mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
956fdf268c
* short test file for MolVS standardize_sm * short test file for MolVS fragment * short test file for MolVS metals * short test file for MolVS normalize * short test file for MolVS reionize * short test file for MolVS tautomer * short test file for MolVS validate * long test file for MolVS standardize smiles * long test file for MolVS fragment * long test file for MolVS metals * long test file for MolVS normalize * long test file for MolVS reionize * long test file for MolVS tautomer * long test file for MolVS validate * Unit tests for MolVS steps * dropping support for Python2 * molvs/__init__.py * molvs/charge.py * molvs/errors.py * molvs/fragment.py * molvs/metal.py * molvs/normalize.py * molvs/resonance.py * molvs/standardize.py * molvs/tautomer.py * molvs/utils.py * molvs/validate.py * molvs/validations.py * molvs/cli.py * adapted and renamed molvs/cli.py to work within $RDBASE/Contrib/MolVS/ * setup MolStandardize directories, source with empty cleanup function, header, CMake files * corrections to empty source, header and test1.cpp * adding empty functions and initializers to MolStandardize * empty Metal source, header and added test * added most of Metal.cpp functionality and made some more tests * empty functions and initializers to Normalize * empty functions and initializers to Validate * added most code for RDKitDefault mode, along with some tests * restructure for abstract base class ValidateMethod * written in isNoneValidation for MolVSValidation * took out isNoneValidation, put in noAtomValidation, neutralValidation, isotopeValidation for MolVSValidation * added in AllowedAtoms * added in disallowedAtoms * corrections to Validate * added code for FragmentRemover * extended fragment functionality to include choose largest fragment, added in tests for fragment catalog, fragment remover. Also added fragmentValidation method in MolStandardize * added another test to testValidate test_fragment * corrections to fragment * corrections to Metal * added code for Normalize * added normalize member function to MolStandardize and added tests * added multi fragment functionality to Normalize.cpp and additional tests * TransformCatalog * tests for Normalize.cpp * first bit of cleanup * added most of Charge functionality and some tests * some corrections to Charge.cpp and some more tests to testCharge.cpp * corrections to Charge.cpp * start of Tautomer Enumerate with some tests * added BondType option to Tautomer Enumeration * correcting for some memory leakage * a few alterations to formatting * sorting out some memory leaks * sorting out some memory leaks * some corrections for PCS test set * redo tests with updated RDKit * fixing memory leak * more fixes after 100kPCS set testing * using tab as delimiter in CSVs rather than comma * tutorial for MolStandardize * still working on Tautomer enumeration * deleted some empty tests * starting writing tautomer canonicalize * rename test_data -> data (the source still needs to be updated) * automatic source reformatting * adjust to directory rename * move the fragment catalog test into the MolStandardize directory do not create separate library for FragmentCatalog * stop building separate libraries for the catalogs * move the CleanupParameters into the MolStandardize namespace * first pass at python wrapper * move the py module to the correct dir; add some python tests; add standardizeSmiles to python wrapper * disabling the compareMolVSTest since that requires command line arguments to run * get this building on windows * put the python lib in the right place * further work on python wrapper for rdMolStandardize * added get and set functions to Metal and wrapped them * added get and set functions to Metal and wrapped them * changed construstor of Reionizer class and input args for reionize, wrapped this default * overload Reionizer constructor so user can input own AcidBaseFile from python * added Uncharger class to Charge and added test for Uncharger * wrapped Fragment, fixed some memory leakage, changed some args and return types, added some tests * wrapped Normalized and changed how Normalizer class is initiated * changing MolVSValidation structure so user can choose which MolVS submethod they want * starting to write Wrap for Validate * now it compiles with Wrap/Validate.cpp * a couple refactorings around validate * move the validate code into the rdMolStandardize module * make sure a valid pointer is returned for standardizeSmiles * rdMolStandardize.MolVSValidation done and tests added * half way through AllowedAtomsValidation * finished AllowedAtomsValidation and DisallowedAtomsValidation * moved charge, fragment, metal, normalize into the rdMolStandardize module * changed tutorial to use wrapped code * added copyrights * added copyrights * move the data files * modify source files to adjust to the move * added validateSmiles functionality * removed std::cout * redid some of the 100k PCS tests * working on the tutorial * adding some documentation * deleting some comment lines * some changes after pull review * More changes after pull review * start of trying to make java wrap * remove some warnings, add some questions * additional warning removals, a bit more reporting * some test cleanups * enable testing of the java code
63 lines
2.0 KiB
Plaintext
63 lines
2.0 KiB
Plaintext
// Name SMARTS
|
|
hydrogen [H]
|
|
fluorine [F]
|
|
chlorine [Cl]
|
|
bromine [Br]
|
|
iodine [I]
|
|
lithium [Li]
|
|
sodium [Na]
|
|
potassium [K]
|
|
calcium [Ca]
|
|
magnesium [Mg]
|
|
aluminium [Al]
|
|
barium [Ba]
|
|
bismuth [Bi]
|
|
silver [Ag]
|
|
strontium [Sr]
|
|
zinc [Zn]
|
|
ammonia/ammonium [#7]
|
|
water/hydroxide [#8]
|
|
methyl amine [#6]-[#7]
|
|
sulfide S
|
|
nitrate [#7](=[#8])(-[#8])-[#8]
|
|
phosphate [P](=[#8])(-[#8])(-[#8])-[#8]
|
|
hexafluorophosphate [P](-[#9])(-[#9])(-[#9])(-[#9])(-[#9])-[#9]
|
|
sulfate [S](=[#8])(=[#8])(-[#8])-[#8]
|
|
methyl sulfonate [#6]-[S](=[#8])(=[#8])(-[#8])
|
|
trifluoromethanesulfonic acid [#8]-[S](=[#8])(=[#8])-[#6](-[#9])(-[#9])-[#9]
|
|
trifluoroacetic acid [#9]-[#6](-[#9])(-[#9])-[#6](=[#8])-[#8]
|
|
1,2-dichloroethane [Cl]-[#6]-[#6]-[Cl]
|
|
1,2-dimethoxyethane [#6]-[#8]-[#6]-[#6]-[#8]-[#6]
|
|
1,4-dioxane [#6]-1-[#6]-[#8]-[#6]-[#6]-[#8]-1
|
|
1-methyl-2-pyrrolidinone [#6]-[#7]-1-[#6]-[#6]-[#6]-[#6]-1=[#8]
|
|
2-butanone [#6]-[#6]-[#6](-[#6])=[#8]
|
|
acetate/acetic acid [#8]-[#6](-[#6])=[#8]
|
|
acetone [#6]-[#6](-[#6])=[#8]
|
|
acetonitrile [#6]-[#6]#[N]
|
|
benzene [#6]1[#6][#6][#6][#6][#6]1
|
|
butanol [#8]-[#6]-[#6]-[#6]-[#6]
|
|
t-butanol [#8]-[#6](-[#6])(-[#6])-[#6]
|
|
chloroform [Cl]-[#6](-[Cl])-[Cl]
|
|
cycloheptane [#6]-1-[#6]-[#6]-[#6]-[#6]-[#6]-[#6]-1
|
|
cyclohexane [#6]-1-[#6]-[#6]-[#6]-[#6]-[#6]-1
|
|
dichloromethane [Cl]-[#6]-[Cl]
|
|
diethyl ether [#6]-[#6]-[#8]-[#6]-[#6]
|
|
diisopropyl ether [#6]-[#6](-[#6])-[#8]-[#6](-[#6])-[#6]
|
|
dimethyl formamide [#6]-[#7](-[#6])-[#6]=[#8]
|
|
dimethyl sulfoxide [#6]-[S](-[#6])=[#8]
|
|
ethanol [#8]-[#6]-[#6]
|
|
ethyl acetate [#6]-[#6]-[#8]-[#6](-[#6])=[#8]
|
|
formic acid [#8]-[#6]=[#8]
|
|
heptane [#6]-[#6]-[#6]-[#6]-[#6]-[#6]-[#6]
|
|
hexane [#6]-[#6]-[#6]-[#6]-[#6]-[#6]
|
|
isopropanol [#8]-[#6](-[#6])-[#6]
|
|
methanol [#8]-[#6]
|
|
N,N-dimethylacetamide [#6]-[#7](-[#6])-[#6](-[#6])=[#8]
|
|
pentane [#6]-[#6]-[#6]-[#6]-[#6]
|
|
propanol [#8]-[#6]-[#6]-[#6]
|
|
pyridine [#6]-1=[#6]-[#6]=[#7]-[#6]=[#6]-1
|
|
t-butyl methyl ether [#6]-[#8]-[#6](-[#6])(-[#6])-[#6]
|
|
tetrahydrofurane [#6]-1-[#6]-[#6]-[#8]-[#6]-1
|
|
toluene [#6]-[#6]~1~[#6]~[#6]~[#6]~[#6]~[#6]~1
|
|
xylene [#6]-[#6]~1~[#6](-[#6])~[#6]~[#6]~[#6]~[#6]~1
|