def _det_pdb_element(self, atom_name):
"""Try to determine the element from the PDB atom name.
@param atom_name: The PDB atom name.
@type atom_name: str
@return: The element name, or None if unsuccessful.
@rtype: str or None
"""
# Strip away the "'" character (for RNA, etc.).
element = atom_name.strip("'")
# Strip away atom numbering, from the front and end.
element = element.strip(digits)
# Amino acid atom translation table (note, numbers have been stripped already!).
table = {'C': ['CA', 'CB', 'CG', 'CD', 'CE', 'CH', 'CZ'],
'N': ['ND', 'NE', 'NH', 'NZ'],
'H': ['HA', 'HB', 'HG', 'HD', 'HE', 'HH', 'HT', 'HZ'],
'O': ['OG', 'OD', 'OE', 'OH', 'OT'],
'S': ['SD', 'SG']
}
# Translate amino acids.
for key in table:
if element in table[key]:
element = key
break
# Return the element if it is in the periodic table.
if periodic_table.has_element(symbol=element):
return element
# Else, throw a warning.
warn(RelaxWarning("Cannot determine the element associated with atom '%s'." % atom_name))
def _det_pdb_element(self, atom_name):
"""Try to determine the element from the PDB atom name.
@param atom_name: The PDB atom name.
@type atom_name: str
@return: The element name, or None if unsuccessful.
@rtype: str or None
"""
# Strip away the "'" character (for RNA, etc.).
element = atom_name.strip("'")
# Strip away atom numbering, from the front and end.
element = element.strip(digits)
# Amino acid atom translation table (note, numbers have been stripped already!).
table = {
'C': ['CA', 'CB', 'CG', 'CD', 'CE', 'CH', 'CZ'],
'N': ['ND', 'NE', 'NH', 'NZ'],
'H': ['HA', 'HB', 'HG', 'HD', 'HE', 'HH', 'HT', 'HZ'],
'O': ['OG', 'OD', 'OE', 'OH', 'OT'],
'S': ['SD', 'SG']
}
# NMR Pseudo-atoms (with trailing numbers stripped).
table['H'] += [
'QA', 'QB', 'QD', 'QE', 'QG', 'QH', 'QQD', 'QQG', 'QR', 'QZ'
]
# Translate amino acids.
for key in table:
if element in table[key]:
element = key
break
# Return the element if it is in the periodic table.
if periodic_table.has_element(symbol=element):
return element
# Else, throw a warning.
warn(
RelaxWarning(
"Cannot determine the element associated with atom '%s'." %
atom_name))
def test_has_element_XYZ(self):
"""Test of the Periodic_table.has_element() method with the symbol 'XYZ'."""
# Check.
self.assertTrue(not periodic_table.has_element('XYZ'))
def test_has_element_Ni(self):
"""Test of the Periodic_table.has_element() method with the symbol 'Ni'."""
# Check.
self.assertTrue(periodic_table.has_element('Ni'))
def test_has_element_XYZ(self):
"""Test of the Periodic_table.has_element() method with the symbol 'XYZ'."""
# Check.
self.assertTrue(not periodic_table.has_element("XYZ"))
def test_has_element_Ni(self):
"""Test of the Periodic_table.has_element() method with the symbol 'Ni'."""
# Check.
self.assertTrue(periodic_table.has_element("Ni"))
