def CCP4Sequence(aa_sequence):
'''From a list of amino acids as three letter codes construct the
one-letter code, number of residues and total mass.'''
list_type = type([])
assert(type(aa_sequence) is list_type)
three_to_one = {'CYS': 'C', 'ASP': 'D', 'SER': 'S', 'GLN': 'Q',
'LYS': 'K', 'ILE': 'I', 'PRO': 'P', 'THR': 'T',
'PHE': 'F', 'ALA': 'A', 'GLY': 'G', 'HIS': 'H',
'GLU': 'E', 'LEU': 'L', 'ARG': 'R', 'TRP': 'W',
'VAL': 'V', 'ASN': 'N', 'TYR': 'Y', 'MET': 'M',
'MSE': 'M'}
three_to_mass = {'CYS': 121, 'ASP': 133, 'SER': 105, 'GLN': 146,
'LYS': 146, 'ASN': 132, 'PRO': 115, 'THR': 119,
'PHE': 165, 'ALA': 89, 'HIS': 155, 'GLY': 75,
'ILE': 131, 'LEU': 131, 'ARG': 174, 'TRP': 204,
'VAL': 117, 'GLU': 147, 'TYR': 181, 'MET': 149,
'MSE': 149}
sequence = ''
mass = 0
number = 0
for aa in aa_sequence:
sequence += three_to_one[aa]
mass += three_to_mass[aa]
number += 1
return _CCP4Sequence(oneLetterCode = _XSDataString(sequence),
numberOfResidues = _XSDataInteger(number),
molecularMass = _XSDataFloat(mass))
def CCP4SpaceGroup(space_group_name):
'''From a space group name, construct and populate a CCP4SpaceGroup
object. N.B. that this will parse the spacegroup information from CCTBX
to get the required information.'''
string_type = type(' ')
assert(type(space_group_name) is string_type)
space_group_symbols = cctbx_space_group_symbols(space_group_name)
space_group_number = space_group_symbols.number()
space_group_name = space_group_symbols.hermann_mauguin()
ccp4_space_group = _CCP4SpaceGroup(
name = _XSDataString(space_group_name),
number = _XSDataInteger(space_group_number))
# now unpack and populate the symmetry operations
space_group = cctbx_space_group(space_group_symbols)
for ltr in space_group.ltr():
for smx in space_group.smx():
symop = smx + ltr
ccp4_space_group.addSymmetryOperations(
CCP4SymmetryOperation(symop.as_xyz()))
return ccp4_space_group
def CCP4SpaceGroup(space_group_name):
'''From a space group name, construct and populate a CCP4SpaceGroup
object. N.B. that this will parse the spacegroup information from CCTBX
to get the required information.'''
string_type = type(' ')
assert (type(space_group_name) is string_type)
space_group_symbols = cctbx_space_group_symbols(space_group_name)
space_group_number = space_group_symbols.number()
space_group_name = space_group_symbols.hermann_mauguin()
ccp4_space_group = _CCP4SpaceGroup(
name=_XSDataString(space_group_name),
number=_XSDataInteger(space_group_number))
# now unpack and populate the symmetry operations
space_group = cctbx_space_group(space_group_symbols)
for ltr in space_group.ltr():
for smx in space_group.smx():
symop = smx + ltr
ccp4_space_group.addSymmetryOperations(
CCP4SymmetryOperation(symop.as_xyz()))
return ccp4_space_group
def CCP4ReturnStatus(code = 0, message = ''):
'''Generate a ccp4 return status - by default assumes all is well.'''
integer_type = type(0)
string_type = type(' ')
assert(type(code) is integer_type)
assert(type(message) is string_type)
return _CCP4ReturnStatus(code = _XSDataInteger(code),
message = _XSDataString(message))
def CCP4ReturnStatus(code=0, message=''):
'''Generate a ccp4 return status - by default assumes all is well.'''
integer_type = type(0)
string_type = type(' ')
assert (type(code) is integer_type)
assert (type(message) is string_type)
return _CCP4ReturnStatus(code=_XSDataInteger(code),
message=_XSDataString(message))
def CCP4Sequence(aa_sequence):
'''From a list of amino acids as three letter codes construct the
one-letter code, number of residues and total mass.'''
list_type = type([])
assert (type(aa_sequence) is list_type)
three_to_one = {
'CYS': 'C',
'ASP': 'D',
'SER': 'S',
'GLN': 'Q',
'LYS': 'K',
'ILE': 'I',
'PRO': 'P',
'THR': 'T',
'PHE': 'F',
'ALA': 'A',
'GLY': 'G',
'HIS': 'H',
'GLU': 'E',
'LEU': 'L',
'ARG': 'R',
'TRP': 'W',
'VAL': 'V',
'ASN': 'N',
'TYR': 'Y',
'MET': 'M',
'MSE': 'M'
}
three_to_mass = {
'CYS': 121,
'ASP': 133,
'SER': 105,
'GLN': 146,
'LYS': 146,
'ASN': 132,
'PRO': 115,
'THR': 119,
'PHE': 165,
'ALA': 89,
'HIS': 155,
'GLY': 75,
'ILE': 131,
'LEU': 131,
'ARG': 174,
'TRP': 204,
'VAL': 117,
'GLU': 147,
'TYR': 181,
'MET': 149,
'MSE': 149
}
sequence = ''
mass = 0
number = 0
for aa in aa_sequence:
sequence += three_to_one[aa]
mass += three_to_mass[aa]
number += 1
return _CCP4Sequence(oneLetterCode=_XSDataString(sequence),
numberOfResidues=_XSDataInteger(number),
molecularMass=_XSDataFloat(mass))
