Allowed (
        self,
        h,
        k,
        l,
        )

See if the reflection hkl is allowed

CMatrix ( self,  p=None )

Find matrix that converts HKL->oriented C vector.

CVector ( self,  hkl )

Calculate a c-vector in 0-goniometer position for a reflection.

parameters:

hkl

a single reflection (array of 3 elements)

return value : the c-vector of hkl (3-vector)

ConventionalCell ( self )

Calculate the parameters of the direct conventional cell.

return value: a 6-tuple of (a, b, c, alpha, beta, gamma)

DataSet (
        self,
        thetamax,
        thetamin=1.5 * projtls.degrees,
        maxaxis=None,
        userhmin=-512,
        userkmin=-512,
        userlmin=-512,
        userhmax=512,
        userkmax=512,
        userlmax=512,
        safetymargin=0,
        )

Make an array of reflection indices respecting given theta limits.

parameters:

thetamax

maximum diffraction angle for the dataset

optional parameters:

thetamin

minimum diffraction angle for the dataset maxaxis -- try to get axis lengths below this value, producing an equivalent smaller dataset.

**user?min, user*max**

limit the output data set to the given hkl limits.

safetymargin

used for debugging purposes to see if reflections were missed.

return value: uniquified dataset object with appropriate symmetry

DataSet2 (
        self,
        invdmin,
        invdmax,
        maxaxis=None,
        thetamax=None,
        thetamin=None,
        userhmin=-512,
        userkmin=-512,
        userlmin=-512,
        userhmax=512,
        userkmax=512,
        userlmax=512,
        safetymargin=0,
        )

Same as DataSet(), but instead of specifying thetamax and thetamin (1/d)max and min must be given. This can be used without knowledge of the wavelength at which the measurement is performed.

DenzoRots (
        self,
        p,
        alternative=0,
        )

Calculate X/Y/Z rotations of crystal at specified goniostat position

parameters: p : desired goniostat position

optional parameters: alternative=0 : if 1, return alternative angles with same setting

return value: 3-tuple of (rotz,roty,rotx)

DirectVector ( self,  indices )

Calculate a direct vector pointing to the named lattice point.

FriedelAxes ( self )

Return list of axes that measure Friedels in same frame when rotating around them.

InputCell ( self )

Calculate the parameters of the direct input cell.

return value: a 6-tuple of (a, b, c, alpha, beta, gamma)

InverseConventionalCell ( self )

Calculate the parameters of the reciprocal conventional cell.

return value: a 6-tuple of (a, b, c, alpha, beta, gamma)

InverseInputCell ( self )

Calculate the parameters of the reciprocal input cell.

return value: a 6-tuple of (a, b, c, alpha, beta, gamma)

InverseReducedCell ( self )

Calculate the parameters of the reciprocal reduced cell.

return value: a 6-tuple of (a, b, c, alpha, beta, gamma)

LowestSpacegroup ( self )

Returns the name of the lowest-symmetry space group that is compatible with the lattice defined by this cell.

PointgroupValid ( self,  pointgroup=None )

Checks whether the given pointgroup is compatible with the cell. If no point group is specified, checks the validity of the point group this cell thinks it has.

ReducedCell ( self )

Calculate the parameters of the direct reduced cell.

return value: a 6-tuple of (a, b, c, alpha, beta, gamma)

ReducedInverseCell ( self )

Calculate the parameters of the reduced reciprocal cell.

return value: a 6-tuple of (a, b, c, alpha, beta, gamma)

ReducedVolume ( self )

Return the volume of the reduced cell

SetHardware (
        self,
        hardware,
        wavelength=None,
        )

Set hardware or wavelength when they appear at a later stage.

SetSigma ( self,  sig )

Set the sigma (6-tuple or 7-tuple) of the unit cell. If the sigma on the volume is not given, it is calculated.

Shkl (
        self,
        p,
        hkl,
        )

Calculate diffracted vector Shkl for a dataset

parameters:

p

position of the goniometer hkl -- dataset

return value: Diffraction vector for each of the reflections in the dataset (3xN array)

ShortestReciprocalLatticeVector ( self )

Return the shortest reciprocal lattice vector as a 3-vector

Theta ( self,  hkl )

Calculate theta for a reflection.

parameters:

hkl

a single reflection (array of 3 elements)

return value: theta for the reflection

ValidPointgroups ( self )

Returns a list of all point groups that are compatible with the current cell. Depending on the (protein?) environment, this may give only acentric point groups!

Volume ( self )

Return the volume of the conventional cell

__init__ (
        self,
        orientationmatrix,
        bravaistype='P',
        transformedbravaistype=None,
        axcrit=None,
        hardware=None,
        wavelength=None,
        pointgroup=None,
        standardize=1,
        system=None,
        triclinic=0,
        transformtrigonal=1,
        transformationmatrix=None,
        xtra={},
        )

Constructor.

Construction will generate an input cell, a Buerger reduced cell, and a standardized cell. The orientation matrix for the input cell must be specified as an argument. Unless a transformation matrix is given or the "standardize=0" argument is passed, the standardized cell is calculated by the algorithm of Y.Le Page.

parameters:

orientationmatrix

Represents a 3x3 matrix with as elements the x,y and z coordinates of a*, b* and c* in the "all zero" position of the goniostat. The associated cell is called the "input cell".

optional parameters:

bravaistype

Bravais type of the input cell transformedbravaistype -- Bravais type of transformed cell (only used if transformation matrix is also specified) axcrit -- Criterion used to decide whether two axes are coinciding. Decrease to prevent pseudo- symmetry. Value in radians. hardware -- a hardware object. wavelength -- Wavelength. Extracted from hardware if not specified. standardize -- if 1, attempt to derive conventional cell triclinic -- if 1 and standardize=0 and no transformation matrix is given, use triclinic crystal system independent of unit cell constants. transformtrigonal -- if 1, trigonal cells will be standardized to hexagonal if 0, they will be kept primitive. transformationmatrix -- pre-specify the input to conventional cell transformation matrix system -- specify crystal system of transformed cell (only used if a t-mat is given!) pointgroup -- point group of the data set. If not specified, or if equal to the string "Default", this will be deduced from the crystal system.

angle30 (
        self,
        v1,
        v2,
        )

Return true if the angle between v1 and v2 is 30 degrees within axcrit

angle45 (
        self,
        v1,
        v2,
        )

Return true if the angle between v1 and v2 is 45 degrees within axcrit

angle60 (
        self,
        v1,
        v2,
        )

Return true if the angle between v1 and v2 is 60 degrees within axcrit

angle90 (
        self,
        v1,
        v2,
        )

Return true if the angle between v1 and v2 is 90 degrees within axcrit

guesssystem ( self )

Guess the crystal system based on the conventional cell parameters

hkl ( self,  c )

Calculate the HKL indices for the given C vector

input2conventionaltransformation ( self )

Returns the transformation matrix that can be used to transform the input cell into the conventional cell

inputrmatstr ( self )

Return the contents of a .rmat file that would reconstruct the current Cell() object completely

reduced2conventionaltransformation ( self )

Returns the transformation matrix that can be used to transform the reduced cell into the conventional cell

rmatstr ( self )

Return the contents of a .rmat file that is the standard description of the current Cell(): the reduced cell plus the standardization matrix

transformedrmatstr ( self )

Return the contents of a .rmat file that contains the conventional cell as rmatrix.