Properties

Properties

class 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

charmm_names(**kwargs)

Parameters:kwargs – optional future arguments Returns:dictionary : atom_name and list of atom names for hydrogen, carbon, nitrogen, oxygen, sulfur, phosphorus, other Return type:charmm_names

Examples

>>> import sasmol.properties as properties
>>> properties = properties.Atomic()
>>> properties.charmm_names()['sulfur']
['SG', 'SD', '1SG', '2SG']

create_fasta(**kwargs)

Method to make a fasta file compatible lists of residue names

http://en.wikipedia.org/wiki/FASTA_format

Parameters:kwargs – optional future arguments Returns:sets the fasta attribute in a system object Return type:self._fasta

Examples

>>> import sasmol.system as system
>>> molecule = system.Molecule("hiv1_gag.pdb")
>>> molecule.create_fasta()
>>> molecule.fasta()[:5]
['G', 'A', 'R', 'A', 'S']
>>> m.create_fasta(fasta_format=True)
>>> print molecule.fasta()[:5]
>
GAR
>>> m.create_fasta(fasta_format=True,width='60')
>>> print molecule.fasta()
>
GARASVLSGGELDKWEKIRLRPGGKKQYKLKHIVWASRELERFAVNPGLLETSEGCRQIL
GQLQPSLQTGSEELRSLYNTIAVLYCVHQRIDVKDTKEALDKIEEEQNKSKKKAQQAAAD
TGNNSQVSQNYPIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATP
QDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTS
TLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFY
KTLRAEQASQEVKNAATETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKAR
VIAEAMSQVTNSATIMMQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGH
QMKDCTERQAN

>>> molecule.create_fasta(fasta_format=True,width='60',name='aar')
>>> print molecule.fasta()[:90]
>aar
GARASVLSGGELDKWEKIRLRPGGKKQYKLKHIVWASRELERFAVNPGLLETSEGCRQIL
GQLQPSLQTGSEELRSLYNTIAVL

Note

Other use types below

molecule.create_fasta(fasta_format=True,exclude_hetatm=True,by_chain=True) print molecule.fasta()

print ‘>>> testing by_chain with HETATM (t.py): ‘

molecule.create_fasta(fasta_format=True,by_chain=True) print molecule.fasta()

print ‘>>> testing by_segname (t.py): ‘

molecule.create_fasta(fasta_format=True,exclude_hetatm=True,by_segname=True) print molecule.fasta()

Note that this creates a simple string that is associated with the molecule (self) and it will return without assigning a string if a non-standard three letter code is supplied.

set_average_vdw(**kwargs)

Parameters:kwargs – optional future arguments Returns: Return type:self._atom_vdw updated in system object

Examples

>>> import sasmol.system as system
>>> molecule = system.Molecule('hiv1_gag.pdb')
>>> molecule.set_average_vdw()
>>> molecule.atom_vdw()[0]
[-0.2, 1.85]

Note

Need to add citations.