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#!/usr/bin/env python
import unittest
import gemmi
from gemmi import Element, IT92_get_exact, IT92_set_ignore_charge
class TestElem(unittest.TestCase):
def test_name(self):
for name in ELEMENT_MASS:
el = Element(name)
self.assertEqual(el.name, name)
self.assertEqual(Element('AL').name, 'Al')
self.assertEqual(Element('al').name, 'Al')
# We check only the first two characters now.
self.assertEqual(Element('alt').name, 'Al')
self.assertEqual(Element('Q').name, 'X')
self.assertEqual(Element('QQ').name, 'X')
self.assertEqual(Element('--').name, 'X')
self.assertEqual(Element('').name, 'X')
def test_weight(self):
for name, mass in ELEMENT_MASS.items():
self.assertAlmostEqual(Element(name).weight, mass, delta=1e-3)
def test_atomic_number(self):
self.assertEqual(Element('O').atomic_number, 8)
self.assertEqual(Element('D').atomic_number, 1)
self.assertEqual(Element('X').atomic_number, 0)
for n in range(119):
self.assertEqual(Element(n).atomic_number, n)
def test_properties(self):
self.assertEqual(Element('K').vdw_r, 2.75)
def test_coef(self):
h = Element('H')
d = Element('D')
fe = Element('Fe')
cf = Element('Cf')
es = Element('Es')
self.assertIsNotNone(cf.it92)
self.assertIsNotNone(cf.c4322)
self.assertIsNone(es.it92)
self.assertIsNone(es.c4322)
self.assertEqual(h.it92.get_coefs(), d.it92.get_coefs())
self.assertEqual(h.c4322.get_coefs(), d.c4322.get_coefs())
self.assertEqual(Element('X').it92.get_coefs(),
Element('O').it92.get_coefs())
fe_coefs = fe.it92.get_coefs()
fe0_coefs = IT92_get_exact(fe, 0).get_coefs()
IT92_set_ignore_charge(False)
fe2_coefs = IT92_get_exact(fe, 2).get_coefs()
self.assertIsNone(IT92_get_exact(fe, 4))
self.assertEqual(fe_coefs, fe0_coefs)
self.assertNotEqual(fe_coefs, fe2_coefs)
def test_resinfo(self):
for i in gemmi.resinfo_table():
ri = gemmi.find_tabulated_residue(i.name)
self.assertEqual(ri.name, i.name)
ELEMENT_MASS = {
'H': 1.00794, 'He': 4.0026, 'Li': 6.941, 'Be': 9.012182, 'B': 10.811,
'C': 12.0107, 'N': 14.0067, 'O': 15.9994, 'F': 18.998403, 'Ne': 20.1797,
'Na': 22.98977, 'Mg': 24.305, 'Al': 26.981539, 'Si': 28.0855,
'P': 30.973761, 'S': 32.065, 'Cl': 35.453, 'Ar': 39.948,
'K': 39.0983, 'Ca': 40.078, 'Sc': 44.95591, 'Ti': 47.867, 'V': 50.9415,
'Cr': 51.9961, 'Mn': 54.93805, 'Fe': 55.845, 'Co': 58.9332,
'Ni': 58.6934, 'Cu': 63.546, 'Zn': 65.38, 'Ga': 69.723, 'Ge': 72.64,
'As': 74.9216, 'Se': 78.96, 'Br': 79.904, 'Kr': 83.798,
'Rb': 85.4678, 'Sr': 87.62, 'Y': 88.90585, 'Zr': 91.224, 'Nb': 92.9064,
'Mo': 95.95, 'Tc': 98, 'Ru': 101.07, 'Rh': 102.9055, 'Pd': 106.42,
'Ag': 107.8682, 'Cd': 112.411, 'In': 114.818, 'Sn': 118.71, 'Sb': 121.76,
'Te': 127.6, 'I': 126.90447, 'Xe': 131.293, 'Cs': 132.905, 'Ba': 137.327,
'La': 138.905, 'Ce': 140.116, 'Pr': 140.908, 'Nd': 144.24, 'Pm': 145,
'Sm': 150.36, 'Eu': 151.964, 'Gd': 157.25, 'Tb': 158.925, 'Dy': 162.5,
'Ho': 164.93, 'Er': 167.259, 'Tm': 168.934, 'Yb': 173.05, 'Lu': 174.967,
'Hf': 178.49, 'Ta': 180.948, 'W': 183.84, 'Re': 186.207, 'Os': 190.23,
'Ir': 192.217, 'Pt': 195.084, 'Au': 196.967, 'Hg': 200.59, 'Tl': 204.383,
'Pb': 207.2, 'Bi': 208.98, 'Po': 209, 'At': 210, 'Rn': 222,
'Fr': 223, 'Ra': 226, 'Ac': 227, 'Th': 232.038, 'Pa': 231.036,
'U': 238.029, 'Np': 237, 'Pu': 244, 'Am': 243, 'Cm': 247,
'Bk': 247, 'Cf': 251, 'Es': 252, 'Fm': 257, 'Md': 258,
'No': 259, 'Lr': 262, 'Rf': 267, 'Db': 268, 'Sg': 271,
'Bh': 272, 'Hs': 270, 'Mt': 276,
'D': 2.0141, 'X': 1,
}
if __name__ == '__main__':
unittest.main()
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