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# 05_rna_ghosts.py
# Copyright 2008 by The University of York
# Author: Bernhard Lohkamp
# Copyright 2007, 2008 by The University of Oxford
# Author: Paul Emsley
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or (at
# your option) any later version.
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
# 02110-1301, USA
import unittest
import os
import coot
import coot_utils
class TestRNAGhostsFunctions(unittest.TestCase):
def test01_0(self):
"""RNA NCS Ghosts"""
import random
jiggle_random = random.uniform(-0.5, 0.5)
# a bit of ugliness here, we set! additions to
# atom-attribute-settings, rather than consing them with
# recursion over chain-id, serial-number and atom-list.
# Hmm... Come back to improve one day?
#
def jiggle_atoms_of_mol(imol):
atom_attribute_settings = []
for chain_id in coot_utils.chain_ids(imol):
if (not coot_utils.is_solvent_chain_qm(imol, chain_id)):
n_residues = coot.chain_n_residues(chain_id, imol)
print(" There are %s residues in chain %s" %(n_residues, chain_id))
for serial_number in range(n_residues):
res_name = coot.resname_from_serial_number(imol, chain_id, serial_number)
res_no = coot.seqnum_from_serial_number (imol, chain_id, serial_number)
ins_code = coot.insertion_code_from_serial_number(imol, chain_id, serial_number)
atom_ls = coot.residue_info_py(imol, chain_id, res_no, ins_code)
for atom in atom_ls:
compound_name = atom[0]
atom_name = compound_name[0]
alt_conf = compound_name[1]
xyz = atom[2]
x = xyz[0]
y = xyz[1]
z = xyz[2]
atom_attribute_settings.append([imol, chain_id, res_no, ins_code, atom_name, alt_conf,
"x", (24 + x + 0.3 * jiggle_random)])
atom_attribute_settings.append([imol, chain_id, res_no, ins_code, atom_name, alt_conf,
"y", (24 + y + 0.3 * jiggle_random)])
atom_attribute_settings.append([imol, chain_id, res_no, ins_code, atom_name, alt_conf,
"z", (24 + z + 0.3 * jiggle_random)])
coot.set_atom_attributes_py(atom_attribute_settings)
# main body
rna_mol = coot.ideal_nucleic_acid("RNA", "A", 0, "GACUCUAG")
copy_rna_mol = coot.copy_molecule(rna_mol)
# move the view over a bit so we can see the atoms being jiggled
rc = coot_utils.rotation_centre()
coot.set_rotation_centre(rc[0] + 12,
rc[1] + 3,
rc[2])
view_number = coot_utils.add_view([74.7079, 10.6267, 24.3308],
[-0.713385, -0.0433099, -0.105865, -0.691373],
70.3919,
"RNA-builder-view")
coot.go_to_view_number(view_number, 1)
# now jiggle the atoms of copy-rna-mol
jiggle_atoms_of_mol(copy_rna_mol)
coot.merge_molecules_py([copy_rna_mol], rna_mol)
imol_copy = coot.copy_molecule(rna_mol)
coot.clear_lsq_matches()
coot.add_lsq_match(1, 6, "A", 1, 6, "C", 0) # ref mov - all atoms
rrtop = coot.apply_lsq_matches_py(imol_copy, imol_copy)
rtop = []
for r in rrtop:
rtop.extend(r)
#close_molecule(imol_copy)
#close_molecule(copy_rna_mol)
self.assertTrue(rtop, "Failed to get matching matrix")
coot.set_draw_ncs_ghosts(rna_mol, 1)
coot.add_ncs_matrix(rna_mol, "C", "A", *rtop)
view_number = coot_utils.add_view([72.3306, 10.6899, 24.073],
[-0.240736, -0.674651, -0.690658, -0.0994136],
14.9021,
"RNA-ghots-view")
coot.go_to_view_number(view_number, 1)
# coot.rotate_y_scene(coot.rotate_n_frames(200), 1)
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