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Pydoc: module atomAction

atomAction

index

Perform some action on an AtomSel. Available actions are the following functions randomizeDomainPos randomizeVelocities translateFit and the following classes PrintPos SetProperty RandomizeVelocities TranslateFit The classes are used like AtomSel("name C").apply(PrintPos()) or AtomSel("resname GLY").apply(SetProperty("residueName","G"))

Classes

atomSelAction.PyAtomSelAction(atomSelAction.Base)

PrintPos
RandomizeVelocities
SetPropertyArr
TranslateFit

class PrintPos(atomSelAction.PyAtomSelAction)

PrintPos(otherCoords=0)

print position of atoms in selection

Method resolution order:: PrintPos; atomSelAction.PyAtomSelAction; atomSelAction.Base; builtins.object

Methods defined here:

__init__(s, otherCoords=0): Initialize self. See help(type(self)) for accurate signature.

init(s, sel)

run(s, sim, index)

Methods inherited from atomSelAction.PyAtomSelAction:

__repr__ = _swig_repr(self)

pyXplorHelp(self, *args, **kwargs) -> 'String'

Static methods inherited from atomSelAction.PyAtomSelAction:

__swig_destroy__ = delete_PyAtomSelAction(...)

Data descriptors inherited from atomSelAction.PyAtomSelAction:

thisown: The membership flag

Methods inherited from atomSelAction.Base:

finish_unused(self, *args, **kwargs) -> 'void'

init_unused(self, *args, **kwargs) -> 'void'

returnMethodName(self, *args, **kwargs) -> 'String'

Data descriptors inherited from atomSelAction.Base:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

class RandomizeVelocities(atomSelAction.PyAtomSelAction)

RandomizeVelocities(temperature)

randomize atomic velocities according to a Maxwell distribution
corresponding to the given temperature.

Method resolution order:: RandomizeVelocities; atomSelAction.PyAtomSelAction; atomSelAction.Base; builtins.object

Methods defined here:

__init__(s, temperature): Initialize self. See help(type(self)) for accurate signature.

run(s, sim, index)

Methods inherited from atomSelAction.PyAtomSelAction:

__repr__ = _swig_repr(self)

pyXplorHelp(self, *args, **kwargs) -> 'String'

Static methods inherited from atomSelAction.PyAtomSelAction:

__swig_destroy__ = delete_PyAtomSelAction(...)

Data descriptors inherited from atomSelAction.PyAtomSelAction:

thisown: The membership flag

Methods inherited from atomSelAction.Base:

finish_unused(self, *args, **kwargs) -> 'void'

init_unused(self, *args, **kwargs) -> 'void'

returnMethodName(self, *args, **kwargs) -> 'String'

Data descriptors inherited from atomSelAction.Base:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

class SetPropertyArr(atomSelAction.PyAtomSelAction)

SetPropertyArr(name, val)

set named property of all atom.Atoms in a selection
usage:
sel = AtomSel("string")
sel.apply(SetProperty(name,val)
where
name is a property of an atom (e.g. pos) and val is the value to set
that property. If val is an sequence of length len(sel), values will be
set appropriately.

atomSelAction.SetProperty is an optimized version of this class which
allows atom properties top be set to a constant value.

Method resolution order:: SetPropertyArr; atomSelAction.PyAtomSelAction; atomSelAction.Base; builtins.object

Methods defined here:

__init__(s, name, val): Initialize self. See help(type(self)) for accurate signature.

run(s, sim, index)

Methods inherited from atomSelAction.PyAtomSelAction:

__repr__ = _swig_repr(self)

pyXplorHelp(self, *args, **kwargs) -> 'String'

Static methods inherited from atomSelAction.PyAtomSelAction:

__swig_destroy__ = delete_PyAtomSelAction(...)

Data descriptors inherited from atomSelAction.PyAtomSelAction:

thisown: The membership flag

Methods inherited from atomSelAction.Base:

finish_unused(self, *args, **kwargs) -> 'void'

init_unused(self, *args, **kwargs) -> 'void'

returnMethodName(self, *args, **kwargs) -> 'String'

Data descriptors inherited from atomSelAction.Base:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

class TranslateFit(atomSelAction.PyAtomSelAction)

TranslateFit(fitCoords, fitSel=0)

translate atom positions to best-fit coordinates specified by fitCoords.
fitCoords must have size sim.numAtoms()

Method resolution order:: TranslateFit; atomSelAction.PyAtomSelAction; atomSelAction.Base; builtins.object

Methods defined here:

__init__(s, fitCoords, fitSel=0): fitCoords- coordinates to use for fitting.
fitSel - subset of atoms to use in calculating fit (default: known)

After construction, the fit is calculated and stored in member trans.

run(s, sim, index)

Methods inherited from atomSelAction.PyAtomSelAction:

__repr__ = _swig_repr(self)

pyXplorHelp(self, *args, **kwargs) -> 'String'

Static methods inherited from atomSelAction.PyAtomSelAction:

__swig_destroy__ = delete_PyAtomSelAction(...)

Data descriptors inherited from atomSelAction.PyAtomSelAction:

thisown: The membership flag

Methods inherited from atomSelAction.Base:

finish_unused(self, *args, **kwargs) -> 'void'

init_unused(self, *args, **kwargs) -> 'void'

returnMethodName(self, *args, **kwargs) -> 'String'

Data descriptors inherited from atomSelAction.Base:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

Functions

centerOfMass(sel='not PSEUDO', useMass=True): Return the center of mass of the specified atoms.

The returned object is a vec3.Vec3 instance representing the center of
mass (if useMass is True) or centroid (if useMass is False) of the atoms
specified by the argument sel. sel can be either an atom selection string
or an atomSel.AtomSel instance.

copyAtomCoords(sel1, sel2): copy atomic coordinates from sel2 to sel1.
The two selections must contain the same number of atoms. This is most
useful for copying coordinates between segments or between separate
simulation.Simulations. The two selections must contain the same number
of atoms.

The current implementation requires that identical ordering of the atoms
in the two selections, but there may be gaps.

genRandomCoords(selection='not pseudo', xyzInterval=10.0): Assign atoms in the specified atom selection random x,y,z, coordinates in the
interval -xyzInterval .. +xyzInterval.

getProperty(name, sel): get array corresponding to the named property for the given selection.

mass(selection='not PSEUDO'): Return the mass of the specified atomSel.AtomSel.

maxwellDist(temperature, factor)

randomizeDomainPos(sel, deltaPos=20, deltaAngle=3.141592653589793, centerSel=None, rotAxis='all'): Randomly rotate and translate the given atom selection,
as a rigid-body about its center of mass.

The deltaPos parameter specifies the maximum displacement to apply.

The deltaAngle parameter specifies the maximal +/- angle (in
radians) to rotate. mat3.randRot() is used to generate a random
rotation matrix of deltaAngle.

If centerSel is specified, atoms in sel at first centered around the
average position of centerSel before rotation/translation.

The rotAxis argument can be specified to restrict rotation to occur
about the specified axis. Allowed values of the argument are "all" for
full 3D rotation using mat3.randRot, "x", "y", or "z" for rotation
about these axes, or a sequence convertible to a vec3.Vec specifying
an arbitrary axis.

randomizeVelocities(temperature, sel='known'): randomize atomic velocities according to a Maxwell distribution
corresponding to the given temperature. The default selection
contains all known atoms.

sqrt(x, /): Return the square root of x.

translateFit(fitCoords, atomSel=0): Return array of atom positions which best-fit coordinates
specified by fitCoords. fitCoords must have size sim.numAtoms()
This routine does not change the current coordinates.
the default atomSel is known atoms.

Data
		pi = 3.141592653589793