RMG-Py v2.1.7 release

ReactionMechanismGenerator · May 2, 2018 · ee33147 · ee33147
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diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,4 +1,4 @@
-Copyright (c) 2002-2017 Prof. William H. Green (whgreen@mit.edu), 
+Copyright (c) 2002-2018 Prof. William H. Green (whgreen@mit.edu),
 Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)
 
 Permission is hereby granted, free of charge, to any person obtaining a

diff --git a/cantherm.py b/cantherm.py
@@ -1,32 +1,32 @@
 #!/usr/bin/env python
-# encoding: utf-8
+# -*- coding: utf-8 -*-
 
-################################################################################
-#
-#   RMG - Reaction Mechanism Generator
-#
-#   Copyright (c) 2002-2015 Prof. William H. Green (whgreen@mit.edu), 
-#   Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)
-#
-#   Permission is hereby granted, free of charge, to any person obtaining a
-#   copy of this software and associated documentation files (the "Software"),
-#   to deal in the Software without restriction, including without limitation
-#   the rights to use, copy, modify, merge, publish, distribute, sublicense,
-#   and/or sell copies of the Software, and to permit persons to whom the
-#   Software is furnished to do so, subject to the following conditions:
-#
-#   The above copyright notice and this permission notice shall be included in
-#   all copies or substantial portions of the Software.
-#
-#   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-#   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-#   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
-#   THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-#   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-#   FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-#   DEALINGS IN THE SOFTWARE.
-#
-################################################################################
+###############################################################################
+#                                                                             #
+# RMG - Reaction Mechanism Generator                                          #
+#                                                                             #
+# Copyright (c) 2002-2018 Prof. William H. Green (whgreen@mit.edu),           #
+# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)   #
+#                                                                             #
+# Permission is hereby granted, free of charge, to any person obtaining a     #
+# copy of this software and associated documentation files (the 'Software'),  #
+# to deal in the Software without restriction, including without limitation   #
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,    #
+# and/or sell copies of the Software, and to permit persons to whom the       #
+# Software is furnished to do so, subject to the following conditions:        #
+#                                                                             #
+# The above copyright notice and this permission notice shall be included in  #
+# all copies or substantial portions of the Software.                         #
+#                                                                             #
+# THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR  #
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,    #
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE #
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER      #
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING     #
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER         #
+# DEALINGS IN THE SOFTWARE.                                                   #
+#                                                                             #
+###############################################################################
 
 """
 This is the main executable script for CanTherm, a tool for computing chemical

diff --git a/documentation/source/reference/molecule/atomtype.rst b/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:
 
-=============== ============================================================
+=============== ==============================================================================================================================================================
 Atom type       Description
-=============== ============================================================
+=============== ==============================================================================================================================================================
 *General atom types*
-----------------------------------------------------------------------------
+--------------- --------------------------------------------------------------------------------------------------------------------------------------------------------------
 ``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*
-----------------------------------------------------------------------------
+--------------- --------------------------------------------------------------------------------------------------------------------------------------------------------------
 ``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*
-----------------------------------------------------------------------------
-``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*
-----------------------------------------------------------------------------
+--------------- --------------------------------------------------------------------------------------------------------------------------------------------------------------
 ``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*
-----------------------------------------------------------------------------
+--------------- --------------------------------------------------------------------------------------------------------------------------------------------------------------
 ``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*
-----------------------------------------------------------------------------
+--------------- --------------------------------------------------------------------------------------------------------------------------------------------------------------
 ``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
-=============== ============================================================
+``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
+=============== ==============================================================================================================================================================