├── .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 | -------------------------------------------------------------------------------- /.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 | -------------------------------------------------------------------------------- /.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 | -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 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 | -------------------------------------------------------------------------------- /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 | > 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/methoxyphenyl.sdf: -------------------------------------------------------------------------------- 1 | methoxyphenyl 2 | xed2sdf_05210316543D 3 | 4 | 22 22 0 0 0 0 0 0 0 0999 V2000 5 | -0.1585 1.4748 0.1000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 1.1225 0.9539 0.1099 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 1.2806 -0.4228 0.0852 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | 0.1836 -1.2500 0.0523 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | -1.0840 -0.7147 0.0448 C 0 0 0 0 0 0 0 0 0 0 0 0 10 | -1.2608 0.6522 0.0690 C 0 0 0 0 0 0 0 0 0 0 0 0 11 | -2.6316 1.3111 0.0641 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | 2.1606 1.8017 0.1453 O 0 0 0 0 0 0 0 0 0 0 0 0 13 | -3.8569 0.3778 0.0688 C 0 0 0 0 0 0 0 0 0 0 0 0 14 | 3.4969 1.2635 0.2126 C 0 0 0 0 0 0 0 0 0 0 0 0 15 | -0.2884 2.4665 0.1172 H 0 0 0 0 0 0 0 0 0 0 0 0 16 | 2.1976 -0.8208 0.0921 H 0 0 0 0 0 0 0 0 0 0 0 0 17 | -1.8800 -1.3197 0.0221 H 0 0 0 0 0 0 0 0 0 0 0 0 18 | 0.3068 -2.2421 0.0347 H 0 0 0 0 0 0 0 0 0 0 0 0 19 | -2.7037 2.0145 1.0335 H 0 0 0 0 0 0 0 0 0 0 0 0 20 | -2.7034 2.0086 -0.9095 H 0 0 0 0 0 0 0 0 0 0 0 0 21 | -4.8596 1.0369 0.0780 H 0 0 0 0 0 0 0 0 0 0 0 0 22 | -3.8418 -0.3111 -0.9138 H 0 0 0 0 0 0 0 0 0 0 0 0 23 | -3.8282 -0.3186 1.0455 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | 4.2832 2.1686 0.2573 H 0 0 0 0 0 0 0 0 0 0 0 0 25 | 3.6166 0.5883 1.1979 H 0 0 0 0 0 0 0 0 0 0 0 0 26 | 3.7160 0.5967 -0.7607 H 0 0 0 0 0 0 0 0 0 0 0 0 27 | 1 6 2 0 28 | 2 1 1 0 29 | 2 8 1 0 30 | 3 2 2 0 31 | 4 3 1 0 32 | 5 4 2 0 33 | 6 5 1 0 34 | 6 7 1 0 35 | 7 9 1 0 36 | 8 10 1 0 37 | 1 11 1 0 38 | 3 12 1 0 39 | 4 14 1 0 40 | 5 13 1 0 41 | 7 15 1 0 42 | 7 16 1 0 43 | 9 17 1 0 44 | 9 18 1 0 45 | 9 19 1 0 46 | 10 20 1 0 47 | 10 21 1 0 48 | 10 22 1 0 49 | M END 50 | > 51 | false 52 | 53 | > 54 | 0.500 55 | 56 | > 57 | 0 58 | 59 | > 60 | 0 61 | 62 | > 63 | 136.2 64 | 65 | > <#Atoms_cresset> 66 | 10 67 | 68 | > 69 | 2.3 70 | 71 | > 72 | 9.2 73 | 74 | > 75 | 1.5 76 | 77 | > 78 | 0 79 | 80 | > 81 | chlorophenyl.sdf 82 | 83 | > <_cresset_fieldpoints> 84 | -5 -0.082070 0.473916 -2.803974 -5.1538 85 | -5 -0.195031 0.354307 2.962966 -5.0846 86 | -5 1.972906 3.533776 -1.411186 -4.6610 87 | -6 4.157138 -1.750635 0.177501 3.9004 88 | -6 -3.375947 -2.938108 -0.018562 2.0565 89 | -6 -1.163018 -4.046505 -0.010580 2.1068 90 | -7 -0.153810 0.336377 -3.143410 -1.9334 91 | -7 -1.785540 4.466249 0.052127 -1.4694 92 | -7 -0.244473 0.216666 3.295629 -1.9482 93 | -7 -2.062251 0.182993 3.209208 -1.9351 94 | -7 -3.159267 -2.738538 -1.547379 -1.3941 95 | -7 -2.103495 0.204531 -3.082617 -1.9140 96 | -7 -4.696292 3.783460 0.052209 -1.1421 97 | -7 2.052454 0.873200 -2.991764 -1.6967 98 | -7 -3.676788 -2.927246 0.094666 -1.4579 99 | -7 4.319685 -1.965214 0.293586 -1.3773 100 | -7 1.677182 0.660007 3.285535 -1.7356 101 | -8 -0.016914 0.096790 0.077272 7.0595 102 | -8 -2.324149 0.235605 0.057507 5.6089 103 | -8 4.214501 0.845845 0.246698 2.5009 104 | 105 | $$$$ 106 | -------------------------------------------------------------------------------- /test/transforms/napthyl.sdf: -------------------------------------------------------------------------------- 1 | Napthyl 2 | xed2sdf_05210316543D 3 | 4 | 24 25 0 0 0 0 0 0 0 0999 V2000 5 | -0.1769 1.5660 0.1864 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 1.0971 0.9820 0.2259 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 1.2227 -0.4151 0.3046 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | 0.1139 -1.1889 0.3412 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | -1.1608 -0.6062 0.3007 C 0 0 0 0 0 0 0 0 0 0 0 0 10 | -1.3220 0.7392 0.2249 C 0 0 0 0 0 0 0 0 0 0 0 0 11 | -2.7192 1.3516 0.1806 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | -0.2643 2.9708 0.1090 C 0 0 0 0 0 0 0 0 0 0 0 0 13 | 0.8541 3.7329 0.0731 C 0 0 0 0 0 0 0 0 0 0 0 0 14 | 2.1231 3.1382 0.1122 C 0 0 0 0 0 0 0 0 0 0 0 0 15 | 2.2457 1.7924 0.1871 C 0 0 0 0 0 0 0 0 0 0 0 0 16 | -3.9203 0.3904 0.2516 C 0 0 0 0 0 0 0 0 0 0 0 0 17 | 2.1291 -0.8363 0.3334 H 0 0 0 0 0 0 0 0 0 0 0 0 18 | -1.9687 -1.1946 0.3282 H 0 0 0 0 0 0 0 0 0 0 0 0 19 | 0.2037 -2.1832 0.3974 H 0 0 0 0 0 0 0 0 0 0 0 0 20 | -1.1628 3.4091 0.0803 H 0 0 0 0 0 0 0 0 0 0 0 0 21 | 3.1537 1.3742 0.2146 H 0 0 0 0 0 0 0 0 0 0 0 0 22 | 0.7742 4.7282 0.0183 H 0 0 0 0 0 0 0 0 0 0 0 0 23 | 2.9419 3.7115 0.0848 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | -2.8104 2.1201 1.0974 H 0 0 0 0 0 0 0 0 0 0 0 0 25 | -2.8114 1.9778 -0.8390 H 0 0 0 0 0 0 0 0 0 0 0 0 26 | -4.9404 1.0213 0.2110 H 0 0 0 0 0 0 0 0 0 0 0 0 27 | -3.8740 -0.2311 1.2770 H 0 0 0 0 0 0 0 0 0 0 0 0 28 | -3.8807 -0.3669 -0.6784 H 0 0 0 0 0 0 0 0 0 0 0 0 29 | 1 6 2 0 30 | 1 8 1 0 31 | 2 1 1 0 32 | 3 2 2 0 33 | 4 3 1 0 34 | 5 4 2 0 35 | 6 5 1 0 36 | 6 7 1 0 37 | 7 12 1 0 38 | 8 9 2 0 39 | 9 10 1 0 40 | 10 11 2 0 41 | 11 2 1 0 42 | 3 13 1 0 43 | 4 15 1 0 44 | 5 14 1 0 45 | 7 20 1 0 46 | 7 21 1 0 47 | 8 16 1 0 48 | 9 18 1 0 49 | 10 19 1 0 50 | 11 17 1 0 51 | 12 22 1 0 52 | 12 23 1 0 53 | 12 24 1 0 54 | M END 55 | > 56 | false 57 | 58 | > 59 | 0.450 60 | 61 | > 62 | 0 63 | 64 | > 65 | 0 66 | 67 | > 68 | 156.2 69 | 70 | > <#Atoms_cresset> 71 | 12 72 | 73 | > 74 | 3.4 75 | 76 | > 77 | 0 78 | 79 | > 80 | 1 81 | 82 | > 83 | 0 84 | 85 | > <_cresset_fieldpoints> 86 | -5 0.236695 1.199721 3.093871 -6.3156 87 | -5 0.275087 0.895251 -2.660867 -6.3121 88 | -6 4.401994 -0.540823 0.330344 2.6825 89 | -6 2.659118 -3.168469 0.470992 2.0591 90 | -6 -3.398940 -2.865561 0.424310 2.1519 91 | -6 2.775770 6.235390 -0.054850 2.0074 92 | -6 -3.065450 4.500637 -0.004352 2.6469 93 | -6 5.275425 2.507179 0.165309 2.0910 94 | -7 2.672053 -3.450489 0.407526 -1.0019 95 | -7 -0.042770 0.714234 -2.961401 -2.3527 96 | -7 -0.080150 1.058757 3.410365 -2.3533 97 | -7 -3.308448 4.542226 -0.073623 -1.6452 98 | -7 5.504169 2.646835 0.196844 -1.0009 99 | -7 2.899687 6.437018 -0.081827 -0.9771 100 | -7 -3.653175 -2.907872 0.506991 -1.4728 101 | -8 -0.035626 0.200547 0.263339 7.1831 102 | -8 -1.286272 1.812153 0.167362 5.7692 103 | -8 0.970024 2.346114 0.149491 7.1694 104 | -8 -2.389894 0.296813 0.251022 5.7047 105 | 106 | $$$$ 107 | -------------------------------------------------------------------------------- /test/transforms/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/transforms/phenylamide.sdf: -------------------------------------------------------------------------------- 1 | phenylamide 2 | xed2sdf_05210316543D 3 | 4 | 22 22 0 0 0 0 0 0 0 0999 V2000 5 | -0.0723 1.4117 0.1745 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 1.1833 0.8176 0.1859 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 1.2469 -0.5663 0.1017 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | 0.1052 -1.3234 0.0102 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | -1.1278 -0.7122 0.0009 C 0 0 0 0 0 0 0 0 0 0 0 0 10 | -1.2202 0.6610 0.0846 C 0 0 0 0 0 0 0 0 0 0 0 0 11 | -2.5471 1.4052 0.0807 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | -3.8255 0.5473 0.1032 C 0 0 0 0 0 0 0 0 0 0 0 0 13 | 2.4425 1.6058 0.2877 C 0 0 0 0 0 0 0 0 0 0 0 0 14 | 3.4961 0.9774 0.3563 O 0 0 0 0 0 0 0 0 0 0 0 0 15 | 2.4135 2.9527 0.3030 N 0 0 0 0 0 0 0 0 0 0 0 0 16 | -0.1515 2.4051 0.2346 H 0 0 0 0 0 0 0 0 0 0 0 0 17 | 2.1384 -1.0192 0.1085 H 0 0 0 0 0 0 0 0 0 0 0 0 18 | -1.9584 -1.2652 -0.0657 H 0 0 0 0 0 0 0 0 0 0 0 0 19 | 0.1695 -2.3195 -0.0495 H 0 0 0 0 0 0 0 0 0 0 0 0 20 | -2.5781 2.1240 1.0416 H 0 0 0 0 0 0 0 0 0 0 0 0 21 | -2.5802 2.0934 -0.9018 H 0 0 0 0 0 0 0 0 0 0 0 0 22 | -4.7867 1.2657 0.1112 H 0 0 0 0 0 0 0 0 0 0 0 0 23 | -3.8298 -0.1383 1.0881 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | -3.8567 -0.1515 -0.8718 H 0 0 0 0 0 0 0 0 0 0 0 0 25 | 1.6551 3.3909 0.2356 H 0 0 0 0 0 0 0 0 0 0 0 0 26 | 3.1659 3.4036 0.3796 H 0 0 0 0 0 0 0 0 0 0 0 0 27 | 1 6 2 0 28 | 2 1 1 0 29 | 2 9 1 0 30 | 3 2 2 0 31 | 4 3 1 0 32 | 5 4 2 0 33 | 6 5 1 0 34 | 6 7 1 0 35 | 7 8 1 0 36 | 9 10 2 0 37 | 9 11 1 0 38 | 1 12 1 0 39 | 3 13 1 0 40 | 4 15 1 0 41 | 5 14 1 0 42 | 7 16 1 0 43 | 7 17 1 0 44 | 8 18 1 0 45 | 8 19 1 0 46 | 8 20 1 0 47 | 11 21 1 0 48 | 11 22 1 0 49 | M END 50 | > 51 | false 52 | 53 | > 54 | 0.693 55 | 56 | > 57 | 0 58 | 59 | > 60 | 0 61 | 62 | > 63 | 149.2 64 | 65 | > <#Atoms_cresset> 66 | 11 67 | 68 | > 69 | 1.3 70 | 71 | > 72 | 43.1 73 | 74 | > 75 | 1.3 76 | 77 | > 78 | 0 79 | 80 | > 81 | phenylethyl.sdf 82 | 83 | > <_cresset_fieldpoints> 84 | -5 4.578770 -0.588242 0.501506 -9.7221 85 | -5 0.689473 0.024166 -2.853223 -4.0362 86 | -6 -0.025433 4.521160 0.169816 7.8105 87 | -6 -3.617255 -2.678400 -0.169259 2.7762 88 | -7 -0.121615 0.458577 -3.117829 -1.9227 89 | -7 1.301958 2.979746 2.822188 -1.7705 90 | -7 -0.436786 0.048682 3.307398 -1.9379 91 | -7 -1.987003 0.188294 3.215451 -1.9533 92 | -7 -2.162801 0.291594 -3.074581 -1.8969 93 | -7 2.566756 -3.667961 -0.167998 -0.9841 94 | -7 -3.826093 -2.764576 0.267275 -1.4618 95 | -7 2.282754 -3.342749 1.674834 -0.9766 96 | -7 -4.457544 3.998811 0.048403 -1.1425 97 | -7 1.566510 2.970659 -2.365492 -1.7523 98 | -7 3.192187 0.029492 2.814797 -1.4946 99 | -7 3.622202 0.218361 -2.165971 -1.4875 100 | -7 -1.341210 4.497324 -0.073318 -1.5912 101 | -8 0.009500 0.049496 0.091921 7.1482 102 | -8 -2.303695 0.311719 0.056819 5.6158 103 | 104 | $$$$ 105 | -------------------------------------------------------------------------------- /test/transforms/phenylethyl.sdf: -------------------------------------------------------------------------------- 1 | phenylethyl 2 | xed2sdf_05210316543D 3 | 4 | 24 24 0 0 0 0 0 0 0 0999 V2000 5 | -0.0991 1.4012 0.1478 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 1.1369 0.7939 0.1488 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 1.2120 -0.5808 0.0800 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | 0.0641 -1.3360 0.0144 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | -1.1655 -0.7194 0.0155 C 0 0 0 0 0 0 0 0 0 0 0 0 10 | -1.2537 0.6544 0.0824 C 0 0 0 0 0 0 0 0 0 0 0 0 11 | -2.5766 1.4035 0.0856 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | -3.8570 0.5484 0.1062 C 0 0 0 0 0 0 0 0 0 0 0 0 13 | 2.3659 1.6876 0.2210 C 0 0 0 0 0 0 0 0 0 0 0 0 14 | 3.7226 0.9829 0.4019 C 0 0 0 0 0 0 0 0 0 0 0 0 15 | -0.1586 2.3983 0.1955 H 0 0 0 0 0 0 0 0 0 0 0 0 16 | 2.1051 -1.0309 0.0783 H 0 0 0 0 0 0 0 0 0 0 0 0 17 | -1.9988 -1.2702 -0.0325 H 0 0 0 0 0 0 0 0 0 0 0 0 18 | 0.1235 -2.3332 -0.0344 H 0 0 0 0 0 0 0 0 0 0 0 0 19 | -2.5944 2.1164 1.0508 H 0 0 0 0 0 0 0 0 0 0 0 0 20 | -2.6099 2.0982 -0.8924 H 0 0 0 0 0 0 0 0 0 0 0 0 21 | -4.8183 1.2666 0.1186 H 0 0 0 0 0 0 0 0 0 0 0 0 22 | -3.8605 -0.1428 1.0871 H 0 0 0 0 0 0 0 0 0 0 0 0 23 | -3.8880 -0.1456 -0.8723 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | 2.2301 2.4451 1.1423 H 0 0 0 0 0 0 0 0 0 0 0 0 25 | 2.4146 2.3324 -0.7898 H 0 0 0 0 0 0 0 0 0 0 0 0 26 | 4.5910 1.8068 0.4826 H 0 0 0 0 0 0 0 0 0 0 0 0 27 | 3.7007 0.3249 1.4056 H 0 0 0 0 0 0 0 0 0 0 0 0 28 | 3.9324 0.2706 -0.5406 H 0 0 0 0 0 0 0 0 0 0 0 0 29 | 1 6 2 0 30 | 2 1 1 0 31 | 2 9 1 0 32 | 3 2 2 0 33 | 4 3 1 0 34 | 5 4 2 0 35 | 6 5 1 0 36 | 6 7 1 0 37 | 7 8 1 0 38 | 9 10 1 0 39 | 1 11 1 0 40 | 3 12 1 0 41 | 4 14 1 0 42 | 5 13 1 0 43 | 7 15 1 0 44 | 7 16 1 0 45 | 8 17 1 0 46 | 8 18 1 0 47 | 8 19 1 0 48 | 9 20 1 0 49 | 9 21 1 0 50 | 10 22 1 0 51 | 10 23 1 0 52 | 10 24 1 0 53 | M END 54 | > 55 | false 56 | 57 | > 58 | 0.500 59 | 60 | > 61 | 0 62 | 63 | > 64 | 0 65 | 66 | > 67 | 134.2 68 | 69 | > <#Atoms_cresset> 70 | 10 71 | 72 | > 73 | 2.8 74 | 75 | > 76 | 0 77 | 78 | > 79 | 2 80 | 81 | > 82 | 0 83 | 84 | > 85 | toluyl.sdf 86 | 87 | > <_cresset_fieldpoints> 88 | -5 0.046961 0.257858 -2.758512 -5.6242 89 | -5 -0.089515 -0.021557 2.926796 -5.6659 90 | -6 0.696206 4.481197 0.297846 2.0378 91 | -6 -3.654353 -2.738937 -0.123452 1.8353 92 | -6 3.910108 -2.313369 0.105175 1.8343 93 | -6 -1.270840 4.362006 0.259752 2.0429 94 | -7 0.906729 4.595091 -0.208989 -1.5353 95 | -7 -1.457266 4.486713 -0.006382 -1.5327 96 | -7 4.059931 -2.301287 0.726863 -1.4674 97 | -7 2.414018 0.458147 -2.908001 -1.8945 98 | -7 -3.881440 -2.761655 0.219283 -1.4608 99 | -7 -1.983285 0.213894 3.223105 -1.9633 100 | -7 -4.485461 3.998049 0.087740 -1.1420 101 | -7 -2.156379 0.301472 -3.075269 -1.9152 102 | -7 1.594988 0.485297 3.341693 -1.9850 103 | -7 0.034261 0.453143 -3.113448 -2.0241 104 | -7 3.976911 4.478362 0.229606 -1.1420 105 | -7 -0.085356 0.130770 3.299682 -2.0462 106 | -8 -0.019180 0.041631 0.081513 7.2189 107 | -8 -2.340223 0.306503 0.066015 5.6253 108 | -8 2.250464 0.570390 0.216862 5.6269 109 | 110 | $$$$ 111 | -------------------------------------------------------------------------------- /test/transforms/phenylisoxazole.sdf: -------------------------------------------------------------------------------- 1 | phenylisoxazole 2 | xed2sdf_05210316543D 3 | 4 | 24 25 0 0 0 0 0 0 0 0999 V2000 5 | -0.0733 1.4514 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 0.0667 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | -1.1037 -0.6899 0.1060 C 0 0 0 0 0 0 0 0 0 0 0 0 10 | -1.2145 0.6842 0.0767 C 0 0 0 0 0 0 0 0 0 0 0 0 11 | -2.5499 1.4090 0.1181 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 | 2.5307 -1.1254 -0.0415 C 0 0 0 0 0 0 0 0 0 0 0 0 14 | 3.6849 -0.3388 -0.1357 O 0 0 0 0 0 0 0 0 0 0 0 0 15 | 4.7919 -1.1956 -0.1570 N 0 0 0 0 0 0 0 0 0 0 0 0 16 | 4.3219 -2.5119 -0.0760 C 0 0 0 0 0 0 0 0 0 0 0 0 17 | 2.9243 -2.4685 -0.0048 C 0 0 0 0 0 0 0 0 0 0 0 0 18 | -0.1456 2.4484 -0.0125 H 0 0 0 0 0 0 0 0 0 0 0 0 19 | 1.9906 1.4174 -0.0799 H 0 0 0 0 0 0 0 0 0 0 0 0 20 | -1.9280 -1.2540 0.1558 H 0 0 0 0 0 0 0 0 0 0 0 0 21 | 0.2079 -2.2869 0.0878 H 0 0 0 0 0 0 0 0 0 0 0 0 22 | -2.5699 2.0921 1.1041 H 0 0 0 0 0 0 0 0 0 0 0 0 23 | -2.6068 2.1324 -0.8377 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | -4.7890 1.2260 0.1573 H 0 0 0 0 0 0 0 0 0 0 0 0 25 | -3.7986 -0.1875 1.0849 H 0 0 0 0 0 0 0 0 0 0 0 0 26 | -3.8372 -0.1426 -0.8725 H 0 0 0 0 0 0 0 0 0 0 0 0 27 | 2.2350 -3.1899 0.0622 H 0 0 0 0 0 0 0 0 0 0 0 0 28 | 4.9684 -3.2747 -0.0773 H 0 0 0 0 0 0 0 0 0 0 0 0 29 | 1 6 2 0 30 | 2 1 1 0 31 | 3 2 2 0 32 | 3 9 1 0 33 | 4 3 1 0 34 | 5 4 2 0 35 | 6 5 1 0 36 | 6 7 1 0 37 | 7 8 1 0 38 | 9 10 1 0 39 | 10 11 1 0 40 | 11 12 2 0 41 | 12 13 1 0 42 | 13 9 2 0 43 | 1 14 1 0 44 | 2 15 1 0 45 | 4 17 1 0 46 | 5 16 1 0 47 | 7 18 1 0 48 | 7 19 1 0 49 | 8 20 1 0 50 | 8 21 1 0 51 | 8 22 1 0 52 | 12 24 1 0 53 | 13 23 1 0 54 | M END 55 | > 56 | false 57 | 58 | > 59 | 0.550 60 | 61 | > 62 | 0 63 | 64 | > 65 | 0 66 | 67 | > 68 | 173.2 69 | 70 | > <#Atoms_cresset> 71 | 13 72 | 73 | > 74 | 2.3 75 | 76 | > 77 | 26 78 | 79 | > 80 | 1 81 | 82 | > 83 | 0 84 | 85 | > 86 | phenyl.sdf 87 | 88 | > <_cresset_fieldpoints> 89 | -5 5.807463 0.299429 -0.281584 -9.8757 90 | -5 0.100359 0.198399 -2.918842 -3.8478 91 | -5 0.355847 0.349634 2.966742 -3.7906 92 | -6 0.484286 -4.410237 0.173158 5.6214 93 | -6 -1.423225 4.325241 0.038814 2.6682 94 | -6 -4.080558 4.065814 0.177759 1.9555 95 | -7 -1.557828 4.514069 0.184418 -1.4557 96 | -7 -2.037056 0.235232 -3.042981 -1.9605 97 | -7 2.000574 4.067716 0.542722 -1.0385 98 | -7 -2.033468 -3.878738 0.455314 -1.1506 99 | -7 -4.509751 3.963223 0.191063 -1.1403 100 | -7 -2.012259 0.239650 3.243213 -1.9263 101 | -7 3.939780 1.014209 -2.084403 -1.7433 102 | -7 -3.779285 -2.784319 -0.057526 -1.4687 103 | -7 -0.156526 -0.022742 -3.164770 -2.0423 104 | -7 4.166566 1.120264 1.685257 -1.7507 105 | -7 0.151635 0.128005 3.246658 -2.0380 106 | -8 0.028482 0.080576 0.038788 7.2066 107 | -8 -2.290104 0.315856 0.110994 5.6310 108 | -8 1.441722 -1.554108 0.024676 5.2846 109 | 110 | $$$$ 111 | -------------------------------------------------------------------------------- /test/transforms/phenylmethylamino.sdf: -------------------------------------------------------------------------------- 1 | phenylmethylamino 2 | xed2sdf_05210316543D 3 | 4 | 23 23 0 0 0 0 0 0 0 0999 V2000 5 | -0.0728 1.4064 0.1467 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 1.1617 0.7956 0.1461 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 1.2339 -0.5792 0.0825 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | 0.0848 -1.3331 0.0223 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | -1.1434 -0.7138 0.0234 C 0 0 0 0 0 0 0 0 0 0 0 0 10 | -1.2289 0.6604 0.0859 C 0 0 0 0 0 0 0 0 0 0 0 0 11 | -2.5547 1.4049 0.0888 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | -3.8297 0.5414 0.1067 C 0 0 0 0 0 0 0 0 0 0 0 0 13 | 2.3956 1.6819 0.2131 C 0 0 0 0 0 0 0 0 0 0 0 0 14 | 3.6631 0.9502 0.3287 N 0 0 0 0 0 0 0 0 0 0 0 0 15 | -0.1307 2.4037 0.1914 H 0 0 0 0 0 0 0 0 0 0 0 0 16 | 2.1261 -1.0310 0.0808 H 0 0 0 0 0 0 0 0 0 0 0 0 17 | -1.9778 -1.2630 -0.0211 H 0 0 0 0 0 0 0 0 0 0 0 0 18 | 0.1423 -2.3304 -0.0226 H 0 0 0 0 0 0 0 0 0 0 0 0 19 | -2.5767 2.1157 1.0553 H 0 0 0 0 0 0 0 0 0 0 0 0 20 | -2.5908 2.1003 -0.8886 H 0 0 0 0 0 0 0 0 0 0 0 0 21 | -4.7968 1.2519 0.1205 H 0 0 0 0 0 0 0 0 0 0 0 0 22 | -3.8279 -0.1526 1.0854 H 0 0 0 0 0 0 0 0 0 0 0 0 23 | -3.8555 -0.1509 -0.8732 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | 2.2893 2.4075 1.1631 H 0 0 0 0 0 0 0 0 0 0 0 0 25 | 2.4344 2.3563 -0.7780 H 0 0 0 0 0 0 0 0 0 0 0 0 26 | 4.4791 1.5741 0.3189 H 0 0 0 0 0 0 0 0 0 0 0 0 27 | 3.6752 0.3088 1.1308 H 0 0 0 0 0 0 0 0 0 0 0 0 28 | 1 6 2 0 29 | 2 1 1 0 30 | 2 9 1 0 31 | 3 2 2 0 32 | 4 3 1 0 33 | 5 4 2 0 34 | 6 5 1 0 35 | 6 7 1 0 36 | 7 8 1 0 37 | 9 10 1 0 38 | 1 11 1 0 39 | 3 12 1 0 40 | 4 14 1 0 41 | 5 13 1 0 42 | 7 15 1 0 43 | 7 16 1 0 44 | 8 17 1 0 45 | 8 18 1 0 46 | 8 19 1 0 47 | 9 20 1 0 48 | 9 21 1 0 49 | 10 22 1 0 50 | 10 23 1 0 51 | M END 52 | > 53 | false 54 | 55 | > 56 | 0.550 57 | 58 | > 59 | 0 60 | 61 | > 62 | 0 63 | 64 | > 65 | 135.2 66 | 67 | > <#Atoms_cresset> 68 | 10 69 | 70 | > 71 | 1.7 72 | 73 | > 74 | 26 75 | 76 | > 77 | 3 78 | 79 | > 80 | 0 81 | 82 | > 83 | toluyl.sdf 84 | 85 | > <_cresset_fieldpoints> 86 | -5 0.395762 0.247335 -2.744022 -6.7291 87 | -5 3.903036 -0.005166 -1.398705 -8.5141 88 | -5 -0.190976 0.016265 2.923435 -5.4455 89 | -6 -1.263682 4.365343 0.366333 1.8617 90 | -6 5.824788 2.411765 0.510411 6.0424 91 | -6 4.110423 -0.724088 2.264121 5.7701 92 | -6 -3.643663 -2.735030 -0.004680 1.6747 93 | -6 0.677359 4.495087 0.478243 1.7940 94 | -7 -0.067546 0.438738 -3.120080 -1.9895 95 | -7 0.898208 4.622214 -0.095316 -1.4601 96 | -7 -0.240684 0.132922 3.305414 -1.9957 97 | -7 -1.975393 0.215523 3.226414 -1.9582 98 | -7 -1.445917 4.489990 0.021034 -1.5248 99 | -7 2.467713 -3.370214 1.432371 -0.9974 100 | -7 2.644385 0.113484 3.095536 -1.7094 101 | -7 -3.848198 -2.772517 0.207848 -1.4604 102 | -7 3.698784 -0.188589 -2.145090 -1.5465 103 | -7 -2.118168 0.309373 -3.071733 -1.9164 104 | -7 2.575742 -3.662223 -0.085573 -0.9982 105 | -7 -4.482294 3.985474 0.088126 -1.1406 106 | -7 4.525843 -1.447106 -0.010091 -1.4370 107 | -8 -0.000681 0.042771 0.083428 7.1942 108 | -8 -2.312739 0.308029 0.072469 5.6391 109 | 110 | $$$$ 111 | -------------------------------------------------------------------------------- /test/transforms/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/transforms/toluyl2.sdf: -------------------------------------------------------------------------------- 1 | toluyl2 2 | xed2sdf_05210316543D 3 | 4 | 21 21 0 0 0 0 0 0 0 0999 V2000 5 | -0.0708 1.4438 0.0347 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 1.1626 0.8358 -0.0202 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 1.2531 -0.5371 -0.0369 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | 0.1099 -1.3030 0.0022 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | -1.1210 -0.6897 0.0563 C 0 0 0 0 0 0 0 0 0 0 0 0 10 | -1.2195 0.6854 0.0723 C 0 0 0 0 0 0 0 0 0 0 0 0 11 | -2.5508 1.4176 0.1307 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | -3.8184 0.5431 0.1291 C 0 0 0 0 0 0 0 0 0 0 0 0 13 | 0.1859 -2.8161 -0.0135 C 0 0 0 0 0 0 0 0 0 0 0 0 14 | -0.1330 2.4417 0.0471 H 0 0 0 0 0 0 0 0 0 0 0 0 15 | 1.9934 1.3919 -0.0470 H 0 0 0 0 0 0 0 0 0 0 0 0 16 | 2.1495 -0.9784 -0.0767 H 0 0 0 0 0 0 0 0 0 0 0 0 17 | -1.9513 -1.2463 0.0833 H 0 0 0 0 0 0 0 0 0 0 0 0 18 | -2.5634 2.0863 1.1271 H 0 0 0 0 0 0 0 0 0 0 0 0 19 | -2.6088 2.1540 -0.8151 H 0 0 0 0 0 0 0 0 0 0 0 0 20 | -4.7912 1.2449 0.1639 H 0 0 0 0 0 0 0 0 0 0 0 0 21 | -3.8083 -0.1755 1.0902 H 0 0 0 0 0 0 0 0 0 0 0 0 22 | -3.8407 -0.1244 -0.8679 H 0 0 0 0 0 0 0 0 0 0 0 0 23 | 1.3271 -3.1883 -0.0111 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | -0.3620 -3.2308 -0.9974 H 0 0 0 0 0 0 0 0 0 0 0 0 25 | -0.3706 -3.2486 0.9578 H 0 0 0 0 0 0 0 0 0 0 0 0 26 | 1 6 2 0 27 | 2 1 1 0 28 | 3 2 2 0 29 | 4 3 1 0 30 | 4 9 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 | 2 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 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 -0.208107 0.046785 -2.823760 -5.5987 80 | -5 0.020563 -0.006284 2.866388 -5.5931 81 | -6 -1.340263 4.382851 0.123869 1.9602 82 | -6 3.744526 -2.551824 -0.149559 1.8221 83 | -6 4.309177 0.301359 -0.157313 1.6625 84 | -6 1.823918 3.973166 -0.020138 1.6910 85 | -6 -3.296678 -2.986730 0.142460 2.0676 86 | -6 0.890557 -5.825451 -0.094911 1.0929 87 | -7 -1.531366 4.515393 0.223742 -1.4532 88 | -7 -1.993195 0.062172 3.213668 -1.9695 89 | -7 1.689084 3.891094 1.463686 -0.9995 90 | -7 -2.094836 0.191407 -3.045323 -1.9873 91 | -7 4.529216 0.270790 -0.123302 -0.9959 92 | -7 -0.448503 0.030427 -3.181023 -2.0022 93 | -7 1.914684 4.167435 0.025501 -1.0014 94 | -7 -4.499644 3.980006 0.253265 -1.1398 95 | -7 -0.172328 -0.023764 3.244221 -1.9944 96 | -7 -2.871802 -2.540846 2.014582 -1.7864 97 | -7 -3.024872 -2.581937 -1.720256 -1.7991 98 | -8 0.015958 0.070891 0.017648 7.2092 99 | -8 -2.303046 0.320625 0.102078 5.6455 100 | 101 | $$$$ 102 | -------------------------------------------------------------------------------- /test/transforms/toluyl3.sdf: -------------------------------------------------------------------------------- 1 | toluyl3 2 | xed2sdf_05210316543D 3 | 4 | 21 21 0 0 0 0 0 0 0 0999 V2000 5 | -0.0812 1.4210 0.0536 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 1.1420 0.7906 0.0596 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 1.2105 -0.5841 0.0738 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | 0.0512 -1.3243 0.0834 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | -1.1711 -0.6920 0.0777 C 0 0 0 0 0 0 0 0 0 0 0 0 10 | -1.2442 0.6845 0.0633 C 0 0 0 0 0 0 0 0 0 0 0 0 11 | -2.5620 1.4426 0.0607 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | -3.8485 0.5963 0.0863 C 0 0 0 0 0 0 0 0 0 0 0 0 13 | 2.5489 -1.2932 0.0833 C 0 0 0 0 0 0 0 0 0 0 0 0 14 | -0.1255 2.4202 0.0433 H 0 0 0 0 0 0 0 0 0 0 0 0 15 | 1.9826 1.3324 0.0534 H 0 0 0 0 0 0 0 0 0 0 0 0 16 | -2.0115 -1.2339 0.0850 H 0 0 0 0 0 0 0 0 0 0 0 0 17 | -2.5746 2.1592 1.0231 H 0 0 0 0 0 0 0 0 0 0 0 0 18 | -2.5900 2.1322 -0.9209 H 0 0 0 0 0 0 0 0 0 0 0 0 19 | -4.8033 1.3223 0.1212 H 0 0 0 0 0 0 0 0 0 0 0 0 20 | -3.8453 -0.1065 1.0590 H 0 0 0 0 0 0 0 0 0 0 0 0 21 | -3.8994 -0.0865 -0.8994 H 0 0 0 0 0 0 0 0 0 0 0 0 22 | 0.0965 -2.3232 0.0945 H 0 0 0 0 0 0 0 0 0 0 0 0 23 | 3.4368 -0.5308 -0.1859 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | 2.7427 -1.7574 1.1728 H 0 0 0 0 0 0 0 0 0 0 0 0 25 | 2.5319 -2.1793 -0.7259 H 0 0 0 0 0 0 0 0 0 0 0 0 26 | 1 6 2 0 27 | 2 1 1 0 28 | 3 2 2 0 29 | 3 9 1 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 | 2 11 1 0 37 | 4 18 1 0 38 | 5 12 1 0 39 | 7 13 1 0 40 | 7 14 1 0 41 | 8 15 1 0 42 | 8 16 1 0 43 | 8 17 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 | > 79 | toluyl2.sdf 80 | 81 | > <_cresset_fieldpoints> 82 | -5 -0.055397 0.018591 -2.778954 -5.5841 83 | -5 -0.051866 0.084559 2.916857 -5.5798 84 | -6 -1.296847 4.381678 0.022220 1.9578 85 | -6 4.165454 1.856216 0.039939 1.8371 86 | -6 1.922042 3.881525 0.029434 1.6905 87 | -6 1.248310 -4.296092 0.138114 1.8454 88 | -6 -3.678680 -2.693708 0.094298 1.8422 89 | -6 5.590796 -1.903549 0.328236 1.1026 90 | -7 -1.495314 4.523250 0.005527 -1.4543 91 | -7 2.005681 4.044226 0.469180 -1.0254 92 | -7 -2.056366 0.312835 3.218956 -1.9382 93 | -7 -0.165135 0.063559 -3.148152 -1.9676 94 | -7 -3.914292 -2.713564 0.024454 -1.4613 95 | -7 -2.121762 0.229845 -3.070182 -1.9271 96 | -7 -4.452307 4.051045 0.034997 -1.1404 97 | -7 -0.149893 0.126008 3.283943 -1.9775 98 | -7 1.459768 -4.237873 1.051547 -1.3881 99 | -8 -0.018727 0.049203 0.068398 7.2106 100 | -8 -2.332775 0.348253 0.076337 5.6306 101 | 102 | $$$$ 103 | --------------------------------------------------------------------------------