def rmsd_residual(trajectory,
reference_structure=False,
gmx="gmx",
output=False,
group_selection="1"):
"""
Args:
trajectory:
reference_structure:
gmx:
output:
group_selection:
"""
if (not output):
output = os.path.dirname(
trajectory) + "/rmsd_residual_" + os.path.basename(trajectory)
if (reference_structure):
reference_structure = trajectory
command = "cd " + os.path.dirname(
output
) + "\necho \"" + group_selection + "\" | " + gmx + " rmsf -f " + trajectory + " -s " + reference_structure + " -od " + output + " -res\n"
bash.execute(command)
return output
def solvate_box(self,
gro_file,
top_file,
output_name=False,
watersNum="none",
gromacs="gmx"):
"""
Args:
gro_file:
top_file:
output_name:
watersNum:
gromacs: path to gromacs binary (default: gmx)
"""
output_name = str(output_name) if (
output_name) else os.path.splitext(gro_file)[0]
if (watersNum != "none"):
solvate_command = gromacs + " solvate -cp " + gro_file + " -cs spc216.gro -o " + output_name + ".gro -maxsol " + str(
watersNum
) + " -p " + top_file + " &> " + output_name + ".log \n"
else:
solvate_command = gromacs + " solvate -cp " + gro_file + " -cs spc216.gro -o " + output_name + ".gro -p " + top_file + ".top &> " + output_name + ".log \n"
bash.execute(solvate_command)
return output_name
def sasa(structure_file,
ref_file,
index_file,
select_1,
output,
gmx="gmx",
residual=False):
"""
Args:
structure_file:
ref_file:
index_file:
select_1:
output:
gmx:
residual:
"""
if (residual):
sasa_res = "-or " + str(residual) + "\n"
else:
sasa_res = ""
if (not os.path.isdir(output)):
output_file = output
output_dir = os.path.dirname(output)
else:
output_file = output + "/rdf_" + select_1
output_dir = output
selection = "echo \"" + select_1 + "\" "
sasa_command = "cd " + output_dir + " \n" + selection + " | " + gmx + " sasa -f " + structure_file + " -s " + ref_file + " -n " + index_file + " -o " + output_file + " " + sasa_res + "\n"
bash.execute(sasa_command)
return output_file
def make_ndx(self,
gro_file,
gromacs="make_ndx_mpi",
index_file=False,
output_name=False,
selection=False):
"""
Args:
gro_file:
gromacs:
index_file:
output_name:
selection:
"""
if (not output_name):
output_name = gro_file
if (selection):
selection_string = "\"" + str(selection) + " \n q\""
print("Got selection " + selection_string)
else:
selection_string = "\"q\""
if (index_file):
gro_file += " -n " + index_file + " "
print("making index file:\t" + output_name)
make_ndx_command = gromacs + " -f " + gro_file + " -o " + output_name + " <<< $(echo -e \"" + selection_string + "\")"
bash.execute(make_ndx_command)
return output_name
def rmsd_fit(trajectory,
reference_structure,
fit_to,
index_file=False,
gmx="gmx",
output=False):
"""
Args:
trajectory:
reference_structure:
fit_to:
index_file:
gmx:
output:
"""
if (not output):
output = os.path.dirname(
trajectory) + "/selection_" + os.path.basename(trajectory)
if (not reference_structure):
reference_structure = trajectory
if (index_file):
command = gmx + " select -f " + trajectory + " -s " + reference_structure + " -n " + index_file + " -on " + output + " -select " + fit_to + " \n"
else:
command = "cd " + os.path.dirname(
output
) + "\n " + gmx + " select -f " + trajectory + " -s " + reference_structure + " -select " + fit_to + " -on " + output + " \n"
bash.execute(command)
return output
def pdb2gmx(self,
pdb_file,
force_field,
watermodel,
output_path=False,
gromacs="gmx",
additional_options=" "):
"""
Args:
pdb_file:
force_field:
watermodel:
output_path:
gromacs: path to gromacs binary (default: gmx)
additional_options:
"""
print("converting pdb to gmx")
output_path = output_path if (
output_path) else os.path.splitext(pdb_file)[0]
if (str(force_field).isdigit()):
pdb2gmx_command = "cd " + os.path.dirname(
output_path
) + "\n echo \"" + str(
force_field
) + "\" | " + gromacs + " pdb2gmx -f " + pdb_file + " -water " + watermodel + " -o " + output_path + ".gro -p " + output_path + " -n " + output_path + " " + additional_options
else:
pdb2gmx_command = "cd " + os.path.dirname(
output_path
) + "\n " + gromacs + " pdb2gmx -f " + pdb_file + " -ff " + force_field + " -water " + watermodel + " -o " + output_path + ".gro -p " + output_path + " -n " + output_path + " " + additional_options
bash.execute(pdb2gmx_command)
return output_path
def md(self,
workdir,
gro_file,
top_file,
ndx_file,
in_protocol,
out_prefix=False,
restriction_gro=False,
gromacs_run="gmx mdrun",
gromacs_grompp="gmx grompp"):
"""This starts an initial run for a simulation "step". very crude and
easy ;) :param workdir: absolute path to folder with step prefix as last
part ("absolutePath/prefix") :param gromacs_run: contains the string,
executing the gromacs command: "gmx mdrun" "gmx_mpi mdrun" ... :param
gro_file:absolute path to .gro file input (build input or previous
simulation step) :param top_file: absolute path to .top file input
(build input folder) :param ndx_file: absolute path to .ndx file input
(build input folder) :return: stepcounter (updates the gro_file for next
step)
Args:
workdir:
gro_file:
top_file:
ndx_file:
in_protocol:
out_prefix:
restriction_gro:
gromacs_run:
gromacs_grompp:
"""
if (out_prefix):
step_name = out_prefix
else:
step_name = os.path.splitext(
os.path.basename(in_protocol))[0] # prefix of the step
if (not restriction_gro):
restriction_gro = gro_file
output = workdir + "/" + step_name
# Formulate commands
grompp_command = gromacs_grompp + " -f " + output + ".mdp -c " + gro_file + " -p " + top_file + " -n " + ndx_file + " -r " + restriction_gro + " -o " + output + ".tpr 1> " + output + "_grompp.log 2>" + output + "_grompp.err\n"
mdrun_command = gromacs_run + " -s " + output + ".tpr -deffnm " + output + " 1> " + output + "_mdrun.log 2>" + output + "_mdrun.err\n"
try:
# execute commands:
print("\tCopy_protocol: " + step_name)
bash.copy_file(in_protocol, output + ".mdp")
print("\tgrompp command: " + step_name)
bash.execute("cd " + workdir + "\n" + grompp_command)
print("\trun_sim: " + step_name)
bash.execute("cd " + workdir + "\n" + mdrun_command)
except Exception as err:
raise bash.increment_error_level("simple sim failed!\n", err)
return output
def grompp(self,
workdir,
gro_file,
top_file,
ndx_file,
in_protocol,
gromacs_grompp="grompp_mpi",
out_prefix=False):
"""This starts grompp to build a tpr file. :param workdir: absolute path
to folder with step prefix as last part ("absolutePath/prefix") :param
gro_file:absolute path to .gro file input (build input or previous
simulation step) :param top_file: absolute path to .top file input
(build input folder) :param ndx_file: absolute path to .ndx file input
(build input folder) :return: stepcounter (updates the gro_file for next
step)
Args:
workdir:
gro_file:
top_file:
ndx_file:
in_protocol:
gromacs_grompp:
out_prefix:
"""
if (out_prefix):
step_name = out_prefix
else:
step_name = os.path.splitext(
os.path.basename(in_protocol))[0] # prefix of the step
output = workdir + "/" + step_name
# Formulate commands
grompp_command = gromacs_grompp + " -f " + output + ".mdp -c " + gro_file + " -p " + top_file + " -n " + ndx_file + " -o " + output + ".tpr 1> " + output + "_grompp.log 2>" + output + "_grompp.err\n"
try:
# execute commands:
print("\tCopy_protocol: " + step_name)
bash.copy_file(in_protocol, output + ".mdp")
print("\tgrompp command: " + step_name)
bash.execute("cd " + workdir + "\n" + grompp_command)
except Exception as err:
raise bash.increment_error_level("grompp failed!\n", err)
return output
def make_posres(self,
gro_file,
output_name,
selection="1",
fc="1000",
gromacs="gmx"):
"""
Args:
gro_file:
output_name:
selection:
fc:
gromacs:
"""
print("making posrestriction file:\t" + output_name)
make_posres_command = "echo \"" + selection + " 0\" | " + gromacs + " genrestr -f " + gro_file + " -o " + output_name + ".itp -fc " + fc + " \n"
bash.execute(make_posres_command)
return output_name
def mdrun(self,
workdir,
tpr_file,
out_prefix=False,
gromacs="gmx ",
additional_options: str = " "):
"""This starts an initial run for a simulation "step". very crude and
easy ;) :param workdir: absolute path to folder with step prefix as last
part ("absolutePath/prefix") :param gromacs_run: contains the string,
executing the gromacs command: "gmx mdrun" "gmx_mpi mdrun" ... :param
gro_file:absolute path to .gro file input (build input or previous
simulation step) :param top_file: absolute path to .top file input
(build input folder) :param ndx_file: absolute path to .ndx file input
(build input folder) :return: stepcounter (updates the gro_file for next
step)
Args:
workdir:
tpr_file:
out_prefix:
gromacs:
additional_options (str):
"""
if (out_prefix):
step_name = out_prefix
else:
step_name = os.path.splitext(
os.path.basename(tpr_file))[0] # prefix of the step
output = workdir + "/" + step_name
# Formulate commands
mdrun_command = gromacs + " mdrun -s " + tpr_file + " -deffnm " + output + " " + additional_options + " 1> " + output + "_mdrun.log 2>" + output + "_mdrun.err"
try:
# execute commands:
print("\tCopy_protocol: " + step_name)
if (not os.path.exists(output + ".tpr")):
bash.copy_file(tpr_file, output + ".tpr")
print("\trun_sim: " + step_name)
bash.execute("cd " + workdir + " && " + mdrun_command)
except Exception as err:
raise bash.increment_error_level("mdrun failed!\n", err)
return output
def editconf(self,
input_file,
output_name=False,
gromacs="gmx",
additional_options=" "):
"""
Args:
input_file:
output_name:
gromacs: path to gromacs binary (default: gmx)
additional_options:
"""
output_name = output_name if (
output_name) else os.path.splitext(input_file)[0]
editconf_command = "cd " + os.path.dirname(
output_name
) + "\n " + gromacs + " editconf -f " + input_file + " -o " + output_name + " " + additional_options
bash.execute(editconf_command)
return output_name
def dist(structure_file,
index_file,
selection,
output,
oav=True,
oallstat=True,
oh=True,
gmx="gmx"):
"""
Args:
structure_file:
index_file:
selection:
output:
oav:
oallstat:
oh:
gmx:
"""
if (not os.path.isdir(output)):
output_file = output
output_dir = os.path.dirname(output)
else:
output_file = output + "/dist_" + selection
output_dir = output
executes = []
if (oav):
executes.append("oav ")
if (oallstat):
executes.append("oallstat ")
if (oh):
executes.append("oh ")
for ex in executes:
dist_command = "cd " + output_dir + " \n" + gmx + " distance -f " + structure_file + " -n " + index_file + " -select " + selection + " -" + ex + " " + output_file + "_" + ex + "\n" # shows numbers of H-bonds over time
bash.execute(dist_command)
return output
def rdf(structure_file, index_file, select_1, select_2, output, gmx="gmx"):
"""
Args:
structure_file:
index_file:
select_1:
select_2:
output:
gmx:
"""
if (not os.path.isdir(output)):
output_file = output
output_dir = os.path.dirname(output)
else:
output_file = output + "/rdf_" + select_1 + "_" + select_2
output_dir = output
selection = "echo \"" + select_1 + "\" "
rdf_command = "cd " + output_dir + " \n" + selection + " | " + gmx + " rdf -f " + structure_file + " -n " + index_file + " -sel " + select_2 + " -o " + output_file + " \n" # shows numbers of H-bonds over time
bash.execute(rdf_command)
return output
def set_box(self,
gro_file,
border_distance,
box_form="dodecahedron",
output_name=False,
gromacs="gmx",
additional_options=""):
"""
Args:
gro_file:
border_distance:
box_form:
output_name:
gromacs: path to gromacs binary (default: gmx)
additional_options:
"""
output_name = str(output_name) if (output_name) else gro_file
# box command for gmx editconf
editconf_command = gromacs + " editconf -f " + gro_file + " -o " + output_name + ".gro -bt " + box_form + " -d " + str(
border_distance
) + " " + additional_options + " &> " + output_name + ".log"
bash.execute(editconf_command)
return output_name
def hbond(structure_file,
tpr_file,
group_1,
group_2,
output,
index_file=False,
gmx=" gmx ",
num=False,
dist=False,
life=False,
hbn=False,
hbm=False,
ac=False,
hx=False):
"""
Args:
structure_file:
tpr_file:
group_1:
group_2:
output:
index_file:
gmx:
num:
dist:
life:
hbn:
hbm:
ac:
hx:
"""
selection = "echo \"" + group_1 + " " + group_2 + "\" "
executes = []
ndx = ""
if (num):
executes.append("num")
if (dist):
executes.append("dist")
if (life):
executes.append("life")
if (hbn):
executes.append("hbn")
if (hbm):
executes.append("hbm")
if (ac):
executes.append("ac")
if (hx):
executes.append("hx")
if (index_file):
ndx = " -n " + str(index_file) + " "
if (os.path.isfile(output)):
output_dir = os.path.dirname(output)
else:
output_dir = output
for ex in executes:
if (ex == "hbm"):
hbond_command = "cd " + selection + " \n" + output_dir + " | " + gmx + " hbond -f " + structure_file + " -s " + tpr_file + " " + ndx + " -" + ex + " " + output + "_" + ex + "\n" # shows numbers of H-bonds over time
hbond_command += "cd " + output_dir + "\n gmx xpm2ps -f " + output + "_" + ex + ".xpm -o " + output + "_" + "ex \n"
else:
hbond_command = "cd " + output_dir + " \n" + selection + " | " + gmx + " hbond -f " + structure_file + " -s " + tpr_file + " " + ndx + " -" + ex + " " + output + "_" + ex + "\n" # shows numbers of H-bonds over time
bash.execute(hbond_command)
def add_ions(self,
gro_file,
top_file,
group_sel,
output_name,
conc="0.15",
np=False,
nn=False,
additional_options="",
gromacs="gmx"):
"""
Args:
gro_file:
top_file:
group_sel:
output_name:
conc:
np:
nn:
additional_options:
gromacs: path to gromacs binary (default: gmx)
"""
folder = os.path.dirname(output_name)
ion_mdp_path = folder + "/ion"
# generating an ion_protocol
print("writing dummy protocol to: " + ion_mdp_path)
ion_mdp = open(ion_mdp_path + ".mdp", "w")
ion_mdp.write(";this is a generic em-protocol to execute grompp\n"
"integrator = steep\n"
"emtol = 250.0\n"
"nsteps = 50000\n"
"nstenergy = 1\n"
"energygrps = System\n"
"nstlist = 1\n"
"ns_type = grid\n"
"coulombtype = PME\n"
"rlist = 1.0\n"
"rcoulomb = 1.0\n"
"rvdw = 1.0\n"
"constraints = none\n"
"pbc = xyz")
ion_mdp.close()
print("grompp")
# salting command for gmx genion
grompp = ("cd " + folder + "\n" + gromacs + " grompp -f " +
ion_mdp_path + " -c " + gro_file + " -p " + top_file +
" -o " + output_name + ".tpr 1> " + output_name +
"_grompp.log 2> " + output_name + "_grompp.err\n")
bash.execute(grompp)
print("salting")
if (np and nn):
add_salt = ("cd " + folder + "\necho -e " + str(group_sel) +
" | " + gromacs + " genion -s " + output_name +
".tpr -o " + output_name + ".gro -nn " + str(nn) +
" -np " + str(np) + " -p " + output_name + ".top " +
additional_options + " 1> " + output_name +
"_mdrun.log 2> " + output_name + "_mdrun.err\n")
else:
add_salt = ("cd " + folder + "\necho -e " + str(group_sel) +
" | " + gromacs + " genion -s " + output_name +
".tpr -o " + output_name + ".gro -neutral -conc " +
str(conc) + " -p " + output_name + ".top " +
additional_options + " 1> " + output_name +
".log 2> " + output_name + "_mdrun.err\n")
bash.execute(add_salt)
return output_name
def trajectory_convert(self,
struct_file,
s_file,
gromacs="gmx",
output_name=False,
format=False,
index_file=False,
frames_file=False,
begin_frame=False,
end_frame=False,
time_unit=False,
timestep=False,
split=False,
pbc=False,
unit_cell_rep=False,
center=False,
dt=False,
fit=False,
additional_options=False,
group_sel="0"):
"""
Args:
struct_file:
s_file:
gromacs: path to gromacs binary (default: gmx)
output_name:
format:
index_file:
frames_file:
begin_frame:
end_frame:
time_unit:
timestep:
split:
pbc:
unit_cell_rep:
center:
dt:
fit:
additional_options:
group_sel:
"""
if (not output_name):
output_name = struct_file
if (format):
output_name = os.path.splitext(output_name)[0] + "." + str(format)
if (not group_sel):
group_sel = 0
options = " "
options += " -n " + str(index_file) + " " if (index_file) else ""
options += " -fr " + str(frames_file) + " " if (frames_file) else ""
options += " -b " + str(begin_frame) + " " if (begin_frame) else ""
options += " -e " + str(end_frame) + " " if (end_frame) else ""
options += " -tu " + str(time_unit) + " " if (time_unit) else ""
options += " -timestep " + str(timestep) + " " if (timestep) else ""
options += " -dt " + str(dt) + " " if (dt) else ""
options += " -split " + str(split) + " " if (split) else ""
options += " -pbc " + str(pbc) + " " if (pbc) else ""
options += " -ur " + str(unit_cell_rep) + " " if (
unit_cell_rep) else ""
options += " -center " if (center) else ""
options += " -fit " + str(fit) + " " if (fit) else ""
options += additional_options if (additional_options) else ""
trjconv_command = "echo -e \"" + group_sel + "\" | " + gromacs + " trjconv -f " + struct_file + " -s " + s_file + " -o " + output_name + " " + options + "\n"
bash.execute(trjconv_command)
return output_name