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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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1 parent bc5da39 commit 2e4e634
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4 changes: 2 additions & 2 deletions .github/workflows/python-linter.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -59,11 +59,11 @@ jobs:
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install mypy types-setuptools types-PyYAML types-requests
pip install mypy types-setuptools types-PyYAML types-requests types-tensorflow types-beautifulsoup4 pandas-stubs PyQt5-stubs
- name: Typecheck with mypy
run: |
# Exclude parts of Informatics for now
mypy --ignore-missing-imports --exclude '(frag_functionalizer.py|bridge_functionalizer.py|macrocycle_synthesis.py)' molSimplify
mypy --ignore-missing-imports molSimplify
- name: Report Status
# Slack notifications only on the main repo
Expand Down
2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ repos:
- id: end-of-file-fixer
- id: trailing-whitespace
- repo: https://github.com/pycqa/flake8
rev: '6.1.0'
rev: '7.0.0'
hooks:
- id: flake8
args: ['--select=E9,F63,F7,F82', '--exclude=fragment_classes.py,frag_functionalizer.py,bridge_functionalizer.py']
34 changes: 29 additions & 5 deletions molSimplify/Classes/globalvars.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
import platform
import sys
import subprocess
from typing import Dict, Tuple
from molSimplify.utils.metaclasses import Singleton

# Dictionary containing atomic mass, atomic number, covalent radius, num valence electrons
Expand Down Expand Up @@ -402,27 +403,46 @@
'devi_linear_avrg': 20, 'devi_linear_max': 28}
}

dict_eightcoord_check = {"mono": {'num_coord_metal': 8,
'rmsd_max': 0.4, 'atom_dist_max': 0.6,
'oct_angle_devi_max': 16, 'max_del_sig_angle': 27,
'dist_del_eq': 0.45, 'dist_del_all': 1.25,
'devi_linear_avrg': 35, 'devi_linear_max': 40},
"multi": {'num_coord_metal': 8,
'rmsd_max': 0.4, 'atom_dist_max': 0.6,
'oct_angle_devi_max': 20, 'max_del_sig_angle': 35,
'dist_del_eq': 0.45, 'dist_del_all': 1.25,
'devi_linear_avrg': 35, 'devi_linear_max': 40}
}

dict_staus = {'good': 1, 'bad': 0}

oct_angle_ref = [[90, 90, 90, 90, 180] for x in range(6)]
tetra_angle_ref = [[109.47, 109.47, 109.47] for x in range(4)]
oneempty_angle_ref = [[90, 90, 90, 90], [180, 90, 90, 90], [180, 90, 90, 90],
[180, 90, 90, 90], [180, 90, 90, 90]]
eightcoord_angle_ref = [[73.7, 73.7, 76.8, 76.8, 116.1, 142.1, 142.1] for x in range(8)]
geo_check_dictionary = {"dict_oct_check_loose": dict_oct_check_loose,
"dict_oct_check_st": dict_oct_check_st,
"dict_oneempty_check_st": dict_oneempty_check_st,
"dict_oneempty_check_loose": dict_oneempty_check_loose,
"dict_staus": dict_staus,
"oct_angle_ref": oct_angle_ref,
"oneempty_angle_ref": oneempty_angle_ref}
"oneempty_angle_ref": oneempty_angle_ref,
"eightcoord_angle_ref": eightcoord_angle_ref}
all_geometries = {
2: ["linear", "bent"],
3: ["trigonal planar", "T shape", "trigonal pyramidal"],
4: ["tetrahedral", "square planar", "seesaw"],
5: ["trigonal bipyramidal", "square pyramidal", "pentagonal planar"],
6: ["octahedral", "pentagonal pyramidal", "trigonal prismatic"],
7: ["pentagonal bipyramidal"],
8: ["square antiprismatic"],
9: ["tricapped trigonal prismatic"]
}
all_angle_refs = {
"linear": [[180] for x in range(2)],
"bent": [[120] for x in range(2)],
"trigonal planar": [[120, 120] for x in range(3)],
"T shape": [[90, 90], [90, 180], [90, 180]],
"tetrahedral": [[109.47, 109.47, 109.47] for x in range(4)],
Expand All @@ -435,10 +455,14 @@
"octahedral": [[90, 90, 90, 90, 180] for x in range(6)],
"pentagonal pyramidal": [[90, 90, 90, 90, 90]] + [[36, 36, 72, 72, 90] for x in range(5)],
"trigonal prismatic": [[75.3, 86.5, 86.5, 133.3, 133.3] for x in range(6)],
"pentagonal bipyramidal": [[90, 90, 90, 90, 90, 180] for x in range(2)] + [[72, 72, 144, 144, 90, 90] for x in range(5)]
"pentagonal bipyramidal": [[90, 90, 90, 90, 90, 180] for x in range(2)] +
[[72, 72, 144, 144, 90, 90] for x in range(5)],
"square antiprismatic": [[73.7, 73.7, 76.8, 76.8, 116.1, 142.1, 142.1] for x in range(8)],
"tricapped trigonal prismatic": [[70.5, 70.5, 120, 67.7, 67.7, 135.5, 135.5, 120] for x in range(4)] +
[[76.3, 79, 138.2, 70.5, 67.7, 76.3, 138.2, 135.5] for x in range(4)] +
[[70.5, 70.5, 67.7, 67.7, 120, 120, 135.5, 135.5]]
}


# Module for running bash commands
# @param cmd String containing command to be run
# @return bash output string
Expand Down Expand Up @@ -563,7 +587,7 @@ def __init__(self):
# Returns atomic mass dictionary
# @param self The object pointer
# @return Atomic mass dictionary
def amass(self):
def amass(self) -> Dict[str, Tuple[float, int, float, int]]:
"""Get the atomic mass dictionary.
Returns
Expand All @@ -573,7 +597,7 @@ def amass(self):
"""
return amassdict

def polarizability(self):
def polarizability(self) -> Dict[str, float]:
"""Get the polarizability dictionary.
Returns
Expand Down
1 change: 1 addition & 0 deletions molSimplify/Classes/ligand.py
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Original file line number Diff line number Diff line change
Expand Up @@ -286,6 +286,7 @@ def ligand_breakdown(mol, BondedOct=False, silent=True, transition_metals_only=T
# this function takes an octahedral
# complex and returns ligands
metal_index = mol.findMetal(transition_metals_only=transition_metals_only)[0]
# print(BondedOct)
bondedatoms = mol.getBondedAtomsSmart(metal_index, oct=BondedOct)
# print('!!!!!boundatoms', bondedatoms)
# print('from get oct' + str(bondedatoms))
Expand Down
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