Python Matrix.multiply_matrices方法代码示例

# 需要导入模块: import Matrix [as 别名]
# 或者: from Matrix import multiply_matrices [as 别名]
def parameter_xform(rotq, rotc, trans):

    import Matrix as m
    ttf = m.translation_matrix(trans)
    sa2 = m.norm(rotq[:3])
    ca2 = rotq[3]
    from math import atan2, pi
    angle = 2*atan2(sa2,ca2) * 180.0/pi
    axis = m.normalize_vector(rotq[:3])
    rtf = m.rotation_transform(axis, angle, rotc)
    tf = m.multiply_matrices(ttf, rtf)
    xf = m.chimera_xform(tf)
    return xf

# 需要导入模块: import Matrix [as 别名]
# 或者: from Matrix import multiply_matrices [as 别名]
def texture_surface_piece(p, t, txf, border_color, offset = 0):

    p.textureId = t.texture_id()
    p.useTextureTransparency = ('a' in t.color_mode)
    p.textureModulationColor = t.modulation_rgba()
    p.textureBorderColor = border_color
    va = offset_vertices(p, offset)
    s2tc = t.texture_matrix()
    p2s = p.model.openState.xform
    p2s.premultiply(txf.inverse())
    import Matrix
    p2tc = Matrix.multiply_matrices(s2tc, Matrix.xform_matrix(p2s))
    import _contour
    _contour.affine_transform_vertices(va, p2tc)
    p.textureCoordinates = va
    p.using_surface_coloring = True

# 需要导入模块: import Matrix [as 别名]
# 或者: from Matrix import multiply_matrices [as 别名]
def fit_map_in_map(map1, map2,
		initial_map1_transform = None,
		map1_threshold = None,
		ijk_step_size_min = 0.01,		# Grid index units
		ijk_step_size_max = 1.5,		 # Grid index units
		max_steps = 10000,
		optimize_translation = True,
		optimize_rotation = True):

	# Files have to have file suffix indicating volume format.
	if initial_map1_transform:
		xf = Matrix.chimera_xform(initial_map1_transform)
		map1.surface_model().openState.globalXform(xf)
		
	use_threshold = (map1_threshold != None)
	points, point_weights = map_points_and_weights(map1, use_threshold)

	if len(points) == 0:
		if use_threshold:
			print 'No grid points above map threshold.'
		else:
			print 'Map has no non-zero values.'
		return

	move_tf, stats = motion_to_maximum(points, point_weights, map2, max_steps,
		ijk_step_size_min, ijk_step_size_max,
		optimize_translation, optimize_rotation)

	if initial_map1_transform:
		move_tf = Matrix.multiply_matrices(move_tf, initial_map1_transform)

	header = ('\nFit map %s in map %s using %d points\n'
		% (map1.name, map2.name, stats['points']) +
		'	correlation = %.4g, overlap = %.4g\n'
		% (stats['correlation'], stats['overlap']) +
		'	steps = %d, shift = %.3g, angle = %.3g degrees\n'
		% (stats['steps'], stats['shift'], stats['angle']))
	print header

	#tfs = Matrix.transformation_description(move_tf)
	#print tfs

	xf = Matrix.chimera_xform(move_tf)
	map1.surface_model().openState.globalXform(xf)

# 需要导入模块: import Matrix [as 别名]
# 或者: from Matrix import multiply_matrices [as 别名]
def group_symmetries(group, center, axis, mol):

    from Commands import CommandError

    g0 = group[:1].lower()
    if g0 in ('c', 'd'):
        # Cyclic or dihedral symmetry: C<n>, D<n>
        try:
            n = int(group[1:])
        except ValueError:
            raise CommandError, 'Invalid symmetry group syntax "%s"' % group
        if n < 2:
            raise CommandError, 'Cn or Dn with n = %d < 2' % (n,)
        if g0 == 'c':
            tflist = cyclic_symmetries(n)
        else:
            tflist = dihedral_symmetries(n)
    elif g0 == 'i':
        # Icosahedral symmetry: i[,<orientation>]
        import Icosahedron as icos
        gfields = group.split(',')
        if len(gfields) == 1:
            orientation = '222'
        elif len(gfields) == 2:
            orientation = gfields[1]
            if not orientation in icos.coordinate_system_names:
                raise CommandError, ('Unknown icosahedron orientation "%s"'
                                     % orientation)
        else:
            raise CommandError, 'Invalid symmetry group syntax "%s"' % group
        tflist = icos.icosahedral_symmetry_matrices(orientation)
    elif g0 == 'h':
        # Helical symmetry: h,<repeat>,<rise>[,<angle>[,<n>,<offet>]]
        gfields = group.split(',')
        nf = len(gfields)
        if nf < 3 or nf > 6:
            raise CommandError, 'Invalid symmetry group syntax "%s"' % group
        try:
            param = [float(f) for f in gfields[1:]]
        except ValueError:
            raise CommandError, 'Invalid symmetry group syntax "%s"' % group
        if len(param) == 2:
            param.append(360.0)
        if len(param) == 3:
            param.append(int(param[0]))
        if len(param) == 4:
            param.append(0)
        repeat, rise, angle, n, offset = param
        tflist = helical_symmetry(repeat, rise, angle, n, offset)
    elif g0 == 't':
        # Translation symmetry: t,<n>,<distance> or t,<n>,<dx>,<dy>,<dz>
        gfields = group.split(',')
        nf = len(gfields)
        if nf != 3 and nf != 5:
            raise CommandError, 'Invalid symmetry group syntax "%s"' % group
        try:
            param = [float(f) for f in gfields[1:]]
        except ValueError:
            raise CommandError, 'Invalid symmetry group syntax "%s"' % group
        n = param[0]
        if n != int(n):
            raise CommandError, 'Invalid symmetry group syntax "%s"' % group
        if nf == 3:
          delta = (0,0,param[1])
        else:
          delta = param[1:]
        tflist = translation_symmetry(n, delta)
    elif group.lower() == 'biomt':
        # BIOMT biological unit matrices from PDB file header.
        if not hasattr(mol, 'pdbHeaders'):
            msg = 'Molecule %s has no BIOMT matrices or PDB headers' % mol.name
            raise CommandError, msg
        from PDBmatrices import pdb_biomt_matrices
        tflist = pdb_biomt_matrices(mol.pdbHeaders)
        if len(tflist) == 0:
            msg = 'Molecule %s has no BIOMT matrices in PDB header' % mol.name
            raise CommandError, msg
        from Matrix import is_identity_matrix
        if len(tflist) == 1 and is_identity_matrix(tflist[0]):
            msg = 'Molecule %s has only identity BIOMT matrix in PDB header' % mol.name
            raise CommandError, msg
    else:
        raise CommandError, 'Unknown symmetry group "%s"' % group

    # Apply center and axis transformation.
    if tuple(center) != (0,0,0) or tuple(axis) != (0,0,1):
        import Matrix as m
        tf = m.multiply_matrices(m.vector_rotation_transform(axis, (0,0,1)),
                                 m.translation_matrix([-c for c in center]))
        tfinv = m.invert_matrix(tf)
        tflist = [m.multiply_matrices(tfinv, t, tf) for t in tflist]

    return tflist