)]
description = ('Adds information from the PDB file (e.g., CHAIN IDs) to '
'the topology file')
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('addPDB', amber_prmtop, widget_list,
var_list, description)
cmd_window.wait_window()
# See if we got any variables back
vars_found = True in [bool(v.get()) for v in var_list]
if not vars_found: return
newvars = [fname]
# If we did, pass them through
if var_list[0] == 'yes': newvars.append('strict')
if var_list[1] == 'yes': newvars.append('elem')
if var_list[1] == 'yes': newvars.append('allicodes')
try:
action = actions.addPDB(amber_prmtop, ArgumentList(newvars))
messages.write('%s\n' % action)
action.execute()
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
def changeljpair(root, amber_prmtop, messages):
""" Changes a pair-wise LJ interaction for pre-combined epsilon/Rmin """
# The variables we need for changeljpair
widget_list = [('MaskEntry', 'Atom(s) Type 1 Mask'),
('MaskEntry', 'Atom(s) Type 2 Mask'),
('Entry', 'Combined Radius'),
('Entry', 'Combined Well Depth')]
# Variable list -- we need 2 masks and 2 floats
var_list = [StringVar(), StringVar(), StringVar(), StringVar()]
# description
description = ' '.join(actions.changeLJPair.__doc__.split())
cmd_window = _guiwidgets.ActionWindow('changeLJPair', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# Make sure we didn't cancel (or just press OK with no input), or just leave
vars_exist = True in [bool(v.get()) for v in var_list]
if not vars_exist: return
# Now that we did something, do it
var_list = [v.get() for v in var_list]
try:
action = actions.changeLJPair(amber_prmtop,ArgumentList(var_list))
messages.write('%s\n' % action)
action.execute()
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
def setangle(root, amber_prmtop, messages):
""" Sets (adds or changes) an angle in the topology file """
# We need 3 masks, a force constant, and an equilibrium angle
widget_list = [('MaskEntry', 'First atom in angle'),
('MaskEntry', 'Second (middle) atom in angle'),
('MaskEntry', 'Third atom in angle'),
('Entry', 'Force constant (kcal/mol rad**2)'),
('Entry', 'Equilibrium Angle (Degrees)')]
# We need 5 variables
var_list = [StringVar(), StringVar(), StringVar(), StringVar(), StringVar()]
description = ('Sets an angle in the topology file with the given Force '
'constant in kcal/mol/rad**2\nand the given equilibrium '
'angle in Degrees. All three masks must specify only a\n'
'single atom. If the angle exists, it will be replaced. If '
'it doesn\'t, it will be added.')
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('setAngle', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# See if we got any variables back
vars_found = True in [bool(v.get()) for v in var_list]
if not vars_found: return
# If we did, pass them through
var_list = [v.get() for v in var_list]
try:
action = actions.setAngle(amber_prmtop, ArgumentList(var_list))
messages.write('%s\n' % action)
action.execute()
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
def deletedihedral(root, amber_prmtop, messages):
""" Deletes a dihedral between 4 given atoms """
# We need 4 masks
widget_list = [('MaskEntry', 'First (end) atom in dihedral'),
('MaskEntry', 'Second (middle) atom in dihedral'),
('MaskEntry', 'Third (middle) atom in dihedral'),
('MaskEntry', 'Fourth (end) atom in dihedral')]
# We need 4 variables
var_list = [StringVar() for i in range(4)]
description = ('Deletes dihedrals between the atoms specified in mask1, ' +
'mask2, mask3, and mask4.\nIt will try to match dihedrals ' +
'only in the order given or reverse order. Dihedrals are\n' +
'specified by atom N in mask1, mask2, mask3, and mask4,' +
'where N is the selected\natom in that mask.')
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('deleteDihedral', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# See if we got any variables back
vars_found = True in [bool(v.get()) for v in var_list]
if not vars_found: return
# If we did, pass them through
var_list = [v.get() for v in var_list]
try:
action = actions.deleteDihedral(amber_prmtop,
ArgumentList(var_list))
messages.write('%s\n' % action)
action.execute()
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
def printdihedrals(root, amber_prmtop, messages):
""" Prints dihedrals containing atoms from a given mask """
widget_list = [('MaskEntry', 'Atoms 1 or Atoms to analyze for dihedrals'),
('MaskEntry', 'Atoms 2 (optional)'),
('MaskEntry', 'Atoms 3 (optional)'),
('MaskEntry', 'Atoms 4 (optional)')]
var_list = [StringVar(), StringVar(), StringVar(), StringVar()]
desc = 'Prints all dihedrals containing at least 1 atom in the given mask'
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('printDihedrals', amber_prmtop,
widget_list, var_list, desc)
cmd_window.wait_window()
# See if we got any variables back
var = ' '.join([x.get() for x in var_list]).strip()
if not var: return
try:
action = actions.printDihedrals(amber_prmtop, ArgumentList(var))
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
messages.write('Printed DIHEDRALs for %s\n' % var)
# Now make the text window
window = Toplevel(root)
window.resizable(True, True)
window.title('DIHEDRAL list in %s' % amber_prmtop.parm)
text = _guiwidgets.ExitingScrollText(window, None, spacing3=5, padx=5,
pady=5, width=140, height=20)
text.pack(fill=BOTH, expand=1)
text.write(action)
window.wait_window()
def printljtypes(root, amber_prmtop, messages):
"""
Prints all of the atoms that have the same LJ type as atoms in a given mask
"""
# We need a mask
widget_list = [('MaskEntry', 'Atom Mask or Atom Type Name')]
var_list = [StringVar()]
description = ('Get a list of all atoms that share a common LJ type')
cmd_window = _guiwidgets.ActionWindow('printLJTypes', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
var = var_list[0].get()
# Bail out if we didn't get any variables
if not var: return
# Instantiate our action
try:
action = actions.printLJTypes(amber_prmtop, ArgumentList(var))
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
# Create our Info window
window = Toplevel(root)
window.resizable(True, True)
window.title('LJ Type List')
text = _guiwidgets.ExitingScrollText(window, None, spacing3=2, padx=5,
pady=5, width=45, height=30)
text.pack(fill=BOTH, expand=1)
text.write(action)
messages.write('Printed LJ types for [%s]\n' % var)
window.wait_window()
def printljmatrix(root, amber_prmtop, messages):
""" Prints A/B matrix coefficients """
# We need 1 mask
widget_list = [('MaskEntry', 'Atoms To Find LJ Interactions')]
# We need 1 variable
var_list = [StringVar()]
description = ('Prints all A- and B-Coefficient elements between the atom '
'types specified in <mask> with every other atom type')
# Create the window, open it, and wait for it to close
cmd_window = _guiwidgets.ActionWindow('printLJMatrix', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# Bail out if we cancelled or something
var = var_list[0].get()
if not var: return
try:
action = actions.printLJMatrix(amber_prmtop, ArgumentList(var))
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
# Create our Info window
window = Toplevel(root)
window.resizable(True, True)
window.title('LJ Type List')
text = _guiwidgets.ExitingScrollText(window, None, spacing3=2, padx=5,
pady=5, width=45, height=30)
text.pack(fill=BOTH, expand=1)
text.write(action)
messages.write('Printed LJ matrix for types [%s]\n' % var)
window.wait_window()
def gui_action_dispatcher(root, amber_prmtop, action_name, messages):
"""
Dispatches all of the GUI actions given the action name. This is the only
externally accessible *thing* in this module. All of the action-specific
methods are in _guiactions with the same name as those found in
parmed.tools.actions
"""
if not hasattr(_guiactions, action_name.lower()):
showerror("Not Implemented.", action_name + " is not implemented in xParmEd! Use parmed instead.")
return None
# Call the function to establish our action
getattr(_guiactions, action_name.lower())(root, amber_prmtop, messages)
def gui_action_dispatcher(root, amber_prmtop, action_name, messages):
"""
Dispatches all of the GUI actions given the action name. This is the only
externally accessible *thing* in this module. All of the action-specific
methods are in _guiactions with the same name as those found in
parmed.tools.actions
"""
if not hasattr(_guiactions, action_name.lower()):
showerror('Not Implemented.', action_name +
' is not implemented in xParmEd! Use parmed instead.')
return None
# Call the function to establish our action
getattr(_guiactions, action_name.lower())(root, amber_prmtop, messages)
def add12_6_4(root, amber_prmtop, messages):
"""
Adds 12-6-4 potential energy terms
"""
# The variables we need for changeljpair
widget_list = [('MaskEntry', 'Divalent ion mask'),
('FileSelector', 'C4 Parameter File'),
('Entry', 'Water model (instead of C4 Params)'),
('FileSelector', 'Pol. Param File'),
('Entry', 'tunfactor')]
# Variable list -- we need 2 masks and 2 floats
var_list = [StringVar(), StringVar(), StringVar(), StringVar(), StringVar()]
var_list[1].set('Pick C4 File')
var_list[3].set('Pick Pol. File')
# description
description = ('Add the r^-4 Lennard-Jones parameter for the 12-6-4 term\n'
'used typically for multi-valent ion parameters')
cmd_window = _guiwidgets.ActionWindow('add12_6_4', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# Make sure we didn't cancel (or just press OK with no input), or just leave
vars_exist = [bool(v.get()) for v in var_list]
if var_list[1].get() == 'Pick C4 File': vars_exist[1] = False
if var_list[3].get() == 'Pick Pol. File': vars_exist[3] = False
if vars_exist[1] and vars_exist[2]:
showerror('Cannot select both C4 parameter file AND water model')
return
vars_exist = True in vars_exist
if not vars_exist: return
# Now that we did something, do it
var_list = [v.get() for v in var_list]
if var_list[1] == 'Pick C4 File': var_list[1] = ''
if var_list[3] == 'Pick Pol. File': var_list[3] = ''
args = [var_list[0]]
if var_list[1]: args.extend(['c4file', var_list[1]])
if var_list[2]: args.extend(['watermodel', var_list[2]])
if var_list[3]: args.extend(['polfile', var_list[3]])
if var_list[4]: args.extend(['tunfactor', var_list[4]])
try:
action = actions.add12_6_4(amber_prmtop, ArgumentList(args))
messages.write('%s\n' % action)
action.execute()
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
def adddihedral(root, amber_prmtop, messages):
""" Adds a dihedral (improper, multiterm, or normal) to the prmtop """
# We need 4 masks, phi_k, periodicity, phase, scee/scnb, dihedral type
widget_list = [
('MaskEntry', 'First (end) atom in dihedral'),
('MaskEntry', 'Second (middle) atom in dihedral'),
('MaskEntry', 'Third (middle) atom in dihedral'),
('MaskEntry', 'Fourth (end) atom in dihedral'),
('Entry', 'Phi Force constant (kcal/mol)'),
('Entry', 'Periodicity'),
('Entry', 'Phase (Degrees)'),
('Entry', 'EEL scaling factor'),
('Entry', 'VDW scaling factor'),
('Spinbox', 'Dihedral type', 'normal', 'improper')
]
# We need 10 variables
var_list = [StringVar() for i in range(10)]
description = ('Adds a dihedral in the topology file with the given Phi '
'Force constant in kcal/mol the\ngiven phase in Degrees '
'and the given periodicity. All masks must specify only \n'
'a single atom. The default Amber values for SCEE/SCNB are '
'1.2 and 2.0, respectively.\nSee the Amber manual for '
'details about normal, multiterm, and improper dihedrals')
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('setDihedral', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# See if we got any variables back
vars_found = True in [bool(v.get()) for v in var_list]
if not vars_found: return
# If we did, pass them through
var_list = [v.get() for v in var_list]
# Fill scee/scnb in with default values
if var_list[7] is None: var_list[7] = '1.2'
if var_list[8] is None: var_list[8] = '2.0'
# The last argument is a keyword, so append that, then swap the last 2 args
var_list.insert(9, 'type')
try:
action = actions.addDihedral(amber_prmtop, ArgumentList(var_list))
messages.write('%s\n' % action)
action.execute()
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
def addcoarsegrain(root, amber_prmtop, messages):
""" Adds coarse graining to topology file via Lula's algo """
# This implementation doesn't exist anywhere yet, so disable it
showerror('Warning', 'This functionality is not implemented in Amber yet!')
return
# We need a file
fname = file_chooser('Coarse Grain Parameter',
[('Coarse Grain Parameters', '*.cgparm'),
('All Files', '*')]
)
if not fname: return
try:
action = actions.addCoarseGrain(amber_prmtop, ArgumentList(fname))
messages.write('%s\n' % action)
action.execute()
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
def addljtype(root, amber_prmtop, messages):
""" Turns given mask into a new LJ atom type """
# We need a mask, new radius, new epsilon, and for chamber topologies,
# a new radius-1-4 and epsilon-1-4. Don't add the latter ones until we
# know if we have a chamber prmtop or not.
widget_list = [('MaskEntry', 'Atoms to make new LJ Type'),
('Entry', 'New Radius (default old radius)'),
('Entry', 'New Depth (default old depth)')]
# We need 5 string variables, then get the description.
var_list = [StringVar(), StringVar(), StringVar(), StringVar(), StringVar()]
description=('Turns given mask into a new LJ atom type. Uses the radius\n'
'and well depth from the first atom type in <mask> if none\n'
'are provided.')
if amber_prmtop.parm.chamber:
widget_list += [('Entry', 'New Radius for 1-4 Terms'),
('Entry', 'New Depth for 1-4 Terms')]
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('addLJType', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# See if we got any variables back
vars_found = True in [bool(v.get()) for v in var_list]
if not vars_found: return
# addljtype expects any _non_specified variables to be None
var_list = [v.get().strip() for v in var_list]
kw_var_list = [var_list[0]]
if var_list[1]: kw_var_list.extend(['radius', var_list[1]])
if var_list[2]: kw_var_list.extend(['epsilon', var_list[2]])
if amber_prmtop.parm.chamber and var_list[3]:
kw_var_list.extend(['radius_14', var_list[3]])
if amber_prmtop.parm.chamber and var_list[4]:
kw_var_list.extend(['epsilon_14', var_list[4]])
try:
action = actions.addLJType(amber_prmtop,ArgumentList(kw_var_list))
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
action.execute()
messages.write('%s\n' % action)
def scnb(root, amber_prmtop, messages):
# We need a value
widget_list = [('Entry', '1-4 van der Waals Scaling Factor')]
var_list = [StringVar()]
description = 'Adjust the scaling factor for 1-4 van der Waals interactions'
cmd_window = _guiwidgets.ActionWindow('scee', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
var = var_list[0].get()
# Bail out if we didn't get any variables
if not var: return
try:
action = actions.scnb(amber_prmtop, ArgumentList(var))
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
messages.write('%s\n' % action)
action.execute()
def definesolvent(root, amber_prmtop, messages):
""" Allows you to define what you consider to be solvent molecules """
# We need a molecule #
widget_list = [('Entry', 'List of solvent residue names')]
var_list = [StringVar()]
description =('Tell ParmEd that these residue names should be considered\n'
'to be solvent residues. This should be a comma-delimited '
'list')
cmd_window = _guiwidgets.ActionWindow('defineSolvent', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# See if we got any variables back
var = var_list[0].get()
if not var: return
# addljtype expects any _non_specified variables to be None
try:
action = actions.defineSolvent(amber_prmtop, ArgumentList(var))
messages.write('%s\n' % action)
action.execute()
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
def timerge(root, amber_prmtop, messages):
""" Merges a topology file with 2 molecules into a single prmtop for TI """
# We need coordinates, so check for that
if amber_prmtop.parm.coords is None:
showerror(root, 'tiMerge requires you to load coordinates first!')
return
# We need 2 masks, a force constant, and an equilibrium distance
widget_list = [('MaskEntry', 'Mask Unique to Lambda = 0'),
('MaskEntry', 'Mask Unique to Lambda = 1'),
('MaskEntry', 'Softcore Mask in Lambda = 0'),
('MaskEntry', 'Softcore Mask in Lambda = 1'),
('MaskEntry', 'Softcore Mols NOT to Merge (Lambda=0)'),
('MaskEntry', 'Softcore Mols NOT to Merge (Lambda=1)'),
('Entry', 'Tolerance')]
# We need 4 variables
var_list = [StringVar() for i in range(7)]
var_list[6].set('0.0001')
description = 'Merges 2 molecules inside a prmtop for use with softcore TI'
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('tiMerge', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# See if we got any variables back
vars_found = True in [bool(v.get()) for v in var_list]
if not vars_found: return
# If we did, pass them through
var_list = [v.get() for v in var_list]
if not var_list[6].strip():
var_list[6] = '0.0001'
var_list.insert(6, 'tol')
actions.tiMerge.output = messages
try:
action = actions.tiMerge(amber_prmtop, ArgumentList(var_list))
messages.write('%s\n' % action)
action.execute()
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
def changeprotstate(root, amber_prmtop, messages):
# We need a mask and a state
widget_list = [('MaskEntry', 'Residue to change protonation state'),
('Entry', 'Protonation state to change to')]
var_list = [StringVar(), StringVar()]
description=('Changes the protonation state of a titratable residue that\n'
'can be treated with constant pH MD in Amber.')
cmd_window = _guiwidgets.ActionWindow('changeProtState', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# Bail out if we didn't get any variables
if not True in [bool(v.get()) for v in var_list]: return
var_list = [v.get() for v in var_list]
try:
action = actions.changeProtState(amber_prmtop,
ArgumentList(var_list))
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
action.execute()
messages.write('%s\n' % action)
def hmassrepartition(root, amber_prmtop, messages):
"""
Repartitions mass by making H-atoms heavier and attached heteroatoms
lighter by the same amount to preserve the same total mass
"""
# The spinbox is sent with the Spinbox, label, and then a list of all of the
# values to give to it
widget_list = [('Entry', 'New hydrogen mass (daltons)'),
('Checkbutton', 'Repartition waters?')]
# We need 2 string variables, then get the description
var_list = [StringVar(value='3.024'), StringVar(value='no')]
description = ('Repartitions atomic masses to keep total mass the same '
'while increasing H-atom masses to allow using a larger '
'time step.')
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('HMassChange', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# See if we got any variables back
vars_found = var_list[0].get() or var_list[1].get()
if not vars_found: return
# If we did, store them and pass it to the class
var_list = [v.get() for v in var_list]
# Convert the check button into the correct keyword
if var_list[1] == 'yes':
var_list[1] = 'dowater'
else:
var_list[1] = ''
try:
action = actions.HMassRepartition(amber_prmtop,
ArgumentList(var_list))
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
action.execute()
messages.write('%s\n' % action)
def __init__(self, title, amber_prmtop, widget_list, var_list, description):
self.cancelled = False
self.var_list = var_list
# widget_list: list of tuples having widget class names and description
# title: title of the window (action name)
# var_list: list of variables that go in each widget
# description: Description to print out on the window
BaseParmedWindow.__init__(self, amber_prmtop, title)
# Add description label
main_desc = Label(self, text=description, justify=CENTER,
pady=5, padx=10)
main_desc.grid(column=0, row=0, sticky=N+S+E+W)
# Make a frame to put all of our widgets in
main_frame = Frame(self, padx=10, pady=5)
# Now add all of our widgets to our
for i, wtemp in enumerate(widget_list):
wname, wdesc = wtemp[0], wtemp[1]
var = var_list[i]
local_frame = Frame(main_frame)
if wname == 'MaskEntry':
mywidget = MaskEntry(local_frame, self.amber_prmtop,
wdesc, var, self)
mywidget.grid(row=0, column=0, sticky=N+S+E+W)
elif wname == 'Entry':
wlab = Label(local_frame, text=wdesc)
wlab.grid(row=0, column=0, sticky=N+S+E+W)
mywidget = Entry(local_frame, width=40, textvariable=var)
mywidget.grid(row=1, column=0, sticky=N+S+E+W)
elif wname == 'Spinbox':
wlab = Label(local_frame, text=wdesc)
wlab.grid(row=0, column=0, sticky=N+S+E+W)
mywidget = Spinbox(local_frame, textvariable=var,
values=wtemp[2:])
mywidget.grid(row=1, column=0, sticky=N+S+E+W)
elif wname == 'Checkbutton':
mywidget = Checkbutton(local_frame, text=wdesc, variable=var,
onvalue='yes', offvalue='no')
mywidget.grid(row=0, column=0, sticky=N+S+E+W)
elif wname == 'FileSelector':
def callback():
file_chooser('C4 Parameter File',
extensions=[('All files', '*')], set_var=var)
mywidget = Button(local_frame, textvariable=var,
command=callback)
wlab = Label(local_frame, text=wdesc)
wlab.grid(row=0, column=0, sticky=N+S+E+W)
mywidget.grid(row=1, column=0, sticky=N+S+E+W)
else:
showerror('Error!', '%s not implemented yet!' % wname)
self.destroy()
local_frame.grid(row=i//2, column=i%2, sticky=N+S+E+W)
# Now pack the main frame
main_frame.grid(column=0, row=1, sticky=N+S+E+W)
# Now make the OK and Cancel buttons
ok_can_frame = Frame(self, padx=10, pady=5)
ok_can_frame.grid(column=0, row=2)
button = Button(ok_can_frame, text='OK', command=self.destroy)
button.grid(row=0, column=0, sticky=N+S+E+W, padx=10)
button = Button(ok_can_frame, text='Cancel', command=self.cancel)
button.grid(row=0, column=1, sticky=N+S+E+W, padx=10)