def run_dials(proj, filters, options):
# Modules list for HPC env
softwares = ["gopresto", versions.DIALS_MOD]
jobs = JobsSet("XIA2/DIALS")
hpc = SITE.get_hpc_runner()
epoch = str(round(time.time()))
for num, dset in enumerate(get_proc_datasets(proj, filters, "dials")):
outdir, image_file = _get_dataset_params(proj, dset)
spg = get_space_group_argument(Tools.DIALS, options["spacegroup"])
if options["cellparam"] != "":
cellpar = ",".join(options["cellparam"].split(","))
cellpar = cellpar.replace("(", "").replace(")", "")
unit_cell = f"unit_cell={cellpar}"
else:
unit_cell = ""
customdials = options["customdials"]
if options["friedel_law"] == "true":
friedel = "atom=X"
else:
friedel = ""
dials_commands, cpus = get_xia_dials_commands(spg, unit_cell,
customdials, friedel,
image_file, dset.images)
batch = hpc.new_batch_file(
"DIALS",
project_script(proj, f"dials_fragmax_part{num}.sh"),
project_log_path(proj, f"multi_xia2DIALS_{epoch}_%j_out.txt"),
project_log_path(proj, f"multi_xia2DIALS_{epoch}_%j_err.txt"),
cpus,
)
batch.set_options(
time=Duration(hours=168),
exclusive=True,
nodes=1,
)
batch.purge_modules()
batch.load_modules(softwares)
batch.add_commands(
f"mkdir -p {outdir}/dials",
f"cd {outdir}/dials",
*dials_commands,
)
batch.save()
jobs.add_job(batch)
add_update_job(jobs, hpc, proj, "dials", dset, batch)
jobs.submit()
def run_xdsapp(project, filters, options):
# Modules list for HPC env
softwares = ["gopresto", versions.XDSAPP_MOD]
jobs = JobsSet("XDSAPP")
hpc = SITE.get_hpc_runner()
epoch = str(round(time.time()))
for num, dset in enumerate(get_proc_datasets(project, filters, "xdsapp")):
outdir, image_file = _get_dataset_params(project, dset)
if options["spacegroup"] is not None:
cellpar = " ".join(options["cellparam"].split(","))
spacegroup = get_space_group_argument(Tools.XDSAPP,
options["spacegroup"])
spg = f"--spacegroup='{spacegroup} {cellpar}'"
else:
spg = ""
customxdsapp = options["customxdsapp"]
if options["friedel_law"] == "true":
friedel = "--fried=True"
else:
friedel = "--fried=False"
xdsapp_command, cpus = get_xdsapp_command(outdir, spg, customxdsapp,
friedel, image_file,
dset.images)
batch = hpc.new_batch_file(
"XDSAPP",
project_script(project, f"xdsapp_fragmax_part{num}.sh"),
project_log_path(project, f"multi_xdsapp_{epoch}_%j_out.txt"),
project_log_path(project, f"multi_xdsapp_{epoch}_%j_err.txt"),
cpus,
)
batch.set_options(
time=Duration(hours=168),
exclusive=True,
nodes=1,
)
batch.purge_modules()
batch.load_modules(softwares)
batch.add_commands(
f"mkdir -p {outdir}/xdsapp",
f"cd {outdir}/xdsapp",
xdsapp_command,
)
batch.save()
jobs.add_job(batch)
add_update_job(jobs, hpc, project, "xdsapp", dset, batch)
jobs.submit()
def run_autoproc(proj, filters, options):
# Modules list for HPC env
softwares = [
"gopresto",
versions.CCP4_MOD,
versions.AUTOPROC_MOD,
versions.DURIN_MOD,
]
jobs = JobsSet("autoPROC")
hpc = SITE.get_hpc_runner()
epoch = str(round(time.time()))
for num, dset in enumerate(get_proc_datasets(proj, filters, "autoproc")):
batch = hpc.new_batch_file(
"autoPROC",
project_script(proj, f"autoproc_fragmax_part{num}.sh"),
project_log_path(proj, f"multi_autoproc_{epoch}_%j_out.txt"),
project_log_path(proj, f"multi_autoproc_{epoch}_%j_err.txt"),
)
batch.set_options(
time=Duration(hours=168),
exclusive=True,
nodes=1,
cpus_per_task=64,
memory=DataSize(gigabyte=300),
)
batch.purge_modules()
batch.load_modules(softwares)
outdir, h5master, sample, num_images = _get_dataset_params(proj, dset)
if options["spacegroup"] != "":
spacegroup = options["spacegroup"]
spg = f"symm='{spacegroup}'"
else:
spg = ""
if options["cellparam"] != "":
cellpar = " ".join(options["cellparam"].split(","))
cellpar = cellpar.replace("(", "").replace(")", "")
unit_cell = f"cell='{cellpar}'"
else:
unit_cell = ""
customautoproc = options["customautoproc"]
if options["friedel_law"] == "true":
friedel = "-ANO"
else:
friedel = "-noANO"
batch.add_commands(
f"rm -rf {outdir}/autoproc",
f"mkdir -p {outdir}",
f"cd {outdir}",
get_autoproc_command(outdir, spg, unit_cell, customautoproc,
friedel, h5master, num_images),
)
batch.save()
jobs.add_job(batch)
add_update_job(jobs, hpc, proj, "autoproc", dset, batch)
jobs.submit()
def launch_refine_jobs(
project: Project,
filters,
pdb_file,
space_group,
run_aimless,
refine_tool,
refine_tool_commands,
cpus,
):
epoch = round(time.time())
jobs = JobsSet("Refine")
hpc = SITE.get_hpc_runner()
for dset in get_refine_datasets(project, filters, refine_tool):
for tool, input_mtz in _find_input_mtzs(project, dset):
batch = hpc.new_batch_file(
f"refine {tool} {dset.name}",
project_script(project,
f"refine_{tool}_{refine_tool}_{dset.name}.sh"),
project_log_path(
project, f"refine_{tool}_{dset.name}_{epoch}_%j_out.txt"),
project_log_path(
project, f"refine_{tool}_{dset.name}_{epoch}_%j_err.txt"),
cpus,
)
batch.set_options(
time=Duration(hours=12),
nodes=1,
mem_per_cpu=DataSize(gigabyte=5),
)
batch.add_commands(crypt_shell.crypt_cmd(project))
batch.assign_variable("WORK_DIR", "`mktemp -d`")
batch.add_commands(
"cd $WORK_DIR",
crypt_shell.fetch_file(project, pdb_file, "model.pdb"),
crypt_shell.fetch_file(project, input_mtz, "input.mtz"),
)
# TODO: load tool specific modules?
batch.load_modules(HPC_MODULES)
if run_aimless:
batch.add_commands(
_aimless_cmd(space_group.short_name, "input.mtz"))
results_dir = Path(project.get_dataset_results_dir(dset), tool)
batch.add_commands(
*refine_tool_commands,
_upload_result_cmd(project, results_dir),
"cd",
"rm -rf $WORK_DIR",
)
batch.save()
jobs.add_job(batch)
add_update_job(jobs, hpc, project, refine_tool, dset, batch)
jobs.submit()
def _write_main_script(
project: Project, pandda_dir: Path, method, methodshort, options
):
epoch = round(time.time())
log_prefix = project_log_path(project, f"PanDDA_{method}_{epoch}_%j_")
pandda_script = project_script(project, PANDDA_WORKER)
giant_cluster = "/mxn/groups/biomax/wmxsoft/pandda/bin/giant.datasets.cluster"
if options["reprocessZmap"]:
pandda_cluster = ""
else:
pandda_cluster = f"{giant_cluster} ./*/final.pdb pdb_label=foldername"
hpc = SITE.get_hpc_runner()
batch = hpc.new_batch_file(
f"PDD{methodshort}",
project_script(project, f"pandda_{method}.sh"),
f"{log_prefix}out.txt",
f"{log_prefix}err.txt",
cpus=40,
)
batch.set_options(
time=Duration(hours=99),
exclusive=True,
nodes=1,
)
if project.encrypted:
# TODO: implement this?
raise NotImplementedError("pandda for encrypted projects")
# batch.add_command(crypt_shell.crypt_cmd(project))
# batch.assign_variable("WORK_DIR", "`mktemp -d`")
# batch.add_commands(
# "cd $WORK_DIR", crypt_shell.fetch_dir(project, data_dir, ".")
# )
#
# batch.load_modules(["gopresto", versions.CCP4_MOD, versions.PYMOL_MOD])
# batch.add_commands(
# pandda_cluster,
# f'python {pandda_script} . {project.protein} "{options}"',
# crypt_shell.upload_dir(
# project, "$WORK_DIR/pandda", path.join(data_dir, "pandda")
# ),
# crypt_shell.upload_dir(
# project,
# "$WORK_DIR/clustered-datasets",
# path.join(data_dir, "clustered-datasets"),
# ),
# )
else:
batch.add_command(f"cd {pandda_dir}")
add_pandda_init_commands(batch)
batch.add_commands(
pandda_cluster,
f'python {pandda_script} {pandda_dir} {project.protein} "{options}"',
f"chmod -R 777 {project.pandda_dir}",
)
# add commands to fix symlinks
ln_command = '\'ln -f "$(readlink -m "$0")" "$0"\' {} \\;'
batch.add_commands(
f"cd {project.pandda_dir}; find -type l -iname *-pandda-input.* -exec bash -c {ln_command}",
f"cd {project.pandda_dir}; find -type l -iname *pandda-model.pdb -exec bash -c {ln_command}",
)
batch.save()
return batch
def _write_prepare_script(
project: Project,
rn,
method,
dataset,
pdb,
mtz,
resHigh,
free_r_flag,
native_f,
sigma_fp,
cif_method,
):
epoch = round(time.time())
output_dir = Path(project.pandda_method_dir(method), dataset.name)
hpc = SITE.get_hpc_runner()
batch = hpc.new_batch_file(
f"PnD{rn}",
project_script(project, f"pandda_prepare_{method}_{dataset.name}.sh"),
project_log_path(project, f"{dataset.name}_PanDDA_{epoch}_%j_out.txt"),
project_log_path(project, f"{dataset.name}_PanDDA_{epoch}_%j_err.txt"),
cpus=1,
)
batch.set_options(time=Duration(minutes=15), memory=DataSize(gigabyte=5))
batch.add_command(crypt_shell.crypt_cmd(project))
batch.assign_variable("DEST_DIR", output_dir)
batch.assign_variable("WORK_DIR", "`mktemp -d`")
batch.add_commands(
"cd $WORK_DIR",
crypt_shell.fetch_file(project, pdb, "final.pdb"),
crypt_shell.fetch_file(project, mtz, "final.mtz"),
)
batch.purge_modules()
batch.load_modules(
["gopresto", versions.PHENIX_MOD, versions.CCP4_MOD, versions.BUSTER_MOD]
)
if not dataset.crystal.is_apo():
fragment = get_crystals_fragment(dataset.crystal)
# non-apo crystal should have a fragment
assert fragment
if cif_method == "elbow":
cif_cmd = f"phenix.elbow --smiles='{fragment.smiles}' --output=$WORK_DIR/{fragment.code} --opt\n"
else:
assert cif_method == "grade"
cif_cmd = (
f"grade '{fragment.smiles}' -ocif $WORK_DIR/{fragment.code}.cif "
f"-opdb $WORK_DIR/{fragment.code}.pdb -nomogul\n"
)
batch.add_command(cif_cmd)
batch.add_commands(
f'printf "monitor BRIEF\\n labin file 1 -\\n ALL\\n resolution file 1 999.0 {resHigh}\\n" | \\\n'
" cad hklin1 $WORK_DIR/final.mtz hklout $WORK_DIR/final.mtz",
"uniqueify -f FreeR_flag $WORK_DIR/final.mtz $WORK_DIR/final.mtz",
f'printf "COMPLETE FREE={free_r_flag} \\nEND\\n" | \\\n'
" freerflag hklin $WORK_DIR/final.mtz hklout $WORK_DIR/final_rfill.mtz",
f"phenix.maps final_rfill.mtz final.pdb maps.input.reflection_data.labels='{native_f},{sigma_fp}'",
"mv final.mtz final_original.mtz",
"mv final_map_coeffs.mtz final.mtz",
"rm -rf $DEST_DIR",
crypt_shell.upload_dir(project, "$WORK_DIR", "$DEST_DIR"),
"rm -rf $WORK_DIR",
)
batch.save()
return batch
def auto_ligand_fit(project, useLigFit, useRhoFit, filters, cifMethod,
custom_ligfit, custom_rhofit):
# Modules for HPC env
softwares = ["gopresto", versions.BUSTER_MOD, versions.PHENIX_MOD]
jobs = JobsSet("Ligand Fit")
hpc = SITE.get_hpc_runner()
refine_results = _get_refine_results(project, filters, useLigFit,
useRhoFit)
for num, result in enumerate(refine_results):
dataset = result.dataset
if dataset.crystal.is_apo():
# don't try to fit ligand to an apo crystal
continue
fragment = get_crystals_fragment(dataset.crystal)
result_dir = project.get_refine_result_dir(result)
pdb = Path(result_dir, "final.pdb")
clear_tmp_cmd = ""
cif_out = Path(result_dir, fragment.code)
if cifMethod == "elbow":
cif_cmd = f"phenix.elbow --smiles='{fragment.smiles}' --output={cif_out}\n"
elif cifMethod == "acedrg":
cif_cmd = f"acedrg -i '{fragment.smiles}' -o {cif_out}\n"
clear_tmp_cmd = f"rm -rf {cif_out}_TMP/\n"
elif cifMethod == "grade":
cif_cmd = (
f"rm -f {cif_out}.cif {cif_out}.pdb\n"
f"grade '{fragment.smiles}' -ocif {cif_out}.cif -opdb {cif_out}.pdb -nomogul\n"
)
else:
cif_cmd = ""
rhofit_cmd = ""
ligfit_cmd = ""
ligCIF = f"{cif_out}.cif"
ligPDB = f"{cif_out}.pdb"
rhofit_outdir = Path(result_dir, "rhofit")
ligfit_outdir = Path(result_dir, "ligfit")
mtz_input = Path(result_dir, "final.mtz")
if useRhoFit:
if rhofit_outdir.exists():
rhofit_cmd += f"rm -rf {rhofit_outdir}\n"
rhofit_cmd += f"rhofit -l {ligCIF} -m {mtz_input} -p {pdb} -d {rhofit_outdir} {custom_rhofit}\n"
if useLigFit:
if ligfit_outdir.exists():
ligfit_cmd += f"rm -rf {ligfit_outdir}\n"
ligfit_cmd += f"mkdir -p {ligfit_outdir}\n"
ligfit_cmd += f"cd {ligfit_outdir} \n"
ligfit_cmd += (
f"phenix.ligandfit data={mtz_input} model={pdb} ligand={ligPDB} "
f"fill=True clean_up=True {custom_ligfit}\n")
batch = hpc.new_batch_file(
"autoLigfit",
project_script(project, f"autoligand_{dataset.name}_{num}.sh"),
project_log_path(project, "auto_ligfit_%j_out.txt"),
project_log_path(project, "auto_ligfit_%j_err.txt"),
cpus=1,
)
batch.set_options(time=Duration(hours=1))
batch.purge_modules()
batch.load_modules(softwares)
batch.add_commands(
cif_cmd,
rhofit_cmd,
ligfit_cmd,
)
batch.add_commands(clear_tmp_cmd)
batch.save()
jobs.add_job(batch)
# NOTE: all the update commands needs to be chained to run after each other,
# due to limitations (bugs!) in jobsd handling of 'run_after' dependencies.
# Currently it does not work to specify that multiple jobs should be run after
# a job is finished.
#
if useRhoFit:
batch = add_update_job(jobs, hpc, project, "rhofit", dataset,
batch)
if useLigFit:
add_update_job(jobs, hpc, project, "ligandfit", dataset, batch)
jobs.submit()