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f5a54af475
* Swap to using a data structure for default normalization parameters * bring the default fragment data into the code too * cleanup * add reionizer parameters via data change fragment parse failures to ValueErrorExceptions * tautomer parameters in the code * got a little over-enthusiastic in that last cleanup * use boost::flyweight to cache normalization and charge data params * a bit more cleanup * support reading params from JSON * fragments from JSON single-call for fragment removal * add a one-liner for the canonical tautomer * quick refactor * Fixes #4115 * complete the parents * docs * move the definitions to a namespace and make them const * see if switching to c++14 fixes the CI compile problems with g++ 5.5 * somewhat uglier way of solving the initalizer list problem
63 lines
2.0 KiB
Plaintext
63 lines
2.0 KiB
Plaintext
// Name SMARTS
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hydrogen [H]
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fluorine [F]
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chlorine [Cl]
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bromine [Br]
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iodine [I]
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lithium [Li]
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sodium [Na]
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potassium [K]
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calcium [Ca]
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magnesium [Mg]
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aluminium [Al]
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barium [Ba]
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bismuth [Bi]
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silver [Ag]
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strontium [Sr]
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zinc [Zn]
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ammonia/ammonium [#7]
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water/hydroxide [#8]
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methyl amine [#6]-[#7]
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sulfide S
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nitrate [#7](=[#8])(-[#8])-[#8]
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phosphate [P](=[#8])(-[#8])(-[#8])-[#8]
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hexafluorophosphate [P](-[#9])(-[#9])(-[#9])(-[#9])(-[#9])-[#9]
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sulfate [S](=[#8])(=[#8])(-[#8])-[#8]
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methyl sulfonate [#6]-[S](=[#8])(=[#8])(-[#8])
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trifluoromethanesulfonic acid [#8]-[S](=[#8])(=[#8])-[#6](-[#9])(-[#9])-[#9]
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trifluoroacetic acid [#9]-[#6](-[#9])(-[#9])-[#6](=[#8])-[#8]
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1,2-dichloroethane [Cl]-[#6]-[#6]-[Cl]
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1,2-dimethoxyethane [#6]-[#8]-[#6]-[#6]-[#8]-[#6]
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1,4-dioxane [#6]-1-[#6]-[#8]-[#6]-[#6]-[#8]-1
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1-methyl-2-pyrrolidinone [#6]-[#7]-1-[#6]-[#6]-[#6]-[#6]-1=[#8]
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2-butanone [#6]-[#6]-[#6](-[#6])=[#8]
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acetate/acetic acid [#8]-[#6](-[#6])=[#8]
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acetone [#6]-[#6](-[#6])=[#8]
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acetonitrile [#6]-[#6]#[N]
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benzene [#6]1[#6][#6][#6][#6][#6]1
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butanol [#8]-[#6]-[#6]-[#6]-[#6]
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t-butanol [#8]-[#6](-[#6])(-[#6])-[#6]
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chloroform [Cl]-[#6](-[Cl])-[Cl]
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cycloheptane [#6]-1-[#6]-[#6]-[#6]-[#6]-[#6]-[#6]-1
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cyclohexane [#6]-1-[#6]-[#6]-[#6]-[#6]-[#6]-1
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dichloromethane [Cl]-[#6]-[Cl]
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diethyl ether [#6]-[#6]-[#8]-[#6]-[#6]
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diisopropyl ether [#6]-[#6](-[#6])-[#8]-[#6](-[#6])-[#6]
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dimethyl formamide [#6]-[#7](-[#6])-[#6]=[#8]
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dimethyl sulfoxide [#6]-[S](-[#6])=[#8]
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ethanol [#8]-[#6]-[#6]
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ethyl acetate [#6]-[#6]-[#8]-[#6](-[#6])=[#8]
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formic acid [#8]-[#6]=[#8]
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heptane [#6]-[#6]-[#6]-[#6]-[#6]-[#6]-[#6]
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hexane [#6]-[#6]-[#6]-[#6]-[#6]-[#6]
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isopropanol [#8]-[#6](-[#6])-[#6]
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methanol [#8]-[#6]
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N,N-dimethylacetamide [#6]-[#7](-[#6])-[#6](-[#6])=[#8]
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pentane [#6]-[#6]-[#6]-[#6]-[#6]
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propanol [#8]-[#6]-[#6]-[#6]
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pyridine [#6]-1=[#6]-[#6]=[#7]-[#6]=[#6]-1
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t-butyl methyl ether [#6]-[#8]-[#6](-[#6])(-[#6])-[#6]
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tetrahydrofurane [#6]-1-[#6]-[#6]-[#8]-[#6]-1
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toluene [#6]-[#6]~1~[#6]~[#6]~[#6]~[#6]~[#6]~1
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xylene [#6]-[#6]~1~[#6](-[#6])~[#6]~[#6]~[#6]~[#6]~1
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