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 CCP4ResolutionLimit(resolution_limit):
'''Construct a resolution limit object.'''
float_type = type(0.0)
assert (type(resolution_limit) is float_type)
return _CCP4ResolutionLimit(resolution=_XSDataFloat(resolution_limit))
def CCP4ResolutionLimit(resolution_limit):
'''Construct a resolution limit object.'''
float_type = type(0.0)
assert(type(resolution_limit) is float_type)
return _CCP4ResolutionLimit(
resolution = _XSDataFloat(resolution_limit))
def CCP4UnitCell(a, b, c, alpha, beta, gamma):
'''Usefully create a unit cell object from the Python floats for the
cell constants. N.B. for reasons unclear this must first pun the floats.'''
float_type = type(0.0)
assert (type(a) is float_type)
assert (type(b) is float_type)
assert (type(c) is float_type)
assert (type(alpha) is float_type)
assert (type(beta) is float_type)
assert (type(gamma) is float_type)
_a = _XSDataFloat(a)
_b = _XSDataFloat(b)
_c = _XSDataFloat(c)
_alpha = _XSDataFloat(alpha)
_beta = _XSDataFloat(beta)
_gamma = _XSDataFloat(gamma)
return _CCP4UnitCell(a=_a,
b=_b,
c=_c,
alpha=_alpha,
beta=_beta,
gamma=_gamma)
def CCP4UnitCell(a, b, c, alpha, beta, gamma):
'''Usefully create a unit cell object from the Python floats for the
cell constants. N.B. for reasons unclear this must first pun the floats.'''
float_type = type(0.0)
assert(type(a) is float_type)
assert(type(b) is float_type)
assert(type(c) is float_type)
assert(type(alpha) is float_type)
assert(type(beta) is float_type)
assert(type(gamma) is float_type)
_a = _XSDataFloat(a)
_b = _XSDataFloat(b)
_c = _XSDataFloat(c)
_alpha = _XSDataFloat(alpha)
_beta = _XSDataFloat(beta)
_gamma = _XSDataFloat(gamma)
return _CCP4UnitCell(a = _a, b = _b, c = _c,
alpha = _alpha, beta = _beta, gamma = _gamma)
def CCP4RTMatrix(e11, e12, e13,
e21, e22, e23,
e31, e32, e33,
e41, e42, e43):
'''A useful constructor for RT matrices.'''
float_type = type(0.0)
assert(type(e11) is float_type)
assert(type(e12) is float_type)
assert(type(e13) is float_type)
assert(type(e21) is float_type)
assert(type(e22) is float_type)
assert(type(e23) is float_type)
assert(type(e31) is float_type)
assert(type(e32) is float_type)
assert(type(e33) is float_type)
assert(type(e41) is float_type)
assert(type(e42) is float_type)
assert(type(e43) is float_type)
_e11 = _XSDataFloat(e11)
_e12 = _XSDataFloat(e12)
_e13 = _XSDataFloat(e13)
_e21 = _XSDataFloat(e21)
_e22 = _XSDataFloat(e22)
_e23 = _XSDataFloat(e23)
_e31 = _XSDataFloat(e31)
_e32 = _XSDataFloat(e32)
_e33 = _XSDataFloat(e33)
_e41 = _XSDataFloat(e41)
_e42 = _XSDataFloat(e42)
_e43 = _XSDataFloat(e43)
return _CCP4RTMatrix(e11 = _e11, e12 = _e12, e13 = _e13,
e21 = _e21, e22 = _e22, e23 = _e23,
e31 = _e31, e32 = _e32, e33 = _e33,
e41 = _e41, e42 = _e42, e43 = _e43)
def CCP4RTMatrix(e11, e12, e13, e21, e22, e23, e31, e32, e33, e41, e42, e43):
'''A useful constructor for RT matrices.'''
float_type = type(0.0)
assert (type(e11) is float_type)
assert (type(e12) is float_type)
assert (type(e13) is float_type)
assert (type(e21) is float_type)
assert (type(e22) is float_type)
assert (type(e23) is float_type)
assert (type(e31) is float_type)
assert (type(e32) is float_type)
assert (type(e33) is float_type)
assert (type(e41) is float_type)
assert (type(e42) is float_type)
assert (type(e43) is float_type)
_e11 = _XSDataFloat(e11)
_e12 = _XSDataFloat(e12)
_e13 = _XSDataFloat(e13)
_e21 = _XSDataFloat(e21)
_e22 = _XSDataFloat(e22)
_e23 = _XSDataFloat(e23)
_e31 = _XSDataFloat(e31)
_e32 = _XSDataFloat(e32)
_e33 = _XSDataFloat(e33)
_e41 = _XSDataFloat(e41)
_e42 = _XSDataFloat(e42)
_e43 = _XSDataFloat(e43)
return _CCP4RTMatrix(e11=_e11,
e12=_e12,
e13=_e13,
e21=_e21,
e22=_e22,
e23=_e23,
e31=_e31,
e32=_e32,
e33=_e33,
e41=_e41,
e42=_e42,
e43=_e43)
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))
