def run(pluginManager):
"""
Entry point for the plugin manager
:param configx: plugin manager instance
:return: None
"""
printer = pluginManager.setup()
molecule = quickLoad(pluginManager, pluginManager.arg('load'))
printer('Filtering Atoms:')
for atom in iter_atoms(molecule):
if filter_atom(pluginManager, atom, 'atomfilter'):
printer(atom)
printer.spacer()
printer('\nFiltering Atom Pairs:')
for atom1, atom2 in iter_atom_pairs(molecule, bound=False, unique=False):
if filter_atom_pair(pluginManager, atom1, atom2, 'atomfilter', 'secondfilter'):
printer('{} {}'.format(atom1.get_name(), atom2.get_name()))
printer.spacer()
printer('\nUsing Custom Filter Function:')
filter.register_custom_fuction('firstOf', firstOfElement)
for atom in iter_atoms(molecule):
if filter_atom(pluginManager, atom, 'customfilter'):
printer(atom)
def run(pluginManager):
"""
Entry point for the plugin manager
:param pluginManager: plugin manager instance
:return: None
"""
printer = pluginManager.setup()
molecule = quickLoad(pluginManager, pluginManager.arg("load"))
printer("Filtering Atoms:")
for atom in iter_atoms(molecule):
if filter_atom(pluginManager, atom, "atomfilter"):
printer(atom)
printer.spacer()
printer("\nFiltering Atom Pairs:")
for atom1, atom2 in iter_atom_pairs(molecule, bound=False, unique=False):
if filter_atom_pair(pluginManager, atom1, atom2, "atomfilter", "secondfilter"):
printer("{} {}".format(atom1.get_name(), atom2.get_name()))
printer.spacer()
printer("\nUsing Custom Filter Function:")
filter.register_custom_fuction("firstOf", firstOfElement)
for atom in iter_atoms(molecule):
if filter_atom(pluginManager, atom, "customfilter"):
printer(atom)
def Uiso(data, logfile):
"""
Method for calculating the size of U_iso hydrogen ADP
relative the the U_iso ADP of the bonding partner.
"""
printer.register_file(logfile, 'log', mode='a')
# isofilters, isopartnerfilters = set_filter()
#===========================================================================
# keys=['cart_int','cart_ext','cart_sum','cart_meas','iso_meas']
#===========================================================================
use1, use2 = None, None
try:
use = config.arg('iso').split(':')
use1 = use[0]
use2 = use[1]
except:
use1 = 'cart_sum'
use2 = 'cart_sum'
# printer('\nSelected filters:\n\n Attribute | Value | True | Function'
# '\n===================================================\nAtom filter: | | |')
# for isofilter in isofilters:
# printer('{:15s} | {:12s} | {:5s} | {}'.format(isofilter[0], isofilter[1], isofilter[2], isofilter[3]))
# printer('-----------------|--------------|-------|----------\nPartner filter: | | |')
# for isofilter in isopartnerfilters:
# printer('{:15s} | {:12s} | {:5s} | {}'.format(isofilter[0], isofilter[1], isofilter[2], isofilter[3]))
printer('\nComparing {} of hydrogen atoms\nwith {} of parent atoms.\n'.format(use1, use2))
printer(' Riding | Parent | U_rel | U_rel\n atom | atom | geom | arith')
printer(' ================================')
geom_sum = []
arit_sum = []
for atom in data['exp'].atoms:
# if apply_filter(atom, isofilters):
for heavy_atom in cg.get_framework_neighbours(atom, useH=True):
if not atom == heavy_atom and filter_atom_pair(config, atom, heavy_atom):
U_rel_geom = cg.Uiso(atom.adp[use1]) / cg.Uiso(heavy_atom.adp[use2])
geom_sum.append(U_rel_geom)
U_rel_arith = cg.Uiso(atom.adp[use1], mean='arithmetic') / \
cg.Uiso(heavy_atom.adp[use2], mean='arithmetic')
arit_sum.append(U_rel_arith)
printer(' {light:5s} | {heavy:5s} | {U:5.3f} | {U2:5.3f}'.format(light=atom.name,
heavy=heavy_atom,
U=U_rel_geom,
U2=U_rel_arith))
printer(' -------|--------|-------|-------')
printer(' {light:5s} | {heavy:5s} | {U:5.3f} | {U2:5.3f}'.format(light='mean',
heavy='---',
U=np.mean(geom_sum),
U2=np.mean(arit_sum)))
printer(' {light:5s} | {heavy:5s} | {U:5.3f} | {U2:5.3f}'.format(light='SD',
heavy='---',
U=np.std(geom_sum),
U2=np.std(arit_sum)))
printer('{temp:.1f} {U:5.3f} {Uer:5.3f} {U2:5.3f} {U2er:5.3f}'.format(temp=data.temperature,
U=np.mean(geom_sum),
Uer=np.std(geom_sum),
U2=np.mean(arit_sum),
U2er=np.std(arit_sum)),
use=['log'])
printer.spacer()
