diff --git a/Dockerfile-dmpk b/Dockerfile-dmpk
index c7b8135..0cab9b1 100644
--- a/Dockerfile-dmpk
+++ b/Dockerfile-dmpk
@@ -18,7 +18,6 @@ WORKDIR ${HOME}
 
 # numpy is pinned below 2 because this matplotlib release predates
 # NumPy 2.0 and its compiled extensions are not ABI-compatible with it
-RUN pip install "numpy<2" matplotlib==3.7.1 im-data-manager-job-utilities==1.0.1
+RUN pip install "numpy<2" matplotlib==3.7.1 sigfig "im-data-manager-job-utilities>=1.4.0"
 
-COPY utils.py ./
 COPY dmpk/*.py ./dmpk/
\ No newline at end of file
diff --git a/Dockerfile-fns b/Dockerfile-fns
index 71a5f9c..610b6c2 100644
--- a/Dockerfile-fns
+++ b/Dockerfile-fns
@@ -14,7 +14,7 @@ WORKDIR ${HOME}
 RUN pip install \
   neo4j-driver==4.4.11 \
   im-standardize-molecule==0.1.0 \
-  im-data-manager-job-utilities==1.1.1
+  "im-data-manager-job-utilities>=1.4.0"
 
-COPY fn_*.py utils.py ./
+COPY fn_*.py ./
 
diff --git a/Dockerfile-jaqpot b/Dockerfile-jaqpot
index 44d5010..b8382ea 100644
--- a/Dockerfile-jaqpot
+++ b/Dockerfile-jaqpot
@@ -4,9 +4,9 @@ RUN apt-get -y update &&\
   apt-get -y install procps &&\
   apt-get clean
 
-RUN pip install im-data-manager-job-utilities==1.3.0 im-rdkit-utilities==1.0.0
+RUN pip install "im-data-manager-job-utilities>=1.4.0" "im-rdkit-utilities>=1.1.2"
 
 ENV HOME=/code
 WORKDIR ${HOME}
 
-COPY utils.py jaqpot*.py ./
\ No newline at end of file
+COPY jaqpot*.py ./
\ No newline at end of file
diff --git a/Dockerfile-moldb b/Dockerfile-moldb
index 74ef9ed..215594b 100644
--- a/Dockerfile-moldb
+++ b/Dockerfile-moldb
@@ -17,8 +17,8 @@ RUN apt-get update && apt-get install -y gcc libpq-dev &&\
 RUN pip install sqlalchemy==1.4.49\
     psycopg2-binary==2.9.6\
     im-standardize-molecule==0.1.0\
-    im-data-manager-job-utilities==1.3.0\
-    im-rdkit-utilities==1.0.0
+    "im-data-manager-job-utilities>=1.4.0"\
+    "im-rdkit-utilities>=1.1.2"
 
 COPY *.py site_substructures.smarts ./
 COPY moldb/* ./moldb/
diff --git a/Dockerfile-mordred b/Dockerfile-mordred
index 5cb4b55..9680e48 100644
--- a/Dockerfile-mordred
+++ b/Dockerfile-mordred
@@ -13,8 +13,7 @@ WORKDIR ${HOME}
 # install our requirements. RDKit is present in base container
 RUN pip install mordredcommunity==2.0.4 \
   im-standardize-molecule==0.1.0 \
-  im-data-manager-job-utilities>=1.4.0 \
-  im-rdkit-utilities>=1.1.2
+  "im-data-manager-job-utilities>=1.4.0" \
+  "im-rdkit-utilities>=1.1.2"
 
 COPY im_mordred/descriptor_generator.py ./im_mordred/
-COPY utils.py ./
diff --git a/Dockerfile-oddt b/Dockerfile-oddt
index 75aa54a..4b0ae2b 100644
--- a/Dockerfile-oddt
+++ b/Dockerfile-oddt
@@ -15,8 +15,8 @@ ENV HOME=/code
 WORKDIR ${HOME}
 
 RUN pip install wheel six &&\
-  pip install im-data-manager-job-utilities==1.3.0\
-  im-rdkit-utilities==1.0.0\
+  pip install "im-data-manager-job-utilities>=1.4.0"\
+  "im-rdkit-utilities>=1.1.2"\
   git+https://github.com/oddt/oddt.git@master
 
 COPY *.py ./
\ No newline at end of file
diff --git a/Dockerfile-plants b/Dockerfile-plants
index c6f0ca4..2b1fc3d 100644
--- a/Dockerfile-plants
+++ b/Dockerfile-plants
@@ -13,7 +13,7 @@ RUN apt-get update &&\
     python3-openbabel &&\
   apt-get clean
 
-COPY pharmacophore.py utils.py /code/
+COPY pharmacophore.py /code/
 
 RUN chmod a+x /code/*.py &&\
-    pip install im-data-manager-job-utilities==1.1.1
+    pip install "im-data-manager-job-utilities>=1.4.0"
diff --git a/Dockerfile-prep b/Dockerfile-prep
index 9578773..9c62e14 100644
--- a/Dockerfile-prep
+++ b/Dockerfile-prep
@@ -23,8 +23,8 @@ WORKDIR ${HOME}
 RUN pip install scikit-learn==1.2.2\
   pdb2pqr==3.6.1\
   im-standardize-molecule==0.1.0\
-  im-data-manager-job-utilities>=1.4.0\
-  im-rdkit-utilities>=1.1.2\
+  "im-data-manager-job-utilities>=1.4.0"\
+  "im-rdkit-utilities>=1.1.2"\
   sigfig==1.3.19
 
 COPY *.py fpscores.pkl.gz site_substructures.smarts ./
diff --git a/align_mol.py b/align_mol.py
index ffba10a..066577a 100755
--- a/align_mol.py
+++ b/align_mol.py
@@ -21,7 +21,7 @@
 from rdkit.Chem import rdMolAlign
 from rdkit.Chem import rdFMCS
 
-import utils
+from dm_job_utilities import utils
 
 
 def align(query_mol, inputs_sdf, outputs_sdf, query_atoms=None, keep_all=False, mcs_params={}, interval=None):
diff --git a/assemble_conformers.py b/assemble_conformers.py
index cef7e0a..62b4127 100755
--- a/assemble_conformers.py
+++ b/assemble_conformers.py
@@ -24,7 +24,9 @@
 """
 
 import argparse, os, time, gzip
-import utils, rdkit_utils
+import rdkit_utils
+from dm_job_utilities import utils
+from digest_utils import get_path_from_digest
 from dm_job_utilities.dm_log import DmLog
 
 from rdkit import Chem
@@ -66,7 +68,7 @@ def execute(input, output, data_dir, mode,
                 uid = tokens[1]
                 digest = tokens[2]
                 parts = [data_dir]
-                parts.extend(utils.get_path_from_digest(digest))
+                parts.extend(get_path_from_digest(digest))
                 path = os.path.join(*parts)
                 if not os.path.isdir(path):
                     utils.log('WARNING, path', path, 'not found')
diff --git a/cluster_butina.py b/cluster_butina.py
index 8e18fb2..da33371 100755
--- a/cluster_butina.py
+++ b/cluster_butina.py
@@ -20,7 +20,7 @@
 from rdkit.Chem import AllChem, MACCSkeys
 from rdkit.ML.Cluster import Butina
 
-import utils
+from dm_job_utilities import utils
 import rdkit_utils
 from dm_job_utilities.dm_log import DmLog
 
diff --git a/digest_utils.py b/digest_utils.py
new file mode 100644
index 0000000..da49235
--- /dev/null
+++ b/digest_utils.py
@@ -0,0 +1,40 @@
+# Copyright 2025 Informatics Matters Ltd.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Mapping a molecule digest onto the sharded directory layout used by the
+enumeration/conformer pipeline.
+
+This lives here rather than in dm_job_utilities: the shared package
+deliberately dropped get_path_from_digest as obsolete, but the layout it
+describes is still what prepare_enum_conf_lists.py writes and
+assemble_conformers.py reads back.
+"""
+
+default_num_chars = 2
+default_num_levels = 2
+
+
+def get_path_from_digest(
+    digest, num_chars=default_num_chars, num_levels=default_num_levels
+):
+    """Split a digest into the directory components that locate its files,
+    e.g. 'abcdef...' -> ['ab', 'cd'] for the default 2 chars over 2 levels.
+    """
+    parts = []
+    start = 0
+    for _ in range(0, num_levels):
+        end = start + num_chars
+        parts.append(digest[start:end])
+        start = start + num_chars
+    return parts
diff --git a/dmpk/pk_tmax_cmax_sim.py b/dmpk/pk_tmax_cmax_sim.py
index fba99c4..9ce9ff0 100644
--- a/dmpk/pk_tmax_cmax_sim.py
+++ b/dmpk/pk_tmax_cmax_sim.py
@@ -23,7 +23,15 @@
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 
-import utils
+from dm_job_utilities import utils
+from sigfig import round as _sigfig_round
+
+
+def sigfig_round(value, sigfigs):
+    """Round to N significant figures. warn=False keeps sigfig quiet when a
+    value carries fewer significant figures than requested, which is common
+    here and was silent under the previous implementation."""
+    return _sigfig_round(value, sigfigs=sigfigs, warn=False)
 
 
 def generatePlot(t_hf, t_hf_a, D, AUC, tn, quiet=False, plot_height=4, plot_width=10, font_size=12, basename='output'):
@@ -37,11 +45,11 @@ def generatePlot(t_hf, t_hf_a, D, AUC, tn, quiet=False, plot_height=4, plot_widt
     V_F = D/kel/AUC
 
     outputs = collections.OrderedDict()
-    outputs['Tmax(hr)'] = utils.round_to_significant_number(Tmax, 3)
-    outputs['Cmax(mg/L)'] = utils.round_to_significant_number(Cmax, 3)
-    outputs['Kel(hr-1)'] = utils.round_to_significant_number(kel, 3)
-    outputs['Ka(hr-1)'] = utils.round_to_significant_number(ka, 3)
-    outputs['V/F(L)'] = utils.round_to_significant_number(V_F, 3)
+    outputs['Tmax(hr)'] = sigfig_round(Tmax, 3)
+    outputs['Cmax(mg/L)'] = sigfig_round(Cmax, 3)
+    outputs['Kel(hr-1)'] = sigfig_round(kel, 3)
+    outputs['Ka(hr-1)'] = sigfig_round(ka, 3)
+    outputs['V/F(L)'] = sigfig_round(V_F, 3)
 
     if not quiet:
         utils.log('------------------------------------------------------------------------------------------')
diff --git a/enumerate.py b/enumerate.py
index e9b9e9a..c4ab0f3 100755
--- a/enumerate.py
+++ b/enumerate.py
@@ -26,7 +26,8 @@
 
 """
 import os, sys, argparse, traceback, uuid, gzip
-import utils, rdkit_utils
+import rdkit_utils
+from dm_job_utilities import utils
 from dm_job_utilities.cli import ProgressReporter, add_reporting_args
 from dm_job_utilities.dm_log import DmLog
 
diff --git a/fn_expand.py b/fn_expand.py
index c92fa31..cf4847c 100755
--- a/fn_expand.py
+++ b/fn_expand.py
@@ -25,7 +25,7 @@
 
 import os, argparse, time
 
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 from standardize_molecule import standardize_to_noniso_smiles
 
diff --git a/fn_find_synthons.py b/fn_find_synthons.py
index 34723ec..796b163 100755
--- a/fn_find_synthons.py
+++ b/fn_find_synthons.py
@@ -25,7 +25,7 @@
 
 import os, argparse, time
 
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 from standardize_molecule import standardize_to_noniso_smiles
 
diff --git a/fn_synthon_expansion.py b/fn_synthon_expansion.py
index 49297f2..1652eb3 100755
--- a/fn_synthon_expansion.py
+++ b/fn_synthon_expansion.py
@@ -55,7 +55,7 @@
 
 import os, argparse, time
 
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 from standardize_molecule import standardize_to_noniso_smiles
 
diff --git a/im_mordred/descriptor_generator.py b/im_mordred/descriptor_generator.py
index 3035df3..a0187fb 100644
--- a/im_mordred/descriptor_generator.py
+++ b/im_mordred/descriptor_generator.py
@@ -20,7 +20,8 @@
 
 from rdkit import Chem
 
-import utils, rdkit_utils
+import rdkit_utils
+from dm_job_utilities import utils
 from dm_job_utilities.cli import ProgressReporter, add_reporting_args
 from dm_job_utilities.dm_log import DmLog
 
diff --git a/le_conformers.py b/le_conformers.py
index a7213ff..e9306d1 100755
--- a/le_conformers.py
+++ b/le_conformers.py
@@ -23,7 +23,8 @@
 """
 import os, sys, argparse, traceback, time, gzip
 
-import utils, rdkit_utils
+import rdkit_utils
+from dm_job_utilities import utils
 from dm_job_utilities.cli import ProgressReporter, add_reporting_args
 from dm_job_utilities.dm_log import DmLog
 
diff --git a/le_conformers_for_mol.py b/le_conformers_for_mol.py
index da7c337..2d2d1fc 100755
--- a/le_conformers_for_mol.py
+++ b/le_conformers_for_mol.py
@@ -16,7 +16,8 @@
 
 
 import time, argparse
-import utils, le_conformers
+import le_conformers
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 
 from rdkit import Chem
diff --git a/max_min_picker.py b/max_min_picker.py
index cd01900..3c00da9 100755
--- a/max_min_picker.py
+++ b/max_min_picker.py
@@ -16,7 +16,7 @@
 
 
 import argparse, time
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 
 from rdkit import Chem, SimDivFilters
diff --git a/minimize.py b/minimize.py
index 566f220..35de5af 100755
--- a/minimize.py
+++ b/minimize.py
@@ -16,7 +16,7 @@
 
 
 import sys, argparse, time
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 
 from rdkit import Chem
diff --git a/moldb/analyse.py b/moldb/analyse.py
index 33f00d2..590bd6d 100644
--- a/moldb/analyse.py
+++ b/moldb/analyse.py
@@ -16,7 +16,7 @@
 
 import argparse, datetime, time
 
-import utils
+from dm_job_utilities import utils
 from . import models, filter, moldb_utils
 
 from dm_job_utilities.dm_log import DmLog
diff --git a/moldb/conformers.py b/moldb/conformers.py
index 0bbaa55..f3e8616 100755
--- a/moldb/conformers.py
+++ b/moldb/conformers.py
@@ -20,7 +20,7 @@
 same methodology that this module uses.
 """
 import os, argparse, traceback, time, gzip
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 
 from rdkit import Chem
diff --git a/moldb/enumerate.py b/moldb/enumerate.py
index c31bc0a..0dde371 100755
--- a/moldb/enumerate.py
+++ b/moldb/enumerate.py
@@ -26,7 +26,8 @@
 
 """
 import os, sys, argparse, traceback, logging
-import utils, rdkit_utils
+import rdkit_utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 
 from rdkit import Chem
diff --git a/moldb/extract_need_molprops.py b/moldb/extract_need_molprops.py
index 085e594..22b9d88 100755
--- a/moldb/extract_need_molprops.py
+++ b/moldb/extract_need_molprops.py
@@ -14,7 +14,7 @@
 
 import argparse, time, os, random, string, traceback
 
-import utils
+from dm_job_utilities import utils
 from . import models
 
 from sqlalchemy import text
diff --git a/moldb/filter.py b/moldb/filter.py
index cacea84..c458926 100755
--- a/moldb/filter.py
+++ b/moldb/filter.py
@@ -14,7 +14,7 @@
 
 
 import os, glob, argparse, time
-import utils
+from dm_job_utilities import utils
 
 from sqlalchemy import text
 from sqlalchemy.orm import Session
diff --git a/moldb/models.py b/moldb/models.py
index 5ae854d..d720583 100644
--- a/moldb/models.py
+++ b/moldb/models.py
@@ -21,7 +21,7 @@
 
 import sqlalchemy
 
-import utils
+from dm_job_utilities import utils
 
 utils.log('sqlalchemy version:', sqlalchemy.__version__)
 
diff --git a/moldb/moldb_utils.py b/moldb/moldb_utils.py
index 3e89fc3..0effdb2 100644
--- a/moldb/moldb_utils.py
+++ b/moldb/moldb_utils.py
@@ -12,7 +12,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import utils
+from dm_job_utilities import utils
 
 def add_filter_args(parser):
     parser.add_argument('--min-hac', type=int, help="Min value for heavy atom count")
diff --git a/moldb/standardize.py b/moldb/standardize.py
index 5d9b83d..49dfbfe 100755
--- a/moldb/standardize.py
+++ b/moldb/standardize.py
@@ -16,7 +16,7 @@
 
 
 import argparse, os, json, gzip, time, logging
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 
 from rdkit import Chem, RDLogger
diff --git a/oddt_ifp.py b/oddt_ifp.py
index 30804ee..c298716 100755
--- a/oddt_ifp.py
+++ b/oddt_ifp.py
@@ -16,7 +16,7 @@
 
 
 import sys, argparse
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 
 from oddt import toolkit, fingerprints
diff --git a/oddt_interactions.py b/oddt_interactions.py
index 1f6be21..8b3e525 100755
--- a/oddt_interactions.py
+++ b/oddt_interactions.py
@@ -81,7 +81,8 @@
 import argparse, traceback
 import json, sys
 
-import utils, interact
+import interact
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 
 import oddt
diff --git a/open3dalign.py b/open3dalign.py
index 8e4352c..b015c5d 100755
--- a/open3dalign.py
+++ b/open3dalign.py
@@ -19,7 +19,7 @@
 """
 
 import argparse, sys
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 
 from rdkit import Chem
diff --git a/pharmacophore.py b/pharmacophore.py
index 15942e8..b041671 100755
--- a/pharmacophore.py
+++ b/pharmacophore.py
@@ -14,7 +14,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 from openbabel import pybel, openbabel
 from jinja2 import Template
diff --git a/prepare_enum_conf_lists.py b/prepare_enum_conf_lists.py
index 6f983a9..b591a46 100755
--- a/prepare_enum_conf_lists.py
+++ b/prepare_enum_conf_lists.py
@@ -16,8 +16,8 @@
 
 
 import argparse, os
-import utils
-from utils import get_path_from_digest
+from dm_job_utilities import utils
+from digest_utils import get_path_from_digest
 from dm_job_utilities.dm_log import DmLog
 
 
diff --git a/ranker.py b/ranker.py
index 48a5ab1..f596ea6 100755
--- a/ranker.py
+++ b/ranker.py
@@ -19,7 +19,7 @@
 
 from rdkit import Chem
 
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 
 
diff --git a/rdkit_dedup.py b/rdkit_dedup.py
index 7be79ef..a788691 100755
--- a/rdkit_dedup.py
+++ b/rdkit_dedup.py
@@ -18,7 +18,8 @@
 import argparse, os, gzip, time
 import traceback
 
-import utils, rdkit_utils
+import rdkit_utils
+from dm_job_utilities import utils
 from dm_job_utilities.cli import ProgressReporter, add_reporting_args
 from dm_job_utilities.dm_log import DmLog
 
diff --git a/rdkit_props.py b/rdkit_props.py
index c96db65..e3ed806 100755
--- a/rdkit_props.py
+++ b/rdkit_props.py
@@ -17,7 +17,8 @@
 
 import argparse, os, gzip, time
 
-import utils, rdkit_utils
+import rdkit_utils
+from dm_job_utilities import utils
 from dm_job_utilities.cli import ProgressReporter, add_reporting_args
 from dm_job_utilities.dm_log import DmLog
 
diff --git a/reactor.py b/reactor.py
index 9e01d8a..565e1ba 100755
--- a/reactor.py
+++ b/reactor.py
@@ -37,7 +37,7 @@
 from rdkit import Chem
 from rdkit.Chem import AllChem, TemplateAlign
 
-import utils
+from dm_job_utilities import utils
 import rdkit_utils
 from dm_job_utilities.dm_log import DmLog
 
diff --git a/sa_score.py b/sa_score.py
index 417b81a..f7c6fab 100755
--- a/sa_score.py
+++ b/sa_score.py
@@ -28,7 +28,8 @@
 import argparse, time, os, pickle, traceback, math
 from sigfig import round
 
-import utils, rdkit_utils
+import rdkit_utils
+from dm_job_utilities import utils
 from dm_job_utilities.cli import ProgressReporter, add_reporting_args
 from dm_job_utilities.dm_log import DmLog
 
diff --git a/screen.py b/screen.py
index d0e650f..122b096 100755
--- a/screen.py
+++ b/screen.py
@@ -17,7 +17,8 @@
 import argparse, time
 import traceback
 
-import utils, rdkit_utils
+import rdkit_utils
+from dm_job_utilities import utils
 from dm_job_utilities.cli import add_reporting_args
 from dm_job_utilities.dm_log import DmLog
 
diff --git a/sdf_manip.py b/sdf_manip.py
index e6a6b0e..ae1312a 100644
--- a/sdf_manip.py
+++ b/sdf_manip.py
@@ -101,7 +101,7 @@
 
 from rdkit import Chem
 
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 
 
diff --git a/sucos.py b/sucos.py
index 950accb..a33bcdb 100755
--- a/sucos.py
+++ b/sucos.py
@@ -29,7 +29,7 @@
 from rdkit import rdBase, RDConfig
 from rdkit.Chem import AllChem, rdShapeHelpers
 from rdkit.Chem.FeatMaps import FeatMaps
-import utils
+from dm_job_utilities import utils
 import rdkit_utils
 from dm_job_utilities.dm_log import DmLog
 
diff --git a/usr.py b/usr.py
index 155db4d..0191deb 100755
--- a/usr.py
+++ b/usr.py
@@ -32,7 +32,7 @@
 """
 
 import argparse, time
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 
 from oddt import toolkit
diff --git a/utils.py b/utils.py
deleted file mode 100755
index 0cbf2e9..0000000
--- a/utils.py
+++ /dev/null
@@ -1,157 +0,0 @@
-from __future__ import print_function
-
-import os, sys
-from math import log10, floor
-
-default_num_chars = 2
-default_num_levels = 2
-
-
-def log(*args, **kwargs):
-    """Log output to STDERR
-    """
-    print(*args, file=sys.stderr, **kwargs)
-
-
-def get_path_from_digest(digest, num_chars=default_num_chars, num_levels=default_num_levels):
-    parts = []
-    start = 0
-    for l in range(0, num_levels):
-        end = start + num_chars
-        p = digest[start:end]
-        parts.append(p)
-        start = start + num_chars
-    return parts
-
-
-def expand_path(path):
-    """
-    Create any necessary directories to ensure that the file path is valid
-    
-    :param path: a filename or directory that might or not exist
-    """
-    head_tail = os.path.split(path)
-    if head_tail[0]:
-        if not os.path.isdir(head_tail[0]):
-            log('Creating directories for', head_tail[0])
-            os.makedirs(head_tail[0], exist_ok=True)
-
-
-def UpdateChargeFlagInAtomBlock(mb):
-    """
-    See https://sourceforge.net/p/rdkit/mailman/message/36425493/
-    """
-    f="{:>10s}"*3+"{:>2}{:>4s}"+"{:>3s}"*11
-    chgs = []    # list of charges
-    lines = mb.split("\n")
-    if mb[0] == '' or mb[0] == "\n":
-        del lines[0]
-    CTAB = lines[2]
-    atomCount = int(CTAB.split()[0])
-    # parse mb line per line
-    for l in lines:
-        # look for M CHG property
-        if l[0:6] == "M  CHG":
-            records = l.split()[3:]    # M  CHG X is not needed for parsing, the info we want comes afterwards
-            # record each charge into a list
-            for i in range(0,len(records),2):
-                idx = records[i]
-                chg = records[i+1]
-                chgs.append((int(idx), int(chg)))    # sort tuples by first element?
-            break    # stop iterating
-
-    # sort by idx in order to parse the molblock only once more
-    chgs = sorted(chgs, key=lambda x: x[0])
-
-    # that we have a list for the current molblock, attribute each charges
-    for chg in chgs:
-        i=3
-        while i < 3+atomCount:    # do not read from beginning each time, rather continue parsing mb!
-            # when finding the idx of the atom we want to update, extract all fields and rewrite whole sequence
-            if i-2 == chg[0]:    # -4 to take into account the CTAB headers, +1 because idx begin at 1 and not 0
-                fields = lines[i].split()
-                x=fields[0]
-                y=fields[1]
-                z=fields[2]
-                symb=fields[3]
-                massDiff=fields[4]
-                charge=fields[5]
-                sp=fields[6]
-                hc=fields[7]
-                scb=fields[8]
-                v=fields[9]
-                hd=fields[10]
-                nu1=fields[11]
-                nu2=fields[12]
-                aamn=fields[13]
-                irf=fields[14]
-                ecf=fields[15]
-                # update charge flag
-                if chg[1] == -1:
-                    charge = '5'
-                elif chg[1] == -2:
-                    charge = '6'
-                elif chg[1] == -3:
-                    charge = '7'
-                elif chg[1] == 1:
-                    charge = '3'
-                elif chg[1] == 2:
-                    charge = '2'
-                elif chg[1] == 3:
-                    charge = '1'
-                else:
-                    print("ERROR! " + str(lines[0]) + "unknown charge flag: " + str(chg[1]))    # print name then go to next chg
-                    break
-                # update modatom block line
-                lines[i] = f.format(x,y,z,symb,massDiff,charge,sp,hc,scb,v,hd,nu1,nu2,aamn,irf,ecf)
-            i+=1
-    #print("\n".join(lines))
-    del lines[-1]    # remove empty element left because last character before $$$$ is \n
-    upmb = "\n" + "\n".join(lines)
-    return(upmb)
-
-
-def read_delimiter(input):
-    if input:
-        if 'tab' == input:
-            delimiter = '\t'
-        elif 'space' == input:
-            delimiter = None
-        elif 'comma' == input:
-            delimiter = ','
-        elif 'pipe' == input:
-            delimiter = '|'
-        else:
-            delimiter = input
-    else:
-        delimiter = None
-    return delimiter
-
-
-def calc_geometric_mean(scores):
-    total = 1.0
-    for score in scores:
-        total = total * score
-    result = total ** (1.0/len(scores))
-    return result
-
-
-def round_to_significant_number(val, sig):
-    """
-    Round the value to the specified number of significant numbers
-    :param val: The number to round
-    :param sig: Number of significant numbers
-    :return:
-    """
-    return round(val, sig - int(floor(log10(abs(val))))-1)
-
-
-def is_type(value, typ):
-    if value is not None:
-        try:
-            i = typ(value)
-            return 1, i
-        except:
-            return -1, value
-    else:
-        return 0, value
\ No newline at end of file