def getParams(self):
# obtain LJ and Elec params
#*********************************************************************************#
vdw = [None,] # combined list of all vdw params from all ct's
chg = [0.0,] # combined list of all charges from all ct's
ct_list = [e for e in ffiostructure.CMSReader(self.cmsname)]
struct_ct = ct_list[1:] # this means this works only on cms files with separate CT blocks
# get tota number of solute atoms
for ct in struct_ct:
ct_chg = []
ct_vdw = []
vdw_type = {} # dict of vdw types, Vdw object in this list are uninitialized
for e in ct.ffio.vdwtype :
vdw_type[e.name] = Vdw( (e.name,), e.funct, (e.c1, e.c2,) )
#print (e.name,), e.funct, (e.c1, e.c2,)
for e in ct.ffio.site: # for each site (i.e., an atom in most cases)
ct_vdw.append( vdw_type[e.vdwtype] ) # add to vdw list for this ct
ct_chg.append(e.charge)
#print e.index, e.charge*18.2223
ct_vdw *= int(ct.atom_total / len( ct.ffio.site ))
ct_chg *= int(ct.atom_total / len( ct.ffio.site ))
#print int(ct.atom_total / len( ct.ffio.site ))
vdw.extend( ct_vdw )
chg.extend( ct_chg)
chg = np.asarray(chg)*18.2223
vdw_params = [[0,0],]
#print len(chg)
#print len(all_at_ids)
for v in vdw[1:]:
vdw_params.extend([v.c])
vdw_params = np.asarray(vdw_params)
return (chg, vdw_params)
def write_nonbonded_parameters(cms_file):
vdw = [] # combined list of all vdw params from all ct's
chg = [] # combined list of all charges from all ct's
ct_list = [e for e in ffiostructure.CMSReader(cms_file)]
# this means this works only on cms files with separate CT blocks
struct_ct = ct_list[1:]
# get total number of solute atoms
for ct in struct_ct:
# print ct.atom_total, len(ct.ffio.site), len(ct.ffio.pseudo)
# else: # do the normal parsing
ct_vdw = [] # list of vdw objects for each ct
ct_chg = []
ct_pseudo_vdw = []
ct_pseudo_chg = []
n_atomic_sites = 0
n_pseudo_sites = 0
vdw_type = {
} # dict of vdw types, Vdw object in this list are uninitialized
for e in ct.ffio.vdwtype:
vdw_type[e.name] = Vdw((e.name, ), e.funct, (
e.c1,
e.c2,
))
#print (e.name,), e.funct, (e.c1, e.c2,)
# for each site (i.e., an atom in most cases)
for e in ct.ffio.site:
# print e.type.lower()
if e.type.lower() == 'pseudo':
# add to vdw list for this ct
ct_pseudo_vdw.append(vdw_type[e.vdwtype])
ct_pseudo_chg.append(e.charge)
n_pseudo_sites += 1
else:
# add to vdw list for this ct
ct_vdw.append(vdw_type[e.vdwtype])
ct_chg.append(e.charge)
n_atomic_sites += 1
# print e.index, e.charge
# check if this site belongs to pseudoparticle, if yes raise corresponding number
# print n_atomic_sites, n_pseudo_sites
ct_vdw *= int(ct.atom_total / n_atomic_sites)
ct_chg *= int(ct.atom_total / n_atomic_sites)
vdw.extend(ct_vdw)
chg.extend(ct_chg)
if n_pseudo_sites != 0:
ct_pseudo_vdw *= int(len(ct.ffio.pseudo) / n_pseudo_sites)
ct_pseudo_chg *= int(len(ct.ffio.pseudo) / n_pseudo_sites)
# print int(ct.atom_total / len( ct.ffio.site ))
vdw.extend(ct_pseudo_vdw)
chg.extend(ct_pseudo_chg)
chg = np.asarray(chg) * 18.2223
vdw_params = []
for v in vdw:
vdw_params.extend([v.c])
vdw_params = np.asarray(vdw_params)
with open(cms_file[0:-4] + "_cms_nb_parms.txt", "w") as f:
for i in range(vdw_params.shape[0]):
f.write("{0:.8f} {1:.8f} {2:.8f}\n".format(chg[i], vdw_params[i,
0],
vdw_params[i, 1]))
def _getNonbondedParams(self):
# obtain LJ and Elec params
#*********************************************************************************#
vdw = [] # combined list of all vdw params from all ct's
chg = [] # combined list of all charges from all ct's
ct_list = [e for e in ffiostructure.CMSReader(self.cmsname)]
struct_ct = ct_list[
1:] # this means this works only on cms files with separate CT blocks
# get total number of solute atoms
for ct in struct_ct:
#print ct.atom_total, len(ct.ffio.site), len(ct.ffio.pseudo)
#else: # do the normal parsing
ct_vdw = [] # list of vdw objects for each ct
ct_chg = []
ct_pseudo_vdw = []
ct_pseudo_chg = []
n_atomic_sites = 0
n_pseudo_sites = 0
vdw_type = {
} # dict of vdw types, Vdw object in this list are uninitialized
for e in ct.ffio.vdwtype:
vdw_type[e.name] = Vdw((e.name, ), e.funct, (
e.c1,
e.c2,
))
#print (e.name,), e.funct, (e.c1, e.c2,)
for e in ct.ffio.site: # for each site (i.e., an atom in most cases)
#print e.type.lower()
if e.type.lower() == 'pseudo':
ct_pseudo_vdw.append(
vdw_type[e.vdwtype]) # add to vdw list for this ct
ct_pseudo_chg.append(e.charge)
n_pseudo_sites += 1
else:
ct_vdw.append(
vdw_type[e.vdwtype]) # add to vdw list for this ct
ct_chg.append(e.charge)
n_atomic_sites += 1
#print e.index, e.charge
# check if this site belongs to pseudoparticle, if yes raise corresponding number
#print n_atomic_sites, n_pseudo_sites
ct_vdw *= int(ct.atom_total / n_atomic_sites)
ct_chg *= int(ct.atom_total / n_atomic_sites)
vdw.extend(ct_vdw)
chg.extend(ct_chg)
if n_pseudo_sites != 0:
ct_pseudo_vdw *= int(len(ct.ffio.pseudo) / n_pseudo_sites)
ct_pseudo_chg *= int(len(ct.ffio.pseudo) / n_pseudo_sites)
#print int(ct.atom_total / len( ct.ffio.site ))
vdw.extend(ct_pseudo_vdw)
chg.extend(ct_pseudo_chg)
chg = np.asarray(chg) * 18.2223
vdw_params = []
for v in vdw:
vdw_params.extend([v.c])
vdw_params = np.asarray(vdw_params)
#tmp_wat_ids = self.getWaterIndices(np.asarray([self.wat_atom_ids[0]]))[0]
#tmp_wat_gids = self.getWaterIndices(np.asarray([self.wat_atom_ids[0]]))[1]
#print tmp_wat_ids, tmp_wat_gids
#print chg[tmp_wat_gids]
#print vdw_params[tmp_wat_gids]
#print vdw_params[self.water_atom_ids-1]
return (chg, vdw_params)