"1i07",
"1a7y"]
pdb_dir_p1 = os.path.join(qrefine,"regression","datasets","p1")
complete_pdbs(expected_list_cluster, pdb_dir_cluster)
complete_pdbs(expected_list_p1, pdb_dir_p1)
def complete_pdbs(expected_list, pdb_dir):
if(not (os.path.isdir(pdb_dir))):
raise Sorry(pdb_dir + " not exist. Please get its repository on GitHub")
#input_var = str(
# raw_input("run finalise.py for all pdbs in %s will take quite a while (30~60 minutes), continue Y/N : " % pdb_dir))
if 1: #(input_var == "Y") or 1:
print '"%s"' % pdb_dir
no_error_list = batch_run_finalise.run(pdb_dir,
nproc=1,
#only_code='1il5',
)
print no_error_list
#shutil.rmtree("./tmp")
expected_list.sort()
no_error_list.sort()
print expected_list
print no_error_list
assert approx_equal(expected_list, no_error_list),'%s has different pdbs passing finalise.py'%pdb_dir
else:
print "skip"
if(__name__ == "__main__"):
rc = run_tests.runner(function=run, prefix="tst_11", disable=False)
assert not rc, 'tst_00 rc: %s' % rc
ATOM 1172 HB3 CYS A 78 9.453 11.155 18.172 1.00 9.23 H
HETATM 1832 CU CU A 201 7.545 9.241 20.314 0.40 8.15 Cu
ANISOU 1832 CU CU A 201 503 1903 690 -55 119 0 Cu
'''
def run(prefix):
fn='test_cu_cys.pdb'
f=file(fn, 'wb')
f.write(pdb_lines)
f.close()
cmd = 'qr.finalise %s action="capping"' % (fn)
if 0: print cmd
rc = easy_run.go(cmd)
os.remove(fn)
fnc = '%s_capping.pdb' % fn.replace('.pdb','')
f=file(fnc, 'rb')
lines=f.read()
f.close()
assert ' HG CYS A 78' not in lines
cmd = 'qr.charges %s verbose=1' % (fnc)
if 0: print cmd
rc = easy_run.go(cmd)
assert 'Charge: 0' in rc.stdout_lines
os.remove(fnc)
return rc
if __name__=='__main__':
prefix='tst_24'
rc = run_tests.runner(function=run, prefix=prefix, disable=False)
assert not rc, '%s rc: %s' % (prefix, rc)
crystal_symmetry=cs,
clustering=True,
)
fm = fragments(working_folder=os.path.split("./ase/tmp_ase.pdb")[0] + "/",
clustering_method=betweenness_centrality_clustering,
maxnum_residues_in_cluster=8,
charge_embedding=False,
pdb_hierarchy=ph,
qm_engine_name="mopac",
crystal_symmetry=cs)
fc = from_cluster(
restraints_manager=fq,
fragment_manager=fm,
parallel_params=get_master_phil().extract(),
)
energy, gradients = fc.target_and_gradients(sites_cart=sites_cart)
energy = energy * (kcal / mol) * (kcal / mol) / Hartree
gradients = gradients * (kcal / mol) * (kcal / mol) * (Bohr / Hartree)
gradients = list(gradients.as_double())
os.system("rm -rf ase")
assert approx_equal(energy, e, 1.0E-4)
#assert approx_equal(gradients, g, 1.0E-4)
if (__name__ == "__main__"):
rc = run_tests.runner(function=run, prefix="tst_10", disable=True)
assert not rc, 'tst_00 rc: %s' % rc
clustering_method = betweenness_centrality_clustering,
maxnum_residues_in_cluster = 8,
charge_embedding = False,
pdb_hierarchy = ph,
qm_engine_name = "mopac",
crystal_symmetry = cs)
restraints = from_cluster(
restraints_manager = fq,
fragment_manager =fm,
parallel_params = get_master_phil().extract())
else:
restraints = fq
return restraints
def qm_gradient(ph, restraints):
sites_cart = ph.atoms().extract_xyz()
e,g = restraints.target_and_gradients(sites_cart)
return g
def qm_opt(restraints, file):
sys = ase_io_read(os.path.join(qr_unit_tests,"data_files/helix.pdb"))
opt = lbfgs_gradient(sys, restraints)
opt.run(5)
opt.write(file)
if(__name__ == "__main__"):
disable = False
if(os.environ.get("MOPAC_COMMAND") is None): disable = True
rc = run_tests.runner(function=run, prefix="tst_13", disable=disable)
assert not rc, 'tst_00 rc: %s' % rc
if 0:
print list(phW.atoms())[0].name
print esW.gradients[0]
print
print list(ph.atoms())[0].name
print es.gradients[0]
print esA.gradients[0]
print esB.gradients[0]
print
print list(phA.atoms())[5].name, list(ph.atoms())[5].name
print es.gradients[5]
print esA.gradients[5]
print
print list(phB.atoms())[5].name, list(ph.atoms())[12].name
print es.gradients[12]
print esB.gradients[5]
print
print "-------"
result = list(
flex.double(esA.gradients[0]) + flex.double(esB.gradients[0]) -
flex.double(esW.gradients[0]))
assert approx_equal(result, es.gradients[0])
if __name__ == '__main__':
rc = run_tests.runner(function=run1, prefix="tst_17", disable=False)
rc += run_tests.runner(function=run2, prefix="tst_17", disable=False)
rc += run_tests.runner(function=run3, prefix="tst_17", disable=False)
assert not rc, 'tst_17 rc: %s' % rc