def calc_gii_pymatgen(self, struct, scale_factor=0.965):
"""Calculates global instability index using Pymatgen's bond valence sum
Args:
struct: Pymatgen Structure object
scale: Float, tunable scale factor for bond valence
Returns:
gii: Float, global instability index
"""
deviations = []
cutoff=self.r_cut
if struct.is_ordered:
for site in struct:
nn = struct.get_neighbors(site,r=cutoff)
bvs = bond_valence.calculate_bv_sum(site,
nn,
scale_factor=scale_factor)
deviations.append(bvs - site.species.elements[0].oxi_state)
gii = np.linalg.norm(deviations) / np.sqrt(len(deviations))
else:
for site in struct:
nn = struct.get_neighbors(site,r=cutoff)
bvs = bond_valence.calculate_bv_sum_unordered(site,
nn,
scale_factor=scale_factor)
min_diff = min(
[bvs - spec.oxi_state for spec in site.species.elements]
)
deviations.append(min_diff)
gii = np.linalg.norm(deviations) / np.sqrt(len(deviations))
return gii
def oxstates(structure, Bsite):
# This function estimates the oxidation state of the Bsite using bond valence methods
sites = structure.sites
Bsite_indexes = []
Bsite_ox = []
oxstate = 0
for site in sites:
if Bsite in str(site):
neighbors = structure.get_neighbors(site, r = 2.5)
oxstate = calculate_bv_sum(site, neighbors)
Bsite_ox.append(oxstate)
Bsite_specie = site.specie
if Bsite not in str(site) and 'O' not in str(site):
Asite_specie = site.specie
Bsite_ox = ceil(sum(Bsite_ox)/len(Bsite_ox))
Asite_ox = 6-Bsite_ox
# catch unusual oxidation states resulting from calculating on the Bsite oxidation state
if Asite_ox not in Asite_specie.common_oxidation_states or Bsite_ox not in Bsite_specie.common_oxidation_states:
if 3 in Asite_specie.common_oxidation_states:
Asite_ox = 3
else:
Asite_ox = max(Asite_specie.common_oxidation_states)
Bsite_ox = 6-Asite_ox
final_ox = {str(Asite_specie): Asite_ox, Bsite: Bsite_ox, 'O': -2}
return final_ox
def test_calculate_bv_sum(self):
s = Structure.from_file(os.path.join(test_dir, "LiMn2O4.json"))
neighbors = s.get_neighbors(s[0], 3.0)
bv_sum = calculate_bv_sum(s[0], neighbors)
self.assertAlmostEqual(bv_sum, 0.7723402182087497, places=5)
equi_sites = [[site] for site in structure]
# Sort the equivalent sites by decreasing electronegativity.
equi_sites = sorted(equi_sites,
key=lambda sites: -sites[0].species.average_electroneg)
# Get a list of valences and probabilities for each symmetrically
# distinct site.
all_prob = []
if structure.is_ordered:
for sites in equi_sites:
test_site = sites[0]
# print(test_site)
nn = structure.get_neighbors(test_site, 3.0)
bv_sum.append(pma.calculate_bv_sum(test_site, nn))
bv_elem.append(test_site.specie.symbol)
bv_type.append('Mineral')
#protein
d = '/home/kenneth/proj/proMin/proteins/feS'
with open(os.path.join(d, 'pdbNames.txt')) as f:
for i in f.readlines():
fi = os.path.join(d, i.strip() + '.pdb')
mol = Molecule.from_file(fi)
# print(dir(parser))
print('test1')
print(list(BV_PARAMS.keys()))
els = [
Element(el.symbol) for el in mol.composition.elements
if Element(el.symbol) in list(BV_PARAMS.keys())
# Sort the equivalent sites by decreasing electronegativity.
equi_sites = sorted(equi_sites,
key=lambda sites: -sites[0].species.average_electroneg)
# Get a list of valences and probabilities for each symmetrically
# distinct site.
all_prob = []
if structure.is_ordered:
for sites in equi_sites:
test_site = sites[0]
if test_site.specie.symbol in ['Fe']:
# print(test_site)
nn = structure.get_neighbors(test_site, 3.0)
bv_sum.append(round(pma.calculate_bv_sum(test_site, nn), 2))
bv_elem.append(test_site.specie.symbol)
bv_type.append('Mineral')
bv_name.append(m)
# print(bv_sum)
# exit()
#protein
# d = '/home/kenneth/proj/pro-min/proteins/feS/clusters/findGeo/combineFindGeoResults'
d = '/home/kenneth/proj/pro-min/proteins/feS/sites'
xyzs = glob(os.path.join(d, '*.xyz'))
for xyz in xyzs:
print(xyz)
if xyz != os.path.join(d, 'pdb.xyz'):
xyzObj = XYZ.from_file(xyz)