diff --git a/docker/Dockerfile b/docker/Dockerfile
index eb66f1288064bb14d6c47caeb4309591a0e39022..81ac08c13930527c2648f2ed78c7a4836815b2d7 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -249,10 +249,10 @@ RUN set -eo pipefail; \
cd ${SRC_FLDR}; \
/usr/bin/rm -rf ost; \
# make the compounds.chemlib interchangeable: move to its own dir and link
- /usr/bin/mkdir /compound_lib; \
+ /usr/bin/mkdir /qmtl; \
/usr/bin/mv /usr/local/share/openstructure/compounds.chemlib \
- /compound_lib/; \
- ln -s /compound_lib/compounds.chemlib /usr/local/share/openstructure/; \
+ /qmtl/; \
+ ln -s /qmtl/compounds.chemlib /usr/local/share/openstructure/; \
# \
# Cleanup packages only needed to compile/ install things \
# \
diff --git a/docker/run_qmean.py b/docker/run_qmean.py
index 84ffc096290b3bb0eeb7d852444e896a7f483e30..15e21a22d156abc973c6296f29f25be085ded813 100755
--- a/docker/run_qmean.py
+++ b/docker/run_qmean.py
@@ -165,10 +165,10 @@ def _run_accpro(fasta_file, msa, workdir, seqlen):
def _get_dc(
- workdir, target_seq, hh, a3m_file, smtldir, datefilter=None, store_dc=True
+ workdir, target_seq, hh, a3m_file, qmtldir, datefilter=None, store_dc=True
):
- db = os.path.join(smtldir, "smtl_uniq")
+ db = os.path.join(qmtldir, "smtl_uniq")
# hhblits prints stuff in stderr, let's setup yet another logger and swallow
# everything. Check later if something went wrong...
@@ -181,15 +181,15 @@ def _get_dc(
LogError("HHblits search did not produce any results, aborting")
sys.exit(-1)
- index_file = os.path.join(smtldir, "CHAINCLUSTERINDEX")
- dates_file = os.path.join(smtldir, "dates.csv")
+ index_file = os.path.join(qmtldir, "CHAINCLUSTERINDEX")
+ dates_file = os.path.join(qmtldir, "dates.csv")
chain_cluster_index = _ChainClusterIndex(index_file, dates_file)
binary_tpl = DisCoDataContainers(
- os.path.join(smtldir, "indexer.dat"),
- os.path.join(smtldir, "seqres_data.dat"),
- os.path.join(smtldir, "atomseq_data.dat"),
- os.path.join(smtldir, "ca_pos_data.dat"),
+ os.path.join(qmtldir, "indexer.dat"),
+ os.path.join(qmtldir, "seqres_data.dat"),
+ os.path.join(qmtldir, "atomseq_data.dat"),
+ os.path.join(qmtldir, "ca_pos_data.dat"),
)
dc = DisCoContainer(target_seq)
@@ -210,7 +210,7 @@ def _get_dc(
pdb_id, assembly_id, chain_name = tpl.split(".")
# use try except block, if certain template cannot be
- # found in binary SMTL...
+ # found in binary TPL...
try:
binary_tpl_assembly = ".".join([pdb_id, assembly_id])
tpl_data = ExtractTemplateDataDisCo(
@@ -239,7 +239,7 @@ def _get_dc(
return dc
-def _seqanno(target_seq, workdir, uniclust30, do_disco, smtldir, datefilter):
+def _seqanno(target_seq, workdir, uniclust30, do_disco, qmtldir, datefilter):
md5_hash = target_seq.GetName()
seqanno_workdir = os.path.join(workdir, md5_hash)
@@ -291,7 +291,7 @@ def _seqanno(target_seq, workdir, uniclust30, do_disco, smtldir, datefilter):
accpro_handler = ACCPROHandler(data)
if do_disco:
- dc = _get_dc(seqanno_workdir, target_seq, hh, a3m, smtldir, datefilter)
+ dc = _get_dc(seqanno_workdir, target_seq, hh, a3m, qmtldir, datefilter)
else:
dc = None
@@ -648,7 +648,7 @@ class ModelScorerContainer:
seqres,
workdir,
uniclust30,
- smtldir,
+ qmtldir,
datefilter,
):
self.method = method
@@ -663,7 +663,7 @@ class ModelScorerContainer:
# - self.psipred_handler
# - self.accpro_handler
# - self.disco_container
- self._do_seqres_features(workdir, uniclust30, smtldir, datefilter)
+ self._do_seqres_features(workdir, uniclust30, qmtldir, datefilter)
# perform scoring on all models
self._score()
@@ -689,7 +689,7 @@ class ModelScorerContainer:
added_sequences.add(s.GetName())
return self._seqres_list
- def _do_seqres_features(self, workdir, uniclust30, smtldir, datefilter):
+ def _do_seqres_features(self, workdir, uniclust30, qmtldir, datefilter):
self.psipred_handler = dict()
self.accpro_handler = dict()
self.disco_container = dict()
@@ -699,7 +699,7 @@ class ModelScorerContainer:
workdir,
uniclust30,
self.method == "QMEANDisCo",
- smtldir,
+ qmtldir,
datefilter,
)
self.psipred_handler[s.GetName()] = p
@@ -768,11 +768,11 @@ def _get_uniclust30():
raise RuntimeError(msg)
-def _check_smtl(args):
- # expect smtl to be mounted at /smtl
- if not os.path.exists("/smtl"):
+def _check_qmtl(args):
+ # expect qmtl to be mounted at /qmtl
+ if not os.path.exists("/qmtl"):
raise RuntimeError(
- "For running QMEANDisCo you need to mount the downloadable SMTL data to /smtl"
+ "For running QMEANDisCo you need to mount the downloadable QMTL data to /qmtl"
)
expected_files = [
@@ -789,16 +789,16 @@ def _check_smtl(args):
]
for f in expected_files:
- p = os.path.join("/smtl", f)
+ p = os.path.join("/qmtl", f)
if not os.path.exists(p):
raise RuntimeError(f"expect {p} to be present")
# only if date-filter is specified, we additionally need dates.csv'
if args.datefilter:
- p = os.path.join("/smtl", "dates.csv")
+ p = os.path.join("/qmtl", "dates.csv")
if not os.path.exists(p):
raise RuntimeError(
- f"If datefilter argument is provided, you additionally need to provide the SMTL specific {p}"
+ f"If datefilter argument is provided, you additionally need to provide the QMTL specific {p}"
)
@@ -930,9 +930,9 @@ def _parse_args():
args.uniclust30 = _get_uniclust30()
ost.LogInfo(f"Use UniClust30: {args.uniclust30}")
- # Check for valid SMTL in case of QMEANDisCo
+ # Check for valid QMTL in case of QMEANDisCo
if args.method == "QMEANDisCo":
- _check_smtl(args)
+ _check_qmtl(args)
# check what complib is used and report to logger
creation_date = conop.GetDefaultLib().GetCreationDate()
@@ -963,10 +963,10 @@ def _main():
out["seqres_uploaded"].append(
{"name": s.GetName(), "sequence": str(s)}
)
- out["smtl_version"] = None
+ out["qmtl_version"] = None
if args.method == "QMEANDisCo":
- with open("/smtl/VERSION", "r") as fh:
- out["smtl_version"] = fh.read().strip()
+ with open("/qmtl/VERSION", "r") as fh:
+ out["qmtl_version"] = fh.read().strip()
######################################
# Load/process models and do scoring #
@@ -977,7 +977,7 @@ def _main():
args.seqres,
args.workdir,
args.uniclust30,
- "/smtl",
+ "/qmtl",
args.datefilter,
)