本文整理匯總了Python中ParmedTools.ParmedActions.timerge方法的典型用法代碼示例。如果您正苦於以下問題：Python ParmedActions.timerge方法的具體用法？Python ParmedActions.timerge怎麽用？Python ParmedActions.timerge使用的例子？那麽, 這裏精選的方法代碼示例或許可以為您提供幫助。您也可以進一步了解該方法所在類ParmedTools.ParmedActions的用法示例。
在下文中一共展示了ParmedActions.timerge方法的1個代碼示例，這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚，您的評價將有助於係統推薦出更棒的Python代碼示例。
示例1: timerge
# 需要導入模塊: from ParmedTools import ParmedActions [as 別名]
# 或者: from ParmedTools.ParmedActions import timerge [as 別名]
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 not hasattr(amber_prmtop, 'coords'):
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 two 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')
try:
action = ParmedActions.timerge(amber_prmtop, ArgumentList(var_list))
messages.write('%s\n' % action)
action.execute()
except Exception, err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return