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tma.py
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tma.py
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# TrajectoryMergeAssist v2.1
# A python based GUI tool that helps in merging two trajectories on Desmond MD
# Copyright (C) 2019 Avimanyu Bandyopadhyay
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import Tkinter
import tkFileDialog
import os
root = Tkinter.Tk()
root.withdraw()
class MergeMDs(Tkinter.Tk):
def __init__(self, parent):
Tkinter.Tk.__init__(self, parent)
self.parent = parent
self.initialize()
def initialize(self):
self.grid()
button = Tkinter.Button(self, text='Browse Desmond "-out.cms" file', command=self.AskDesmondInputFile)
button.grid(column=0, row=1)
button2 = Tkinter.Button(self, text='Choose Desmond Trajectory 1', command=self.AskDesmondTrajectory1)
button2.grid(column=0, row=2)
button3 = Tkinter.Button(self, text='Choose Desmond Trajectory 2', command=self.AskDesmondTrajectory2)
button3.grid(column=0, row=3)
button4 = Tkinter.Button(self, text='Merge Desmond Trajectories', command=self.MergeDesmondTrajectories)
button4.grid(column=0, row=4)
button5 = Tkinter.Button(self, text='Browse GROMACS Trajectory 1 ".xtc" file', command=self.AskGROMACSTrajectory1)
button5.grid(column=1, row=1)
button6 = Tkinter.Button(self, text='Browse GROMACS Trajectory 2 ".xtc" file', command=self.AskGROMACSTrajectory2)
button6.grid(column=1, row=2)
button7 = Tkinter.Button(self, text='Merge GROMACS Trajectories', command=self.MergeGROMACSTrajectories)
button7.grid(column=1, row=3)
self.grid_columnconfigure(0, weight=1)
self.resizable(False, False)
self.update()
self.geometry("490x120")
def AskDesmondInputFile(self):
global cms
cms = tkFileDialog.askopenfilename(parent=root, initialdir="pwd", title='Choose -out.cms file')
if len(cms) > 0:
print "%s selected" % cms
def AskDesmondTrajectory1(self):
global in1_trj
in1_trj = tkFileDialog.askdirectory(parent=root, initialdir="pwd", title='Please Select Desmond Trajectory 1')
if len(in1_trj) > 0:
print "You chose %s" % in1_trj
def AskDesmondTrajectory2(self):
global in2_trj
in2_trj = tkFileDialog.askdirectory(parent=root, initialdir="pwd", title='Please Select Desmond Trajectory 2')
if len(in2_trj) > 0:
print "You chose %s" % in2_trj
def MergeDesmondTrajectories(self):
if os.path.exists(os.path.expandvars("$SCHRODINGER")):
print "\t"
os.system("echo You are using Desmond MD via $SCHRODINGER")
print "\t"
else:
print "Desmond MD not installed or $SCHRODINGER path not set correctly. Exiting..."
exit()
print "-------------------------------------------------------------"
print "Merging both trajectories into one and generating -out.cms..."
print "-------------------------------------------------------------"
# For Desmond Version >= 2018.1 https://www.schrodinger.com/kb/282357
if os.path.exists(os.path.expandvars("$SCHRODINGER/internal/bin/trj_merge.py")):
os.system("$SCHRODINGER/run trj_merge.py %s %s %s -o NewMergedTrajectory" % (
cms, in1_trj, in2_trj))
os.system("mv NewMergedTrajectory.cms NewMergedTrajectory-out.cms")
else: # For Desmond Version < 2018.1 https://www.schrodinger.com/kb/90
os.system("$SCHRODINGER/run -FROM desmond manipulate_trj.py %s NewMergedTrajectory %s %s" % (
cms, in1_trj, in2_trj))
if os.path.exists("NewMergedTrajectory-out.cms"):
print "...Done!"
print "Check your current working directory for new merged trajectory and -out.cms file."
print "Thank you for using TrajectoryMergeAssist."
print "\t"
else:
print "Error! New Merged Trajectory not created! Please contact author."
print "\t"
exit()
def AskGROMACSTrajectory1(self):
global xtc1
xtc1 = tkFileDialog.askopenfilename(parent=root, initialdir="pwd", title='Please Select GROMACS Trajectory 1 .xtc file')
if len(xtc1) > 0:
print "You chose %s" % xtc1
def AskGROMACSTrajectory2(self):
global xtc2
xtc2 = tkFileDialog.askopenfilename(parent=root, initialdir="pwd", title='Please Select GROMACS Trajectory 2 .xtc file')
if len(xtc2) > 0:
print "You chose %s" % xtc2
def MergeGROMACSTrajectories(self):
if os.path.exists("/usr/local/gromacs"):
print "You are using GROMACS via /usr/local/gromacs"
elif os.path.exists("/usr/share/gromacs"):
print "You are using GROMACS via /usr/share/gromacs"
else:
print "Default GROMACS installation not found. Exiting."
exit()
print "---------------------------------------------------------"
print "Merging both trajectories into one and generating .xtc..."
print "---------------------------------------------------------"
# For GROMACS 2019.1 http://manual.gromacs.org/current/onlinehelp/gmx-trjcat.html
os.system("gmx trjcat -f %s %s -o NewMergedTrajectory.xtc" % (
xtc1, xtc2))
if os.path.exists("NewMergedTrajectory.xtc"):
print "...Done!"
print "Check your current working directory for new merged trajectory (.xtc) file."
print "Thank you for using TrajectoryMergeAssist."
print "\t"
else:
print "Error! New Merged Trajectory not created! Please contact author."
print "\t"
exit()
if __name__ == "__main__":
app = MergeMDs(None)
app.title('TrajectoryMergeAssist v2.1: Merge Molecular Dynamics Extended Trajectories')
app.mainloop()