Properties

Properties

class sasmol.properties.Atomic

Bases: object

Class containing methods to define physical properties

and atomic information used by other modules.

http://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=&ascii=html&isotype=some

standard atomic weight is based on the natural istopic composition

Examples

>>> import sasmol.properties as properties
>>> properties = properties.Atomic()
>>> properties.amu()['FE']
55.8452

Note

self parameter is not shown in the Parameters section in the documentation

amino_acid_sld(**kwargs)

Parameters

kwargs – optional future arguments

Returns

dictionary : residue name, and sld information residue name : [vol Ang^3, eSL, SLprot Ang, SLdeut Ang, #exchngH]

Return type

residue_scattering

Examples

>>> import sasmol.properties as properties
>>> properties = properties.Atomic()
>>> properties.amino_acid_sld()['PRO']
[112.7, 52, 22.2207, 95.104, 0]

Note

Need to validate units here used in neutron reflectivity versus small-angle scattering

amu(**kwargs)

Parameters

kwargs – optional future arguments

Returns

dictionary : containing standard atomic weights

Return type

standard_atomic_weights

Examples

>>> import sasmol.properties as properties
>>> properties = properties.Atomic()
>>> properties.amu()['FE']
55.8452

dna_scattering_lengths(**kwargs)

Parameters

kwargs – optional future arguments

Returns

dictionary : DNA scattering information

Return type

dna_scattering_lengths

dna_sl(**kwargs)

element_scattering_lengths(**kwargs)

Parameters

kwargs – optional future arguments

Returns

dictionary : element name and scattering information

Return type

element_scattering_lengths

element_sl(**kwargs)

nucleotide_scattering_lengths(**kwargs)

Parameters

kwargs – optional future arguments

Returns

dictionary : nucleotide scattering information

Return type

nucleotide_scattering_lengths

nucleotide_sl(**kwargs)

one_to_three_letter_nucleic_residue_dictionary = {'A': 'ADE', 'C': 'CYT', 'G': 'GUA', 'T': 'THY', 'U': 'URA'}

one_to_three_letter_protein_residue_dictionary = {'A': 'ALA', 'C': 'CYS', 'D': 'ASP', 'E': 'GLU', 'F': 'PHE', 'G': 'GLY', 'H': 'HSE', 'I': 'ILE', 'K': 'LYS', 'L': 'LEU', 'M': 'MET', 'N': 'ASN', 'P': 'PRO', 'Q': 'GLN', 'R': 'ARG', 'S': 'SER', 'T': 'THR', 'V': 'VAL', 'W': 'TRP', 'Y': 'TYR'}

protein_scattering_lengths(**kwargs)

Parameters

kwargs – optional future arguments

Returns

dictionary : protein scattering information

Return type

protein_scattering_lengths

protein_sl(**kwargs)

rna_scattering_lengths(**kwargs)

Parameters

kwargs – optional future arguments

Returns

dictionary : RNA scattering information

Return type

rna_scattering_lengths

rna_sl(**kwargs)

van_der_Waals_radii(**kwargs)

van_der_waals_radii(**kwargs)

Parameters

kwargs – optional future arguments

Returns

dictionary : element name and van der Waals radius

Return type

van_der_waals_radii