System

System

class system.Atom(*args, **kwargs)

Base class containing methods to define system objects.

Atom is the base class to build and deal with molecular systems. The class inherits file input/output, calcuation, manipulation, subset, atom properties, topology, and viewing from other samsol classes.

Class has several initialization options

Parameters:

• args – optional integer : self._id
• kwargs –

  optional keyword arguments {

  string filename (filename = ‘hiv1_gag.pdb’) : default = None integet id (id=3) : default = 0 boolean debug (debug = True) : default = None

  }

Returns:

if called with string (or with filename kwarg) returns an initialized system object with data read in using file_io.read_pdb()

Return type:

system object

Examples

Define instance of class and read in PDB file at same time

>>> import sasmol.system as system
>>> molecule = system.Molecule(filename='hiv1_gag.pdb')

Other instance definition examples (not-exhaustive)

>>> molecule = system.Molecule()
>>> molecule = system.Molecule(id=7)
>>> molecule = system.Molecule(debug=True)
>>> molecule = system.Molecule('hiv1_gag.pdb')
>>> molecule = system.Molecule(filename='hiv1_gag.pdb', id=0, debug=False)

Example of how setters and getters work. Below, the original index values are adjusted by a value (-10) and setIndex() is used to assign the new list to the molecule

>>> molecule.index()[0]
1
>>> offset = -10
>>> index = [x + offset for x in xrange(molecule.natoms())]
>>> molecule.setIndex(index)
>>> molecule.index()[0]
-10

Note

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

Many “setters” and “getters” methods are defined in this class. See source code for details.

atom()

atom_charge()

atom_vdw()

beta()

betas()

betas_mask()

chain()

chains()

chains_mask()

charge()

charmm_type()

com()

conect()

coor()

delete()

delframes()

effective_charge()

effective_van_der_waals()

element()

elements()

elements_mask()

energy()

fasta()

filename()

formula()

header()

id()

index()

load()

loc()

long_range_potential()

maketop()

mass()

maximum()

minimum()

moltype()

moltypes()

name()

names()

names_mask()

natoms()

number_of_betas()

number_of_chains()

number_of_elements()

number_of_frames()

number_of_moltypes()

number_of_names()

number_of_occupancies()

number_of_resids()

number_of_resnames()

number_of_segnames()

occupancies()

occupancies_mask()

occupancy()

one_letter_resname()

original_index()

original_resid()

pmi()

rescode()

resid()

resids()

resids_mask()

residue_charge()

residue_flag()

resname()

resnames()

resnames_mask()

rg()

save()

segname()

segnames()

segnames_mask()

setAtom(newValue)

setAtom_charge(newValue)

setAtom_vdw(newValue)

setBeta(newValue)

setBetas(newValue)

setBetas_mask(newValue)

setChain(newValue)

setChains(newValue)

setChains_mask(newValue)

setCharge(newValue)

setCharmm_type(newValue)

setCom(newValue)

setConect(newValue)

setCoor(newValue)

setEffective_charge(newValue)

setEffective_van_der_waals(newValue)

setElement(newValue)

setElements(newValue)

setElements_mask(newValue)

setEnergy(newValue)

setFasta(newValue)

setFilename(newValue)

setFormula(newValue)

setHeader(newValue)

setId(newValue)

setIndex(newValue)

setLoc(newValue)

setLong_range_potential(newValue)

setMass(newValue)

setMaximum(newValue)

setMinimum(newValue)

setMoltype(newValue)

setMoltypes(newValue)

setName(newValue)

setNames(newValue)

setNames_mask(newValue)

setNatoms(newValue)

setNumber_of_betas(newValue)

setNumber_of_chains(newValue)

setNumber_of_elements(newValue)

setNumber_of_frames(newValue)

setNumber_of_moltypes(newValue)

setNumber_of_names(newValue)

setNumber_of_occupancies(newValue)

setNumber_of_resids(newValue)

setNumber_of_resnames(newValue)

setNumber_of_segnames(newValue)

setOccupancies(newValue)

setOccupancies_mask(newValue)

setOccupancy(newValue)

setOne_letter_resname(newValue)

setOriginal_index(newValue)

setOriginal_resid(newValue)

setPmi(newValue)

setRescode(newValue)

setResid(newValue)

setResids(newValue)

setResids_mask(newValue)

setResidue_charge(newValue)

setResidue_flag(newValue)

setResname(newValue)

setResnames(newValue)

setResnames_mask(newValue)

setRg(newValue)

setSegname(newValue)

setSegnames(newValue)

setSegnames_mask(newValue)

setShape(newValue)

setShort_range_potential(newValue)

setTotal_mass(newValue)

setType(newValue)

setUnitcell(newValue)

shape()

short_range_potential()

total_mass()

type()

unitcell()

class system.Molecule(*args, **kwargs)

Molecule is a class that is used to describe molecules. It inherits all of attributes from Atom. An example of a molecule is a single protein, a single nucleic acid strand.

Class has several initialization options

Parameters:

• args – optional integer : self._id
• kwargs –

  optional keyword arguments {

  string filename (filename = ‘hiv1_gag.pdb’) : default = None integet id (id=3) : default = 0 boolean debug (debug = True) : default = None

  }

Returns:

if called with string (or with filename kwarg) returns an initialized system object with data read in using file_io.read_pdb()

Return type:

system object

Examples

>>> import sasmol.system as system
>>> molecule = system.Molecule(filename='hiv1_gag.pdb')

>>> molecule = system.Molecule()
>>> molecule = system.Molecule(id=7)
>>> molecule = system.Molecule(debug=True)
>>> molecule = system.Molecule('hiv1_gag.pdb')
>>> molecule = system.Molecule(filename='hiv1_gag.pdb', id=0, debug=False)

class system.Molecule_Maker(natoms, atom='ATOM', index=None, name='C', loc=' ', resname='DUM', chain='A', resid=None, rescode=' ', coor=None, occupancy='0.00', beta='0.00', segname='DUM', element='C', charge=' ', **kwargs)

This class is used to define the minimum number of fields required to use within sasmol to use read_pdb() and write_pdb() methods in file_io.

Default inputs are listed in the variables in __init__ and itemized below. The values are assigned to all atoms in the molecule.

Once defined, attributes can be set using setters in the Atom class.

Class has several initialization options

Parameters:

• natoms – integer : number of atoms in the molecule
• atom – string : name of ATOM keyword, typically either ATOM or HETATM
• index – integer list : atom number
• name – string : atom name
• loc – string : alt loc
• resname – string : residue name
• chain – string : chain name
• resid – integer list : residue number
• rescode – string : residue code
• coor – numpy float array : x, y, z coordinates
• occupancy – string : occupancy value
• beta – string : beta value
• segname – string : segment name
• element – string : element name
• charge – string : element charge
• kwargs – optional future arguments

Returns:

Return type:

system object

Examples

>>> import sasmol.system as system
>>> molecule = system.Molecule_Maker(2048)
>>> molecule = system.Molecule_Maker(2048, name='Ar')
>>> molecule = system.Molecule_Maker(2048, name='Ar', segname='ARG0')
>>> index = [x for x in xrange(340,1000)]
>>> molecule = system.Molecule_Maker(660, name='Ar', index=index)
>>> molecule.index()[0]
340

class system.System(*args, **kwargs)

System is a class that is used to aggregate all components. It inherits all of attributes from Atom.

Class has several initialization options

Parameters:

• args – optional integer : self._id
• kwargs –

  optional keyword arguments {

  string filename (filename = ‘hiv1_gag.pdb’) : default = None integet id (id=3) : default = 0 boolean debug (debug = True) : default = None

  }

Returns:

if called with string (or with filename kwarg) returns an initialized system object with data read in using file_io.read_pdb()

Return type:

system object

Examples

>>> import sasmol.system as system
>>> molecule = system.Molecule(filename='hiv1_gag.pdb')

>>> molecule = system.Molecule()
>>> molecule = system.Molecule(id=7)
>>> molecule = system.Molecule(debug=True)
>>> molecule = system.Molecule('hiv1_gag.pdb')
>>> molecule = system.Molecule(filename='hiv1_gag.pdb', id=0, debug=False)