Charged atom types

documentation/source/reference/molecule/atomtype.rst

@@ -16,46 +16,103 @@ molecular substructure patterns via an RMG-style adjacency list.
 
 We define the following basic atom types:
 
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 Atom type       Description
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 *General atom types*
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+--------------- --------------------------------------------------------------------------------------------------------------------------------------------------------------
 ``R``           any atom with any local bond structure
 ``R!H``         any non-hydrogen atom with any local bond structure
+*Hydrogen atom types*
+--------------- --------------------------------------------------------------------------------------------------------------------------------------------------------------
+``H``           hydrogen atom with up to one single bond
 *Carbon atom types*
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+--------------- --------------------------------------------------------------------------------------------------------------------------------------------------------------
 ``C``           carbon atom with any local bond structure
-``Cs``          carbon atom with four single bonds
-``Cd``          carbon atom with one double bond (to carbon) and two single bonds
+``Ca``          carbon atom with two lone pairs and no bonds
+``Cs``          carbon atom with up to four single bonds
+``Csc``         charged carbon atom with up to three single bonds
+``Cd``          carbon atom with one double bond (not to O or S) and up to two single bonds
+``Cdc``         charged carbon atom with one double bond and up to one single bond
+``CO``          carbon atom with one double bond to oxygen and up to two single bonds
+``CS``          carbon atom with one double bond to sulfur and up to two single bonds
 ``Cdd``         carbon atom with two double bonds
-``Ct``          carbon atom with one triple bond and one single bond
-``CO``          carbon atom with one double bond (to oxygen) and two single bonds
-``Cb``          carbon atom with two benzene bonds and one single bond
+``Ct``          carbon atom with one triple bond and up to one single bond
+``Cb``          carbon atom with up to two benzene bonds and up to one single bond
 ``Cbf``         carbon atom with three benzene bonds
-*Hydrogen atom types*
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-``H``           hydrogen atom with one single bond
+``C2s``         carbon atom with one lone pair (valance 2) and up to two single bonds
+``C2sc``        charged carbon atom with one lone pair (valance 2) and up to three single bonds
+``C2d``         carbon atom with one lone pair (valance 2) and one double bond
+``C2dc``        charged carbon atom with one lone pair (valance 2), one double bond and up to one single bond
+``C2tc``        charged carbon atom with one lone pair (valance 2), one triple bond
+*Nitrogen atom types*
+--------------- --------------------------------------------------------------------------------------------------------------------------------------------------------------
+``N``           nitrogen atom with any local bond structure
+``N0sc``        charged nitrogen atom with three lone pairs (valance 0) with up to one single bond
+``N1s``         nitrogen atom with two lone pairs (valance 1) and up to one single bond
+``N1sc``        charged nitrogen atom with two lone pairs (valance 1) up to two single bonds
+``N1dc``        charged nitrogen atom with two lone pairs (valance 1), one double bond
+``N3s``         nitrogen atom with one lone pair (valance 3) with up to three single bonds
+``N3d``         nitrogen atom with one lone pair (valance 3), one double bond and up to one single bond
+``N3t``         nitrogen atom with one lone pair (valance 3) and one triple bond
+``N3b``         nitrogen atom with one lone pair (valance 3) and two benzene bonds
+``N5sc``        charged nitrogen atom with no lone pairs (valance 5) with up to four single bonds
+``N5dc``        charged nitrogen atom with no lone pairs (valance 5), one double bond and up to two single bonds
+``N5ddc``       charged nitrogen atom with with no lone pairs (valance 5) and two double bonds
+``N5dddc``      charged nitrogen atom with with no lone pairs (valance 5) and three double bonds
+``N5t``         nitrogen atom with with no lone pairs (valance 5), one triple bond and up to two single bonds
+``N5tc``        charged nitrogen atom with with no lone pairs (valance 5), one triple bond and up to one single bond
+``N5b``         nitrogen atom with with no lone pairs (valance 5) and two benzene bonds (one of the lone pairs also participates in the aromatic bond) and up to one single bond
+``N5bd``        nitrogen atom with with no lone pairs (valance 5), two benzene bonds, and one double bond
 *Oxygen atom types*
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+--------------- --------------------------------------------------------------------------------------------------------------------------------------------------------------
 ``O``           oxygen atom with any local bond structure
-``Os``          oxygen atom with two single bonds
-``Od``          oxygen atom with one double bond
-``Oa``          oxygen atom with no bonds
+``Oa``          oxygen atom with three lone pairs and no bonds
+``O0sc``        charged oxygen with three lone pairs (valance 0) and up to one single bond
+``O0dc``        charged oxygen atom with three lone pairs (valance 0) and one double bond
+``O2s``         oxygen atom with two lone pairs (valance 2) and up to two single bonds
+``O2sc``        charged oxygen atom with two lone pairs (valance 2) and up to one single bond
+``O2d``         oxygen atom with two lone pairs (valance 2) and one doubel bond
+``O4sc``        charged oxygen atom with one one pair (valance 4) and up to three single bonds
+``O4dc``        charged oxygen atom with one one pair (valance 4), one double bond and up to one single bond
+``O4tc``        charged oxygen atom with one one pair (valance 4) and one triple bond
+``O4b``         oxygen atom with one one pair (valance 4) and and two benzene bonds
 *Silicon atom types*
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+--------------- --------------------------------------------------------------------------------------------------------------------------------------------------------------
 ``Si``          silicon atom with any local bond structure
 ``Sis``         silicon atom with four single bonds
 ``Sid``         silicon atom with one double bond (to carbon) and two single bonds
+``SiO``         silicon atom with one double bond (to oxygen) and two single bonds
 ``Sidd``        silicon atom with two double bonds
 ``Sit``         silicon atom with one triple bond and one single bond
-``SiO``         silicon atom with one double bond (to oxygen) and two single bonds
 ``Sib``         silicon atom with two benzene bonds and one single bond
 ``Sibf``        silicon atom with three benzene bonds
 *Sulfur atom types*
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+--------------- --------------------------------------------------------------------------------------------------------------------------------------------------------------
 ``S``           sulfur atom with any local bond structure
-``Ss``          sulfur atom with two single bonds
-``Sd``          sulfur atom with one double bond
-``Sa``          sulfur atom with no bonds
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+``Sa``          sulfur atom with three lone pairs and no bonds
+``S0sc``        charged sulfur atom with three lone pairs (valance 0) and up to one single bonds
+``S2s``         sulfur atom with two lone pairs (valance 2) and up to two single bonds
+``S2sc``        charged sulfur atom with two lone pairs (valance 2) and up to three single bonds
+``S2d``         sulfur atom with two lone pairs (valance 2) and one double bond
+``S2dc``        charged sulfur atom with two lone pairs (valance 2), one double bond and up to one single bond
+``S2tc``        charged sulfur atom with two lone pairs (valance 2) and one triple bond
+``S4s``         sulfur atom with one lone pair (valance 4) and up to four single bonds
+``S4sc``        charged sulfur atom with one lone pair (valance 4) and up to five single bonds
+``S4d``         sulfur atom with one lone pair (valance 4), one double bond and up to two single bonds
+``S4dd``        sulfur atom with one lone pair (valance 4) and two double bonds
+``S4dc``        charged sulfur atom with one lone pair (valance 4), one to three double bonds and up to three single bonds
+``S4b``         sulfur atom with one lone pair (valance 4) and two benzene bonds (one of the lone pairs also participates in the aromatic bond)
+``S4t``         sulfur atom with one lone pair (valance 4), one triple bond and up to one single bond
+``S4tdc``       charged sulfur atom with one lone pair (valance 4) one to two triple bonds, up to two double bonds, and up to three single bonds
+``S6s``         sulfur atom with no lone pairs (valance 6) and up to six single bonds
+``S6sc``        charged sulfur atom with no lone pairs (valance 6) and up to seven single bonds
+``S6d``         sulfur atom with no lone pairs (valance 6), one double bond and up to four single bonds
+``S6dd``        sulfur atom with no lone pairs (valance 6), two double bonds and up to two single bonds
+``S6ddd``       sulfur atom with no lone pairs (valance 6) and three double bonds
+``S6dc``        charged sulfur atom with no lone pairs (valance 6), one to three double bonds and up to five single bonds
+``S6t``         sulfur atom with no lone pairs (valance 6), one triple bond and up to three single bonds
+``S6td``        sulfur atom with no lone pairs (valance 6), one triple bond, one double bond and up to one single bond
+``S6tt``        sulfur atom with no lone pairs (valance 6) and two triple bonds
+``S6tdc``       charged sulfur atom with no lone pairs (valance 6), one to two triple bonds, up to two double bonds, and up to four single bonds
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