movie.py

#!/usr/bin/env python
import os
import argparse
import sys
from time import sleep
import subprocess
# import imp
from small_script.myFunctions import shrinkage
import fileinput

parser = argparse.ArgumentParser(description="written by Wei Lu.")
parser.add_argument("protein", help="The name of the protein")
parser.add_argument("-p", "--plot", help="only plot mode",
                    action="store_true")
# parser.add_argument("-d", "--debug", action="store_true", default=False)
parser.add_argument("-d", "--dump", default="dump.lammpstrj")
parser.add_argument("-l", "--last", action="store_true", default=False)
parser.add_argument("-m", "--mode",
                    type=int, default=2)
parser.add_argument("-s", "--submode",
                    type=int, default=-1)
parser.add_argument("-c", "--membraneCenter",
                    type=int, default=0)
parser.add_argument("--fix", help="convert pdb period box, number of chain", type=int, default=-1)
parser.add_argument("--mem", help="show membrane",
                    action="store_true")
parser.add_argument("--cys", help="show Cys",
                    action="store_true")
parser.add_argument("-v", "--visual", default="movie.tcl")
args = parser.parse_args()
# render Tachyon frame450.dat '/Applications/VMD 1.9.2.app/Contents/vmd/tachyon_MACOSXX86' -aasamples 12 %s -format TARGA -o frame450.tga -res 2000 2000

# print(args.dump)
do = os.system
cd = os.chdir

def replace(TARGET, FROM, TO):
    os.system("sed -i.bak 's@{}@{}@g' {}".format(FROM,TO,TARGET))

def replace_v2(TARGET, FROM, TO):
    with fileinput.FileInput(TARGET, inplace=True) as file:
        for line in file:
            tmp = line.replace(FROM, TO)
            print(tmp, end='')
if args.fix >= 0:
    do(f"python ~/opt/small_script/PBC_fixer.py -n {args.fix}")

if args.mode == 4 or args.mode == 5 or args.mode == 6:
    # add the native as initial frames.
    if args.submode == 1:
        for i in range(5):
            do("cat native.pdb >> tmp.pdb")
    do("cat movie.pdb >> tmp.pdb")
    do("mv tmp.pdb movie.pdb")
    do("python ~/openmmawsem/helperFunctions/convertOpenmmTrajectoryToStandardMovie.py movie.pdb")
    do("cp ~/opt/plot_scripts/movie.tcl .")
    do("cp ~/opt/plot_scripts/with_membrane.tcl .")
    # do("/Applications/VMD\ 1.9.3.app/Contents/MacOS/startup.command -e movie.tcl")

    replace("with_membrane.tcl", "MEMUP", str(args.membraneCenter+15))
    replace("with_membrane.tcl", "MEMDOWN", str(args.membraneCenter-15))
    if args.mem:
        plot_script = "with_membrane.tcl"
    else:
        plot_script = "movie.tcl"
    if args.cys:
        showCYS = '''\
mol selection resname CYS and type CB
mol color ColorID 0
mol addrep top
mol modstyle 1 0 VDW 1 12
mol smoothrep 0 1 5
'''
        replace_v2(plot_script, "#CYS", showCYS)
    if args.mode == 5:
        exit()
    if args.mode == 6:
        do("/Applications/VMD\ 1.9.3.app/Contents/MacOS/startup.command -e ../../visual_with_ligands.vmd")
        exit()
    if args.visual != "movie.tcl":
        plot_script = args.visual
    do(f"/Applications/VMD\ 1.9.3.app/Contents/MacOS/startup.command -e {plot_script}")

protein_name = args.protein.split('.')[0]


if args.mode == 3:
    # do("python3 ~/opt/small_script/delete_lammps_frame.py")
    if args.submode == -1:
        shrinkage(shrink_size=6, max_frame=2000,fileName=f"{args.dump}")
    else:
        shrinkage(shrink_size=6, max_frame=2000,fileName=f"{args.dump}.{args.submode}")
    # shrinkage()
    do("cp ../{}.seq .".format(protein_name))
    do("python2 ~/opt/script/BuildAllAtomsFromLammps_seq.py small.lammpstrj movie "+protein_name+".seq")
    do("cp ~/opt/plot_scripts/2xov_movie_bicelle.tcl .")
    do("cp ~/opt/plot_scripts/movie_bicelle_no_smooth.tcl .")
    do("cp ~/opt/plot_scripts/movie.tcl .")
    if args.plot:
        do("/Applications/VMD\ 1.9.3.app/Contents/MacOS/startup.command -e 2xov_movie_bicelle.tcl")


if args.mode == 1:
    # do("python3 ~/opt/small_script/delete_lammps_frame.py")
    shrinkage(shrink_size=1, max_frame=1000,fileName=f"{args.dump}")
    # shrinkage()
    do("cp ../{}.seq .".format(protein_name))
    do("python2 ~/opt/script/BuildAllAtomsFromLammps_seq.py small.lammpstrj movie "+protein_name+".seq")
    do("cp ~/opt/plot_scripts/2xov_movie_bicelle.tcl .")
    do("cp ~/opt/plot_scripts/movie_bicelle_no_smooth.tcl .")
    do("cp ~/opt/plot_scripts/movie.tcl .")
    if args.plot:
        do("/Applications/VMD\ 1.9.3.app/Contents/MacOS/startup.command -e 2xov_movie_bicelle.tcl")

if args.mode == 2:
    if not args.last:
        fail = do("cp ../{}.seq .".format(protein_name))
        print(fail)
        if fail > 0:
            do(f"cp ../crystal.seq {protein_name}.seq")
        if args.submode == -1:
            do(f"python2 ~/opt/script/BuildAllAtomsFromLammps_seq.py {args.dump} movie "+protein_name+".seq")
        else:
            do(f"python2 ~/opt/script/BuildAllAtomsFromLammps_seq.py {args.dump}.{args.submode} movie "+protein_name+".seq")
        # do("cp ~/opt/plot_scripts/2xov_movie_bicelle.tcl .")
        # do("cp ~/opt/plot_scripts/movie_bicelle_no_smooth.tcl .")
        # do("cp ~/opt/plot_scripts/2xov_movie_bicelle_no_smooth.tcl .")
        # do(f"cp ~/opt/plot_scripts/{protein_name}.tcl .")
        # do(f"cp ~/opt/plot_scripts/{protein_name}_no_smooth.tcl .")
        do(f"cp ~/opt/plot_scripts/{protein_name}* .")
        do("cp ~/opt/plot_scripts/movie.tcl .")
    else:
        x = os.listdir()
        y = [int(int(f.split(".")[1])/1000) for f in os.listdir() if f.startswith("restart.")]
        last_frame = max(y)
        print("last Frame: {}".format(last_frame))
        do(f"python2 ~/opt/script/BuildAllAtomsFromLammps_seq.py {args.dump} last "+protein_name+f".seq {last_frame}")
        do("cp ~/opt/plot_scripts/last_frame.pml .")
        do("pymol last_frame.pml")

    if args.plot:
        # do("/Applications/VMD\ 1.9.3.app/Contents/MacOS/startup.command -e 2xov_movie_bicelle.tcl")
        if not os.path.exists(f"{protein_name}.tcl"):
            do("/Applications/VMD\ 1.9.3.app/Contents/MacOS/startup.command -e movie.tcl")
        else:
            do(f"/Applications/VMD\ 1.9.3.app/Contents/MacOS/startup.command -e {protein_name}.tcl")


# if(args.number == -1):
#     # do("cp ~/opt/pulling/2xov.seq .")
#     if(not args.plot):
#         os.system("python2 ~/opt/script/BuildAllAtomsFromLammps_seq.py dump.lammpstrj movie "+protein_name+".seq")
#         # os.system(
#         #     "python2 ~/opt/script/BuildAllAtomsFromLammps.py \
#         #     dump.lammpstrj movie")
# else:
#     os.system("ghead -n 399648 dump.lammpstrj > part_dump")
#     if(not args.plot):
#         os.system("python2 ~/opt/script/BuildAllAtomsFromLammps_seq.py dump.lammpstrj movie "+protein_name+".seq")
#         # os.system(
#         #     "python2 ~/opt/script/BuildAllAtomsFromLammps.py \
#         #     part_dump movie")
# os.system("cp ~/opt/plot_scripts/*.tcl .")