tma_py3.py

#!/usr/bin/python
# -*- coding: utf-8 -*-
# TrajectoryMergeAssist v2.1.1
# A python3 based GUI tool that helps in merging two trajectories on Desmond MD

# Copyright (C) 2021 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 os
from tkinter import filedialog

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 1 ".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 = tkinter.filedialog.askopenfilename(
            parent=root, initialdir="pwd", title='Choose Desmond "-out.cms" file'
        )
        if len(cms) > 0:
            print("%s selected" % cms)

    def AskDesmondTrajectory1(self):
        global in1_trj
        in1_trj = tkinter.filedialog.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 = tkinter.filedialog.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 = tkinter.filedialog.askopenfilename(
            parent=root,
            initialdir="pwd",
            title="Please Select GROMACS Trajectory 1 .xtc file",
        )
        if len(xtc1) > 0:
            print("%s selected" % xtc1)

    def AskGROMACSTrajectory2(self):

        global xtc2
        xtc2 = tkinter.filedialog.askopenfilename(
            parent=root,
            initialdir="pwd",
            title="Please Select GROMACS Trajectory 2 .xtc file",
        )
        if len(xtc2) > 0:
            print("%s selected" % 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()