def progress_bar(proc, func_input_dict, tail_line_num=20):
""" Monitor ``.log`` file timestep.
The ``func_input_dict`` should contains several keys:
* `nsteps`: Total number of steps during the simulation
* `log`: path of the log file (Defined in ``os_command.run_background()``)
* `refresh_time`: time interval to refresh log extract (default=1.0 s)
:param proc: running subprocess
:type proc: subprocess object
:param func_input_dict: dictionnary containing parameters for log extract
:type func_input_dict: dict
:param tail_line_num: number of line to read at the end of ``.log`` file
:type tail_line_num: int, default=20
Example:
>>> TEST_OUT = str(getfixture('tmpdir'))
>>> import sys
>>> sys.path.insert(0, os.path.abspath(os.path.join(MONITOR_LIB_DIR, \
'../..')))
>>> from gromacs_py import gmx #doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
<BLANKLINE>
...
>>> prot = gmx.GmxSys(name='1y0m', coor_file=TEST_PATH+'/1y0m.pdb')
>>> ###################################
>>> #### Create the topologie: ###
>>> ###################################
>>> prot.prepare_top(out_folder=os.path.join(TEST_OUT, 'top_SH3'), \
vsite='hydrogens') #doctest: +ELLIPSIS
pdb2pqr... --ff CHARMM --ffout CHARMM --chain --ph-calc-method=propka \
--with-ph=7.00 tmp_pdb2pqr.pdb 00_1y0m.pqr
gmx pdb2gmx -f 01_1y0m_good_his.pdb -o 1y0m_pdb2gmx.pdb -p \
1y0m_pdb2gmx.top -i 1y0m_posre.itp -water tip3p -ff charmm36-jul2017 -ignh \
-vsite hydrogens
>>> ######################################
>>> ### Monitor an energy minimisation ###
>>> ######################################
>>> monitor = PROGRESS_BAR
>>> prot.em(out_folder=os.path.join(TEST_OUT, 'em_SH3'), nsteps=50,\
constraints='none', create_box_flag=True, monitor=monitor, nstlog=1)\
#doctest: +ELLIPSIS
gmx editconf -f .../top_SH3/1y0m_pdb2gmx.pdb -o \
.../top_SH3/1y0m_pdb2gmx_box.pdb -bt dodecahedron -d 1.0
gmx grompp -f 1y0m.mdp -c ../top_SH3/1y0m_pdb2gmx_box.pdb -r \
../top_SH3/1y0m_pdb2gmx_box.pdb -p ../top_SH3/1y0m_pdb2gmx.top -po \
out_1y0m.mdp -o 1y0m.tpr -maxwarn 1
gmx mdrun -s 1y0m.tpr -deffnm 1y0m -nt 0 -ntmpi 0 -nsteps -2 \
-nocopyright
"""
if isnotebook():
from tqdm.notebook import tqdm
else:
from tqdm import tqdm
log_to_check = func_input_dict['log']
time_modif = None
file_time = None
count = 1
if 'refresh_time' in func_input_dict:
refresh_time = func_input_dict['refresh_time']
else:
refresh_time = 1.0
pbar = tqdm(total=func_input_dict['nsteps'])
last_time = 0
while proc.poll() is None:
time.sleep(refresh_time)
count += 1
if os_command.check_file_exist(log_to_check):
file_time = os.stat(log_to_check).st_mtime
if time_modif != file_time:
time_modif = file_time
log_dict = extract_log_dict(func_input_dict)
if 'step' in log_dict:
pbar.update(log_dict['step'] - last_time)
last_time = log_dict['step']
pbar.update(func_input_dict['nsteps'] - last_time)
pbar.close()
def print_log_file(proc, func_input_dict, tail_line_num=20):
""" Monitor ``.log`` file information.
The ``func_input_dict`` should contains several keys:
* `terms`: list of energetic terms to extract, eg. ['Potential',
'Temperature']
* `log`: path of the log file (Defined in ``os_command.run_background()``)
* `refresh_time`: time interval to refresh log extract (default=1.0 s)
:param proc: running subprocess
:type proc: subprocess object
:param func_input_dict: dictionnary containing parameters for log extract
:type func_input_dict: dict
:param tail_line_num: number of line to read at the end of ``.log`` file
:type tail_line_num: int, default=20
Example:
>>> TEST_OUT = str(getfixture('tmpdir'))
>>> import sys
>>> sys.path.insert(0, os.path.abspath(os.path.join(MONITOR_LIB_DIR, \
'../..')))
>>> from gromacs_py import gmx #doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
<BLANKLINE>
...
>>> prot = gmx.GmxSys(name='1y0m', coor_file=TEST_PATH+'/1y0m.pdb')
>>> ###################################
>>> #### Create the topologie: ###
>>> ###################################
>>> prot.prepare_top(out_folder=os.path.join(TEST_OUT, 'top_SH3'), \
vsite='hydrogens') #doctest: +ELLIPSIS
pdb2pqr... --ff CHARMM --ffout CHARMM --chain --ph-calc-method=propka \
--with-ph=7.00 tmp_pdb2pqr.pdb 00_1y0m.pqr
gmx pdb2gmx -f 01_1y0m_good_his.pdb -o 1y0m_pdb2gmx.pdb -p \
1y0m_pdb2gmx.top -i 1y0m_posre.itp -water tip3p -ff charmm36-jul2017 -ignh \
-vsite hydrogens
>>> ######################################
>>> ### Monitor an energy minimisation ###
>>> ######################################
>>> monitor = {'function': print_log_file,\
'terms':['Potential'],\
'file_check_ext':'log'}
>>> prot.em(out_folder=os.path.join(TEST_OUT, 'em_SH3'), nsteps=50,\
constraints='none', create_box_flag=True, monitor=monitor, nstlog=1)\
#doctest: +ELLIPSIS
gmx editconf -f .../top_SH3/1y0m_pdb2gmx.pdb -o \
.../top_SH3/1y0m_pdb2gmx_box.pdb -bt dodecahedron -d 1.0
gmx grompp -f 1y0m.mdp -c ../top_SH3/1y0m_pdb2gmx_box.pdb -r \
../top_SH3/1y0m_pdb2gmx_box.pdb -p ../top_SH3/1y0m_pdb2gmx.top -po \
out_1y0m.mdp -o 1y0m.tpr -maxwarn 1
gmx mdrun -s 1y0m.tpr -deffnm 1y0m -nt 0 -ntmpi 0 -nsteps -2 \
-nocopyright...
"""
log_to_check = func_input_dict['log']
time_modif = None
file_time = None
count = 1
if 'refresh_time' in func_input_dict:
refresh_time = func_input_dict['refresh_time']
else:
refresh_time = 1.0
while proc.poll() is None:
time.sleep(refresh_time)
count += 1
if os_command.check_file_exist(log_to_check):
file_time = os.stat(log_to_check).st_mtime
if time_modif != file_time:
time_modif = file_time
log_dict = extract_log_dict(func_input_dict)
if 'time' in log_dict:
print("time = {:6.1f} ".format(log_dict['time']), end='')
for keys in func_input_dict['terms']:
if keys in log_dict:
print(" {} = {:5.1f} ".format(keys, log_dict[keys]),
end='')
print()
def correct_charge_type(self, forcefield, index_list=None):
""" Correct the charge and atom type of an itp object,
base on a ff `.rtp` file.
This is specially usefull, to correct charge of termini resiudes
of a cyclicized peptide.
if index_list is None, will correct all atom charges, if not, only
atoms listed in index_list.
"""
# First extract charge and type from the ff .rtp file
forcefield_path = forcefield['path']
rtp_path = os.path.abspath(
os.path.join(os_command.get_directory(forcefield_path),
'aminoacids.rtp'))
if not os_command.check_file_exist(rtp_path):
rtp_path = os.path.abspath(
os.path.join(os_command.get_directory(forcefield_path),
'merged.rtp'))
logger.info('Read rtp file : {}'.format(rtp_path))
ff_rtp = Rtp(rtp_path)
# Correct charges and type:
# for atom_num, atom in self.atom_dict.items():
if index_list is None:
index_list = self.atom_dict.keys()
for atom_num in index_list:
atom = self.atom_dict[atom_num]
res_name = atom['res_name']
resid = atom['res_num']
atom_name = atom['atom_name']
# With Amber disulfide cys are called CYX in the rtp and CYS in
# the itp.
# Don't get sense but need to check the protonation state of cys
# By counting atoms
# With charmm disuldie cys is CYS2
if res_name == 'CYS':
if len(
self.get_selection_index(selec_dict={
'res_num': [resid],
'res_name': ['CYS']
})) == 10:
if forcefield['name'].startswith('amber'):
res_name = 'CYX'
elif forcefield['name'].startswith('charmm'):
res_name = 'CYS2'
# print(res_name)
# With gromacs all histidine are called HIS !
if res_name == 'HIS':
if len(
self.get_selection_index(selec_dict={
'res_num': [resid],
'res_name': ['HIS']
})) == 18:
if forcefield['name'].startswith('amber'):
res_name = 'HIP'
elif forcefield['name'].startswith('charmm'):
res_name = 'HSP'
elif len(
self.get_selection_index(selec_dict={
'res_num': [resid],
'atom_name': ['HE2']
})) == 1:
if forcefield['name'].startswith('amber'):
res_name = 'HIE'
elif forcefield['name'].startswith('charmm'):
res_name = 'HSE'
else:
if forcefield['name'].startswith('amber'):
res_name = 'HID'
elif forcefield['name'].startswith('charmm'):
res_name = 'HSD'
# print(atom)
# print(ff_rtp.res_dict[res_name]['atom'][atom_name])
if atom_name in ff_rtp.res_dict[res_name]['atom']:
atom_type = \
ff_rtp.res_dict[res_name]['atom'][atom_name]['type']
atom_charge = \
ff_rtp.res_dict[res_name]['atom'][atom_name]['charge']
# print('Correct residue {:4} atom {:4} atom type {:4} '
# 'to {:4}'.format(res_name, atom['atom_name'],
# atom['atom_type'], atom_type))
# print('Correct charge {:4} '
# 'to {:4}'.format(self.atom_dict[atom_num]['charge'],
# atom_charge))
if atom_type != atom['atom_type']:
logger.warning('Correct residue {:4} atom {:4} atom '
'type {:4} to {:4}'.format(
res_name, atom['atom_name'],
atom['atom_type'], atom_type))
else:
logger.warning('Can\'t find residue {:4} atom {:4} atom '
'type {:4} parameters in forcefield'.format(
res_name, atom['atom_name'],
atom['atom_type']))
self.atom_dict[atom_num]['atom_type'] = atom_type
self.atom_dict[atom_num]['charge'] = atom_charge
def simulation_plot(proc, func_input_dict, refresh_time=1.0):
""" This function is used for monitoring a simulation in real time.
Function can be excecuted by the gromacs.tools.os_command.run_background()
function.
The function monitors a trajectory file, and launch the analysis if the
file has been modified.
It can plot as function of time an analysis of a simulation.
Analysis is passed as input function.
.. warning::
Need to add the following lines to be run in jupyter notebook:
* ``%matplotlib notebook``
Example:
>>> TEST_OUT = str(getfixture('tmpdir'))
>>> import sys
>>> # print(os.path.abspath(os.path.join(MONITOR_LIB_DIR, \
'../..')))
>>> sys.path.insert(0, os.path.abspath(os.path.join(MONITOR_LIB_DIR, \
'../..')))
>>> from gromacs_py import gmx #doctest: +ELLIPSIS
>>> prot = gmx.GmxSys(name='1y0m', coor_file=TEST_PATH+'/1y0m.pdb')
>>> ###################################
>>> #### Create the topologie: ###
>>> ###################################
>>> prot.prepare_top(out_folder=os.path.join(TEST_OUT, 'top_SH3'), \
vsite='hydrogens') #doctest: +ELLIPSIS
pdb2pqr... --ff CHARMM --ffout CHARMM --chain --ph-calc-method=propka \
--with-ph=7.00 tmp_pdb2pqr.pdb 00_1y0m.pqr
gmx pdb2gmx -f 01_1y0m_good_his.pdb -o 1y0m_pdb2gmx.pdb -p \
1y0m_pdb2gmx.top -i 1y0m_posre.itp -water tip3p -ff charmm36-jul2017 -ignh \
-vsite hydrogens
>>> ######################################
>>> ### Monitor an energy minimisation ###
>>> ######################################
>>> monitor = {'function': simulation_plot,\
'extract_func': [{'func': extract_log_dict,\
'term': 'Potential'},\
{'func': extract_log_dict,\
'term': 'Temperature'}],\
'file_check_ext':'log'}
>>> prot.em(out_folder=os.path.join(TEST_OUT, 'em_SH3'), nsteps=50,\
constraints='none', create_box_flag=True, monitor=monitor, nstlog=10)\
#doctest: +ELLIPSIS
gmx editconf -f ...top_SH3/1y0m_pdb2gmx.pdb -o \
...top_SH3/1y0m_pdb2gmx_box.pdb -bt dodecahedron -d 1.0
gmx grompp -f 1y0m.mdp -c .../top_SH3/1y0m_pdb2gmx_box.pdb \
-r .../top_SH3/1y0m_pdb2gmx_box.pdb -p .../top_SH3/1y0m_pdb2gmx.top \
-po out_1y0m.mdp -o 1y0m.tpr -maxwarn 1
gmx mdrun -s 1y0m.tpr -deffnm 1y0m -nt 0 -ntmpi 0 -nsteps -2 -nocopyright
"""
file_to_check = func_input_dict[func_input_dict['file_check_ext']]
function_list = func_input_dict['extract_func']
time_modif = None
file_time = None
count = 1
x_list = []
y_list = []
notebook = isnotebook()
###################
# Set up the plot #
###################
# Remove the matplotlib window buttons:
matplotlib.rcParams['toolbar'] = 'None'
# Create the plot in interactive mode
plt.ion()
# fig = plt.figure()
fig, axarr = plt.subplots(len(function_list), sharex=True)
for i, function in enumerate(function_list):
y_list.append([])
x_list.append([])
axarr[i].set_xlabel('time (ps)')
axarr[i].set_ylabel(function['term'])
axarr[i].plot(x_list[i],
y_list[i],
'ko-',
markersize=2,
linewidth=0.5,
color='blue')
# show the window
# figure will be in foreground, but the user may move it to background
if not notebook:
fig.show()
fig.canvas.set_window_title(file_to_check[:-4])
while proc.poll() is None:
time.sleep(refresh_time)
count += 1
if os_command.check_file_exist(file_to_check):
file_time = os.stat(file_to_check).st_mtime
if time_modif != file_time:
time_modif = file_time
for i, function in enumerate(function_list):
anal = function['func'](func_input_dict)
# print(anal)
if 'time' in anal and function['term'] in anal:
x_list[i].append(anal['time'])
y_list[i].append(anal[function['term']])
# set plot data
axarr[i].lines[0].set_data(x_list[i], y_list[i])
# recompute the data limits
axarr[i].relim()
# automatic axis scaling
axarr[i].autoscale_view()
# except KeyError:
# print('Energy could not be extract,
# simulation is probably finished.')
# Update the plot and take care of window events
# (like resizing etc.)
fig.canvas.flush_events()
if notebook:
# Needed when launched in notebook
fig.canvas.draw()
def read_file(self, top_in):
field = None
ifdef = False
bond_list = []
angle_list = []
dihed_list = []
with open(top_in) as topfile:
for line in topfile:
# print("line: ",line)
# Check #ifdef field:
if line[:6] == '#ifdef':
ifdef = True
if line[:6] == '#endif':
ifdef = False
# Check include files
if not ifdef and line.startswith('#include'):
# get the file name to include:
file_name = line.split()[1][1:-1]
# remove '"' , path and .itp:
include = (file_name.split("/")[-1]).split(".")[0]
# Look if the itp is in the top path:
# print("Path 1: ",self.folder+"/"+file_name)
# print("Path 2: ",FORCEFIELD_PATH_LIST+"/"+file_name)
itp_found = False
if os_command.check_file_exist(
os.path.join(self.folder, file_name)):
path = os.path.abspath(
os.path.join(self.folder, file_name))
itp_found = True
else:
for forcefield in FORCEFIELD_PATH_LIST:
if os_command.check_file_exist(
os.path.join(forcefield, file_name)):
path = os.path.abspath(
os.path.join(forcefield, file_name))
itp_found = True
break
if not itp_found:
raise IOError('Itp ' + file_name + ' not found')
# print("name =", include, "fullname =", file_name,
# "path =",path)
if include == "forcefield":
self.forcefield = {
'name': file_name.split('.')[0],
'fullname': file_name,
'path': path
}
else:
self.add_mol_itp(path)
# Check field
elif not ifdef and line.startswith("["):
# Remove space and [ ]
field = line.strip()[1:-1].strip()
# print(field)
# As intermolecular_inter field is empty
# (filled with bonds, angles, ...)
# It has to be checked now:
if field == 'intermolecular_interactions':
self.inter_interact = True
continue
# Check in the field :
elif (not ifdef and not line[0].startswith(";")
and line.strip() != ""):
if field == 'moleculetype':
# in the case where mol param are present in the top
# file, convert the top to an itp
# If mol_name variable is defined, give to the mol
# param this name
name_itp = os.path.basename(top_in)[:-3] + "itp"
logger.info("Molecule topologie present in {} "
", extract the topologie in a separate"
" file: {}".format(top_in, name_itp))
# Store and write the itp file:
top_itp = Itp(name=name_itp,
fullname=name_itp,
path=os.path.abspath(top_in))
top_itp.write_file(os.path.join(self.folder, name_itp))
top_itp.display()
# Add the itp to the itp_list
self.add_mol_itp(os.path.join(self.folder, name_itp))
self.include_itp = True
# Name of the system
elif field == 'system':
self.name = line.strip()
# Molecule composition of the system
elif field == 'molecules':
line_list = line.strip().split()
self.mol_comp.append({
'name': line_list[0],
'num': line_list[1]
})
# Following command concern
# intermolecular interactions
elif field == 'bonds':
bond_list.append(line.strip().split())
elif field == 'angles':
angle_list.append(line.strip().split())
elif field == 'dihedrals':
dihed_list.append(line.strip().split())
if self.inter_interact:
self.add_intermolecular_restr(bond_list=bond_list,
angle_list=angle_list,
dihed_list=dihed_list)