xfab.structure

Help on module xfab.structure in [xfab]:

NAME
xfab.structure

CLASSES
atom_entry
atomlist
build_atomlist

class atom_entry
| Methods defined here: | | init(self, label=None, atomtype=None, pos=None, adp_type=None, adp=None, occ=None, symmulti=None)

class atomlist
| Methods defined here: | | init(self, sgname=None, sgno=None, cell=None) | | add_atom(self, label=None, atomtype=None, pos=None, adp_type=None, adp=None, occ=None, symmulti=None)

class build_atomlist
| Methods defined here: | | CIFopen(self, ciffile=None, cifblkname=None) | | CIFread(self, ciffile=None, cifblkname=None, cifblk=None) | | PDBread(self, pdbfile=None) | function to read pdb file (www.pdb.org) and make | atomlist structure | | init(self) | | remove_esd(self, a) | This function will remove the esd part of the entry, | e.g. '1.234(56)' to '1.234'.

FUNCTIONS
FormFactor(atomtype, stl)
Calculation of the atomic form factor at a specified sin(theta)/lambda
using the analytic fit to the form factors from
Int. Tab. Cryst Sect. C 6.1.1.4

INPUT: atomtype: Atom type (string) e.g. 'C'
stl: form factor calculated sin(theta)/lambda = stl
OUTPUT: atomic form factor (no dispersion)

Henning Osholm Sorensen, Risoe National Laboratory, April 9, 2008.

StructureFactor(hkl, ucell, sgname, atoms, disper=None)
Calculation of the structure factor of reflection hkl

[Freal Fimg] = StructureFactor(hkl,unit_cell,sg,atoms)

INPUT : hkl = [h, k, l]
unit_cell = [a, b, c, alpha, beta, gamma]
sgname: space group name (e.g. 'P 21/c')
atoms: structural parameters (as an object)
OUTPUT: The real and imaginary parts of the the structure factor

Henning Osholm Sorensen, June 23, 2006.
Translated to python code April 8, 2008

Uij2betaij(adp, ucell)
Uij2betaij transform the ADP U-matrix into the beta form

betaij = Uij2betaij(adp,unit_cell)

INPUT: adp: anisotropic displacement parameter U matrix
Uijs are given in this order: [U11, U22, U33, U23, U13, U12]
unit_cell = [a, b, c, alpha, beta, gamma]

OUTPUT: betaij: beta displacement matrix

Henning Osholm Sorensen, Risoe National Laboratory, June 23, 2006.
Translated to python code March 29, 2008

int_intensity(F2, L, P, I0, wavelength, cell_vol, cryst_vol)
Calculate the reflection intensities scaling factor

INPUT:
F2 : the structure factor squared
L : Lorentz factor
P : Polarisation factor
I0 : Incoming beam flux
wavelength: in Angstroem
cell_vol : Volume of unit cell in AA^3
cryst_vol : Volume of crystal in mm^3

OUTPUT:
int_intensity: integrated intensity

multiplicity(position, sgname)