def run_multiprocessing(a_grofileName):
# --------------------------------------------------------------------
# Getting topology for molec0 and molec1
# --------------------------------------------------------------------
itpmolec0 = Topology.fromItpFile(workdir, molec0_ipt, Hydros0)
itpmolec0.fromGroFile(workdir, a_grofileName)
itpmolec1 = Topology.fromItpFile(workdir, molec1_itp, Hydros1)
itpmolec1.fromGroFile(workdir, a_grofileName)
# --------------------------------------------------------------------
# Getting the molecules0 and molecules1 corresponding to the itpmolec0 and itpmolec1, respectvely
# --------------------------------------------------------------------
grofile = FileUtil.FileReader(workdir, a_grofileName).file
print('\nGetting all molec0 molecules present in grofile: {}\n'.format(a_grofileName))
molecs0_dict = add.get_molecules(itpmolec0, grofile)
print('\nGetting all molec1 molecules present in grofile: {}\n'.format(a_grofileName))
molecs1_dict = add.get_molecules(itpmolec1, grofile)
# --------------------------------------------------------------------
# Getting h-bonds interactions
# --------------------------------------------------------------------
# h-bonds interactions between molec0 and molec1. Where in molec0 we get X-H bond and in molec 1 we get Y
# ------------------------------
print('\nThe hydrogen bonds found between X-H from molec0 and Y from molec1 present in grofile {} are:\n'.format(a_grofileName))
hbonds0_list = add.get_bonded_interactions(molecs0_dict, itpmolec0, molecs1_dict, Hydros1, Alkali1, dist_thres, angle_thres)
if not hbonds0_list:
print('\nNo hydrogen bonds found between X-H from molec0 and Y from molec1 present in grofile {}\n'.format(a_grofileName))
else:
print('\nA total of {} hydrogen bonds found between X-H from molec0 and Y from molec1 present in grofile {}\n'.format(str(len(hbonds0_list)), a_grofileName))
# h-bonds interactions between molec0 and molec1. Where in molec0 we get X-H bond and in molec 1 we get Y
# ------------------------------
print('\nThe hydrogen bonds found between X-H from molec1 and Y from molec0 present in grofile {} are:\n'.format(a_grofileName))
hbonds1_list = add.get_bonded_interactions(molecs1_dict, itpmolec1, molecs0_dict, Hydros0, Alkali0, dist_thres, angle_thres)
if not hbonds1_list:
print('\nNo hydrogen bonds found between X-H from molec1 and Y from molec0 present in grofile {}\n'.format(a_grofileName))
else:
print('\nA total of {} hydrogen bonds found between X-H from molec1 and Y from molec0 present in grofile {}\n'.format(str(len(hbonds1_list)), a_grofileName))
# adding both list
# ------------------------------
hbond_list = hbonds0_list + hbonds1_list # we just add them
del(itpmolec0, itpmolec1, grofile, molecs0_dict, molecs1_dict, hbonds0_list, hbonds1_list) # delete things to free space in case we run out of memory during the multiprocessing
return hbond_list
# -------------------------------------------------------------------------------------------------
# Plotting the number of hydrogen bonds for each one of the different grofiles
# -------------------------------------------------------------------------------------------------
plotObj = HbondsPlotter(all_hbonds) # creating the HbondsPlotter object from the all_bonds list
plotObj.plot(workdir, frame_time) # method to print all the h-bonds plots.
print('\nFinished all plots!\n')
# -------------------------------------------------------------------------------------------------
# Getting the density profile using gmx density
# -------------------------------------------------------------------------------------------------
# Getting the residue name for molec0 and molec1 (see Topology.py for more info)
# ------------------------------
molec0_residue= Topology.fromItpFile(workdir, molec0_ipt, Hydros0).residue
molec1_residue = Topology.fromItpFile(workdir, molec1_itp, Hydros1).residue
# Getting the z-axis length of the grofile (any grofile can be used)
# ------------------------------
zBoxLen = float(FileUtil.FileReader(workdir, grofiles[-1]).file[-1].split()[2]) # Any grofile can be used. The last was selected.
# Getting the density file file
# ------------------------------
add.get_gmx_index_density_files(workdir, all_hbonds, molec0_residue, molec1_residue,
zBoxLen, gmx_call, grofiles[-1], xtc_filename,
tpr_filename, outdens_xvg)
print('\nDensity profile was calculated sucessfully!\n')
