schrodinger.application.desmond.packages.analysis.OrderParameter

Class OrderParameter

Given the director (local or global), and the descriptor (local or global), calculate the order parameter <P2> for each frame S = 1/N sum_i ((3 * (n dot m_i)^2 -1) / 2) Where n is the director vector and m is the descriptor vector. For example, n is the z axis and m is the electric dipole moment. Typical usage includes Director Descriptor result Axis Lipid avg over carbon type Axis Smarts avg over bond type Axis Dipole avg over molecule SystemDipole Dipole avg over molecule Dipole Smarts avg over bond type To extend its functionality, implement to the L{GeomAnalyzerBase} interface and provide the reduction rule as callable.

Instance Methods

[hide private]

__init__(self, vec1, vec2, reducer)
@param vec1: a L{GeomAnalyzerBase} that computes director @param vec2: a L{GeomAnalyzerBase} that computes descriptor @type reducer: a callable that reduces the results of C{vec1} and C{vec2} to order parameter for each frame

_precalc(self, calc)

_postcalc(self, *args)

Inherited from GeomAnalyzerBase: __call__

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

init(self, vec1, vec2, reducer)
(Constructor)


@param   vec1: a L{GeomAnalyzerBase} that computes director
@param   vec2: a L{GeomAnalyzerBase} that computes descriptor
@type reducer: a callable that reduces the results of C{vec1} and
               C{vec2} to order parameter for each frame

Typically both director and descriptor return Nx3 vectors for each
frame, where N depends on the context. In this case, one should make
sure that the orders of these vectors match. For example, if both
director and descriptor give one vector per molecule, then the
implementation should guarantee the molecule orders are the same in
vec1() and vec2().

For axis director which returns 1x3 vector, reduction with descriptor
is taken care of by numpy broadcasting. For more complicated cases
where director and descriptor have incompatible dimensions, the user
needs to provide special-purpose reduce function, see
L{SmartsDirector.reduce_vec} for example.

Overrides: object.__init__

_precalc(self, calc)

Overrides: GeomAnalyzerBase._precalc: (inherited documentation)

_postcalc(self, *args)

Overrides: GeomAnalyzerBase._postcalc: (inherited documentation)

Class OrderParameter

__init__(self, vec1, vec2, reducer) (Constructor)

_precalc(self, calc)

_postcalc(self, *args)

init(self, vec1, vec2, reducer)
(Constructor)