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# 03_ligand.oy
# Copyright (C) 2008 Bernhard Lohkamp, The University of York
#
# 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, see <http://www.gnu.org/licenses/>.
import os
import unittest
import coot
import coot_utils
import coot_testing_utils
class TestLigandFunctions(unittest.TestCase):
def test01_0(self):
"""Get monomer test"""
imol = coot.get_monomer("3GP")
if (coot_utils.valid_model_molecule_qm(imol)):
coot.delete_residue_hydrogens(imol, "A", 1, "", "")
self.assertFalse(not coot_utils.valid_model_molecule_qm(imol), "not valid molecule for 3GP")
def test03_0(self):
"""Delete all-molecule Hydrogens"""
imol = coot_testing_utils.unittest_pdb("monomer-3GP.pdb")
self.assertTrue(coot_utils.valid_model_molecule_qm(imol))
print("here 1")
n = coot.delete_hydrogens(imol)
self.assertTrue(n > 0)
# I don't understand this test any more.
# def test04_0(self):
# """Non-Autoloads"""
# def get_ccp4_version():
# s = coot_utils.shell_command_to_string("cad -i").split("\n")
# if s:
# for line in s:
# if "CCP4 software suite: patch level" in line:
# sl = line.split()
# return sl[-1]
# return False
# def old_ccp4_restraints_qm():
# global have_ccp4_qm
# if (not have_ccp4_qm):
# return False
# else:
# v = get_ccp4_version()
# # will always be string
# return v < "6.2"
# r_1 = coot.monomer_restraints_py("LIG")
# o = old_ccp4_restraints_qm()
# coot_testing_utils.unittest_pdb("test-LIG.pdb")
# r_2 = coot.monomer_restraints_py("LIG")
# coot.remove_non_auto_load_residue_name("LIG")
# coot_testing_utils.unittest_pdb("test-LIG.pdb")
# r_3 = coot.monomer_restraints_py("LIG")
# coot.delete_restraints("LIG")
# coot.add_non_auto_load_residue_name("LIG")
# r_4 = coot.monomer_restraints_py("LIG")
# # r_1, r_2, r_4 should be False, r_3 should be filled
# #
# # just to be clear here: either this is modern
# # restraints and we should get a list in r-3... or
# # this is old restraints. Either of those should
# # result in a PASS.
# self.assertTrue(all([r_1 == False,
# r_2 == False,
# r_4 == False,
# old_ccp4_restraints_qm() if \
# old_ccp4_restraints_qm() else \
# isinstance(r_3, dict)]))
def test05_0(self):
"""Merge molecules of a ligand with a spec"""
imol = coot_testing_utils.unittest_pdb("tutorial-modern.pdb")
imol_lig = coot.get_monomer("3GP")
spec = ["L", 1, ""]
coot.set_merge_molecules_ligand_spec_py(spec)
coot.merge_molecules_py([imol_lig], imol)
# now check that L1 exists in imol
# residue_spec_to_residue_name expects a 4-ele spec. Hmm
spec[0:0] = [True]
rn = coot_utils.residue_spec_to_residue_name(imol, spec)
self.assertTrue(isinstance(rn, str))
self.assertTrue(rn == "3GP")
def test05_1(self):
"""Move and Refine Ligand test"""
imol = coot_testing_utils.unittest_pdb("tutorial-modern.pdb")
self.assertTrue(coot_utils.valid_model_molecule_qm(imol))
new_rc = [55.3, 9.1, 20.6]
# set the view
view_number = coot_utils.add_view([54.5698, 8.7148, 20.5308],
[0.046229, -0.157139, -0.805581, 0.569395],
19.8858,
"ligand-view")
coot.go_to_view_number(view_number, 1)
# update the map
coot.set_rotation_centre(*new_rc)
coot_utils.move_molecule_here(imol)
backup_mode = coot.backup_state(imol)
alt_conf = ""
replacement_state = coot.refinement_immediate_replacement_state()
coot.turn_off_backup(imol)
coot.set_refinement_immediate_replacement(1)
coot.refine_zone(imol, "A", 1, 1, alt_conf)
coot.accept_regularizement()
coot.rotate_y_scene(600, 0.1)
if replacement_state == 0:
coot.set_refinement_immediate_replacement(0)
if backup_mode == 1:
coot.turn_on_backup(imol)
# ok. no fail.
def test06_0(self):
"""Many Molecules - Ligand Fitting"""
npo_pdb = os.path.join(coot_testing_utils.unittest_data_dir, "monomer-NPO.pdb")
pdb43ca_pdb = os.path.join(coot_testing_utils.unittest_data_dir, "pdb43ca-sans-NPO-refmaced.pdb")
pdb43ca_mtz = os.path.join(coot_testing_utils.unittest_data_dir, "pdb43ca-sans-NPO-refmaced.mtz")
imol_npo = coot.handle_read_draw_molecule_with_recentre(npo_pdb, 0)
self.assertTrue(coot_utils.valid_model_molecule_qm(imol_npo), "no valid molecule")
for i in range(0, 5):
imol_copy = coot.copy_molecule(imol_npo)
coot.set_mol_displayed(imol_copy, 0)
imol_protein = coot.read_pdb(pdb43ca_pdb)
imol_map = coot.auto_read_make_and_draw_maps(pdb43ca_mtz)
imol_map_1 = imol_map[0]
imol_map_2 = imol_map[1]
coot.add_ligand_clear_ligands()
coot.set_ligand_search_protein_molecule(imol_protein)
coot.set_ligand_search_map_molecule(imol_map_1)
coot.add_ligand_search_ligand_molecule(imol_npo)
solutions = coot.execute_ligand_search() # crash?
print(" Fitting NPO gave these results: ", solutions)
coot.set_map_displayed(imol_map_1, 0)
coot.set_map_displayed(imol_map_2, 0)
coot.set_mol_displayed(imol_protein, 0)
coot.set_mol_displayed(imol_npo, 0)
# checked for non crash
def test07_0(self):
"""flip residue (around eigen vectors)"""
# new version
imol_orig = coot_testing_utils.unittest_pdb("monomer-3GP.pdb")
imol_copy = coot.copy_molecule(imol_orig)
self.assertFalse(not coot_utils.valid_model_molecule_qm(imol_orig),
"not valid molecule for monomer-3GP.pdb")
# we need this, otherwise active-atom is (accidentally) the wrong
# molecule
coot.set_go_to_atom_molecule(imol_copy)
coot.set_go_to_atom_chain_residue_atom_name("A", 1, " C8 ")
active_atom = coot.active_residue_py()
self.assertTrue(active_atom, "No active atom")
imol = active_atom[0]
chain_id = active_atom[1]
res_no = active_atom[2]
ins_code = active_atom[3]
atom_name = active_atom[4]
alt_conf = active_atom[5]
self.assertFalse(imol == imol_orig, "oops - didn't pick the copy for active res")
coot.flip_ligand(imol, chain_id, res_no)
atom_orig_1 = coot_utils.get_atom(imol_orig, "A", 1, "", " C8 ")
atom_move_1 = coot_utils.get_atom(imol , "A", 1, "", " C8 ")
self.assertTrue(isinstance(atom_orig_1, list), "atom_orig_1 not found")
self.assertTrue(isinstance(atom_move_1, list), "atom_move_1 not found")
d = coot_testing_utils.bond_length(atom_orig_1[2], atom_move_1[2])
print("distance: ", d)
self.assertTrue(d > 2.1, "fail to move test atom d1")
coot.flip_ligand(imol, chain_id, res_no)
coot.flip_ligand(imol, chain_id, res_no)
coot.flip_ligand(imol, chain_id, res_no)
# having flipped it round the axes 4
# times, we should be back where we
# started.
atom_orig_1 = coot_utils.get_atom(imol_orig, "A", 1, "", " C8 ")
atom_move_1 = coot_utils.get_atom(imol , "A", 1, "", " C8 ")
d2 = coot_testing_utils.bond_length(atom_orig_1[2], atom_move_1[2])
print("distance d2: ", d2)
self.assertTrue(d2 < 0.001, "fail to move atom back to start d2")
# no partial charges in dictionary.
# def test08_0(self):
# """Test dipole"""
# imol = coot_testing_utils.unittest_pdb("dipole-residues.pdb")
# self.assertTrue(coot_utils.valid_model_molecule_qm(imol), "dipole-residues.pdb not found")
# residue_specs = [["A", 1, ""],
# ["A", 2, ""],
# ["A", 3, ""]]
# dipole = coot.add_dipole_for_residues_py(imol, residue_specs)
# self.assertFalse(not dipole, "bad dipole %s" %dipole)
# d = dipole[0]
# dip = dipole[1]
# dip_x = dip[0]
# dip_y = dip[1]
# dip_z = dip[2]
# print("info:: dipole components", dip)
# self.assertAlmostEqual(dip_y, 0.0, 2, "bad dipole y component %s" %dip_y)
# self.assertAlmostEqual(dip_z, 0.0, 2, "bad dipole z component %s" %dip_z)
# self.assertTrue(dip_x < 0 and dip_x > -20)
# def test10_0(self):
# """Pyrogen Runs OK?"""
# # bad things may well happen if we run the wrong version of pyrogen.
# # so force pyrogen to be the one that is installed alongside this version of coot
# # that we are running. We do that by looking and manipulating sys.argv[0]
# import os, sys
# coot_dir = os.path.abspath(os.path.dirname(sys.argv[0]))
# prefix_dir = os.path.normpath(os.path.join(coot_dir, ".."))
# pyrogen_exe = "pyrogen"
# pyrogen_bin = pyrogen_exe # test installed pyrogen
# if coot_utils.is_windows():
# pyrogen_exe = "pyrogen.bat"
# pyrogen_bin = os.path.normpath(os.path.join(prefix_dir, "bin", pyrogen_exe))
# smiles = "C1CNC1"
# tlc_text = "XXX"
# log_file_name = "pyrogen.log"
# # do we have pass now?
# if not coot.enhanced_ligand_coot_p():
# # dont test pyrogen
# # not needed any more. Tested above.
# return
# else:
# arg_list = ["--no-mogul", "--residue-type", tlc_text, smiles] # --no-mogul is the default now
# popen_status = coot_utils.popen_command(pyrogen_bin, arg_list, [], log_file_name, True)
# # self.assertTrue(popen_status == 0)
# self.assertEqual(popen_status, 0,
# "WARNING:: pyrogen exited with status %i\n" %popen_status)
# pdb_file_name = tlc_text + "-pyrogen.pdb"
# cif_file_name = tlc_text + "-pyrogen.cif"
# imol = coot.handle_read_draw_molecule_with_recentre(pdb_file_name, 0)
# print("INFO:: pyrogen will try to read pdb file %s" %pdb_file_name)
# # add test for chirality in the dictionary here
# self.assertTrue(coot_utils.valid_model_molecule_qm(imol))
# def test11_0(self):
# """pyrogen dictionary does not make double-quoted atom names"""
# # make sure that you are running the correct pyrogen
# import os
# if os.path.isfile("UVP-pyrogen.cif"):
# os.remove("UVP-pyrogen.cif")
# popen_status = coot_utils.popen_command("pyrogen",
# # ["-nM", "-r", "UVP",
# ["-n", "-r", "UVP",
# "CO[C@@H]1[C@H](O)[C@H](O[C@H]1[n+]1ccc(O)nc1O)\\C=C\\P(O)(O)=O"],
# [], "pyrogen.log", False)
# self.assertEqual(popen_status, 0,
# "Fail to correctly run pyrogen\n")
# coot.read_cif_dictionary("UVP-pyrogen.cif")
# imol = coot.get_monomer("UVP")
# self.assertTrue(coot_utils.valid_model_molecule_qm(imol),
# "Fail to load molecule from pyrogen dictionary\n")
# atom_info = coot.residue_info(imol, "A", 1, "")
# FLEV will not make a PNG if it is not compiled with
# C++-11 - and that is OK for 0.8.9.x.
#
# def test12_0(self):
# """FLEV makes a PNG"""
# import os
# if self.skip_test(not enhanced_ligand_coot_p(),
# "No ligand enhanced version, skipping FLEV test"):
# return
# fn = "test-flev-greg-testcase.png"
# if os.path.exists(fn):
# os.remove(fn)
# imol = unittest_data_dir("tutorial-modern.pdb")
# imol_ligand = get_monomer("3GP")
# set_rotation_centre(54, 10, 20)
# move_molecule_to_screen_centre(imol_ligand)
# set_merge_molecules_ligand_spec(["L", 1, ""])
# merge_molecules([imol_ligand], imol)
# fle_view_with_rdkit_to_png(imol, "L", 1, "", 4.8, fn)
# self.failUnless(os.path.exists(fn))
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