OpenFreeEnergy · atravitz · Sep 3, 2025 · Sep 3, 2025
diff --git a/LICENCE.txt → LICENSE.txt b/LICENCE.txt → LICENSE.txt
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,14 +1,14 @@
-graft lomap
-recursive-include lomap/tests  *sdf
-recursive-include lomap/tests  *mol2
-recursive-include lomap/tests  *gpickle
-recursive-include lomap/tests  *pickle
-recursive-include lomap/tests  *txt
+graft src/lomap
+recursive-include src/lomap/tests  *sdf
+recursive-include src/lomap/tests  *mol2
+recursive-include src/lomap/tests  *gpickle
+recursive-include src/lomap/tests  *pickle
+recursive-include src/lomap/tests  *txt
 
 
 include MANIFEST.in
 include README.md
-include LICENCE.txt
+include LICENSE.txt
 include examples/example.py
 include versioneer.py
-include lomap/_version.py
+include src/lomap/_version.py
diff --git a/docs/conf.py b/docs/conf.py
@@ -7,7 +7,7 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../'))
+sys.path.insert(0, os.path.abspath('../src'))
 
 project = 'lomap'
 copyright = '2023, Lomap developers'

diff --git a/lomap/__init__.py → src/lomap/__init__.py b/lomap/__init__.py → src/lomap/__init__.py
diff --git a/lomap/_due.py → src/lomap/_due.py b/lomap/_due.py → src/lomap/_due.py
diff --git a/lomap/dbmol.py → src/lomap/dbmol.py b/lomap/dbmol.py → src/lomap/dbmol.py
diff --git a/lomap/fp.py → src/lomap/fp.py b/lomap/fp.py → src/lomap/fp.py
diff --git a/lomap/graphgen.py → src/lomap/graphgen.py b/lomap/graphgen.py → src/lomap/graphgen.py
diff --git a/lomap/gufe_bindings/__init__.py → src/lomap/gufe_bindings/__init__.py b/lomap/gufe_bindings/__init__.py → src/lomap/gufe_bindings/__init__.py
diff --git a/lomap/gufe_bindings/mapper.py → src/lomap/gufe_bindings/mapper.py b/lomap/gufe_bindings/mapper.py → src/lomap/gufe_bindings/mapper.py
diff --git a/lomap/gufe_bindings/network_generation.py → ...lomap/gufe_bindings/network_generation.py b/lomap/gufe_bindings/network_generation.py → ...lomap/gufe_bindings/network_generation.py
diff --git a/lomap/gufe_bindings/scorers.py → src/lomap/gufe_bindings/scorers.py b/lomap/gufe_bindings/scorers.py → src/lomap/gufe_bindings/scorers.py
diff --git a/lomap/mcs.py → src/lomap/mcs.py b/lomap/mcs.py → src/lomap/mcs.py
diff --git a/lomap/tests/__init__.py → src/lomap/tests/__init__.py b/lomap/tests/__init__.py → src/lomap/tests/__init__.py
diff --git a/...sts/basic/1,3,7-trimethylnaphthalene.mol2 → ...sts/basic/1,3,7-trimethylnaphthalene.mol2 b/...sts/basic/1,3,7-trimethylnaphthalene.mol2 → ...sts/basic/1,3,7-trimethylnaphthalene.mol2
diff --git a/.../tests/basic/1-butyl-4-methylbenzene.mol2 → .../tests/basic/1-butyl-4-methylbenzene.mol2 b/.../tests/basic/1-butyl-4-methylbenzene.mol2 → .../tests/basic/1-butyl-4-methylbenzene.mol2
diff --git a/.../tests/basic/2,6-dimethylnaphthalene.mol2 → .../tests/basic/2,6-dimethylnaphthalene.mol2 b/.../tests/basic/2,6-dimethylnaphthalene.mol2 → .../tests/basic/2,6-dimethylnaphthalene.mol2
diff --git a/...s/basic/2-methyl-6-propylnaphthalene.mol2 → ...s/basic/2-methyl-6-propylnaphthalene.mol2 b/...s/basic/2-methyl-6-propylnaphthalene.mol2 → ...s/basic/2-methyl-6-propylnaphthalene.mol2
diff --git a/lomap/tests/basic/2-methylnaphthalene.mol2 → ...omap/tests/basic/2-methylnaphthalene.mol2 b/lomap/tests/basic/2-methylnaphthalene.mol2 → ...omap/tests/basic/2-methylnaphthalene.mol2
diff --git a/lomap/tests/basic/2-naftanol.mol2 → src/lomap/tests/basic/2-naftanol.mol2 b/lomap/tests/basic/2-naftanol.mol2 → src/lomap/tests/basic/2-naftanol.mol2
diff --git a/lomap/tests/basic/MCS.pickle → src/lomap/tests/basic/MCS.pickle b/lomap/tests/basic/MCS.pickle → src/lomap/tests/basic/MCS.pickle
diff --git a/lomap/tests/basic/__init__.py → src/lomap/tests/basic/__init__.py b/lomap/tests/basic/__init__.py → src/lomap/tests/basic/__init__.py
diff --git a/lomap/tests/basic/chlorophenyl.sdf → src/lomap/tests/basic/chlorophenyl.sdf b/lomap/tests/basic/chlorophenyl.sdf → src/lomap/tests/basic/chlorophenyl.sdf
diff --git a/lomap/tests/basic/methylcyclohexane.mol2 → src/lomap/tests/basic/methylcyclohexane.mol2 b/lomap/tests/basic/methylcyclohexane.mol2 → src/lomap/tests/basic/methylcyclohexane.mol2
diff --git a/lomap/tests/basic/molecules.gpickle → src/lomap/tests/basic/molecules.gpickle b/lomap/tests/basic/molecules.gpickle → src/lomap/tests/basic/molecules.gpickle
diff --git a/lomap/tests/basic/thrombin_ligands.sdf → src/lomap/tests/basic/thrombin_ligands.sdf b/lomap/tests/basic/thrombin_ligands.sdf → src/lomap/tests/basic/thrombin_ligands.sdf
diff --git a/lomap/tests/basic/toluene.mol2 → src/lomap/tests/basic/toluene.mol2 b/lomap/tests/basic/toluene.mol2 → src/lomap/tests/basic/toluene.mol2
diff --git a/lomap/tests/basic/toluyl.sdf → src/lomap/tests/basic/toluyl.sdf b/lomap/tests/basic/toluyl.sdf → src/lomap/tests/basic/toluyl.sdf
diff --git a/lomap/tests/chiral/Chiral1R.sdf → src/lomap/tests/chiral/Chiral1R.sdf b/lomap/tests/chiral/Chiral1R.sdf → src/lomap/tests/chiral/Chiral1R.sdf
diff --git a/lomap/tests/chiral/Chiral1S.sdf → src/lomap/tests/chiral/Chiral1S.sdf b/lomap/tests/chiral/Chiral1S.sdf → src/lomap/tests/chiral/Chiral1S.sdf
diff --git a/lomap/tests/chiral/Chiral2R.sdf → src/lomap/tests/chiral/Chiral2R.sdf b/lomap/tests/chiral/Chiral2R.sdf → src/lomap/tests/chiral/Chiral2R.sdf
diff --git a/lomap/tests/chiral/Chiral3RS.sdf → src/lomap/tests/chiral/Chiral3RS.sdf b/lomap/tests/chiral/Chiral3RS.sdf → src/lomap/tests/chiral/Chiral3RS.sdf
diff --git a/lomap/tests/chiral/Chiral3SR.sdf → src/lomap/tests/chiral/Chiral3SR.sdf b/lomap/tests/chiral/Chiral3SR.sdf → src/lomap/tests/chiral/Chiral3SR.sdf
diff --git a/lomap/tests/chiral/Chiral3SS.sdf → src/lomap/tests/chiral/Chiral3SS.sdf b/lomap/tests/chiral/Chiral3SS.sdf → src/lomap/tests/chiral/Chiral3SS.sdf
diff --git a/lomap/tests/chiral/Chiral4RR.sdf → src/lomap/tests/chiral/Chiral4RR.sdf b/lomap/tests/chiral/Chiral4RR.sdf → src/lomap/tests/chiral/Chiral4RR.sdf
diff --git a/lomap/tests/chiral/Chiral4RS.sdf → src/lomap/tests/chiral/Chiral4RS.sdf b/lomap/tests/chiral/Chiral4RS.sdf → src/lomap/tests/chiral/Chiral4RS.sdf
diff --git a/lomap/tests/chiral/RingChiralR.sdf → src/lomap/tests/chiral/RingChiralR.sdf b/lomap/tests/chiral/RingChiralR.sdf → src/lomap/tests/chiral/RingChiralR.sdf
diff --git a/lomap/tests/chiral/RingChiralS.sdf → src/lomap/tests/chiral/RingChiralS.sdf b/lomap/tests/chiral/RingChiralS.sdf → src/lomap/tests/chiral/RingChiralS.sdf
diff --git a/lomap/tests/chiral/SpiroR.sdf → src/lomap/tests/chiral/SpiroR.sdf b/lomap/tests/chiral/SpiroR.sdf → src/lomap/tests/chiral/SpiroR.sdf
diff --git a/lomap/tests/chiral/SpiroS.sdf → src/lomap/tests/chiral/SpiroS.sdf b/lomap/tests/chiral/SpiroS.sdf → src/lomap/tests/chiral/SpiroS.sdf
diff --git a/lomap/tests/chiral/__init__.py → src/lomap/tests/chiral/__init__.py b/lomap/tests/chiral/__init__.py → src/lomap/tests/chiral/__init__.py
diff --git a/lomap/tests/chiral/bace_cat_13d.sdf → src/lomap/tests/chiral/bace_cat_13d.sdf b/lomap/tests/chiral/bace_cat_13d.sdf → src/lomap/tests/chiral/bace_cat_13d.sdf
diff --git a/lomap/tests/chiral/bace_cat_13d_inverted.sdf → ...ap/tests/chiral/bace_cat_13d_inverted.sdf b/lomap/tests/chiral/bace_cat_13d_inverted.sdf → ...ap/tests/chiral/bace_cat_13d_inverted.sdf
diff --git a/lomap/tests/chiral/bace_cat_13d_perm1.sdf → ...lomap/tests/chiral/bace_cat_13d_perm1.sdf b/lomap/tests/chiral/bace_cat_13d_perm1.sdf → ...lomap/tests/chiral/bace_cat_13d_perm1.sdf
diff --git a/lomap/tests/chiral/bace_cat_13d_perm2.sdf → ...lomap/tests/chiral/bace_cat_13d_perm2.sdf b/lomap/tests/chiral/bace_cat_13d_perm2.sdf → ...lomap/tests/chiral/bace_cat_13d_perm2.sdf
diff --git a/lomap/tests/chiral/bace_cat_13d_perm3.sdf → ...lomap/tests/chiral/bace_cat_13d_perm3.sdf b/lomap/tests/chiral/bace_cat_13d_perm3.sdf → ...lomap/tests/chiral/bace_cat_13d_perm3.sdf
diff --git a/lomap/tests/chiral/bace_cat_13d_perm4.sdf → ...lomap/tests/chiral/bace_cat_13d_perm4.sdf b/lomap/tests/chiral/bace_cat_13d_perm4.sdf → ...lomap/tests/chiral/bace_cat_13d_perm4.sdf
diff --git a/lomap/tests/chiral/bace_cat_13d_perm5.sdf → ...lomap/tests/chiral/bace_cat_13d_perm5.sdf b/lomap/tests/chiral/bace_cat_13d_perm5.sdf → ...lomap/tests/chiral/bace_cat_13d_perm5.sdf
diff --git a/lomap/tests/chiral/bace_mk1.sdf → src/lomap/tests/chiral/bace_mk1.sdf b/lomap/tests/chiral/bace_mk1.sdf → src/lomap/tests/chiral/bace_mk1.sdf
diff --git a/lomap/tests/chiral/tpbs2_lig1.sdf → src/lomap/tests/chiral/tpbs2_lig1.sdf b/lomap/tests/chiral/tpbs2_lig1.sdf → src/lomap/tests/chiral/tpbs2_lig1.sdf
diff --git a/lomap/tests/chiral/tpbs2_lig1a.sdf → src/lomap/tests/chiral/tpbs2_lig1a.sdf b/lomap/tests/chiral/tpbs2_lig1a.sdf → src/lomap/tests/chiral/tpbs2_lig1a.sdf
diff --git a/lomap/tests/chiral/tpbs2_lig2.sdf → src/lomap/tests/chiral/tpbs2_lig2.sdf b/lomap/tests/chiral/tpbs2_lig2.sdf → src/lomap/tests/chiral/tpbs2_lig2.sdf
diff --git a/lomap/tests/data/__init__.py → src/lomap/tests/data/__init__.py b/lomap/tests/data/__init__.py → src/lomap/tests/data/__init__.py
diff --git a/lomap/tests/data/lig_41.sdf → src/lomap/tests/data/lig_41.sdf b/lomap/tests/data/lig_41.sdf → src/lomap/tests/data/lig_41.sdf
diff --git a/lomap/tests/data/lig_74.sdf → src/lomap/tests/data/lig_74.sdf b/lomap/tests/data/lig_74.sdf → src/lomap/tests/data/lig_74.sdf
diff --git a/lomap/tests/linksfile/__init__.py → src/lomap/tests/linksfile/__init__.py b/lomap/tests/linksfile/__init__.py → src/lomap/tests/linksfile/__init__.py
diff --git a/lomap/tests/linksfile/links1.txt → src/lomap/tests/linksfile/links1.txt b/lomap/tests/linksfile/links1.txt → src/lomap/tests/linksfile/links1.txt
diff --git a/lomap/tests/linksfile/links2.txt → src/lomap/tests/linksfile/links2.txt b/lomap/tests/linksfile/links2.txt → src/lomap/tests/linksfile/links2.txt
diff --git a/lomap/tests/linksfile/links3.txt → src/lomap/tests/linksfile/links3.txt b/lomap/tests/linksfile/links3.txt → src/lomap/tests/linksfile/links3.txt
diff --git a/lomap/tests/linksfile/phenyl.sdf → src/lomap/tests/linksfile/phenyl.sdf b/lomap/tests/linksfile/phenyl.sdf → src/lomap/tests/linksfile/phenyl.sdf
diff --git a/lomap/tests/linksfile/phenylcyclobutyl.sdf → ...omap/tests/linksfile/phenylcyclobutyl.sdf b/lomap/tests/linksfile/phenylcyclobutyl.sdf → ...omap/tests/linksfile/phenylcyclobutyl.sdf
diff --git a/lomap/tests/linksfile/phenylfuran.sdf → src/lomap/tests/linksfile/phenylfuran.sdf b/lomap/tests/linksfile/phenylfuran.sdf → src/lomap/tests/linksfile/phenylfuran.sdf
diff --git a/lomap/tests/linksfile/toluyl.sdf → src/lomap/tests/linksfile/toluyl.sdf b/lomap/tests/linksfile/toluyl.sdf → src/lomap/tests/linksfile/toluyl.sdf
diff --git a/lomap/tests/radial/__init__.py → src/lomap/tests/radial/__init__.py b/lomap/tests/radial/__init__.py → src/lomap/tests/radial/__init__.py
diff --git a/lomap/tests/radial/ejm_31.mol2 → src/lomap/tests/radial/ejm_31.mol2 b/lomap/tests/radial/ejm_31.mol2 → src/lomap/tests/radial/ejm_31.mol2
diff --git a/lomap/tests/radial/ejm_42.mol2 → src/lomap/tests/radial/ejm_42.mol2 b/lomap/tests/radial/ejm_42.mol2 → src/lomap/tests/radial/ejm_42.mol2
diff --git a/lomap/tests/radial/ejm_43.mol2 → src/lomap/tests/radial/ejm_43.mol2 b/lomap/tests/radial/ejm_43.mol2 → src/lomap/tests/radial/ejm_43.mol2
diff --git a/lomap/tests/radial/ejm_44.mol2 → src/lomap/tests/radial/ejm_44.mol2 b/lomap/tests/radial/ejm_44.mol2 → src/lomap/tests/radial/ejm_44.mol2
diff --git a/lomap/tests/radial/ejm_45.mol2 → src/lomap/tests/radial/ejm_45.mol2 b/lomap/tests/radial/ejm_45.mol2 → src/lomap/tests/radial/ejm_45.mol2
diff --git a/lomap/tests/radial/ejm_46.mol2 → src/lomap/tests/radial/ejm_46.mol2 b/lomap/tests/radial/ejm_46.mol2 → src/lomap/tests/radial/ejm_46.mol2
diff --git a/lomap/tests/radial/ejm_47.mol2 → src/lomap/tests/radial/ejm_47.mol2 b/lomap/tests/radial/ejm_47.mol2 → src/lomap/tests/radial/ejm_47.mol2
diff --git a/lomap/tests/radial/ejm_48.mol2 → src/lomap/tests/radial/ejm_48.mol2 b/lomap/tests/radial/ejm_48.mol2 → src/lomap/tests/radial/ejm_48.mol2
diff --git a/lomap/tests/radial/ejm_49.mol2 → src/lomap/tests/radial/ejm_49.mol2 b/lomap/tests/radial/ejm_49.mol2 → src/lomap/tests/radial/ejm_49.mol2
diff --git a/lomap/tests/radial/ejm_50.mol2 → src/lomap/tests/radial/ejm_50.mol2 b/lomap/tests/radial/ejm_50.mol2 → src/lomap/tests/radial/ejm_50.mol2
diff --git a/lomap/tests/radial/ejm_54.mol2 → src/lomap/tests/radial/ejm_54.mol2 b/lomap/tests/radial/ejm_54.mol2 → src/lomap/tests/radial/ejm_54.mol2
diff --git a/lomap/tests/radial/ejm_55.mol2 → src/lomap/tests/radial/ejm_55.mol2 b/lomap/tests/radial/ejm_55.mol2 → src/lomap/tests/radial/ejm_55.mol2
diff --git a/lomap/tests/radial/jmc_23.mol2 → src/lomap/tests/radial/jmc_23.mol2 b/lomap/tests/radial/jmc_23.mol2 → src/lomap/tests/radial/jmc_23.mol2
diff --git a/lomap/tests/radial/jmc_27.mol2 → src/lomap/tests/radial/jmc_27.mol2 b/lomap/tests/radial/jmc_27.mol2 → src/lomap/tests/radial/jmc_27.mol2
diff --git a/lomap/tests/radial/jmc_28.mol2 → src/lomap/tests/radial/jmc_28.mol2 b/lomap/tests/radial/jmc_28.mol2 → src/lomap/tests/radial/jmc_28.mol2
diff --git a/lomap/tests/radial/jmc_30.mol2 → src/lomap/tests/radial/jmc_30.mol2 b/lomap/tests/radial/jmc_30.mol2 → src/lomap/tests/radial/jmc_30.mol2
diff --git a/lomap/tests/radial/molecules.gpickle → src/lomap/tests/radial/molecules.gpickle b/lomap/tests/radial/molecules.gpickle → src/lomap/tests/radial/molecules.gpickle
diff --git a/lomap/tests/radial/radial.gpickle → src/lomap/tests/radial/radial.gpickle b/lomap/tests/radial/radial.gpickle → src/lomap/tests/radial/radial.gpickle
diff --git a/lomap/tests/radial/radial_hub.gpickle → src/lomap/tests/radial/radial_hub.gpickle b/lomap/tests/radial/radial_hub.gpickle → src/lomap/tests/radial/radial_hub.gpickle
diff --git a/...sts/radial/radial_hub_fingerprint.gpickle → ...sts/radial/radial_hub_fingerprint.gpickle b/...sts/radial/radial_hub_fingerprint.gpickle → ...sts/radial/radial_hub_fingerprint.gpickle
diff --git a/...adial/radial_hub_fingerprint_fast.gpickle → ...adial/radial_hub_fingerprint_fast.gpickle b/...adial/radial_hub_fingerprint_fast.gpickle → ...adial/radial_hub_fingerprint_fast.gpickle
diff --git a/lomap/tests/test_lomap.py → src/lomap/tests/test_lomap.py b/lomap/tests/test_lomap.py → src/lomap/tests/test_lomap.py
diff --git a/lomap/tests/test_lomapatommapper.py → src/lomap/tests/test_lomapatommapper.py b/lomap/tests/test_lomapatommapper.py → src/lomap/tests/test_lomapatommapper.py
diff --git a/lomap/tests/test_mcs.py → src/lomap/tests/test_mcs.py b/lomap/tests/test_mcs.py → src/lomap/tests/test_mcs.py
diff --git a/lomap/tests/test_new_api.py → src/lomap/tests/test_new_api.py b/lomap/tests/test_new_api.py → src/lomap/tests/test_new_api.py
diff --git a/lomap/tests/test_scorer.py → src/lomap/tests/test_scorer.py b/lomap/tests/test_scorer.py → src/lomap/tests/test_scorer.py
diff --git a/lomap/tests/transforms/__init__.py → src/lomap/tests/transforms/__init__.py b/lomap/tests/transforms/__init__.py → src/lomap/tests/transforms/__init__.py
diff --git a/lomap/tests/transforms/bromophenyl.sdf → src/lomap/tests/transforms/bromophenyl.sdf b/lomap/tests/transforms/bromophenyl.sdf → src/lomap/tests/transforms/bromophenyl.sdf
diff --git a/lomap/tests/transforms/cdk2_lig1.sdf → src/lomap/tests/transforms/cdk2_lig1.sdf b/lomap/tests/transforms/cdk2_lig1.sdf → src/lomap/tests/transforms/cdk2_lig1.sdf
diff --git a/lomap/tests/transforms/cdk2_lig11.sdf → src/lomap/tests/transforms/cdk2_lig11.sdf b/lomap/tests/transforms/cdk2_lig11.sdf → src/lomap/tests/transforms/cdk2_lig11.sdf
diff --git a/lomap/tests/transforms/cdk2_lig13.sdf → src/lomap/tests/transforms/cdk2_lig13.sdf b/lomap/tests/transforms/cdk2_lig13.sdf → src/lomap/tests/transforms/cdk2_lig13.sdf
diff --git a/lomap/tests/transforms/cdk2_lig14.sdf → src/lomap/tests/transforms/cdk2_lig14.sdf b/lomap/tests/transforms/cdk2_lig14.sdf → src/lomap/tests/transforms/cdk2_lig14.sdf
diff --git a/...ests/transforms/cdk2_lig14_translated.sdf → ...ests/transforms/cdk2_lig14_translated.sdf b/...ests/transforms/cdk2_lig14_translated.sdf → ...ests/transforms/cdk2_lig14_translated.sdf
diff --git a/lomap/tests/transforms/cdk2_lig15.sdf → src/lomap/tests/transforms/cdk2_lig15.sdf b/lomap/tests/transforms/cdk2_lig15.sdf → src/lomap/tests/transforms/cdk2_lig15.sdf
diff --git a/lomap/tests/transforms/cdk2_lig16.sdf → src/lomap/tests/transforms/cdk2_lig16.sdf b/lomap/tests/transforms/cdk2_lig16.sdf → src/lomap/tests/transforms/cdk2_lig16.sdf
diff --git a/lomap/tests/transforms/cdk2_lig2.sdf → src/lomap/tests/transforms/cdk2_lig2.sdf b/lomap/tests/transforms/cdk2_lig2.sdf → src/lomap/tests/transforms/cdk2_lig2.sdf
diff --git a/lomap/tests/transforms/chlorophenol.sdf → src/lomap/tests/transforms/chlorophenol.sdf b/lomap/tests/transforms/chlorophenol.sdf → src/lomap/tests/transforms/chlorophenol.sdf
diff --git a/lomap/tests/transforms/chlorophenyl.sdf → src/lomap/tests/transforms/chlorophenyl.sdf b/lomap/tests/transforms/chlorophenyl.sdf → src/lomap/tests/transforms/chlorophenyl.sdf
diff --git a/lomap/tests/transforms/chlorophenyl2.sdf → src/lomap/tests/transforms/chlorophenyl2.sdf b/lomap/tests/transforms/chlorophenyl2.sdf → src/lomap/tests/transforms/chlorophenyl2.sdf
diff --git a/lomap/tests/transforms/chlorotoluyl1.sdf → src/lomap/tests/transforms/chlorotoluyl1.sdf b/lomap/tests/transforms/chlorotoluyl1.sdf → src/lomap/tests/transforms/chlorotoluyl1.sdf
diff --git a/lomap/tests/transforms/chlorotoluyl2.sdf → src/lomap/tests/transforms/chlorotoluyl2.sdf b/lomap/tests/transforms/chlorotoluyl2.sdf → src/lomap/tests/transforms/chlorotoluyl2.sdf
diff --git a/lomap/tests/transforms/fluorophenyl.sdf → src/lomap/tests/transforms/fluorophenyl.sdf b/lomap/tests/transforms/fluorophenyl.sdf → src/lomap/tests/transforms/fluorophenyl.sdf
diff --git a/lomap/tests/transforms/iodophenyl.sdf → src/lomap/tests/transforms/iodophenyl.sdf b/lomap/tests/transforms/iodophenyl.sdf → src/lomap/tests/transforms/iodophenyl.sdf
diff --git a/lomap/tests/transforms/methoxyphenyl.sdf → src/lomap/tests/transforms/methoxyphenyl.sdf b/lomap/tests/transforms/methoxyphenyl.sdf → src/lomap/tests/transforms/methoxyphenyl.sdf
diff --git a/lomap/tests/transforms/napthyl.sdf → src/lomap/tests/transforms/napthyl.sdf b/lomap/tests/transforms/napthyl.sdf → src/lomap/tests/transforms/napthyl.sdf
diff --git a/lomap/tests/transforms/napthyl2.sdf → src/lomap/tests/transforms/napthyl2.sdf b/lomap/tests/transforms/napthyl2.sdf → src/lomap/tests/transforms/napthyl2.sdf
diff --git a/lomap/tests/transforms/napthyl3.sdf → src/lomap/tests/transforms/napthyl3.sdf b/lomap/tests/transforms/napthyl3.sdf → src/lomap/tests/transforms/napthyl3.sdf
diff --git a/lomap/tests/transforms/phenyl.sdf → src/lomap/tests/transforms/phenyl.sdf b/lomap/tests/transforms/phenyl.sdf → src/lomap/tests/transforms/phenyl.sdf
diff --git a/lomap/tests/transforms/phenylamide.sdf → src/lomap/tests/transforms/phenylamide.sdf b/lomap/tests/transforms/phenylamide.sdf → src/lomap/tests/transforms/phenylamide.sdf
diff --git a/lomap/tests/transforms/phenylcyclobutyl.sdf → ...map/tests/transforms/phenylcyclobutyl.sdf b/lomap/tests/transforms/phenylcyclobutyl.sdf → ...map/tests/transforms/phenylcyclobutyl.sdf
diff --git a/lomap/tests/transforms/phenylcyclononyl.sdf → ...map/tests/transforms/phenylcyclononyl.sdf b/lomap/tests/transforms/phenylcyclononyl.sdf → ...map/tests/transforms/phenylcyclononyl.sdf
diff --git a/lomap/tests/transforms/phenylcyclopentyl.sdf → ...ap/tests/transforms/phenylcyclopentyl.sdf b/lomap/tests/transforms/phenylcyclopentyl.sdf → ...ap/tests/transforms/phenylcyclopentyl.sdf
diff --git a/...s/transforms/phenylcyclopentylmethyl1.sdf → ...s/transforms/phenylcyclopentylmethyl1.sdf b/...s/transforms/phenylcyclopentylmethyl1.sdf → ...s/transforms/phenylcyclopentylmethyl1.sdf
diff --git a/...s/transforms/phenylcyclopentylmethyl2.sdf → ...s/transforms/phenylcyclopentylmethyl2.sdf b/...s/transforms/phenylcyclopentylmethyl2.sdf → ...s/transforms/phenylcyclopentylmethyl2.sdf
diff --git a/lomap/tests/transforms/phenylcyclopropyl.sdf → ...ap/tests/transforms/phenylcyclopropyl.sdf b/lomap/tests/transforms/phenylcyclopropyl.sdf → ...ap/tests/transforms/phenylcyclopropyl.sdf
diff --git a/lomap/tests/transforms/phenylethyl.sdf → src/lomap/tests/transforms/phenylethyl.sdf b/lomap/tests/transforms/phenylethyl.sdf → src/lomap/tests/transforms/phenylethyl.sdf
diff --git a/lomap/tests/transforms/phenylfuran.sdf → src/lomap/tests/transforms/phenylfuran.sdf b/lomap/tests/transforms/phenylfuran.sdf → src/lomap/tests/transforms/phenylfuran.sdf
diff --git a/lomap/tests/transforms/phenylimidazole.sdf → ...omap/tests/transforms/phenylimidazole.sdf b/lomap/tests/transforms/phenylimidazole.sdf → ...omap/tests/transforms/phenylimidazole.sdf
diff --git a/lomap/tests/transforms/phenylisoxazole.sdf → ...omap/tests/transforms/phenylisoxazole.sdf b/lomap/tests/transforms/phenylisoxazole.sdf → ...omap/tests/transforms/phenylisoxazole.sdf
diff --git a/lomap/tests/transforms/phenylmethylamino.sdf → ...ap/tests/transforms/phenylmethylamino.sdf b/lomap/tests/transforms/phenylmethylamino.sdf → ...ap/tests/transforms/phenylmethylamino.sdf
diff --git a/lomap/tests/transforms/phenyloxazole.sdf → src/lomap/tests/transforms/phenyloxazole.sdf b/lomap/tests/transforms/phenyloxazole.sdf → src/lomap/tests/transforms/phenyloxazole.sdf
diff --git a/lomap/tests/transforms/phenylphenyl.sdf → src/lomap/tests/transforms/phenylphenyl.sdf b/lomap/tests/transforms/phenylphenyl.sdf → src/lomap/tests/transforms/phenylphenyl.sdf
diff --git a/lomap/tests/transforms/phenylpyrazole.sdf → ...lomap/tests/transforms/phenylpyrazole.sdf b/lomap/tests/transforms/phenylpyrazole.sdf → ...lomap/tests/transforms/phenylpyrazole.sdf
diff --git a/lomap/tests/transforms/phenylpyridine1.sdf → ...omap/tests/transforms/phenylpyridine1.sdf b/lomap/tests/transforms/phenylpyridine1.sdf → ...omap/tests/transforms/phenylpyridine1.sdf
diff --git a/lomap/tests/transforms/phenylpyridine2.sdf → ...omap/tests/transforms/phenylpyridine2.sdf b/lomap/tests/transforms/phenylpyridine2.sdf → ...omap/tests/transforms/phenylpyridine2.sdf
diff --git a/lomap/tests/transforms/phenylpyrimidine.sdf → ...map/tests/transforms/phenylpyrimidine.sdf b/lomap/tests/transforms/phenylpyrimidine.sdf → ...map/tests/transforms/phenylpyrimidine.sdf
diff --git a/lomap/tests/transforms/phenylpyrrole.sdf → src/lomap/tests/transforms/phenylpyrrole.sdf b/lomap/tests/transforms/phenylpyrrole.sdf → src/lomap/tests/transforms/phenylpyrrole.sdf
diff --git a/lomap/tests/transforms/phenylsulfonamide.sdf → ...ap/tests/transforms/phenylsulfonamide.sdf b/lomap/tests/transforms/phenylsulfonamide.sdf → ...ap/tests/transforms/phenylsulfonamide.sdf
diff --git a/lomap/tests/transforms/sulfonamide.sdf → src/lomap/tests/transforms/sulfonamide.sdf b/lomap/tests/transforms/sulfonamide.sdf → src/lomap/tests/transforms/sulfonamide.sdf
diff --git a/lomap/tests/transforms/sulfone.sdf → src/lomap/tests/transforms/sulfone.sdf b/lomap/tests/transforms/sulfone.sdf → src/lomap/tests/transforms/sulfone.sdf
diff --git a/...p/tests/transforms/tetrahydronaphthyl.sdf → ...p/tests/transforms/tetrahydronaphthyl.sdf b/...p/tests/transforms/tetrahydronaphthyl.sdf → ...p/tests/transforms/tetrahydronaphthyl.sdf
diff --git a/lomap/tests/transforms/toluyl.sdf → src/lomap/tests/transforms/toluyl.sdf b/lomap/tests/transforms/toluyl.sdf → src/lomap/tests/transforms/toluyl.sdf
diff --git a/lomap/tests/transforms/toluyl2.sdf → src/lomap/tests/transforms/toluyl2.sdf b/lomap/tests/transforms/toluyl2.sdf → src/lomap/tests/transforms/toluyl2.sdf
diff --git a/lomap/tests/transforms/toluyl3.sdf → src/lomap/tests/transforms/toluyl3.sdf b/lomap/tests/transforms/toluyl3.sdf → src/lomap/tests/transforms/toluyl3.sdf
diff --git a/lomap/utils.py → src/lomap/utils.py b/lomap/utils.py → src/lomap/utils.py