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))