def tst_adding_disulfur_hydrogen_atoms(switch):
element = 'H'
if switch.endswith('_D'): element = 'D'
fn = 'tst_ready_hydrogens_%s.pdb' % (switch)
f = file(fn, 'wb')
f.write(pdb_strings[switch])
del f
pdb_inp = pdb_input(fn)
hierarchy = pdb_inp.construct_hierarchy()
from mmtbx.conformation_dependent_library.testing_utils import get_geometry_restraints_manager
grm = get_geometry_restraints_manager(pdb_filename=fn)
add_disulfur_hydrogen_atoms(grm, hierarchy, element=element)
hierarchy.write_pdb_file(fn.replace('.pdb', '_updated.pdb'))
if switch == 'CYS_1':
f = file(fn.replace('.pdb', '_updated.pdb'), 'rb')
lines = f.read()
del f
assert lines.find('HG') == -1
else:
cmd = 'phenix.pdb_interpretation %s write_geo=True' % fn.replace(
'.pdb', '_updated.pdb')
print(cmd)
easy_run.go(cmd)
assert_lines_in_file(file_name='%s.geo' %
fn.replace('.pdb', '_updated.pdb'),
lines=geo_strings[switch])
def run_bond(prefix):
edits = """
refinement {
geometry_restraints.edits {
bond {
action = %s
atom_selection_1 = %s
atom_selection_2 = %s
distance_ideal = 2.0
sigma = 1.0
}
}
}
"""
sel_old_1 = "chain A and resseq 7 and name C"
sel_old_2 = "chain A and resseq 7 and name O"
sel_new_1 = "chain A and resseq 7 and name CA"
sel_new_2 = "chain A and resseq 7 and name O"
cntr=0
for action in ["add","delete","change"]:
for kind in ["new","old"]:
prefix_ = "%s_bond_%s_%s"%(prefix, kind, action)
with open("%s.eff"%prefix_, "w") as f:
f.write(edits%(action, eval("sel_%s_1"%kind), eval("sel_%s_2"%kind)))
cmd = cmd_base%(prefix, prefix_)
print (cmd)
r = easy_run.fully_buffered(cmd)
if action == "delete":
cntr+=1
assert r.stderr_lines[0] == \
'Sorry: geometry_restraints.edits.bond.action = delete not implemented.'
else:
if kind == "new":
if action == 'add':
cntr+=1
assert_lines_in_file(
file_name = "%s.pdb.geo"%prefix,
lines = """bond pdb=" CA ILE A 7 "
pdb=" O ILE A 7 "
ideal model delta sigma weight residual
2.000 2.394 -0.394 1.00e+00 1.00e+00 1.56e-01""")
elif action == 'change':
cntr += 1
assert r.stderr_lines[0] == "Sorry: Bond below does not exists, use action=add instead."
elif(kind == "old"):
if action == 'add':
cntr += 1
assert r.stderr_lines[0] == "Sorry: Bond below exists, use action=change instead."
elif action == 'change':
cntr+=1
assert_lines_in_file(
file_name = "%s.pdb.geo"%prefix,
lines = """bond pdb=" C ILE A 7 "
pdb=" O ILE A 7 "
ideal model delta sigma weight residual
2.000 1.229 0.771 1.00e+00 1.00e+00 5.94e-01""")
assert cntr==6
def exercise_2(prefix="tst_pdb_link_records_2"):
with open('%s_mcm.cif' % prefix, 'w') as f:
f.write(restr_cif_txt)
with open('%s.pdb' % prefix, 'w') as f:
f.write(pdb_2c_id)
cmd = "phenix.geometry_minimization %s.pdb %s_mcm.cif write_geo=False" % (
prefix, prefix)
assert not easy_run.call(cmd)
assert_lines_in_file(
'%s_minimized.pdb' % prefix,
"LINK C ALYaC 5 N MCMaC 6 ",
remove_white_spaces=False)
def main():
for code, item in pdbs.items():
print(code)
pf = 'tst_fe_s_%s.pdb' % code
with open(pf, 'w') as f:
f.write(item[0])
cmd = 'phenix.pdb_interpretation %(pf)s > %(pf)s.log' % locals()
print(cmd)
easy_run.go(cmd)
print(item[1])
for line in item[1].split('\n'):
print(line)
assert_lines_in_file(file_name='%s.log' % pf, lines=line)
def test_3():
""" test for command-line tool iotbx.unique_with_biomt"""
inp = iotbx.pdb.input(source_info=None, lines=pdb_str_0)
model = mmtbx.model.manager(model_input=inp)
model.expand_with_BIOMT_records()
model = shift_and_box_model(model)
sel = model.selection("chain '0' or chain 'C' or chain 'F' or chain 'I' or chain 'L' or chain 'O' or chain 'R' or chain 'U' or chain 'X'")
model = model.select(sel)
pdb_str = model.model_as_pdb()
fname = 'tst_reduce_model_with_biomt_test3.pdb'
with open(fname, 'w') as f:
f.write(pdb_str)
assert os.path.isfile(fname)
cmd = "iotbx.unique_with_biomt %s" % fname
print(cmd)
easy_run.call(cmd)
res_fname = 'tst_reduce_model_with_biomt_test3_unique_biomt_000.cif'
assert_lines_in_file(res_fname, """
ATOM 1 N . LYS 0 151 ? 72.74200 43.65400 193.22800 14.010 14.01000 N ? A ? 1 1""")
assert_lines_in_file(res_fname, """
_pdbx_struct_assembly_gen.asym_id_list
1 (1-9) A""")
cmd = "iotbx.unique_with_biomt %s chain_id_to_leave='C' output.serial=1" % fname
print(cmd)
easy_run.call(cmd)
res_fname = 'tst_reduce_model_with_biomt_test3_unique_biomt_001.cif'
assert_lines_in_file(res_fname, """
ATOM 1 N . LYS C 151 ? 186.74500 185.38200 236.77300 14.010 14.01000 N ? A ? 1 1""")
assert_lines_in_file(res_fname, """
_pdbx_struct_assembly_gen.asym_id_list
1 (1-9) A""")
def exercise(prefix="tst_pdb_box_around_mol"):
# test pdb format
with open("%s.pdb" % prefix, 'w') as f:
f.write(pdb_str)
assert not easy_run.call("iotbx.pdb.box_around_molecule %s.pdb" % (
prefix))
assert_lines_in_file(file_name="%s_box_000.pdb" % prefix,
lines="""\
CRYST1 10.847 12.316 12.145 90.00 90.00 90.00 P 1
SCALE1 0.092191 0.000000 0.000000 0.00000
SCALE2 0.000000 0.081195 0.000000 0.00000
SCALE3 0.000000 0.000000 0.082338 0.00000
ATOM 1 N SER 1 71 5.439 5.000 5.057 1.00300.00 N
ATOM 2 CA SER 1 71 5.000 6.424 5.000 1.00300.00 C
ATOM 3 C SER 1 71 5.847 7.316 5.915 1.00300.00 C
ATOM 4 O SER 1 71 5.736 7.242 7.145 1.00300.00 O
TER""")
# test mmcif format
if libtbx.env.find_in_repositories(relative_path='chem_data') is not None:
with open("%s.cif" % prefix, 'w') as f:
f.write(cif_str)
assert not easy_run.call("iotbx.pdb.box_around_molecule %s.cif" % (
prefix))
assert_lines_in_file(file_name="%s_box_000.cif" % prefix,
lines="""\
data_default
_cell.angle_beta 90.000
_cell.angle_gamma 90.000
_cell.length_b 11.563
_cell.length_c 11.512
_cell.angle_alpha 90.000
_cell.volume 1650.205
_cell.length_a 12.397
_space_group.crystal_system triclinic
_space_group.name_H-M_alt 'P 1'
_space_group.IT_number 1
_space_group.name_Hall ' P 1'
_symmetry.space_group_name_H-M 'P 1'
_symmetry.Int_Tables_number 1
_symmetry.space_group_name_Hall ' P 1'
loop_
_space_group_symop.id
_space_group_symop.operation_xyz
1 x,y,z""")
else:
print('chem_data is not available, skipping')
print("OK")
def exercise(prefix="tst_pdb_box_around_mol"):
with open("%s.pdb" % prefix, 'w') as f:
f.write(pdb_str)
assert not easy_run.call(
"iotbx.pdb.box_around_molecule %s.pdb > %s_boxed.pdb" %
(prefix, prefix))
assert_lines_in_file(file_name="%s_boxed.pdb" % prefix,
lines="""\
CRYST1 10.847 12.316 12.145 90.00 90.00 90.00 P 1
SCALE1 0.092191 0.000000 0.000000 0.00000
SCALE2 0.000000 0.081195 0.000000 0.00000
SCALE3 0.000000 0.000000 0.082338 0.00000
ATOM 1 N SER 1 71 5.439 5.000 5.057 1.00300.00 N
ATOM 2 CA SER 1 71 5.000 6.424 5.000 1.00300.00 C
ATOM 3 C SER 1 71 5.847 7.316 5.915 1.00300.00 C
ATOM 4 O SER 1 71 5.736 7.242 7.145 1.00300.00 O
TER""")
print "OK"
def tst_adding_side_chain_acid_hydrogen_atoms(switch):
element = 'H'
if switch.endswith('_D'): element = 'D'
for i in range(4):
fn = 'tst_ready_hydrogens_%s_%d.pdb' % (switch, i)
with open(fn, 'w') as f:
f.write(pdb_strings[switch])
pdb_inp = pdb_input(fn)
hierarchy = pdb_inp.construct_hierarchy()
add_side_chain_acid_hydrogens(hierarchy,
configuration_index=i,
element=element)
hierarchy.write_pdb_file(fn.replace('.pdb', '_updated.pdb'))
cmd = 'phenix.pdb_interpretation %s flip_sym=0 write_geo=True' % fn.replace(
'.pdb', '_updated.pdb')
print(cmd)
easy_run.go(cmd)
assert_lines_in_file(file_name='%s.geo' %
fn.replace('.pdb', '_updated.pdb'),
lines=geo_strings[switch][i])
def tst_1(prefix="tst_ref_model_ligands_1"):
with open("%s.pdb" % prefix, 'w') as f:
f.write(pdb_str)
with open("%s.cif" % prefix, 'w') as f:
f.write(restr_string)
cmd = " ".join([
"phenix.geometry_minimization",
"%s.pdb" % prefix,
"%s.cif" % prefix,
"reference_model.enabled=True",
"reference_model.file=%s.pdb" % prefix,
">%s.log" % prefix])
print(cmd)
assert not easy_run.call(cmd)
assert_lines_in_file(
file_name="%s.log" % prefix,
lines=
"""Model: Reference:
LIG A 1 <=====> LIG A 1
Total # of matched residue pairs: 1
Total # of reference model restraints: 1""")
def exercise(prefix="tst_pdb_box_around_mol"):
# test pdb format
with open("%s.pdb" % prefix, 'w') as f:
f.write(pdb_str)
assert not easy_run.call("iotbx.pdb.box_around_molecule %s.pdb" % (prefix))
assert_lines_in_file(file_name="%s_box_000.pdb" % prefix,
lines="""\
CRYST1 10.847 12.316 12.145 90.00 90.00 90.00 P 1
SCALE1 0.092191 0.000000 0.000000 0.00000
SCALE2 0.000000 0.081195 0.000000 0.00000
SCALE3 0.000000 0.000000 0.082338 0.00000
ATOM 1 N SER 1 71 5.439 5.000 5.057 1.00300.00 N
ATOM 2 CA SER 1 71 5.000 6.424 5.000 1.00300.00 C
ATOM 3 C SER 1 71 5.847 7.316 5.915 1.00300.00 C
ATOM 4 O SER 1 71 5.736 7.242 7.145 1.00300.00 O
TER""")
# test mmcif format
if libtbx.env.find_in_repositories(relative_path='chem_data') is not None:
with open("%s.cif" % prefix, 'w') as f:
f.write(cif_str)
assert not easy_run.call("iotbx.pdb.box_around_molecule %s.cif" %
(prefix))
# XXX temp fix for python3 failure
# XXX changes in python 3 because _cell.length_a and other order differs
# Python 3 behavior looks better.
# Reason for this discrepancy is that starting from Python 3.7
# "the insertion-order preservation nature of dict objects has been
# declared to be an official part of the Python language spec."
# https://docs.python.org/3/whatsnew/3.7.html
# Basically, dict.keys() in Py3 preserves the order in which keys were added
# to the dict.
#
# Sorting of mmCIF keys here
# cctbx_project/iotbx/cif/__init__.py, def category_sort_function()
# should be improved to address such issues universally (sorting within
# category), note the diference in _space_group and _symmetry categories
# as well.
import sys
if sys.version.startswith("3.8"):
assert_lines_in_file(file_name="%s_box_000.cif" % prefix,
lines="""\
data_default
_cell.length_a 12.397
_cell.length_b 11.563
_cell.length_c 11.512
_cell.angle_alpha 90.000
_cell.angle_beta 90.000
_cell.angle_gamma 90.000
_cell.volume 1650.205
_space_group.crystal_system triclinic
_space_group.IT_number 1
_space_group.name_H-M_alt 'P 1'
_space_group.name_Hall ' P 1'
_symmetry.space_group_name_H-M 'P 1'
_symmetry.space_group_name_Hall ' P 1'
_symmetry.Int_Tables_number 1
loop_
_space_group_symop.id
_space_group_symop.operation_xyz
1 x,y,z""")
else: # version 2.7
assert_lines_in_file(file_name="%s_box_000.cif" % prefix,
lines="""\
data_default
_cell.angle_beta 90.000
_cell.angle_gamma 90.000
_cell.length_b 11.563
_cell.length_c 11.512
_cell.angle_alpha 90.000
_cell.volume 1650.205
_cell.length_a 12.397
_space_group.crystal_system triclinic
_space_group.name_H-M_alt 'P 1'
_space_group.IT_number 1
_space_group.name_Hall ' P 1'
_symmetry.space_group_name_H-M 'P 1'
_symmetry.Int_Tables_number 1
_symmetry.space_group_name_Hall ' P 1'
loop_
_space_group_symop.id
_space_group_symop.operation_xyz
1 x,y,z""")
else:
print('chem_data is not available, skipping')
print("OK")
def run():
fn = '4udx_sf4.pdb'
f = file(fn, 'wb')
f.write(pdbs[fn])
f.close()
for i, superpose in enumerate(['None', 'all']):
cmd = 'phenix.geometry_minimization %s superpose_ideal=%s' % (
fn,
superpose,
)
print cmd
rc = easy_run.go(cmd)
for line in rc.stdout_lines:
#print line
if line.find('bond_residual_sum') > -1:
bond_value = round(float(line.split()[-1]))
if line.find('angle_residual_sum') > -1:
angle_value = round(float(line.split()[-1]))
# in the second iteration bond_value and angle_value are expected to be 0!
# assert bond_value, "%f %f" % (bond_value, results[fn][i][0])
# assert angle_value, angle_value
assert bond_value == results[fn][i][0], 'not matching %s to %s' % (
bond_value,
results[fn][i][0],
)
assert angle_value == results[fn][i][1], 'not matching %s to %s' % (
angle_value,
results[fn][i][1],
)
for i, superpose in enumerate(['None', 'all']):
cmd = 'phenix.pdb_interpretation %s superpose_ideal=%s' % (
fn,
superpose,
)
print cmd
rc = easy_run.go(cmd)
for line in rc.stdout_lines:
#print line
if line.find('bond_residual_sum') > -1:
value = round(float(line.split()[-1]))
print 'value', value
assert value == results[fn][i][2], 'not matching %s to %s' % (
value,
results[fn][i][2],
)
if line.find('angle_residual_sum') > -1:
value = round(float(line.split()[-1]))
print 'value', value
assert value == results[fn][i][3], 'not matching %s to %s' % (
value,
results[fn][i][3],
)
fn = '4udx_sf4_cys.pdb'
f = file(fn, 'wb')
f.write(pdbs[fn])
f.close()
# lines = '''
# SF4/F3S coordination
# SF4 X1001
# pdb="FE1 SF4 X1001 " - pdb=" SG CYS X 51 "
# pdb="FE2 SF4 X1001 " - pdb=" SG CYS X 48 "
# pdb="FE3 SF4 X1001 " - pdb=" SG CYS X 56 "
# pdb="FE4 SF4 X1001 " - pdb=" SG CYS X 70 "'''
from libtbx.test_utils import assert_lines_in_file
lines = [
'SF4/F3S coordination',
'SF4 X1001',
'pdb="FE1 SF4 X1001 " - pdb=" SG CYS X 51 "',
'pdb="FE4 SF4 X1001 " - pdb=" SG CYS X 70 "',
'pdb="FE3 SF4 X1001 " - pdb=" SG CYS X 56 "',
'pdb="FE2 SF4 X1001 " - pdb=" SG CYS X 48 "',
]
cmd = 'phenix.pdb_interpretation %s link_all=True > %s.log' % (fn, fn)
print cmd
assert not easy_run.call(cmd)
for line in lines:
print line
assert_lines_in_file(file_name='%s.log' % fn, lines=line)
return 0
def run_angle(prefix):
edits = """
refinement {
geometry_restraints.edits {
angle {
action = %s
atom_selection_1 = %s
atom_selection_2 = %s
atom_selection_3 = %s
angle_ideal = 10
sigma = 1
}
}
}
"""
sel_old_1 = "chain A and resseq 7 and name N"
sel_old_2 = "chain A and resseq 7 and name CA"
sel_old_3 = "chain A and resseq 7 and name CB"
sel_new_1 = "chain A and resseq 7 and name N"
sel_new_2 = "chain A and resseq 7 and name CA"
sel_new_3 = "chain A and resseq 7 and name CG2"
cntr = 0
for action in ["add", "delete", "change"]:
for kind in ["new", "old"]:
prefix_ = "%s_angle_%s_%s" % (prefix, kind, action)
with open("%s.eff" % prefix_, "w") as f:
f.write(edits %
(action, eval("sel_%s_1" % kind),
eval("sel_%s_2" % kind), eval("sel_%s_3" % kind)))
cmd = cmd_base % (prefix, prefix_)
print(cmd)
r = easy_run.fully_buffered(cmd)
if action == "add":
if kind == "new":
cntr += 1
assert_lines_in_file(file_name="%s.pdb.geo" % prefix,
lines="""
angle pdb=" N ILE A 7 "
pdb=" CA ILE A 7 "
pdb=" CG2 ILE A 7 "
ideal model delta sigma weight residual
10.00 143.31 -133.31 1.00e+00 1.00e+00 1.78e+04""")
elif kind == "old":
cntr += 1
assert r.stderr_lines[0] == \
"Sorry: Some restraints were not added because they are already present."
if action == "delete":
cntr += 1
assert r.stderr_lines[0] == \
'Sorry: geometry_restraints.edits.angle.action = delete not implemented.'
if action == "change":
if kind == "new":
cntr += 1
assert r.stderr_lines[0] == \
'Sorry: Angle below is not restrained, nothing to change.'
elif kind == "old":
cntr += 1
assert_lines_in_file(file_name="%s.pdb.geo" % prefix,
lines="""
angle pdb=" N ILE A 7 "
pdb=" CA ILE A 7 "
pdb=" CB ILE A 7 "
ideal model delta sigma weight residual
10.00 109.54 -99.54 1.00e+00 1.00e+00 9.91e+03""")
assert cntr == 6
