def transforms(self, molecule):
import PDBmatrices
sm = []
h = pdb_headers(molecule)
if self.use_smtry_records.get():
sm = PDBmatrices.pdb_smtry_matrices(h)
if len(sm) == 0 and self.use_cryst1_smtry.get():
sm = PDBmatrices.pdb_space_group_matrices(h)
from Matrix import identity_matrix, matrix_products
mm = [identity_matrix()]
if self.use_mtrix_records.get():
mm = PDBmatrices.pdb_mtrix_matrices(h)
if sm:
tflist = matrix_products(sm, mm)
else:
tflist = mm
# Adjust transforms so centers of models are in unit cell box
from Molecule import unit_cell_parameters, molecule_center
uc = unit_cell_parameters(molecule)
if uc:
mc = molecule_center(molecule)
tflist = PDBmatrices.pack_unit_cell(uc, self.grid_origin(), mc, tflist)
# Make multiple unit cells
nc = self.number_of_cells()
if nc != (1,1,1):
tflist = PDBmatrices.unit_cell_translations(uc, nc, tflist)
return tflist
def transforms(self, molecule):
import PDBmatrices
sm = []
h = pdb_headers(molecule)
if self.use_smtry_records.get():
sm = PDBmatrices.pdb_smtry_matrices(h)
if len(sm) == 0 and self.use_cryst1_smtry.get():
sm = PDBmatrices.pdb_space_group_matrices(h)
from Matrix import identity_matrix, matrix_products
mm = [identity_matrix()]
if self.use_mtrix_records.get():
mm = PDBmatrices.pdb_mtrix_matrices(h)
if sm:
tflist = matrix_products(sm, mm)
else:
tflist = mm
# Adjust transforms so centers of models are in unit cell box
from Molecule import unit_cell_parameters, molecule_center
uc = unit_cell_parameters(molecule)
if uc:
mc = molecule_center(molecule)
tflist = PDBmatrices.pack_unit_cell(uc, self.grid_origin(), mc,
tflist)
# Make multiple unit cells
nc = self.number_of_cells()
if nc != (1, 1, 1):
tflist = PDBmatrices.unit_cell_translations(uc, nc, tflist)
return tflist
def dihedral_symmetries(n):
clist = cyclic_symmetries(n)
reflect = ((-1,0,0,0),(0,1,0,0),(0,0,-1,0))
from Matrix import matrix_products, identity_matrix
tflist = matrix_products([identity_matrix(), reflect], clist)
return tflist
def dihedral_symmetries(n):
clist = cyclic_symmetries(n)
reflect = ((-1, 0, 0, 0), (0, 1, 0, 0), (0, 0, -1, 0))
from Matrix import matrix_products, identity_matrix
tflist = matrix_products([identity_matrix(), reflect], clist)
return tflist
def unit_cell_translations(uc, nc, tflist): ranges = [(0,n-1) for n in nc] cell_axes = unit_cell_axes(*uc) mlist = translation_matrices(cell_axes, ranges) from Matrix import matrix_products tlist = matrix_products(mlist, tflist) return tlist
def unit_cell_translations(uc, nc, tflist):
ranges = [(0, n - 1) for n in nc]
cell_axes = unit_cell_axes(*uc)
mlist = translation_matrices(cell_axes, ranges)
from Matrix import matrix_products
tlist = matrix_products(mlist, tflist)
return tlist
def pdb_3x3x3_unit_cell_matrices(pdb_headers): cell_axes = pdb_unit_cell_axes(pdb_headers) mlist = translation_matrices(cell_axes, ((-1,1), (-1,1), (-1,1))) clist = pdb_unit_cell_matrices(pdb_headers) from Matrix import matrix_products plist = matrix_products(mlist, clist) return plist
def pdb_3x3x3_unit_cell_matrices(pdb_headers):
cell_axes = pdb_unit_cell_axes(pdb_headers)
mlist = translation_matrices(cell_axes, ((-1, 1), (-1, 1), (-1, 1)))
clist = pdb_unit_cell_matrices(pdb_headers)
from Matrix import matrix_products
plist = matrix_products(mlist, clist)
return plist
def pdb_unit_cell_matrices(pdb_headers):
slist = crystal_symmetry_matrices(pdb_headers)
import parsepdb
mlist = parsepdb.pdb_mtrix_matrices(pdb_headers)
if slist and mlist:
from Matrix import matrix_products
smlist = matrix_products(slist, mlist)
return smlist
elif slist:
return slist
elif mlist:
return mlist
from Matrix import identity_matrix
return [identity_matrix()]
def pdb_unit_cell_matrices(pdb_headers):
slist = crystal_symmetry_matrices(pdb_headers)
import parsepdb
mlist = parsepdb.pdb_mtrix_matrices(pdb_headers)
if slist and mlist:
from Matrix import matrix_products
smlist = matrix_products(slist, mlist)
return smlist
elif slist:
return slist
elif mlist:
return mlist
from Matrix import identity_matrix
return [identity_matrix()]