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RMG-Py v2.1.7 release
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‎LICENSE.txt‎

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Copyright (c) 2002-2017 Prof. William H. Green ([email protected]),
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Copyright (c) 2002-2018 Prof. William H. Green ([email protected]),
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Prof. Richard H. West ([email protected]) and the RMG Team ([email protected])
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Permission is hereby granted, free of charge, to any person obtaining a

‎cantherm.py‎

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#!/usr/bin/env python
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# encoding: utf-8
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# -*- coding: utf-8 -*-
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################################################################################
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#
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# RMG - Reaction Mechanism Generator
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#
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# Copyright (c) 2002-2015 Prof. William H. Green ([email protected]),
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# Prof. Richard H. West ([email protected]) and the RMG Team ([email protected])
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#
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# Permission is hereby granted, free of charge, to any person obtaining a
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# copy of this software and associated documentation files (the "Software"),
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# to deal in the Software without restriction, including without limitation
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# the rights to use, copy, modify, merge, publish, distribute, sublicense,
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# and/or sell copies of the Software, and to permit persons to whom the
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# Software is furnished to do so, subject to the following conditions:
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#
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# The above copyright notice and this permission notice shall be included in
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# all copies or substantial portions of the Software.
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#
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# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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# DEALINGS IN THE SOFTWARE.
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#
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################################################################################
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###############################################################################
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# #
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# RMG - Reaction Mechanism Generator #
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# #
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# Copyright (c) 2002-2018 Prof. William H. Green ([email protected]), #
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# Prof. Richard H. West ([email protected]) and the RMG Team ([email protected]) #
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# #
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# Permission is hereby granted, free of charge, to any person obtaining a #
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# copy of this software and associated documentation files (the 'Software'), #
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# to deal in the Software without restriction, including without limitation #
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# the rights to use, copy, modify, merge, publish, distribute, sublicense, #
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# and/or sell copies of the Software, and to permit persons to whom the #
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# Software is furnished to do so, subject to the following conditions: #
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# #
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# The above copyright notice and this permission notice shall be included in #
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# all copies or substantial portions of the Software. #
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# #
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# THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR #
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# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, #
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# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE #
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# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER #
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# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING #
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# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER #
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# DEALINGS IN THE SOFTWARE. #
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# #
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###############################################################################
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"""
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This is the main executable script for CanTherm, a tool for computing chemical

‎documentation/source/reference/molecule/atomtype.rst‎

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

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