本文整理汇总了Python中ParmedTools.ParmedActions.timerge方法的典型用法代码示例。如果您正苦于以下问题：Python ParmedActions.timerge方法的具体用法？Python ParmedActions.timerge怎么用？Python ParmedActions.timerge使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类ParmedTools.ParmedActions的用法示例。
在下文中一共展示了ParmedActions.timerge方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: timerge
# 需要导入模块: from ParmedTools import ParmedActions [as 别名]
# 或者: from ParmedTools.ParmedActions import timerge [as 别名]
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