def _save_pdb(project: Project, pdb_id, filename, pdb_data):
name = path.splitext(filename)[0]
nohet_filename = f"{name}_noHETATM.pdb"
noanisou_filename = f"{name}_noANISOU.pdb"
nohetanisou_filename = f"{name}_noANISOU_noHETATM.pdb"
txc_filename = f"{name}_txc.pdb"
orig_pdb = _add_pdb_entry(project, filename, pdb_id)
nohet_pdb = _add_pdb_entry(project, nohet_filename, pdb_id)
noanisou_pdb = _add_pdb_entry(project, noanisou_filename, pdb_id)
nohetnoanisou_pdb = _add_pdb_entry(project, nohetanisou_filename, pdb_id)
# write original pdb file 'as-is' to models folder
with open_proj_file(project, project.get_pdb_file(orig_pdb)) as dest:
dest.write(pdb_data)
# filter out all non-ATOM entries from pdb and write it as *_noHETATM.pdb
with open_proj_file(project, project.get_pdb_file(nohetnoanisou_pdb)) as dest:
for line in pdb_data.splitlines(keepends=True):
if not line.startswith(b"HETATM") or not line.startswith(b"ANISOU"):
dest.write(line)
with open_proj_file(project, project.get_pdb_file(nohet_pdb)) as dest:
for line in pdb_data.splitlines(keepends=True):
if not line.startswith(b"HETATM"):
dest.write(line)
with open_proj_file(project, project.get_pdb_file(noanisou_pdb)) as dest:
for line in pdb_data.splitlines(keepends=True):
if not line.startswith(b"ANISOU"):
dest.write(line)
n_chains = pdb_chains(pdb_data.splitlines(keepends=True))
if n_chains > 1:
txc_pdb = _add_pdb_entry(project, txc_filename, pdb_id)
input_pdb_name = path.join(project.models_dir, f"{name}.pdb")
jobs = JobsSet("phenix ensembler")
batch = SITE.get_hpc_runner().new_batch_file(
"phenix ensembler",
project_script(project, "phenix_ensembler.sh"),
project_syslog_path(project, "phenix_ensembler_%j.out"),
project_syslog_path(project, "phenix_ensembler_%j.err"),
)
batch.load_modules(["gopresto", PHENIX_MOD])
batch.add_commands(
f"cd {project.models_dir}",
f"phenix.ensembler {input_pdb_name} trim=TRUE output.location='{project.models_dir}'",
f"mv {project.models_dir}/ensemble_merged.pdb {project.get_pdb_file(txc_pdb)}",
)
batch.save()
jobs.add_job(batch)
jobs.submit()
def _delete_pdb(project: Project, pdb):
project.get_pdb_file(pdb).unlink()
pdb.delete()