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| Line 15: |
Line 15: |
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| <source lang="python"> | | <source lang="python"> |
| run supercell.py | | # import psico.xtal, or run the standalone script: |
| | run https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/xtal.py |
| | |
| fetch 2x19, async=0 | | fetch 2x19, async=0 |
| supercell 2,1,1, 2x19, green | | supercell 2,1,1, 2x19, green |
| supercell 1,1,2, 2x19, orange, name=super2 | | supercell 1,1,2, 2x19, orange, name=super2 |
| </source>
| |
|
| |
| == The Code ==
| |
|
| |
| <source lang="python">
| |
| '''
| |
| (c) 2010 Thomas Holder
| |
|
| |
| PyMOL python script (load with `run supercell.py`)
| |
| Usage: See "help supercell" and "help symexpcell"
| |
| '''
| |
|
| |
| from pymol import cmd, cgo, xray
| |
| from math import cos, sin, radians, sqrt
| |
| import numpy
| |
|
| |
| def cellbasis(angles, edges):
| |
| '''
| |
| For the unit cell with given angles and edge lengths calculate the basis
| |
| transformation (vectors) as a 4x4 numpy.array
| |
| '''
| |
| rad = [radians(i) for i in angles]
| |
| basis = numpy.identity(4)
| |
| basis[0][1] = cos(rad[2])
| |
| basis[1][1] = sin(rad[2])
| |
| basis[0][2] = cos(rad[1])
| |
| basis[1][2] = (cos(rad[0]) - basis[0][1]*basis[0][2])/basis[1][1]
| |
| basis[2][2] = sqrt(1 - basis[0][2]**2 - basis[1][2]**2)
| |
| edges.append(1.0)
| |
| return basis * edges # numpy.array multiplication!
| |
|
| |
| def supercell(a=1, b=1, c=1, object=None, color='blue', name='supercell', withmates=1):
| |
| '''
| |
| DESCRIPTION
| |
|
| |
| Draw a supercell, as requested by Nicolas Bock on the pymol-users
| |
| mailing list (Subject: [PyMOL] feature request: supercell construction
| |
| Date: 04/12/2010 10:12:17 PM (Mon, 12 Apr 2010 14:12:17 -0600))
| |
|
| |
| USAGE
| |
|
| |
| supercell a, b, c [, object [, color [, name [, withmates]]]]
| |
|
| |
| ARGUMENTS
| |
|
| |
| a, b, c = integer: repeat cell in x,y,z direction a,b,c times
| |
| {default: 1,1,1}
| |
|
| |
| object = string: name of object to take cell definition from
| |
|
| |
| color = string: color of cell {default: blue}
| |
|
| |
| name = string: name of the cgo object to create {default: supercell}
| |
|
| |
| withmates = bool: also create symmetry mates in displayed cells
| |
| {default: 1}
| |
|
| |
| SEE ALSO
| |
|
| |
| show cell
| |
|
| |
| '''
| |
| if object is None:
| |
| object = cmd.get_object_list()[0]
| |
| withmates = int(withmates)
| |
|
| |
| sym = cmd.get_symmetry(object)
| |
| cell_edges = sym[0:3]
| |
| cell_angles = sym[3:6]
| |
|
| |
| basis = cellbasis(cell_angles, cell_edges)
| |
| assert isinstance(basis, numpy.ndarray)
| |
|
| |
| ts = list()
| |
| for i in range(int(a)):
| |
| for j in range(int(b)):
| |
| for k in range(int(c)):
| |
| ts.append([i,j,k])
| |
|
| |
| obj = [
| |
| cgo.BEGIN,
| |
| cgo.LINES,
| |
| cgo.COLOR,
| |
| ]
| |
| obj.extend(cmd.get_color_tuple(color))
| |
|
| |
| for t in ts:
| |
| shift = basis[0:3,0:3] * t
| |
| shift = shift[:,0] + shift[:,1] + shift[:,2]
| |
|
| |
| for i in range(3):
| |
| vi = basis[0:3,i]
| |
| vj = [
| |
| numpy.array([0.,0.,0.]),
| |
| basis[0:3,(i+1)%3],
| |
| basis[0:3,(i+2)%3],
| |
| basis[0:3,(i+1)%3] + basis[0:3,(i+2)%3]
| |
| ]
| |
| for j in range(4):
| |
| obj.append(cgo.VERTEX)
| |
| obj.extend((shift + vj[j]).tolist())
| |
| obj.append(cgo.VERTEX)
| |
| obj.extend((shift + vj[j] + vi).tolist())
| |
|
| |
| if withmates:
| |
| symexpcell('m%d%d%d_' % tuple(t), object, *t)
| |
|
| |
| obj.append(cgo.END)
| |
|
| |
| cmd.delete(name)
| |
| cmd.load_cgo(obj, name)
| |
|
| |
| def symexpcell(prefix='mate', object=None, a=0, b=0, c=0):
| |
| '''
| |
| DESCRIPTION
| |
|
| |
| Creates all symmetry-related objects for the specified object that
| |
| occur with their bounding box center within the unit cell.
| |
|
| |
| USAGE
| |
|
| |
| symexpcell prefix, object, [a, b, c]
| |
|
| |
| ARGUMENTS
| |
|
| |
| prefix = string: prefix of new objects
| |
|
| |
| object = string: object for which to create symmetry mates
| |
|
| |
| a, b, c = integer: create neighboring cell {default: 0,0,0}
| |
|
| |
| SEE ALSO
| |
|
| |
| symexp, http://www.pymolwiki.org/index.php/SuperSym
| |
| '''
| |
| if object is None:
| |
| object = cmd.get_object_list()[0]
| |
|
| |
| sym = cmd.get_symmetry(object)
| |
| cell_edges = sym[0:3]
| |
| cell_angles = sym[3:6]
| |
| spacegroup = sym[6]
| |
|
| |
| basis = cellbasis(cell_angles, cell_edges)
| |
| basis = numpy.matrix(basis)
| |
|
| |
| extent = cmd.get_extent(object)
| |
| center = sum(numpy.array(extent)) * 0.5
| |
| center = numpy.matrix(center.tolist() + [1.0]).T
| |
| center_cell = basis.I * center
| |
|
| |
| extra_shift = [[float(i)] for i in (a,b,c)]
| |
|
| |
| i = 0
| |
| matrices = xray.sg_sym_to_mat_list(spacegroup)
| |
| for mat in matrices:
| |
| i += 1
| |
|
| |
| mat = numpy.matrix(mat)
| |
| shift = numpy.floor(mat * center_cell)
| |
| mat[0:3,3] -= shift[0:3,0]
| |
| mat[0:3,3] += extra_shift
| |
|
| |
| mat = basis * mat * basis.I
| |
| mat_list = list(mat.flat)
| |
|
| |
| name = '%s%d' % (prefix, i)
| |
| cmd.create(name, object)
| |
| cmd.transform_object(name, mat_list, 0)
| |
| cmd.color(i+1, name)
| |
|
| |
| cmd.extend('symexpcell', symexpcell)
| |
| cmd.extend('supercell', supercell)
| |
|
| |
| # tab-completion of arguments
| |
| cmd.auto_arg[3]['supercell'] = [ cmd.object_sc, 'object', '']
| |
| </source> | | </source> |
|
| |
|
