Add minimal example for issue 127 #202
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ralf-meyer
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Feb 26, 2024
commit 9481fd8 Merge: 21b7db1 5369b24 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 26 16:11:39 2024 -0500 Merge pull request #169 from hjkgrp/type-hinting Type hinting commit 21b7db1 Merge: 56ab21b 04ad929 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 19 21:40:41 2024 -0500 Merge pull request #203 from hjkgrp/more_ligand_fixes Improve documentation of the test case commit 04ad929 Merge: d8cd523 56ab21b Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 19 21:27:56 2024 -0500 Merge branch 'master' into more_ligand_fixes commit 56ab21b Merge: e5a4d04 82640c5 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 19 21:20:13 2024 -0500 Merge pull request #202 from hjkgrp/rmsd Add minimal example for issue 127 commit 82640c5 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 19 21:14:11 2024 -0500 Add minimal example for issue 127 commit e5a4d04 Merge: 5ad401e 8ecc724 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 12 21:30:50 2024 -0500 Merge pull request #201 from hjkgrp/mol3D_from_smiles mol3D from smiles commit 8ecc724 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 12 20:45:28 2024 -0500 Add from_smiles constructor commit 650a222 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 12 20:44:36 2024 -0500 Fix get_geometry_type default argument commit 5ad401e Author: Gianmarco Terrones <78051991+gianmarco-terrones@users.noreply.github.com> Date: Sat Feb 10 16:54:37 2024 -0500 Update fragment_MOFs_for_pormake.py commit e96d424 Merge: 9e42836 4836f07 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 5 16:29:06 2024 -0500 Merge pull request #199 from hjkgrp/pre-commit-ci-update-config [pre-commit.ci] pre-commit autoupdate commit 4836f07 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon Feb 5 21:13:58 2024 +0000 [pre-commit.ci] pre-commit autoupdate updates: - [github.com/pycqa/flake8: 6.1.0 → 7.0.0](PyCQA/flake8@6.1.0...7.0.0) commit 9e42836 Merge: e8ee975 e5570d6 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 5 16:07:27 2024 -0500 Merge pull request #197 from hjkgrp/jwt_edits Jwt edits commit e5570d6 Author: jwtoney <jwt@mit.edu> Date: Mon Feb 5 13:45:46 2024 -0500 Flake fixes commit 71c2af1 Author: jwtoney <jwt@mit.edu> Date: Mon Feb 5 13:44:25 2024 -0500 Remove print statement commit e8ee975 Author: davut-m <155399887+davut-m@users.noreply.github.com> Date: Wed Jan 24 10:11:50 2024 -0500 Added a line to check geomnames (#195) * Added a line to check geomnames * [pre-commit.ci] auto fixes from pre-commit hooks --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 5369b24 Merge: dd92b55 4e6d826 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Fri Nov 10 19:00:41 2023 -0500 Merge branch 'master' into type-hinting commit 58c9384 Merge: 9203f21 62526bd Author: jwtoney <jwt@mit.edu> Date: Fri Oct 13 12:50:51 2023 -0400 Merge branch 'master' into tutorial4 Merge latest updates from master commit 9203f21 Author: jwtoney <jwt@mit.edu> Date: Fri Sep 29 11:04:19 2023 -0400 Passed transition_metals_only flag commit dd92b55 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sat Aug 26 18:53:45 2023 -0400 Fix mypy test for pandas index type commit 944f9c6 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sat Aug 26 18:46:54 2023 -0400 type hints for rungen commit fb50e10 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sat Aug 26 18:08:22 2023 -0400 Intermediate commit of new type hints commit 65394d8 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Fri Aug 25 16:24:30 2023 -0400 remove mypy exclusions commit d8cd523 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Tue Aug 9 22:08:35 2022 -0400 Improve documentation of the test case
ralf-meyer
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Mar 21, 2024
commit ecda58b Merge: 3b66225 48035f4 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Thu Mar 21 16:32:04 2024 -0400 Merge pull request #200 from hjkgrp/get_geometry_edits Updated get_geometry commit 3b66225 Merge: 35714b8 6b78b7f Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Thu Mar 7 13:10:28 2024 -0500 Merge pull request #206 from hjkgrp/from_smiles Add option to skip 3D generation in getOBMol() commit 6b78b7f Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Thu Mar 7 12:54:15 2024 -0500 Add option to skip 3D generation in getOBMol() commit 35714b8 Merge: 292cc44 3d21d04 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sun Mar 3 17:25:42 2024 -0500 Merge pull request #204 from hjkgrp/geo_free_RACs Fixes a bug in geo_free_RACs notebook commit 3d21d04 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 26 17:06:40 2024 -0500 Move macrocycle functions to its own directory commit e76c897 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 26 17:05:03 2024 -0500 Fix from SMILES function commit 292cc44 Merge: 9481fd8 e8dbfdc Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 26 16:38:59 2024 -0500 Merge pull request #192 from hjkgrp/additional_tests Additional tests commit e8dbfdc Merge: b8b7922 9481fd8 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 26 16:25:29 2024 -0500 Merge branch 'master' into additional_tests commit b8b7922 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 26 16:20:54 2024 -0500 Squashed commit of the following: commit 9481fd8 Merge: 21b7db1 5369b24 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 26 16:11:39 2024 -0500 Merge pull request #169 from hjkgrp/type-hinting Type hinting commit 21b7db1 Merge: 56ab21b 04ad929 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 19 21:40:41 2024 -0500 Merge pull request #203 from hjkgrp/more_ligand_fixes Improve documentation of the test case commit 04ad929 Merge: d8cd523 56ab21b Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 19 21:27:56 2024 -0500 Merge branch 'master' into more_ligand_fixes commit 56ab21b Merge: e5a4d04 82640c5 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 19 21:20:13 2024 -0500 Merge pull request #202 from hjkgrp/rmsd Add minimal example for issue 127 commit 82640c5 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 19 21:14:11 2024 -0500 Add minimal example for issue 127 commit e5a4d04 Merge: 5ad401e 8ecc724 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 12 21:30:50 2024 -0500 Merge pull request #201 from hjkgrp/mol3D_from_smiles mol3D from smiles commit 8ecc724 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 12 20:45:28 2024 -0500 Add from_smiles constructor commit 650a222 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 12 20:44:36 2024 -0500 Fix get_geometry_type default argument commit 5ad401e Author: Gianmarco Terrones <78051991+gianmarco-terrones@users.noreply.github.com> Date: Sat Feb 10 16:54:37 2024 -0500 Update fragment_MOFs_for_pormake.py commit e96d424 Merge: 9e42836 4836f07 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 5 16:29:06 2024 -0500 Merge pull request #199 from hjkgrp/pre-commit-ci-update-config [pre-commit.ci] pre-commit autoupdate commit 4836f07 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon Feb 5 21:13:58 2024 +0000 [pre-commit.ci] pre-commit autoupdate updates: - [github.com/pycqa/flake8: 6.1.0 → 7.0.0](PyCQA/flake8@6.1.0...7.0.0) commit 9e42836 Merge: e8ee975 e5570d6 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 5 16:07:27 2024 -0500 Merge pull request #197 from hjkgrp/jwt_edits Jwt edits commit e5570d6 Author: jwtoney <jwt@mit.edu> Date: Mon Feb 5 13:45:46 2024 -0500 Flake fixes commit 71c2af1 Author: jwtoney <jwt@mit.edu> Date: Mon Feb 5 13:44:25 2024 -0500 Remove print statement commit e8ee975 Author: davut-m <155399887+davut-m@users.noreply.github.com> Date: Wed Jan 24 10:11:50 2024 -0500 Added a line to check geomnames (#195) * Added a line to check geomnames * [pre-commit.ci] auto fixes from pre-commit hooks --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 5369b24 Merge: dd92b55 4e6d826 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Fri Nov 10 19:00:41 2023 -0500 Merge branch 'master' into type-hinting commit 58c9384 Merge: 9203f21 62526bd Author: jwtoney <jwt@mit.edu> Date: Fri Oct 13 12:50:51 2023 -0400 Merge branch 'master' into tutorial4 Merge latest updates from master commit 9203f21 Author: jwtoney <jwt@mit.edu> Date: Fri Sep 29 11:04:19 2023 -0400 Passed transition_metals_only flag commit dd92b55 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sat Aug 26 18:53:45 2023 -0400 Fix mypy test for pandas index type commit 944f9c6 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sat Aug 26 18:46:54 2023 -0400 type hints for rungen commit fb50e10 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sat Aug 26 18:08:22 2023 -0400 Intermediate commit of new type hints commit 65394d8 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Fri Aug 25 16:24:30 2023 -0400 remove mypy exclusions commit d8cd523 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Tue Aug 9 22:08:35 2022 -0400 Improve documentation of the test case commit d0e8443 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 26 16:18:22 2024 -0500 Add failing test cases as commented lines commit 9481fd8 Merge: 21b7db1 5369b24 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 26 16:11:39 2024 -0500 Merge pull request #169 from hjkgrp/type-hinting Type hinting commit 21b7db1 Merge: 56ab21b 04ad929 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 19 21:40:41 2024 -0500 Merge pull request #203 from hjkgrp/more_ligand_fixes Improve documentation of the test case commit 04ad929 Merge: d8cd523 56ab21b Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 19 21:27:56 2024 -0500 Merge branch 'master' into more_ligand_fixes commit 56ab21b Merge: e5a4d04 82640c5 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 19 21:20:13 2024 -0500 Merge pull request #202 from hjkgrp/rmsd Add minimal example for issue 127 commit 82640c5 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 19 21:14:11 2024 -0500 Add minimal example for issue 127 commit 48035f4 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sun Feb 18 14:07:57 2024 -0500 Expand test_get_geometry_type_sandwich() test case commit fee143f Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sun Feb 18 13:52:42 2024 -0500 Test cases for is_edge_compound commit b8116af Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sun Feb 18 13:51:56 2024 -0500 Add typing commit 2e2313b Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sat Feb 17 17:04:01 2024 -0500 Add test cases for is_sandwich_compound commit 84d56c0 Merge: ec69c0e e5a4d04 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sat Feb 17 16:43:57 2024 -0500 Merge remote-tracking branch 'origin/master' into get_geometry_edits commit ec69c0e Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sat Feb 17 16:40:37 2024 -0500 Add test cases for new geometries commit 5a70add Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Fri Feb 16 14:38:21 2024 -0500 compare to all_geometries dict instead of static list commit 21a0d65 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Fri Feb 16 13:43:57 2024 -0500 Remove list() cast commit e5a4d04 Merge: 5ad401e 8ecc724 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 12 21:30:50 2024 -0500 Merge pull request #201 from hjkgrp/mol3D_from_smiles mol3D from smiles commit 8ecc724 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 12 20:45:28 2024 -0500 Add from_smiles constructor commit 650a222 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 12 20:44:36 2024 -0500 Fix get_geometry_type default argument commit 5ad401e Author: Gianmarco Terrones <78051991+gianmarco-terrones@users.noreply.github.com> Date: Sat Feb 10 16:54:37 2024 -0500 Update fragment_MOFs_for_pormake.py commit 12adbf5 Author: jwtoney <jwt@mit.edu> Date: Tue Feb 6 17:12:08 2024 -0500 Updated get_geometry to properly classify edge / sandwich ligands and coordination numbers > 7 commit e96d424 Merge: 9e42836 4836f07 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 5 16:29:06 2024 -0500 Merge pull request #199 from hjkgrp/pre-commit-ci-update-config [pre-commit.ci] pre-commit autoupdate commit 4836f07 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon Feb 5 21:13:58 2024 +0000 [pre-commit.ci] pre-commit autoupdate updates: - [github.com/pycqa/flake8: 6.1.0 → 7.0.0](PyCQA/flake8@6.1.0...7.0.0) commit 9e42836 Merge: e8ee975 e5570d6 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Mon Feb 5 16:07:27 2024 -0500 Merge pull request #197 from hjkgrp/jwt_edits Jwt edits commit e5570d6 Author: jwtoney <jwt@mit.edu> Date: Mon Feb 5 13:45:46 2024 -0500 Flake fixes commit 71c2af1 Author: jwtoney <jwt@mit.edu> Date: Mon Feb 5 13:44:25 2024 -0500 Remove print statement commit c33449c Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Tue Dec 19 19:52:18 2023 -0500 Add test case for MOFs from Aditya's JACS paper commit 93fbfe2 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Tue Dec 19 11:18:08 2023 -0500 Remove dead code commit 65ee867 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sun Dec 17 19:43:53 2023 -0500 Replace df.append with pd.concat commit 22ff357 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sun Dec 17 18:45:53 2023 -0500 Remove unnecessay code commit 2912003 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sun Dec 17 18:45:15 2023 -0500 Add references for the MOF csv files commit 877481d Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sun Dec 17 15:15:35 2023 -0500 Convert .cif files to primitive unit cell commit 8f3ed8f Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sun Dec 17 14:23:18 2023 -0500 Added more type hints commit 450c8dd Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sat Dec 16 20:38:49 2023 -0500 Move pymatgen import to get_primitive() function commit 91d0b45 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sat Dec 16 20:14:55 2023 -0500 Remove checkpoint file commit 06040bf Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sat Dec 16 14:50:12 2023 -0500 Add test cases for MOF_descriptors commit 7861aae Merge: 0ecbea3 07dffb1 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sat Dec 16 10:44:53 2023 -0500 Merge remote-tracking branch 'origin/HEAD' into additional_tests commit 0ecbea3 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Fri Dec 15 14:51:12 2023 -0500 Removed duplicate file commit 8e0f9f4 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Fri Nov 10 23:17:59 2023 -0500 Switch report comparison to proper helper function commit 5cc7c87 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Fri Nov 10 23:03:52 2023 -0500 Add tests for ligand class commit 252eb1b Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Fri Nov 10 22:58:37 2023 -0500 Add test for deprecated ligand assign commit 613082a Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Fri Nov 10 22:57:55 2023 -0500 Add geometry tests commit 4528a42 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Fri Nov 10 22:57:37 2023 -0500 Add io tests commit 69d5b63 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Fri Nov 10 22:57:07 2023 -0500 Add test for cli commit 5369b24 Merge: dd92b55 4e6d826 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Fri Nov 10 19:00:41 2023 -0500 Merge branch 'master' into type-hinting commit 58c9384 Merge: 9203f21 62526bd Author: jwtoney <jwt@mit.edu> Date: Fri Oct 13 12:50:51 2023 -0400 Merge branch 'master' into tutorial4 Merge latest updates from master commit 9203f21 Author: jwtoney <jwt@mit.edu> Date: Fri Sep 29 11:04:19 2023 -0400 Passed transition_metals_only flag commit dd92b55 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sat Aug 26 18:53:45 2023 -0400 Fix mypy test for pandas index type commit 944f9c6 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sat Aug 26 18:46:54 2023 -0400 type hints for rungen commit fb50e10 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Sat Aug 26 18:08:22 2023 -0400 Intermediate commit of new type hints commit 65394d8 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Fri Aug 25 16:24:30 2023 -0400 remove mypy exclusions commit d8cd523 Author: Ralf Meyer <meyer.ralf@yahoo.com> Date: Tue Aug 9 22:08:35 2022 -0400 Improve documentation of the test case
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Added a test case that showcases the current issue with #127