def exercise_3():
if (not libtbx.env.has_module(name="phaser")):
print "phaser module not available: skipping advanced tests"
return
import iotbx.phil
import phaser.phenix_interface
master_phil = phaser.phenix_interface.master_phil()
i = interface.index(master_phil=master_phil, parse=iotbx.phil.parse)
i.merge_phil(phil_string="""\
phaser {
hklin = "/Users/nat/Documents/beta-blip/beta_blip_P3221.mtz"
labin = Fobs,Sigma
composition {
chain {
sequence_file = "/Users/nat/Documents/beta-blip/beta.seq"
}
chain {
sequence_file = "/Users/nat/Documents/beta-blip/blip.seq"
}
}
ensemble {
model_id = "beta"
coordinates {
pdb = "/Users/nat/Documents/beta-blip/beta.pdb"
}
}
ensemble {
model_id = "blip"
coordinates {
pdb = "/Users/nat/Documents/beta-blip/blip.pdb"
}
}
}
""")
files_in = [('/Users/nat/Documents/beta-blip/beta_blip_P3221.mtz',
'Data file', 'phaser.hklin'),
('/Users/nat/Documents/beta-blip/blip.seq', 'Sequence file',
'phaser.composition.chain.sequence_file'),
('/Users/nat/Documents/beta-blip/blip.pdb', 'Ensemble model',
'phaser.ensemble.coordinates.pdb')]
assert (i.get_input_files() == files_in)
i.save_param_file(file_name="phaser.eff",
extra_phil="""
phaser.search {
ensembles = beta
copies = 1
}
phaser.search {
ensembles = blip
copies = 1
}""",
replace_path="/Users/nat/Documents/beta-blip")
i = interface.index(master_phil=master_phil, parse=iotbx.phil.parse)
i.merge_phil(phil_file="phaser.eff")
p = i.get_python_object().phaser
assert (i.get_input_files() == files_in)
assert (p.hklin == "/Users/nat/Documents/beta-blip/beta_blip_P3221.mtz")
assert (len(p.search) == 2)
assert (p.search[0].ensembles == ["beta"])
# update file in-place (with variable substitution)
interface.update_phil_file_paths(
master_phil=master_phil,
file_name="phaser.eff",
old_path="/Users/nat/Documents/beta-blip",
new_path="/Users/nat/Documents/projects/beta-blip",
use_iotbx_parser=True)
i = interface.index(master_phil=master_phil, parse=iotbx.phil.parse)
i.merge_phil(phil_file="phaser.eff")
p = i.get_python_object().phaser
assert (p.hklin ==
"/Users/nat/Documents/projects/beta-blip/beta_blip_P3221.mtz")
# update file in-place, by modifying phil objects directly
i.save_param_file(file_name="phaser2.eff")
interface.update_phil_file_paths(
master_phil=master_phil,
file_name="phaser2.eff",
old_path="/Users/nat/Documents/projects/beta-blip",
new_path="/home/nat/projects/beta-blip",
use_iotbx_parser=True)
i = interface.index(master_phil=master_phil, parse=iotbx.phil.parse)
i.merge_phil(phil_file="phaser2.eff")
p = i.get_python_object().phaser
assert (p.hklin == "/home/nat/projects/beta-blip/beta_blip_P3221.mtz")
i.set_prefix("phaser")
assert (i.get_full_path(".hklin") == "phaser.hklin")
assert (i.get_scope_by_name(".keywords") is not None)
# and now with Windows-style paths
interface.update_phil_file_paths(
master_phil=master_phil,
file_name="phaser2.eff",
old_path="/home/nat/projects/beta-blip",
new_path="C:\\projects\\xtal\\beta-blip", # \x and \b are key here
use_iotbx_parser=True)
i = interface.index(master_phil=master_phil, parse=iotbx.phil.parse)
i.merge_phil(phil_file="phaser2.eff")
p = i.get_python_object().phaser
# XXX obviously these are not entirely transferrable between Unix and
# Windows - we need to caution users against this
assert (p.hklin == "C:\\projects\\xtal\\beta-blip/beta_blip_P3221.mtz")
def exercise_2(verbose=False):
if (not libtbx.env.has_module(name="phenix")):
print "phenix module not available: skipping advanced tests"
return
from phenix.refinement import runtime
import iotbx.phil
from time import time
phil_str = """
refinement.pdb_interpretation.secondary_structure.protein {
helix {
selection = "chain A and resseq 10:20"
}
helix {
selection = "chain A and resseq 30:40"
}
helix {
selection = "chain A and resseq 50:60"
}
}
"""
phil_str_2 = """
refinement.pdb_interpretation.secondary_structure.protein {
helix {
selection = "chain B and resseq 10:20"
}
helix {
selection = "chain B and resseq 30:40"
}
helix {
selection = "chain B and resseq 50:60"
}
}
"""
master_phil = runtime.master_phil()
i = interface.index(master_phil=master_phil, parse=iotbx.phil.parse)
t1 = time()
i.merge_phil(phil_string=phil_str)
t2 = time()
params = i.get_python_object()
assert (params.refinement.pdb_interpretation.secondary_structure.\
protein.helix[0].selection == "chain A and resseq 10:20")
t3 = time()
i.merge_phil(
phil_string=phil_str_2,
only_scope="refinement.pdb_interpretation.secondary_structure")
t4 = time()
params = i.get_python_object()
assert (params.refinement.pdb_interpretation.secondary_structure.\
protein.helix[0].selection == "chain B and resseq 10:20")
scope = i.get_scope_by_name(
"refinement.pdb_interpretation.secondary_structure")
params2 = scope.extract()
assert (params2.protein.helix[0].selection == "chain B and resseq 10:20")
if verbose:
print "Merge with global fetch: %6.1fms" % ((t2 - t1) * 1000)
print "Merge with local fetch: %6.1fms" % ((t4 - t3) * 1000)
i.merge_phil(phil_string="""
refinement.input.pdb.file_name = protein.pdb
refinement.input.pdb.file_name = ligand.pdb
refinement.input.xray_data.file_name = data.mtz
refinement.input.monomers.file_name = ligand.cif
refinement.output.job_title = Test refinement run
""")
names = i.search_phil_text("CIF")
assert (set(names) == {
'refinement.output.write_model_cif_file',
'refinement.output.write_reflection_cif_file',
'refinement.input.monomers.file_name',
})
assert (i.get_input_files() == [
('protein.pdb', 'Input model', 'refinement.input.pdb.file_name'),
('ligand.pdb', 'Input model', 'refinement.input.pdb.file_name'),
('data.mtz', 'Reflections file',
'refinement.input.xray_data.file_name'),
('ligand.cif', 'Restraints (CIF)',
'refinement.input.monomers.file_name')
])
assert (i.get_job_title() == "Test refinement run")
#
# .style processing
style = i.get_scope_style("refinement.refine.strategy")
#assert (style.auto_launch_dialog == [
# 'refinement.refine.sites.individual', 'refinement.refine.sites.individual',
# 'refinement.refine.sites.rigid_body', 'refinement.refine.adp.individual',
# 'refinement.refine.adp.group', 'refinement.refine.adp.tls',
# 'refinement.refine.occupancies', 'refinement.refine.anomalous_scatterers'])
assert (style.file_type is None)
style = i.get_scope_style("refinement.input.xray_data.file_name")
assert (style.get_list("file_type") == ["hkl"])
assert (style.get_child_params() == {
'fobs': 'labels',
'd_max': 'low_resolution',
'd_min': 'high_resolution',
'rfree_file': 'r_free_flags.file_name'
})
assert i.is_list_type("refinement.input.xray_data.labels")
style = i.get_scope_style("refinement.input.xray_data.labels")
assert (style.get_parent_params() == {"file_name": "file_name"})
file_map = i.get_file_type_map("pdb")
assert (file_map.get_multiple_params() == \
['refinement.input.pdb.file_name',
'refinement.reference_model.file'])
assert (file_map.get_default_param() == "refinement.input.pdb.file_name")
file_map = i.get_file_type_map("hkl")
assert (file_map.get_overall_max_count() == 5)
assert (len(file_map.get_multiple_params()) == 0)
assert (
file_map.get_max_count("refinement.input.xray_data.file_name") == 1)
menu = i.get_menu_db()
assert (len(menu.get_items()) > 15) # XXX ballpark (currently 17)
submenu = menu.get_submenu("Atom_selections")
assert (str(submenu.get_items()[0]) == "refinement.refine.sites")
{
include scope xia2.Modules.Analysis.phil_scope
}
symmetry
.short_caption = "symmetry"
{
chirality = chiral nonchiral centrosymmetric
.type = choice
program = *pointless dials
.type = choice
}
}
""",
process_includes=True,
)
# override default resolution parameters
master_phil = master_phil.fetch(source=parse("""\
xia2.settings {
resolution {
isigma = None
misigma = None
}
}
"""))
PhilIndex = interface.index(master_phil=master_phil)
if __name__ == "__main__":
PhilIndex.working_phil.show()
def exercise_3 () :
if (not libtbx.env.has_module(name="phaser")):
print "phaser module not available: skipping advanced tests"
return
import iotbx.phil
import phaser.phenix_interface
master_phil = phaser.phenix_interface.master_phil()
i = interface.index(master_phil=master_phil,
parse=iotbx.phil.parse)
i.merge_phil(phil_string="""\
phaser {
hklin = "/Users/nat/Documents/beta-blip/beta_blip_P3221.mtz"
labin = Fobs,Sigma
composition {
chain {
sequence_file = "/Users/nat/Documents/beta-blip/beta.seq"
}
chain {
sequence_file = "/Users/nat/Documents/beta-blip/blip.seq"
}
}
ensemble {
model_id = "beta"
coordinates {
pdb = "/Users/nat/Documents/beta-blip/beta.pdb"
}
}
ensemble {
model_id = "blip"
coordinates {
pdb = "/Users/nat/Documents/beta-blip/blip.pdb"
}
}
}
""")
files_in = [
('/Users/nat/Documents/beta-blip/beta_blip_P3221.mtz', 'Data file',
'phaser.hklin'),
('/Users/nat/Documents/beta-blip/blip.seq', 'Sequence file',
'phaser.composition.chain.sequence_file'),
('/Users/nat/Documents/beta-blip/blip.pdb', 'Ensemble model',
'phaser.ensemble.coordinates.pdb')
]
assert (i.get_input_files() == files_in)
i.save_param_file(
file_name="phaser.eff",
extra_phil="""
phaser.search {
ensembles = beta
copies = 1
}
phaser.search {
ensembles = blip
copies = 1
}""",
replace_path="/Users/nat/Documents/beta-blip")
i = interface.index(master_phil=master_phil,
parse=iotbx.phil.parse)
i.merge_phil(phil_file="phaser.eff")
p = i.get_python_object().phaser
assert (i.get_input_files() == files_in)
assert (p.hklin == "/Users/nat/Documents/beta-blip/beta_blip_P3221.mtz")
assert (len(p.search) == 2)
assert (p.search[0].ensembles == ["beta"])
# update file in-place (with variable substitution)
interface.update_phil_file_paths(
master_phil=master_phil,
file_name="phaser.eff",
old_path="/Users/nat/Documents/beta-blip",
new_path="/Users/nat/Documents/projects/beta-blip",
use_iotbx_parser=True)
i = interface.index(master_phil=master_phil,
parse=iotbx.phil.parse)
i.merge_phil(phil_file="phaser.eff")
p = i.get_python_object().phaser
assert (p.hklin ==
"/Users/nat/Documents/projects/beta-blip/beta_blip_P3221.mtz")
# update file in-place, by modifying phil objects directly
i.save_param_file(file_name="phaser2.eff")
interface.update_phil_file_paths(
master_phil=master_phil,
file_name="phaser2.eff",
old_path="/Users/nat/Documents/projects/beta-blip",
new_path="/home/nat/projects/beta-blip",
use_iotbx_parser=True)
i = interface.index(master_phil=master_phil,
parse=iotbx.phil.parse)
i.merge_phil(phil_file="phaser2.eff")
p = i.get_python_object().phaser
assert (p.hklin == "/home/nat/projects/beta-blip/beta_blip_P3221.mtz")
i.set_prefix("phaser")
assert (i.get_full_path(".hklin") == "phaser.hklin")
assert (i.get_scope_by_name(".keywords") is not None)
# and now with Windows-style paths
interface.update_phil_file_paths(
master_phil=master_phil,
file_name="phaser2.eff",
old_path="/home/nat/projects/beta-blip",
new_path="C:\\projects\\xtal\\beta-blip", # \x and \b are key here
use_iotbx_parser=True)
i = interface.index(master_phil=master_phil,
parse=iotbx.phil.parse)
i.merge_phil(phil_file="phaser2.eff")
p = i.get_python_object().phaser
# XXX obviously these are not entirely transferrable between Unix and
# Windows - we need to caution users against this
assert (p.hklin == "C:\\projects\\xtal\\beta-blip/beta_blip_P3221.mtz")
def exercise_2 (verbose=False) :
if (not libtbx.env.has_module(name="phenix")):
print "phenix module not available: skipping advanced tests"
return
from phenix.refinement import runtime
import iotbx.phil
from time import time
phil_str = """
refinement.pdb_interpretation.secondary_structure.protein {
helix {
selection = "chain A and resseq 10:20"
}
helix {
selection = "chain A and resseq 30:40"
}
helix {
selection = "chain A and resseq 50:60"
}
}
"""
phil_str_2 = """
refinement.pdb_interpretation.secondary_structure.protein {
helix {
selection = "chain B and resseq 10:20"
}
helix {
selection = "chain B and resseq 30:40"
}
helix {
selection = "chain B and resseq 50:60"
}
}
"""
master_phil = runtime.master_phil()
i = interface.index(master_phil=master_phil,
parse=iotbx.phil.parse)
t1 = time()
i.merge_phil(phil_string=phil_str)
t2 = time()
params = i.get_python_object()
assert (params.refinement.pdb_interpretation.secondary_structure.\
protein.helix[0].selection == "chain A and resseq 10:20")
t3 = time()
i.merge_phil(phil_string=phil_str_2,
only_scope="refinement.pdb_interpretation.secondary_structure")
t4 = time()
params = i.get_python_object()
assert (params.refinement.pdb_interpretation.secondary_structure.\
protein.helix[0].selection == "chain B and resseq 10:20")
scope = i.get_scope_by_name("refinement.pdb_interpretation.secondary_structure")
params2 = scope.extract()
assert (params2.protein.helix[0].selection == "chain B and resseq 10:20")
if verbose :
print "Merge with global fetch: %6.1fms" % ((t2-t1) * 1000)
print "Merge with local fetch: %6.1fms" % ((t4-t3) * 1000)
i.merge_phil(phil_string="""
refinement.input.pdb.file_name = protein.pdb
refinement.input.pdb.file_name = ligand.pdb
refinement.input.xray_data.file_name = data.mtz
refinement.input.monomers.file_name = ligand.cif
refinement.output.job_title = Test refinement run
""")
names = i.search_phil_text("CIF")
assert (set(names) == {
'refinement.output.write_model_cif_file',
'refinement.output.write_reflection_cif_file',
'refinement.input.monomers.file_name',}
)
assert (i.get_input_files() == [
('protein.pdb', 'Input model', 'refinement.input.pdb.file_name'),
('ligand.pdb', 'Input model', 'refinement.input.pdb.file_name'),
('data.mtz', 'Reflections file', 'refinement.input.xray_data.file_name'),
('ligand.cif', 'Restraints (CIF)', 'refinement.input.monomers.file_name')])
assert (i.get_job_title() == "Test refinement run")
#
# .style processing
style = i.get_scope_style("refinement.refine.strategy")
#assert (style.auto_launch_dialog == [
# 'refinement.refine.sites.individual', 'refinement.refine.sites.individual',
# 'refinement.refine.sites.rigid_body', 'refinement.refine.adp.individual',
# 'refinement.refine.adp.group', 'refinement.refine.adp.tls',
# 'refinement.refine.occupancies', 'refinement.refine.anomalous_scatterers'])
assert (style.file_type is None)
style = i.get_scope_style("refinement.input.xray_data.file_name")
assert (style.get_list("file_type") == ["hkl"])
assert (style.get_child_params() == {'fobs': 'labels',
'd_max': 'low_resolution', 'd_min': 'high_resolution',
'rfree_file': 'r_free_flags.file_name'})
assert i.is_list_type("refinement.input.xray_data.labels")
style = i.get_scope_style("refinement.input.xray_data.labels")
assert (style.get_parent_params() == {"file_name" : "file_name"})
file_map = i.get_file_type_map("pdb")
assert (file_map.get_multiple_params() == \
['refinement.input.pdb.file_name',
'refinement.reference_model.file'])
assert (file_map.get_default_param() == "refinement.input.pdb.file_name")
file_map = i.get_file_type_map("hkl")
assert (file_map.get_overall_max_count() == 5)
assert (len(file_map.get_multiple_params()) == 0)
assert (file_map.get_max_count("refinement.input.xray_data.file_name") == 1)
menu = i.get_menu_db()
assert (len(menu.get_items()) > 15) # XXX ballpark (currently 17)
submenu = menu.get_submenu("Atom_selections")
assert (str(submenu.get_items()[0]) == "refinement.refine.sites")
.expert_level = 1
multiprocessing
.short_caption = "Multiprocessing"
.expert_level = 1
{
mode = *serial parallel
.type = choice
.help = "Whether to process each sweep in serial (using n processes per"
" sweep) or to process sweeps in parallel (using 1 process per"
" sweep)."
nproc = Auto
.type = int(value_min=1)
.help = "The number of processors to use per job."
njob = Auto
.type = int(value_min=1)
.help = "The number of sweeps to process simultaneously."
type = *simple qsub
.type = choice
.help = "How to run the parallel processing jobs, e.g. over a cluster"
qsub_command = ''
.type = str
.help = "The command to use to submit qsub jobs"
}
}
""", process_includes=True)
PhilIndex = interface.index(master_phil=master_phil)
if __name__ == '__main__':
PhilIndex.working_phil.show()