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Crystallographic symmetry related commands.
(c) 2010-2012 Thomas Holder
License: BSD-2-Clause
from pymol import cmd, CmdException
def cellbasis(angles, edges):
API only. For the unit cell with given angles and edge lengths calculate
the basis transformation (vectors) as a 4x4 numpy.array
from math import cos, sin, radians, sqrt
import numpy
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)
return basis * edges # numpy.array multiplication!
def supercell(a=1, b=1, c=1, object=None, color='green', name='supercell', withmates=1):
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))
supercell a, b, c [, object [, color [, name [, withmates]]]]
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}
show cell
import numpy
from pymol import cgo
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)):
obj = [
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 = [
basis[0:3,(i+1)%3] + basis[0:3,(i+2)%3]
for j in range(4):
obj.extend((shift + vj[j]).tolist())
obj.extend((shift + vj[j] + vi).tolist())
if withmates:
groupname = 'm%d%d%d' % tuple(t)
symexpcell(groupname + '_', object, *t), groupname + '_*')
cmd.load_cgo(obj, name)
cmd.color(color, name)
def symexpcell(prefix='mate', object=None, a=0, b=0, c=0):
Creates all symmetry-related objects for the specified object that
occur with their bounding box center within the unit cell.
symexpcell prefix, object, [a, b, c]
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}
import numpy
from pymol import xray
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)]
spacegroup = xray.space_group_map.get(spacegroup, spacegroup)
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)
def pdbremarks(filename):
API only. Read REMARK lines from PDB file. Return dictionary with
remarkNum as key and list of lines as value.
remarks = dict()
if not cmd.is_string(filename):
f = filename
elif filename[-3:] == '.gz':
import gzip
f =
f = open(filename)
for line in f:
recname = line[0:6]
if recname == 'REMARK':
num = int(line[7:10])
lstring = line[11:]
remarks.setdefault(num, []).append(lstring)
return remarks
def biomolecule(name=None, filename=None, prefix=None, number=1, suffix=None,
Create biological unit (quaternary structure) as annotated by the REMARK
350 BIOMOLECULE record.
biomolecule name [, filename [, prefix [, number ]]]
name = string: name of object and basename of PDB file, if
filename is not given {default: first loaded object}
filename = string: file to read remarks from {default: <name>.pdb}
prefix = string: prefix for new objects {default: <name>}
fetch 1rmv, async=0
biomolecule 1rmv
import os
from .importing import local_mirror_pdb
import numpy
except ImportError:
numpy = None
number, quiet = int(number), int(quiet)
if name is None:
name = cmd.get_object_list()[0]
if prefix is None:
prefix = name
if suffix is None:
suffix = str(number)
if filename is None:
candidates = [
'%s.pdb' % (name),
'%s/%s.pdb' % (cmd.get('fetch_path'), name),
for filename in candidates:
if os.path.exists(filename):
print('please provide filename')
raise CmdException
if not quiet:
print('loading from %s' % (filename))
remarks = pdbremarks(filename)
if 350 not in remarks:
print('There is no REMARK 350 in ' + filename)
raise CmdException
current = 1
biomt = {current: {}}
chains = tuple()
for line in remarks[350]:
if line.startswith('BIOMOLECULE:'):
current = int(line[12:])
biomt[current] = {}
elif line.startswith('APPLY THE FOLLOWING TO CHAINS:'):
chains = tuple(chain.strip() for chain in line[30:].split(','))
elif line.startswith(' AND CHAINS:'):
chains += tuple(chain.strip() for chain in line[30:].split(','))
elif line.startswith(' BIOMT'):
row = int(line[7])
num = int(line[8:12])
vec = line[12:].split()
vec = list(map(float, vec))
biomt[current].setdefault(chains, dict()).setdefault(num, []).extend(vec)
if number not in biomt or len(biomt[number]) == 0:
print(' Error: no BIOMOLECULE number %d' % (number))
raise CmdException
if numpy is not None:
mat_source = numpy.reshape(cmd.get_object_matrix(name), (4,4))
mat_source = numpy.matrix(mat_source)
for chains, matrices in biomt[number].items():
for num in matrices:
mat = matrices[num][0:12]
copy = '%s_%s_%d' % (prefix, suffix, num)
if not quiet:
print('creating %s' % (copy))
cmd.create(copy, 'model %s and chain %s' % (name, '+'.join(chains)))
cmd.alter(copy, 'segi="%d"' % (num))
if numpy is not None:
mat = mat_source * numpy.reshape(mat, (4,4)) * mat_source.I
mat = list(mat.flat)
cmd.transform_object(copy, mat)
cmd.disable(name)'%s_%s' % (prefix, suffix), '%s_%s_*' % (prefix, suffix))
cmd.extend('supercell', supercell)
cmd.extend('symexpcell', symexpcell)
cmd.extend('biomolecule', biomolecule)
# tab-completion of arguments
cmd.auto_arg[0]['biomolecule'] = cmd.auto_arg[0]['pseudoatom']
cmd.auto_arg[3]['supercell'] = cmd.auto_arg[0]['pseudoatom']
# vi: ts=4:sw=4:smarttab:expandtab