├── .gitattributes
├── .gitignore
├── .travis.yml
├── CHANGELOG
├── LICENCE.txt
├── MANIFEST.in
├── README.md
├── devtools
├── conda-recipe
│ ├── build.sh
│ └── meta.yaml
└── travis-ci
│ └── install.sh
├── examples
├── example.py
└── example_radial_graph.py
├── lomap
├── __init__.py
├── _version.py
├── dbmol.py
├── fp.py
├── graphgen.py
└── mcs.py
├── setup.cfg
├── setup.py
├── test
├── basic
│ ├── 1,3,7-trimethylnaphthalene.mol2
│ ├── 1-butyl-4-methylbenzene.mol2
│ ├── 2,6-dimethylnaphthalene.mol2
│ ├── 2-methyl-6-propylnaphthalene.mol2
│ ├── 2-methylnaphthalene.mol2
│ ├── 2-naftanol.mol2
│ ├── MCS.pickle
│ ├── chlorophenyl.sdf
│ ├── methylcyclohexane.mol2
│ ├── molecules.gpickle
│ ├── toluene.mol2
│ └── toluyl.sdf
├── chiral
│ ├── Chiral1R.sdf
│ ├── Chiral1S.sdf
│ ├── Chiral2R.sdf
│ ├── Chiral3RS.sdf
│ ├── Chiral3SR.sdf
│ ├── Chiral3SS.sdf
│ ├── Chiral4RR.sdf
│ ├── Chiral4RS.sdf
│ ├── RingChiralR.sdf
│ ├── RingChiralS.sdf
│ ├── SpiroR.sdf
│ ├── SpiroS.sdf
│ ├── bace_cat_13d.sdf
│ ├── bace_cat_13d_inverted.sdf
│ ├── bace_cat_13d_perm1.sdf
│ ├── bace_cat_13d_perm2.sdf
│ ├── bace_cat_13d_perm3.sdf
│ ├── bace_cat_13d_perm4.sdf
│ ├── bace_cat_13d_perm5.sdf
│ ├── bace_mk1.sdf
│ ├── tpbs2_lig1.sdf
│ ├── tpbs2_lig1a.sdf
│ └── tpbs2_lig2.sdf
├── linksfile
│ ├── links1.txt
│ ├── links2.txt
│ ├── links3.txt
│ ├── phenyl.sdf
│ ├── phenylcyclobutyl.sdf
│ ├── phenylfuran.sdf
│ └── toluyl.sdf
├── radial
│ ├── ejm_31.mol2
│ ├── ejm_42.mol2
│ ├── ejm_43.mol2
│ ├── ejm_44.mol2
│ ├── ejm_45.mol2
│ ├── ejm_46.mol2
│ ├── ejm_47.mol2
│ ├── ejm_48.mol2
│ ├── ejm_49.mol2
│ ├── ejm_50.mol2
│ ├── ejm_54.mol2
│ ├── ejm_55.mol2
│ ├── jmc_23.mol2
│ ├── jmc_27.mol2
│ ├── jmc_28.mol2
│ ├── jmc_30.mol2
│ ├── molecules.gpickle
│ ├── radial.gpickle
│ ├── radial_hub.gpickle
│ ├── radial_hub_fingerprint.gpickle
│ └── radial_hub_fingerprint_fast.gpickle
├── test_lomap.py
└── transforms
│ ├── bromophenyl.sdf
│ ├── cdk2_lig1.sdf
│ ├── cdk2_lig11.sdf
│ ├── cdk2_lig13.sdf
│ ├── cdk2_lig14.sdf
│ ├── cdk2_lig14_translated.sdf
│ ├── cdk2_lig15.sdf
│ ├── cdk2_lig16.sdf
│ ├── cdk2_lig2.sdf
│ ├── chlorophenol.sdf
│ ├── chlorophenyl.sdf
│ ├── chlorophenyl2.sdf
│ ├── chlorotoluyl1.sdf
│ ├── chlorotoluyl2.sdf
│ ├── fluorophenyl.sdf
│ ├── iodophenyl.sdf
│ ├── methoxyphenyl.sdf
│ ├── napthyl.sdf
│ ├── napthyl2.sdf
│ ├── napthyl3.sdf
│ ├── phenyl.sdf
│ ├── phenylamide.sdf
│ ├── phenylcyclobutyl.sdf
│ ├── phenylcyclononyl.sdf
│ ├── phenylcyclopentyl.sdf
│ ├── phenylcyclopentylmethyl1.sdf
│ ├── phenylcyclopentylmethyl2.sdf
│ ├── phenylcyclopropyl.sdf
│ ├── phenylethyl.sdf
│ ├── phenylfuran.sdf
│ ├── phenylimidazole.sdf
│ ├── phenylisoxazole.sdf
│ ├── phenylmethylamino.sdf
│ ├── phenyloxazole.sdf
│ ├── phenylphenyl.sdf
│ ├── phenylpyrazole.sdf
│ ├── phenylpyridine1.sdf
│ ├── phenylpyridine2.sdf
│ ├── phenylpyrimidine.sdf
│ ├── phenylpyrrole.sdf
│ ├── phenylsulfonamide.sdf
│ ├── sulfonamide.sdf
│ ├── sulfone.sdf
│ ├── test.py
│ ├── tetrahydronaphthyl.sdf
│ ├── toluyl.sdf
│ ├── toluyl2.sdf
│ └── toluyl3.sdf
└── versioneer.py
/.gitattributes:
--------------------------------------------------------------------------------
1 | Lomap/_version.py export-subst
2 | lomap/_version.py export-subst
3 |
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/.gitignore:
--------------------------------------------------------------------------------
1 | # Byte-compiled / optimized / DLL files
2 | __pycache__/
3 | *.py[cod]
4 | *$py.class
5 |
6 | # C extensions
7 | *.so
8 |
9 | # Distribution / packaging
10 | .Python
11 | build/
12 | develop-eggs/
13 | dist/
14 | downloads/
15 | eggs/
16 | .eggs/
17 | lib/
18 | lib64/
19 | parts/
20 | sdist/
21 | var/
22 | wheels/
23 | *.egg-info/
24 | .installed.cfg
25 | *.egg
26 | MANIFEST
27 |
28 | # PyInstaller
29 | # Usually these files are written by a python script from a template
30 | # before PyInstaller builds the exe, so as to inject date/other infos into it.
31 | *.manifest
32 | *.spec
33 |
34 | # Installer logs
35 | pip-log.txt
36 | pip-delete-this-directory.txt
37 |
38 | # Unit test / coverage reports
39 | htmlcov/
40 | .tox/
41 | .nox/
42 | .coverage
43 | .coverage.*
44 | .cache
45 | nosetests.xml
46 | coverage.xml
47 | *.cover
48 | .hypothesis/
49 | .pytest_cache/
50 |
51 | # Translations
52 | *.mo
53 | *.pot
54 |
55 | # Django stuff:
56 | *.log
57 | local_settings.py
58 | db.sqlite3
59 |
60 | # Flask stuff:
61 | instance/
62 | .webassets-cache
63 |
64 | # Scrapy stuff:
65 | .scrapy
66 |
67 | # Sphinx documentation
68 | docs/_build/
69 |
70 | # PyBuilder
71 | target/
72 |
73 | # Jupyter Notebook
74 | .ipynb_checkpoints
75 |
76 | # IPython
77 | profile_default/
78 | ipython_config.py
79 |
80 | # pyenv
81 | .python-version
82 |
83 | # celery beat schedule file
84 | celerybeat-schedule
85 |
86 | # SageMath parsed files
87 | *.sage.py
88 |
89 | # Environments
90 | .env
91 | .venv
92 | env/
93 | venv/
94 | ENV/
95 | env.bak/
96 | venv.bak/
97 |
98 | # Spyder project settings
99 | .spyderproject
100 | .spyproject
101 |
102 | # Rope project settings
103 | .ropeproject
104 |
105 | # mkdocs documentation
106 | /site
107 |
108 | # mypy
109 | .mypy_cache/
110 | .dmypy.json
111 | dmypy.json
112 |
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/.travis.yml:
--------------------------------------------------------------------------------
1 | language: python
2 | matrix:
3 | include:
4 | - os: linux
5 | python: 3.6
6 | env:
7 | - PYTHON_VER=3.6
8 | - os: linux
9 | python: 3.5
10 | env:
11 | - PYTHON_VER=3.5
12 |
13 | branches:
14 | only:
15 | - devel
16 | - master
17 | - feat_pytest
18 |
19 | before_install:
20 | - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
21 | - bash miniconda.sh -b -p $HOME/miniconda
22 | - export PATH="$HOME/miniconda/bin:$PATH"
23 | - hash -r
24 | - conda config --set always_yes yes --set changeps1 no
25 | - conda update -q conda
26 | - conda info -a
27 | - conda create -q -n test-env python=$TRAVIS_PYTHON_VERSION
28 | - source activate test-env
29 | - conda install networkx
30 | - conda install numpy
31 | - conda install matplotlib
32 | - conda install -c rdkit rdkit=2018.03.4
33 | - conda install pip pytest
34 | - pip install codecov
35 | install: yes
36 |
37 | script:
38 | - python setup.py install
39 | - pytest -v test/test_lomap.py
40 |
41 | after_success:
42 | - echo "...DONE..."
43 | - codecov
44 | notifications:
45 | email: false
46 |
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/CHANGELOG:
--------------------------------------------------------------------------------
1 | *********
2 | CHANGELOG
3 | *********
4 |
5 | 0.0.x
6 | =====
7 |
8 | Internal Alpha version
9 | ----------------------
10 | - Basic functionality of preparing a Perturbation map for alchemical free energy calculations
11 |
12 | 1.0.0
13 | =====
14 |
15 | - added versioning
16 | - support for python 3.5 and networkx2
17 | - improved visualisation of output networks
18 | - better enforcement of PEP8 style python
19 | - no longer support for python 2.7
20 |
--------------------------------------------------------------------------------
/LICENCE.txt:
--------------------------------------------------------------------------------
1 | Copyright (c) 2016-2017, Mobley Lab at UC Irvine.
2 |
3 | Permission is hereby granted, free of charge, to any person obtaining a copy
4 | of this software and associated documentation files (the "Software"), to deal
5 | in the Software without restriction, including without limitation the rights
6 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
7 | copies of the Software, and to permit persons to whom the Software is
8 | furnished to do so, subject to the following conditions:
9 |
10 | The above copyright notice and this permission notice shall be included in all
11 | copies or substantial portions of the Software.
12 |
13 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
14 | EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
15 | MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
16 | IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
17 | DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
18 | OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE
19 | OR OTHER DEALINGS IN THE SOFTWARE.
20 |
--------------------------------------------------------------------------------
/MANIFEST.in:
--------------------------------------------------------------------------------
1 | recursive-include test *
2 |
3 | include MANIFEST.in
4 | include README.md
5 | include LICENCE.txt
6 | include examples/example.py
7 | include versioneer.py
8 | include lomap/_version.py
9 |
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/devtools/conda-recipe/build.sh:
--------------------------------------------------------------------------------
1 | $PYTHON setup.py install # Python command to install the script
2 |
--------------------------------------------------------------------------------
/devtools/conda-recipe/meta.yaml:
--------------------------------------------------------------------------------
1 | package:
2 | name: lomap
3 | version: "0.0.0"
4 |
5 | source:
6 | path: ../..
7 |
8 | build:
9 | preserve_egg_dir: True
10 | number: 0
11 | skip:
12 | - [not unix]
13 |
14 | requirements:
15 | build:
16 | - python
17 | - boost
18 | - setuptools
19 | - rdkit
20 | - matplotlib
21 | - pyqt ==4.11.4
22 | - networkx >=2.0
23 | - graphviz
24 | - pygraphviz
25 | - pillow
26 | - nose
27 |
28 | run:
29 | - python
30 | - boost
31 | - rdkit
32 | - matplotlib
33 | - pyqt ==4.11.4
34 | - networkx >=2.0
35 | - graphviz
36 | - pygraphviz
37 | - pillow
38 |
39 | test:
40 | requires:
41 | - nose
42 | imports:
43 | - lomap
44 | commands:
45 | - which lomap
46 | - lomap -h
47 | - nosetests -v
48 |
49 | about:
50 | home: https://github.com/MobleyLab/Lomap
51 | license: LGPL
52 | license_file: LICENCE.txt
53 | summary: Alchemical free-energy calculations planner
54 |
--------------------------------------------------------------------------------
/devtools/travis-ci/install.sh:
--------------------------------------------------------------------------------
1 | MINICONDA=Miniconda3-latest-Linux-x86_64.sh
2 | MINICONDA_MD5=$(curl -s https://repo.continuum.io/miniconda/ | grep -A3 $MINICONDA | sed -n '4p' | sed -n 's/ *
\(.*\)<\/td> */\1/p')
3 | wget http://repo.continuum.io/miniconda/$MINICONDA
4 | if [[ $MINICONDA_MD5 != $(md5sum $MINICONDA | cut -d ' ' -f 1) ]]; then
5 | echo "Miniconda MD5 mismatch"
6 | exit 1
7 | fi
8 | bash $MINICONDA -b -p $HOME/miniconda
9 | PIP_ARGS="-U"
10 |
11 | export PATH=$HOME/miniconda/bin:$PATH
12 |
13 | conda install --yes pip
14 |
15 |
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/examples/example.py:
--------------------------------------------------------------------------------
1 | # Import lomap
2 | import lomap
3 | import sys
4 | import networkx as nx
5 |
6 |
7 | # Create the molecule database by using .mol2 files
8 | # The DBMolecule class must be created with a valid
9 | # directory name
10 |
11 | db_mol = lomap.DBMolecules('../test/basic/', output=True)
12 |
13 | # db_mol = lomap.DBMolecules('test/basic/', output=True, display=True)
14 |
15 |
16 | # Generate the strict and loose symmetric similarity
17 | # score matrices
18 |
19 | strict, loose = db_mol.build_matrices()
20 |
21 | # Convert the matrices in standard numpy matrices
22 |
23 | strict_numpy = strict.to_numpy_2D_array()
24 | loose_numpy = loose.to_numpy_2D_array()
25 |
26 |
27 | # Networkx graph generation based on the similarity
28 | # score matrices
29 |
30 | nx_graph = db_mol.build_graph()
31 | #print(nx_graph.edges(data=True))
32 |
33 |
34 | # Calculate the Maximum Common Subgraph (MCS) between
35 | # the first two molecules in the molecule database
36 | # ignoring hydrogens and depicting the mapping in a file
37 |
38 | MC = lomap.MCS.getMapping(db_mol[0].getMolecule(), db_mol[1].getMolecule(), hydrogens=False, fname='mcs.png')
39 |
--------------------------------------------------------------------------------
/examples/example_radial_graph.py:
--------------------------------------------------------------------------------
1 | # Import lomap
2 | import lomap
3 | import sys
4 | import networkx as nx
5 |
6 | # Create the molecule database by using .mol2 files
7 | # The DBMolecule class must be created with a valid
8 | # directory name
9 |
10 | db_mol = lomap.DBMolecules('../test/radial/', output=True, radial=True )
11 | #use the radial option with hub ligand set as
12 | #db_mol = lomap.DBMolecules('test/radial/', output=True, radial=True, hub="ejm_46.mol2")
13 |
14 | # Generate the strict and loose symmetric similarity
15 | # score matrices
16 |
17 | strict, loose = db_mol.build_matrices()
18 |
19 | # Convert the matrices in standard numpy matrices
20 |
21 | strict_numpy = strict.to_numpy_2D_array()
22 | loose_numpy = loose.to_numpy_2D_array()
23 |
24 |
25 | # Networkx graph generation based on the similarity
26 | # score matrices
27 |
28 | nx_graph = db_mol.build_graph()
29 | #print(nx_graph.edges(data=True))
30 |
31 |
32 | # Calculate the Maximum Common Subgraph (MCS) between
33 | # the first two molecules in the molecule database
34 | # ignoring hydrogens and depicting the mapping in a file
35 |
36 | MC = lomap.MCS.getMapping(db_mol[0].getMolecule(), db_mol[1].getMolecule(), hydrogens=False, fname='mcs.png')
37 |
--------------------------------------------------------------------------------
/lomap/__init__.py:
--------------------------------------------------------------------------------
1 | """
2 | Lomap2
3 | ======
4 |
5 | Alchemical free energy calculations hold increasing promise as an aid to drug
6 | discovery efforts. However, applications of these techniques in discovery
7 | projects have been relatively few, partly because of the difficulty of planning
8 | and setting up calculations. The Lead Optimization Mapper (LOMAP) is an
9 | automated algorithm to plan efficient relative free energy calculations between
10 | potential ligands within a substantial of compounds.
11 |
12 | Authors: Gaetano Calabro'
13 | David Mobley
14 |
15 |
16 | Licence: LGPL
17 |
18 | URL: https://github.com/nividic/Lomap
19 |
20 |
21 | Using
22 | -----
23 | Just write in Python
24 |
25 | # Import Lomap
26 | import lomap
27 |
28 | # Generate the molecule database starting from
29 | # a directory containing .mol2 files
30 |
31 | db_mol = lomap.DBMolecules("lomap/test/basic", output=True)
32 |
33 | # Calculate the similarity matrix betweeen the database
34 | # molecules. Two molecules are generated related to the
35 | # scrict rule and loose rule
36 |
37 | strict, loose = db_mol.build_matrices()
38 |
39 | # Generate the NetworkX graph and output the results
40 | nx_graph = db_mol.build_graph()
41 |
42 |
43 | # Calculate the Maximum Common Subgraph (MCS) between
44 | # the first two molecules in the molecule database
45 | # ignoring hydrogens and depicting the mapping in a file
46 |
47 | MC = lomap.MCS.getMapping(db_mol[0].getMolecule(), db_mol[1].getMolecule(), hydrogens=False, fname='mcs.png')
48 |
49 |
50 | # Alchemical transformation are usually performed between molecules with
51 | # the same charges. However, it is possible to allow these transformations
52 | # manually setting the electrostatic score for the whole set of molecules
53 | # producing a connected graph. The electrostatic scrore must be in the
54 | # range [0,1]
55 |
56 |
57 | db_mol = lomap.DBMolecules("python string pointing to a directory with mol2 files", output=True, ecrscore=0.1)
58 | strict, loose = db_mol.build_matrices()
59 | nx_graph = db_mol.build_graph()
60 | """
61 |
62 | from .dbmol import DBMolecules
63 | from .dbmol import SMatrix
64 | from .dbmol import Molecule
65 | from .mcs import MCS
66 |
67 | del dbmol
68 | del mcs
69 |
70 | from ._version import get_versions
71 | __version__ = get_versions()['version']
72 | del get_versions
73 |
--------------------------------------------------------------------------------
/lomap/fp.py:
--------------------------------------------------------------------------------
1 | # ******************
2 | # MODULE DOCSTRING
3 | # ******************
4 |
5 | """
6 |
7 | LOMAP: fingerprint calculations
8 | =====
9 |
10 | Alchemical free energy calculations hold increasing promise as an aid to drug
11 | discovery efforts. However, applications of these techniques in discovery
12 | projects have been relatively few, partly because of the difficulty of planning
13 | and setting up calculations. The Lead Optimization Mapper (LOMAP) is an
14 | automated algorithm to plan efficient relative free energy calculations between
15 | potential ligands within a substantial of compounds.
16 |
17 | """
18 |
19 | # *****************************************************************************
20 | # Lomap2: A toolkit to plan alchemical relative binding affinity calculations
21 | # Copyright 2015 - 2016 UC Irvine and the Authors
22 | #
23 | # Authors: Dr Gaetano Calabro' and Dr David Mobley
24 | #
25 | # This library is free software; you can redistribute it and/or
26 | # modify it under the terms of the GNU Lesser General Public
27 | # License as published by the Free Software Foundation; either
28 | # version 2.1 of the License, or (at your option) any later version.
29 | #
30 | # This library is distributed in the hope that it will be useful,
31 | # but WITHOUT ANY WARRANTY; without even the implied warranty of
32 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
33 | # Lesser General Public License for more details.
34 | #
35 | # You should have received a copy of the GNU Lesser General Public
36 | # License along with this library; if not, see http://www.gnu.org/licenses/
37 | # *****************************************************************************
38 |
39 |
40 | # ****************
41 | # MODULE IMPORTS
42 | # ****************
43 |
44 |
45 | from rdkit import Chem
46 | from rdkit.Chem import rdFMCS
47 | from rdkit.Chem import AllChem
48 | from rdkit.Chem.Draw.MolDrawing import DrawingOptions
49 | from rdkit.Chem import Draw
50 | from rdkit import DataStructs
51 | from rdkit.Chem.Fingerprints import FingerprintMols
52 | import sys
53 | import math
54 | from rdkit import RDLogger
55 | import logging
56 | import argparse
57 |
58 | # *******************************
59 | # Figureprint Class
60 | # *******************************
61 |
62 |
63 | __all__ = ['FIGUREPRINT']
64 |
65 |
66 | class Figureprint(object):
67 | """
68 |
69 | This class is used to compute the Maximum Common Subgraph (MCS) between two
70 | RDkit molecule objects and to score their similarity by using defined rules
71 |
72 | """
73 |
74 | def __init__(self, moli, molj):
75 | """
76 | Inizialization function
77 |
78 | Parameters
79 | ----------
80 |
81 | moli : RDKit molecule object
82 | the first molecule used to perform the Figureprint calculation
83 | molj : RDKit molecule object
84 | the second molecule used to perform the Figureprint calculation
85 | options : argparse python object
86 | the list of user options
87 |
88 | """
89 |
90 | # Set logging level and format
91 | logging.basicConfig(format='%(levelname)s:\t%(message)s', level=logging.INFO)
92 |
93 | # Local pointers to the passed molecules
94 | self.moli = moli
95 | self.molj = molj
96 |
97 | if not options.verbose == 'pedantic':
98 | lg = RDLogger.logger()
99 | lg.setLevel(RDLogger.CRITICAL)
100 |
101 | self.fps_moli = FingerprintMols.FingerprintMol(self.moli)
102 | self.fps_molj = FingerprintMols.FingerprintMol(self.molj)
103 | self.fps_tan = DataStructs.FingerprintSimilarity(self.fps_moli, self.fps_molj)
104 |
105 | def get_fps_tan(self):
106 | return self.fps_tan
107 |
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/setup.cfg:
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1 | [versioneer]
2 | # Automatic version numbering scheme
3 | VCS = git
4 | style = pep440
5 | versionfile_source = lomap/_version.py
6 | versionfile_build = lomap/_version.py
7 | tag_prefix = ''
8 |
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/setup.py:
--------------------------------------------------------------------------------
1 | """
2 | Setup script for Lomap2
3 |
4 | You can install lomap with
5 |
6 | python setup.py install
7 | """
8 |
9 | import sys,os
10 | from os.path import relpath, join
11 | import versioneer
12 |
13 | from setuptools import setup, find_packages
14 |
15 | if sys.argv[-1] == 'setup.py':
16 | print("To install, run 'python setup.py install'")
17 | print()
18 |
19 | if sys.version_info[:2] < (2, 7):
20 | print("Lomap requires Python 2.7 or later (%d.%d detected)." %
21 | sys.version_info[:2])
22 | sys.exit(-1)
23 |
24 |
25 | descr = """
26 | The Lead Optimization Mapper (LOMAP) is an automated algorithm
27 | to plan efficient relative free energy calculations between
28 | potential ligands within a substantial of compounds'
29 | """
30 |
31 | setup(
32 | name = 'lomap',
33 | version = versioneer.get_version(),
34 | cmdclass = versioneer.get_cmdclass(),
35 | description = 'Lead Optimization Mapper 2',
36 | long_description = descr,
37 | classifiers=[
38 | 'Development Status :: 3 - Alpha',
39 | 'Environment :: Console',
40 | 'Intended Audience :: Science/Research',
41 | 'Natural Language :: English',
42 | 'Operating System :: MacOS :: MacOS X',
43 | 'Operating System :: POSIX :: Linux',
44 | 'Programming Language :: Python :: 3.5',
45 | 'Topic :: Scientific/Engineering :: Bio-Informatics',
46 | 'Topic :: Scientific/Engineering :: Chemistry',
47 | 'Topic :: Scientific/Engineering :: Mathematics',
48 | 'Topic :: Scientific/Engineering :: Physics'
49 | ],
50 | keywords=[ 'alchemical free energy setup', 'perturbation network' ],
51 | url = 'https://github.com/MobleyLab/Lomap',
52 | author = 'Gaetano Calabro and David Mobley',
53 | maintainer = 'Antonia Mey and David Mobley',
54 | author_email = 'gcalabro -at- uci.edu',
55 | license = 'MIT',
56 | platforms = ['Linux-64', 'Mac OSX-64', 'Unix-64'],
57 | packages = find_packages()+['test'],
58 | include_package_data = True,
59 |
60 | entry_points = {'console_scripts':['lomap=lomap.dbmol:startup']},
61 | zip_safe = False
62 | )
63 |
64 |
--------------------------------------------------------------------------------
/test/basic/1,3,7-trimethylnaphthalene.mol2:
--------------------------------------------------------------------------------
1 | @MOLECULE
2 | *****
3 | 27 28 0 0 0
4 | SMALL
5 | GASTEIGER
6 |
7 | @ATOM
8 | 1 C 0.9251 0.1494 -0.0025 C.3 1 LIG1 -0.0397
9 | 2 C 2.4242 0.1552 0.0465 C.ar 1 LIG1 -0.0498
10 | 3 C 3.1297 -1.0574 0.0810 C.ar 1 LIG1 -0.0509
11 | 4 C 4.5422 -1.1042 0.1427 C.ar 1 LIG1 -0.0147
12 | 5 C 5.2861 -2.3145 0.1727 C.ar 1 LIG1 -0.0425
13 | 6 C 6.6903 -2.2735 0.2331 C.ar 1 LIG1 -0.0553
14 | 7 C 7.3760 -1.0578 0.2620 C.ar 1 LIG1 -0.0496
15 | 8 C 6.6436 0.1328 0.2358 C.ar 1 LIG1 -0.0511
16 | 9 C 5.2413 0.1261 0.1765 C.ar 1 LIG1 -0.0174
17 | 10 C 4.5298 1.3362 0.1522 C.ar 1 LIG1 -0.0538
18 | 11 C 3.1361 1.3519 0.0914 C.ar 1 LIG1 -0.0582
19 | 12 C 8.8737 -1.0147 0.3281 C.3 1 LIG1 -0.0397
20 | 13 C 4.6094 -3.6603 0.1443 C.3 1 LIG1 -0.0391
21 | 14 H 0.5282 1.1476 -0.2149 H 1 LIG1 0.0278
22 | 15 H 0.5194 -0.1845 0.9575 H 1 LIG1 0.0278
23 | 16 H 0.5728 -0.5198 -0.7944 H 1 LIG1 0.0278
24 | 17 H 2.5577 -1.9826 0.0575 H 1 LIG1 0.0626
25 | 18 H 7.2540 -3.2043 0.2569 H 1 LIG1 0.0623
26 | 19 H 7.1781 1.0810 0.2619 H 1 LIG1 0.0626
27 | 20 H 5.0603 2.2854 0.1820 H 1 LIG1 0.0624
28 | 21 H 2.6157 2.3065 0.0777 H 1 LIG1 0.0620
29 | 22 H 9.3069 -2.0200 0.3015 H 1 LIG1 0.0278
30 | 23 H 9.1960 -0.5332 1.2567 H 1 LIG1 0.0278
31 | 24 H 9.2731 -0.4567 -0.5249 H 1 LIG1 0.0278
32 | 25 H 5.3371 -4.4789 0.1591 H 1 LIG1 0.0278
33 | 26 H 4.0157 -3.7691 -0.7690 H 1 LIG1 0.0278
34 | 27 H 3.9645 -3.7798 1.0209 H 1 LIG1 0.0278
35 | @BOND
36 | 1 6 7 ar
37 | 2 5 6 ar
38 | 3 7 8 ar
39 | 4 8 9 ar
40 | 5 9 10 ar
41 | 6 4 9 ar
42 | 7 10 11 ar
43 | 8 2 11 ar
44 | 9 2 3 ar
45 | 10 3 4 ar
46 | 11 4 5 ar
47 | 12 1 2 1
48 | 13 5 13 1
49 | 14 7 12 1
50 | 15 1 14 1
51 | 16 1 15 1
52 | 17 1 16 1
53 | 18 3 17 1
54 | 19 6 18 1
55 | 20 8 19 1
56 | 21 10 20 1
57 | 22 11 21 1
58 | 23 12 22 1
59 | 24 12 23 1
60 | 25 12 24 1
61 | 26 13 25 1
62 | 27 13 26 1
63 | 28 13 27 1
64 |
--------------------------------------------------------------------------------
/test/basic/1-butyl-4-methylbenzene.mol2:
--------------------------------------------------------------------------------
1 | @MOLECULE
2 | *****
3 | 27 27 0 0 0
4 | SMALL
5 | GASTEIGER
6 |
7 | @ATOM
8 | 1 C 1.9899 -1.5496 1.4095 C.3 1 LIG1 -0.0653
9 | 2 C 3.0612 -0.6401 0.8303 C.3 1 LIG1 -0.0556
10 | 3 C 3.5100 0.4139 1.8419 C.3 1 LIG1 -0.0493
11 | 4 C 4.5859 1.3256 1.2470 C.3 1 LIG1 -0.0277
12 | 5 C 5.0777 2.3433 2.2464 C.ar 1 LIG1 -0.0473
13 | 6 C 4.4793 3.6056 2.3316 C.ar 1 LIG1 -0.0583
14 | 7 C 4.9350 4.5439 3.2608 C.ar 1 LIG1 -0.0586
15 | 8 C 5.9858 4.2317 4.1299 C.ar 1 LIG1 -0.0504
16 | 9 C 6.5860 2.9711 4.0431 C.ar 1 LIG1 -0.0586
17 | 10 C 6.1309 2.0320 3.1146 C.ar 1 LIG1 -0.0583
18 | 11 C 6.4975 5.2565 5.0979 C.3 1 LIG1 -0.0397
19 | 12 H 1.6931 -2.3034 0.6726 H 1 LIG1 0.0230
20 | 13 H 1.0980 -0.9785 1.6885 H 1 LIG1 0.0230
21 | 14 H 2.3560 -2.0720 2.3000 H 1 LIG1 0.0230
22 | 15 H 2.6700 -0.1517 -0.0688 H 1 LIG1 0.0263
23 | 16 H 3.9190 -1.2484 0.5229 H 1 LIG1 0.0263
24 | 17 H 3.8957 -0.0824 2.7418 H 1 LIG1 0.0268
25 | 18 H 2.6473 1.0144 2.1583 H 1 LIG1 0.0268
26 | 19 H 4.1939 1.8426 0.3620 H 1 LIG1 0.0313
27 | 20 H 5.4358 0.7279 0.8940 H 1 LIG1 0.0313
28 | 21 H 3.6566 3.8691 1.6710 H 1 LIG1 0.0620
29 | 22 H 4.4634 5.5233 3.3010 H 1 LIG1 0.0620
30 | 23 H 7.4138 2.7097 4.6988 H 1 LIG1 0.0620
31 | 24 H 6.6080 1.0557 3.0700 H 1 LIG1 0.0620
32 | 25 H 7.0175 4.7827 5.9374 H 1 LIG1 0.0278
33 | 26 H 5.6710 5.8412 5.5155 H 1 LIG1 0.0278
34 | 27 H 7.1937 5.9336 4.5926 H 1 LIG1 0.0278
35 | @BOND
36 | 1 5 6 ar
37 | 2 6 7 ar
38 | 3 5 10 ar
39 | 4 9 10 ar
40 | 5 8 9 ar
41 | 6 7 8 ar
42 | 7 1 2 1
43 | 8 2 3 1
44 | 9 3 4 1
45 | 10 4 5 1
46 | 11 8 11 1
47 | 12 1 12 1
48 | 13 1 13 1
49 | 14 1 14 1
50 | 15 2 15 1
51 | 16 2 16 1
52 | 17 3 17 1
53 | 18 3 18 1
54 | 19 4 19 1
55 | 20 4 20 1
56 | 21 6 21 1
57 | 22 7 22 1
58 | 23 9 23 1
59 | 24 10 24 1
60 | 25 11 25 1
61 | 26 11 26 1
62 | 27 11 27 1
63 |
--------------------------------------------------------------------------------
/test/basic/2,6-dimethylnaphthalene.mol2:
--------------------------------------------------------------------------------
1 | @MOLECULE
2 | *****
3 | 24 25 0 0 0
4 | SMALL
5 | GASTEIGER
6 |
7 | @ATOM
8 | 1 C 0.8817 -0.0759 0.0737 C.3 1 LIG1 -0.0397
9 | 2 C 2.3811 -0.0540 0.0354 C.ar 1 LIG1 -0.0499
10 | 3 C 3.0834 1.1532 0.0347 C.ar 1 LIG1 -0.0582
11 | 4 C 4.4799 1.1582 -0.0011 C.ar 1 LIG1 -0.0538
12 | 5 C 5.2032 -0.0442 -0.0356 C.ar 1 LIG1 -0.0176
13 | 6 C 6.6087 -0.0550 -0.0772 C.ar 1 LIG1 -0.0511
14 | 7 C 7.3242 -1.2594 -0.1176 C.ar 1 LIG1 -0.0499
15 | 8 C 8.8235 -1.2393 -0.1486 C.3 1 LIG1 -0.0397
16 | 9 C 6.6224 -2.4667 -0.0984 C.ar 1 LIG1 -0.0582
17 | 10 C 5.2258 -2.4717 -0.0573 C.ar 1 LIG1 -0.0538
18 | 11 C 4.5024 -1.2692 -0.0283 C.ar 1 LIG1 -0.0176
19 | 12 C 3.0971 -1.2586 0.0081 C.ar 1 LIG1 -0.0511
20 | 13 H 0.4638 0.9355 0.0362 H 1 LIG1 0.0278
21 | 14 H 0.5354 -0.5508 0.9973 H 1 LIG1 0.0278
22 | 15 H 0.4903 -0.6304 -0.7856 H 1 LIG1 0.0278
23 | 16 H 2.5515 2.1015 0.0601 H 1 LIG1 0.0620
24 | 17 H 5.0016 2.1125 -0.0033 H 1 LIG1 0.0624
25 | 18 H 7.1539 0.8869 -0.0807 H 1 LIG1 0.0626
26 | 19 H 9.2330 -2.2332 -0.3578 H 1 LIG1 0.0278
27 | 20 H 9.2150 -0.9034 0.8167 H 1 LIG1 0.0278
28 | 21 H 9.1785 -0.5651 -0.9354 H 1 LIG1 0.0278
29 | 22 H 7.1546 -3.4149 -0.1177 H 1 LIG1 0.0620
30 | 23 H 4.7045 -3.4261 -0.0479 H 1 LIG1 0.0624
31 | 24 H 2.5515 -2.2003 0.0134 H 1 LIG1 0.0626
32 | @BOND
33 | 1 2 3 ar
34 | 2 3 4 ar
35 | 3 2 12 ar
36 | 4 11 12 ar
37 | 5 10 11 ar
38 | 6 5 11 ar
39 | 7 9 10 ar
40 | 8 7 9 ar
41 | 9 6 7 ar
42 | 10 5 6 ar
43 | 11 4 5 ar
44 | 12 1 2 1
45 | 13 7 8 1
46 | 14 1 13 1
47 | 15 1 14 1
48 | 16 1 15 1
49 | 17 3 16 1
50 | 18 4 17 1
51 | 19 6 18 1
52 | 20 8 19 1
53 | 21 8 20 1
54 | 22 8 21 1
55 | 23 9 22 1
56 | 24 10 23 1
57 | 25 12 24 1
58 |
--------------------------------------------------------------------------------
/test/basic/2-methyl-6-propylnaphthalene.mol2:
--------------------------------------------------------------------------------
1 | @MOLECULE
2 | *****
3 | 30 31 0 0 0
4 | SMALL
5 | GASTEIGER
6 |
7 | @ATOM
8 | 1 C 0.7969 1.3147 -1.5722 C.3 1 LIG1 -0.0650
9 | 2 C 2.3162 1.3551 -1.5843 C.3 1 LIG1 -0.0519
10 | 3 C 2.8874 1.3784 -0.1657 C.3 1 LIG1 -0.0279
11 | 4 C 4.3949 1.4239 -0.1763 C.ar 1 LIG1 -0.0468
12 | 5 C 5.1419 0.2376 -0.2084 C.ar 1 LIG1 -0.0508
13 | 6 C 6.5466 0.2630 -0.2482 C.ar 1 LIG1 -0.0176
14 | 7 C 7.2164 1.5056 -0.2598 C.ar 1 LIG1 -0.0176
15 | 8 C 6.4634 2.6893 -0.2285 C.ar 1 LIG1 -0.0538
16 | 9 C 5.0678 2.6494 -0.1901 C.ar 1 LIG1 -0.0580
17 | 10 C 8.6208 1.5306 -0.3057 C.ar 1 LIG1 -0.0511
18 | 11 C 9.3673 0.3447 -0.3470 C.ar 1 LIG1 -0.0499
19 | 12 C 8.6960 -0.8804 -0.3232 C.ar 1 LIG1 -0.0582
20 | 13 C 7.3000 -0.9207 -0.2780 C.ar 1 LIG1 -0.0538
21 | 14 C 10.8656 0.4019 -0.3796 C.3 1 LIG1 -0.0397
22 | 15 H 0.4106 1.2994 -2.5961 H 1 LIG1 0.0230
23 | 16 H 0.3854 2.1942 -1.0670 H 1 LIG1 0.0230
24 | 17 H 0.4325 0.4199 -1.0579 H 1 LIG1 0.0230
25 | 18 H 2.6477 2.2415 -2.1391 H 1 LIG1 0.0266
26 | 19 H 2.6945 0.4813 -2.1292 H 1 LIG1 0.0266
27 | 20 H 2.5534 0.4943 0.3922 H 1 LIG1 0.0313
28 | 21 H 2.5001 2.2454 0.3843 H 1 LIG1 0.0313
29 | 22 H 4.6215 -0.7184 -0.2065 H 1 LIG1 0.0626
30 | 23 H 6.9606 3.6568 -0.2384 H 1 LIG1 0.0624
31 | 24 H 4.5102 3.5829 -0.1747 H 1 LIG1 0.0620
32 | 25 H 9.1424 2.4858 -0.3125 H 1 LIG1 0.0626
33 | 26 H 9.2523 -1.8147 -0.3422 H 1 LIG1 0.0620
34 | 27 H 6.8033 -1.8881 -0.2657 H 1 LIG1 0.0624
35 | 28 H 11.2977 -0.5759 -0.6162 H 1 LIG1 0.0278
36 | 29 H 11.2498 0.7216 0.5938 H 1 LIG1 0.0278
37 | 30 H 11.2028 1.1048 -1.1483 H 1 LIG1 0.0278
38 | @BOND
39 | 1 4 9 ar
40 | 2 8 9 ar
41 | 3 4 5 ar
42 | 4 5 6 ar
43 | 5 6 13 ar
44 | 6 6 7 ar
45 | 7 12 13 ar
46 | 8 11 12 ar
47 | 9 10 11 ar
48 | 10 7 10 ar
49 | 11 7 8 ar
50 | 12 1 2 1
51 | 13 2 3 1
52 | 14 3 4 1
53 | 15 11 14 1
54 | 16 1 15 1
55 | 17 1 16 1
56 | 18 1 17 1
57 | 19 2 18 1
58 | 20 2 19 1
59 | 21 3 20 1
60 | 22 3 21 1
61 | 23 5 22 1
62 | 24 8 23 1
63 | 25 9 24 1
64 | 26 10 25 1
65 | 27 12 26 1
66 | 28 13 27 1
67 | 29 14 28 1
68 | 30 14 29 1
69 | 31 14 30 1
70 |
--------------------------------------------------------------------------------
/test/basic/2-methylnaphthalene.mol2:
--------------------------------------------------------------------------------
1 | @MOLECULE
2 | *****
3 | 21 22 0 0 0
4 | SMALL
5 | GASTEIGER
6 |
7 | @ATOM
8 | 1 C 0.9750 -0.0348 0.0833 C.3 1 LIG1 -0.0397
9 | 2 C 2.4749 -0.0532 0.0754 C.ar 1 LIG1 -0.0499
10 | 3 C 3.2098 1.1400 0.0597 C.ar 1 LIG1 -0.0511
11 | 4 C 4.6141 1.1264 -0.0127 C.ar 1 LIG1 -0.0176
12 | 5 C 5.3554 2.3190 -0.0614 C.ar 1 LIG1 -0.0540
13 | 6 C 6.7465 2.2894 -0.1768 C.ar 1 LIG1 -0.0612
14 | 7 C 7.4142 1.0702 -0.2321 C.ar 1 LIG1 -0.0612
15 | 8 C 6.6939 -0.1236 -0.1628 C.ar 1 LIG1 -0.0540
16 | 9 C 5.2934 -0.1107 -0.0560 C.ar 1 LIG1 -0.0179
17 | 10 C 4.5528 -1.3018 -0.0057 C.ar 1 LIG1 -0.0538
18 | 11 C 3.1574 -1.2723 0.0551 C.ar 1 LIG1 -0.0582
19 | 12 H 0.5850 0.9882 0.1017 H 1 LIG1 0.0278
20 | 13 H 0.5915 -0.5586 0.9643 H 1 LIG1 0.0278
21 | 14 H 0.5924 -0.5209 -0.8204 H 1 LIG1 0.0278
22 | 15 H 2.6835 2.0917 0.0844 H 1 LIG1 0.0626
23 | 16 H 4.8512 3.2813 -0.0218 H 1 LIG1 0.0624
24 | 17 H 7.3059 3.2198 -0.2301 H 1 LIG1 0.0618
25 | 18 H 8.4962 1.0459 -0.3322 H 1 LIG1 0.0618
26 | 19 H 7.2331 -1.0669 -0.2063 H 1 LIG1 0.0624
27 | 20 H 5.0575 -2.2644 -0.0289 H 1 LIG1 0.0624
28 | 21 H 2.6062 -2.2099 0.0730 H 1 LIG1 0.0620
29 | @BOND
30 | 1 1 2 1
31 | 2 2 3 ar
32 | 3 3 4 ar
33 | 4 4 5 ar
34 | 5 5 6 ar
35 | 6 6 7 ar
36 | 7 7 8 ar
37 | 8 8 9 ar
38 | 9 4 9 ar
39 | 10 9 10 ar
40 | 11 10 11 ar
41 | 12 2 11 ar
42 | 13 1 12 1
43 | 14 1 13 1
44 | 15 1 14 1
45 | 16 3 15 1
46 | 17 5 16 1
47 | 18 6 17 1
48 | 19 7 18 1
49 | 20 8 19 1
50 | 21 10 20 1
51 | 22 11 21 1
52 |
--------------------------------------------------------------------------------
/test/basic/2-naftanol.mol2:
--------------------------------------------------------------------------------
1 | @MOLECULE
2 | *****
3 | 19 20 0 0 0
4 | SMALL
5 | GASTEIGER
6 |
7 | @ATOM
8 | 1 O 9.9477 -4.1875 1.4569 O.3 1 LIG1 -0.5067
9 | 2 C 9.0676 -3.1850 1.1716 C.ar 1 LIG1 0.1175
10 | 3 C 7.7820 -3.1808 1.6974 C.ar 1 LIG1 -0.0196
11 | 4 C 6.9153 -2.1329 1.3798 C.ar 1 LIG1 -0.0506
12 | 5 C 7.3294 -1.0867 0.5375 C.ar 1 LIG1 -0.0177
13 | 6 C 6.4703 -0.0252 0.2106 C.ar 1 LIG1 -0.0540
14 | 7 C 6.8977 1.0066 -0.6271 C.ar 1 LIG1 -0.0612
15 | 8 C 8.1878 0.9906 -1.1489 C.ar 1 LIG1 -0.0612
16 | 9 C 9.0548 -0.0574 -0.8344 C.ar 1 LIG1 -0.0539
17 | 10 C 8.6411 -1.1023 0.0071 C.ar 1 LIG1 -0.0144
18 | 11 C 9.5008 -2.1625 0.3346 C.ar 1 LIG1 -0.0125
19 | 12 H 9.5144 -4.8197 2.0534 H 1 LIG1 0.2921
20 | 13 H 7.4363 -3.9757 2.3505 H 1 LIG1 0.0654
21 | 14 H 5.9102 -2.1360 1.7951 H 1 LIG1 0.0625
22 | 15 H 5.4583 0.0059 0.6080 H 1 LIG1 0.0624
23 | 16 H 6.2223 1.8225 -0.8713 H 1 LIG1 0.0618
24 | 17 H 8.5216 1.7931 -1.8011 H 1 LIG1 0.0618
25 | 18 H 10.0593 -0.0532 -1.2512 H 1 LIG1 0.0624
26 | 19 H 10.5134 -2.1967 -0.0603 H 1 LIG1 0.0660
27 | @BOND
28 | 1 2 3 ar
29 | 2 2 11 ar
30 | 3 3 4 ar
31 | 4 4 5 ar
32 | 5 5 6 ar
33 | 6 5 10 ar
34 | 7 6 7 ar
35 | 8 7 8 ar
36 | 9 8 9 ar
37 | 10 9 10 ar
38 | 11 10 11 ar
39 | 12 1 2 1
40 | 13 1 12 1
41 | 14 3 13 1
42 | 15 4 14 1
43 | 16 6 15 1
44 | 17 7 16 1
45 | 18 8 17 1
46 | 19 9 18 1
47 | 20 11 19 1
48 |
--------------------------------------------------------------------------------
/test/basic/chlorophenyl.sdf:
--------------------------------------------------------------------------------
1 | chlorophenyl
2 | xed2sdf_05210316543D
3 |
4 | 18 18 0 0 0 0 0 0 0 0999 V2000
5 | -0.2078 1.4341 0.0950 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | 1.0621 0.9009 0.0874 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | 1.2340 -0.4650 0.0630 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 0.1359 -1.2932 0.0457 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | -1.1320 -0.7566 0.0534 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | -1.3107 0.6105 0.0784 C 0 0 0 0 0 0 0 0 0 0 0 0
11 | -2.6779 1.2763 0.0882 C 0 0 0 0 0 0 0 0 0 0 0 0
12 | 2.4475 1.9524 0.1083 Cl 0 0 0 0 0 0 0 0 0 0 0 0
13 | -3.9112 0.3543 0.0807 C 0 0 0 0 0 0 0 0 0 0 0 0
14 | -0.3295 2.4266 0.1128 H 0 0 0 0 0 0 0 0 0 0 0 0
15 | 2.1553 -0.8540 0.0577 H 0 0 0 0 0 0 0 0 0 0 0 0
16 | -1.9279 -1.3621 0.0406 H 0 0 0 0 0 0 0 0 0 0 0 0
17 | 0.2588 -2.2856 0.0273 H 0 0 0 0 0 0 0 0 0 0 0 0
18 | -2.7414 1.9674 1.0669 H 0 0 0 0 0 0 0 0 0 0 0 0
19 | -2.7452 1.9886 -0.8751 H 0 0 0 0 0 0 0 0 0 0 0 0
20 | -4.9067 1.0246 0.0934 H 0 0 0 0 0 0 0 0 0 0 0 0
21 | -3.9009 -0.3248 -0.9085 H 0 0 0 0 0 0 0 0 0 0 0 0
22 | -3.8935 -0.3513 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0
23 | 1 6 2 0
24 | 2 1 1 0
25 | 2 8 1 0
26 | 3 2 2 0
27 | 4 3 1 0
28 | 5 4 2 0
29 | 6 5 1 0
30 | 6 7 1 0
31 | 7 9 1 0
32 | 1 10 1 0
33 | 3 11 1 0
34 | 4 13 1 0
35 | 5 12 1 0
36 | 7 14 1 0
37 | 7 15 1 0
38 | 9 16 1 0
39 | 9 17 1 0
40 | 9 18 1 0
41 | M END
42 | >
43 | false
44 |
45 | >
46 | 0.500
47 |
48 | >
49 | 0
50 |
51 | >
52 | 0
53 |
54 | >
55 | 140.6
56 |
57 | > <#Atoms_cresset>
58 | 9
59 |
60 | >
61 | 2.9
62 |
63 | >
64 | 0
65 |
66 | >
67 | 1
68 |
69 | >
70 | 0
71 |
72 | > <_cresset_fieldpoints>
73 | -5 -0.094680 0.222177 -2.835047 -4.4581
74 | -5 -0.106375 0.113757 2.978022 -4.4593
75 | -5 1.510659 4.458917 0.152585 -1.6575
76 | -5 4.616120 0.384842 0.081066 -1.6555
77 | -6 -1.778282 4.242813 0.142253 2.0977
78 | -6 2.229008 -3.559570 0.011913 2.1330
79 | -6 -1.889942 -3.774020 -0.000153 2.3037
80 | -6 -4.416456 3.826114 0.131633 1.5745
81 | -6 -3.468552 -2.916028 0.008702 2.4074
82 | -7 -1.817315 4.429328 0.113080 -1.4787
83 | -7 -0.372788 0.191227 3.299193 -1.9188
84 | -7 1.313214 2.027709 -2.951936 -1.4564
85 | -7 2.712362 -3.511066 -0.038950 -0.9773
86 | -7 -3.744973 -2.950735 0.051607 -1.4580
87 | -7 -4.713938 3.772743 0.128011 -1.1435
88 | -7 -2.157252 0.189870 -3.072170 -1.9199
89 | -7 -0.352324 0.309023 -3.153058 -1.9175
90 | -7 -2.126824 0.100978 3.215595 -1.9246
91 | -8 -0.041996 0.074380 0.068595 7.1954
92 | -8 1.239143 1.041456 0.093815 5.6090
93 | -8 -2.370005 0.207171 0.070073 5.5944
94 |
95 | $$$$
96 |
--------------------------------------------------------------------------------
/test/basic/methylcyclohexane.mol2:
--------------------------------------------------------------------------------
1 | @MOLECULE
2 | *****
3 | 21 21 0 0 0
4 | SMALL
5 | GASTEIGER
6 |
7 | @ATOM
8 | 1 C 0.9730 0.1554 0.1412 C.3 1 LIG1 -0.0624
9 | 2 C 2.4934 0.1043 -0.0303 C.3 1 LIG1 -0.0439
10 | 3 C 2.9737 -1.3048 -0.4072 C.3 1 LIG1 -0.0505
11 | 4 C 2.6388 -1.6853 -1.8487 C.3 1 LIG1 -0.0528
12 | 5 C 3.1458 -0.6424 -2.8397 C.3 1 LIG1 -0.0530
13 | 6 C 2.6503 0.7581 -2.4959 C.3 1 LIG1 -0.0528
14 | 7 C 2.9839 1.1382 -1.0536 C.3 1 LIG1 -0.0505
15 | 8 H 0.6557 1.1542 0.4607 H 1 LIG1 0.0232
16 | 9 H 0.6478 -0.5562 0.9081 H 1 LIG1 0.0232
17 | 10 H 0.4392 -0.0840 -0.7835 H 1 LIG1 0.0232
18 | 11 H 2.9316 0.3596 0.9431 H 1 LIG1 0.0298
19 | 12 H 2.5484 -2.0480 0.2778 H 1 LIG1 0.0268
20 | 13 H 4.0632 -1.3509 -0.2778 H 1 LIG1 0.0268
21 | 14 H 3.0861 -2.6588 -2.0822 H 1 LIG1 0.0265
22 | 15 H 1.5550 -1.8040 -1.9616 H 1 LIG1 0.0265
23 | 16 H 4.2430 -0.6482 -2.8423 H 1 LIG1 0.0265
24 | 17 H 2.8244 -0.9091 -3.8522 H 1 LIG1 0.0265
25 | 18 H 3.1052 1.4851 -3.1790 H 1 LIG1 0.0265
26 | 19 H 1.5667 0.8148 -2.6555 H 1 LIG1 0.0265
27 | 20 H 4.0736 1.2348 -0.9613 H 1 LIG1 0.0268
28 | 21 H 2.5648 2.1260 -0.8271 H 1 LIG1 0.0268
29 | @BOND
30 | 1 2 7 1
31 | 2 2 3 1
32 | 3 6 7 1
33 | 4 5 6 1
34 | 5 4 5 1
35 | 6 3 4 1
36 | 7 1 2 1
37 | 8 1 8 1
38 | 9 1 9 1
39 | 10 1 10 1
40 | 11 2 11 1
41 | 12 3 12 1
42 | 13 3 13 1
43 | 14 4 14 1
44 | 15 4 15 1
45 | 16 5 16 1
46 | 17 5 17 1
47 | 18 6 18 1
48 | 19 6 19 1
49 | 20 7 20 1
50 | 21 7 21 1
51 |
--------------------------------------------------------------------------------
/test/basic/molecules.gpickle:
--------------------------------------------------------------------------------
1 | ccopy_reg
2 | _reconstructor
3 | p0
4 | (cnetworkx.classes.graph
5 | Graph
6 | p1
7 | c__builtin__
8 | object
9 | p2
10 | Ntp3
11 | Rp4
12 | (dp5
13 | S'adjlist_inner_dict_factory'
14 | p6
15 | c__builtin__
16 | dict
17 | p7
18 | sS'node_dict_factory'
19 | p8
20 | g7
21 | sS'edge_attr_dict_factory'
22 | p9
23 | g7
24 | sS'_node'
25 | p10
26 | (dp11
27 | I0
28 | (dp12
29 | S'fname_comp'
30 | p13
31 | S'1,3,7-trimethylnaphthalene.mol2'
32 | p14
33 | sS'ID'
34 | p15
35 | I0
36 | ssI1
37 | (dp16
38 | g13
39 | S'1-butyl-4-methylbenzene.mol2'
40 | p17
41 | sg15
42 | I1
43 | ssI2
44 | (dp18
45 | g13
46 | S'2,6-dimethylnaphthalene.mol2'
47 | p19
48 | sg15
49 | I2
50 | ssI3
51 | (dp20
52 | g13
53 | S'2-methyl-6-propylnaphthalene.mol2'
54 | p21
55 | sg15
56 | I3
57 | ssI4
58 | (dp22
59 | g13
60 | S'2-methylnaphthalene.mol2'
61 | p23
62 | sg15
63 | I4
64 | ssI5
65 | (dp24
66 | g13
67 | S'2-naftanol.mol2'
68 | p25
69 | sg15
70 | I5
71 | ssI6
72 | (dp26
73 | g13
74 | S'methylcyclohexane.mol2'
75 | p27
76 | sg15
77 | I6
78 | ssI7
79 | (dp28
80 | g13
81 | S'toluene.mol2'
82 | p29
83 | sg15
84 | I7
85 | sssS'graph'
86 | p30
87 | (dp31
88 | sS'root_graph'
89 | p32
90 | g4
91 | sS'_adj'
92 | p33
93 | (dp34
94 | I0
95 | (dp35
96 | I2
97 | (dp36
98 | S'strict_flag'
99 | p37
100 | I01
101 | sS'similarity'
102 | p38
103 | cnumpy.core.multiarray
104 | scalar
105 | p39
106 | (cnumpy
107 | dtype
108 | p40
109 | (S'f8'
110 | p41
111 | I0
112 | I1
113 | tp42
114 | Rp43
115 | (I3
116 | S'<'
117 | p44
118 | NNNI-1
119 | I-1
120 | I0
121 | tp45
122 | bS':+\xd5\x99m\xf4\xec?'
123 | p46
124 | tp47
125 | Rp48
126 | ssI5
127 | (dp49
128 | g37
129 | I01
130 | sg38
131 | g39
132 | (g43
133 | S'Ya\x16\xd6\n3\xea?'
134 | p50
135 | tp51
136 | Rp52
137 | sssI1
138 | (dp53
139 | I6
140 | (dp54
141 | g37
142 | I01
143 | sg38
144 | g39
145 | (g43
146 | S'\xeepr\x06Cs\xe5?'
147 | p55
148 | tp56
149 | Rp57
150 | ssI7
151 | (dp58
152 | g37
153 | I01
154 | sg38
155 | g39
156 | (g43
157 | S'\xeepr\x06Cs\xe5?'
158 | p59
159 | tp60
160 | Rp61
161 | sssI2
162 | (dp62
163 | I0
164 | g36
165 | sI3
166 | (dp63
167 | g37
168 | I01
169 | sg38
170 | g39
171 | (g43
172 | S'Ya\x16\xd6\n3\xea?'
173 | p64
174 | tp65
175 | Rp66
176 | ssI4
177 | (dp67
178 | g37
179 | I01
180 | sg38
181 | g39
182 | (g43
183 | S':+\xd5\x99m\xf4\xec?'
184 | p68
185 | tp69
186 | Rp70
187 | sssI3
188 | (dp71
189 | I2
190 | g63
191 | sI5
192 | (dp72
193 | g37
194 | I01
195 | sg38
196 | g39
197 | (g43
198 | S'\x05|\xc3i\xc8\xb4\xe7?'
199 | p73
200 | tp74
201 | Rp75
202 | sssI4
203 | (dp76
204 | I2
205 | g67
206 | sI5
207 | (dp77
208 | g37
209 | I01
210 | sg38
211 | g39
212 | (g43
213 | S'\x00\x00\x00\x00\x00\x00\xf0?'
214 | p78
215 | tp79
216 | Rp80
217 | ssI7
218 | (dp81
219 | g37
220 | I00
221 | sg38
222 | g39
223 | (g43
224 | S'\xeepr\x06Cs\xe5?'
225 | p82
226 | tp83
227 | Rp84
228 | sssI5
229 | (dp85
230 | I0
231 | g49
232 | sI3
233 | g72
234 | sI4
235 | g77
236 | sI7
237 | (dp86
238 | g37
239 | I00
240 | sg38
241 | g39
242 | (g43
243 | S'\xeepr\x06Cs\xe5?'
244 | p87
245 | tp88
246 | Rp89
247 | sssI6
248 | (dp90
249 | I1
250 | g54
251 | sI7
252 | (dp91
253 | g37
254 | I01
255 | sg38
256 | g39
257 | (g43
258 | S'\x00\x00\x00\x00\x00\x00\xf0?'
259 | p92
260 | tp93
261 | Rp94
262 | sssI7
263 | (dp95
264 | I1
265 | g58
266 | sI4
267 | g81
268 | sI5
269 | g86
270 | sI6
271 | g91
272 | sssS'adjlist_outer_dict_factory'
273 | p96
274 | g7
275 | sb.
--------------------------------------------------------------------------------
/test/basic/toluene.mol2:
--------------------------------------------------------------------------------
1 | @MOLECULE
2 | *****
3 | 15 15 0 0 0
4 | SMALL
5 | GASTEIGER
6 |
7 | @ATOM
8 | 1 C 0.9562 0.0874 0.1225 C.3 1 LIG1 -0.0397
9 | 2 C 2.4532 0.1169 0.0327 C.ar 1 LIG1 -0.0504
10 | 3 C 3.1480 1.3313 -0.0192 C.ar 1 LIG1 -0.0588
11 | 4 C 4.5410 1.3447 -0.1106 C.ar 1 LIG1 -0.0615
12 | 5 C 5.2502 0.1457 -0.1538 C.ar 1 LIG1 -0.0617
13 | 6 C 4.5672 -1.0681 -0.1065 C.ar 1 LIG1 -0.0615
14 | 7 C 3.1745 -1.0830 -0.0148 C.ar 1 LIG1 -0.0588
15 | 8 H 0.5405 1.0944 0.2295 H 1 LIG1 0.0278
16 | 9 H 0.6412 -0.4972 0.9928 H 1 LIG1 0.0278
17 | 10 H 0.5343 -0.3590 -0.7834 H 1 LIG1 0.0278
18 | 11 H 2.6097 2.2757 0.0116 H 1 LIG1 0.0620
19 | 12 H 5.0726 2.2915 -0.1488 H 1 LIG1 0.0618
20 | 13 H 6.3343 0.1573 -0.2252 H 1 LIG1 0.0618
21 | 14 H 5.1186 -2.0039 -0.1418 H 1 LIG1 0.0618
22 | 15 H 2.6530 -2.0368 0.0195 H 1 LIG1 0.0620
23 | @BOND
24 | 1 2 3 ar
25 | 2 3 4 ar
26 | 3 2 7 ar
27 | 4 6 7 ar
28 | 5 5 6 ar
29 | 6 4 5 ar
30 | 7 1 2 1
31 | 8 1 8 1
32 | 9 1 9 1
33 | 10 1 10 1
34 | 11 3 11 1
35 | 12 4 12 1
36 | 13 5 13 1
37 | 14 6 14 1
38 | 15 7 15 1
39 |
--------------------------------------------------------------------------------
/test/basic/toluyl.sdf:
--------------------------------------------------------------------------------
1 | toluyl
2 | xed2sdf_05210316543D
3 |
4 | 21 21 0 0 0 0 0 0 0 0999 V2000
5 | -0.1287 1.4436 0.1374 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | 1.1199 0.8649 0.1388 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | 1.2396 -0.5053 0.0866 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 0.1122 -1.2920 0.0314 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | -1.1344 -0.7088 0.0291 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | -1.2615 0.6632 0.0829 C 0 0 0 0 0 0 0 0 0 0 0 0
11 | -2.6032 1.3787 0.0842 C 0 0 0 0 0 0 0 0 0 0 0 0
12 | -3.8657 0.4974 0.1005 C 0 0 0 0 0 0 0 0 0 0 0 0
13 | 2.3483 1.7493 0.2016 C 0 0 0 0 0 0 0 0 0 0 0 0
14 | -0.2139 2.4390 0.1765 H 0 0 0 0 0 0 0 0 0 0 0 0
15 | 2.1454 -0.9288 0.0884 H 0 0 0 0 0 0 0 0 0 0 0 0
16 | -1.9522 -1.2830 -0.0112 H 0 0 0 0 0 0 0 0 0 0 0 0
17 | 0.1985 -2.2876 -0.0070 H 0 0 0 0 0 0 0 0 0 0 0 0
18 | -2.6373 2.0884 1.0514 H 0 0 0 0 0 0 0 0 0 0 0 0
19 | -2.6511 2.0753 -0.8916 H 0 0 0 0 0 0 0 0 0 0 0 0
20 | -4.8399 1.1972 0.1325 H 0 0 0 0 0 0 0 0 0 0 0 0
21 | -3.8493 -0.2093 1.0702 H 0 0 0 0 0 0 0 0 0 0 0 0
22 | -3.8932 -0.1806 -0.8892 H 0 0 0 0 0 0 0 0 0 0 0 0
23 | 3.3420 1.1166 -0.0301 H 0 0 0 0 0 0 0 0 0 0 0 0
24 | 2.4321 2.2313 1.2974 H 0 0 0 0 0 0 0 0 0 0 0 0
25 | 2.2434 2.6282 -0.6084 H 0 0 0 0 0 0 0 0 0 0 0 0
26 | 1 6 2 0
27 | 2 1 1 0
28 | 2 9 1 0
29 | 3 2 2 0
30 | 4 3 1 0
31 | 5 4 2 0
32 | 6 5 1 0
33 | 6 7 1 0
34 | 7 8 1 0
35 | 1 10 1 0
36 | 3 11 1 0
37 | 4 13 1 0
38 | 5 12 1 0
39 | 7 14 1 0
40 | 7 15 1 0
41 | 8 16 1 0
42 | 8 17 1 0
43 | 8 18 1 0
44 | 9 19 1 0
45 | 9 20 1 0
46 | 9 21 1 0
47 | M END
48 | >
49 | false
50 |
51 | >
52 | 0.500
53 |
54 | >
55 | 0
56 |
57 | >
58 | 0
59 |
60 | >
61 | 120.2
62 |
63 | > <#Atoms_cresset>
64 | 9
65 |
66 | >
67 | 2.6
68 |
69 | >
70 | 0
71 |
72 | >
73 | 1
74 |
75 | >
76 | 0
77 |
78 | > <_cresset_fieldpoints>
79 | -5 0.008522 0.267777 -2.758281 -5.5867
80 | -5 -0.119070 0.043230 2.931842 -5.5917
81 | -6 0.590387 4.546290 0.268672 1.9514
82 | -6 -1.393872 4.371596 0.210859 2.0098
83 | -6 2.537503 -3.388101 -0.009318 1.6456
84 | -6 -3.587573 -2.777867 -0.081397 1.8350
85 | -6 4.381054 -1.155498 0.128075 1.8272
86 | -6 5.148639 3.042823 0.415846 1.1109
87 | -7 -1.578198 4.493007 0.009328 -1.5215
88 | -7 -0.236002 0.186086 3.302474 -1.9984
89 | -7 -3.815108 -2.813158 0.111945 -1.4591
90 | -7 -0.102794 0.440597 -3.122239 -1.9844
91 | -7 2.657345 -3.561917 -0.075642 -0.9960
92 | -7 -2.147875 0.280342 -3.072160 -1.9153
93 | -7 -4.554007 3.938925 0.097355 -1.1432
94 | -7 -2.019970 0.204714 3.221865 -1.9540
95 | -8 -0.010391 0.081569 0.083822 7.2096
96 | -8 -2.335089 0.293857 0.068131 5.6072
97 |
98 | $$$$
99 |
--------------------------------------------------------------------------------
/test/chiral/Chiral1R.sdf:
--------------------------------------------------------------------------------
1 | Chiral1R
2 | xed2sdf_05210316543D
3 |
4 | 17 16 0 0 1 0 0 0 0 0999 V2000
5 | -0.3058 -0.4631 -1.9568 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | -0.3164 -0.2219 -0.4360 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | -1.7737 -0.1746 0.0580 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 0.4422 -1.3289 0.3240 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | 1.9514 -1.3091 0.0248 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | 2.5898 0.3492 0.1257 Cl 0 0 0 0 0 0 0 0 0 0 0 0
11 | -2.4018 -1.3887 -0.2037 F 0 0 0 0 0 0 0 0 0 0 0 0
12 | -1.0348 0.3245 -2.4935 H 0 0 0 0 0 0 0 0 0 0 0 0
13 | -0.6848 -1.5780 -2.1880 H 0 0 0 0 0 0 0 0 0 0 0 0
14 | 0.8034 -0.3148 -2.3887 H 0 0 0 0 0 0 0 0 0 0 0 0
15 | 0.1987 0.8369 -0.2036 H 0 0 0 0 0 0 0 0 0 0 0 0
16 | -2.3627 0.7061 -0.5055 H 0 0 0 0 0 0 0 0 0 0 0 0
17 | -1.7954 0.0375 1.2389 H 0 0 0 0 0 0 0 0 0 0 0 0
18 | -0.0120 -2.4021 0.0373 H 0 0 0 0 0 0 0 0 0 0 0 0
19 | 0.2993 -1.1475 1.5016 H 0 0 0 0 0 0 0 0 0 0 0 0
20 | 2.1547 -1.7497 -1.0723 H 0 0 0 0 0 0 0 0 0 0 0 0
21 | 2.5164 -2.0010 0.8262 H 0 0 0 0 0 0 0 0 0 0 0 0
22 | 2 1 1 0
23 | 3 2 1 0
24 | 3 7 1 0
25 | 4 2 1 0
26 | 5 4 1 0
27 | 6 5 1 0
28 | 1 8 1 0
29 | 1 9 1 0
30 | 1 10 1 0
31 | 2 11 1 0
32 | 3 12 1 0
33 | 3 13 1 0
34 | 4 14 1 0
35 | 4 15 1 0
36 | 5 16 1 0
37 | 5 17 1 0
38 | M END
39 | >
40 | false
41 |
42 | >
43 | 0.500
44 |
45 | >
46 | 0
47 |
48 | >
49 | 0
50 |
51 | >
52 | 124.6
53 |
54 | > <#Atoms_cresset>
55 | 7
56 |
57 | >
58 | 2.2
59 |
60 | >
61 | 0
62 |
63 | >
64 | 3
65 |
66 | >
67 | 0
68 |
69 | >
70 | chiral1.sdf
71 |
72 | > <_cresset_fieldpoints>
73 | -5 3.293315 1.124753 -2.359326 -1.6776
74 | -5 -3.683935 -1.675065 -2.732728 -1.9696
75 | -5 4.817850 1.890634 0.585638 -1.6945
76 | -6 -1.513595 2.610760 1.006982 2.4387
77 | -6 1.930667 -4.312699 -0.242293 1.9644
78 | -7 1.542804 2.247766 -1.958592 -1.7740
79 | -7 0.623769 1.331181 2.333789 -2.0640
80 | -7 -3.583742 0.107118 -2.885224 -1.3838
81 | -7 -1.002519 2.845980 -1.475811 -1.5479
82 | -7 -4.498881 0.959383 1.384988 -0.9011
83 | -7 0.981321 -3.812348 2.273848 -1.1684
84 | -7 0.728875 -3.732660 -2.084903 -1.7377
85 | -7 3.291013 0.013838 -2.785055 -1.5417
86 | -7 -1.600251 -2.220802 2.866382 -1.4741
87 | -8 1.196516 -0.431650 -0.085633 5.9612
88 | -8 -0.774478 -0.802442 -0.480920 6.0785
89 |
90 | $$$$
91 |
--------------------------------------------------------------------------------
/test/chiral/Chiral1S.sdf:
--------------------------------------------------------------------------------
1 | Chiral1S
2 | xed2sdf_05210316543D
3 |
4 | 17 16 0 0 1 0 0 0 0 0999 V2000
5 | -0.0574 1.3872 -0.0749 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | -0.4638 -0.0733 -0.3431 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | -1.9453 -0.2399 0.0359 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 0.3930 -1.0503 0.4888 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | 1.8049 -1.2359 -0.0969 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | 2.7910 0.2353 0.0797 Cl 0 0 0 0 0 0 0 0 0 0 0 0
11 | -2.3661 -1.5295 -0.2691 F 0 0 0 0 0 0 0 0 0 0 0 0
12 | 1.0681 1.5780 -0.4414 H 0 0 0 0 0 0 0 0 0 0 0 0
13 | -0.1445 1.6215 1.0987 H 0 0 0 0 0 0 0 0 0 0 0 0
14 | -0.7860 2.1252 -0.6783 H 0 0 0 0 0 0 0 0 0 0 0 0
15 | -0.3423 -0.3138 -1.5123 H 0 0 0 0 0 0 0 0 0 0 0 0
16 | -2.6123 0.5387 -0.5877 H 0 0 0 0 0 0 0 0 0 0 0 0
17 | -2.0864 -0.0353 1.2099 H 0 0 0 0 0 0 0 0 0 0 0 0
18 | -0.1292 -2.1303 0.4908 H 0 0 0 0 0 0 0 0 0 0 0 0
19 | 0.4717 -0.6608 1.6209 H 0 0 0 0 0 0 0 0 0 0 0 0
20 | 1.7322 -1.5354 -1.2565 H 0 0 0 0 0 0 0 0 0 0 0 0
21 | 2.3483 -2.1256 0.4971 H 0 0 0 0 0 0 0 0 0 0 0 0
22 | 2 1 1 0
23 | 3 2 1 0
24 | 3 7 1 0
25 | 4 2 1 0
26 | 5 4 1 0
27 | 6 5 1 0
28 | 1 8 1 0
29 | 1 9 1 0
30 | 1 10 1 0
31 | 2 11 1 0
32 | 3 12 1 0
33 | 3 13 1 0
34 | 4 14 1 0
35 | 4 15 1 0
36 | 5 16 1 0
37 | 5 17 1 0
38 | M END
39 | >
40 | false
41 |
42 | >
43 | 0.500
44 |
45 | >
46 | 0
47 |
48 | >
49 | 0
50 |
51 | >
52 | 124.6
53 |
54 | > <#Atoms_cresset>
55 | 7
56 |
57 | >
58 | 2.2
59 |
60 | >
61 | 0
62 |
63 | >
64 | 3
65 |
66 | >
67 | 0
68 |
69 | >
70 | chiral2.sdf
71 |
72 | > <_cresset_fieldpoints>
73 | -5 5.308778 1.134607 0.677239 -1.8290
74 | -5 -4.566900 -2.292121 -1.977420 -1.7783
75 | -6 0.789240 -1.272119 -3.428989 1.3159
76 | -6 -1.064255 0.678985 3.178056 2.5202
77 | -6 1.388079 -4.280977 -0.155582 1.6220
78 | -6 1.296165 -3.628495 2.119094 1.6241
79 | -6 -2.798126 2.415992 1.198739 2.7943
80 | -7 -0.227325 -2.912244 -2.287760 -1.8376
81 | -7 -0.878330 0.604629 3.363729 -1.6423
82 | -7 -1.489834 -1.930124 2.984459 -1.6211
83 | -7 1.767116 0.663536 -2.825933 -2.0685
84 | -7 1.241088 -3.100492 2.806798 -1.1822
85 | -7 1.856483 1.198134 2.732960 -1.8774
86 | -7 -2.749444 2.644858 1.308583 -1.4670
87 | -7 -1.862990 1.234476 -3.052495 -1.5920
88 | -8 0.907872 -0.142969 -0.020819 5.8661
89 | -8 -0.541785 -0.035449 0.143963 5.8888
90 | -8 -0.883094 -0.682621 0.091185 5.8287
91 |
92 | $$$$
93 |
--------------------------------------------------------------------------------
/test/chiral/Chiral2R.sdf:
--------------------------------------------------------------------------------
1 | Chiral2R
2 | xed2sdf_05210316543D
3 |
4 | 17 16 0 0 1 0 0 0 0 0999 V2000
5 | -0.4824 -0.3628 -2.0588 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | -0.3824 -0.1734 -0.5329 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | -1.7998 -0.1610 0.0706 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 0.4426 -1.2987 0.1258 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | 1.9379 -1.2157 -0.2298 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | 2.5771 0.4081 0.1214 Cl 0 0 0 0 0 0 0 0 0 0 0 0
11 | -2.4331 -1.3746 -0.1811 F 0 0 0 0 0 0 0 0 0 0 0 0
12 | 2.8461 -2.4188 0.7164 Cl 0 0 0 0 0 0 0 0 0 0 0 0
13 | -1.2812 0.4083 -2.5139 H 0 0 0 0 0 0 0 0 0 0 0 0
14 | -0.8328 -1.4845 -2.3024 H 0 0 0 0 0 0 0 0 0 0 0 0
15 | 0.5806 -0.1513 -2.5727 H 0 0 0 0 0 0 0 0 0 0 0 0
16 | 0.1368 0.8834 -0.3012 H 0 0 0 0 0 0 0 0 0 0 0 0
17 | -2.4425 0.7284 -0.4149 H 0 0 0 0 0 0 0 0 0 0 0 0
18 | -1.7388 0.0154 1.2559 H 0 0 0 0 0 0 0 0 0 0 0 0
19 | 0.0070 -2.3654 -0.2089 H 0 0 0 0 0 0 0 0 0 0 0 0
20 | 0.3499 -1.1994 1.3180 H 0 0 0 0 0 0 0 0 0 0 0 0
21 | 2.0955 -1.4609 -1.3932 H 0 0 0 0 0 0 0 0 0 0 0 0
22 | 2 1 1 0
23 | 3 2 1 0
24 | 3 7 1 0
25 | 4 2 1 0
26 | 5 4 1 0
27 | 5 8 1 0
28 | 6 5 1 0
29 | 1 9 1 0
30 | 1 10 1 0
31 | 1 11 1 0
32 | 2 12 1 0
33 | 3 13 1 0
34 | 3 14 1 0
35 | 4 15 1 0
36 | 4 16 1 0
37 | 5 17 1 0
38 | M END
39 | >
40 | false
41 |
42 | >
43 | 0.500
44 |
45 | >
46 | 0
47 |
48 | >
49 | 0
50 |
51 | >
52 | 159
53 |
54 | > <#Atoms_cresset>
55 | 8
56 |
57 | >
58 | 2.8
59 |
60 | >
61 | 0
62 |
63 | >
64 | 3
65 |
66 | >
67 | 0
68 |
69 | >
70 | chiral1extended.sdf
71 |
72 | > <_cresset_fieldpoints>
73 | -5 -4.938744 -1.933373 -1.507140 -1.6623
74 | -5 -3.861631 -3.244622 1.533432 -1.6453
75 | -5 4.636777 -0.564024 1.782508 -2.4922
76 | -5 1.116724 -4.057750 2.215973 -1.1789
77 | -6 1.296604 -2.737301 -3.156195 2.0987
78 | -6 -1.329453 2.652410 0.844085 3.1133
79 | -7 0.824863 -3.535106 -2.386636 -1.8630
80 | -7 -1.196681 2.908851 -1.427763 -1.5424
81 | -7 0.585093 1.229750 2.307772 -2.1445
82 | -7 2.150530 -0.414124 3.006948 -1.8195
83 | -7 -4.438163 0.890712 1.620558 -0.9023
84 | -7 -0.904563 -3.980512 -1.874143 -1.4908
85 | -7 2.913202 0.763784 -2.814165 -1.6302
86 | -7 5.072411 -1.060383 -0.976542 -1.3561
87 | -7 -3.851872 0.195330 -2.700142 -1.3736
88 | -7 1.594174 2.224336 -2.034774 -1.8222
89 | -7 -1.401802 -2.348287 2.769437 -1.4859
90 | -7 0.461819 -3.859462 2.028636 -1.4971
91 | -8 -0.832461 -0.762936 -0.559133 6.0732
92 | -8 2.043660 -1.067383 0.243947 5.7866
93 | -8 1.223379 -0.384685 -0.148382 5.9129
94 |
95 | $$$$
96 |
--------------------------------------------------------------------------------
/test/chiral/Chiral4RR.sdf:
--------------------------------------------------------------------------------
1 | Chiral4RR
2 | xed2sdf_05210316543D
3 |
4 | 11 10 0 0 1 0 0 0 0 0999 V2000
5 | -1.2596 -0.0598 -0.5509 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | -0.0495 0.8508 -0.2939 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | 1.2201 -0.0165 -0.2155 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 2.8481 1.0257 0.0715 Br 0 0 0 0 0 0 0 0 0 0 0 0
9 | -0.2474 1.5305 0.9045 F 0 0 0 0 0 0 0 0 0 0 0 0
10 | 1.0569 -1.2278 1.0786 Cl 0 0 0 0 0 0 0 0 0 0 0 0
11 | -2.2528 0.6078 -0.6401 H 0 0 0 0 0 0 0 0 0 0 0 0
12 | -1.0943 -0.6724 -1.5692 H 0 0 0 0 0 0 0 0 0 0 0 0
13 | -1.3776 -0.8288 0.3626 H 0 0 0 0 0 0 0 0 0 0 0 0
14 | 0.0570 1.6385 -1.1931 H 0 0 0 0 0 0 0 0 0 0 0 0
15 | 1.3350 -0.5987 -1.2584 H 0 0 0 0 0 0 0 0 0 0 0 0
16 | 1 2 1 0
17 | 2 3 1 0
18 | 2 5 1 0
19 | 3 4 1 0
20 | 3 6 1 0
21 | 1 7 1 0
22 | 1 8 1 0
23 | 1 9 1 0
24 | 2 10 1 0
25 | 3 11 1 0
26 | M END
27 | >
28 | false
29 |
30 | >
31 | 0.500
32 |
33 | >
34 | 0
35 |
36 | >
37 | 0
38 |
39 | >
40 | 175.4
41 |
42 | > <#Atoms_cresset>
43 | 6
44 |
45 | >
46 | 2.3
47 |
48 | >
49 | 0
50 |
51 | >
52 | 1
53 |
54 | >
55 | 0
56 |
57 | > <_cresset_fieldpoints>
58 | -5 1.508038 0.779073 3.106345 -4.1098
59 | -6 0.438205 0.305714 -3.275494 4.6226
60 | -7 0.693873 0.543747 -3.507240 -1.6656
61 | -7 1.461404 1.064601 -3.330812 -1.6800
62 | -7 0.101277 -3.030353 -1.136788 -1.7518
63 | -7 1.227761 3.973117 -0.901803 -1.4810
64 | -7 -2.134232 3.178537 -1.458603 -1.2556
65 | -7 1.714188 0.599247 3.363103 -1.7144
66 | -7 -1.229293 -0.794016 2.958261 -1.5761
67 | -7 3.333307 -2.470699 -0.574931 -1.5031
68 | -8 0.204473 -0.101976 0.250962 6.0910
69 | -8 1.446425 0.439644 0.181052 5.6899
70 |
71 | $$$$
72 |
--------------------------------------------------------------------------------
/test/chiral/Chiral4RS.sdf:
--------------------------------------------------------------------------------
1 | Chiral4RS
2 | xed2sdf_05210316543D
3 |
4 | 11 10 0 0 1 0 0 0 0 0999 V2000
5 | -1.2647 -0.0920 -0.4955 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | -0.0175 0.7895 -0.3322 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | 1.2461 -0.0895 -0.3103 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 1.1900 -1.4706 1.0708 Br 0 0 0 0 0 0 0 0 0 0 0 0
9 | -0.1165 1.5226 0.8470 F 0 0 0 0 0 0 0 0 0 0 0 0
10 | 2.6892 0.9248 -0.0721 Cl 0 0 0 0 0 0 0 0 0 0 0 0
11 | -2.2429 0.6025 -0.5218 H 0 0 0 0 0 0 0 0 0 0 0 0
12 | -1.1853 -0.7073 -1.5229 H 0 0 0 0 0 0 0 0 0 0 0 0
13 | -1.3411 -0.8576 0.4249 H 0 0 0 0 0 0 0 0 0 0 0 0
14 | 0.0515 1.5504 -1.2576 H 0 0 0 0 0 0 0 0 0 0 0 0
15 | 1.3394 -0.6347 -1.3753 H 0 0 0 0 0 0 0 0 0 0 0 0
16 | 1 2 1 0
17 | 2 3 1 0
18 | 2 5 1 0
19 | 3 4 1 0
20 | 3 6 1 0
21 | 1 7 1 0
22 | 1 8 1 0
23 | 1 9 1 0
24 | 2 10 1 0
25 | 3 11 1 0
26 | M END
27 | >
28 | false
29 |
30 | >
31 | 0.500
32 |
33 | >
34 | 0
35 |
36 | >
37 | 0
38 |
39 | >
40 | 175.4
41 |
42 | > <#Atoms_cresset>
43 | 6
44 |
45 | >
46 | 2.3
47 |
48 | >
49 | 0
50 |
51 | >
52 | 1
53 |
54 | >
55 | 0
56 |
57 | > <_cresset_fieldpoints>
58 | -5 2.107218 1.284684 2.720385 -4.1286
59 | -6 0.239154 0.140943 -3.337858 4.5515
60 | -7 0.081873 -2.943421 -1.883405 -1.6885
61 | -7 0.269152 0.254273 -3.601748 -1.5492
62 | -7 -2.135021 3.127711 -1.438432 -1.2430
63 | -7 2.426515 1.225641 2.911015 -1.6941
64 | -7 3.984715 -1.656326 -1.149291 -1.4881
65 | -7 -1.595955 -0.468800 2.977931 -1.5804
66 | -7 2.006131 1.510912 -3.035895 -1.5648
67 | -7 1.749793 3.563557 -1.144164 -1.4934
68 | -8 0.493687 -0.307031 0.300215 5.8793
69 | -8 1.195270 0.700094 0.020633 5.7738
70 |
71 | $$$$
72 |
--------------------------------------------------------------------------------
/test/chiral/RingChiralR.sdf:
--------------------------------------------------------------------------------
1 | RingChiralR
2 | xed2sdf_05210316543D
3 |
4 | 16 16 0 0 1 0 0 0 0 0999 V2000
5 | -1.6141 1.4460 0.2377 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | -1.1814 0.2709 -0.3885 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | 0.2186 0.2708 -0.3884 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 0.6512 0.3163 0.9423 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | 0.1517 1.4897 1.5198 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | -1.2458 1.4453 1.4502 O 0 0 0 0 0 0 0 0 0 0 0 0
11 | 1.5958 0.5496 0.4357 Cl 0 0 0 0 0 0 0 0 0 0 0 0
12 | 0.8150 -0.1604 1.8538 F 0 0 0 0 0 0 0 0 0 0 0 0
13 | -1.5382 -0.5055 0.1313 H 0 0 0 0 0 0 0 0 0 0 0 0
14 | 0.5276 -0.5684 -0.8357 H 0 0 0 0 0 0 0 0 0 0 0 0
15 | 0.4607 1.5222 2.4703 H 0 0 0 0 0 0 0 0 0 0 0 0
16 | -1.5382 0.2691 -1.3226 H 0 0 0 0 0 0 0 0 0 0 0 0
17 | 0.5276 1.0779 -0.8918 H 0 0 0 0 0 0 0 0 0 0 0 0
18 | 0.5102 2.2661 1.0015 H 0 0 0 0 0 0 0 0 0 0 0 0
19 | -1.2322 2.3156 -0.2768 H 0 0 0 0 0 0 0 0 0 0 0 0
20 | -2.6932 1.4747 0.2063 H 0 0 0 0 0 0 0 0 0 0 0 0
21 | 1 2 1 0
22 | 2 3 1 0
23 | 3 4 1 0
24 | 4 5 1 0
25 | 4 7 1 0
26 | 4 8 1 0
27 | 5 6 1 0
28 | 6 1 1 0
29 | 1 15 1 0
30 | 1 16 1 0
31 | 2 9 1 0
32 | 2 12 1 0
33 | 3 10 1 0
34 | 3 13 1 0
35 | 5 11 1 0
36 | 5 14 1 0
37 | M END
38 | >
39 | false
40 |
41 | >
42 | 0.500
43 |
44 | >
45 | 0
46 |
47 | >
48 | 0
49 |
50 | >
51 | 138.6
52 |
53 | > <#Atoms_cresset>
54 | 8
55 |
56 | >
57 | 1.7
58 |
59 | >
60 | 9.2
61 |
62 | >
63 | 1
64 |
65 | >
66 | 0
67 |
68 | > <_cresset_fieldpoints>
69 | -5 -2.222526 0.748098 2.988486 -7.5701
70 | -5 3.550467 -0.955037 2.231292 -2.2420
71 | -6 0.725299 3.362092 -1.189131 4.1816
72 | -7 -2.314700 -0.432978 2.764491 -2.1089
73 | -7 -0.441107 2.535762 -2.783427 -1.6404
74 | -7 -0.272483 -2.910644 0.329646 -1.7540
75 | -7 2.797442 0.395927 -2.301421 -1.4586
76 | -7 3.195543 2.379205 2.188208 -1.6662
77 | -7 -1.159105 4.428876 1.469106 -1.3292
78 | -7 2.353556 -2.363265 -0.193691 -1.6406
79 | -7 1.084728 3.489602 -1.127328 -2.0627
80 | -8 0.480923 0.582395 0.577355 8.5161
81 |
82 | $$$$
83 |
--------------------------------------------------------------------------------
/test/chiral/RingChiralS.sdf:
--------------------------------------------------------------------------------
1 | RingChiralS
2 | xed2sdf_05210316543D
3 |
4 | 16 16 0 0 1 0 0 0 0 0999 V2000
5 | -1.7596 1.8003 0.0572 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | -1.5131 0.4293 -0.6043 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | -0.0066 0.1089 -0.5632 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 0.5009 0.1889 0.8883 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | 0.1725 1.5819 1.4581 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | -1.2473 1.8262 1.4052 O 0 0 0 0 0 0 0 0 0 0 0 0
11 | -0.2462 -1.0836 1.8831 Cl 0 0 0 0 0 0 0 0 0 0 0 0
12 | 1.8747 -0.0199 0.9187 F 0 0 0 0 0 0 0 0 0 0 0 0
13 | -2.1132 -0.4149 0.0016 H 0 0 0 0 0 0 0 0 0 0 0 0
14 | 0.1878 -0.9907 -1.0025 H 0 0 0 0 0 0 0 0 0 0 0 0
15 | 0.5434 1.6404 2.5977 H 0 0 0 0 0 0 0 0 0 0 0 0
16 | -1.8928 0.4518 -1.7425 H 0 0 0 0 0 0 0 0 0 0 0 0
17 | 0.5840 0.9147 -1.2280 H 0 0 0 0 0 0 0 0 0 0 0 0
18 | 0.7435 2.4173 0.8129 H 0 0 0 0 0 0 0 0 0 0 0 0
19 | -1.2167 2.6538 -0.5880 H 0 0 0 0 0 0 0 0 0 0 0 0
20 | -2.9398 2.0161 0.0819 H 0 0 0 0 0 0 0 0 0 0 0 0
21 | 1 2 1 0
22 | 2 3 1 0
23 | 3 4 1 0
24 | 4 5 1 0
25 | 4 7 1 0
26 | 4 8 1 0
27 | 5 6 1 0
28 | 6 1 1 0
29 | 1 15 1 0
30 | 1 16 1 0
31 | 2 9 1 0
32 | 2 12 1 0
33 | 3 10 1 0
34 | 3 13 1 0
35 | 5 11 1 0
36 | 5 14 1 0
37 | M END
38 | >
39 | false
40 |
41 | >
42 | 0.500
43 |
44 | >
45 | 0
46 |
47 | >
48 | 0
49 |
50 | >
51 | 138.6
52 |
53 | > <#Atoms_cresset>
54 | 8
55 |
56 | >
57 | 1.7
58 |
59 | >
60 | 9.2
61 |
62 | >
63 | 1
64 |
65 | >
66 | 0
67 |
68 | > <_cresset_fieldpoints>
69 | -5 -2.324977 1.238472 2.889834 -7.2779
70 | -5 2.124333 -2.179902 2.885112 -3.0598
71 | -6 -0.335882 2.449165 -2.821344 3.9025
72 | -6 0.871542 3.202595 -1.489519 4.0444
73 | -7 -0.456459 2.407712 -3.105993 -1.5115
74 | -7 1.101088 3.353064 -1.534007 -1.6887
75 | -7 -1.336596 -2.966091 -0.168522 -1.7482
76 | -7 -4.737803 0.162704 -0.760286 -1.0804
77 | -7 2.656934 -0.558879 -2.282709 -1.1791
78 | -7 3.118690 2.805954 2.155334 -1.1199
79 | -7 2.409875 2.662501 -1.093646 -1.5637
80 | -7 -0.951264 4.608456 1.465051 -1.2578
81 | -7 -2.725216 0.306735 2.704386 -2.2001
82 | -7 1.417473 -0.210058 4.245065 -1.5015
83 | -7 0.935772 -3.200377 0.117219 -1.5900
84 | -8 0.288471 -0.093568 0.894646 6.0645
85 |
86 | $$$$
87 |
--------------------------------------------------------------------------------
/test/chiral/SpiroR.sdf:
--------------------------------------------------------------------------------
1 | SpiroR
2 | xed2sdf_05210316543D
3 |
4 | 24 25 0 0 1 0 0 0 0 0999 V2000
5 | -1.9647 0.6421 0.2364 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | -1.4327 1.9982 -0.2639 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | 0.1087 1.9994 -0.1929 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 0.7238 0.7740 -0.9094 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | 0.0490 -0.5061 -0.3739 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | -1.3846 -0.4430 -0.5145 O 0 0 0 0 0 0 0 0 0 0 0 0
11 | 0.5623 0.8575 -2.4452 C 0 0 0 0 0 0 0 0 0 0 0 0
12 | 1.9796 0.6485 -2.9956 C 0 0 0 0 0 0 0 0 0 0 0 0
13 | 2.8656 1.0881 -1.8260 C 0 0 0 0 0 0 0 0 0 0 0 0
14 | 2.1377 0.7105 -0.6482 O 0 0 0 0 0 0 0 0 0 0 0 0
15 | -1.7884 2.1620 -1.3978 H 0 0 0 0 0 0 0 0 0 0 0 0
16 | 0.5400 3.0164 -0.6619 H 0 0 0 0 0 0 0 0 0 0 0 0
17 | 0.4610 -1.4489 -0.9916 H 0 0 0 0 0 0 0 0 0 0 0 0
18 | -1.8691 2.8828 0.4196 H 0 0 0 0 0 0 0 0 0 0 0 0
19 | 0.4256 1.9494 0.9635 H 0 0 0 0 0 0 0 0 0 0 0 0
20 | 0.3315 -0.6471 0.7837 H 0 0 0 0 0 0 0 0 0 0 0 0
21 | -1.7005 0.5156 1.4002 H 0 0 0 0 0 0 0 0 0 0 0 0
22 | -3.1570 0.6192 0.1020 H 0 0 0 0 0 0 0 0 0 0 0 0
23 | 0.1825 1.9437 -2.7860 H 0 0 0 0 0 0 0 0 0 0 0 0
24 | -0.1821 0.0190 -2.8740 H 0 0 0 0 0 0 0 0 0 0 0 0
25 | 2.1845 1.2971 -3.9844 H 0 0 0 0 0 0 0 0 0 0 0 0
26 | 2.1565 -0.5189 -3.2100 H 0 0 0 0 0 0 0 0 0 0 0 0
27 | 3.9487 0.5734 -1.8661 H 0 0 0 0 0 0 0 0 0 0 0 0
28 | 2.9715 2.2834 -1.8482 H 0 0 0 0 0 0 0 0 0 0 0 0
29 | 1 2 1 0
30 | 2 3 1 0
31 | 3 4 1 0
32 | 4 5 1 0
33 | 4 7 1 0
34 | 5 6 1 0
35 | 6 1 1 0
36 | 7 8 1 0
37 | 8 9 1 0
38 | 9 10 1 0
39 | 10 4 1 0
40 | 1 17 1 0
41 | 1 18 1 0
42 | 2 11 1 0
43 | 2 14 1 0
44 | 3 12 1 0
45 | 3 15 1 0
46 | 5 13 1 0
47 | 5 16 1 0
48 | 7 19 1 0
49 | 7 20 1 0
50 | 8 21 1 0
51 | 8 22 1 0
52 | 9 23 1 0
53 | 9 24 1 0
54 | M END
55 | >
56 | false
57 |
58 | >
59 | 0.500
60 |
61 | >
62 | 0
63 |
64 | >
65 | 0
66 |
67 | >
68 | 142.2
69 |
70 | > <#Atoms_cresset>
71 | 10
72 |
73 | >
74 | 1.3
75 |
76 | >
77 | 18.5
78 |
79 | >
80 | 1.5
81 |
82 | >
83 | 0
84 |
85 | > <_cresset_fieldpoints>
86 | -5 -2.377949 -1.646142 -1.561537 -7.7821
87 | -5 2.990018 0.238047 0.965016 -7.4187
88 | -6 -1.402575 2.552930 2.879059 2.0503
89 | -6 1.465789 3.999984 -2.878239 2.8861
90 | -6 -0.352163 4.265409 -2.580418 2.5770
91 | -7 -4.503424 2.695160 -1.020521 -1.0872
92 | -7 -1.071703 2.486838 3.040231 -1.4995
93 | -7 0.284664 0.547079 3.054670 -1.6400
94 | -7 -2.687412 -0.095094 -2.737669 -2.1076
95 | -7 -1.945918 -2.410372 1.287207 -1.2541
96 | -7 -0.645490 4.326442 -2.578669 -1.6837
97 | -7 1.450552 4.136094 -2.817268 -1.9720
98 | -7 2.649354 0.569781 1.675497 -2.0012
99 | -7 3.021010 -1.891289 -0.773170 -1.9632
100 | -7 -0.126872 1.505058 -5.527009 -1.1672
101 | -7 0.400530 -2.462969 -3.346998 -1.5994
102 | -7 4.798400 -0.141982 -4.386024 -1.0563
103 | -8 -0.412689 1.263979 -0.370706 5.4822
104 | -8 1.359296 0.987774 -2.293681 5.1604
105 |
106 | $$$$
107 |
--------------------------------------------------------------------------------
/test/chiral/SpiroS.sdf:
--------------------------------------------------------------------------------
1 | SpiroS
2 | xed2sdf_05210316543D
3 |
4 | 24 25 0 0 1 0 0 0 0 0999 V2000
5 | -1.9646 0.6421 0.2364 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | -1.4327 1.9981 -0.2640 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | 0.1086 1.9995 -0.1928 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 0.7237 0.7740 -0.9094 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | 0.0490 -0.5060 -0.3740 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | -1.3845 -0.4430 -0.5145 O 0 0 0 0 0 0 0 0 0 0 0 0
11 | 2.2563 0.7487 -0.7047 C 0 0 0 0 0 0 0 0 0 0 0 0
12 | 2.8376 1.0424 -2.0945 C 0 0 0 0 0 0 0 0 0 0 0 0
13 | 1.7143 0.5926 -3.0337 C 0 0 0 0 0 0 0 0 0 0 0 0
14 | 0.5008 0.8879 -2.3267 O 0 0 0 0 0 0 0 0 0 0 0 0
15 | -1.7885 2.1620 -1.3978 H 0 0 0 0 0 0 0 0 0 0 0 0
16 | 0.5399 3.0164 -0.6620 H 0 0 0 0 0 0 0 0 0 0 0 0
17 | 0.4610 -1.4489 -0.9916 H 0 0 0 0 0 0 0 0 0 0 0 0
18 | -1.8692 2.8828 0.4195 H 0 0 0 0 0 0 0 0 0 0 0 0
19 | 0.4255 1.9494 0.9635 H 0 0 0 0 0 0 0 0 0 0 0 0
20 | 0.3316 -0.6470 0.7837 H 0 0 0 0 0 0 0 0 0 0 0 0
21 | -1.7005 0.5156 1.4001 H 0 0 0 0 0 0 0 0 0 0 0 0
22 | -3.1569 0.6193 0.1020 H 0 0 0 0 0 0 0 0 0 0 0 0
23 | 2.6332 -0.3377 -0.3610 H 0 0 0 0 0 0 0 0 0 0 0 0
24 | 2.6269 1.5713 0.0871 H 0 0 0 0 0 0 0 0 0 0 0 0
25 | 3.8593 0.4456 -2.2963 H 0 0 0 0 0 0 0 0 0 0 0 0
26 | 3.0060 2.2243 -2.2153 H 0 0 0 0 0 0 0 0 0 0 0 0
27 | 1.7631 1.1552 -4.0923 H 0 0 0 0 0 0 0 0 0 0 0 0
28 | 1.7916 -0.5949 -3.1893 H 0 0 0 0 0 0 0 0 0 0 0 0
29 | 1 2 1 0
30 | 2 3 1 0
31 | 3 4 1 0
32 | 4 5 1 0
33 | 4 7 1 0
34 | 5 6 1 0
35 | 6 1 1 0
36 | 7 8 1 0
37 | 8 9 1 0
38 | 9 10 1 0
39 | 10 4 1 0
40 | 1 17 1 0
41 | 1 18 1 0
42 | 2 11 1 0
43 | 2 14 1 0
44 | 3 12 1 0
45 | 3 15 1 0
46 | 5 13 1 0
47 | 5 16 1 0
48 | 7 19 1 0
49 | 7 20 1 0
50 | 8 21 1 0
51 | 8 22 1 0
52 | 9 23 1 0
53 | 9 24 1 0
54 | M END
55 | >
56 | false
57 |
58 | >
59 | 0.500
60 |
61 | >
62 | 0
63 |
64 | >
65 | 0
66 |
67 | >
68 | 142.2
69 |
70 | > <#Atoms_cresset>
71 | 10
72 |
73 | >
74 | 1.3
75 |
76 | >
77 | 18.5
78 |
79 | >
80 | 1.5
81 |
82 | >
83 | 0
84 |
85 | > <_cresset_fieldpoints>
86 | -5 -1.345069 0.039015 -2.711090 -12.6182
87 | -6 1.811603 0.483092 2.356957 3.7706
88 | -6 5.129586 0.052126 0.095784 2.7268
89 | -6 3.485332 -2.093464 -1.741062 2.7093
90 | -7 1.828098 0.482656 2.523491 -1.9081
91 | -7 0.406009 0.533677 3.011635 -1.7814
92 | -7 -4.524868 2.782874 -0.818787 -1.0713
93 | -7 2.312422 -2.695601 0.516834 -1.3218
94 | -7 -0.089898 3.196458 -3.240538 -2.3086
95 | -7 -1.044432 2.468679 3.044927 -1.5188
96 | -7 -1.645321 0.063842 -3.088746 -2.5670
97 | -7 2.834908 4.116484 -0.396392 -1.6982
98 | -7 5.383923 0.365731 0.021490 -1.1386
99 | -7 4.277779 1.998691 -4.835410 -1.0568
100 | -7 -1.824008 -2.327997 1.527919 -1.2547
101 | -7 2.776996 -2.475135 -1.739168 -1.8786
102 | -8 -0.410264 1.203638 -0.073934 5.3102
103 | -8 0.937500 0.847616 -0.147577 5.2063
104 | -8 2.133675 0.665013 -1.506051 5.1581
105 |
106 | $$$$
107 |
--------------------------------------------------------------------------------
/test/chiral/bace_cat_13d_perm1.sdf:
--------------------------------------------------------------------------------
1 | CAT-13d
2 | xed2sdf_05210316543D
3 |
4 | 43 46 0 0 1 0 0 0 0 0999 V2000
5 | 14.9444 4.0910 -2.8732 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | 15.2486 3.6732 -0.5009 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | 14.9243 4.5522 -1.5465 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 11.7860 -2.3271 1.0538 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | 13.4812 -2.9579 -0.7768 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | 16.1894 -2.3496 -3.0284 C 0 0 0 0 0 0 0 0 0 0 0 0
11 | 15.2648 2.7464 -3.1489 C 0 0 0 0 0 0 0 0 0 0 0 0
12 | 14.3652 -2.2938 2.6004 N 0 0 0 0 0 0 0 0 0 0 0 0
13 | 15.8080 0.4004 -2.4044 C 0 0 0 0 0 0 0 0 0 0 0 0
14 | 15.3469 -2.7616 0.5345 N 0 3 0 0 0 0 0 0 0 0 0 0
15 | 16.6159 -1.3547 -3.9204 C 0 0 0 0 0 0 0 0 0 0 0 0
16 | 15.0192 -3.0683 -0.8497 C 0 0 0 0 0 0 0 0 0 0 0 0
17 | 16.7355 -4.7540 -2.0801 C 0 0 0 0 0 0 0 0 0 0 0 0
18 | 16.4013 0.0015 -3.6209 C 0 0 0 0 0 0 0 0 0 0 0 0
19 | 15.4125 -0.6168 -1.5039 C 0 0 0 0 0 0 0 0 0 0 0 0
20 | 15.5899 -4.4689 -1.1332 C 0 0 0 0 0 0 0 0 0 0 0 0
21 | 15.5647 2.3288 -0.7836 C 0 0 0 0 0 0 0 0 0 0 0 0
22 | 12.6571 -3.1079 -1.6844 O 0 0 0 0 0 0 0 0 0 0 0 0
23 | 14.2729 -2.5333 1.2874 C 0 0 0 0 0 0 0 0 0 0 0 0
24 | 15.2426 4.2511 1.1245 Cl 0 0 0 0 0 0 0 0 0 0 0 0
25 | 15.5634 -1.9948 -1.8100 C 0 0 0 0 0 0 0 0 0 0 0 0
26 | 15.5587 1.8326 -2.1090 C 0 0 0 0 0 0 0 0 0 0 0 0
27 | 13.1444 -2.5995 0.5661 N 0 0 0 0 0 0 0 0 0 0 0 0
28 | 15.3463 -5.2332 -2.4204 C 0 0 0 0 0 0 0 0 0 0 0 0
29 | 14.9319 -0.3282 -0.5818 H 0 0 0 0 0 0 0 0 0 0 0 0
30 | 15.2371 2.4076 -4.1742 H 0 0 0 0 0 0 0 0 0 0 0 0
31 | 11.0292 -2.7766 0.4106 H 0 0 0 0 0 0 0 0 0 0 0 0
32 | 14.6865 4.7672 -3.6749 H 0 0 0 0 0 0 0 0 0 0 0 0
33 | 16.3098 -2.7539 0.8773 H 0 0 0 0 0 0 0 0 0 0 0 0
34 | 16.6981 0.7398 -4.3492 H 0 0 0 0 0 0 0 0 0 0 0 0
35 | 17.1286 -3.9418 -2.6801 H 0 0 0 0 0 0 0 0 0 0 0 0
36 | 11.6181 -1.2506 1.0770 H 0 0 0 0 0 0 0 0 0 0 0 0
37 | 14.6583 5.5770 -1.3284 H 0 0 0 0 0 0 0 0 0 0 0 0
38 | 11.6524 -2.7177 2.0625 H 0 0 0 0 0 0 0 0 0 0 0 0
39 | 15.8089 1.6730 0.0351 H 0 0 0 0 0 0 0 0 0 0 0 0
40 | 14.8362 -4.7371 -3.2436 H 0 0 0 0 0 0 0 0 0 0 0 0
41 | 16.3451 -3.3789 -3.3174 H 0 0 0 0 0 0 0 0 0 0 0 0
42 | 15.2860 -2.2903 3.0398 H 0 0 0 0 0 0 0 0 0 0 0 0
43 | 13.5838 -2.0392 3.2009 H 0 0 0 0 0 0 0 0 0 0 0 0
44 | 15.5716 -5.0931 -0.2434 H 0 0 0 0 0 0 0 0 0 0 0 0
45 | 15.1570 -6.3019 -2.3389 H 0 0 0 0 0 0 0 0 0 0 0 0
46 | 17.0896 -1.6334 -4.8518 H 0 0 0 0 0 0 0 0 0 0 0 0
47 | 17.4697 -5.4962 -1.7713 H 0 0 0 0 0 0 0 0 0 0 0 0
48 | 14 9 2 0
49 | 7 1 2 0
50 | 12 5 1 0
51 | 1 28 1 0
52 | 10 12 1 0
53 | 23 19 1 0
54 | 5 18 2 0
55 | 4 32 1 0
56 | 22 17 2 0
57 | 4 27 1 0
58 | 2 20 1 0
59 | 16 13 1 0
60 | 7 26 1 0
61 | 24 41 1 0
62 | 6 37 1 0
63 | 2 17 1 0
64 | 21 15 2 0
65 | 24 36 1 0
66 | 23 5 1 0
67 | 12 16 1 0
68 | 3 2 2 0
69 | 16 24 1 0
70 | 22 7 1 0
71 | 10 29 1 0
72 | 11 14 1 0
73 | 1 3 1 0
74 | 4 34 1 0
75 | 16 40 1 0
76 | 6 11 2 0
77 | 8 38 1 0
78 | 19 8 1 0
79 | 17 35 1 0
80 | 11 42 1 0
81 | 3 33 1 0
82 | 4 23 1 0
83 | 14 30 1 0
84 | 9 22 1 0
85 | 13 31 1 0
86 | 24 13 1 0
87 | 13 43 1 0
88 | 12 21 1 0
89 | 8 39 1 0
90 | 21 6 1 0
91 | 15 25 1 0
92 | 9 15 1 0
93 | 19 10 2 0
94 | M CHG 1 10 1
95 | M END
96 | $$$$
97 |
--------------------------------------------------------------------------------
/test/chiral/bace_cat_13d_perm2.sdf:
--------------------------------------------------------------------------------
1 | CAT-13d
2 | xed2sdf_05210316543D
3 |
4 | 43 46 0 0 1 0 0 0 0 0999 V2000
5 | 16.6159 -1.3547 -3.9204 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | 15.4125 -0.6168 -1.5039 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | 14.2729 -2.5333 1.2874 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 16.1894 -2.3496 -3.0284 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | 15.5587 1.8326 -2.1089 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | 14.3652 -2.2938 2.6004 N 0 0 0 0 0 0 0 0 0 0 0 0
11 | 12.6571 -3.1079 -1.6844 O 0 0 0 0 0 0 0 0 0 0 0 0
12 | 15.5647 2.3288 -0.7836 C 0 0 0 0 0 0 0 0 0 0 0 0
13 | 15.3469 -2.7616 0.5345 N 0 0 0 0 0 0 0 0 0 0 0 0
14 | 15.2649 2.7464 -3.1489 C 0 0 0 0 0 0 0 0 0 0 0 0
15 | 13.4812 -2.9579 -0.7767 C 0 0 0 0 0 0 0 0 0 0 0 0
16 | 13.1444 -2.5995 0.5661 N 0 3 0 0 0 0 0 0 0 0 0 0
17 | 15.2486 3.6732 -0.5009 C 0 0 0 0 0 0 0 0 0 0 0 0
18 | 15.0192 -3.0683 -0.8497 C 0 0 0 0 0 0 0 0 0 0 0 0
19 | 15.8080 0.4004 -2.4044 C 0 0 0 0 0 0 0 0 0 0 0 0
20 | 14.9444 4.0910 -2.8732 C 0 0 0 0 0 0 0 0 0 0 0 0
21 | 16.4013 0.0015 -3.6209 C 0 0 0 0 0 0 0 0 0 0 0 0
22 | 15.5634 -1.9948 -1.8100 C 0 0 0 0 0 0 0 0 0 0 0 0
23 | 11.7860 -2.3271 1.0538 C 0 0 0 0 0 0 0 0 0 0 0 0
24 | 14.9243 4.5522 -1.5465 C 0 0 0 0 0 0 0 0 0 0 0 0
25 | 16.7355 -4.7539 -2.0801 C 0 0 0 0 0 0 0 0 0 0 0 0
26 | 15.2426 4.2511 1.1245 Cl 0 0 0 0 0 0 0 0 0 0 0 0
27 | 15.3463 -5.2332 -2.4204 C 0 0 0 0 0 0 0 0 0 0 0 0
28 | 15.5900 -4.4689 -1.1332 C 0 0 0 0 0 0 0 0 0 0 0 0
29 | 14.8362 -4.7371 -3.2436 H 0 0 0 0 0 0 0 0 0 0 0 0
30 | 14.6583 5.5769 -1.3284 H 0 0 0 0 0 0 0 0 0 0 0 0
31 | 15.5716 -5.0931 -0.2434 H 0 0 0 0 0 0 0 0 0 0 0 0
32 | 15.2371 2.4076 -4.1742 H 0 0 0 0 0 0 0 0 0 0 0 0
33 | 11.0292 -2.7766 0.4106 H 0 0 0 0 0 0 0 0 0 0 0 0
34 | 13.5838 -2.0392 3.2009 H 0 0 0 0 0 0 0 0 0 0 0 0
35 | 17.4697 -5.4962 -1.7713 H 0 0 0 0 0 0 0 0 0 0 0 0
36 | 15.2860 -2.2903 3.0398 H 0 0 0 0 0 0 0 0 0 0 0 0
37 | 15.8089 1.6730 0.0351 H 0 0 0 0 0 0 0 0 0 0 0 0
38 | 15.1570 -6.3019 -2.3389 H 0 0 0 0 0 0 0 0 0 0 0 0
39 | 17.1286 -3.9418 -2.6801 H 0 0 0 0 0 0 0 0 0 0 0 0
40 | 14.9319 -0.3282 -0.5818 H 0 0 0 0 0 0 0 0 0 0 0 0
41 | 16.3451 -3.3789 -3.3174 H 0 0 0 0 0 0 0 0 0 0 0 0
42 | 16.6981 0.7398 -4.3492 H 0 0 0 0 0 0 0 0 0 0 0 0
43 | 11.6524 -2.7177 2.0625 H 0 0 0 0 0 0 0 0 0 0 0 0
44 | 16.3098 -2.7539 0.8773 H 0 0 0 0 0 0 0 0 0 0 0 0
45 | 11.6181 -1.2506 1.0770 H 0 0 0 0 0 0 0 0 0 0 0 0
46 | 14.6865 4.7672 -3.6749 H 0 0 0 0 0 0 0 0 0 0 0 0
47 | 17.0896 -1.6334 -4.8519 H 0 0 0 0 0 0 0 0 0 0 0 0
48 | 3 9 1 0
49 | 20 13 2 0
50 | 13 8 1 0
51 | 19 41 1 0
52 | 19 29 1 0
53 | 20 26 1 0
54 | 3 6 1 0
55 | 9 40 1 0
56 | 24 21 1 0
57 | 1 17 1 0
58 | 21 35 1 0
59 | 17 15 2 0
60 | 16 20 1 0
61 | 16 42 1 0
62 | 12 3 2 0
63 | 10 28 1 0
64 | 14 11 1 0
65 | 5 10 1 0
66 | 19 12 1 0
67 | 24 27 1 0
68 | 18 4 1 0
69 | 15 5 1 0
70 | 24 23 1 0
71 | 23 34 1 0
72 | 6 32 1 0
73 | 9 14 1 0
74 | 8 33 1 0
75 | 17 38 1 0
76 | 21 31 1 0
77 | 10 16 2 0
78 | 18 2 2 0
79 | 1 43 1 0
80 | 6 30 1 0
81 | 11 7 2 0
82 | 4 37 1 0
83 | 23 21 1 0
84 | 13 22 1 0
85 | 19 39 1 0
86 | 14 24 1 0
87 | 5 8 2 0
88 | 15 2 1 0
89 | 2 36 1 0
90 | 23 25 1 0
91 | 4 1 2 0
92 | 12 11 1 0
93 | 14 18 1 0
94 | M CHG 1 12 1
95 | M END
96 | $$$$
97 |
--------------------------------------------------------------------------------
/test/chiral/bace_cat_13d_perm3.sdf:
--------------------------------------------------------------------------------
1 | CAT-13d
2 | xed2sdf_05210316543D
3 |
4 | 43 46 0 0 1 0 0 0 0 0999 V2000
5 | 15.4125 -0.6168 -1.5039 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | 14.3652 -2.2938 2.6004 N 0 0 0 0 0 0 0 0 0 0 0 0
7 | 15.8080 0.4004 -2.4044 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 15.2426 4.2511 1.1245 Cl 0 0 0 0 0 0 0 0 0 0 0 0
9 | 15.3463 -5.2332 -2.4204 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | 14.9444 4.0910 -2.8732 C 0 0 0 0 0 0 0 0 0 0 0 0
11 | 13.4812 -2.9579 -0.7768 C 0 0 0 0 0 0 0 0 0 0 0 0
12 | 15.5647 2.3288 -0.7836 C 0 0 0 0 0 0 0 0 0 0 0 0
13 | 15.5587 1.8326 -2.1090 C 0 0 0 0 0 0 0 0 0 0 0 0
14 | 16.1894 -2.3496 -3.0284 C 0 0 0 0 0 0 0 0 0 0 0 0
15 | 15.0192 -3.0683 -0.8497 C 0 0 0 0 0 0 0 0 0 0 0 0
16 | 16.4013 0.0015 -3.6209 C 0 0 0 0 0 0 0 0 0 0 0 0
17 | 15.5634 -1.9948 -1.8100 C 0 0 0 0 0 0 0 0 0 0 0 0
18 | 14.9243 4.5522 -1.5465 C 0 0 0 0 0 0 0 0 0 0 0 0
19 | 11.7860 -2.3271 1.0538 C 0 0 0 0 0 0 0 0 0 0 0 0
20 | 15.5900 -4.4689 -1.1332 C 0 0 0 0 0 0 0 0 0 0 0 0
21 | 12.6571 -3.1079 -1.6844 O 0 0 0 0 0 0 0 0 0 0 0 0
22 | 13.1444 -2.5995 0.5661 N 0 0 0 0 0 0 0 0 0 0 0 0
23 | 15.2649 2.7464 -3.1489 C 0 0 0 0 0 0 0 0 0 0 0 0
24 | 16.7355 -4.7539 -2.0801 C 0 0 0 0 0 0 0 0 0 0 0 0
25 | 15.3469 -2.7616 0.5345 N 0 3 0 0 0 0 0 0 0 0 0 0
26 | 16.6159 -1.3547 -3.9204 C 0 0 0 0 0 0 0 0 0 0 0 0
27 | 14.2729 -2.5333 1.2874 C 0 0 0 0 0 0 0 0 0 0 0 0
28 | 15.2486 3.6732 -0.5009 C 0 0 0 0 0 0 0 0 0 0 0 0
29 | 15.2372 2.4076 -4.1742 H 0 0 0 0 0 0 0 0 0 0 0 0
30 | 11.0292 -2.7766 0.4106 H 0 0 0 0 0 0 0 0 0 0 0 0
31 | 13.5838 -2.0392 3.2009 H 0 0 0 0 0 0 0 0 0 0 0 0
32 | 16.6981 0.7398 -4.3492 H 0 0 0 0 0 0 0 0 0 0 0 0
33 | 15.8089 1.6730 0.0351 H 0 0 0 0 0 0 0 0 0 0 0 0
34 | 15.1570 -6.3019 -2.3389 H 0 0 0 0 0 0 0 0 0 0 0 0
35 | 17.4697 -5.4962 -1.7713 H 0 0 0 0 0 0 0 0 0 0 0 0
36 | 15.2860 -2.2903 3.0398 H 0 0 0 0 0 0 0 0 0 0 0 0
37 | 14.9319 -0.3282 -0.5818 H 0 0 0 0 0 0 0 0 0 0 0 0
38 | 11.6524 -2.7177 2.0625 H 0 0 0 0 0 0 0 0 0 0 0 0
39 | 17.1286 -3.9418 -2.6801 H 0 0 0 0 0 0 0 0 0 0 0 0
40 | 16.3098 -2.7539 0.8773 H 0 0 0 0 0 0 0 0 0 0 0 0
41 | 11.6181 -1.2506 1.0770 H 0 0 0 0 0 0 0 0 0 0 0 0
42 | 15.5716 -5.0932 -0.2434 H 0 0 0 0 0 0 0 0 0 0 0 0
43 | 17.0896 -1.6334 -4.8519 H 0 0 0 0 0 0 0 0 0 0 0 0
44 | 16.3451 -3.3789 -3.3174 H 0 0 0 0 0 0 0 0 0 0 0 0
45 | 14.6583 5.5769 -1.3284 H 0 0 0 0 0 0 0 0 0 0 0 0
46 | 14.8362 -4.7371 -3.2436 H 0 0 0 0 0 0 0 0 0 0 0 0
47 | 14.6865 4.7672 -3.6749 H 0 0 0 0 0 0 0 0 0 0 0 0
48 | 11 13 1 0
49 | 14 41 1 0
50 | 16 38 1 0
51 | 19 6 2 0
52 | 6 43 1 0
53 | 8 29 1 0
54 | 5 30 1 0
55 | 10 40 1 0
56 | 2 32 1 0
57 | 12 28 1 0
58 | 24 8 1 0
59 | 5 42 1 0
60 | 11 16 1 0
61 | 14 24 2 0
62 | 16 5 1 0
63 | 11 7 1 0
64 | 9 8 2 0
65 | 20 35 1 0
66 | 10 22 1 0
67 | 3 9 1 0
68 | 13 10 2 0
69 | 15 18 1 0
70 | 19 25 1 0
71 | 2 27 1 0
72 | 23 2 1 0
73 | 21 11 1 0
74 | 21 36 1 0
75 | 3 1 2 0
76 | 22 12 2 0
77 | 24 4 1 0
78 | 15 37 1 0
79 | 1 33 1 0
80 | 22 39 1 0
81 | 15 34 1 0
82 | 13 1 1 0
83 | 5 20 1 0
84 | 9 19 1 0
85 | 18 23 1 0
86 | 16 20 1 0
87 | 12 3 1 0
88 | 6 14 1 0
89 | 18 7 1 0
90 | 15 26 1 0
91 | 7 17 2 0
92 | 20 31 1 0
93 | 23 21 2 0
94 | M CHG 1 21 1
95 | M END
96 | $$$$
97 |
--------------------------------------------------------------------------------
/test/chiral/bace_cat_13d_perm4.sdf:
--------------------------------------------------------------------------------
1 | CAT-13d
2 | xed2sdf_05210316543D
3 |
4 | 43 46 0 0 1 0 0 0 0 0999 V2000
5 | 15.5587 1.8326 -2.1090 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | 15.4125 -0.6168 -1.5039 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | 16.1894 -2.3496 -3.0284 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 15.8080 0.4004 -2.4044 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | 15.3463 -5.2332 -2.4204 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | 16.7355 -4.7539 -2.0801 C 0 0 0 0 0 0 0 0 0 0 0 0
11 | 13.1444 -2.5995 0.5661 N 0 0 0 0 0 0 0 0 0 0 0 0
12 | 15.5900 -4.4689 -1.1332 C 0 0 0 0 0 0 0 0 0 0 0 0
13 | 15.0192 -3.0683 -0.8497 C 0 0 0 0 0 0 0 0 0 0 0 0
14 | 15.5634 -1.9948 -1.8100 C 0 0 0 0 0 0 0 0 0 0 0 0
15 | 14.9243 4.5522 -1.5465 C 0 0 0 0 0 0 0 0 0 0 0 0
16 | 15.5647 2.3288 -0.7836 C 0 0 0 0 0 0 0 0 0 0 0 0
17 | 15.2649 2.7464 -3.1489 C 0 0 0 0 0 0 0 0 0 0 0 0
18 | 15.3469 -2.7616 0.5345 N 0 3 0 0 0 0 0 0 0 0 0 0
19 | 13.4812 -2.9579 -0.7768 C 0 0 0 0 0 0 0 0 0 0 0 0
20 | 14.3652 -2.2938 2.6004 N 0 0 0 0 0 0 0 0 0 0 0 0
21 | 15.2426 4.2511 1.1245 Cl 0 0 0 0 0 0 0 0 0 0 0 0
22 | 12.6571 -3.1079 -1.6844 O 0 0 0 0 0 0 0 0 0 0 0 0
23 | 11.7860 -2.3271 1.0538 C 0 0 0 0 0 0 0 0 0 0 0 0
24 | 16.4013 0.0015 -3.6209 C 0 0 0 0 0 0 0 0 0 0 0 0
25 | 14.9444 4.0910 -2.8732 C 0 0 0 0 0 0 0 0 0 0 0 0
26 | 16.6159 -1.3547 -3.9204 C 0 0 0 0 0 0 0 0 0 0 0 0
27 | 14.2729 -2.5333 1.2874 C 0 0 0 0 0 0 0 0 0 0 0 0
28 | 15.2486 3.6732 -0.5009 C 0 0 0 0 0 0 0 0 0 0 0 0
29 | 17.0896 -1.6334 -4.8519 H 0 0 0 0 0 0 0 0 0 0 0 0
30 | 11.0292 -2.7766 0.4106 H 0 0 0 0 0 0 0 0 0 0 0 0
31 | 14.8362 -4.7371 -3.2436 H 0 0 0 0 0 0 0 0 0 0 0 0
32 | 15.5716 -5.0931 -0.2434 H 0 0 0 0 0 0 0 0 0 0 0 0
33 | 15.1570 -6.3019 -2.3389 H 0 0 0 0 0 0 0 0 0 0 0 0
34 | 16.3451 -3.3789 -3.3174 H 0 0 0 0 0 0 0 0 0 0 0 0
35 | 15.2371 2.4076 -4.1742 H 0 0 0 0 0 0 0 0 0 0 0 0
36 | 14.6865 4.7672 -3.6749 H 0 0 0 0 0 0 0 0 0 0 0 0
37 | 17.4697 -5.4962 -1.7713 H 0 0 0 0 0 0 0 0 0 0 0 0
38 | 14.6583 5.5769 -1.3284 H 0 0 0 0 0 0 0 0 0 0 0 0
39 | 15.2860 -2.2903 3.0398 H 0 0 0 0 0 0 0 0 0 0 0 0
40 | 15.8089 1.6730 0.0351 H 0 0 0 0 0 0 0 0 0 0 0 0
41 | 13.5838 -2.0392 3.2009 H 0 0 0 0 0 0 0 0 0 0 0 0
42 | 14.9319 -0.3282 -0.5817 H 0 0 0 0 0 0 0 0 0 0 0 0
43 | 16.6981 0.7398 -4.3492 H 0 0 0 0 0 0 0 0 0 0 0 0
44 | 16.3098 -2.7539 0.8773 H 0 0 0 0 0 0 0 0 0 0 0 0
45 | 11.6181 -1.2506 1.0770 H 0 0 0 0 0 0 0 0 0 0 0 0
46 | 17.1286 -3.9418 -2.6801 H 0 0 0 0 0 0 0 0 0 0 0 0
47 | 11.6524 -2.7177 2.0625 H 0 0 0 0 0 0 0 0 0 0 0 0
48 | 22 25 1 0
49 | 24 12 2 0
50 | 15 18 2 0
51 | 7 15 1 0
52 | 14 9 1 0
53 | 7 23 1 0
54 | 6 33 1 0
55 | 11 24 1 0
56 | 3 30 1 0
57 | 11 34 1 0
58 | 12 36 1 0
59 | 10 2 1 0
60 | 9 15 1 0
61 | 9 10 1 0
62 | 5 6 1 0
63 | 13 21 1 0
64 | 8 28 1 0
65 | 19 26 1 0
66 | 1 12 1 0
67 | 20 39 1 0
68 | 4 1 1 0
69 | 19 41 1 0
70 | 21 11 2 0
71 | 3 22 1 0
72 | 23 14 2 0
73 | 5 27 1 0
74 | 5 29 1 0
75 | 1 13 2 0
76 | 16 35 1 0
77 | 4 2 2 0
78 | 19 7 1 0
79 | 10 3 2 0
80 | 8 5 1 0
81 | 14 40 1 0
82 | 16 37 1 0
83 | 2 38 1 0
84 | 22 20 2 0
85 | 8 6 1 0
86 | 21 32 1 0
87 | 24 17 1 0
88 | 13 31 1 0
89 | 6 42 1 0
90 | 23 16 1 0
91 | 9 8 1 0
92 | 20 4 1 0
93 | 19 43 1 0
94 | M CHG 1 14 1
95 | M END
96 | $$$$
97 |
--------------------------------------------------------------------------------
/test/chiral/bace_cat_13d_perm5.sdf:
--------------------------------------------------------------------------------
1 | CAT-13d
2 | xed2sdf_05210316543D
3 |
4 | 43 46 0 0 1 0 0 0 0 0999 V2000
5 | 15.4125 -0.6168 -1.5039 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | 14.2729 -2.5333 1.2874 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | 16.6159 -1.3547 -3.9204 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 15.5634 -1.9948 -1.8100 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | 15.8080 0.4004 -2.4044 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | 15.3469 -2.7616 0.5345 N 0 3 0 0 0 0 0 0 0 0 0 0
11 | 13.4812 -2.9579 -0.7768 C 0 0 0 0 0 0 0 0 0 0 0 0
12 | 11.7860 -2.3271 1.0538 C 0 0 0 0 0 0 0 0 0 0 0 0
13 | 15.2486 3.6732 -0.5009 C 0 0 0 0 0 0 0 0 0 0 0 0
14 | 15.5647 2.3288 -0.7836 C 0 0 0 0 0 0 0 0 0 0 0 0
15 | 15.5587 1.8326 -2.1090 C 0 0 0 0 0 0 0 0 0 0 0 0
16 | 16.7355 -4.7539 -2.0801 C 0 0 0 0 0 0 0 0 0 0 0 0
17 | 15.3463 -5.2332 -2.4204 C 0 0 0 0 0 0 0 0 0 0 0 0
18 | 15.5900 -4.4689 -1.1332 C 0 0 0 0 0 0 0 0 0 0 0 0
19 | 15.2426 4.2511 1.1245 Cl 0 0 0 0 0 0 0 0 0 0 0 0
20 | 15.2649 2.7464 -3.1489 C 0 0 0 0 0 0 0 0 0 0 0 0
21 | 14.9444 4.0910 -2.8732 C 0 0 0 0 0 0 0 0 0 0 0 0
22 | 14.3652 -2.2938 2.6004 N 0 0 0 0 0 0 0 0 0 0 0 0
23 | 14.9243 4.5522 -1.5465 C 0 0 0 0 0 0 0 0 0 0 0 0
24 | 12.6571 -3.1079 -1.6844 O 0 0 0 0 0 0 0 0 0 0 0 0
25 | 16.4013 0.0015 -3.6209 C 0 0 0 0 0 0 0 0 0 0 0 0
26 | 15.0192 -3.0683 -0.8497 C 0 0 0 0 0 0 0 0 0 0 0 0
27 | 13.1444 -2.5996 0.5661 N 0 0 0 0 0 0 0 0 0 0 0 0
28 | 16.1894 -2.3496 -3.0284 C 0 0 0 0 0 0 0 0 0 0 0 0
29 | 11.6181 -1.2506 1.0770 H 0 0 0 0 0 0 0 0 0 0 0 0
30 | 15.1570 -6.3019 -2.3389 H 0 0 0 0 0 0 0 0 0 0 0 0
31 | 14.9319 -0.3282 -0.5818 H 0 0 0 0 0 0 0 0 0 0 0 0
32 | 15.5716 -5.0931 -0.2434 H 0 0 0 0 0 0 0 0 0 0 0 0
33 | 16.3098 -2.7539 0.8773 H 0 0 0 0 0 0 0 0 0 0 0 0
34 | 11.0292 -2.7766 0.4106 H 0 0 0 0 0 0 0 0 0 0 0 0
35 | 16.3451 -3.3789 -3.3174 H 0 0 0 0 0 0 0 0 0 0 0 0
36 | 15.2860 -2.2903 3.0398 H 0 0 0 0 0 0 0 0 0 0 0 0
37 | 16.6981 0.7398 -4.3492 H 0 0 0 0 0 0 0 0 0 0 0 0
38 | 17.4698 -5.4962 -1.7713 H 0 0 0 0 0 0 0 0 0 0 0 0
39 | 15.8089 1.6730 0.0351 H 0 0 0 0 0 0 0 0 0 0 0 0
40 | 17.0896 -1.6334 -4.8519 H 0 0 0 0 0 0 0 0 0 0 0 0
41 | 13.5838 -2.0392 3.2009 H 0 0 0 0 0 0 0 0 0 0 0 0
42 | 11.6524 -2.7177 2.0625 H 0 0 0 0 0 0 0 0 0 0 0 0
43 | 17.1286 -3.9418 -2.6801 H 0 0 0 0 0 0 0 0 0 0 0 0
44 | 14.8362 -4.7371 -3.2436 H 0 0 0 0 0 0 0 0 0 0 0 0
45 | 14.6583 5.5769 -1.3284 H 0 0 0 0 0 0 0 0 0 0 0 0
46 | 14.6865 4.7672 -3.6749 H 0 0 0 0 0 0 0 0 0 0 0 0
47 | 15.2371 2.4076 -4.1742 H 0 0 0 0 0 0 0 0 0 0 0 0
48 | 6 22 1 0
49 | 1 27 1 0
50 | 17 42 1 0
51 | 9 10 2 0
52 | 8 38 1 0
53 | 5 1 2 0
54 | 18 32 1 0
55 | 17 19 2 0
56 | 3 36 1 0
57 | 6 29 1 0
58 | 14 13 1 0
59 | 21 33 1 0
60 | 19 9 1 0
61 | 21 5 1 0
62 | 5 11 1 0
63 | 13 40 1 0
64 | 13 26 1 0
65 | 22 4 1 0
66 | 8 23 1 0
67 | 11 10 1 0
68 | 4 24 2 0
69 | 22 14 1 0
70 | 12 39 1 0
71 | 13 12 1 0
72 | 7 20 2 0
73 | 22 7 1 0
74 | 23 7 1 0
75 | 19 41 1 0
76 | 3 21 2 0
77 | 9 15 1 0
78 | 14 12 1 0
79 | 11 16 2 0
80 | 16 17 1 0
81 | 8 25 1 0
82 | 18 37 1 0
83 | 10 35 1 0
84 | 23 2 1 0
85 | 4 1 1 0
86 | 2 6 2 0
87 | 12 34 1 0
88 | 24 31 1 0
89 | 14 28 1 0
90 | 2 18 1 0
91 | 8 30 1 0
92 | 24 3 1 0
93 | 16 43 1 0
94 | M CHG 1 6 1
95 | M END
96 | $$$$
97 |
--------------------------------------------------------------------------------
/test/linksfile/links1.txt:
--------------------------------------------------------------------------------
1 | phenyl.sdf phenylfuran.sdf
2 |
--------------------------------------------------------------------------------
/test/linksfile/links2.txt:
--------------------------------------------------------------------------------
1 | phenyl.sdf phenylfuran.sdf 0.77777
2 | phenyl.sdf toluyl.sdf 0.88888
3 |
--------------------------------------------------------------------------------
/test/linksfile/links3.txt:
--------------------------------------------------------------------------------
1 | phenyl.sdf phenylcyclobutyl.sdf 0.1 force
2 | phenyl.sdf phenylfuran.sdf 0.2 force
3 | phenyl.sdf toluyl.sdf 0.3
4 | phenylcyclobutyl.sdf phenylfuran.sdf 0.4 force
5 | phenylcyclobutyl.sdf toluyl.sdf 0.5 force
6 | phenylfuran.sdf toluyl.sdf 0.6 force
7 |
--------------------------------------------------------------------------------
/test/linksfile/phenyl.sdf:
--------------------------------------------------------------------------------
1 | phenyl
2 | xed2sdf_05210316543D
3 |
4 | 18 18 0 0 0 0 0 0 0 0999 V2000
5 | -0.0733 1.4513 0.0087 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | 1.1660 0.8543 -0.0305 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | 1.2703 -0.5172 -0.0016 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 0.1342 -1.2899 0.0666 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | -1.1037 -0.6898 0.1060 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | -1.2144 0.6842 0.0767 C 0 0 0 0 0 0 0 0 0 0 0 0
11 | -2.5500 1.4090 0.1180 C 0 0 0 0 0 0 0 0 0 0 0 0
12 | -3.8135 0.5283 0.1220 C 0 0 0 0 0 0 0 0 0 0 0 0
13 | -0.1456 2.4485 -0.0124 H 0 0 0 0 0 0 0 0 0 0 0 0
14 | 1.9906 1.4175 -0.0799 H 0 0 0 0 0 0 0 0 0 0 0 0
15 | 2.1706 -0.9517 -0.0301 H 0 0 0 0 0 0 0 0 0 0 0 0
16 | -1.9279 -1.2539 0.1558 H 0 0 0 0 0 0 0 0 0 0 0 0
17 | 0.2079 -2.2870 0.0878 H 0 0 0 0 0 0 0 0 0 0 0 0
18 | -2.5700 2.0922 1.1041 H 0 0 0 0 0 0 0 0 0 0 0 0
19 | -2.6068 2.1325 -0.8377 H 0 0 0 0 0 0 0 0 0 0 0 0
20 | -4.7890 1.2260 0.1573 H 0 0 0 0 0 0 0 0 0 0 0 0
21 | -3.7986 -0.1875 1.0849 H 0 0 0 0 0 0 0 0 0 0 0 0
22 | -3.8372 -0.1426 -0.8726 H 0 0 0 0 0 0 0 0 0 0 0 0
23 | 1 6 2 0
24 | 2 1 1 0
25 | 3 2 2 0
26 | 4 3 1 0
27 | 5 4 2 0
28 | 6 5 1 0
29 | 6 7 1 0
30 | 7 8 1 0
31 | 1 9 1 0
32 | 2 10 1 0
33 | 3 11 1 0
34 | 4 13 1 0
35 | 5 12 1 0
36 | 7 14 1 0
37 | 7 15 1 0
38 | 8 16 1 0
39 | 8 17 1 0
40 | 8 18 1 0
41 | M END
42 | >
43 | false
44 |
45 | >
46 | 0.500
47 |
48 | >
49 | 0
50 |
51 | >
52 | 0
53 |
54 | >
55 | 106.2
56 |
57 | > <#Atoms_cresset>
58 | 8
59 |
60 | >
61 | 2.2
62 |
63 | >
64 | 0
65 |
66 | >
67 | 1
68 |
69 | >
70 | 0
71 |
72 | > <_cresset_fieldpoints>
73 | -5 -0.234587 0.055735 -2.814415 -5.2903
74 | -5 0.023247 0.186111 2.901422 -5.2784
75 | -6 -1.360068 4.380095 0.012308 2.0290
76 | -6 4.311040 0.423086 -0.154910 1.7344
77 | -6 1.796086 3.993629 -0.131632 1.7638
78 | -6 2.457426 -3.464894 0.017965 1.7181
79 | -6 -3.547228 -2.758875 0.235646 1.9077
80 | -7 -2.092885 0.259874 -3.046483 -1.9365
81 | -7 -1.558968 4.517028 0.188562 -1.4531
82 | -7 -0.605739 0.184744 -3.174024 -1.8883
83 | -7 -0.268997 0.343572 3.282107 -1.8771
84 | -7 4.533032 0.415883 -0.168589 -0.9682
85 | -7 1.880946 4.193428 -0.148368 -1.0007
86 | -7 2.563035 -3.662832 0.003794 -0.9683
87 | -7 -3.785009 -2.780910 -0.050233 -1.4601
88 | -7 -4.509257 3.964528 0.208243 -1.1401
89 | -7 -2.046873 0.245953 3.244507 -1.9060
90 | -8 0.025932 0.085791 0.037910 7.1877
91 | -8 -2.291075 0.318835 0.112898 5.6294
92 |
93 | $$$$
94 |
--------------------------------------------------------------------------------
/test/linksfile/toluyl.sdf:
--------------------------------------------------------------------------------
1 | toluyl
2 | xed2sdf_05210316543D
3 |
4 | 21 21 0 0 0 0 0 0 0 0999 V2000
5 | -0.1287 1.4436 0.1374 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | 1.1199 0.8649 0.1388 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | 1.2396 -0.5053 0.0866 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 0.1122 -1.2920 0.0314 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | -1.1344 -0.7088 0.0291 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | -1.2615 0.6632 0.0829 C 0 0 0 0 0 0 0 0 0 0 0 0
11 | -2.6032 1.3787 0.0842 C 0 0 0 0 0 0 0 0 0 0 0 0
12 | -3.8657 0.4974 0.1005 C 0 0 0 0 0 0 0 0 0 0 0 0
13 | 2.3483 1.7493 0.2016 C 0 0 0 0 0 0 0 0 0 0 0 0
14 | -0.2139 2.4390 0.1765 H 0 0 0 0 0 0 0 0 0 0 0 0
15 | 2.1454 -0.9288 0.0884 H 0 0 0 0 0 0 0 0 0 0 0 0
16 | -1.9522 -1.2830 -0.0112 H 0 0 0 0 0 0 0 0 0 0 0 0
17 | 0.1985 -2.2876 -0.0070 H 0 0 0 0 0 0 0 0 0 0 0 0
18 | -2.6373 2.0884 1.0514 H 0 0 0 0 0 0 0 0 0 0 0 0
19 | -2.6511 2.0753 -0.8916 H 0 0 0 0 0 0 0 0 0 0 0 0
20 | -4.8399 1.1972 0.1325 H 0 0 0 0 0 0 0 0 0 0 0 0
21 | -3.8493 -0.2093 1.0702 H 0 0 0 0 0 0 0 0 0 0 0 0
22 | -3.8932 -0.1806 -0.8892 H 0 0 0 0 0 0 0 0 0 0 0 0
23 | 3.3420 1.1166 -0.0301 H 0 0 0 0 0 0 0 0 0 0 0 0
24 | 2.4321 2.2313 1.2974 H 0 0 0 0 0 0 0 0 0 0 0 0
25 | 2.2434 2.6282 -0.6084 H 0 0 0 0 0 0 0 0 0 0 0 0
26 | 1 6 2 0
27 | 2 1 1 0
28 | 2 9 1 0
29 | 3 2 2 0
30 | 4 3 1 0
31 | 5 4 2 0
32 | 6 5 1 0
33 | 6 7 1 0
34 | 7 8 1 0
35 | 1 10 1 0
36 | 3 11 1 0
37 | 4 13 1 0
38 | 5 12 1 0
39 | 7 14 1 0
40 | 7 15 1 0
41 | 8 16 1 0
42 | 8 17 1 0
43 | 8 18 1 0
44 | 9 19 1 0
45 | 9 20 1 0
46 | 9 21 1 0
47 | M END
48 | >
49 | false
50 |
51 | >
52 | 0.500
53 |
54 | >
55 | 0
56 |
57 | >
58 | 0
59 |
60 | >
61 | 120.2
62 |
63 | > <#Atoms_cresset>
64 | 9
65 |
66 | >
67 | 2.6
68 |
69 | >
70 | 0
71 |
72 | >
73 | 1
74 |
75 | >
76 | 0
77 |
78 | > <_cresset_fieldpoints>
79 | -5 0.008522 0.267777 -2.758281 -5.5867
80 | -5 -0.119070 0.043230 2.931842 -5.5917
81 | -6 0.590387 4.546290 0.268672 1.9514
82 | -6 -1.393872 4.371596 0.210859 2.0098
83 | -6 2.537503 -3.388101 -0.009318 1.6456
84 | -6 -3.587573 -2.777867 -0.081397 1.8350
85 | -6 4.381054 -1.155498 0.128075 1.8272
86 | -6 5.148639 3.042823 0.415846 1.1109
87 | -7 -1.578198 4.493007 0.009328 -1.5215
88 | -7 -0.236002 0.186086 3.302474 -1.9984
89 | -7 -3.815108 -2.813158 0.111945 -1.4591
90 | -7 -0.102794 0.440597 -3.122239 -1.9844
91 | -7 2.657345 -3.561917 -0.075642 -0.9960
92 | -7 -2.147875 0.280342 -3.072160 -1.9153
93 | -7 -4.554007 3.938925 0.097355 -1.1432
94 | -7 -2.019970 0.204714 3.221865 -1.9540
95 | -8 -0.010391 0.081569 0.083822 7.2096
96 | -8 -2.335089 0.293857 0.068131 5.6072
97 |
98 | $$$$
99 |
--------------------------------------------------------------------------------
/test/radial/ejm_31.mol2:
--------------------------------------------------------------------------------
1 | @MOLECULE
2 | ejm_31
3 | 32 33 0 0 0
4 | SMALL
5 | GASTEIGER
6 |
7 | @ATOM
8 | 1 C 5.5936 -1.0358 -0.9810 C.ar 1 LIG1 -0.0590
9 | 2 C 4.4624 -1.4147 -1.7043 C.ar 1 LIG1 -0.0426
10 | 3 C 3.2394 -0.7670 -1.4957 C.ar 1 LIG1 0.0545
11 | 4 C 3.1453 0.2734 -0.5445 C.ar 1 LIG1 0.0735
12 | 5 C 4.2984 0.6559 0.1752 C.ar 1 LIG1 0.0545
13 | 6 C 5.5127 -0.0032 -0.0466 C.ar 1 LIG1 -0.0426
14 | 7 CL 4.2493 1.9292 1.3915 Cl 1 LIG1 -0.0827
15 | 8 C 1.8615 0.9632 -0.3092 C.2 1 LIG1 0.2511
16 | 9 O 1.7837 2.2042 -0.5173 O.2 1 LIG1 -0.2698
17 | 10 N 0.7124 0.2207 0.1320 N.am 1 LIG1 -0.2813
18 | 11 C -0.5488 0.8170 0.4777 C.ar 1 LIG1 0.0384
19 | 12 C -0.6196 2.0442 1.1553 C.ar 1 LIG1 -0.0222
20 | 13 C -1.8671 2.5813 1.4753 C.ar 1 LIG1 0.0314
21 | 14 N -3.0026 1.9073 1.1560 N.ar 1 LIG1 -0.2400
22 | 15 C -2.9742 0.6955 0.5372 C.ar 1 LIG1 0.1266
23 | 16 C -1.7359 0.1350 0.1789 C.ar 1 LIG1 -0.0003
24 | 17 N -4.2159 0.0509 0.2127 N.am 1 LIG1 -0.2706
25 | 18 C -4.4015 -1.3720 0.1574 C.2 1 LIG1 0.2152
26 | 19 O -3.5392 -2.1533 0.6422 O.2 1 LIG1 -0.2757
27 | 20 C -5.6736 -1.9344 -0.3878 C.3 1 LIG1 0.0125
28 | 21 CL 1.8658 -1.2447 -2.4900 Cl 1 LIG1 -0.0827
29 | 22 H 6.5362 -1.5408 -1.1483 H 1 LIG1 0.0618
30 | 23 H 4.5394 -2.2088 -2.4363 H 1 LIG1 0.0632
31 | 24 H 6.3964 0.2827 0.5098 H 1 LIG1 0.0632
32 | 25 H 0.7742 -0.8225 0.1402 H 1 LIG1 0.1551
33 | 26 H 0.2757 2.5743 1.4511 H 1 LIG1 0.0651
34 | 27 H -1.9328 3.5330 1.9855 H 1 LIG1 0.0831
35 | 28 H -1.6875 -0.8012 -0.3614 H 1 LIG1 0.0671
36 | 29 H -5.0598 0.6567 0.0989 H 1 LIG1 0.1562
37 | 30 H -6.0059 -1.3387 -1.2637 H 1 LIG1 0.0323
38 | 31 H -5.5239 -2.9868 -0.7098 H 1 LIG1 0.0323
39 | 32 H -6.4583 -1.9009 0.3962 H 1 LIG1 0.0323
40 | @BOND
41 | 1 1 2 ar
42 | 2 1 6 ar
43 | 3 2 3 ar
44 | 4 3 4 ar
45 | 5 3 21 1
46 | 6 4 5 ar
47 | 7 4 8 1
48 | 8 5 6 ar
49 | 9 5 7 1
50 | 10 8 9 2
51 | 11 8 10 am
52 | 12 10 11 1
53 | 13 11 12 ar
54 | 14 11 16 ar
55 | 15 12 13 ar
56 | 16 13 14 ar
57 | 17 14 15 ar
58 | 18 15 16 ar
59 | 19 15 17 1
60 | 20 17 18 am
61 | 21 18 19 2
62 | 22 18 20 1
63 | 23 1 22 1
64 | 24 2 23 1
65 | 25 6 24 1
66 | 26 10 25 1
67 | 27 12 26 1
68 | 28 13 27 1
69 | 29 16 28 1
70 | 30 17 29 1
71 | 31 20 30 1
72 | 32 20 31 1
73 | 33 20 32 1
74 |
--------------------------------------------------------------------------------
/test/radial/ejm_42.mol2:
--------------------------------------------------------------------------------
1 | @MOLECULE
2 | ejm_42
3 | 35 36 0 0 0
4 | SMALL
5 | GASTEIGER
6 |
7 | @ATOM
8 | 1 C -6.4057 -0.4955 -0.0625 C.ar 1 LIG1 -0.0590
9 | 2 C -5.8247 -0.9633 -1.2414 C.ar 1 LIG1 -0.0426
10 | 3 C -4.4946 -0.6527 -1.5455 C.ar 1 LIG1 0.0545
11 | 4 C -3.7314 0.1335 -0.6549 C.ar 1 LIG1 0.0735
12 | 5 C -4.3315 0.6106 0.5318 C.ar 1 LIG1 0.0545
13 | 6 C -5.6631 0.2901 0.8193 C.ar 1 LIG1 -0.0426
14 | 7 CL -3.4698 1.6637 1.6509 Cl 1 LIG1 -0.0827
15 | 8 C -2.3263 0.4586 -0.9703 C.2 1 LIG1 0.2511
16 | 9 O -2.0661 1.1016 -2.0230 O.2 1 LIG1 -0.2698
17 | 10 N -1.2742 0.0622 -0.0747 N.am 1 LIG1 -0.2813
18 | 11 C 0.1257 0.2436 -0.3451 C.ar 1 LIG1 0.0384
19 | 12 C 0.6532 0.0721 -1.6348 C.ar 1 LIG1 -0.0222
20 | 13 C 2.0228 0.2391 -1.8441 C.ar 1 LIG1 0.0314
21 | 14 N 2.8394 0.5459 -0.8027 N.ar 1 LIG1 -0.2400
22 | 15 C 2.3698 0.6862 0.4669 C.ar 1 LIG1 0.1266
23 | 16 C 0.9972 0.5390 0.7115 C.ar 1 LIG1 -0.0003
24 | 17 N 3.2532 1.0304 1.5477 N.am 1 LIG1 -0.2703
25 | 18 C 4.6836 0.8704 1.5504 C.2 1 LIG1 0.2180
26 | 19 O 5.3620 1.5206 2.3903 O.2 1 LIG1 -0.2754
27 | 20 C 5.4021 -0.0989 0.6475 C.3 1 LIG1 0.0215
28 | 21 CL -3.8049 -1.2992 -3.0319 Cl 1 LIG1 -0.0827
29 | 22 C 4.9666 -1.5369 0.9153 C.3 1 LIG1 -0.0570
30 | 23 H -7.4353 -0.7388 0.1662 H 1 LIG1 0.0618
31 | 24 H -6.4096 -1.5727 -1.9187 H 1 LIG1 0.0632
32 | 25 H -6.1278 0.6585 1.7252 H 1 LIG1 0.0632
33 | 26 H -1.5421 -0.3235 0.8589 H 1 LIG1 0.1551
34 | 27 H 0.0222 -0.2107 -2.4664 H 1 LIG1 0.0651
35 | 28 H 2.4390 0.1174 -2.8352 H 1 LIG1 0.0831
36 | 29 H 0.6086 0.6584 1.7156 H 1 LIG1 0.0671
37 | 30 H 2.8266 1.4505 2.4049 H 1 LIG1 0.1562
38 | 31 H 6.4968 -0.0291 0.8307 H 1 LIG1 0.0356
39 | 32 H 5.2470 0.1623 -0.4178 H 1 LIG1 0.0356
40 | 33 H 3.8892 -1.6733 0.6872 H 1 LIG1 0.0234
41 | 34 H 5.1512 -1.8027 1.9782 H 1 LIG1 0.0234
42 | 35 H 5.5509 -2.2268 0.2707 H 1 LIG1 0.0234
43 | @BOND
44 | 1 1 2 ar
45 | 2 1 6 ar
46 | 3 2 3 ar
47 | 4 3 4 ar
48 | 5 3 21 1
49 | 6 4 5 ar
50 | 7 4 8 1
51 | 8 5 6 ar
52 | 9 5 7 1
53 | 10 8 9 2
54 | 11 8 10 am
55 | 12 10 11 1
56 | 13 11 12 ar
57 | 14 11 16 ar
58 | 15 12 13 ar
59 | 16 13 14 ar
60 | 17 14 15 ar
61 | 18 15 16 ar
62 | 19 15 17 1
63 | 20 17 18 am
64 | 21 18 19 2
65 | 22 18 20 1
66 | 23 20 22 1
67 | 24 1 23 1
68 | 25 2 24 1
69 | 26 6 25 1
70 | 27 10 26 1
71 | 28 12 27 1
72 | 29 13 28 1
73 | 30 16 29 1
74 | 31 17 30 1
75 | 32 20 31 1
76 | 33 20 32 1
77 | 34 22 33 1
78 | 35 22 34 1
79 | 36 22 35 1
80 |
--------------------------------------------------------------------------------
/test/radial/ejm_43.mol2:
--------------------------------------------------------------------------------
1 | @MOLECULE
2 | ejm_43
3 | 38 39 0 0 0
4 | SMALL
5 | GASTEIGER
6 |
7 | @ATOM
8 | 1 C 7.1678 -0.2887 0.4794 C.ar 1 LIG1 -0.0590
9 | 2 C 6.8755 -0.0925 -0.8705 C.ar 1 LIG1 -0.0426
10 | 3 C 5.5688 -0.2590 -1.3423 C.ar 1 LIG1 0.0545
11 | 4 C 4.5365 -0.6223 -0.4500 C.ar 1 LIG1 0.0735
12 | 5 C 4.8442 -0.8286 0.9133 C.ar 1 LIG1 0.0545
13 | 6 C 6.1569 -0.6581 1.3671 C.ar 1 LIG1 -0.0426
14 | 7 CL 3.6277 -1.3628 2.0703 Cl 1 LIG1 -0.0827
15 | 8 C 3.1554 -0.7923 -0.9432 C.2 1 LIG1 0.2511
16 | 9 O 2.9218 -1.6583 -1.8290 O.2 1 LIG1 -0.2698
17 | 10 N 2.0913 0.0088 -0.4027 N.am 1 LIG1 -0.2813
18 | 11 C 0.7379 -0.0154 -0.8862 C.ar 1 LIG1 0.0384
19 | 12 C 0.4486 -0.1403 -2.2542 C.ar 1 LIG1 -0.0222
20 | 13 C -0.8808 -0.1332 -2.6786 C.ar 1 LIG1 0.0314
21 | 14 N -1.8849 0.0091 -1.7746 N.ar 1 LIG1 -0.2400
22 | 15 C -1.6428 0.1535 -0.4419 C.ar 1 LIG1 0.1266
23 | 16 C -0.3183 0.1517 0.0193 C.ar 1 LIG1 -0.0003
24 | 17 N -2.7254 0.3081 0.4932 N.am 1 LIG1 -0.2701
25 | 18 C -4.1171 0.3301 0.1290 C.2 1 LIG1 0.2208
26 | 19 O -4.4668 0.2339 -1.0794 O.2 1 LIG1 -0.2752
27 | 20 C -5.1743 0.4853 1.1937 C.3 1 LIG1 0.0303
28 | 21 CL 5.2537 0.0352 -3.0503 Cl 1 LIG1 -0.0827
29 | 22 C -6.1514 -0.6943 1.1590 C.3 1 LIG1 -0.0544
30 | 23 C -5.9148 1.8145 1.0196 C.3 1 LIG1 -0.0544
31 | 24 H 8.1809 -0.1584 0.8376 H 1 LIG1 0.0618
32 | 25 H 7.6673 0.1943 -1.5510 H 1 LIG1 0.0632
33 | 26 H 6.3973 -0.8200 2.4103 H 1 LIG1 0.0632
34 | 27 H 2.2965 0.5983 0.4355 H 1 LIG1 0.1551
35 | 28 H 1.2377 -0.2143 -2.9903 H 1 LIG1 0.0651
36 | 29 H -1.1147 -0.2313 -3.7303 H 1 LIG1 0.0831
37 | 30 H -0.1099 0.2681 1.0759 H 1 LIG1 0.0671
38 | 31 H -2.4848 0.4101 1.5052 H 1 LIG1 0.1562
39 | 32 H -4.6922 0.4936 2.1958 H 1 LIG1 0.0389
40 | 33 H -6.6973 -0.7284 0.1914 H 1 LIG1 0.0237
41 | 34 H -6.8915 -0.6007 1.9824 H 1 LIG1 0.0237
42 | 35 H -5.6003 -1.6497 1.2948 H 1 LIG1 0.0237
43 | 36 H -6.6585 1.9469 1.8343 H 1 LIG1 0.0237
44 | 37 H -6.4449 1.8470 0.0432 H 1 LIG1 0.0237
45 | 38 H -5.1951 2.6600 1.0661 H 1 LIG1 0.0237
46 | @BOND
47 | 1 1 2 ar
48 | 2 1 6 ar
49 | 3 2 3 ar
50 | 4 3 4 ar
51 | 5 3 21 1
52 | 6 4 5 ar
53 | 7 4 8 1
54 | 8 5 6 ar
55 | 9 5 7 1
56 | 10 8 9 2
57 | 11 8 10 am
58 | 12 10 11 1
59 | 13 11 12 ar
60 | 14 11 16 ar
61 | 15 12 13 ar
62 | 16 13 14 ar
63 | 17 14 15 ar
64 | 18 15 16 ar
65 | 19 15 17 1
66 | 20 17 18 am
67 | 21 18 19 2
68 | 22 18 20 1
69 | 23 20 22 1
70 | 24 20 23 1
71 | 25 1 24 1
72 | 26 2 25 1
73 | 27 6 26 1
74 | 28 10 27 1
75 | 29 12 28 1
76 | 30 13 29 1
77 | 31 16 30 1
78 | 32 17 31 1
79 | 33 20 32 1
80 | 34 22 33 1
81 | 35 22 34 1
82 | 36 22 35 1
83 | 37 23 36 1
84 | 38 23 37 1
85 | 39 23 38 1
86 |
--------------------------------------------------------------------------------
/test/radial/ejm_45.mol2:
--------------------------------------------------------------------------------
1 | @MOLECULE
2 | ejm_45
3 | 39 41 0 0 0
4 | SMALL
5 | GASTEIGER
6 |
7 | @ATOM
8 | 1 C 7.4556 0.3365 0.4003 C.ar 1 LIG1 -0.0590
9 | 2 C 6.4844 1.2952 0.6895 C.ar 1 LIG1 -0.0426
10 | 3 C 5.1384 0.9273 0.8007 C.ar 1 LIG1 0.0545
11 | 4 C 4.7565 -0.4202 0.6093 C.ar 1 LIG1 0.0735
12 | 5 C 5.7495 -1.3843 0.3270 C.ar 1 LIG1 0.0545
13 | 6 C 7.0906 -0.9983 0.2248 C.ar 1 LIG1 -0.0426
14 | 7 CL 5.3443 -3.0744 0.0389 Cl 1 LIG1 -0.0827
15 | 8 C 3.3397 -0.8250 0.7124 C.2 1 LIG1 0.2511
16 | 9 O 3.0063 -1.6840 1.5732 O.2 1 LIG1 -0.2698
17 | 10 N 2.3524 -0.2357 -0.1498 N.am 1 LIG1 -0.2813
18 | 11 C 0.9958 -0.6994 -0.2430 C.ar 1 LIG1 0.0384
19 | 12 C 0.6879 -2.0681 -0.2110 C.ar 1 LIG1 -0.0222
20 | 13 C -0.6395 -2.4768 -0.3453 C.ar 1 LIG1 0.0314
21 | 14 N -1.6228 -1.5554 -0.5172 N.ar 1 LIG1 -0.2400
22 | 15 C -1.3602 -0.2202 -0.5696 C.ar 1 LIG1 0.1266
23 | 16 C -0.0375 0.2261 -0.4366 C.ar 1 LIG1 -0.0003
24 | 17 N -2.4235 0.7325 -0.7413 N.am 1 LIG1 -0.2703
25 | 18 C -3.7751 0.3813 -1.0800 C.2 1 LIG1 0.2185
26 | 19 O -4.0884 -0.8135 -1.3287 O.2 1 LIG1 -0.2754
27 | 20 C -4.8420 1.4326 -1.1007 C.3 1 LIG1 0.0271
28 | 21 CL 3.9732 2.1709 1.2492 Cl 1 LIG1 -0.0827
29 | 22 C -5.4534 1.5765 0.2973 C.3 1 LIG1 -0.0328
30 | 23 C -6.8752 2.1161 0.3254 C.3 1 LIG1 -0.0495
31 | 24 C -6.6139 0.6437 0.6052 C.3 1 LIG1 -0.0495
32 | 25 H 8.4954 0.6285 0.3149 H 1 LIG1 0.0618
33 | 26 H 6.7808 2.3255 0.8428 H 1 LIG1 0.0632
34 | 27 H 7.8524 -1.7322 -0.0052 H 1 LIG1 0.0632
35 | 28 H 2.6155 0.6137 -0.6975 H 1 LIG1 0.1551
36 | 29 H 1.4647 -2.8145 -0.1116 H 1 LIG1 0.0651
37 | 30 H -0.8879 -3.5295 -0.3215 H 1 LIG1 0.0831
38 | 31 H 0.1859 1.2846 -0.4751 H 1 LIG1 0.0671
39 | 32 H -2.2013 1.7463 -0.6171 H 1 LIG1 0.1562
40 | 33 H -5.6046 1.1659 -1.8656 H 1 LIG1 0.0361
41 | 34 H -4.3999 2.4092 -1.3940 H 1 LIG1 0.0361
42 | 35 H -4.8193 1.8657 1.1621 H 1 LIG1 0.0305
43 | 36 H -7.3556 2.3043 -0.6589 H 1 LIG1 0.0268
44 | 37 H -7.1405 2.6958 1.2349 H 1 LIG1 0.0268
45 | 38 H -6.9250 -0.0393 -0.2141 H 1 LIG1 0.0268
46 | 39 H -6.7039 0.3640 1.6761 H 1 LIG1 0.0268
47 | @BOND
48 | 1 1 2 ar
49 | 2 1 6 ar
50 | 3 2 3 ar
51 | 4 3 4 ar
52 | 5 3 21 1
53 | 6 4 5 ar
54 | 7 4 8 1
55 | 8 5 6 ar
56 | 9 5 7 1
57 | 10 8 9 2
58 | 11 8 10 am
59 | 12 10 11 1
60 | 13 11 12 ar
61 | 14 11 16 ar
62 | 15 12 13 ar
63 | 16 13 14 ar
64 | 17 14 15 ar
65 | 18 15 16 ar
66 | 19 15 17 1
67 | 20 17 18 am
68 | 21 18 19 2
69 | 22 18 20 1
70 | 23 20 22 1
71 | 24 22 23 1
72 | 25 22 24 1
73 | 26 23 24 1
74 | 27 1 25 1
75 | 28 2 26 1
76 | 29 6 27 1
77 | 30 10 28 1
78 | 31 12 29 1
79 | 32 13 30 1
80 | 33 16 31 1
81 | 34 17 32 1
82 | 35 20 33 1
83 | 36 20 34 1
84 | 37 22 35 1
85 | 38 23 36 1
86 | 39 23 37 1
87 | 40 24 38 1
88 | 41 24 39 1
89 |
--------------------------------------------------------------------------------
/test/radial/ejm_46.mol2:
--------------------------------------------------------------------------------
1 | @MOLECULE
2 | ejm_46
3 | 36 38 0 0 0
4 | SMALL
5 | GASTEIGER
6 |
7 | @ATOM
8 | 1 C -6.4803 -1.2817 -0.4370 C.ar 1 LIG1 -0.0590
9 | 2 C -6.1972 -0.1094 0.2644 C.ar 1 LIG1 -0.0426
10 | 3 C -4.8720 0.2536 0.5302 C.ar 1 LIG1 0.0545
11 | 4 C -3.8125 -0.5670 0.0829 C.ar 1 LIG1 0.0735
12 | 5 C -4.1100 -1.7564 -0.6175 C.ar 1 LIG1 0.0545
13 | 6 C -5.4411 -2.1033 -0.8743 C.ar 1 LIG1 -0.0426
14 | 7 CL -2.8391 -2.8153 -1.2231 Cl 1 LIG1 -0.0827
15 | 8 C -2.4091 -0.1958 0.3508 C.2 1 LIG1 0.2511
16 | 9 O -1.6879 -0.9725 1.0336 O.2 1 LIG1 -0.2698
17 | 10 N -1.8822 1.0458 -0.1462 N.am 1 LIG1 -0.2813
18 | 11 C -0.5043 1.4385 -0.0328 C.ar 1 LIG1 0.0384
19 | 12 C -0.1891 2.7880 0.1658 C.ar 1 LIG1 -0.0222
20 | 13 C 1.1474 3.1785 0.2554 C.ar 1 LIG1 0.0314
21 | 14 N 2.1366 2.2554 0.1320 N.ar 1 LIG1 -0.2400
22 | 15 C 1.8719 0.9370 -0.0861 C.ar 1 LIG1 0.1266
23 | 16 C 0.5392 0.5091 -0.1783 C.ar 1 LIG1 -0.0003
24 | 17 N 2.9399 -0.0167 -0.2229 N.am 1 LIG1 -0.2701
25 | 18 C 4.3370 0.3179 -0.1857 C.2 1 LIG1 0.2213
26 | 19 O 4.7146 1.5196 -0.1378 O.2 1 LIG1 -0.2751
27 | 20 C 5.3659 -0.7693 -0.2690 C.3 1 LIG1 0.0360
28 | 21 C 5.2982 -1.7909 0.8565 C.3 1 LIG1 -0.0412
29 | 22 C 6.4056 -0.7519 0.8420 C.3 1 LIG1 -0.0412
30 | 23 CL -4.5833 1.7089 1.4801 Cl 1 LIG1 -0.0827
31 | 24 H -7.5078 -1.5564 -0.6382 H 1 LIG1 0.0618
32 | 25 H -7.0118 0.5143 0.6104 H 1 LIG1 0.0632
33 | 26 H -5.6717 -3.0106 -1.4182 H 1 LIG1 0.0632
34 | 27 H -2.5509 1.7342 -0.5597 H 1 LIG1 0.1551
35 | 28 H -0.9738 3.5279 0.2624 H 1 LIG1 0.0651
36 | 29 H 1.3993 4.2173 0.4217 H 1 LIG1 0.0831
37 | 30 H 0.3253 -0.5304 -0.3890 H 1 LIG1 0.0671
38 | 31 H 2.6893 -1.0237 -0.3505 H 1 LIG1 0.1562
39 | 32 H 5.7055 -1.1512 -1.2549 H 1 LIG1 0.0394
40 | 33 H 4.5278 -1.6127 1.6379 H 1 LIG1 0.0273
41 | 34 H 5.6351 -2.8106 0.5740 H 1 LIG1 0.0273
42 | 35 H 6.2878 0.0372 1.6160 H 1 LIG1 0.0273
43 | 36 H 7.3977 -1.1576 0.5515 H 1 LIG1 0.0273
44 | @BOND
45 | 1 1 2 ar
46 | 2 1 6 ar
47 | 3 2 3 ar
48 | 4 3 4 ar
49 | 5 3 23 1
50 | 6 4 5 ar
51 | 7 4 8 1
52 | 8 5 6 ar
53 | 9 5 7 1
54 | 10 8 9 2
55 | 11 8 10 am
56 | 12 10 11 1
57 | 13 11 12 ar
58 | 14 11 16 ar
59 | 15 12 13 ar
60 | 16 13 14 ar
61 | 17 14 15 ar
62 | 18 15 16 ar
63 | 19 15 17 1
64 | 20 17 18 am
65 | 21 18 19 2
66 | 22 18 20 1
67 | 23 20 21 1
68 | 24 20 22 1
69 | 25 21 22 1
70 | 26 1 24 1
71 | 27 2 25 1
72 | 28 6 26 1
73 | 29 10 27 1
74 | 30 12 28 1
75 | 31 13 29 1
76 | 32 16 30 1
77 | 33 17 31 1
78 | 34 20 32 1
79 | 35 21 33 1
80 | 36 21 34 1
81 | 37 22 35 1
82 | 38 22 36 1
83 |
--------------------------------------------------------------------------------
/test/radial/ejm_50.mol2:
--------------------------------------------------------------------------------
1 | @MOLECULE
2 | ejm_50
3 | 33 34 0 0 0
4 | SMALL
5 | GASTEIGER
6 |
7 | @ATOM
8 | 1 C -5.7712 1.1760 0.8320 C.ar 1 LIG1 -0.0590
9 | 2 C -5.0585 2.3620 0.6570 C.ar 1 LIG1 -0.0426
10 | 3 C -3.7732 2.3407 0.1038 C.ar 1 LIG1 0.0545
11 | 4 C -3.1879 1.1119 -0.2797 C.ar 1 LIG1 0.0735
12 | 5 C -3.9219 -0.0837 -0.1014 C.ar 1 LIG1 0.0545
13 | 6 C -5.2059 -0.0414 0.4536 C.ar 1 LIG1 -0.0426
14 | 7 CL -3.2977 -1.6482 -0.6194 Cl 1 LIG1 -0.0827
15 | 8 C -1.8292 1.0764 -0.8637 C.2 1 LIG1 0.2511
16 | 9 O -1.5423 1.8484 -1.8185 O.2 1 LIG1 -0.2698
17 | 10 N -0.8300 0.2046 -0.3118 N.am 1 LIG1 -0.2813
18 | 11 C 0.3962 -0.1401 -0.9792 C.ar 1 LIG1 0.0384
19 | 12 C 0.4628 -0.2541 -2.3768 C.ar 1 LIG1 -0.0222
20 | 13 C 1.6611 -0.6391 -2.9792 C.ar 1 LIG1 0.0314
21 | 14 N 2.7538 -0.9049 -2.2169 N.ar 1 LIG1 -0.2400
22 | 15 C 2.7306 -0.8025 -0.8602 C.ar 1 LIG1 0.1267
23 | 16 C 1.5337 -0.4413 -0.2177 C.ar 1 LIG1 -0.0003
24 | 17 N 3.9144 -1.1326 -0.1170 N.am 1 LIG1 -0.2684
25 | 18 C 4.2754 -0.5322 1.1371 C.2 1 LIG1 0.2438
26 | 19 O 3.7118 0.5271 1.5252 O.2 1 LIG1 -0.2729
27 | 20 C 5.3964 -1.1078 1.9502 C.3 1 LIG1 0.1206
28 | 21 CL -2.9102 3.8701 -0.0401 Cl 1 LIG1 -0.0827
29 | 22 O 5.0252 -1.1969 3.2994 O.3 1 LIG1 -0.3858
30 | 23 H -6.7653 1.2007 1.2597 H 1 LIG1 0.0618
31 | 24 H -5.5051 3.3011 0.9586 H 1 LIG1 0.0632
32 | 25 H -5.7724 -0.9549 0.5839 H 1 LIG1 0.0632
33 | 26 H -0.9749 -0.1421 0.6639 H 1 LIG1 0.1551
34 | 27 H -0.4077 -0.0830 -2.9955 H 1 LIG1 0.0651
35 | 28 H 1.7196 -0.7390 -4.0545 H 1 LIG1 0.0831
36 | 29 H 1.4744 -0.4103 0.8622 H 1 LIG1 0.0671
37 | 30 H 4.5988 -1.7832 -0.5644 H 1 LIG1 0.1563
38 | 31 H 6.3075 -0.4782 1.8304 H 1 LIG1 0.0654
39 | 32 H 5.6395 -2.1287 1.5869 H 1 LIG1 0.0654
40 | 33 H 5.1521 -0.2933 3.6921 H 1 LIG1 0.2100
41 | @BOND
42 | 1 1 2 ar
43 | 2 1 6 ar
44 | 3 2 3 ar
45 | 4 3 4 ar
46 | 5 3 21 1
47 | 6 4 5 ar
48 | 7 4 8 1
49 | 8 5 6 ar
50 | 9 5 7 1
51 | 10 8 9 2
52 | 11 8 10 am
53 | 12 10 11 1
54 | 13 11 12 ar
55 | 14 11 16 ar
56 | 15 12 13 ar
57 | 16 13 14 ar
58 | 17 14 15 ar
59 | 18 15 16 ar
60 | 19 15 17 1
61 | 20 17 18 am
62 | 21 18 19 2
63 | 22 18 20 1
64 | 23 20 22 1
65 | 24 1 23 1
66 | 25 2 24 1
67 | 26 6 25 1
68 | 27 10 26 1
69 | 28 12 27 1
70 | 29 13 28 1
71 | 30 16 29 1
72 | 31 17 30 1
73 | 32 20 31 1
74 | 33 20 32 1
75 | 34 22 33 1
76 |
--------------------------------------------------------------------------------
/test/radial/ejm_54.mol2:
--------------------------------------------------------------------------------
1 | @MOLECULE
2 | ejm_54
3 | 37 38 0 0 0
4 | SMALL
5 | GASTEIGER
6 |
7 | @ATOM
8 | 1 C 7.1409 -0.6193 0.4749 C.ar 1 LIG1 -0.0590
9 | 2 C 6.1396 -0.7849 1.4322 C.ar 1 LIG1 -0.0426
10 | 3 C 4.8411 -0.3253 1.1848 C.ar 1 LIG1 0.0545
11 | 4 C 4.5380 0.3060 -0.0422 C.ar 1 LIG1 0.0735
12 | 5 C 5.5608 0.4776 -1.0005 C.ar 1 LIG1 0.0545
13 | 6 C 6.8534 0.0115 -0.7358 C.ar 1 LIG1 -0.0426
14 | 7 CL 5.2494 1.2358 -2.5597 Cl 1 LIG1 -0.0827
15 | 8 C 3.1720 0.7920 -0.3205 C.2 1 LIG1 0.2511
16 | 9 O 2.9897 2.0202 -0.5392 O.2 1 LIG1 -0.2698
17 | 10 N 2.0648 -0.1246 -0.3208 N.am 1 LIG1 -0.2813
18 | 11 C 0.7200 0.2359 -0.6778 C.ar 1 LIG1 0.0384
19 | 12 C 0.4534 1.1376 -1.7201 C.ar 1 LIG1 -0.0222
20 | 13 C -0.8697 1.4373 -2.0477 C.ar 1 LIG1 0.0314
21 | 14 N -1.8902 0.8481 -1.3716 N.ar 1 LIG1 -0.2400
22 | 15 C -1.6712 -0.0467 -0.3681 C.ar 1 LIG1 0.1278
23 | 16 C -0.3538 -0.3719 -0.0137 C.ar 1 LIG1 -0.0002
24 | 17 N -2.7710 -0.6605 0.3275 N.am 1 LIG1 -0.2541
25 | 18 C -4.1571 -0.4034 0.0478 C.2 1 LIG1 0.3049
26 | 19 O -4.4898 0.3992 -0.8663 O.2 1 LIG1 -0.2525
27 | 20 CL 3.6397 -0.5020 2.4611 Cl 1 LIG1 -0.0827
28 | 21 C -6.5971 -0.8384 0.6127 C.3 1 LIG1 0.0102
29 | 22 C -7.0037 0.5168 1.1817 C.3 1 LIG1 -0.0495
30 | 23 N -5.1685 -1.0751 0.8120 N.am 1 LIG1 -0.2994
31 | 24 H 8.1431 -0.9766 0.6735 H 1 LIG1 0.0618
32 | 25 H 6.3768 -1.2643 2.3736 H 1 LIG1 0.0632
33 | 26 H 7.6375 0.1345 -1.4721 H 1 LIG1 0.0632
34 | 27 H 2.2319 -1.0981 0.0208 H 1 LIG1 0.1551
35 | 28 H 1.2539 1.5848 -2.2939 H 1 LIG1 0.0651
36 | 29 H -1.0862 2.1326 -2.8477 H 1 LIG1 0.0831
37 | 30 H -0.1641 -1.0839 0.7804 H 1 LIG1 0.0671
38 | 31 H -2.5528 -1.3386 1.0923 H 1 LIG1 0.1578
39 | 32 H -6.8445 -0.8909 -0.4695 H 1 LIG1 0.0460
40 | 33 H -7.1758 -1.6304 1.1356 H 1 LIG1 0.0460
41 | 34 H -6.7483 0.5682 2.2615 H 1 LIG1 0.0245
42 | 35 H -6.4847 1.3379 0.6447 H 1 LIG1 0.0245
43 | 36 H -8.0993 0.6552 1.0661 H 1 LIG1 0.0245
44 | 37 H -4.8781 -1.7963 1.5101 H 1 LIG1 0.1502
45 | @BOND
46 | 1 1 2 ar
47 | 2 1 6 ar
48 | 3 2 3 ar
49 | 4 3 4 ar
50 | 5 3 20 1
51 | 6 4 5 ar
52 | 7 4 8 1
53 | 8 5 6 ar
54 | 9 5 7 1
55 | 10 8 9 2
56 | 11 8 10 am
57 | 12 10 11 1
58 | 13 11 12 ar
59 | 14 11 16 ar
60 | 15 12 13 ar
61 | 16 13 14 ar
62 | 17 14 15 ar
63 | 18 15 16 ar
64 | 19 15 17 1
65 | 20 17 18 am
66 | 21 18 19 2
67 | 22 18 23 am
68 | 23 21 22 1
69 | 24 21 23 1
70 | 25 1 24 1
71 | 26 2 25 1
72 | 27 6 26 1
73 | 28 10 27 1
74 | 29 12 28 1
75 | 30 13 29 1
76 | 31 16 30 1
77 | 32 17 31 1
78 | 33 21 32 1
79 | 34 21 33 1
80 | 35 22 34 1
81 | 36 22 35 1
82 | 37 22 36 1
83 | 38 23 37 1
84 |
--------------------------------------------------------------------------------
/test/radial/ejm_55.mol2:
--------------------------------------------------------------------------------
1 | @MOLECULE
2 | ejm_55
3 | 33 34 0 0 0
4 | SMALL
5 | GASTEIGER
6 |
7 | @ATOM
8 | 1 C -6.2779 1.1986 0.1164 C.ar 1 LIG1 -0.0590
9 | 2 C -5.2595 1.8481 -0.5817 C.ar 1 LIG1 -0.0426
10 | 3 C -3.9948 1.2603 -0.6977 C.ar 1 LIG1 0.0545
11 | 4 C -3.7431 0.0044 -0.1016 C.ar 1 LIG1 0.0735
12 | 5 C -4.7835 -0.6493 0.5943 C.ar 1 LIG1 0.0545
13 | 6 C -6.0417 -0.0462 0.7002 C.ar 1 LIG1 -0.0426
14 | 7 CL -4.5346 -2.2060 1.3803 Cl 1 LIG1 -0.0827
15 | 8 C -2.4130 -0.6268 -0.2107 C.2 1 LIG1 0.2511
16 | 9 O -2.3102 -1.7491 -0.7756 O.2 1 LIG1 -0.2698
17 | 10 N -1.2505 0.0436 0.3044 N.am 1 LIG1 -0.2813
18 | 11 C 0.0656 -0.5334 0.3345 C.ar 1 LIG1 0.0384
19 | 12 C 0.2651 -1.8930 0.6220 C.ar 1 LIG1 -0.0222
20 | 13 C 1.5636 -2.4026 0.6658 C.ar 1 LIG1 0.0314
21 | 14 N 2.6256 -1.5840 0.4464 N.ar 1 LIG1 -0.2399
22 | 15 C 2.4725 -0.2561 0.1843 C.ar 1 LIG1 0.1291
23 | 16 C 1.1817 0.2897 0.1342 C.ar 1 LIG1 -0.0002
24 | 17 N 3.6152 0.5891 -0.0377 N.am 1 LIG1 -0.2355
25 | 18 C 4.9781 0.1412 -0.0114 C.2 1 LIG1 0.4054
26 | 19 O 5.2572 -1.0680 0.2167 O.2 1 LIG1 -0.2261
27 | 20 CL -2.7729 2.0986 -1.6506 Cl 1 LIG1 -0.0827
28 | 21 C 7.3767 0.7072 -0.2351 C.3 1 LIG1 0.0833
29 | 22 O 6.0001 1.0663 -0.2431 O.3 1 LIG1 -0.4534
30 | 23 H -7.2538 1.6590 0.2013 H 1 LIG1 0.0618
31 | 24 H -5.4575 2.8080 -1.0418 H 1 LIG1 0.0632
32 | 25 H -6.8387 -0.5416 1.2401 H 1 LIG1 0.0632
33 | 26 H -1.3529 1.0353 0.6178 H 1 LIG1 0.1551
34 | 27 H -0.5673 -2.5490 0.8379 H 1 LIG1 0.0651
35 | 28 H 1.7283 -3.4492 0.8843 H 1 LIG1 0.0831
36 | 29 H 1.0448 1.3447 -0.0702 H 1 LIG1 0.0671
37 | 30 H 3.4535 1.6030 -0.2334 H 1 LIG1 0.1596
38 | 31 H 7.9897 1.6081 -0.4431 H 1 LIG1 0.0661
39 | 32 H 7.6583 0.3020 0.7599 H 1 LIG1 0.0661
40 | 33 H 7.5760 -0.0529 -1.0199 H 1 LIG1 0.0661
41 | @BOND
42 | 1 1 2 ar
43 | 2 1 6 ar
44 | 3 2 3 ar
45 | 4 3 4 ar
46 | 5 3 20 1
47 | 6 4 5 ar
48 | 7 4 8 1
49 | 8 5 6 ar
50 | 9 5 7 1
51 | 10 8 9 2
52 | 11 8 10 am
53 | 12 10 11 1
54 | 13 11 12 ar
55 | 14 11 16 ar
56 | 15 12 13 ar
57 | 16 13 14 ar
58 | 17 14 15 ar
59 | 18 15 16 ar
60 | 19 15 17 1
61 | 20 17 18 am
62 | 21 18 19 2
63 | 22 18 22 1
64 | 23 21 22 1
65 | 24 1 23 1
66 | 25 2 24 1
67 | 26 6 25 1
68 | 27 10 26 1
69 | 28 12 27 1
70 | 29 13 28 1
71 | 30 16 29 1
72 | 31 17 30 1
73 | 32 21 31 1
74 | 33 21 32 1
75 | 34 21 33 1
76 |
--------------------------------------------------------------------------------
/test/radial/jmc_23.mol2:
--------------------------------------------------------------------------------
1 | @MOLECULE
2 | jmc_23
3 | 36 38 0 0 0
4 | SMALL
5 | GASTEIGER
6 |
7 | @ATOM
8 | 1 C -5.1883 0.6983 0.8884 C.ar 1 LIG1 -0.0590
9 | 2 C -4.2771 -0.2671 1.3160 C.ar 1 LIG1 -0.0426
10 | 3 C -3.5098 -0.9773 0.3862 C.ar 1 LIG1 0.0545
11 | 4 C -3.6493 -0.7118 -0.9953 C.ar 1 LIG1 0.0735
12 | 5 C -4.5861 0.2581 -1.4178 C.ar 1 LIG1 0.0545
13 | 6 C -5.3447 0.9576 -0.4730 C.ar 1 LIG1 -0.0426
14 | 7 CL -4.7973 0.6640 -3.1188 Cl 1 LIG1 -0.0827
15 | 8 C -2.8312 -1.4429 -1.9906 C.2 1 LIG1 0.2511
16 | 9 O -3.4107 -2.0828 -2.9083 O.2 1 LIG1 -0.2698
17 | 10 N -1.3973 -1.4846 -1.9098 N.am 1 LIG1 -0.2813
18 | 11 C -0.5905 -0.4910 -1.2542 C.ar 1 LIG1 0.0384
19 | 12 C -0.9537 0.8647 -1.2541 C.ar 1 LIG1 -0.0222
20 | 13 C -0.1353 1.7953 -0.6133 C.ar 1 LIG1 0.0314
21 | 14 N 1.0124 1.3919 -0.0085 N.ar 1 LIG1 -0.2400
22 | 15 C 1.4075 0.0883 -0.0044 C.ar 1 LIG1 0.1266
23 | 16 C 0.6101 -0.8732 -0.6417 C.ar 1 LIG1 -0.0003
24 | 17 N 2.6338 -0.3088 0.6336 N.am 1 LIG1 -0.2700
25 | 18 C 3.4990 0.5836 1.3546 C.2 1 LIG1 0.2242
26 | 19 O 3.1603 1.7775 1.5749 O.2 1 LIG1 -0.2750
27 | 20 C 4.7946 0.0767 1.9122 C.3 1 LIG1 0.0695
28 | 21 C 6.0227 0.8828 1.5059 C.3 1 LIG1 -0.0072
29 | 22 C 5.7558 -0.4685 0.8682 C.3 1 LIG1 0.1129
30 | 23 F 6.5838 -1.4680 1.3467 F 1 LIG1 -0.2447
31 | 24 CL -2.4330 -2.2341 0.9898 Cl 1 LIG1 -0.0827
32 | 25 H -5.7787 1.2432 1.6138 H 1 LIG1 0.0618
33 | 26 H -4.1744 -0.4705 2.3745 H 1 LIG1 0.0632
34 | 27 H -6.0544 1.7096 -0.7939 H 1 LIG1 0.0632
35 | 28 H -0.9138 -2.3059 -2.3393 H 1 LIG1 0.1551
36 | 29 H -1.8464 1.2048 -1.7605 H 1 LIG1 0.0651
37 | 30 H -0.4084 2.8420 -0.6041 H 1 LIG1 0.0831
38 | 31 H 0.9124 -1.9133 -0.6481 H 1 LIG1 0.0671
39 | 32 H 2.9229 -1.3114 0.5670 H 1 LIG1 0.1562
40 | 33 H 4.8298 -0.4000 2.9146 H 1 LIG1 0.0423
41 | 34 H 5.8433 1.7409 0.8228 H 1 LIG1 0.0301
42 | 35 H 6.8423 0.8810 2.2555 H 1 LIG1 0.0301
43 | 36 H 5.4497 -0.4493 -0.2000 H 1 LIG1 0.0659
44 | @BOND
45 | 1 1 2 ar
46 | 2 1 6 ar
47 | 3 2 3 ar
48 | 4 3 4 ar
49 | 5 3 24 1
50 | 6 4 5 ar
51 | 7 4 8 1
52 | 8 5 6 ar
53 | 9 5 7 1
54 | 10 8 9 2
55 | 11 8 10 am
56 | 12 10 11 1
57 | 13 11 12 ar
58 | 14 11 16 ar
59 | 15 12 13 ar
60 | 16 13 14 ar
61 | 17 14 15 ar
62 | 18 15 16 ar
63 | 19 15 17 1
64 | 20 17 18 am
65 | 21 18 19 2
66 | 22 18 20 1
67 | 23 20 21 1
68 | 24 20 22 1
69 | 25 21 22 1
70 | 26 22 23 1
71 | 27 1 25 1
72 | 28 2 26 1
73 | 29 6 27 1
74 | 30 10 28 1
75 | 31 12 29 1
76 | 32 13 30 1
77 | 33 16 31 1
78 | 34 17 32 1
79 | 35 20 33 1
80 | 36 21 34 1
81 | 37 21 35 1
82 | 38 22 36 1
83 |
--------------------------------------------------------------------------------
/test/radial/jmc_27.mol2:
--------------------------------------------------------------------------------
1 | @MOLECULE
2 | jmc_27
3 | 36 38 0 0 0
4 | SMALL
5 | GASTEIGER
6 |
7 | @ATOM
8 | 1 C 6.2677 1.6912 -0.6993 C.ar 1 LIG1 -0.0590
9 | 2 C 5.9943 1.6681 0.6679 C.ar 1 LIG1 -0.0426
10 | 3 C 4.7573 1.2097 1.1349 C.ar 1 LIG1 0.0545
11 | 4 C 3.7761 0.7638 0.2195 C.ar 1 LIG1 0.0735
12 | 5 C 4.0631 0.7964 -1.1648 C.ar 1 LIG1 0.0545
13 | 6 C 5.3061 1.2584 -1.6117 C.ar 1 LIG1 -0.0426
14 | 7 CL 2.8719 0.3289 -2.3761 Cl 1 LIG1 -0.0827
15 | 8 C 2.4663 0.2737 0.7015 C.2 1 LIG1 0.2511
16 | 9 O 1.8073 0.9667 1.5234 O.2 1 LIG1 -0.2698
17 | 10 N 1.9751 -1.0073 0.2761 N.am 1 LIG1 -0.2813
18 | 11 C 0.6130 -1.4397 0.4331 C.ar 1 LIG1 0.0384
19 | 12 C 0.3393 -2.8016 0.6084 C.ar 1 LIG1 -0.0222
20 | 13 C -0.9827 -3.2291 0.7369 C.ar 1 LIG1 0.0314
21 | 14 N -1.9987 -2.3293 0.6757 N.ar 1 LIG1 -0.2400
22 | 15 C -1.7755 -0.9987 0.4878 C.ar 1 LIG1 0.1266
23 | 16 C -0.4587 -0.5344 0.3539 C.ar 1 LIG1 -0.0003
24 | 17 N -2.8721 -0.0715 0.4067 N.am 1 LIG1 -0.2701
25 | 18 C -4.2537 -0.4325 0.5669 C.2 1 LIG1 0.2228
26 | 19 O -4.5832 -1.6000 0.9095 O.2 1 LIG1 -0.2751
27 | 20 C -5.3200 0.6058 0.3888 C.3 1 LIG1 0.0535
28 | 21 C -6.4155 0.2297 -0.6010 C.3 1 LIG1 -0.0235
29 | 22 C -5.3531 1.2435 -0.9930 C.3 1 LIG1 0.0458
30 | 23 CL -5.9368 2.9287 -0.9939 Cl 1 LIG1 -0.1210
31 | 24 CL 4.4983 1.1606 2.8769 Cl 1 LIG1 -0.0827
32 | 25 H 7.2267 2.0475 -1.0529 H 1 LIG1 0.0618
33 | 26 H 6.7500 2.0022 1.3676 H 1 LIG1 0.0632
34 | 27 H 5.5254 1.2906 -2.6715 H 1 LIG1 0.0632
35 | 28 H 2.6695 -1.6925 -0.0998 H 1 LIG1 0.1551
36 | 29 H 1.1448 -3.5238 0.6546 H 1 LIG1 0.0651
37 | 30 H -1.2020 -4.2783 0.8826 H 1 LIG1 0.0831
38 | 31 H -0.2791 0.5159 0.1653 H 1 LIG1 0.0671
39 | 32 H -2.6563 0.9330 0.2130 H 1 LIG1 0.1562
40 | 33 H -5.6364 1.2366 1.2466 H 1 LIG1 0.0409
41 | 34 H -7.4118 0.6584 -0.3617 H 1 LIG1 0.0287
42 | 35 H -6.3020 -0.7551 -1.1036 H 1 LIG1 0.0287
43 | 36 H -4.6147 0.8841 -1.7420 H 1 LIG1 0.0473
44 | @BOND
45 | 1 1 2 ar
46 | 2 1 6 ar
47 | 3 2 3 ar
48 | 4 3 4 ar
49 | 5 3 24 1
50 | 6 4 5 ar
51 | 7 4 8 1
52 | 8 5 6 ar
53 | 9 5 7 1
54 | 10 8 9 2
55 | 11 8 10 am
56 | 12 10 11 1
57 | 13 11 12 ar
58 | 14 11 16 ar
59 | 15 12 13 ar
60 | 16 13 14 ar
61 | 17 14 15 ar
62 | 18 15 16 ar
63 | 19 15 17 1
64 | 20 17 18 am
65 | 21 18 19 2
66 | 22 18 20 1
67 | 23 20 21 1
68 | 24 20 22 1
69 | 25 21 22 1
70 | 26 22 23 1
71 | 27 1 25 1
72 | 28 2 26 1
73 | 29 6 27 1
74 | 30 10 28 1
75 | 31 12 29 1
76 | 32 13 30 1
77 | 33 16 31 1
78 | 34 17 32 1
79 | 35 20 33 1
80 | 36 21 34 1
81 | 37 21 35 1
82 | 38 22 36 1
83 |
--------------------------------------------------------------------------------
/test/radial/jmc_30.mol2:
--------------------------------------------------------------------------------
1 | @MOLECULE
2 | jmc_30
3 | 37 39 0 0 0
4 | SMALL
5 | GASTEIGER
6 |
7 | @ATOM
8 | 1 C 6.2964 0.8445 2.3244 C.ar 1 LIG1 -0.0590
9 | 2 C 6.2248 -0.2362 1.4444 C.ar 1 LIG1 -0.0426
10 | 3 C 4.9845 -0.6930 0.9843 C.ar 1 LIG1 0.0545
11 | 4 C 3.7973 -0.0589 1.4123 C.ar 1 LIG1 0.0735
12 | 5 C 3.8792 1.0250 2.3135 C.ar 1 LIG1 0.0545
13 | 6 C 5.1279 1.4701 2.7602 C.ar 1 LIG1 -0.0426
14 | 7 CL 2.4396 1.8742 2.8697 Cl 1 LIG1 -0.0827
15 | 8 C 2.4830 -0.5193 0.9244 C.2 1 LIG1 0.2511
16 | 9 O 1.6453 -0.9722 1.7506 O.2 1 LIG1 -0.2698
17 | 10 N 2.1784 -0.4693 -0.4797 N.am 1 LIG1 -0.2813
18 | 11 C 0.8836 -0.7443 -1.0421 C.ar 1 LIG1 0.0384
19 | 12 C 0.7984 -1.3080 -2.3211 C.ar 1 LIG1 -0.0222
20 | 13 C -0.4530 -1.5469 -2.8892 C.ar 1 LIG1 0.0314
21 | 14 N -1.5830 -1.2222 -2.2090 N.ar 1 LIG1 -0.2400
22 | 15 C -1.5435 -0.6596 -0.9689 C.ar 1 LIG1 0.1266
23 | 16 C -0.3021 -0.4007 -0.3702 C.ar 1 LIG1 -0.0003
24 | 17 N -2.7566 -0.3085 -0.2806 N.am 1 LIG1 -0.2701
25 | 18 C -4.0777 -0.5896 -0.7727 C.2 1 LIG1 0.2226
26 | 19 O -4.2477 -1.3086 -1.7941 O.2 1 LIG1 -0.2751
27 | 20 C -5.2824 -0.0991 -0.0170 C.3 1 LIG1 0.0526
28 | 21 C -5.2732 1.3938 0.2958 C.3 1 LIG1 -0.0243
29 | 22 C -6.2415 0.8474 -0.7430 C.3 1 LIG1 0.0580
30 | 23 C -5.8978 1.2541 -2.1162 C.1 1 LIG1 0.0667
31 | 24 CL 4.9558 -2.0960 -0.0805 Cl 1 LIG1 -0.0827
32 | 25 N -5.6274 1.5757 -3.1946 N.1 1 LIG1 -0.1963
33 | 26 H 7.2595 1.1944 2.6739 H 1 LIG1 0.0618
34 | 27 H 7.1372 -0.7216 1.1219 H 1 LIG1 0.0632
35 | 28 H 5.1945 2.3079 3.4432 H 1 LIG1 0.0632
36 | 29 H 2.9609 -0.2664 -1.1426 H 1 LIG1 0.1551
37 | 30 H 1.6957 -1.5661 -2.8695 H 1 LIG1 0.0651
38 | 31 H -0.5265 -1.9897 -3.8739 H 1 LIG1 0.0831
39 | 32 H -0.2688 0.0911 0.5926 H 1 LIG1 0.0671
40 | 33 H -2.6774 0.1791 0.6407 H 1 LIG1 0.1562
41 | 34 H -5.7282 -0.7379 0.7741 H 1 LIG1 0.0407
42 | 35 H -4.4059 1.9665 -0.1018 H 1 LIG1 0.0285
43 | 36 H -5.7452 1.6535 1.2667 H 1 LIG1 0.0285
44 | 37 H -7.3042 0.8369 -0.4217 H 1 LIG1 0.0461
45 | @BOND
46 | 1 1 2 ar
47 | 2 1 6 ar
48 | 3 2 3 ar
49 | 4 3 4 ar
50 | 5 3 24 1
51 | 6 4 5 ar
52 | 7 4 8 1
53 | 8 5 6 ar
54 | 9 5 7 1
55 | 10 8 9 2
56 | 11 8 10 am
57 | 12 10 11 1
58 | 13 11 12 ar
59 | 14 11 16 ar
60 | 15 12 13 ar
61 | 16 13 14 ar
62 | 17 14 15 ar
63 | 18 15 16 ar
64 | 19 15 17 1
65 | 20 17 18 am
66 | 21 18 19 2
67 | 22 18 20 1
68 | 23 20 21 1
69 | 24 20 22 1
70 | 25 21 22 1
71 | 26 22 23 1
72 | 27 23 25 3
73 | 28 1 26 1
74 | 29 2 27 1
75 | 30 6 28 1
76 | 31 10 29 1
77 | 32 12 30 1
78 | 33 13 31 1
79 | 34 16 32 1
80 | 35 17 33 1
81 | 36 20 34 1
82 | 37 21 35 1
83 | 38 21 36 1
84 | 39 22 37 1
85 |
--------------------------------------------------------------------------------
/test/radial/molecules.gpickle:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/MobleyLab/Lomap/fe1c196a72949c26169af0df4dbfbe088eadea3d/test/radial/molecules.gpickle
--------------------------------------------------------------------------------
/test/transforms/bromophenyl.sdf:
--------------------------------------------------------------------------------
1 | bromophenyl
2 | xed2sdf_05210316543D
3 |
4 | 18 18 0 0 0 0 0 0 0 0999 V2000
5 | -0.2078 1.4341 0.0951 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | 1.0620 0.9009 0.0874 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | 1.2340 -0.4650 0.0630 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 0.1360 -1.2932 0.0457 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | -1.1321 -0.7567 0.0533 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | -1.3108 0.6105 0.0784 C 0 0 0 0 0 0 0 0 0 0 0 0
11 | -2.6779 1.2763 0.0882 C 0 0 0 0 0 0 0 0 0 0 0 0
12 | 2.4475 1.9523 0.1083 Br 0 0 0 0 0 0 0 0 0 0 0 0
13 | -3.9112 0.3543 0.0807 C 0 0 0 0 0 0 0 0 0 0 0 0
14 | -0.3295 2.4266 0.1128 H 0 0 0 0 0 0 0 0 0 0 0 0
15 | 2.1554 -0.8541 0.0576 H 0 0 0 0 0 0 0 0 0 0 0 0
16 | -1.9279 -1.3622 0.0406 H 0 0 0 0 0 0 0 0 0 0 0 0
17 | 0.2588 -2.2856 0.0273 H 0 0 0 0 0 0 0 0 0 0 0 0
18 | -2.7414 1.9674 1.0670 H 0 0 0 0 0 0 0 0 0 0 0 0
19 | -2.7452 1.9886 -0.8751 H 0 0 0 0 0 0 0 0 0 0 0 0
20 | -4.9067 1.0246 0.0934 H 0 0 0 0 0 0 0 0 0 0 0 0
21 | -3.9009 -0.3248 -0.9085 H 0 0 0 0 0 0 0 0 0 0 0 0
22 | -3.8935 -0.3513 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0
23 | 1 6 2 0
24 | 2 1 1 0
25 | 2 8 1 0
26 | 3 2 2 0
27 | 4 3 1 0
28 | 5 4 2 0
29 | 6 5 1 0
30 | 6 7 1 0
31 | 7 9 1 0
32 | 1 10 1 0
33 | 3 11 1 0
34 | 4 13 1 0
35 | 5 12 1 0
36 | 7 14 1 0
37 | 7 15 1 0
38 | 9 16 1 0
39 | 9 17 1 0
40 | 9 18 1 0
41 | M END
42 | >
43 | false
44 |
45 | >
46 | 0.500
47 |
48 | >
49 | 0
50 |
51 | >
52 | 0
53 |
54 | >
55 | 124.2
56 |
57 | > <#Atoms_cresset>
58 | 9
59 |
60 | >
61 | 2.7
62 |
63 | >
64 | 0
65 |
66 | >
67 | 1
68 |
69 | >
70 | 0
71 |
72 | >
73 | chlorophenyl.sdf
74 |
75 | > <_cresset_fieldpoints>
76 | -5 -0.249634 0.141481 -2.870371 -3.6992
77 | -5 -0.258767 0.038885 3.011418 -3.7006
78 | -5 5.131414 1.088324 0.104046 -2.1699
79 | -5 2.329686 4.767548 0.155661 -2.1605
80 | -6 -1.762562 4.219894 0.131912 2.3877
81 | -6 2.291609 -3.481932 0.008202 2.4738
82 | -6 -1.782707 -3.807055 -0.006433 2.5518
83 | -6 -3.456510 -2.920497 0.018592 2.6231
84 | -7 -1.806085 4.428570 0.123346 -1.4927
85 | -7 2.722434 -3.502663 -0.031210 -0.9845
86 | -7 -3.741013 -2.952006 0.046786 -1.4581
87 | -7 -0.340618 0.200088 3.296729 -1.9382
88 | -7 -4.711312 3.773040 0.126341 -1.1440
89 | -7 -2.148519 0.194150 -3.070925 -1.9240
90 | -7 -0.321952 0.319669 -3.150448 -1.9370
91 | -7 -2.125665 0.115104 3.216287 -1.9291
92 | -8 -0.049161 0.067818 0.069660 7.1681
93 | -8 -2.367455 0.204391 0.074533 5.5931
94 |
95 | $$$$
96 |
--------------------------------------------------------------------------------
/test/transforms/cdk2_lig15.sdf:
--------------------------------------------------------------------------------
1 | 17
2 | xed2sdf_05210316543D
3 |
4 | 45 48 0 0 0 0 0 0 0 0999 V2000
5 | 1.3901 29.1077 6.7935 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | -1.6911 31.9130 8.0794 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | -0.7437 26.3748 8.8319 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | -1.3142 25.5567 9.9914 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | -1.1214 24.0589 9.6854 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | -1.5824 23.1795 10.8502 C 0 0 0 0 0 0 0 0 0 0 0 0
11 | -0.8551 23.5463 12.1491 C 0 0 0 0 0 0 0 0 0 0 0 0
12 | -1.0780 25.0277 12.4857 C 0 0 0 0 0 0 0 0 0 0 0 0
13 | -0.6321 25.9351 11.3273 C 0 0 0 0 0 0 0 0 0 0 0 0
14 | 4.6903 25.7129 5.8380 C 0 0 0 0 0 0 0 0 0 0 0 0
15 | 4.6667 25.1395 7.1233 C 0 0 0 0 0 0 0 0 0 0 0 0
16 | 3.9496 25.7658 8.1576 C 0 0 0 0 0 0 0 0 0 0 0 0
17 | 3.2460 26.9556 7.8985 C 0 0 0 0 0 0 0 0 0 0 0 0
18 | 0.6302 28.2313 7.4508 N 0 0 0 0 0 0 0 0 0 0 0 0
19 | -0.4898 28.6252 8.0923 C 0 0 0 0 0 0 0 0 0 0 0 0
20 | -1.1796 27.7315 8.8832 O 0 0 0 0 0 0 0 0 0 0 0 0
21 | -0.8660 29.9818 8.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
22 | -1.9251 30.7129 8.5212 N 0 0 0 0 0 0 0 0 0 0 0 0
23 | -0.5542 32.0464 7.3306 N 0 0 0 0 0 0 0 0 0 0 0 0
24 | -0.0249 30.7863 7.2610 C 0 0 0 0 0 0 0 0 0 0 0 0
25 | 1.1172 30.4049 6.6113 N 0 0 0 0 0 0 0 0 0 0 0 0
26 | 2.5827 28.6807 6.3360 N 0 0 0 0 0 0 0 0 0 0 0 0
27 | 3.2365 27.5251 6.6032 C 0 0 0 0 0 0 0 0 0 0 0 0
28 | 3.9871 26.9068 5.5819 C 0 0 0 0 0 0 0 0 0 0 0 0
29 | 3.9332 25.0203 9.8943 Br 0 0 0 0 0 0 0 0 0 0 0 0
30 | -2.3542 32.7337 8.2866 H 0 0 0 0 0 0 0 0 0 0 0 0
31 | 0.3421 26.2813 8.8885 H 0 0 0 0 0 0 0 0 0 0 0 0
32 | -1.0533 25.9544 7.8735 H 0 0 0 0 0 0 0 0 0 0 0 0
33 | -2.3846 25.7536 10.0698 H 0 0 0 0 0 0 0 0 0 0 0 0
34 | -1.6745 23.7903 8.7850 H 0 0 0 0 0 0 0 0 0 0 0 0
35 | -0.0713 23.8531 9.4740 H 0 0 0 0 0 0 0 0 0 0 0 0
36 | -2.6489 23.3294 10.9949 H 0 0 0 0 0 0 0 0 0 0 0 0
37 | -1.4335 22.1247 10.6147 H 0 0 0 0 0 0 0 0 0 0 0 0
38 | -1.2175 22.9242 12.9680 H 0 0 0 0 0 0 0 0 0 0 0 0
39 | 0.2126 23.3446 12.0504 H 0 0 0 0 0 0 0 0 0 0 0 0
40 | -2.1337 25.2025 12.7004 H 0 0 0 0 0 0 0 0 0 0 0 0
41 | -0.5350 25.2900 13.3929 H 0 0 0 0 0 0 0 0 0 0 0 0
42 | 0.4518 25.8639 11.2223 H 0 0 0 0 0 0 0 0 0 0 0 0
43 | -0.8463 26.9766 11.5731 H 0 0 0 0 0 0 0 0 0 0 0 0
44 | 5.2554 25.2427 5.0475 H 0 0 0 0 0 0 0 0 0 0 0 0
45 | 5.2165 24.2329 7.3224 H 0 0 0 0 0 0 0 0 0 0 0 0
46 | 2.7083 27.4238 8.7079 H 0 0 0 0 0 0 0 0 0 0 0 0
47 | -0.1784 32.8770 6.8845 H 0 0 0 0 0 0 0 0 0 0 0 0
48 | 3.0167 29.2655 5.6333 H 0 0 0 0 0 0 0 0 0 0 0 0
49 | 4.0234 27.3389 4.5933 H 0 0 0 0 0 0 0 0 0 0 0 0
50 | 14 1 2 0
51 | 21 1 1 0
52 | 22 1 1 0
53 | 18 2 2 0
54 | 19 2 1 0
55 | 26 2 1 0
56 | 4 3 1 0
57 | 16 3 1 0
58 | 27 3 1 0
59 | 28 3 1 0
60 | 5 4 1 0
61 | 9 4 1 0
62 | 29 4 1 0
63 | 6 5 1 0
64 | 30 5 1 0
65 | 31 5 1 0
66 | 7 6 1 0
67 | 32 6 1 0
68 | 33 6 1 0
69 | 8 7 1 0
70 | 34 7 1 0
71 | 35 7 1 0
72 | 9 8 1 0
73 | 36 8 1 0
74 | 37 8 1 0
75 | 38 9 1 0
76 | 39 9 1 0
77 | 11 10 2 0
78 | 24 10 1 0
79 | 40 10 1 0
80 | 12 11 1 0
81 | 41 11 1 0
82 | 13 12 2 0
83 | 25 12 1 0
84 | 23 13 1 0
85 | 42 13 1 0
86 | 15 14 1 0
87 | 16 15 1 0
88 | 17 15 2 0
89 | 18 17 1 0
90 | 20 17 1 0
91 | 20 19 1 0
92 | 43 19 1 0
93 | 21 20 2 0
94 | 23 22 1 0
95 | 44 22 1 0
96 | 24 23 2 0
97 | 45 24 1 0
98 | M END
99 | $$$$
100 |
--------------------------------------------------------------------------------
/test/transforms/cdk2_lig16.sdf:
--------------------------------------------------------------------------------
1 | 1h1q
2 | xed2sdf_05210316543D
3 |
4 | 45 48 0 0 0 0 0 0 0 0999 V2000
5 | 1.3901 29.1077 6.7935 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | -1.6911 31.9130 8.0794 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | -0.7437 26.3748 8.8319 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | -1.3142 25.5567 9.9914 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | -1.1214 24.0589 9.6854 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | -1.5824 23.1795 10.8502 C 0 0 0 0 0 0 0 0 0 0 0 0
11 | -0.8551 23.5463 12.1491 C 0 0 0 0 0 0 0 0 0 0 0 0
12 | -1.0780 25.0277 12.4857 C 0 0 0 0 0 0 0 0 0 0 0 0
13 | -0.6321 25.9351 11.3273 C 0 0 0 0 0 0 0 0 0 0 0 0
14 | 4.6903 25.7129 5.8380 C 0 0 0 0 0 0 0 0 0 0 0 0
15 | 4.6667 25.1395 7.1233 C 0 0 0 0 0 0 0 0 0 0 0 0
16 | 3.9496 25.7658 8.1576 C 0 0 0 0 0 0 0 0 0 0 0 0
17 | 3.2460 26.9556 7.8985 C 0 0 0 0 0 0 0 0 0 0 0 0
18 | 0.6302 28.2313 7.4508 N 0 0 0 0 0 0 0 0 0 0 0 0
19 | -0.4898 28.6252 8.0923 C 0 0 0 0 0 0 0 0 0 0 0 0
20 | -1.1796 27.7315 8.8832 O 0 0 0 0 0 0 0 0 0 0 0 0
21 | -0.8660 29.9818 8.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
22 | -1.9251 30.7129 8.5212 N 0 0 0 0 0 0 0 0 0 0 0 0
23 | -0.5542 32.0464 7.3306 N 0 0 0 0 0 0 0 0 0 0 0 0
24 | -0.0249 30.7863 7.2610 C 0 0 0 0 0 0 0 0 0 0 0 0
25 | 1.1172 30.4049 6.6113 N 0 0 0 0 0 0 0 0 0 0 0 0
26 | 2.5827 28.6807 6.3360 N 0 0 0 0 0 0 0 0 0 0 0 0
27 | 3.2365 27.5251 6.6032 C 0 0 0 0 0 0 0 0 0 0 0 0
28 | 3.9871 26.9068 5.5819 C 0 0 0 0 0 0 0 0 0 0 0 0
29 | -2.3542 32.7337 8.2866 H 0 0 0 0 0 0 0 0 0 0 0 0
30 | 0.3421 26.2813 8.8885 H 0 0 0 0 0 0 0 0 0 0 0 0
31 | -1.0533 25.9544 7.8735 H 0 0 0 0 0 0 0 0 0 0 0 0
32 | -2.3846 25.7536 10.0698 H 0 0 0 0 0 0 0 0 0 0 0 0
33 | -1.6745 23.7903 8.7850 H 0 0 0 0 0 0 0 0 0 0 0 0
34 | -0.0713 23.8531 9.4740 H 0 0 0 0 0 0 0 0 0 0 0 0
35 | -2.6489 23.3294 10.9949 H 0 0 0 0 0 0 0 0 0 0 0 0
36 | -1.4335 22.1247 10.6147 H 0 0 0 0 0 0 0 0 0 0 0 0
37 | -1.2175 22.9242 12.9680 H 0 0 0 0 0 0 0 0 0 0 0 0
38 | 0.2126 23.3446 12.0504 H 0 0 0 0 0 0 0 0 0 0 0 0
39 | -2.1337 25.2025 12.7004 H 0 0 0 0 0 0 0 0 0 0 0 0
40 | -0.5350 25.2900 13.3929 H 0 0 0 0 0 0 0 0 0 0 0 0
41 | 0.4518 25.8639 11.2223 H 0 0 0 0 0 0 0 0 0 0 0 0
42 | -0.8463 26.9766 11.5731 H 0 0 0 0 0 0 0 0 0 0 0 0
43 | 5.2554 25.2427 5.0475 H 0 0 0 0 0 0 0 0 0 0 0 0
44 | 5.2165 24.2329 7.3224 H 0 0 0 0 0 0 0 0 0 0 0 0
45 | 3.9402 25.3397 9.1502 H 0 0 0 0 0 0 0 0 0 0 0 0
46 | 2.7083 27.4238 8.7079 H 0 0 0 0 0 0 0 0 0 0 0 0
47 | -0.1784 32.8770 6.8845 H 0 0 0 0 0 0 0 0 0 0 0 0
48 | 3.0167 29.2655 5.6333 H 0 0 0 0 0 0 0 0 0 0 0 0
49 | 4.0234 27.3389 4.5933 H 0 0 0 0 0 0 0 0 0 0 0 0
50 | 14 1 2 0
51 | 21 1 1 0
52 | 22 1 1 0
53 | 18 2 2 0
54 | 19 2 1 0
55 | 25 2 1 0
56 | 4 3 1 0
57 | 16 3 1 0
58 | 26 3 1 0
59 | 27 3 1 0
60 | 5 4 1 0
61 | 9 4 1 0
62 | 28 4 1 0
63 | 6 5 1 0
64 | 29 5 1 0
65 | 30 5 1 0
66 | 7 6 1 0
67 | 31 6 1 0
68 | 32 6 1 0
69 | 8 7 1 0
70 | 33 7 1 0
71 | 34 7 1 0
72 | 9 8 1 0
73 | 35 8 1 0
74 | 36 8 1 0
75 | 37 9 1 0
76 | 38 9 1 0
77 | 11 10 2 0
78 | 24 10 1 0
79 | 39 10 1 0
80 | 12 11 1 0
81 | 40 11 1 0
82 | 13 12 2 0
83 | 41 12 1 0
84 | 23 13 1 0
85 | 42 13 1 0
86 | 15 14 1 0
87 | 16 15 1 0
88 | 17 15 2 0
89 | 18 17 1 0
90 | 20 17 1 0
91 | 20 19 1 0
92 | 43 19 1 0
93 | 21 20 2 0
94 | 23 22 1 0
95 | 44 22 1 0
96 | 24 23 2 0
97 | 45 24 1 0
98 | M END
99 | $$$$
100 |
--------------------------------------------------------------------------------
/test/transforms/chlorophenol.sdf:
--------------------------------------------------------------------------------
1 | chlorophenol
2 | xed2sdf_05210316543D
3 |
4 | 19 19 0 0 0 0 0 0 0 0999 V2000
5 | -0.2084 1.4846 0.0779 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | 1.0463 0.9145 0.0986 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | 1.1798 -0.4542 0.1262 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 0.0558 -1.2554 0.1330 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | -1.1984 -0.6780 0.1118 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | -1.3352 0.6924 0.0845 C 0 0 0 0 0 0 0 0 0 0 0 0
11 | -2.6887 1.3845 0.0608 C 0 0 0 0 0 0 0 0 0 0 0 0
12 | 2.4617 1.9254 0.0901 Cl 0 0 0 0 0 0 0 0 0 0 0 0
13 | 0.1795 -2.6103 0.1603 O 0 0 0 0 0 0 0 0 0 0 0 0
14 | -3.9300 0.4734 0.0815 C 0 0 0 0 0 0 0 0 0 0 0 0
15 | -0.3014 2.4802 0.0581 H 0 0 0 0 0 0 0 0 0 0 0 0
16 | 2.0898 -0.8686 0.1414 H 0 0 0 0 0 0 0 0 0 0 0 0
17 | -2.0128 -1.2584 0.1166 H 0 0 0 0 0 0 0 0 0 0 0 0
18 | 1.1452 -2.8920 0.1790 H 0 0 0 0 0 0 0 0 0 0 0 0
19 | -2.7417 2.0589 -0.9303 H 0 0 0 0 0 0 0 0 0 0 0 0
20 | -2.7483 2.1109 1.0141 H 0 0 0 0 0 0 0 0 0 0 0 0
21 | -4.9223 1.1481 0.0645 H 0 0 0 0 0 0 0 0 0 0 0 0
22 | -3.9174 -0.1953 1.0778 H 0 0 0 0 0 0 0 0 0 0 0 0
23 | -3.9158 -0.2420 -0.8818 H 0 0 0 0 0 0 0 0 0 0 0 0
24 | 1 6 2 0
25 | 2 1 1 0
26 | 2 8 1 0
27 | 3 2 2 0
28 | 4 3 1 0
29 | 4 9 1 0
30 | 5 4 2 0
31 | 6 5 1 0
32 | 6 7 1 0
33 | 7 10 1 0
34 | 1 11 1 0
35 | 3 12 1 0
36 | 5 13 1 0
37 | 7 15 1 0
38 | 7 16 1 0
39 | 9 14 1 0
40 | 10 17 1 0
41 | 10 18 1 0
42 | 10 19 1 0
43 | M END
44 | >
45 | false
46 |
47 | >
48 | 0.502
49 |
50 | >
51 | 0
52 |
53 | >
54 | 0
55 |
56 | >
57 | 156.6
58 |
59 | > <#Atoms_cresset>
60 | 10
61 |
62 | >
63 | 2.6
64 |
65 | >
66 | 20.2
67 |
68 | >
69 | 1.5
70 |
71 | >
72 | 0
73 |
74 | > <_cresset_fieldpoints>
75 | -5 -0.393715 -0.025480 -2.818253 -4.4367
76 | -5 -0.443449 0.092946 3.027092 -4.4266
77 | -5 -0.981641 -3.635580 -1.212135 -3.8513
78 | -5 -1.019473 -3.596491 1.525997 -3.8345
79 | -5 1.570466 4.459907 0.007438 -1.4435
80 | -6 2.904676 -3.000094 0.198545 6.7627
81 | -6 -1.686634 4.329597 0.006446 2.0741
82 | -7 -2.171090 0.328163 3.238219 -1.9278
83 | -7 1.565037 -2.989100 2.485406 -1.2061
84 | -7 -3.827586 -2.841263 0.186550 -1.4606
85 | -7 -1.750090 4.512656 -0.025477 -1.4767
86 | -7 -4.711824 3.890758 -0.011996 -1.1399
87 | -7 -0.375408 0.241472 -3.125880 -1.9167
88 | -7 -0.435139 0.367664 3.324347 -1.9187
89 | -7 -1.989081 -3.937536 0.176132 -1.2197
90 | -7 -2.162934 0.173577 -3.054674 -1.9217
91 | -7 1.619212 -3.082185 -2.114046 -1.2065
92 | -7 -4.990709 3.176942 -1.701322 -1.0765
93 | -8 -0.086121 0.154449 0.103869 7.0627
94 | -8 -2.415864 0.305511 0.088686 5.6266
95 | -8 1.230534 1.057891 0.098839 5.5928
96 |
97 | $$$$
98 |
--------------------------------------------------------------------------------
/test/transforms/chlorophenyl.sdf:
--------------------------------------------------------------------------------
1 | chlorophenyl
2 | xed2sdf_05210316543D
3 |
4 | 18 18 0 0 0 0 0 0 0 0999 V2000
5 | -0.2078 1.4341 0.0950 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | 1.0621 0.9009 0.0874 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | 1.2340 -0.4650 0.0630 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 0.1359 -1.2932 0.0457 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | -1.1320 -0.7566 0.0534 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | -1.3107 0.6105 0.0784 C 0 0 0 0 0 0 0 0 0 0 0 0
11 | -2.6779 1.2763 0.0882 C 0 0 0 0 0 0 0 0 0 0 0 0
12 | 2.4475 1.9524 0.1083 Cl 0 0 0 0 0 0 0 0 0 0 0 0
13 | -3.9112 0.3543 0.0807 C 0 0 0 0 0 0 0 0 0 0 0 0
14 | -0.3295 2.4266 0.1128 H 0 0 0 0 0 0 0 0 0 0 0 0
15 | 2.1553 -0.8540 0.0577 H 0 0 0 0 0 0 0 0 0 0 0 0
16 | -1.9279 -1.3621 0.0406 H 0 0 0 0 0 0 0 0 0 0 0 0
17 | 0.2588 -2.2856 0.0273 H 0 0 0 0 0 0 0 0 0 0 0 0
18 | -2.7414 1.9674 1.0669 H 0 0 0 0 0 0 0 0 0 0 0 0
19 | -2.7452 1.9886 -0.8751 H 0 0 0 0 0 0 0 0 0 0 0 0
20 | -4.9067 1.0246 0.0934 H 0 0 0 0 0 0 0 0 0 0 0 0
21 | -3.9009 -0.3248 -0.9085 H 0 0 0 0 0 0 0 0 0 0 0 0
22 | -3.8935 -0.3513 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0
23 | 1 6 2 0
24 | 2 1 1 0
25 | 2 8 1 0
26 | 3 2 2 0
27 | 4 3 1 0
28 | 5 4 2 0
29 | 6 5 1 0
30 | 6 7 1 0
31 | 7 9 1 0
32 | 1 10 1 0
33 | 3 11 1 0
34 | 4 13 1 0
35 | 5 12 1 0
36 | 7 14 1 0
37 | 7 15 1 0
38 | 9 16 1 0
39 | 9 17 1 0
40 | 9 18 1 0
41 | M END
42 | >
43 | false
44 |
45 | >
46 | 0.500
47 |
48 | >
49 | 0
50 |
51 | >
52 | 0
53 |
54 | >
55 | 140.6
56 |
57 | > <#Atoms_cresset>
58 | 9
59 |
60 | >
61 | 2.9
62 |
63 | >
64 | 0
65 |
66 | >
67 | 1
68 |
69 | >
70 | 0
71 |
72 | > <_cresset_fieldpoints>
73 | -5 -0.094680 0.222177 -2.835047 -4.4581
74 | -5 -0.106375 0.113757 2.978022 -4.4593
75 | -5 1.510659 4.458917 0.152585 -1.6575
76 | -5 4.616120 0.384842 0.081066 -1.6555
77 | -6 -1.778282 4.242813 0.142253 2.0977
78 | -6 2.229008 -3.559570 0.011913 2.1330
79 | -6 -1.889942 -3.774020 -0.000153 2.3037
80 | -6 -4.416456 3.826114 0.131633 1.5745
81 | -6 -3.468552 -2.916028 0.008702 2.4074
82 | -7 -1.817315 4.429328 0.113080 -1.4787
83 | -7 -0.372788 0.191227 3.299193 -1.9188
84 | -7 1.313214 2.027709 -2.951936 -1.4564
85 | -7 2.712362 -3.511066 -0.038950 -0.9773
86 | -7 -3.744973 -2.950735 0.051607 -1.4580
87 | -7 -4.713938 3.772743 0.128011 -1.1435
88 | -7 -2.157252 0.189870 -3.072170 -1.9199
89 | -7 -0.352324 0.309023 -3.153058 -1.9175
90 | -7 -2.126824 0.100978 3.215595 -1.9246
91 | -8 -0.041996 0.074380 0.068595 7.1954
92 | -8 1.239143 1.041456 0.093815 5.6090
93 | -8 -2.370005 0.207171 0.070073 5.5944
94 |
95 | $$$$
96 |
--------------------------------------------------------------------------------
/test/transforms/chlorophenyl2.sdf:
--------------------------------------------------------------------------------
1 | chlorophenyl2
2 | xed2sdf_05210316543D
3 |
4 | 18 18 0 0 0 0 0 0 0 0999 V2000
5 | -0.2212 1.5007 0.1089 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | 1.0363 0.9416 0.0941 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | 1.1803 -0.4253 0.0472 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 0.0651 -1.2322 0.0149 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | -1.1922 -0.6694 0.0296 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | -1.3414 0.7006 0.0769 C 0 0 0 0 0 0 0 0 0 0 0 0
11 | -2.6932 1.3970 0.0937 C 0 0 0 0 0 0 0 0 0 0 0 0
12 | 0.2475 -2.9607 -0.0443 Cl 0 0 0 0 0 0 0 0 0 0 0 0
13 | -3.9431 0.4988 0.1266 C 0 0 0 0 0 0 0 0 0 0 0 0
14 | -0.3223 2.4950 0.1427 H 0 0 0 0 0 0 0 0 0 0 0 0
15 | 2.0936 -0.8325 0.0364 H 0 0 0 0 0 0 0 0 0 0 0 0
16 | -2.0007 -1.2572 0.0059 H 0 0 0 0 0 0 0 0 0 0 0 0
17 | 1.8450 1.5292 0.1174 H 0 0 0 0 0 0 0 0 0 0 0 0
18 | -2.7263 2.1096 1.0584 H 0 0 0 0 0 0 0 0 0 0 0 0
19 | -2.7615 2.0895 -0.8838 H 0 0 0 0 0 0 0 0 0 0 0 0
20 | -4.9264 1.1869 0.1347 H 0 0 0 0 0 0 0 0 0 0 0 0
21 | -3.9232 -0.1812 1.1150 H 0 0 0 0 0 0 0 0 0 0 0 0
22 | -3.9563 -0.2050 -0.8451 H 0 0 0 0 0 0 0 0 0 0 0 0
23 | 1 6 2 0
24 | 2 1 1 0
25 | 3 2 2 0
26 | 4 3 1 0
27 | 4 8 1 0
28 | 5 4 2 0
29 | 6 5 1 0
30 | 6 7 1 0
31 | 7 9 1 0
32 | 1 10 1 0
33 | 2 13 1 0
34 | 3 11 1 0
35 | 5 12 1 0
36 | 7 14 1 0
37 | 7 15 1 0
38 | 9 16 1 0
39 | 9 17 1 0
40 | 9 18 1 0
41 | M END
42 | >
43 | false
44 |
45 | >
46 | 0.500
47 |
48 | >
49 | 0
50 |
51 | >
52 | 0
53 |
54 | >
55 | 140.6
56 |
57 | > <#Atoms_cresset>
58 | 9
59 |
60 | >
61 | 2.9
62 |
63 | >
64 | 0
65 |
66 | >
67 | 1
68 |
69 | >
70 | 0
71 |
72 | > <_cresset_fieldpoints>
73 | -5 -0.198843 0.166988 -2.847468 -4.4601
74 | -5 -0.236047 -0.039867 2.964649 -4.4711
75 | -5 -2.237623 -3.944314 -0.053438 -1.7618
76 | -5 2.874693 -3.483078 -0.036726 -1.6659
77 | -6 -1.559440 4.378763 0.179717 2.5612
78 | -6 4.120207 0.999217 0.110748 2.1534
79 | -6 1.616211 4.042339 0.205514 2.3411
80 | -6 -3.827843 -2.621763 0.026503 1.4297
81 | -7 -1.780260 4.529726 0.014446 -1.4539
82 | -7 1.635249 4.295853 0.383193 -1.0017
83 | -7 4.419244 0.570176 0.076167 -0.9772
84 | -7 1.570949 4.175596 1.085428 -1.0005
85 | -7 -0.440163 0.314608 -3.160933 -1.9173
86 | -7 -4.682197 3.929051 0.119919 -1.1426
87 | -7 -0.496242 0.090226 3.287114 -1.9257
88 | -7 -2.279541 0.229942 -3.054355 -1.9227
89 | -7 -2.087526 0.180273 3.219336 -1.9495
90 | -7 -2.680445 -3.135392 -1.457509 -1.5394
91 | -7 -2.957559 -2.553493 1.940703 -1.5831
92 | -7 -3.705138 -2.863318 0.372684 -1.5828
93 | -8 -0.084990 0.137444 0.060718 7.1959
94 | -8 0.086330 -1.455865 0.005853 5.6114
95 | -8 -2.408620 0.317752 0.079306 5.6049
96 |
97 | $$$$
98 |
--------------------------------------------------------------------------------
/test/transforms/chlorotoluyl1.sdf:
--------------------------------------------------------------------------------
1 | chlorotoluyl1
2 | xed2sdf_05210316543D
3 |
4 | 21 21 0 0 0 0 0 0 0 0999 V2000
5 | -0.2097 1.4324 0.0777 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | 1.0536 0.8844 0.0961 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | 1.2102 -0.4831 0.1231 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 0.1042 -1.3020 0.1312 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | -1.1563 -0.7484 0.1143 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | -1.3210 0.6204 0.0875 C 0 0 0 0 0 0 0 0 0 0 0 0
11 | -2.6857 1.2905 0.0702 C 0 0 0 0 0 0 0 0 0 0 0 0
12 | 2.4510 1.9194 0.0858 Cl 0 0 0 0 0 0 0 0 0 0 0 0
13 | -3.9137 0.3615 0.0666 C 0 0 0 0 0 0 0 0 0 0 0 0
14 | 0.2636 -2.8086 0.1669 C 0 0 0 0 0 0 0 0 0 0 0 0
15 | -0.3203 2.4262 0.0574 H 0 0 0 0 0 0 0 0 0 0 0 0
16 | 2.1275 -0.8811 0.1374 H 0 0 0 0 0 0 0 0 0 0 0 0
17 | -1.9594 -1.3442 0.1220 H 0 0 0 0 0 0 0 0 0 0 0 0
18 | -2.7602 1.9980 1.0368 H 0 0 0 0 0 0 0 0 0 0 0 0
19 | -2.7442 1.9845 -0.9069 H 0 0 0 0 0 0 0 0 0 0 0 0
20 | -4.9158 1.0214 0.0760 H 0 0 0 0 0 0 0 0 0 0 0 0
21 | -3.8958 -0.3239 -0.9183 H 0 0 0 0 0 0 0 0 0 0 0 0
22 | -3.8858 -0.3393 1.0404 H 0 0 0 0 0 0 0 0 0 0 0 0
23 | 1.3764 -3.1220 -0.1568 H 0 0 0 0 0 0 0 0 0 0 0 0
24 | 0.0542 -3.1999 1.2818 H 0 0 0 0 0 0 0 0 0 0 0 0
25 | -0.5198 -3.3216 -0.5842 H 0 0 0 0 0 0 0 0 0 0 0 0
26 | 1 6 2 0
27 | 2 1 1 0
28 | 2 8 1 0
29 | 3 2 2 0
30 | 4 3 1 0
31 | 4 10 1 0
32 | 5 4 2 0
33 | 6 5 1 0
34 | 6 7 1 0
35 | 7 9 1 0
36 | 1 11 1 0
37 | 3 12 1 0
38 | 5 13 1 0
39 | 7 14 1 0
40 | 7 15 1 0
41 | 9 16 1 0
42 | 9 17 1 0
43 | 9 18 1 0
44 | 10 19 1 0
45 | 10 20 1 0
46 | 10 21 1 0
47 | M END
48 | >
49 | false
50 |
51 | >
52 | 0.475
53 |
54 | >
55 | 0
56 |
57 | >
58 | 0
59 |
60 | >
61 | 154.6
62 |
63 | > <#Atoms_cresset>
64 | 10
65 |
66 | > <2D Sim_cresset>
67 | 1
68 |
69 | >
70 | 3.2
71 |
72 | >
73 | 0
74 |
75 | >
76 | 1
77 |
78 | >
79 | 0
80 |
81 | >
82 | chlorophenyl.sdf
83 |
84 | > <_cresset_fieldpoints>
85 | -5 -0.087605 -0.000034 -2.785532 -4.7614
86 | -5 1.539579 4.431469 0.048729 -1.7239
87 | -5 4.585974 0.309859 0.172488 -1.7423
88 | -5 -0.113217 0.115486 2.996586 -4.7503
89 | -6 3.651323 -2.582189 0.323773 1.7956
90 | -6 -4.486787 3.798370 0.039369 1.5167
91 | -6 -1.764029 4.251424 0.030317 2.0279
92 | -6 -3.234832 -3.115461 0.074574 2.5916
93 | -7 -1.803603 4.434534 0.059936 -1.4779
94 | -7 -0.269931 -0.020888 -3.105073 -2.0286
95 | -7 -2.147747 0.074793 3.219288 -1.9789
96 | -7 -2.074900 0.003885 -3.042543 -1.9810
97 | -7 -0.297152 0.065645 3.313384 -2.0394
98 | -7 -4.742827 3.766482 0.029611 -1.1408
99 | -7 -2.863637 -2.790952 1.910719 -1.7710
100 | -7 -2.831667 -2.571763 -1.922886 -1.7925
101 | -8 -0.057138 0.067216 0.102893 7.2188
102 | -8 1.230757 1.020876 0.098157 5.6179
103 | -8 -2.380938 0.205954 0.088087 5.6374
104 |
105 | $$$$
106 |
--------------------------------------------------------------------------------
/test/transforms/chlorotoluyl2.sdf:
--------------------------------------------------------------------------------
1 | chlorotoluyl2
2 | xed2sdf_05210316543D
3 |
4 | 21 21 0 0 0 0 0 0 0 0999 V2000
5 | -0.1938 1.4830 0.0782 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | 1.0694 0.9354 0.0950 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | 1.2235 -0.4319 0.1229 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 0.1157 -1.2493 0.1334 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | -1.1453 -0.6969 0.1165 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | -1.3062 0.6715 0.0888 C 0 0 0 0 0 0 0 0 0 0 0 0
11 | -2.6713 1.3413 0.0701 C 0 0 0 0 0 0 0 0 0 0 0 0
12 | 2.2775 1.8487 0.0835 C 0 0 0 0 0 0 0 0 0 0 0 0
13 | -3.8992 0.4115 0.0638 C 0 0 0 0 0 0 0 0 0 0 0 0
14 | 0.3079 -2.9769 0.1684 Cl 0 0 0 0 0 0 0 0 0 0 0 0
15 | -0.3038 2.4768 0.0583 H 0 0 0 0 0 0 0 0 0 0 0 0
16 | 2.1400 -0.8313 0.1353 H 0 0 0 0 0 0 0 0 0 0 0 0
17 | -1.9489 -1.2919 0.1244 H 0 0 0 0 0 0 0 0 0 0 0 0
18 | -2.7470 2.0475 1.0372 H 0 0 0 0 0 0 0 0 0 0 0 0
19 | -2.7274 2.0356 -0.9068 H 0 0 0 0 0 0 0 0 0 0 0 0
20 | -4.9037 1.0680 0.0614 H 0 0 0 0 0 0 0 0 0 0 0 0
21 | -3.8712 -0.2802 -0.9163 H 0 0 0 0 0 0 0 0 0 0 0 0
22 | -3.8783 -0.2835 1.0416 H 0 0 0 0 0 0 0 0 0 0 0 0
23 | 3.2958 1.2126 0.0881 H 0 0 0 0 0 0 0 0 0 0 0 0
24 | 2.2450 2.5326 -0.9020 H 0 0 0 0 0 0 0 0 0 0 0 0
25 | 2.2481 2.5522 1.0551 H 0 0 0 0 0 0 0 0 0 0 0 0
26 | 1 6 2 0
27 | 2 1 1 0
28 | 2 8 1 0
29 | 3 2 2 0
30 | 4 3 1 0
31 | 4 10 1 0
32 | 5 4 2 0
33 | 6 5 1 0
34 | 6 7 1 0
35 | 7 9 1 0
36 | 1 11 1 0
37 | 3 12 1 0
38 | 5 13 1 0
39 | 7 14 1 0
40 | 7 15 1 0
41 | 8 19 1 0
42 | 8 20 1 0
43 | 8 21 1 0
44 | 9 16 1 0
45 | 9 17 1 0
46 | 9 18 1 0
47 | M END
48 | >
49 | false
50 |
51 | >
52 | 0.475
53 |
54 | >
55 | 0
56 |
57 | >
58 | 0
59 |
60 | >
61 | 154.6
62 |
63 | > <#Atoms_cresset>
64 | 10
65 |
66 | > <2D Sim_cresset>
67 | 1
68 |
69 | >
70 | 3.2
71 |
72 | >
73 | 0
74 |
75 | >
76 | 1
77 |
78 | >
79 | 0
80 |
81 | >
82 | chlorophenyl.sdf
83 |
84 | > <_cresset_fieldpoints>
85 | -5 -0.067790 0.054922 -2.785769 -4.7563
86 | -5 -0.094023 0.167077 2.996860 -4.7527
87 | -5 -2.172030 -3.975008 0.182330 -1.8171
88 | -5 2.938128 -3.444929 0.211224 -1.7578
89 | -6 0.514643 4.567085 0.022611 2.4631
90 | -6 -1.545493 4.349075 0.021797 2.5160
91 | -6 4.421916 -0.875917 0.145737 1.7708
92 | -6 -3.746627 -2.702787 0.096605 1.3602
93 | -7 -0.171238 0.196556 -3.107582 -2.0318
94 | -7 0.684115 4.737516 0.086476 -1.4510
95 | -7 -1.750846 4.486156 0.061283 -1.5173
96 | -7 -2.879323 -2.662051 -1.742283 -1.5881
97 | -7 -4.729161 3.818013 0.042667 -1.1409
98 | -7 -0.194647 0.329412 3.309833 -2.0312
99 | -7 -2.045084 0.150183 -3.055637 -1.9588
100 | -7 -3.615049 -2.961360 -0.013593 -1.5919
101 | -7 -2.913715 -2.661590 1.952031 -1.5803
102 | -7 -3.304031 -2.957864 1.143089 -1.5738
103 | -7 -2.141198 0.224340 3.232067 -1.9507
104 | -8 -0.041072 0.122617 0.106917 7.2196
105 | -8 -2.376746 0.265933 0.093239 5.6413
106 |
107 | $$$$
108 |
--------------------------------------------------------------------------------
/test/transforms/fluorophenyl.sdf:
--------------------------------------------------------------------------------
1 | fluorophenyl
2 | xed2sdf_05210316543D
3 |
4 | 18 18 0 0 0 0 0 0 0 0999 V2000
5 | -0.2078 1.4341 0.0951 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | 1.0620 0.9009 0.0874 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | 1.2340 -0.4650 0.0630 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 0.1360 -1.2932 0.0457 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | -1.1321 -0.7567 0.0533 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | -1.3108 0.6105 0.0784 C 0 0 0 0 0 0 0 0 0 0 0 0
11 | -2.6779 1.2763 0.0882 C 0 0 0 0 0 0 0 0 0 0 0 0
12 | 2.4475 1.9523 0.1083 F 0 0 0 0 0 0 0 0 0 0 0 0
13 | -3.9112 0.3543 0.0807 C 0 0 0 0 0 0 0 0 0 0 0 0
14 | -0.3295 2.4266 0.1128 H 0 0 0 0 0 0 0 0 0 0 0 0
15 | 2.1554 -0.8541 0.0576 H 0 0 0 0 0 0 0 0 0 0 0 0
16 | -1.9279 -1.3622 0.0406 H 0 0 0 0 0 0 0 0 0 0 0 0
17 | 0.2588 -2.2856 0.0273 H 0 0 0 0 0 0 0 0 0 0 0 0
18 | -2.7414 1.9674 1.0670 H 0 0 0 0 0 0 0 0 0 0 0 0
19 | -2.7452 1.9886 -0.8751 H 0 0 0 0 0 0 0 0 0 0 0 0
20 | -4.9067 1.0246 0.0934 H 0 0 0 0 0 0 0 0 0 0 0 0
21 | -3.9009 -0.3248 -0.9085 H 0 0 0 0 0 0 0 0 0 0 0 0
22 | -3.8935 -0.3513 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0
23 | 1 6 2 0
24 | 2 1 1 0
25 | 2 8 1 0
26 | 3 2 2 0
27 | 4 3 1 0
28 | 5 4 2 0
29 | 6 5 1 0
30 | 6 7 1 0
31 | 7 9 1 0
32 | 1 10 1 0
33 | 3 11 1 0
34 | 4 13 1 0
35 | 5 12 1 0
36 | 7 14 1 0
37 | 7 15 1 0
38 | 9 16 1 0
39 | 9 17 1 0
40 | 9 18 1 0
41 | M END
42 | >
43 | false
44 |
45 | >
46 | 0.500
47 |
48 | >
49 | 0
50 |
51 | >
52 | 0
53 |
54 | >
55 | 124.2
56 |
57 | > <#Atoms_cresset>
58 | 9
59 |
60 | >
61 | 2.7
62 |
63 | >
64 | 0
65 |
66 | >
67 | 1
68 |
69 | >
70 | 0
71 |
72 | >
73 | chlorophenyl.sdf
74 |
75 | > <_cresset_fieldpoints>
76 | -5 -0.249634 0.141481 -2.870371 -3.6992
77 | -5 -0.258767 0.038885 3.011418 -3.7006
78 | -5 5.131414 1.088324 0.104046 -2.1699
79 | -5 2.329686 4.767548 0.155661 -2.1605
80 | -6 -1.762562 4.219894 0.131912 2.3877
81 | -6 2.291609 -3.481932 0.008202 2.4738
82 | -6 -1.782707 -3.807055 -0.006433 2.5518
83 | -6 -3.456510 -2.920497 0.018592 2.6231
84 | -7 -1.806085 4.428570 0.123346 -1.4927
85 | -7 2.722434 -3.502663 -0.031210 -0.9845
86 | -7 -3.741013 -2.952006 0.046786 -1.4581
87 | -7 -0.340618 0.200088 3.296729 -1.9382
88 | -7 -4.711312 3.773040 0.126341 -1.1440
89 | -7 -2.148519 0.194150 -3.070925 -1.9240
90 | -7 -0.321952 0.319669 -3.150448 -1.9370
91 | -7 -2.125665 0.115104 3.216287 -1.9291
92 | -8 -0.049161 0.067818 0.069660 7.1681
93 | -8 -2.367455 0.204391 0.074533 5.5931
94 |
95 | $$$$
96 |
--------------------------------------------------------------------------------
/test/transforms/iodophenyl.sdf:
--------------------------------------------------------------------------------
1 | iodophenyl
2 | xed2sdf_05210316543D
3 |
4 | 18 18 0 0 0 0 0 0 0 0999 V2000
5 | -0.2078 1.4341 0.0951 C 0 0 0 0 0 0 0 0 0 0 0 0
6 | 1.0620 0.9009 0.0874 C 0 0 0 0 0 0 0 0 0 0 0 0
7 | 1.2340 -0.4650 0.0630 C 0 0 0 0 0 0 0 0 0 0 0 0
8 | 0.1360 -1.2932 0.0457 C 0 0 0 0 0 0 0 0 0 0 0 0
9 | -1.1321 -0.7567 0.0533 C 0 0 0 0 0 0 0 0 0 0 0 0
10 | -1.3108 0.6105 0.0784 C 0 0 0 0 0 0 0 0 0 0 0 0
11 | -2.6779 1.2763 0.0882 C 0 0 0 0 0 0 0 0 0 0 0 0
12 | 2.4475 1.9523 0.1083 I 0 0 0 0 0 0 0 0 0 0 0 0
13 | -3.9112 0.3543 0.0807 C 0 0 0 0 0 0 0 0 0 0 0 0
14 | -0.3295 2.4266 0.1128 H 0 0 0 0 0 0 0 0 0 0 0 0
15 | 2.1554 -0.8541 0.0576 H 0 0 0 0 0 0 0 0 0 0 0 0
16 | -1.9279 -1.3622 0.0406 H 0 0 0 0 0 0 0 0 0 0 0 0
17 | 0.2588 -2.2856 0.0273 H 0 0 0 0 0 0 0 0 0 0 0 0
18 | -2.7414 1.9674 1.0670 H 0 0 0 0 0 0 0 0 0 0 0 0
19 | -2.7452 1.9886 -0.8751 H 0 0 0 0 0 0 0 0 0 0 0 0
20 | -4.9067 1.0246 0.0934 H 0 0 0 0 0 0 0 0 0 0 0 0
21 | -3.9009 -0.3248 -0.9085 H 0 0 0 0 0 0 0 0 0 0 0 0
22 | -3.8935 -0.3513 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0
23 | 1 6 2 0
24 | 2 1 1 0
25 | 2 8 1 0
26 | 3 2 2 0
27 | 4 3 1 0
28 | 5 4 2 0
29 | 6 5 1 0
30 | 6 7 1 0
31 | 7 9 1 0
32 | 1 10 1 0
33 | 3 11 1 0
34 | 4 13 1 0
35 | 5 12 1 0
36 | 7 14 1 0
37 | 7 15 1 0
38 | 9 16 1 0
39 | 9 17 1 0
40 | 9 18 1 0
41 | M END
42 | >
43 | false
44 |
45 | >
46 | 0.500
47 |
48 | >
49 | 0
50 |
51 | >
52 | 0
53 |
54 | >
55 | 124.2
56 |
57 | > <#Atoms_cresset>
58 | 9
59 |
60 | >
61 | 2.7
62 |
63 | > |