From f55608e325168e726cb1a4e315b2e94d21c86930 Mon Sep 17 00:00:00 2001 From: Nathan Yee Date: Fri, 3 Jun 2016 16:03:23 -0400 Subject: [PATCH 01/21] Add unitTest for checking sibling relationship A unit test has been added to databaseTest to see if any siblings in a tree shuold actually be parents. For now, I have only implemented it for thermo groups. It should be implemented to kinetics, solvation, statmech and transport as well, but I don't think we have any commits of RMG-database that will pass those tests. --- testing/databaseTest.py | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/testing/databaseTest.py b/testing/databaseTest.py index ddbf58c9aa..5166794ed9 100644 --- a/testing/databaseTest.py +++ b/testing/databaseTest.py @@ -102,6 +102,13 @@ def test_thermo(self): test.description = test_name self.compat_func_name = test_name yield test, group_name + + test = lambda x: self.general_checkSiblingsForParents(group_name, group) + test_name = "Thermo groups {0}: sibling relationships are correct?".format(group_name) + test.description = test_name + self.compat_func_name = test_name + yield test, group_name + def test_solvation(self): for group_name, group in self.database.solvation.groups.iteritems(): @@ -349,5 +356,18 @@ def general_checkChildParentRelationships(self, group_name, group): if isinstance(ancestorNode, Group): nose.tools.assert_true(group.matchNodeToChild(ancestorNode, childNode), "In {group} group, node {ancestor} is not a proper ancestor of its child {child}.".format(group=group_name, ancestor=ancestorNode, child=nodeName)) + + def general_checkSiblingsForParents(self, group_name, group): + """ + This test checks that siblings in a tree are not actually parent/child + """ + for nodeName, node in group.entries.iteritems(): + for index, child1 in enumerate(node.children): + for child2 in node.children[index+1:]: + #Don't check a node against itself + if child1 is child2: continue + nose.tools.assert_false(group.matchNodeToChild(child1, child2), + "In {0} group, node {1} is written as a sibling of {2}, when it is actually a parent.".format(group_name, child1, child2)) + if __name__ == '__main__': nose.run(argv=[__file__, '-v', '--nologcapture'], defaultTest=__name__) From b378e10cfca8627f316045a1b13cdf780843e32b Mon Sep 17 00:00:00 2001 From: Nathan Yee Date: Wed, 1 Jun 2016 17:53:23 -0400 Subject: [PATCH 02/21] Removed all groups with a CS atomType Because CS atomType is not currently recognized correctly, I have removed all thermo groups containing CS, and written them out in a separate directory. --- input/CSThermoGroups/groups/group.py | 1463 ++++++++++++++++++++++ input/thermo/groups/group.py | 1711 ++------------------------ 2 files changed, 1555 insertions(+), 1619 deletions(-) create mode 100644 input/CSThermoGroups/groups/group.py diff --git a/input/CSThermoGroups/groups/group.py b/input/CSThermoGroups/groups/group.py new file mode 100644 index 0000000000..d4db1e2a8e --- /dev/null +++ b/input/CSThermoGroups/groups/group.py @@ -0,0 +1,1463 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Functional Group Additivity Values" +shortDesc = u"" +longDesc = u""" + +""" +entry( + index = -1, + label = "C=S-C=SSs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Ss u0 {1,S} +5 Sd u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Sd)Cs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Cs u0 {1,S} +5 Cdd u0 {3,D} {6,D} +6 Sd u0 {5,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cd)H", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 H u0 {1,S} +5 [Cd,Cdd,CO] u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CbC=S", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cb u0 {1,S} +4 Cd u0 {1,S} {5,D} +5 Sd u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-Ct(Cds-Cdd-Cd)", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Ct u0 {1,S} +4 Cd u0 {1,S} {5,D} +5 Cdd u0 {4,D} {6,D} +6 C u0 {5,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd)(Cds-Cds)", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Cd u0 {1,S} {6,D} +5 Cdd u0 {3,D} +6 Cd u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-Cb(Cds-Cdd-Sd)", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cb u0 {1,S} +4 Cd u0 {1,S} {5,D} +5 Cdd u0 {4,D} {6,D} +6 Sd u0 {5,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cds)Cs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Cs u0 {1,S} +5 Cd u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Cd)H", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 H u0 {1,S} +5 Cdd u0 {3,D} {6,D} +6 C u0 {5,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CbSs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cb u0 {1,S} +4 Ss u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CbCds", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cb u0 {1,S} +4 Cd u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cd)C=S", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} +4 Cd u0 {1,S} {5,D} +5 Sd u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-Ct(Cds-Cds)", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Ct u0 {1,S} +4 Cd u0 {1,S} {5,D} +5 Cd u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CdsSs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} +4 Ss u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cd)(Cds-Cd)", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Cd u0 {1,S} {6,D} +5 [Cd,Cdd,CO] u0 {3,D} +6 [Cd,Cdd,CO] u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cds)C=S", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Cd u0 {1,S} {6,D} +5 Cd u0 {3,D} +6 Sd u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd)H", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 H u0 {1,S} +5 Cdd u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cds)(Cds-Cds)", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Cd u0 {1,S} {6,D} +5 Cd u0 {3,D} +6 Cd u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CtCt", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Ct u0 {1,S} +4 Ct u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-Cb(Cds-Cdd-Cd)", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cb u0 {1,S} +4 Cd u0 {1,S} {5,D} +5 Cdd u0 {4,D} {6,D} +6 C u0 {5,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Cd)(Cds-Cds)", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Cd u0 {1,S} {6,D} +5 Cdd u0 {3,D} {7,D} +6 Cd u0 {4,D} +7 C u0 {5,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Cd)C=S", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Cd u0 {1,S} {7,D} +5 Cdd u0 {3,D} {6,D} +6 C u0 {5,D} +7 Sd u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-SsSs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Ss u0 {1,S} +4 Ss u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CbCb", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cb u0 {1,S} +4 Cb u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-Ct(Cds-Cd)", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Ct u0 {1,S} +4 Cd u0 {1,S} {5,D} +5 [Cd,Cdd,CO] u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd)Cs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Cs u0 {1,S} +5 Cdd u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-Ct(Cds-Cdd)", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Ct u0 {1,S} +4 Cd u0 {1,S} {5,D} +5 Cdd u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Cd)(Cds-Cdd-Cd)", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Cd u0 {1,S} {6,D} +5 Cdd u0 {3,D} {7,D} +6 Cdd u0 {4,D} {8,D} +7 C u0 {5,D} +8 C u0 {6,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-Cb(Cds-Cd)", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cb u0 {1,S} +4 Cd u0 {1,S} {5,D} +5 [Cd,Cdd,CO] u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cd)Ss", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Ss u0 {1,S} +5 [Cd,Cdd,CO] u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-Cb(Cds-Cds)", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cb u0 {1,S} +4 Cd u0 {1,S} {5,D} +5 Cd u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CH", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 C u0 {1,S} +4 H u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd)(Cds-Cdd)", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Cd u0 {1,S} {6,D} +5 Cdd u0 {3,D} +6 Cdd u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-Cb(Cds-Cdd)", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cb u0 {1,S} +4 Cd u0 {1,S} {5,D} +5 Cdd u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CC", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 C u0 {1,S} +4 C u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CtC=S", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Ct u0 {1,S} +4 Cd u0 {1,S} {5,D} +5 Sd u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Cd)Cs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Cs u0 {1,S} +5 Cdd u0 {3,D} {6,D} +6 C u0 {5,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CdsCds", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} +4 Cd u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Sd)(Cds-Cdd-Sd)", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Cd u0 {1,S} {6,D} +5 Cdd u0 {3,D} {7,D} +6 Cdd u0 {4,D} {8,D} +7 Sd u0 {5,D} +8 Sd u0 {6,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CtSs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Ct u0 {1,S} +4 Ss u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cds)Ss", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Ss u0 {1,S} +5 Cd u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Sd)H", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 H u0 {1,S} +5 Cdd u0 {3,D} {6,D} +6 Sd u0 {5,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd)C=S", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Cd u0 {1,S} {6,D} +5 Cdd u0 {3,D} +6 Sd u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Cd)(Cds-Cdd-Sd)", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Cd u0 {1,S} {6,D} +5 Cdd u0 {3,D} {7,D} +6 Cdd u0 {4,D} {8,D} +7 C u0 {5,D} +8 Sd u0 {6,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Cd)Ss", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Ss u0 {1,S} +5 Cdd u0 {3,D} {6,D} +6 C u0 {5,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cds)H", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 H u0 {1,S} +5 Cd u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd)Ss", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Ss u0 {1,S} +5 Cdd u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-Ct(Cds-Cdd-Sd)", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Ct u0 {1,S} +4 Cd u0 {1,S} {5,D} +5 Cdd u0 {4,D} {6,D} +6 Sd u0 {5,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Sd)Ss", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Ss u0 {1,S} +5 Cdd u0 {3,D} {6,D} +6 Sd u0 {5,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CtCds", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Ct u0 {1,S} +4 Cd u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cd)Cs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Cs u0 {1,S} +5 [Cd,Cdd,CO] u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Sd)(Cds-Cds)", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Cd u0 {1,S} {6,D} +5 Cdd u0 {3,D} {7,D} +6 Cd u0 {4,D} +7 Sd u0 {5,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Sd)C=S", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Cd u0 {1,S} {7,D} +5 Cdd u0 {3,D} {6,D} +6 Sd u0 {5,D} +7 Sd u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CbCt", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cb u0 {1,S} +4 Ct u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-C=SC=S", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Cd u0 {1,S} {6,D} +5 Sd u0 {3,D} +6 Sd u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = 1183, + label = "C=S-HH", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 H u0 {1,S} +4 H u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([9.08,10.34,11.51,12.5,14.07,15.25,17.14],'cal/(mol*K)'), + H298 = (27.71,'kcal/mol'), + S298 = (56.51,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1184, + label = "C=S-CsH", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cs u0 {1,S} +4 H u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([8.11,9.03,9.88,10.61,11.74,12.55,13.82],'cal/(mol*K)'), + H298 = (27.32,'kcal/mol'), + S298 = (37.56,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1185, + label = "C=S-CdsH", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} +4 H u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([7.59,9.38,10.81,11.85,13.18,13.95,14.81],'cal/(mol*K)'), + H298 = (24.05,'kcal/mol'), + S298 = (34.35,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1186, + label = "C=S-CtH", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Ct u0 {1,S} +4 H u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([7.46,8.91,10.01,10.83,11.98,12.74,13.87],'cal/(mol*K)'), + H298 = (30.83,'kcal/mol'), + S298 = (37.16,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1187, + label = "C=S-CbH", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cb u0 {1,S} +4 H u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([8.45,9.84,10.94,11.78,12.97,13.76,14.77],'cal/(mol*K)'), + H298 = (24.71,'kcal/mol'), + S298 = (34.15,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1188, + label = "C=S-C=SH", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 H u0 {1,S} +5 Sd u0 {3,D} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([7.79,9.18,10.41,11.42,12.82,13.63,14.54],'cal/(mol*K)'), + H298 = (26.96,'kcal/mol'), + S298 = (35.65,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1189, + label = "C=S-SsH", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Ss u0 {1,S} +4 H u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([8.38,9.78,10.83,11.66,12.86,13.71,14.87],'cal/(mol*K)'), + H298 = (21.55,'kcal/mol'), + S298 = (34.41,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1190, + label = "C=S-CsCs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cs u0 {1,S} +4 Cs u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([6.7,7.44,8.14,8.72,9.52,9.98,10.51],'cal/(mol*K)'), + H298 = (27.2,'kcal/mol'), + S298 = (18,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1191, + label = "C=S-CdsCs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} +4 Cs u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([7.79,9.21,10.13,10.71,11.25,11.42,11.35],'cal/(mol*K)'), + H298 = (26.19,'kcal/mol'), + S298 = (13.44,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1192, + label = "C=S-CtCs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Ct u0 {1,S} +4 Cs u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([6.87,7.88,8.6,9.13,9.8,10.17,10.59],'cal/(mol*K)'), + H298 = (30.12,'kcal/mol'), + S298 = (17.46,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1193, + label = "C=S-CbCs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cb u0 {1,S} +4 Cs u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([8.02,9.02,9.75,10.23,10.75,10.96,11.04],'cal/(mol*K)'), + H298 = (26.6,'kcal/mol'), + S298 = (14.55,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1194, + label = "C=S-C=SCs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Cs u0 {1,S} +5 Sd u0 {3,D} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([6.93,7.93,8.76,9.37,10.11,10.45,10.71],'cal/(mol*K)'), + H298 = (27.48,'kcal/mol'), + S298 = (16.58,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1205, + label = "C=S-CSs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 C u0 {1,S} +4 Ss u0 {1,S} +""", + thermo = u'C=S-CsSs', + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = 1206, + label = "C=S-CsSs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cs u0 {1,S} +4 Ss u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([7.4,8.38,9.16,9.8,10.72,11.25,11.66],'cal/(mol*K)'), + H298 = (21.35,'kcal/mol'), + S298 = (14.52,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1457, + label = "CS-OsH", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Os u0 {1,S} +4 H u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([4.48,5.3,6.09,6.82,8.05,8.99,10.37],'cal/(mol*K)'), + H298 = (2.85,'kcal/mol'), + S298 = (30.14,'cal/(mol*K)'), + ), + shortDesc = u"""CAC 1d-HR calc""", + longDesc = +u""" + +""", +) + +entry( + index = 1458, + label = "CS-CsOs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Os u0 {1,S} +4 Cs u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([3.9,4.17,4.6,5.1,6.08,6.76,7.44],'cal/(mol*K)'), + H298 = (-1.32,'kcal/mol'), + S298 = (8.62,'cal/(mol*K)'), + ), + shortDesc = u"""CAC 1d-HR calc""", + longDesc = +u""" + +""", +) + +entry( + index = 1459, + label = "CS-OsOs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Os u0 {1,S} +4 Os u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([3.08,3.59,3.9,4.03,3.99,3.75,3.23],'cal/(mol*K)'), + H298 = (-22.72,'kcal/mol'), + S298 = (2.67,'cal/(mol*K)'), + ), + shortDesc = u"""CAC CBS-QB3 1Dhr calc""", + longDesc = +u""" + +""", +) + diff --git a/input/thermo/groups/group.py b/input/thermo/groups/group.py index cb57116913..6c2d64eb15 100644 --- a/input/thermo/groups/group.py +++ b/input/thermo/groups/group.py @@ -1753,116 +1753,6 @@ """, ) -entry( - index = 1183, - label = "C=S-HH", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 H u0 {1,S} -4 H u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([9.08,10.34,11.51,12.5,14.07,15.25,17.14],'cal/(mol*K)'), - H298 = (27.71,'kcal/mol'), - S298 = (56.51,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = 1189, - label = "C=S-SsH", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ss u0 {1,S} -4 H u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([8.38,9.78,10.83,11.66,12.86,13.71,14.87],'cal/(mol*K)'), - H298 = (21.55,'kcal/mol'), - S298 = (34.41,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = 1457, - label = "CS-OsH", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Os u0 {1,S} -4 H u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([4.48,5.3,6.09,6.82,8.05,8.99,10.37],'cal/(mol*K)'), - H298 = (2.85,'kcal/mol'), - S298 = (30.14,'cal/(mol*K)'), - ), - shortDesc = u"""CAC 1d-HR calc""", - longDesc = -u""" - -""", -) - -entry( - index = 1459, - label = "CS-OsOs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Os u0 {1,S} -4 Os u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([3.08,3.59,3.9,4.03,3.99,3.75,3.23],'cal/(mol*K)'), - H298 = (-22.72,'kcal/mol'), - S298 = (2.67,'cal/(mol*K)'), - ), - shortDesc = u"""CAC CBS-QB3 1Dhr calc""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-SsSs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ss u0 {1,S} -4 Ss u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - entry( index = 54, label = "Cds-OdCH", @@ -2082,237 +1972,6 @@ """, ) -entry( - index = -1, - label = "C=S-CH", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 C u0 {1,S} -4 H u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = 1184, - label = "C=S-CsH", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cs u0 {1,S} -4 H u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([8.11,9.03,9.88,10.61,11.74,12.55,13.82],'cal/(mol*K)'), - H298 = (27.32,'kcal/mol'), - S298 = (37.56,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = 1185, - label = "C=S-CdsH", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} -4 H u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([7.59,9.38,10.81,11.85,13.18,13.95,14.81],'cal/(mol*K)'), - H298 = (24.05,'kcal/mol'), - S298 = (34.35,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cd)H", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 H u0 {1,S} -5 [Cd,Cdd,CO] u0 {3,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cds)H", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 H u0 {1,S} -5 Cd u0 {3,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd)H", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 H u0 {1,S} -5 Cdd u0 {3,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Sd)H", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 H u0 {1,S} -5 Cdd u0 {3,D} {6,D} -6 Sd u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Cd)H", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 H u0 {1,S} -5 Cdd u0 {3,D} {6,D} -6 C u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = 1188, - label = "C=S-C=SH", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 H u0 {1,S} -5 Sd u0 {3,D} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([7.79,9.18,10.41,11.42,12.82,13.63,14.54],'cal/(mol*K)'), - H298 = (26.96,'kcal/mol'), - S298 = (35.65,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = 1186, - label = "C=S-CtH", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 H u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([7.46,8.91,10.01,10.83,11.98,12.74,13.87],'cal/(mol*K)'), - H298 = (30.83,'kcal/mol'), - S298 = (37.16,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = 1187, - label = "C=S-CbH", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 H u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([8.45,9.84,10.94,11.78,12.97,13.76,14.77],'cal/(mol*K)'), - H298 = (24.71,'kcal/mol'), - S298 = (34.15,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - entry( index = 65, label = "Cds-OdCOs", @@ -2537,217 +2196,6 @@ """, ) -entry( - index = 1205, - label = "C=S-CSs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 C u0 {1,S} -4 Ss u0 {1,S} -""", - thermo = u'C=S-CsSs', - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = 1206, - label = "C=S-CsSs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cs u0 {1,S} -4 Ss u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([7.4,8.38,9.16,9.8,10.72,11.25,11.66],'cal/(mol*K)'), - H298 = (21.35,'kcal/mol'), - S298 = (14.52,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CdsSs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} -4 Ss u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cd)Ss", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Ss u0 {1,S} -5 [Cd,Cdd,CO] u0 {3,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cds)Ss", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Ss u0 {1,S} -5 Cd u0 {3,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd)Ss", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Ss u0 {1,S} -5 Cdd u0 {3,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Sd)Ss", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Ss u0 {1,S} -5 Cdd u0 {3,D} {6,D} -6 Sd u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Cd)Ss", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Ss u0 {1,S} -5 Cdd u0 {3,D} {6,D} -6 C u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-C=SSs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Ss u0 {1,S} -5 Sd u0 {3,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CtSs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 Ss u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CbSs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Ss u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - entry( index = 76, label = "Cds-OdCC", @@ -3608,909 +3056,6 @@ """, ) -entry( - index = -1, - label = "C=S-CC", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 C u0 {1,S} -4 C u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = 1190, - label = "C=S-CsCs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cs u0 {1,S} -4 Cs u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([6.7,7.44,8.14,8.72,9.52,9.98,10.51],'cal/(mol*K)'), - H298 = (27.2,'kcal/mol'), - S298 = (18,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = 1191, - label = "C=S-CdsCs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} -4 Cs u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([7.79,9.21,10.13,10.71,11.25,11.42,11.35],'cal/(mol*K)'), - H298 = (26.19,'kcal/mol'), - S298 = (13.44,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cd)Cs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cs u0 {1,S} -5 [Cd,Cdd,CO] u0 {3,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cds)Cs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cs u0 {1,S} -5 Cd u0 {3,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd)Cs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cs u0 {1,S} -5 Cdd u0 {3,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Sd)Cs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cs u0 {1,S} -5 Cdd u0 {3,D} {6,D} -6 Sd u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Cd)Cs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cs u0 {1,S} -5 Cdd u0 {3,D} {6,D} -6 C u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = 1194, - label = "C=S-C=SCs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cs u0 {1,S} -5 Sd u0 {3,D} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([6.93,7.93,8.76,9.37,10.11,10.45,10.71],'cal/(mol*K)'), - H298 = (27.48,'kcal/mol'), - S298 = (16.58,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CdsCds", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} -4 Cd u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cd)(Cds-Cd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 [Cd,Cdd,CO] u0 {3,D} -6 [Cd,Cdd,CO] u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cds)(Cds-Cds)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Cd u0 {3,D} -6 Cd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd)(Cds-Cds)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Cdd u0 {3,D} -6 Cd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Sd)(Cds-Cds)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Cdd u0 {3,D} {7,D} -6 Cd u0 {4,D} -7 Sd u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Cd)(Cds-Cds)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Cdd u0 {3,D} {7,D} -6 Cd u0 {4,D} -7 C u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd)(Cds-Cdd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Cdd u0 {3,D} -6 Cdd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Sd)(Cds-Cdd-Sd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Cdd u0 {3,D} {7,D} -6 Cdd u0 {4,D} {8,D} -7 Sd u0 {5,D} -8 Sd u0 {6,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Cd)(Cds-Cdd-Sd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Cdd u0 {3,D} {7,D} -6 Cdd u0 {4,D} {8,D} -7 C u0 {5,D} -8 Sd u0 {6,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Cd)(Cds-Cdd-Cd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Cdd u0 {3,D} {7,D} -6 Cdd u0 {4,D} {8,D} -7 C u0 {5,D} -8 C u0 {6,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cd)C=S", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Sd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cds)C=S", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Cd u0 {3,D} -6 Sd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd)C=S", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Cdd u0 {3,D} -6 Sd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Sd)C=S", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {7,D} -5 Cdd u0 {3,D} {6,D} -6 Sd u0 {5,D} -7 Sd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Cd)C=S", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {7,D} -5 Cdd u0 {3,D} {6,D} -6 C u0 {5,D} -7 Sd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-C=SC=S", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Sd u0 {3,D} -6 Sd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = 1192, - label = "C=S-CtCs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 Cs u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([6.87,7.88,8.6,9.13,9.8,10.17,10.59],'cal/(mol*K)'), - H298 = (30.12,'kcal/mol'), - S298 = (17.46,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CtCds", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 Cd u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-Ct(Cds-Cd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 [Cd,Cdd,CO] u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-Ct(Cds-Cds)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Cd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-Ct(Cds-Cdd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Cdd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-Ct(Cds-Cdd-Sd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Cdd u0 {4,D} {6,D} -6 Sd u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-Ct(Cds-Cdd-Cd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Cdd u0 {4,D} {6,D} -6 C u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CtC=S", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Sd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CtCt", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 Ct u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = 1193, - label = "C=S-CbCs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Cs u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([8.02,9.02,9.75,10.23,10.75,10.96,11.04],'cal/(mol*K)'), - H298 = (26.6,'kcal/mol'), - S298 = (14.55,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CbCds", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Cd u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-Cb(Cds-Cd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 [Cd,Cdd,CO] u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-Cb(Cds-Cds)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Cd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-Cb(Cds-Cdd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Cdd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-Cb(Cds-Cdd-Sd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Cdd u0 {4,D} {6,D} -6 Sd u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-Cb(Cds-Cdd-Cd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Cdd u0 {4,D} {6,D} -6 C u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CbC=S", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Sd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CbCt", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Ct u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CbCb", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Cb u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = 1458, - label = "CS-CsOs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Os u0 {1,S} -4 Cs u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([3.9,4.17,4.6,5.1,6.08,6.76,7.44],'cal/(mol*K)'), - H298 = (-1.32,'kcal/mol'), - S298 = (8.62,'cal/(mol*K)'), - ), - shortDesc = u"""CAC 1d-HR calc""", - longDesc = -u""" - -""", -) - entry( index = 120, label = "Cds-CdHH", @@ -7533,7 +6078,7 @@ shortDesc = u"""Cd-COCd from CD/CD2/ jwb est 6/97""", longDesc = u""" -AG Vandeputte, added 7 kcal/mol to the following value (see phd M Sabbe) +AG Vandeputte, added 7 kcal/mol to the following value (see phd M Sabbe) """, ) @@ -33424,6 +31969,49 @@ """, ) +entry( + index = -1, + label = "Cs-CCOsSs", + group = +""" +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 C u0 {1,S} +3 C u0 {1,S} +4 Os u0 {1,S} +5 Ss u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = 1453, + label = "Cs-CsCsOsSs", + group = +""" +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cs u0 {1,S} +3 Cs u0 {1,S} +4 Os u0 {1,S} +5 Ss u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([8.16,10.15,10.69,10.52,9.74,9.01,8.34],'cal/(mol*K)'), + H298 = (-11.26,'kcal/mol'), + S298 = (-39.73,'cal/(mol*K)'), + ), + shortDesc = u"""CAC CBS-QB3 1DHR calc""", + longDesc = +u""" + +""", +) + entry( index = 1467, label = "Cs-COsOsSs", @@ -35225,49 +33813,6 @@ """, ) -entry( - index = -1, - label = "Cs-CCOsSs", - group = -""" -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 C u0 {1,S} -3 C u0 {1,S} -4 Os u0 {1,S} -5 Ss u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = 1453, - label = "Cs-CsCsOsSs", - group = -""" -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cs u0 {1,S} -3 Cs u0 {1,S} -4 Os u0 {1,S} -5 Ss u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([8.16,10.15,10.69,10.52,9.74,9.01,8.34],'cal/(mol*K)'), - H298 = (-11.26,'kcal/mol'), - S298 = (-39.73,'cal/(mol*K)'), - ), - shortDesc = u"""CAC CBS-QB3 1DHR calc""", - longDesc = -u""" - -""", -) - entry( index = -1, label = "Cs-(Cds-Cds)CtCsSs", @@ -40647,9 +39192,9 @@ label = "Os-(Cds-Cd)H", group = """ -1 * Os u0 {2,S} {3,S} -2 Cd u0 {1,S} {4,D} -3 H u0 {1,S} +1 * Os u0 {2,S} {3,S} +2 Cd u0 {1,S} {4,D} +3 H u0 {1,S} 4 [Cd,Cdd,CO] u0 {2,D} """, thermo = ThermoData( @@ -41130,6 +39675,29 @@ """, ) +entry( + index = 1461, + label = "Os-Cs(Cds-Sd)", + group = +""" +1 * Os u0 {2,S} {3,S} +2 Cs u0 {1,S} +3 Cd u0 {1,S} {4,D} +4 Sd u0 {3,D} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([5.56,6.31,7,7.61,8.52,8.99,9.29],'cal/(mol*K)'), + H298 = (-14.54,'kcal/mol'), + S298 = (10.02,'cal/(mol*K)'), + ), + shortDesc = u"""CAC CBS-QB3 1D-HR""", + longDesc = +u""" + +""", +) + entry( index = 1128, label = "Os-Cs(Cds-Cd)", @@ -41800,6 +40368,28 @@ """, ) +entry( + index = 1463, + label = "Ss-CsCO", + group = +""" +1 * Ss u0 {2,S} {3,S} +2 Cs u0 {1,S} +3 CO u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([5.78,6.73,7.6,8.34,9.31,9.77,10.14],'cal/(mol*K)'), + H298 = (-15.33,'kcal/mol'), + S298 = (11.11,'cal/(mol*K)'), + ), + shortDesc = u"""CAC CBS-QB3 1dhr calc""", + longDesc = +u""" + +""", +) + entry( index = 1139, label = "Ss-CsCt", @@ -42354,29 +40944,6 @@ """, ) -entry( - index = 1461, - label = "Os-Cs(Cds-Sd)", - group = -""" -1 * Os u0 {2,S} {3,S} -2 Cs u0 {1,S} -3 Cd u0 {1,S} {4,D} -4 Sd u0 {3,D} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([5.56,6.31,7,7.61,8.52,8.99,9.29],'cal/(mol*K)'), - H298 = (-14.54,'kcal/mol'), - S298 = (10.02,'cal/(mol*K)'), - ), - shortDesc = u"""CAC CBS-QB3 1D-HR""", - longDesc = -u""" - -""", -) - entry( index = 1828, label = "N3s-(CO)CbH", @@ -43141,28 +41708,6 @@ """, ) -entry( - index = 1463, - label = "Ss-CsCO", - group = -""" -1 * Ss u0 {2,S} {3,S} -2 Cs u0 {1,S} -3 CO u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([5.78,6.73,7.6,8.34,9.31,9.77,10.14],'cal/(mol*K)'), - H298 = (-15.33,'kcal/mol'), - S298 = (11.11,'cal/(mol*K)'), - ), - shortDesc = u"""CAC CBS-QB3 1dhr calc""", - longDesc = -u""" - -""", -) - entry( index = 1909, label = "N3d-OdOs", @@ -43529,11 +42074,6 @@ L4: Cds-OdOsOs L4: CO-CsSs L4: CO-OsSs - L4: C=S-HH - L4: C=S-SsH - L4: CS-OsH - L4: CS-OsOs - L4: C=S-SsSs L4: Cds-OdCH L5: Cds-OdCsH L5: Cds-OdCdsH @@ -43545,17 +42085,6 @@ L8: Cds-Od(Cds-Cdd-Cd)H L5: Cds-OdCtH L5: Cds-OdCbH - L4: C=S-CH - L5: C=S-CsH - L5: C=S-CdsH - L6: C=S-(Cds-Cd)H - L7: C=S-(Cds-Cds)H - L7: C=S-(Cds-Cdd)H - L8: C=S-(Cds-Cdd-Sd)H - L8: C=S-(Cds-Cdd-Cd)H - L6: C=S-C=SH - L5: C=S-CtH - L5: C=S-CbH L4: Cds-OdCOs L5: Cds-OdCsOs L5: Cds-OdCdsOs @@ -43567,17 +42096,6 @@ L8: Cds-Od(Cds-Cdd-Cd)Os L5: Cds-OdCtOs L5: Cds-OdCbOs - L4: C=S-CSs - L5: C=S-CsSs - L5: C=S-CdsSs - L6: C=S-(Cds-Cd)Ss - L7: C=S-(Cds-Cds)Ss - L7: C=S-(Cds-Cdd)Ss - L8: C=S-(Cds-Cdd-Sd)Ss - L8: C=S-(Cds-Cdd-Cd)Ss - L6: C=S-C=SSs - L5: C=S-CtSs - L5: C=S-CbSs L4: Cds-OdCC L5: Cds-OdCsCs L5: Cds-OdCdsCs @@ -43622,51 +42140,6 @@ L8: Cds-OdCb(Cds-Cdd-Cd) L5: Cds-OdCbCt L5: Cds-OdCbCb - L4: C=S-CC - L5: C=S-CsCs - L5: C=S-CdsCs - L6: C=S-(Cds-Cd)Cs - L7: C=S-(Cds-Cds)Cs - L7: C=S-(Cds-Cdd)Cs - L8: C=S-(Cds-Cdd-Sd)Cs - L8: C=S-(Cds-Cdd-Cd)Cs - L6: C=S-C=SCs - L5: C=S-CdsCds - L6: C=S-(Cds-Cd)(Cds-Cd) - L7: C=S-(Cds-Cds)(Cds-Cds) - L7: C=S-(Cds-Cdd)(Cds-Cds) - L8: C=S-(Cds-Cdd-Sd)(Cds-Cds) - L8: C=S-(Cds-Cdd-Cd)(Cds-Cds) - L7: C=S-(Cds-Cdd)(Cds-Cdd) - L8: C=S-(Cds-Cdd-Sd)(Cds-Cdd-Sd) - L8: C=S-(Cds-Cdd-Cd)(Cds-Cdd-Sd) - L8: C=S-(Cds-Cdd-Cd)(Cds-Cdd-Cd) - L6: C=S-(Cds-Cd)C=S - L7: C=S-(Cds-Cds)C=S - L7: C=S-(Cds-Cdd)C=S - L8: C=S-(Cds-Cdd-Sd)C=S - L8: C=S-(Cds-Cdd-Cd)C=S - L6: C=S-C=SC=S - L5: C=S-CtCs - L5: C=S-CtCds - L6: C=S-Ct(Cds-Cd) - L7: C=S-Ct(Cds-Cds) - L7: C=S-Ct(Cds-Cdd) - L8: C=S-Ct(Cds-Cdd-Sd) - L8: C=S-Ct(Cds-Cdd-Cd) - L6: C=S-CtC=S - L5: C=S-CtCt - L5: C=S-CbCs - L5: C=S-CbCds - L6: C=S-Cb(Cds-Cd) - L7: C=S-Cb(Cds-Cds) - L7: C=S-Cb(Cds-Cdd) - L8: C=S-Cb(Cds-Cdd-Sd) - L8: C=S-Cb(Cds-Cdd-Cd) - L6: C=S-CbC=S - L5: C=S-CbCt - L5: C=S-CbCb - L4: CS-CsOs L4: Cds-CdHH L5: Cds-CdsHH L5: Cds-CddHH From b46b957addac36750f544a64019598290b1a661d Mon Sep 17 00:00:00 2001 From: Nathan Yee Date: Thu, 2 Jun 2016 17:22:38 -0400 Subject: [PATCH 03/21] Edit adjlist for every instance of (Cds-Cd) ligand in groups.py Previously every instance of Cds-Cd ligand was not comprehensively represented in the adjlist. There would only be one Cd atomType in the adjList, instead of a Cd connected to another C. This is likely to have occurred because the original benson group did not have many heteroatoms, so it was previously a safe assumption. This fix will help with making groups work as intended and make groups more exclusive. --- input/thermo/groups/group.py | 906 +++++++++++++++++++++-------------- 1 file changed, 556 insertions(+), 350 deletions(-) diff --git a/input/thermo/groups/group.py b/input/thermo/groups/group.py index 6c2d64eb15..a826802f64 100644 --- a/input/thermo/groups/group.py +++ b/input/thermo/groups/group.py @@ -278,7 +278,8 @@ group = """ 1 * Cb u0 {2,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {3,D} +3 C u0 {2,D} """, thermo = u'Cb-(Cds-Cds)', shortDesc = u"""""", @@ -778,7 +779,8 @@ """ 1 * Ct u0 {2,T} {3,S} 2 Ct u0 {1,T} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {4,D} +4 C u0 {3,D} """, thermo = u'Ct-Ct(Cds-Cds)', shortDesc = u"""""", @@ -1842,8 +1844,9 @@ """ 1 * CO u0 {2,D} {3,S} {4,S} 2 Od u0 {1,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {5,D} 4 H u0 {1,S} +5 C u0 {3,D} """, thermo = u'Cds-Od(Cds-Cds)H', shortDesc = u"""""", @@ -2061,8 +2064,9 @@ """ 1 * CO u0 {2,D} {3,S} {4,S} 2 Od u0 {1,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {5,D} 4 Os u0 {1,S} +5 C u0 {3,D} """, thermo = u'Cds-Od(Cds-Cds)Os', shortDesc = u"""""", @@ -2285,8 +2289,9 @@ """ 1 * CO u0 {2,D} {3,S} {4,S} 2 Od u0 {1,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {5,D} 4 Cs u0 {1,S} +5 C u0 {3,D} """, thermo = u'Cds-Od(Cds-Cds)Cs', shortDesc = u"""""", @@ -2422,8 +2427,9 @@ """ 1 * CO u0 {2,D} {3,S} {4,S} 2 Od u0 {1,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {5,D} 4 CO u0 {1,S} +5 C u0 {3,D} """, thermo = u'Cds-Od(Cds-Cds)(Cds-Od)', shortDesc = u"""""", @@ -2518,8 +2524,10 @@ """ 1 * CO u0 {2,D} {3,S} {4,S} 2 Od u0 {1,D} -3 Cd u0 {1,S} -4 Cd u0 {1,S} +3 Cd u0 {1,S} {5,D} +4 Cd u0 {1,S} {6,D} +5 C u0 {3,D} +6 C u0 {4,D} """, thermo = u'Cds-Od(Cds-Cds)(Cds-Cds)', shortDesc = u"""""", @@ -2764,7 +2772,8 @@ 1 * CO u0 {2,D} {3,S} {4,S} 2 Od u0 {1,D} 3 Ct u0 {1,S} -4 Cd u0 {1,S} +4 Cd u0 {1,S} {5,D} +5 C u0 {4,D} """, thermo = u'Cds-OdCt(Cds-Cds)', shortDesc = u"""""", @@ -2932,7 +2941,8 @@ 1 * CO u0 {2,D} {3,S} {4,S} 2 Od u0 {1,D} 3 Cb u0 {1,S} -4 Cd u0 {1,S} +4 Cd u0 {1,S} {5,D} +5 C u0 {4,D} """, thermo = u'Cds-OdCb(Cds-Cds)', shortDesc = u"""""", @@ -3654,8 +3664,9 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cd u0 {1,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {5,D} 4 H u0 {1,S} +5 C u0 {3,D} """, thermo = u'Cds-Cds(Cds-Cds)H', shortDesc = u"""""", @@ -3986,9 +3997,10 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 H u0 {1,S} 5 Od u0 {2,D} +6 C u0 {3,D} """, thermo = u'Cds-(Cdd-Od)(Cds-Cds)H', shortDesc = u"""""", @@ -4092,9 +4104,10 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 H u0 {1,S} 5 Sd u0 {2,D} +6 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -4212,9 +4225,10 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 H u0 {1,S} 5 C u0 {2,D} +6 C u0 {3,D} """, thermo = u'Cds-(Cdd-Cd)(Cds-Cds)H', shortDesc = u"""""", @@ -4606,8 +4620,9 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cd u0 {1,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {5,D} 4 Os u0 {1,S} +5 C u0 {3,D} """, thermo = u'Cds-Cds(Cds-Cds)Os', shortDesc = u"""""", @@ -4846,9 +4861,10 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Os u0 {1,S} 5 Od u0 {2,D} +6 C u0 {3,D} """, thermo = u'Cds-(Cdd-Od)(Cds-Cds)Os', shortDesc = u"""""", @@ -4952,9 +4968,10 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Os u0 {1,S} 5 C u0 {2,D} +6 C u0 {3,D} """, thermo = u'Cds-(Cdd-Cd)(Cds-Cds)Os', shortDesc = u"""""", @@ -5222,11 +5239,11 @@ label = "Cds-Cds(Cds-Cd)Ss", group = """ -1 * Cd u0 {2,D} {3,S} {4,S} -2 Cd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Ss u0 {1,S} -5 [Cd,Cdd,CO] u0 {3,D} +1 * Cd u0 {2,D} {3,S} {4,S} +2 Cd u0 {1,D} +3 Cd u0 {1,S} {5,D} +4 Ss u0 {1,S} +5 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -5450,9 +5467,10 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Ss u0 {1,S} 5 Sd u0 {2,D} +6 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -5551,9 +5569,10 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Ss u0 {1,S} 5 C u0 {2,D} +6 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -5866,8 +5885,9 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cd u0 {1,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {5,D} 4 Cs u0 {1,S} +5 C u0 {3,D} """, thermo = u'Cds-Cds(Cds-Cds)Cs', shortDesc = u"""""", @@ -6048,7 +6068,8 @@ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cd u0 {1,D} 3 CO u0 {1,S} -4 Cd u0 {1,S} +4 Cd u0 {1,S} {5,D} +5 C u0 {4,D} """, thermo = u'Cds-Cds(Cds-Od)(Cds-Cds)', shortDesc = u"""""", @@ -6148,8 +6169,10 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cd u0 {1,D} -3 Cd u0 {1,S} -4 Cd u0 {1,S} +3 Cd u0 {1,S} {5,D} +4 Cd u0 {1,S} {6,D} +5 C u0 {3,D} +6 C u0 {4,D} """, thermo = u'Cds-Cds(Cds-Cds)(Cds-Cds)', shortDesc = u"""""", @@ -6405,8 +6428,9 @@ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cd u0 {1,D} 3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} +4 Cd u0 {1,S} {6,D} 5 Sd u0 {3,D} +6 C u0 {4,D} """, thermo = None, shortDesc = u"""""", @@ -6611,7 +6635,8 @@ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cd u0 {1,D} 3 Ct u0 {1,S} -4 Cd u0 {1,S} +4 Cd u0 {1,S} {5,D} +5 C u0 {4,D} """, thermo = u'Cds-Cds(Cds-Cds)Ct', shortDesc = u"""""", @@ -6857,8 +6882,9 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cd u0 {1,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {5,D} 4 Cb u0 {1,S} +5 C u0 {3,D} """, thermo = u'Cds-Cds(Cds-Cds)Cb', shortDesc = u"""""", @@ -7160,9 +7186,10 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Cs u0 {1,S} 5 Od u0 {2,D} +6 C u0 {3,D} """, thermo = u'Cds-(Cdd-Od)(Cds-Cds)Cs', shortDesc = u"""""", @@ -7266,9 +7293,10 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Cs u0 {1,S} 5 Sd u0 {2,D} +6 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -7367,9 +7395,10 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Cs u0 {1,S} 5 C u0 {2,D} +6 C u0 {3,D} """, thermo = u'Cds-(Cdd-Cd)(Cds-Cds)Cs', shortDesc = u"""""", @@ -7546,9 +7575,10 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 CO u0 {1,S} 5 Od u0 {2,D} +6 C u0 {3,D} """, thermo = u'Cds-(Cdd-Od)(Cds-Cds)(Cds-Od)', shortDesc = u"""""", @@ -7647,9 +7677,11 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 Cd u0 {1,S} -4 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} +4 Cd u0 {1,S} {7,D} 5 Od u0 {2,D} +6 C u0 {3,D} +7 C u0 {4,D} """, thermo = u'Cds-(Cdd-Od)(Cds-Cds)(Cds-Cds)', shortDesc = u"""""", @@ -7861,9 +7893,10 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 CO u0 {1,S} -4 Cd u0 {1,S} +3 CO u0 {1,S} +4 Cd u0 {1,S} {6,D} 5 C u0 {2,D} +6 C u0 {4,D} """, thermo = u'Cds-(Cdd-Cd)(Cds-Od)(Cds-Cds)', shortDesc = u"""""", @@ -7962,9 +7995,11 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 Cd u0 {1,S} -4 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} +4 Cd u0 {1,S} {7,D} 5 Sd u0 {2,D} +6 C u0 {3,D} +7 C u0 {4,D} """, thermo = None, shortDesc = u"""""", @@ -8157,9 +8192,11 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 Cd u0 {1,S} -4 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} +4 Cd u0 {1,S} {7,D} 5 C u0 {2,D} +6 C u0 {3,D} +7 C u0 {4,D} """, thermo = u'Cds-(Cdd-Cd)(Cds-Cds)(Cds-Cds)', shortDesc = u"""""", @@ -8420,10 +8457,11 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} 4 Cd u0 {1,S} {6,D} 5 Sd u0 {2,D} 6 Sd u0 {4,D} +7 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -8527,9 +8565,10 @@ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} 3 Cd u0 {1,S} {6,D} -4 Cd u0 {1,S} +4 Cd u0 {1,S} {7,D} 5 C u0 {2,D} 6 Sd u0 {3,D} +7 C u0 {4,D} """, thermo = None, shortDesc = u"""""", @@ -8786,9 +8825,10 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Ct u0 {1,S} 5 Od u0 {2,D} +6 C u0 {3,D} """, thermo = u'Cds-(Cdd-Od)(Cds-Cds)Ct', shortDesc = u"""""", @@ -8887,9 +8927,10 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Ct u0 {1,S} 5 Sd u0 {2,D} +6 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -8988,9 +9029,10 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Ct u0 {1,S} 5 C u0 {2,D} +6 C u0 {3,D} """, thermo = u'Cds-(Cdd-Cd)(Cds-Cds)Ct', shortDesc = u"""""", @@ -9317,9 +9359,10 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Cb u0 {1,S} 5 Od u0 {2,D} +6 C u0 {3,D} """, thermo = u'Cds-(Cdd-Od)(Cds-Cds)Cb', shortDesc = u"""""", @@ -9418,9 +9461,10 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Cb u0 {1,S} 5 Sd u0 {2,D} +6 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -9519,9 +9563,10 @@ """ 1 * Cd u0 {2,D} {3,S} {4,S} 2 Cdd u0 {1,D} {5,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Cb u0 {1,S} 5 C u0 {2,D} +6 C u0 {3,D} """, thermo = u'Cds-(Cdd-Cd)(Cds-Cds)Cb', shortDesc = u"""""", @@ -10848,10 +10893,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 H u0 {1,S} 4 H u0 {1,S} 5 H u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)HHH', shortDesc = u"""""", @@ -11381,10 +11427,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Cs u0 {1,S} 4 H u0 {1,S} 5 H u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CsHH', shortDesc = u"""""", @@ -11608,9 +11655,10 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 H u0 {1,S} 5 H u0 {1,S} +6 C u0 {3,D} """, thermo = u'Cs-(Cds-Od)(Cds-Cds)HH', shortDesc = u"""""", @@ -11713,10 +11761,12 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} -3 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} 4 H u0 {1,S} 5 H u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} """, thermo = u'Cs-(Cds-Cds)(Cds-Cds)HH', shortDesc = u"""""", @@ -11987,10 +12037,11 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} 4 H u0 {1,S} 5 H u0 {1,S} 6 Sd u0 {2,D} +7 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -12205,10 +12256,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Ct u0 {1,S} 4 H u0 {1,S} 5 H u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CtHH', shortDesc = u"""""", @@ -12443,10 +12495,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Cb u0 {1,S} 4 H u0 {1,S} 5 H u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CbHH', shortDesc = u"""""", @@ -12724,10 +12777,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Cs u0 {1,S} 4 Cs u0 {1,S} 5 H u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CsCsH', shortDesc = u"""""", @@ -13024,9 +13078,10 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Cs u0 {1,S} 5 H u0 {1,S} +6 C u0 {3,D} """, thermo = u'Cs-(Cds-Od)(Cds-Cds)CsH', shortDesc = u"""""", @@ -13124,10 +13179,12 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} -3 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} 4 Cs u0 {1,S} 5 H u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} """, thermo = u'Cs-(Cds-Cds)(Cds-Cds)CsH', shortDesc = u"""""", @@ -13398,10 +13455,11 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} 4 Cs u0 {1,S} 5 H u0 {1,S} 6 Sd u0 {2,D} +7 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -13562,10 +13620,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Ct u0 {1,S} 4 Cs u0 {1,S} 5 H u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CtCsH', shortDesc = u"""""", @@ -13747,10 +13806,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Cb u0 {1,S} 4 Cs u0 {1,S} 5 H u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CbCsH', shortDesc = u"""""", @@ -13965,8 +14025,9 @@ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} 3 CO u0 {1,S} -4 Cd u0 {1,S} +4 Cd u0 {1,S} {6,D} 5 H u0 {1,S} +6 C u0 {4,D} """, thermo = u'Cs-(Cds-Od)(Cds-Od)(Cds-Cds)H', shortDesc = u"""""", @@ -14065,9 +14126,11 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} -4 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} +4 Cd u0 {1,S} {7,D} 5 H u0 {1,S} +6 C u0 {3,D} +7 C u0 {4,D} """, thermo = u'Cs-(Cds-Od)(Cds-Cds)(Cds-Cds)H', shortDesc = u"""""", @@ -14259,10 +14322,13 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} -3 Cd u0 {1,S} -4 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} +4 Cd u0 {1,S} {8,D} 5 H u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} +8 C u0 {4,D} """, thermo = u'Cs-(Cds-Cds)(Cds-Cds)(Cds-Cds)H', shortDesc = u"""""", @@ -14736,10 +14802,12 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} -4 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} +4 Cd u0 {1,S} {8,D} 5 H u0 {1,S} 6 Sd u0 {2,D} +7 C u0 {3,D} +8 C u0 {4,D} """, thermo = None, shortDesc = u"""""", @@ -14941,10 +15009,11 @@ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} 3 Cd u0 {1,S} {7,D} -4 Cd u0 {1,S} +4 Cd u0 {1,S} {8,D} 5 H u0 {1,S} 6 Sd u0 {2,D} 7 Sd u0 {3,D} +8 C u0 {4,D} """, thermo = None, shortDesc = u"""""", @@ -15111,9 +15180,10 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Ct u0 {1,S} 5 H u0 {1,S} +6 C u0 {3,D} """, thermo = u'Cs-(Cds-Od)(Cds-Cds)CtH', shortDesc = u"""""", @@ -15211,10 +15281,12 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} -3 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} 4 Ct u0 {1,S} 5 H u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} """, thermo = u'Cs-(Cds-Cds)(Cds-Cds)CtH', shortDesc = u"""""", @@ -15480,10 +15552,11 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} 4 Ct u0 {1,S} 5 H u0 {1,S} 6 Sd u0 {2,D} +7 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -15645,9 +15718,10 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Cb u0 {1,S} 5 H u0 {1,S} +6 C u0 {3,D} """, thermo = u'Cs-(Cds-Od)(Cds-Cds)CbH', shortDesc = u"""""", @@ -15745,10 +15819,12 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} -3 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} 4 Cb u0 {1,S} 5 H u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} """, thermo = u'Cs-(Cds-Cds)(Cds-Cds)CbH', shortDesc = u"""""", @@ -16014,10 +16090,11 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} 4 Cb u0 {1,S} 5 H u0 {1,S} 6 Sd u0 {2,D} +7 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -16180,8 +16257,9 @@ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Ct u0 {1,S} 3 Ct u0 {1,S} -4 Cd u0 {1,S} +4 Cd u0 {1,S} {6,D} 5 H u0 {1,S} +6 C u0 {4,D} """, thermo = u'Cs-CtCt(Cds-Cds)H', shortDesc = u"""""", @@ -16365,8 +16443,9 @@ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cb u0 {1,S} 3 Ct u0 {1,S} -4 Cd u0 {1,S} +4 Cd u0 {1,S} {6,D} 5 H u0 {1,S} +6 C u0 {4,D} """, thermo = u'Cs-CbCt(Cds-Cds)H', shortDesc = u"""""", @@ -16545,8 +16624,9 @@ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cb u0 {1,S} 3 Cb u0 {1,S} -4 Cd u0 {1,S} +4 Cd u0 {1,S} {6,D} 5 H u0 {1,S} +6 C u0 {4,D} """, thermo = None, shortDesc = u"""""", @@ -16857,10 +16937,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Cs u0 {1,S} 4 Cs u0 {1,S} 5 Cs u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CsCsCs', shortDesc = u"""""", @@ -17152,9 +17233,10 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Cs u0 {1,S} 5 Cs u0 {1,S} +6 C u0 {3,D} """, thermo = u'Cs-(Cds-Od)(Cds-Cds)CsCs', shortDesc = u"""""", @@ -17252,10 +17334,12 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} -3 Cd u0 {1,S} -4 Cs u0 {1,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} +4 Cs u0 {1,S} 5 Cs u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} """, thermo = u'Cs-(Cds-Cds)(Cds-Cds)CsCs', shortDesc = u"""""", @@ -17526,10 +17610,11 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} 4 Cs u0 {1,S} 5 Cs u0 {1,S} 6 Sd u0 {2,D} +7 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -17690,10 +17775,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Ct u0 {1,S} 4 Cs u0 {1,S} 5 Cs u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CtCsCs', shortDesc = u"""""", @@ -17875,10 +17961,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Cb u0 {1,S} 4 Cs u0 {1,S} 5 Cs u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CbCsCs', shortDesc = u"""""", @@ -18160,8 +18247,9 @@ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} 3 CO u0 {1,S} -4 Cd u0 {1,S} +4 Cd u0 {1,S} {6,D} 5 Cs u0 {1,S} +6 C u0 {4,D} """, thermo = u'Cs-(Cds-Od)(Cds-Od)(Cds-Cds)Cs', shortDesc = u"""""", @@ -18260,9 +18348,11 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} -4 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} +4 Cd u0 {1,S} {7,D} 5 Cs u0 {1,S} +6 C u0 {3,D} +7 C u0 {4,D} """, thermo = u'Cs-(Cds-Od)(Cds-Cds)(Cds-Cds)Cs', shortDesc = u"""""", @@ -18454,10 +18544,13 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} -3 Cd u0 {1,S} -4 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} +4 Cd u0 {1,S} {8,D} 5 Cs u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} +8 C u0 {4,D} """, thermo = u'Cs-(Cds-Cds)(Cds-Cds)(Cds-Cds)Cs', shortDesc = u"""""", @@ -18931,10 +19024,12 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} -4 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} +4 Cd u0 {1,S} {8,D} 5 Cs u0 {1,S} 6 Sd u0 {2,D} +7 C u0 {3,D} +8 C u0 {4,D} """, thermo = None, shortDesc = u"""""", @@ -19136,10 +19231,11 @@ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} 3 Cd u0 {1,S} {7,D} -4 Cd u0 {1,S} +4 Cd u0 {1,S} {8,D} 5 Cs u0 {1,S} 6 Sd u0 {2,D} 7 Sd u0 {3,D} +8 C u0 {4,D} """, thermo = None, shortDesc = u"""""", @@ -19306,9 +19402,10 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Ct u0 {1,S} 5 Cs u0 {1,S} +6 C u0 {3,D} """, thermo = u'Cs-(Cds-Od)(Cds-Cds)CtCs', shortDesc = u"""""", @@ -19406,10 +19503,12 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} -3 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} 4 Ct u0 {1,S} 5 Cs u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} """, thermo = u'Cs-(Cds-Cds)(Cds-Cds)CtCs', shortDesc = u"""""", @@ -19670,10 +19769,11 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} 4 Ct u0 {1,S} 5 Cs u0 {1,S} 6 Sd u0 {2,D} +7 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -19835,9 +19935,10 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Cb u0 {1,S} 5 Cs u0 {1,S} +6 C u0 {3,D} """, thermo = u'Cs-(Cds-Od)(Cds-Cds)CbCs', shortDesc = u"""""", @@ -19935,10 +20036,12 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} -3 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} 4 Cb u0 {1,S} 5 Cs u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} """, thermo = u'Cs-(Cds-Cds)(Cds-Cds)CbCs', shortDesc = u"""""", @@ -20199,10 +20302,11 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} 4 Cb u0 {1,S} 5 Cs u0 {1,S} 6 Sd u0 {2,D} +7 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -20363,10 +20467,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Ct u0 {1,S} 4 Ct u0 {1,S} 5 Cs u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CtCtCs', shortDesc = u"""""", @@ -20548,10 +20653,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Cb u0 {1,S} 4 Ct u0 {1,S} 5 Cs u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CbCtCs', shortDesc = u"""""", @@ -20738,10 +20844,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Cb u0 {1,S} 4 Cb u0 {1,S} 5 Cs u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CbCbCs', shortDesc = u"""""", @@ -21022,7 +21129,8 @@ 2 CO u0 {1,S} 3 CO u0 {1,S} 4 CO u0 {1,S} -5 Cd u0 {1,S} +5 Cd u0 {1,S} {6,D} +6 C u0 {5,D} """, thermo = u'Cs-(Cds-Od)(Cds-Od)(Cds-Od)(Cds-Cds)', shortDesc = u"""""", @@ -21122,8 +21230,10 @@ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} 3 CO u0 {1,S} -4 Cd u0 {1,S} -5 Cd u0 {1,S} +4 Cd u0 {1,S} {6,D} +5 Cd u0 {1,S} {7,D} +6 C u0 {4,D} +7 C u0 {5,D} """, thermo = u'Cs-(Cds-Od)(Cds-Od)(Cds-Cds)(Cds-Cds)', shortDesc = u"""""", @@ -21316,9 +21426,12 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} -4 Cd u0 {1,S} -5 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} +4 Cd u0 {1,S} {7,D} +5 Cd u0 {1,S} {8,D} +6 C u0 {3,D} +7 C u0 {4,D} +8 C u0 {5,D} """, thermo = u'Cs-(Cds-Od)(Cds-Cds)(Cds-Cds)(Cds-Cds)', shortDesc = u"""""", @@ -21640,10 +21753,14 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} -3 Cd u0 {1,S} -4 Cd u0 {1,S} -5 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} +4 Cd u0 {1,S} {8,D} +5 Cd u0 {1,S} {9,D} +6 C u0 {2,D} +7 C u0 {3,D} +8 C u0 {4,D} +9 C u0 {5,D} """, thermo = u'Cs-(Cds-Cds)(Cds-Cds)(Cds-Cds)(Cds-Cds)', shortDesc = u"""""", @@ -22397,10 +22514,13 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} -4 Cd u0 {1,S} -5 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} +4 Cd u0 {1,S} {8,D} +5 Cd u0 {1,S} {9,D} 6 Sd u0 {2,D} +7 C u0 {3,D} +8 C u0 {4,D} +9 C u0 {5,D} """, thermo = None, shortDesc = u"""""", @@ -22737,10 +22857,12 @@ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} 3 Cd u0 {1,S} {7,D} -4 Cd u0 {1,S} -5 Cd u0 {1,S} +4 Cd u0 {1,S} {8,D} +5 Cd u0 {1,S} {9,D} 6 Sd u0 {2,D} 7 Sd u0 {3,D} +8 C u0 {4,D} +9 C u0 {5,D} """, thermo = None, shortDesc = u"""""", @@ -22951,10 +23073,11 @@ 2 Cd u0 {1,S} {6,D} 3 Cd u0 {1,S} {7,D} 4 Cd u0 {1,S} {8,D} -5 Cd u0 {1,S} +5 Cd u0 {1,S} {9,D} 6 Sd u0 {2,D} 7 Sd u0 {3,D} 8 Sd u0 {4,D} +9 C u0 {5,D} """, thermo = None, shortDesc = u"""""", @@ -23127,8 +23250,9 @@ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} 3 CO u0 {1,S} -4 Cd u0 {1,S} +4 Cd u0 {1,S} {6,D} 5 Ct u0 {1,S} +6 C u0 {4,D} """, thermo = u'Cs-(Cds-Od)(Cds-Od)(Cds-Cds)Ct', shortDesc = u"""""", @@ -23227,9 +23351,11 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} -4 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} +4 Cd u0 {1,S} {7,D} 5 Ct u0 {1,S} +6 C u0 {3,D} +7 C u0 {4,D} """, thermo = u'Cs-(Cds-Od)(Cds-Cds)(Cds-Cds)Ct', shortDesc = u"""""", @@ -23421,10 +23547,13 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} -3 Cd u0 {1,S} -4 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} +4 Cd u0 {1,S} {8,D} 5 Ct u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} +8 C u0 {4,D} """, thermo = u'Cs-(Cds-Cds)(Cds-Cds)(Cds-Cds)Ct', shortDesc = u"""""", @@ -23893,10 +24022,12 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} -4 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} +4 Cd u0 {1,S} {8,D} 5 Ct u0 {1,S} 6 Sd u0 {2,D} +7 C u0 {3,D} +8 C u0 {4,D} """, thermo = None, shortDesc = u"""""", @@ -24098,10 +24229,11 @@ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} 3 Cd u0 {1,S} {7,D} -4 Cd u0 {1,S} +4 Cd u0 {1,S} {8,D} 5 Ct u0 {1,S} 6 Sd u0 {2,D} 7 Sd u0 {3,D} +8 C u0 {4,D} """, thermo = None, shortDesc = u"""""", @@ -24269,8 +24401,9 @@ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} 3 CO u0 {1,S} -4 Cd u0 {1,S} +4 Cd u0 {1,S} {6,D} 5 Cb u0 {1,S} +6 C u0 {4,D} """, thermo = u'Cs-(Cds-Od)(Cds-Od)(Cds-Cds)Cb', shortDesc = u"""""", @@ -24369,9 +24502,11 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} -4 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} +4 Cd u0 {1,S} {7,D} 5 Cb u0 {1,S} +6 C u0 {3,D} +7 C u0 {4,D} """, thermo = u'Cs-(Cds-Od)(Cds-Cds)(Cds-Cds)Cb', shortDesc = u"""""", @@ -24563,10 +24698,13 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} -3 Cd u0 {1,S} -4 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} +4 Cd u0 {1,S} {8,D} 5 Cb u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} +8 C u0 {4,D} """, thermo = u'Cs-(Cds-Cds)(Cds-Cds)(Cds-Cds)Cb', shortDesc = u"""""", @@ -25035,10 +25173,12 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} -4 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} +4 Cd u0 {1,S} {8,D} 5 Cb u0 {1,S} 6 Sd u0 {2,D} +7 C u0 {3,D} +8 C u0 {4,D} """, thermo = None, shortDesc = u"""""", @@ -25240,10 +25380,11 @@ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} 3 Cd u0 {1,S} {7,D} -4 Cd u0 {1,S} +4 Cd u0 {1,S} {8,D} 5 Cb u0 {1,S} 6 Sd u0 {2,D} 7 Sd u0 {3,D} +8 C u0 {4,D} """, thermo = None, shortDesc = u"""""", @@ -25410,9 +25551,10 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Ct u0 {1,S} 5 Ct u0 {1,S} +6 C u0 {3,D} """, thermo = u'Cs-(Cds-Od)(Cds-Cds)CtCt', shortDesc = u"""""", @@ -25510,10 +25652,12 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} -3 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} 4 Ct u0 {1,S} 5 Ct u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} """, thermo = u'Cs-(Cds-Cds)(Cds-Cds)CtCt', shortDesc = u"""""", @@ -25779,10 +25923,11 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} 4 Ct u0 {1,S} 5 Ct u0 {1,S} 6 Sd u0 {2,D} +7 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -25944,9 +26089,10 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Cb u0 {1,S} 5 Ct u0 {1,S} +6 C u0 {3,D} """, thermo = u'Cs-(Cds-Od)(Cds-Cds)CbCt', shortDesc = u"""""", @@ -26044,10 +26190,12 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} -3 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} 4 Cb u0 {1,S} 5 Ct u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} """, thermo = u'Cs-(Cds-Cds)(Cds-Cds)CbCt', shortDesc = u"""""", @@ -26313,10 +26461,11 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} 4 Cb u0 {1,S} 5 Ct u0 {1,S} 6 Sd u0 {2,D} +7 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -26478,9 +26627,10 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Cb u0 {1,S} 5 Cb u0 {1,S} +6 C u0 {3,D} """, thermo = u'Cs-(Cds-Od)(Cds-Cds)CbCb', shortDesc = u"""""", @@ -26578,10 +26728,12 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} -3 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} 4 Cb u0 {1,S} 5 Cb u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} """, thermo = u'Cs-(Cds-Cds)(Cds-Cds)CbCb', shortDesc = u"""""", @@ -26847,10 +26999,11 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} 4 Cb u0 {1,S} 5 Cb u0 {1,S} 6 Sd u0 {2,D} +7 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -27011,10 +27164,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Ct u0 {1,S} 4 Ct u0 {1,S} 5 Ct u0 {1,S} +6 C u0 {2,D} """, thermo = None, shortDesc = u"""""", @@ -27191,10 +27345,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Cb u0 {1,S} 4 Ct u0 {1,S} 5 Ct u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CbCtCt', shortDesc = u"""""", @@ -27371,10 +27526,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Cb u0 {1,S} 4 Cb u0 {1,S} 5 Ct u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CbCbCt', shortDesc = u"""""", @@ -27551,10 +27707,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Cb u0 {1,S} 4 Cb u0 {1,S} 5 Cb u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CbCbCb', shortDesc = u"""""", @@ -27874,10 +28031,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Cs u0 {1,S} 4 Cs u0 {1,S} 5 Os u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CsCsOs', shortDesc = u"""""", @@ -28067,9 +28225,10 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Cs u0 {1,S} 5 Os u0 {1,S} +6 C u0 {3,D} """, thermo = u'Cs-(Cds-Od)(Cds-Cds)CsOs', shortDesc = u"""""", @@ -28167,10 +28326,12 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} -3 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} 4 Cs u0 {1,S} 5 Os u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} """, thermo = u'Cs-(Cds-Cds)(Cds-Cds)CsOs', shortDesc = u"""""", @@ -28405,10 +28566,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Ct u0 {1,S} 4 Cs u0 {1,S} 5 Os u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CtCsOs', shortDesc = u"""""", @@ -28544,10 +28706,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Cb u0 {1,S} 4 Cs u0 {1,S} 5 Os u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CbCsOs', shortDesc = u"""""", @@ -28742,8 +28905,9 @@ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} 3 CO u0 {1,S} -4 Cd u0 {1,S} +4 Cd u0 {1,S} {6,D} 5 Os u0 {1,S} +6 C u0 {4,D} """, thermo = u'Cs-(Cds-Od)(Cds-Od)(Cds-Cds)Os', shortDesc = u"""""", @@ -28842,9 +29006,11 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} -4 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} +4 Cd u0 {1,S} {7,D} 5 Os u0 {1,S} +6 C u0 {3,D} +7 C u0 {4,D} """, thermo = u'Cs-(Cds-Od)(Cds-Cds)(Cds-Cds)Os', shortDesc = u"""""", @@ -29036,10 +29202,13 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} -3 Cd u0 {1,S} -4 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} +4 Cd u0 {1,S} {8,D} 5 Os u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} +8 C u0 {4,D} """, thermo = u'Cs-(Cds-Cds)(Cds-Cds)(Cds-Cds)Os', shortDesc = u"""""", @@ -29400,9 +29569,10 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Ct u0 {1,S} 5 Os u0 {1,S} +6 C u0 {3,D} """, thermo = u'Cs-(Cds-Od)(Cds-Cds)CtOs', shortDesc = u"""""", @@ -29500,10 +29670,12 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} -3 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} 4 Ct u0 {1,S} 5 Os u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} """, thermo = u'Cs-(Cds-Cds)(Cds-Cds)CtOs', shortDesc = u"""""", @@ -29734,9 +29906,10 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Cb u0 {1,S} 5 Os u0 {1,S} +6 C u0 {3,D} """, thermo = u'Cs-(Cds-Od)(Cds-Cds)CbOs', shortDesc = u"""""", @@ -29834,10 +30007,12 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} -3 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} 4 Cb u0 {1,S} 5 Os u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} """, thermo = u'Cs-(Cds-Cds)(Cds-Cds)CbOs', shortDesc = u"""""", @@ -30067,10 +30242,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Ct u0 {1,S} 4 Ct u0 {1,S} 5 Os u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CtCtOs', shortDesc = u"""""", @@ -30206,10 +30382,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Cb u0 {1,S} 4 Ct u0 {1,S} 5 Os u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CbCtOs', shortDesc = u"""""", @@ -30345,10 +30522,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Cb u0 {1,S} 4 Cb u0 {1,S} 5 Os u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CbCbOs', shortDesc = u"""""", @@ -30603,10 +30781,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Cs u0 {1,S} 4 Os u0 {1,S} 5 Os u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CsOsOs', shortDesc = u"""""", @@ -30743,9 +30922,10 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Os u0 {1,S} 5 Os u0 {1,S} +6 C u0 {3,D} """, thermo = u'Cs-(Cds-Od)(Cds-Cds)OsOs', shortDesc = u"""""", @@ -30843,10 +31023,12 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} -3 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} 4 Os u0 {1,S} 5 Os u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} """, thermo = u'Cs-(Cds-Cds)(Cds-Cds)OsOs', shortDesc = u"""""", @@ -31095,10 +31277,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Ct u0 {1,S} 4 Os u0 {1,S} 5 Os u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CtOsOs', shortDesc = u"""""", @@ -31272,10 +31455,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Cb u0 {1,S} 4 Os u0 {1,S} 5 Os u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CbOsOs', shortDesc = u"""""", @@ -31492,10 +31676,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Os u0 {1,S} 4 Os u0 {1,S} 5 Os u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)OsOsOs', shortDesc = u"""""", @@ -31736,10 +31921,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Os u0 {1,S} 4 Os u0 {1,S} 5 H u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)OsOsH', shortDesc = u"""""", @@ -32147,10 +32333,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Cs u0 {1,S} 4 Os u0 {1,S} 5 H u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CsOsH', shortDesc = u"""""", @@ -32297,9 +32484,10 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {6,D} 4 Os u0 {1,S} 5 H u0 {1,S} +6 C u0 {3,D} """, thermo = u'Cs-(Cds-Od)(Cds-Cds)OsH', shortDesc = u"""""", @@ -32397,10 +32585,12 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} -3 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} 4 Os u0 {1,S} 5 H u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} """, thermo = u'Cs-(Cds-Cds)(Cds-Cds)OsH', shortDesc = u"""""", @@ -32654,10 +32844,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Ct u0 {1,S} 4 Os u0 {1,S} 5 H u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CtOsH', shortDesc = u"""""", @@ -32836,10 +33027,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Cb u0 {1,S} 4 Os u0 {1,S} 5 H u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)CbOsH', shortDesc = u"""""", @@ -33061,10 +33253,11 @@ group = """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} +2 Cd u0 {1,S} {6,D} 3 Os u0 {1,S} 4 H u0 {1,S} 5 H u0 {1,S} +6 C u0 {2,D} """, thermo = u'Cs-(Cds-Cds)OsHH', shortDesc = u"""""", @@ -33276,12 +33469,12 @@ label = "Cs-(Cds-Cd)CsCsSs", group = """ -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} {6,D} -3 Cs u0 {1,S} -4 Cs u0 {1,S} -5 Ss u0 {1,S} -6 [Cd,Cdd,CO] u0 {2,D} +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cd u0 {1,S} {6,D} +3 Cs u0 {1,S} +4 Cs u0 {1,S} +5 Ss u0 {1,S} +6 C u0 {2,D} """, thermo = None, shortDesc = u"""""", @@ -33455,13 +33648,13 @@ label = "Cs-(Cds-Cd)(Cds-Cd)CsSs", group = """ -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} {7,D} -4 Cs u0 {1,S} -5 Ss u0 {1,S} -6 [Cd,Cdd,CO] u0 {2,D} -7 [Cd,Cdd,CO] u0 {3,D} +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} +4 Cs u0 {1,S} +5 Ss u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -33654,10 +33847,11 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} 4 Cs u0 {1,S} 5 Ss u0 {1,S} 6 Sd u0 {2,D} +7 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -33798,12 +33992,12 @@ label = "Cs-(Cds-Cd)CtCsSs", group = """ -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} {6,D} -3 Ct u0 {1,S} -4 Cs u0 {1,S} -5 Ss u0 {1,S} -6 [Cd,Cdd,CO] u0 {2,D} +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cd u0 {1,S} {6,D} +3 Ct u0 {1,S} +4 Cs u0 {1,S} +5 Ss u0 {1,S} +6 C u0 {2,D} """, thermo = None, shortDesc = u"""""", @@ -33939,12 +34133,12 @@ label = "Cs-(Cds-Cd)CbCsSs", group = """ -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} {6,D} -3 Cb u0 {1,S} -4 Cs u0 {1,S} -5 Ss u0 {1,S} -6 [Cd,Cdd,CO] u0 {2,D} +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cd u0 {1,S} {6,D} +3 Cb u0 {1,S} +4 Cs u0 {1,S} +5 Ss u0 {1,S} +6 C u0 {2,D} """, thermo = None, shortDesc = u"""""", @@ -34137,14 +34331,14 @@ label = "Cs-(Cds-Cd)(Cds-Cd)(Cds-Cd)Ss", group = """ -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} {7,D} -4 Cd u0 {1,S} {8,D} -5 Ss u0 {1,S} -6 [Cd,Cdd,CO] u0 {2,D} -7 [Cd,Cdd,CO] u0 {3,D} -8 [Cd,Cdd,CO] u0 {4,D} +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} +4 Cd u0 {1,S} {8,D} +5 Ss u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} +8 C u0 {4,D} """, thermo = None, shortDesc = u"""""", @@ -34467,10 +34661,12 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} -4 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} +4 Cd u0 {1,S} {8,D} 5 Ss u0 {1,S} 6 Sd u0 {2,D} +7 C u0 {3,D} +8 C u0 {4,D} """, thermo = None, shortDesc = u"""""", @@ -34672,10 +34868,11 @@ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} 3 Cd u0 {1,S} {7,D} -4 Cd u0 {1,S} +4 Cd u0 {1,S} {8,D} 5 Ss u0 {1,S} 6 Sd u0 {2,D} 7 Sd u0 {3,D} +8 C u0 {4,D} """, thermo = None, shortDesc = u"""""", @@ -34821,13 +35018,13 @@ label = "Cs-(Cds-Cd)(Cds-Cd)CtSs", group = """ -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} {7,D} -4 Ct u0 {1,S} -5 Ss u0 {1,S} -6 [Cd,Cdd,CO] u0 {2,D} -7 [Cd,Cdd,CO] u0 {3,D} +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} +4 Ct u0 {1,S} +5 Ss u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -35020,10 +35217,11 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} 4 Ct u0 {1,S} 5 Ss u0 {1,S} 6 Sd u0 {2,D} +7 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -35164,13 +35362,13 @@ label = "Cs-(Cds-Cd)(Cds-Cd)CbSs", group = """ -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} {7,D} -4 Cb u0 {1,S} -5 Ss u0 {1,S} -6 [Cd,Cdd,CO] u0 {2,D} -7 [Cd,Cdd,CO] u0 {3,D} +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} +4 Cb u0 {1,S} +5 Ss u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -35363,10 +35561,11 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} 4 Cb u0 {1,S} 5 Ss u0 {1,S} 6 Sd u0 {2,D} +7 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -35507,12 +35706,12 @@ label = "Cs-(Cds-Cd)CtCtSs", group = """ -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} {6,D} -3 Ct u0 {1,S} -4 Ct u0 {1,S} -5 Ss u0 {1,S} -6 [Cd,Cdd,CO] u0 {2,D} +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cd u0 {1,S} {6,D} +3 Ct u0 {1,S} +4 Ct u0 {1,S} +5 Ss u0 {1,S} +6 C u0 {2,D} """, thermo = None, shortDesc = u"""""", @@ -35648,12 +35847,12 @@ label = "Cs-(Cds-Cd)CbCtSs", group = """ -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} {6,D} -3 Cb u0 {1,S} -4 Ct u0 {1,S} -5 Ss u0 {1,S} -6 [Cd,Cdd,CO] u0 {2,D} +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cd u0 {1,S} {6,D} +3 Cb u0 {1,S} +4 Ct u0 {1,S} +5 Ss u0 {1,S} +6 C u0 {2,D} """, thermo = None, shortDesc = u"""""", @@ -35789,12 +35988,12 @@ label = "Cs-(Cds-Cd)CbCbSs", group = """ -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} {6,D} -3 Cb u0 {1,S} -4 Cb u0 {1,S} -5 Ss u0 {1,S} -6 [Cd,Cdd,CO] u0 {2,D} +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cd u0 {1,S} {6,D} +3 Cb u0 {1,S} +4 Cb u0 {1,S} +5 Ss u0 {1,S} +6 C u0 {2,D} """, thermo = None, shortDesc = u"""""", @@ -36049,12 +36248,12 @@ label = "Cs-(Cds-Cd)CsSsSs", group = """ -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} {6,D} -3 Cs u0 {1,S} -4 Ss u0 {1,S} -5 Ss u0 {1,S} -6 [Cd,Cdd,CO] u0 {2,D} +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cd u0 {1,S} {6,D} +3 Cs u0 {1,S} +4 Ss u0 {1,S} +5 Ss u0 {1,S} +6 C u0 {2,D} """, thermo = None, shortDesc = u"""""", @@ -36190,13 +36389,13 @@ label = "Cs-(Cds-Cd)(Cds-Cd)SsSs", group = """ -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} {7,D} -4 Ss u0 {1,S} -5 Ss u0 {1,S} -6 [Cd,Cdd,CO] u0 {2,D} -7 [Cd,Cdd,CO] u0 {3,D} +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} +4 Ss u0 {1,S} +5 Ss u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -36389,10 +36588,11 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} 4 Ss u0 {1,S} 5 Ss u0 {1,S} 6 Sd u0 {2,D} +7 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -36552,12 +36752,12 @@ label = "Cs-(Cds-Cd)CtSsSs", group = """ -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} {6,D} -3 Ct u0 {1,S} -4 Ss u0 {1,S} -5 Ss u0 {1,S} -6 [Cd,Cdd,CO] u0 {2,D} +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cd u0 {1,S} {6,D} +3 Ct u0 {1,S} +4 Ss u0 {1,S} +5 Ss u0 {1,S} +6 C u0 {2,D} """, thermo = None, shortDesc = u"""""", @@ -36731,12 +36931,12 @@ label = "Cs-(Cds-Cd)CbSsSs", group = """ -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} {6,D} -3 Cb u0 {1,S} -4 Ss u0 {1,S} -5 Ss u0 {1,S} -6 [Cd,Cdd,CO] u0 {2,D} +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cd u0 {1,S} {6,D} +3 Cb u0 {1,S} +4 Ss u0 {1,S} +5 Ss u0 {1,S} +6 C u0 {2,D} """, thermo = None, shortDesc = u"""""", @@ -36953,12 +37153,12 @@ label = "Cs-(Cds-Cd)SsSsSs", group = """ -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} {6,D} -3 Ss u0 {1,S} -4 Ss u0 {1,S} -5 Ss u0 {1,S} -6 [Cd,Cdd,CO] u0 {2,D} +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cd u0 {1,S} {6,D} +3 Ss u0 {1,S} +4 Ss u0 {1,S} +5 Ss u0 {1,S} +6 C u0 {2,D} """, thermo = None, shortDesc = u"""""", @@ -37194,12 +37394,12 @@ label = "Cs-(Cds-Cd)SsSsH", group = """ -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} {6,D} -3 Ss u0 {1,S} -4 Ss u0 {1,S} -5 H u0 {1,S} -6 [Cd,Cdd,CO] u0 {2,D} +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cd u0 {1,S} {6,D} +3 Ss u0 {1,S} +4 Ss u0 {1,S} +5 H u0 {1,S} +6 C u0 {2,D} """, thermo = None, shortDesc = u"""""", @@ -37421,12 +37621,12 @@ label = "Cs-(Cds-Cd)CsSsH", group = """ -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} {6,D} -3 Cs u0 {1,S} -4 Ss u0 {1,S} -5 H u0 {1,S} -6 [Cd,Cdd,CO] u0 {2,D} +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cd u0 {1,S} {6,D} +3 Cs u0 {1,S} +4 Ss u0 {1,S} +5 H u0 {1,S} +6 C u0 {2,D} """, thermo = None, shortDesc = u"""""", @@ -37567,13 +37767,13 @@ label = "Cs-(Cds-Cd)(Cds-Cd)SsH", group = """ -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} {7,D} -4 Ss u0 {1,S} -5 H u0 {1,S} -6 [Cd,Cdd,CO] u0 {2,D} -7 [Cd,Cdd,CO] u0 {3,D} +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cd u0 {1,S} {6,D} +3 Cd u0 {1,S} {7,D} +4 Ss u0 {1,S} +5 H u0 {1,S} +6 C u0 {2,D} +7 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -37766,10 +37966,11 @@ """ 1 * Cs u0 {2,S} {3,S} {4,S} {5,S} 2 Cd u0 {1,S} {6,D} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {7,D} 4 Ss u0 {1,S} 5 H u0 {1,S} 6 Sd u0 {2,D} +7 C u0 {3,D} """, thermo = None, shortDesc = u"""""", @@ -37934,12 +38135,12 @@ label = "Cs-(Cds-Cd)CtSsH", group = """ -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} {6,D} -3 Ct u0 {1,S} -4 Ss u0 {1,S} -5 H u0 {1,S} -6 [Cd,Cdd,CO] u0 {2,D} +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cd u0 {1,S} {6,D} +3 Ct u0 {1,S} +4 Ss u0 {1,S} +5 H u0 {1,S} +6 C u0 {2,D} """, thermo = None, shortDesc = u"""""", @@ -38118,12 +38319,12 @@ label = "Cs-(Cds-Cd)CbSsH", group = """ -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} {6,D} -3 Cb u0 {1,S} -4 Ss u0 {1,S} -5 H u0 {1,S} -6 [Cd,Cdd,CO] u0 {2,D} +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cd u0 {1,S} {6,D} +3 Cb u0 {1,S} +4 Ss u0 {1,S} +5 H u0 {1,S} +6 C u0 {2,D} """, thermo = None, shortDesc = u"""""", @@ -38345,12 +38546,12 @@ label = "Cs-(Cds-Cd)SsHH", group = """ -1 * Cs u0 {2,S} {3,S} {4,S} {5,S} -2 Cd u0 {1,S} {6,D} -3 Ss u0 {1,S} -4 H u0 {1,S} -5 H u0 {1,S} -6 [Cd,Cdd,CO] u0 {2,D} +1 * Cs u0 {2,S} {3,S} {4,S} {5,S} +2 Cd u0 {1,S} {6,D} +3 Ss u0 {1,S} +4 H u0 {1,S} +5 H u0 {1,S} +6 C u0 {2,D} """, thermo = None, shortDesc = u"""""", @@ -39192,10 +39393,10 @@ label = "Os-(Cds-Cd)H", group = """ -1 * Os u0 {2,S} {3,S} -2 Cd u0 {1,S} {4,D} -3 H u0 {1,S} -4 [Cd,Cdd,CO] u0 {2,D} +1 * Os u0 {2,S} {3,S} +2 Cd u0 {1,S} {4,D} +3 H u0 {1,S} +4 C u0 {2,D} """, thermo = ThermoData( Tdata = ([300,400,500,600,800,1000,1500],'K'), @@ -39362,7 +39563,8 @@ """ 1 * Os u0 {2,S} {3,S} 2 Os u0 {1,S} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {4,D} +4 C u0 {3,D} """, thermo = ThermoData( Tdata = ([300,400,500,600,800,1000,1500],'K'), @@ -39491,7 +39693,8 @@ """ 1 * Os u0 {2,S} {3,S} 2 Ct u0 {1,S} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {4,D} +4 C u0 {3,D} """, thermo = u'Os-(Cds-Cd)(Cds-Cd)', shortDesc = u"""""", @@ -39604,7 +39807,8 @@ """ 1 * Os u0 {2,S} {3,S} 2 CO u0 {1,S} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {4,D} +4 C u0 {3,D} """, thermo = u'Os-(Cds-Cd)(Cds-Cd)', shortDesc = u"""""", @@ -39705,7 +39909,8 @@ """ 1 * Os u0 {2,S} {3,S} 2 Cs u0 {1,S} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {4,D} +4 C u0 {3,D} """, thermo = ThermoData( Tdata = ([300,400,500,600,800,1000,1500],'K'), @@ -39761,7 +39966,8 @@ """ 1 * Os u0 {2,S} {3,S} 2 Cb u0 {1,S} -3 Cd u0 {1,S} +3 Cd u0 {1,S} {4,D} +4 C u0 {3,D} """, thermo = None, shortDesc = u"""""", From cada4c6eaa24a34a9bbefb9f9252e7a6493bc6eb Mon Sep 17 00:00:00 2001 From: Nathan Yee Date: Fri, 3 Jun 2016 13:22:04 -0400 Subject: [PATCH 04/21] Move a few groups around in tree due to changes from last commit Some (CdN3d) ligands were placed underneath (Cd-Cds) because the (Cd-Cds) were previously defined as only Cd in the adjlist. --- input/thermo/groups/group.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/input/thermo/groups/group.py b/input/thermo/groups/group.py index a826802f64..fea5240544 100644 --- a/input/thermo/groups/group.py +++ b/input/thermo/groups/group.py @@ -42724,12 +42724,12 @@ L5: Cs-CdsHHH L6: Cs-(Cds-Od)HHH L6: Cs-(Cds-Cd)HHH - L7: Cs-(CdN3d)HHH L7: Cs-(Cds-Cds)HHH L7: Cs-(Cds-Cdd)HHH L8: Cs-(Cds-Cdd-Od)HHH L8: Cs-(Cds-Cdd-Sd)HHH L8: Cs-(Cds-Cdd-Cd)HHH + L6: Cs-(CdN3d)HHH L6: Cs-C=SHHH L5: Cs-CtHHH L6: Cs-(CtN3t)HHH @@ -42752,7 +42752,7 @@ L8: Cs-(Cds-Cdd-Od)CsHH L8: Cs-(Cds-Cdd-Sd)CsHH L8: Cs-(Cds-Cdd-Cd)CsHH - L7: Cs-(CdN3d)CsHH + L6: Cs-(CdN3d)CsHH L6: Cs-C=SCsHH L5: Cs-CdsCdsHH L6: Cs-(Cds-Od)(Cds-Od)HH @@ -42813,7 +42813,7 @@ L8: Cs-(Cds-Cdd-Od)CsCsH L8: Cs-(Cds-Cdd-Sd)CsCsH L8: Cs-(Cds-Cdd-Cd)CsCsH - L7: Cs-(CdN3d)CsCsH + L6: Cs-(CdN3d)CsCsH L6: Cs-C=SCsCsH L5: Cs-CtCsCsH L6: Cs-(CtN3t)CsCsH @@ -43004,7 +43004,7 @@ L8: Cs-(Cds-Cdd-Od)CsCsCs L8: Cs-(Cds-Cdd-Sd)CsCsCs L8: Cs-(Cds-Cdd-Cd)CsCsCs - L7: Cs-(CdN3d)CsCsCs + L6: Cs-(CdN3d)CsCsCs L6: Cs-C=SCsCsCs L5: Cs-CtCsCsCs L6: Cs-(CtN3t)CsCsCs From 247568d80561b98a030b4bcfeabbb37a8ea654e4 Mon Sep 17 00:00:00 2001 From: Nathan Yee Date: Fri, 3 Jun 2016 13:45:01 -0400 Subject: [PATCH 05/21] Fixes for siblings that should be child/parent in radical.py Used a script to re-order groups that were listed as siblings, but should have been child/parents, moving about 30 groups total. To the best of my knowledge, all these groups with the exception of CO, were previously completely inaccessible. Below is a list of moved groups with the format of newParent/formersibling, newChild: CsJ-S, CsJ-SS CsJ-S, CsJ-SsSsSs cyclopropane, bicyclo[1.1.0]butane-secondary cyclopropane, spiro[2.2]pentane-secondary cyclopropane, bicyclo[2.1.0]pentane-secondary-C3 cyclopropane, bicyclo[2.1.0]pent-2-ene-C5 cyclopropane, tricyclo[1.1.1.0(1,3)]pentane-C2 cyclopropane, bicyclo[3.1.0]hexane-C3 cyclopropane, tricyclo[2.1.1.0(1,4)]hex-2-ene-C5 cyclopropane, tricyclo[2.1.1.0(1,4)]hexane-C5 cyclopropane, bicyclo[4.1.0]heptane-C3-7 cyclopropane, bicyclo[4.1.0]heptane-C3-7 cyclopropane, tricyclo[3.1.1.0(1,5)]heptane-C6 cyclopropane, tricyclo[2.2.1.0(1,4)]heptane-C7 cyclobutane, bicyclo[2.1.0]pentane-secondary-C4 cyclobutane, bicyclo[2.2.0]hexane-secondary cyclobutane, bicyclo[3.2.0]heptane-C5-6 cyclopentene-4, bicyclo[2.1.1]hex-2-ene-C5 bicyclo[2.1.1]hexane-C2, tricyclo[2.1.1.0(1,4)]hexane-C2 cycloheptane, bicyclo[3.2.0]heptane-C5-2 cycloheptane, bicyclo[3.2.0]heptane-C5-3 bicyclo[3.1.1]heptane-C2, tricyclo[3.1.1.0(1,5)]heptane-C2 bicyclo[3.1.1]heptane-C3, tricyclo[3.1.1.0(1,5)]heptane-C3 bicyclo[2.2.2]octane-C2, tricyclo[2.2.2.0(1,4)]octane-C2 bicyclo[2.1.0]pent-2-ene-C5, tricyclo[2.1.1.0(1,4)]hex-2-ene-C5 CsJ-SS, CsJ-SsSsSs cyclobutene-vinyl, bicyclo[2.1.0]pent-2-ene-C2 cyclobutene-vinyl, tricyclo[2.1.1.0(1,4)]hex-2-ene-C2 cyclobutene-vinyl, bicyclo[2.2.0]hexa-2,5-diene-C2 cyclopentene-vinyl, bicyclo[2.1.1]hex-2-ene-C2 cyclobutadiene-C1, bicyclo[2.2.0]hexa-1(4),2,5-triene-C2 bicyclo[2.1.0]pent-2-ene-C2, tricyclo[2.1.1.0(1,4)]hex-2-ene-C2 CJ2_singlet, CO CdJ2_singlet, CCdJ2_singlet CdJ2_singlet, CdJ2-Sd_singlet --- input/thermo/groups/radical.py | 78 +++++++++++++++++----------------- 1 file changed, 39 insertions(+), 39 deletions(-) diff --git a/input/thermo/groups/radical.py b/input/thermo/groups/radical.py index ef805fa3c1..51214ca574 100644 --- a/input/thermo/groups/radical.py +++ b/input/thermo/groups/radical.py @@ -6231,53 +6231,53 @@ L5: Cs_S L6: (Cs)2CsJ L7: cyclopropane + L8: bicyclo[1.1.0]butane-secondary + L8: spiro[2.2]pentane-secondary + L8: bicyclo[2.1.0]pentane-secondary-C3 + L8: bicyclo[2.1.0]pent-2-ene-C5 + L9: tricyclo[2.1.1.0(1,4)]hex-2-ene-C5 + L8: tricyclo[1.1.1.0(1,3)]pentane-C2 + L8: bicyclo[3.1.0]hexane-C3 + L8: tricyclo[2.1.1.0(1,4)]hexane-C5 + L8: bicyclo[4.1.0]heptane-C3-7 + L8: bicyclo[4.1.0]heptane-C3-7 + L8: tricyclo[3.1.1.0(1,5)]heptane-C6 + L8: tricyclo[2.2.1.0(1,4)]heptane-C7 L7: cyclobutane - L7: bicyclo[1.1.0]butane-secondary + L8: bicyclo[2.1.0]pentane-secondary-C4 + L8: bicyclo[2.2.0]hexane-secondary + L8: bicyclo[3.2.0]heptane-C5-6 L7: CCJCOOH - L7: spiro[2.2]pentane-secondary - L7: bicyclo[2.1.0]pentane-secondary-C4 - L7: bicyclo[2.1.0]pentane-secondary-C3 L7: cyclopentene-4 - L7: bicyclo[2.1.0]pent-2-ene-C5 + L8: bicyclo[2.1.1]hex-2-ene-C5 L7: bicyclo[1.1.1]pentane-C2 - L7: tricyclo[1.1.1.0(1,3)]pentane-C2 L7: bicyclo[3.1.0]hexane-C5-2 L7: bicyclo[3.1.0]hexane-C5-3 - L7: bicyclo[3.1.0]hexane-C3 - L7: bicyclo[2.2.0]hexane-secondary - L7: bicyclo[2.1.1]hex-2-ene-C5 - L7: tricyclo[2.1.1.0(1,4)]hex-2-ene-C5 L7: bicyclo[2.1.1]hexane-C2 + L8: tricyclo[2.1.1.0(1,4)]hexane-C2 L7: bicyclo[2.1.1]hexane-C5 - L7: tricyclo[2.1.1.0(1,4)]hexane-C2 - L7: tricyclo[2.1.1.0(1,4)]hexane-C5 L7: 7-norbornyl L7: 2-norbornyl L7: cycloheptane - L7: bicyclo[3.2.0]heptane-C5-2 - L7: bicyclo[3.2.0]heptane-C5-3 - L7: bicyclo[3.2.0]heptane-C5-6 + L8: bicyclo[3.2.0]heptane-C5-2 + L8: bicyclo[3.2.0]heptane-C5-3 L7: bicyclo[4.1.0]heptane-C6-2 L7: bicyclo[4.1.0]heptane-C6-3 - L7: bicyclo[4.1.0]heptane-C3-7 L7: bicyclo[4.1.0]heptane-C6-2 L7: bicyclo[4.1.0]heptane-C6-3 - L7: bicyclo[4.1.0]heptane-C3-7 L7: bicyclo[3.1.1]heptane-C2 + L8: tricyclo[3.1.1.0(1,5)]heptane-C2 L7: bicyclo[3.1.1]heptane-C3 + L8: tricyclo[3.1.1.0(1,5)]heptane-C3 L7: bicyclo[3.1.1]heptane-C6 - L7: tricyclo[3.1.1.0(1,5)]heptane-C2 - L7: tricyclo[3.1.1.0(1,5)]heptane-C3 - L7: tricyclo[3.1.1.0(1,5)]heptane-C6 L7: tricyclo[2.2.1.0(1,4)]heptane-C2 - L7: tricyclo[2.2.1.0(1,4)]heptane-C7 L7: octahydro-pentalene-C5-2 L7: octahydro-pentalene-C5-3 L7: bicyclo[4.2.0]octane-C6-2 L7: bicyclo[4.2.0]octane-C6-3 L7: bicyclo[4.2.0]octane-C4-7 L7: bicyclo[2.2.2]octane-C2 - L7: tricyclo[2.2.2.0(1,4)]octane-C2 + L8: tricyclo[2.2.2.0(1,4)]octane-C2 L7: CCJC L7: RCCJC L7: RCCJCC @@ -6371,15 +6371,15 @@ L7: CsJ-CsCbSs L7: CsJ-CsCdSs L7: CsJ-CsC=SSs - L5: CsJ-SS - L6: CsJ-SsSsH - L6: CsJ-CSS - L7: CsJ-CsSsSs - L7: CsJ-CtSsSs - L7: CsJ-CbSsSs - L7: CsJ-CdSsSs - L7: CsJ-C=SSsSs - L5: CsJ-SsSsSs + L6: CsJ-SS + L7: CsJ-SsSsH + L7: CsJ-CSS + L8: CsJ-CsSsSs + L8: CsJ-CtSsSs + L8: CsJ-CbSsSs + L8: CsJ-CdSsSs + L8: CsJ-C=SSsSs + L7: CsJ-SsSsSs L5: CsJN L5: CCsJN L5: C2CsJN @@ -6407,16 +6407,16 @@ L5: Cds_S L6: C=CJC=C L7: cyclobutadiene-C1 + L8: bicyclo[2.2.0]hexa-1(4),2,5-triene-C2 L7: 1,3-cyclopentadiene-vinyl-2 - L7: bicyclo[2.2.0]hexa-1(4),2,5-triene-C2 L6: cyclopropenyl-vinyl L6: cyclobutene-vinyl + L7: bicyclo[2.1.0]pent-2-ene-C2 + L8: tricyclo[2.1.1.0(1,4)]hex-2-ene-C2 + L7: bicyclo[2.2.0]hexa-2,5-diene-C2 L6: cyclopentene-vinyl + L7: bicyclo[2.1.1]hex-2-ene-C2 L6: 1,3-cyclopentadiene-vinyl-1 - L6: bicyclo[2.1.0]pent-2-ene-C2 - L6: bicyclo[2.1.1]hex-2-ene-C2 - L6: tricyclo[2.1.1.0(1,4)]hex-2-ene-C2 - L6: bicyclo[2.2.0]hexa-2,5-diene-C2 L5: CdsJ-Ss L4: CtJ L5: Acetyl @@ -6466,7 +6466,6 @@ L3: SiJ2_triplet L3: SJ2_triplet L2: RJ2_singlet - L3: CO L3: CJ2_singlet L4: CsJ2_singlet L5: CH2_singlet @@ -6477,8 +6476,9 @@ L6: AllylJ2_singlet L5: CsJ2_S_singlet L4: CdJ2_singlet - L4: CCdJ2_singlet - L4: CdJ2-Sd_singlet + L5: CCdJ2_singlet + L5: CdJ2-Sd_singlet + L4: CO L3: Oa_singlet L3: SiJ2_singlet L3: SJ2_singlet From febb5530e9c082af7f556fa9c3481ea296dffdc9 Mon Sep 17 00:00:00 2001 From: Nathan Yee Date: Sun, 12 Jun 2016 17:24:32 -0400 Subject: [PATCH 06/21] Add in groups with CS atomType Now that CS atomTypes detection has been fixed, I have added back the groups that were previously removed. --- input/CSThermoGroups/groups/group.py | 1463 ------------------------ input/thermo/groups/group.py | 1527 ++++++++++++++++++++++++++ 2 files changed, 1527 insertions(+), 1463 deletions(-) delete mode 100644 input/CSThermoGroups/groups/group.py diff --git a/input/CSThermoGroups/groups/group.py b/input/CSThermoGroups/groups/group.py deleted file mode 100644 index d4db1e2a8e..0000000000 --- a/input/CSThermoGroups/groups/group.py +++ /dev/null @@ -1,1463 +0,0 @@ -#!/usr/bin/env python -# encoding: utf-8 - -name = "Functional Group Additivity Values" -shortDesc = u"" -longDesc = u""" - -""" -entry( - index = -1, - label = "C=S-C=SSs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Ss u0 {1,S} -5 Sd u0 {3,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Sd)Cs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cs u0 {1,S} -5 Cdd u0 {3,D} {6,D} -6 Sd u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cd)H", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 H u0 {1,S} -5 [Cd,Cdd,CO] u0 {3,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CbC=S", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Sd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-Ct(Cds-Cdd-Cd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Cdd u0 {4,D} {6,D} -6 C u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd)(Cds-Cds)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Cdd u0 {3,D} -6 Cd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-Cb(Cds-Cdd-Sd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Cdd u0 {4,D} {6,D} -6 Sd u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cds)Cs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cs u0 {1,S} -5 Cd u0 {3,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Cd)H", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 H u0 {1,S} -5 Cdd u0 {3,D} {6,D} -6 C u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CbSs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Ss u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CbCds", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Cd u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cd)C=S", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Sd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-Ct(Cds-Cds)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Cd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CdsSs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} -4 Ss u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cd)(Cds-Cd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 [Cd,Cdd,CO] u0 {3,D} -6 [Cd,Cdd,CO] u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cds)C=S", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Cd u0 {3,D} -6 Sd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd)H", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 H u0 {1,S} -5 Cdd u0 {3,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cds)(Cds-Cds)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Cd u0 {3,D} -6 Cd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CtCt", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 Ct u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-Cb(Cds-Cdd-Cd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Cdd u0 {4,D} {6,D} -6 C u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Cd)(Cds-Cds)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Cdd u0 {3,D} {7,D} -6 Cd u0 {4,D} -7 C u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Cd)C=S", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {7,D} -5 Cdd u0 {3,D} {6,D} -6 C u0 {5,D} -7 Sd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-SsSs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ss u0 {1,S} -4 Ss u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CbCb", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Cb u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-Ct(Cds-Cd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 [Cd,Cdd,CO] u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd)Cs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cs u0 {1,S} -5 Cdd u0 {3,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-Ct(Cds-Cdd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Cdd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Cd)(Cds-Cdd-Cd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Cdd u0 {3,D} {7,D} -6 Cdd u0 {4,D} {8,D} -7 C u0 {5,D} -8 C u0 {6,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-Cb(Cds-Cd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 [Cd,Cdd,CO] u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cd)Ss", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Ss u0 {1,S} -5 [Cd,Cdd,CO] u0 {3,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-Cb(Cds-Cds)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Cd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CH", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 C u0 {1,S} -4 H u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd)(Cds-Cdd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Cdd u0 {3,D} -6 Cdd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-Cb(Cds-Cdd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Cdd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CC", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 C u0 {1,S} -4 C u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CtC=S", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Sd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Cd)Cs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cs u0 {1,S} -5 Cdd u0 {3,D} {6,D} -6 C u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CdsCds", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} -4 Cd u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Sd)(Cds-Cdd-Sd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Cdd u0 {3,D} {7,D} -6 Cdd u0 {4,D} {8,D} -7 Sd u0 {5,D} -8 Sd u0 {6,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CtSs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 Ss u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cds)Ss", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Ss u0 {1,S} -5 Cd u0 {3,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Sd)H", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 H u0 {1,S} -5 Cdd u0 {3,D} {6,D} -6 Sd u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd)C=S", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Cdd u0 {3,D} -6 Sd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Cd)(Cds-Cdd-Sd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Cdd u0 {3,D} {7,D} -6 Cdd u0 {4,D} {8,D} -7 C u0 {5,D} -8 Sd u0 {6,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Cd)Ss", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Ss u0 {1,S} -5 Cdd u0 {3,D} {6,D} -6 C u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cds)H", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 H u0 {1,S} -5 Cd u0 {3,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd)Ss", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Ss u0 {1,S} -5 Cdd u0 {3,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-Ct(Cds-Cdd-Sd)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 Cd u0 {1,S} {5,D} -5 Cdd u0 {4,D} {6,D} -6 Sd u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Sd)Ss", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Ss u0 {1,S} -5 Cdd u0 {3,D} {6,D} -6 Sd u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CtCds", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 Cd u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cd)Cs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cs u0 {1,S} -5 [Cd,Cdd,CO] u0 {3,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Sd)(Cds-Cds)", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Cdd u0 {3,D} {7,D} -6 Cd u0 {4,D} -7 Sd u0 {5,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-(Cds-Cdd-Sd)C=S", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {7,D} -5 Cdd u0 {3,D} {6,D} -6 Sd u0 {5,D} -7 Sd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-CbCt", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Ct u0 {1,S} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = -1, - label = "C=S-C=SC=S", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cd u0 {1,S} {6,D} -5 Sd u0 {3,D} -6 Sd u0 {4,D} -""", - thermo = None, - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = 1183, - label = "C=S-HH", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 H u0 {1,S} -4 H u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([9.08,10.34,11.51,12.5,14.07,15.25,17.14],'cal/(mol*K)'), - H298 = (27.71,'kcal/mol'), - S298 = (56.51,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = 1184, - label = "C=S-CsH", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cs u0 {1,S} -4 H u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([8.11,9.03,9.88,10.61,11.74,12.55,13.82],'cal/(mol*K)'), - H298 = (27.32,'kcal/mol'), - S298 = (37.56,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = 1185, - label = "C=S-CdsH", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} -4 H u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([7.59,9.38,10.81,11.85,13.18,13.95,14.81],'cal/(mol*K)'), - H298 = (24.05,'kcal/mol'), - S298 = (34.35,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = 1186, - label = "C=S-CtH", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 H u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([7.46,8.91,10.01,10.83,11.98,12.74,13.87],'cal/(mol*K)'), - H298 = (30.83,'kcal/mol'), - S298 = (37.16,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = 1187, - label = "C=S-CbH", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 H u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([8.45,9.84,10.94,11.78,12.97,13.76,14.77],'cal/(mol*K)'), - H298 = (24.71,'kcal/mol'), - S298 = (34.15,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = 1188, - label = "C=S-C=SH", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 H u0 {1,S} -5 Sd u0 {3,D} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([7.79,9.18,10.41,11.42,12.82,13.63,14.54],'cal/(mol*K)'), - H298 = (26.96,'kcal/mol'), - S298 = (35.65,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = 1189, - label = "C=S-SsH", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ss u0 {1,S} -4 H u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([8.38,9.78,10.83,11.66,12.86,13.71,14.87],'cal/(mol*K)'), - H298 = (21.55,'kcal/mol'), - S298 = (34.41,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = 1190, - label = "C=S-CsCs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cs u0 {1,S} -4 Cs u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([6.7,7.44,8.14,8.72,9.52,9.98,10.51],'cal/(mol*K)'), - H298 = (27.2,'kcal/mol'), - S298 = (18,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = 1191, - label = "C=S-CdsCs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} -4 Cs u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([7.79,9.21,10.13,10.71,11.25,11.42,11.35],'cal/(mol*K)'), - H298 = (26.19,'kcal/mol'), - S298 = (13.44,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = 1192, - label = "C=S-CtCs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Ct u0 {1,S} -4 Cs u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([6.87,7.88,8.6,9.13,9.8,10.17,10.59],'cal/(mol*K)'), - H298 = (30.12,'kcal/mol'), - S298 = (17.46,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = 1193, - label = "C=S-CbCs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cb u0 {1,S} -4 Cs u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([8.02,9.02,9.75,10.23,10.75,10.96,11.04],'cal/(mol*K)'), - H298 = (26.6,'kcal/mol'), - S298 = (14.55,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = 1194, - label = "C=S-C=SCs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cd u0 {1,S} {5,D} -4 Cs u0 {1,S} -5 Sd u0 {3,D} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([6.93,7.93,8.76,9.37,10.11,10.45,10.71],'cal/(mol*K)'), - H298 = (27.48,'kcal/mol'), - S298 = (16.58,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = 1205, - label = "C=S-CSs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 C u0 {1,S} -4 Ss u0 {1,S} -""", - thermo = u'C=S-CsSs', - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = 1206, - label = "C=S-CsSs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Cs u0 {1,S} -4 Ss u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([7.4,8.38,9.16,9.8,10.72,11.25,11.66],'cal/(mol*K)'), - H298 = (21.35,'kcal/mol'), - S298 = (14.52,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", - longDesc = -u""" - -""", -) - -entry( - index = 1457, - label = "CS-OsH", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Os u0 {1,S} -4 H u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([4.48,5.3,6.09,6.82,8.05,8.99,10.37],'cal/(mol*K)'), - H298 = (2.85,'kcal/mol'), - S298 = (30.14,'cal/(mol*K)'), - ), - shortDesc = u"""CAC 1d-HR calc""", - longDesc = -u""" - -""", -) - -entry( - index = 1458, - label = "CS-CsOs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Os u0 {1,S} -4 Cs u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([3.9,4.17,4.6,5.1,6.08,6.76,7.44],'cal/(mol*K)'), - H298 = (-1.32,'kcal/mol'), - S298 = (8.62,'cal/(mol*K)'), - ), - shortDesc = u"""CAC 1d-HR calc""", - longDesc = -u""" - -""", -) - -entry( - index = 1459, - label = "CS-OsOs", - group = -""" -1 * CS u0 {2,D} {3,S} {4,S} -2 Sd u0 {1,D} -3 Os u0 {1,S} -4 Os u0 {1,S} -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([3.08,3.59,3.9,4.03,3.99,3.75,3.23],'cal/(mol*K)'), - H298 = (-22.72,'kcal/mol'), - S298 = (2.67,'cal/(mol*K)'), - ), - shortDesc = u"""CAC CBS-QB3 1Dhr calc""", - longDesc = -u""" - -""", -) - diff --git a/input/thermo/groups/group.py b/input/thermo/groups/group.py index fea5240544..abdb505aa7 100644 --- a/input/thermo/groups/group.py +++ b/input/thermo/groups/group.py @@ -9999,6 +9999,1461 @@ """, ) +entry( + index = -1, + label = "C=S-SsSs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Ss u0 {1,S} +4 Ss u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CH", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 C u0 {1,S} +4 H u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = 1184, + label = "C=S-CsH", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cs u0 {1,S} +4 H u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([8.11,9.03,9.88,10.61,11.74,12.55,13.82],'cal/(mol*K)'), + H298 = (27.32,'kcal/mol'), + S298 = (37.56,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1185, + label = "C=S-CdsH", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} +4 H u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([7.59,9.38,10.81,11.85,13.18,13.95,14.81],'cal/(mol*K)'), + H298 = (24.05,'kcal/mol'), + S298 = (34.35,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cd)H", + group = +""" +1 * CS u0 {2,S} {3,D} {4,S} +2 Cd u0 {1,S} {5,D} +3 Sd u0 {1,D} +4 H u0 {1,S} +5 [Cd,Cdd,CO] u0 {2,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd)H", + group = +""" +1 * CS u0 {2,S} {3,D} {4,S} +2 Cd u0 {1,S} {5,D} +3 Sd u0 {1,D} +4 H u0 {1,S} +5 Cdd u0 {2,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Cd)H", + group = +""" +1 * CS u0 {2,S} {4,D} {5,S} +2 Cd u0 {1,S} {3,D} +3 Cdd u0 {2,D} {6,D} +4 Sd u0 {1,D} +5 H u0 {1,S} +6 C u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Sd)H", + group = +""" +1 * CS u0 {2,S} {4,D} {5,S} +2 Cd u0 {1,S} {3,D} +3 Cdd u0 {2,D} {6,D} +4 Sd u0 {1,D} +5 H u0 {1,S} +6 Sd u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cds)H", + group = +""" +1 * CS u0 {2,S} {3,D} {4,S} +2 Cd u0 {1,S} {5,D} +3 Sd u0 {1,D} +4 H u0 {1,S} +5 Cd u0 {2,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = 1188, + label = "C=S-C=SH", + group = +""" +1 * CS u0 {2,S} {3,D} {4,S} +2 Cd u0 {1,S} {5,D} +3 Sd u0 {1,D} +4 H u0 {1,S} +5 Sd u0 {2,D} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([7.79,9.18,10.41,11.42,12.82,13.63,14.54],'cal/(mol*K)'), + H298 = (26.96,'kcal/mol'), + S298 = (35.65,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1186, + label = "C=S-CtH", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Ct u0 {1,S} +4 H u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([7.46,8.91,10.01,10.83,11.98,12.74,13.87],'cal/(mol*K)'), + H298 = (30.83,'kcal/mol'), + S298 = (37.16,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1187, + label = "C=S-CbH", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cb u0 {1,S} +4 H u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([8.45,9.84,10.94,11.78,12.97,13.76,14.77],'cal/(mol*K)'), + H298 = (24.71,'kcal/mol'), + S298 = (34.15,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CC", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 C u0 {1,S} +4 C u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CbCds", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cb u0 {1,S} +4 Cd u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CbC=S", + group = +""" +1 * CS u0 {2,S} {3,D} {4,S} +2 Cd u0 {1,S} {5,D} +3 Sd u0 {1,D} +4 Cb u0 {1,S} +5 Sd u0 {2,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-Cb(Cds-Cd)", + group = +""" +1 * CS u0 {2,S} {3,D} {4,S} +2 Cd u0 {1,S} {5,D} +3 Sd u0 {1,D} +4 Cb u0 {1,S} +5 [Cd,Cdd,CO] u0 {2,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-Cb(Cds-Cds)", + group = +""" +1 * CS u0 {2,S} {3,D} {4,S} +2 Cd u0 {1,S} {5,D} +3 Sd u0 {1,D} +4 Cb u0 {1,S} +5 Cd u0 {2,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-Cb(Cds-Cdd)", + group = +""" +1 * CS u0 {2,S} {3,D} {4,S} +2 Cd u0 {1,S} {5,D} +3 Sd u0 {1,D} +4 Cb u0 {1,S} +5 Cdd u0 {2,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-Cb(Cds-Cdd-Sd)", + group = +""" +1 * CS u0 {2,S} {4,D} {5,S} +2 Cd u0 {1,S} {3,D} +3 Cdd u0 {2,D} {6,D} +4 Sd u0 {1,D} +5 Cb u0 {1,S} +6 Sd u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-Cb(Cds-Cdd-Cd)", + group = +""" +1 * CS u0 {2,S} {4,D} {5,S} +2 Cd u0 {1,S} {3,D} +3 Cdd u0 {2,D} {6,D} +4 Sd u0 {1,D} +5 Cb u0 {1,S} +6 C u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CtCt", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Ct u0 {1,S} +4 Ct u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CbCb", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cb u0 {1,S} +4 Cb u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CdsCds", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} +4 Cd u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cd)C=S", + group = +""" +1 * CS u0 {2,S} {3,D} {4,S} +2 Cd u0 {1,S} {5,D} +3 Sd u0 {1,D} +4 Cd u0 {1,S} +5 Sd u0 {2,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cds)C=S", + group = +""" +1 * CS u0 {2,S} {3,S} {4,D} +2 Cd u0 {1,S} {5,D} +3 Cd u0 {1,S} {6,D} +4 Sd u0 {1,D} +5 Cd u0 {2,D} +6 Sd u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd)C=S", + group = +""" +1 * CS u0 {2,S} {3,S} {4,D} +2 Cd u0 {1,S} {5,D} +3 Cd u0 {1,S} {6,D} +4 Sd u0 {1,D} +5 Cdd u0 {2,D} +6 Sd u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Cd)C=S", + group = +""" +1 * CS u0 {2,S} {3,S} {5,D} +2 Cd u0 {1,S} {4,D} +3 Cd u0 {1,S} {6,D} +4 Cdd u0 {2,D} {7,D} +5 Sd u0 {1,D} +6 Sd u0 {3,D} +7 C u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Sd)C=S", + group = +""" +1 * CS u0 {2,S} {3,S} {5,D} +2 Cd u0 {1,S} {4,D} +3 Cd u0 {1,S} {6,D} +4 Cdd u0 {2,D} {7,D} +5 Sd u0 {1,D} +6 Sd u0 {3,D} +7 Sd u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-C=SC=S", + group = +""" +1 * CS u0 {2,S} {3,S} {4,D} +2 Cd u0 {1,S} {5,D} +3 Cd u0 {1,S} {6,D} +4 Sd u0 {1,D} +5 Sd u0 {2,D} +6 Sd u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cd)(Cds-Cd)", + group = +""" +1 * CS u0 {2,S} {3,S} {4,D} +2 Cd u0 {1,S} {5,D} +3 Cd u0 {1,S} {6,D} +4 Sd u0 {1,D} +5 [Cd,Cdd,CO] u0 {2,D} +6 [Cd,Cdd,CO] u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd)(Cds-Cds)", + group = +""" +1 * CS u0 {2,S} {3,S} {4,D} +2 Cd u0 {1,S} {5,D} +3 Cd u0 {1,S} {6,D} +4 Sd u0 {1,D} +5 Cdd u0 {2,D} +6 Cd u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Cd)(Cds-Cds)", + group = +""" +1 * CS u0 {2,S} {3,S} {5,D} +2 Cd u0 {1,S} {4,D} +3 Cd u0 {1,S} {6,D} +4 Cdd u0 {2,D} {7,D} +5 Sd u0 {1,D} +6 Cd u0 {3,D} +7 C u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Sd)(Cds-Cds)", + group = +""" +1 * CS u0 {2,S} {3,S} {5,D} +2 Cd u0 {1,S} {4,D} +3 Cd u0 {1,S} {6,D} +4 Cdd u0 {2,D} {7,D} +5 Sd u0 {1,D} +6 Cd u0 {3,D} +7 Sd u0 {4,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cds)(Cds-Cds)", + group = +""" +1 * CS u0 {2,S} {3,S} {4,D} +2 Cd u0 {1,S} {5,D} +3 Cd u0 {1,S} {6,D} +4 Sd u0 {1,D} +5 Cd u0 {2,D} +6 Cd u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd)(Cds-Cdd)", + group = +""" +1 * CS u0 {2,S} {3,S} {4,D} +2 Cd u0 {1,S} {5,D} +3 Cd u0 {1,S} {6,D} +4 Sd u0 {1,D} +5 Cdd u0 {2,D} +6 Cdd u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Cd)(Cds-Cdd-Cd)", + group = +""" +1 * CS u0 {2,S} {3,S} {6,D} +2 Cd u0 {1,S} {4,D} +3 Cd u0 {1,S} {5,D} +4 Cdd u0 {2,D} {7,D} +5 Cdd u0 {3,D} {8,D} +6 Sd u0 {1,D} +7 C u0 {4,D} +8 C u0 {5,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Sd)(Cds-Cdd-Sd)", + group = +""" +1 * CS u0 {2,S} {3,S} {6,D} +2 Cd u0 {1,S} {4,D} +3 Cd u0 {1,S} {5,D} +4 Cdd u0 {2,D} {7,D} +5 Cdd u0 {3,D} {8,D} +6 Sd u0 {1,D} +7 Sd u0 {4,D} +8 Sd u0 {5,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Cd)(Cds-Cdd-Sd)", + group = +""" +1 * CS u0 {2,S} {3,S} {6,D} +2 Cd u0 {1,S} {4,D} +3 Cd u0 {1,S} {5,D} +4 Cdd u0 {2,D} {7,D} +5 Cdd u0 {3,D} {8,D} +6 Sd u0 {1,D} +7 C u0 {4,D} +8 Sd u0 {5,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CtCds", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Ct u0 {1,S} +4 Cd u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-Ct(Cds-Cd)", + group = +""" +1 * CS u0 {2,S} {3,D} {4,S} +2 Cd u0 {1,S} {5,D} +3 Sd u0 {1,D} +4 Ct u0 {1,S} +5 [Cd,Cdd,CO] u0 {2,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-Ct(Cds-Cds)", + group = +""" +1 * CS u0 {2,S} {3,D} {4,S} +2 Cd u0 {1,S} {5,D} +3 Sd u0 {1,D} +4 Ct u0 {1,S} +5 Cd u0 {2,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-Ct(Cds-Cdd)", + group = +""" +1 * CS u0 {2,S} {3,D} {4,S} +2 Cd u0 {1,S} {5,D} +3 Sd u0 {1,D} +4 Ct u0 {1,S} +5 Cdd u0 {2,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-Ct(Cds-Cdd-Cd)", + group = +""" +1 * CS u0 {2,S} {4,D} {5,S} +2 Cd u0 {1,S} {3,D} +3 Cdd u0 {2,D} {6,D} +4 Sd u0 {1,D} +5 Ct u0 {1,S} +6 C u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-Ct(Cds-Cdd-Sd)", + group = +""" +1 * CS u0 {2,S} {4,D} {5,S} +2 Cd u0 {1,S} {3,D} +3 Cdd u0 {2,D} {6,D} +4 Sd u0 {1,D} +5 Ct u0 {1,S} +6 Sd u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CtC=S", + group = +""" +1 * CS u0 {2,S} {3,D} {4,S} +2 Cd u0 {1,S} {5,D} +3 Sd u0 {1,D} +4 Ct u0 {1,S} +5 Sd u0 {2,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CbCt", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cb u0 {1,S} +4 Ct u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = 1190, + label = "C=S-CsCs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cs u0 {1,S} +4 Cs u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([6.7,7.44,8.14,8.72,9.52,9.98,10.51],'cal/(mol*K)'), + H298 = (27.2,'kcal/mol'), + S298 = (18,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1191, + label = "C=S-CdsCs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} +4 Cs u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([7.79,9.21,10.13,10.71,11.25,11.42,11.35],'cal/(mol*K)'), + H298 = (26.19,'kcal/mol'), + S298 = (13.44,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cd)Cs", + group = +""" +1 * CS u0 {2,S} {3,D} {4,S} +2 Cd u0 {1,S} {5,D} +3 Sd u0 {1,D} +4 Cs u0 {1,S} +5 [Cd,Cdd,CO] u0 {2,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cds)Cs", + group = +""" +1 * CS u0 {2,S} {3,D} {4,S} +2 Cd u0 {1,S} {5,D} +3 Sd u0 {1,D} +4 Cs u0 {1,S} +5 Cd u0 {2,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd)Cs", + group = +""" +1 * CS u0 {2,S} {3,D} {4,S} +2 Cd u0 {1,S} {5,D} +3 Sd u0 {1,D} +4 Cs u0 {1,S} +5 Cdd u0 {2,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Sd)Cs", + group = +""" +1 * CS u0 {2,S} {4,D} {5,S} +2 Cd u0 {1,S} {3,D} +3 Cdd u0 {2,D} {6,D} +4 Sd u0 {1,D} +5 Cs u0 {1,S} +6 Sd u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Cd)Cs", + group = +""" +1 * CS u0 {2,S} {4,D} {5,S} +2 Cd u0 {1,S} {3,D} +3 Cdd u0 {2,D} {6,D} +4 Sd u0 {1,D} +5 Cs u0 {1,S} +6 C u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = 1194, + label = "C=S-C=SCs", + group = +""" +1 * CS u0 {2,S} {3,D} {4,S} +2 Cd u0 {1,S} {5,D} +3 Sd u0 {1,D} +4 Cs u0 {1,S} +5 Sd u0 {2,D} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([6.93,7.93,8.76,9.37,10.11,10.45,10.71],'cal/(mol*K)'), + H298 = (27.48,'kcal/mol'), + S298 = (16.58,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1192, + label = "C=S-CtCs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Ct u0 {1,S} +4 Cs u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([6.87,7.88,8.6,9.13,9.8,10.17,10.59],'cal/(mol*K)'), + H298 = (30.12,'kcal/mol'), + S298 = (17.46,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1193, + label = "C=S-CbCs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cb u0 {1,S} +4 Cs u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([8.02,9.02,9.75,10.23,10.75,10.96,11.04],'cal/(mol*K)'), + H298 = (26.6,'kcal/mol'), + S298 = (14.55,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1183, + label = "C=S-HH", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 H u0 {1,S} +4 H u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([9.08,10.34,11.51,12.5,14.07,15.25,17.14],'cal/(mol*K)'), + H298 = (27.71,'kcal/mol'), + S298 = (56.51,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1189, + label = "C=S-SsH", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Ss u0 {1,S} +4 H u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([8.38,9.78,10.83,11.66,12.86,13.71,14.87],'cal/(mol*K)'), + H298 = (21.55,'kcal/mol'), + S298 = (34.41,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1205, + label = "C=S-CSs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 C u0 {1,S} +4 Ss u0 {1,S} +""", + thermo = u'C=S-CsSs', + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CbSs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cb u0 {1,S} +4 Ss u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CdsSs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cd u0 {1,S} +4 Ss u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-C=SSs", + group = +""" +1 * CS u0 {2,S} {3,D} {4,S} +2 Cd u0 {1,S} {5,D} +3 Sd u0 {1,D} +4 Ss u0 {1,S} +5 Sd u0 {2,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cd)Ss", + group = +""" +1 * CS u0 {2,S} {3,D} {4,S} +2 Cd u0 {1,S} {5,D} +3 Sd u0 {1,D} +4 Ss u0 {1,S} +5 [Cd,Cdd,CO] u0 {2,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cds)Ss", + group = +""" +1 * CS u0 {2,S} {3,D} {4,S} +2 Cd u0 {1,S} {5,D} +3 Sd u0 {1,D} +4 Ss u0 {1,S} +5 Cd u0 {2,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd)Ss", + group = +""" +1 * CS u0 {2,S} {3,D} {4,S} +2 Cd u0 {1,S} {5,D} +3 Sd u0 {1,D} +4 Ss u0 {1,S} +5 Cdd u0 {2,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Cd)Ss", + group = +""" +1 * CS u0 {2,S} {4,D} {5,S} +2 Cd u0 {1,S} {3,D} +3 Cdd u0 {2,D} {6,D} +4 Sd u0 {1,D} +5 Ss u0 {1,S} +6 C u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-(Cds-Cdd-Sd)Ss", + group = +""" +1 * CS u0 {2,S} {4,D} {5,S} +2 Cd u0 {1,S} {3,D} +3 Cdd u0 {2,D} {6,D} +4 Sd u0 {1,D} +5 Ss u0 {1,S} +6 Sd u0 {3,D} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = -1, + label = "C=S-CtSs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Ct u0 {1,S} +4 Ss u0 {1,S} +""", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = 1206, + label = "C=S-CsSs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Cs u0 {1,S} +4 Ss u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([7.4,8.38,9.16,9.8,10.72,11.25,11.66],'cal/(mol*K)'), + H298 = (21.35,'kcal/mol'), + S298 = (14.52,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 GA 1D-HR Aaron Vandeputte 2010""", + longDesc = +u""" + +""", +) + +entry( + index = 1457, + label = "CS-OsH", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Os u0 {1,S} +4 H u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([4.48,5.3,6.09,6.82,8.05,8.99,10.37],'cal/(mol*K)'), + H298 = (2.85,'kcal/mol'), + S298 = (30.14,'cal/(mol*K)'), + ), + shortDesc = u"""CAC 1d-HR calc""", + longDesc = +u""" + +""", +) + +entry( + index = 1458, + label = "CS-CsOs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Os u0 {1,S} +4 Cs u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([3.9,4.17,4.6,5.1,6.08,6.76,7.44],'cal/(mol*K)'), + H298 = (-1.32,'kcal/mol'), + S298 = (8.62,'cal/(mol*K)'), + ), + shortDesc = u"""CAC 1d-HR calc""", + longDesc = +u""" + +""", +) + +entry( + index = 1459, + label = "CS-OsOs", + group = +""" +1 * CS u0 {2,D} {3,S} {4,S} +2 Sd u0 {1,D} +3 Os u0 {1,S} +4 Os u0 {1,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([3.08,3.59,3.9,4.03,3.99,3.75,3.23],'cal/(mol*K)'), + H298 = (-22.72,'kcal/mol'), + S298 = (2.67,'cal/(mol*K)'), + ), + shortDesc = u"""CAC CBS-QB3 1Dhr calc""", + longDesc = +u""" + +""", +) + entry( index = 329, label = "Cs", @@ -42686,6 +44141,78 @@ L4: Cds-CCN L5: Cd-CdCsN3s L5: Cd-CdCs(N5dOdOs) + L4: C=S-SsSs + L4: C=S-CH + L5: C=S-CsH + L5: C=S-CdsH + L6: C=S-(Cds-Cd)H + L7: C=S-(Cds-Cdd)H + L8: C=S-(Cds-Cdd-Cd)H + L8: C=S-(Cds-Cdd-Sd)H + L7: C=S-(Cds-Cds)H + L6: C=S-C=SH + L5: C=S-CtH + L5: C=S-CbH + L4: C=S-CC + L5: C=S-CbCds + L6: C=S-CbC=S + L6: C=S-Cb(Cds-Cd) + L7: C=S-Cb(Cds-Cds) + L7: C=S-Cb(Cds-Cdd) + L8: C=S-Cb(Cds-Cdd-Sd) + L8: C=S-Cb(Cds-Cdd-Cd) + L5: C=S-CtCt + L5: C=S-CbCb + L5: C=S-CdsCds + L6: C=S-(Cds-Cd)C=S + L7: C=S-(Cds-Cds)C=S + L7: C=S-(Cds-Cdd)C=S + L8: C=S-(Cds-Cdd-Cd)C=S + L8: C=S-(Cds-Cdd-Sd)C=S + L7: C=S-C=SC=S + L6: C=S-(Cds-Cd)(Cds-Cd) + L7: C=S-(Cds-Cdd)(Cds-Cds) + L8: C=S-(Cds-Cdd-Cd)(Cds-Cds) + L8: C=S-(Cds-Cdd-Sd)(Cds-Cds) + L7: C=S-(Cds-Cds)(Cds-Cds) + L7: C=S-(Cds-Cdd)(Cds-Cdd) + L8: C=S-(Cds-Cdd-Cd)(Cds-Cdd-Cd) + L8: C=S-(Cds-Cdd-Sd)(Cds-Cdd-Sd) + L8: C=S-(Cds-Cdd-Cd)(Cds-Cdd-Sd) + L5: C=S-CtCds + L6: C=S-Ct(Cds-Cd) + L7: C=S-Ct(Cds-Cds) + L7: C=S-Ct(Cds-Cdd) + L8: C=S-Ct(Cds-Cdd-Cd) + L8: C=S-Ct(Cds-Cdd-Sd) + L6: C=S-CtC=S + L5: C=S-CbCt + L5: C=S-CsCs + L5: C=S-CdsCs + L6: C=S-(Cds-Cd)Cs + L7: C=S-(Cds-Cds)Cs + L7: C=S-(Cds-Cdd)Cs + L8: C=S-(Cds-Cdd-Sd)Cs + L8: C=S-(Cds-Cdd-Cd)Cs + L6: C=S-C=SCs + L5: C=S-CtCs + L5: C=S-CbCs + L4: C=S-HH + L4: C=S-SsH + L4: C=S-CSs + L5: C=S-CbSs + L5: C=S-CdsSs + L6: C=S-C=SSs + L6: C=S-(Cds-Cd)Ss + L7: C=S-(Cds-Cds)Ss + L7: C=S-(Cds-Cdd)Ss + L8: C=S-(Cds-Cdd-Cd)Ss + L8: C=S-(Cds-Cdd-Sd)Ss + L5: C=S-CtSs + L5: C=S-CsSs + L4: CS-OsH + L4: CS-CsOs + L4: CS-OsOs L3: Cs L4: Cs-NHHH L5: Cs-N3sHHH From db2fae791259a6d8b57bee5e59f494d0c6eee759 Mon Sep 17 00:00:00 2001 From: Nathan Yee Date: Mon, 13 Jun 2016 16:18:46 -0400 Subject: [PATCH 07/21] Set references in training reaction to None instead of empty strings The saveEntry function expects either an Article object or None type. Empty strings cause an error. --- .../families/R_Addition_MultipleBond/training/reactions.py | 2 +- input/kinetics/families/intra_H_migration/training/reactions.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/input/kinetics/families/R_Addition_MultipleBond/training/reactions.py b/input/kinetics/families/R_Addition_MultipleBond/training/reactions.py index 951c9e8050..202b94966f 100644 --- a/input/kinetics/families/R_Addition_MultipleBond/training/reactions.py +++ b/input/kinetics/families/R_Addition_MultipleBond/training/reactions.py @@ -76,7 +76,7 @@ Ea = (6.589, 'kcal/mol', '+|-', 0.024), T0 = (1, 'K'), ), - reference = "", + reference = None, referenceType = "theory", shortDesc = u"""nyee TST calculations at CBS-QB3 level with hindered rotors level""", longDesc = diff --git a/input/kinetics/families/intra_H_migration/training/reactions.py b/input/kinetics/families/intra_H_migration/training/reactions.py index 39b5435032..9cf5b66c84 100644 --- a/input/kinetics/families/intra_H_migration/training/reactions.py +++ b/input/kinetics/families/intra_H_migration/training/reactions.py @@ -101,7 +101,7 @@ Ea = (8.231, 'kcal/mol', '+|-', 1.00), T0 = (1, 'K'), ), - reference = "", + reference = None, referenceType = "theory", shortDesc = u"""TST calculations at M08SO/MG3S level by edames""", longDesc = From 1e91b56310d5e0f264927740cb0883cdbccb61c8 Mon Sep 17 00:00:00 2001 From: Nathan Yee Date: Mon, 13 Jun 2016 17:27:35 -0400 Subject: [PATCH 08/21] Fix parent/child siblings for Disprop family Only changes the location of H rad and a formatting inconsistency in the tree. Functionally shouldn't make a difference but will past new suite of unit tests. --- input/kinetics/families/Disproportionation/groups.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/input/kinetics/families/Disproportionation/groups.py b/input/kinetics/families/Disproportionation/groups.py index f6dace9f0d..e0231c0cfd 100644 --- a/input/kinetics/families/Disproportionation/groups.py +++ b/input/kinetics/families/Disproportionation/groups.py @@ -2720,13 +2720,12 @@ L2: Y_2centerbirad L3: O2b L3: C2b - L3: S2b + L3: S2b L2: Y_1centerbirad L3: CO_birad_triplet L3: O_atom_triplet L3: CH2_triplet L3: NH_triplet - L2: H_rad L2: Y_rad L3: Ct_rad L4: Ct_rad/Ct @@ -2811,6 +2810,7 @@ L5: N3d_rad/N L3: N5_rad L4: N5d_rad + L3: H_rad L1: XH_Rrad_birad L2: XH_Rrad L3: XH_s_Rrad @@ -2852,7 +2852,7 @@ L6: C/H2/Nd_COrad L6: C/H2/Nd_Orad L6: C/H2/Nd_Nrad - L6: C/H2/Nd_Srad + L6: C/H2/Nd_Srad L5: C/H2/De_Rrad L6: C/H2/De_Csrad L7: C/H2/De_Csrad/H/Cd From 3f84e7ce9921bd240a689be7a278e38c5cfa5fde Mon Sep 17 00:00:00 2001 From: Nathan Yee Date: Mon, 13 Jun 2016 17:59:14 -0400 Subject: [PATCH 09/21] Fix Intra_RH_Add family labels All *2 should be *4 under the radadd tree in Intra_RH_Add_Endocyclic and Intra_RH_Add_Exocyclic --- .../Intra_RH_Add_Endocyclic/groups.py | 26 +++++++++---------- .../families/Intra_RH_Add_Exocyclic/groups.py | 26 +++++++++---------- 2 files changed, 26 insertions(+), 26 deletions(-) diff --git a/input/kinetics/families/Intra_RH_Add_Endocyclic/groups.py b/input/kinetics/families/Intra_RH_Add_Endocyclic/groups.py index 604136ef12..eac7abc6cd 100644 --- a/input/kinetics/families/Intra_RH_Add_Endocyclic/groups.py +++ b/input/kinetics/families/Intra_RH_Add_Endocyclic/groups.py @@ -1079,7 +1079,7 @@ group = """ 1 *1 Cs u0 {2,S} {3,S} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 H u0 {1,S} """, kinetics = None, @@ -1091,7 +1091,7 @@ group = """ 1 *1 Cs u0 {2,S} {3,S} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 [Cs,O] u0 {1,S} """, kinetics = None, @@ -1103,7 +1103,7 @@ group = """ 1 *1 Cs u0 {2,S} {3,S} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 [Cd,Ct,Cb,CO] u0 {1,S} """, kinetics = None, @@ -1115,7 +1115,7 @@ group = """ 1 *1 Cs u0 {2,S} {3,S} {4,S} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 [Cs,O] u0 {1,S} 4 [Cs,O] u0 {1,S} """, @@ -1128,7 +1128,7 @@ group = """ 1 *1 Cs u0 {2,S} {3,S} {4,S} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 [Cs,O] u0 {1,S} 4 [Cd,Ct,Cb,CO] u0 {1,S} """, @@ -1141,7 +1141,7 @@ group = """ 1 *1 Cs u0 {2,S} {3,S} {4,S} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 [Cd,Ct,Cb,CO] u0 {1,S} 4 [Cd,Ct,Cb,CO] u0 {1,S} """, @@ -1174,7 +1174,7 @@ group = """ 1 *1 Cd u0 {2,S} {3,S} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 R u0 {1,S} """, kinetics = None, @@ -1186,7 +1186,7 @@ group = """ 1 *1 Cd u0 {2,S} {3,S} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 H u0 {1,S} """, kinetics = None, @@ -1198,7 +1198,7 @@ group = """ 1 *1 Cd u0 {2,S} {3,S} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 [Cs,O] u0 {1,S} """, kinetics = None, @@ -1210,7 +1210,7 @@ group = """ 1 *1 Cd u0 {2,S} {3,S} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 [Cd,Ct,Cb,CO] u0 {1,S} """, kinetics = None, @@ -1222,7 +1222,7 @@ group = """ 1 *1 Cd u0 {2,S} {3,D} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 Cd u0 {1,D} """, kinetics = None, @@ -1234,7 +1234,7 @@ group = """ 1 *1 CO u0 {2,S} {3,D} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 O u0 {1,D} """, kinetics = None, @@ -1246,7 +1246,7 @@ group = """ 1 *1 Ct u0 {2,S} {3,T} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 Ct u0 {1,T} """, kinetics = None, diff --git a/input/kinetics/families/Intra_RH_Add_Exocyclic/groups.py b/input/kinetics/families/Intra_RH_Add_Exocyclic/groups.py index 96aa515df0..eadb841f4a 100644 --- a/input/kinetics/families/Intra_RH_Add_Exocyclic/groups.py +++ b/input/kinetics/families/Intra_RH_Add_Exocyclic/groups.py @@ -2548,7 +2548,7 @@ group = """ 1 *1 Cs u0 {2,S} {3,S} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 H u0 {1,S} """, kinetics = None, @@ -2560,7 +2560,7 @@ group = """ 1 *1 Cs u0 {2,S} {3,S} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 [Cs,O] u0 {1,S} """, kinetics = None, @@ -2572,7 +2572,7 @@ group = """ 1 *1 Cs u0 {2,S} {3,S} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 [Cd,Ct,Cb,CO] u0 {1,S} """, kinetics = None, @@ -2584,7 +2584,7 @@ group = """ 1 *1 Cs u0 {2,S} {3,S} {4,S} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 [Cs,O] u0 {1,S} 4 [Cs,O] u0 {1,S} """, @@ -2597,7 +2597,7 @@ group = """ 1 *1 Cs u0 {2,S} {3,S} {4,S} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 [Cs,O] u0 {1,S} 4 [Cd,Ct,Cb,CO] u0 {1,S} """, @@ -2610,7 +2610,7 @@ group = """ 1 *1 Cs u0 {2,S} {3,S} {4,S} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 [Cd,Ct,Cb,CO] u0 {1,S} 4 [Cd,Ct,Cb,CO] u0 {1,S} """, @@ -2643,7 +2643,7 @@ group = """ 1 *1 Cd u0 {2,S} {3,S} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 R u0 {1,S} """, kinetics = None, @@ -2655,7 +2655,7 @@ group = """ 1 *1 Cd u0 {2,S} {3,S} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 H u0 {1,S} """, kinetics = None, @@ -2667,7 +2667,7 @@ group = """ 1 *1 Cd u0 {2,S} {3,S} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 [Cs,O] u0 {1,S} """, kinetics = None, @@ -2679,7 +2679,7 @@ group = """ 1 *1 Cd u0 {2,S} {3,S} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 [Cd,Ct,Cb,CO] u0 {1,S} """, kinetics = None, @@ -2691,7 +2691,7 @@ group = """ 1 *1 Cd u0 {2,S} {3,D} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 Cd u0 {1,D} """, kinetics = None, @@ -2703,7 +2703,7 @@ group = """ 1 *1 CO u0 {2,S} {3,D} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 O u0 {1,D} """, kinetics = None, @@ -2715,7 +2715,7 @@ group = """ 1 *1 Ct u0 {2,S} {3,T} -2 *2 H u0 {1,S} +2 *4 H u0 {1,S} 3 Ct u0 {1,T} """, kinetics = None, From 9b9242f334a7d0737c0a5ad5dace3ebb332776b4 Mon Sep 17 00:00:00 2001 From: Nathan Yee Date: Mon, 13 Jun 2016 18:22:24 -0400 Subject: [PATCH 10/21] More explictly define groups for Intra_R_Add families I add explicit H atoms to the groups radadd_intra_CsHNd and radadd_intra_CsHDe, renamed and moved to correct place in tree. I'm not sure if this was the original intent, but the previous version had incorrect sibling parent/child relationship. The group labels are not consistent, and there were no rules with sources to help me make the decision, so I just made my best guess There is only one rule for each of these families anyhow, so this minor change won't have any effect for now. --- .../families/Intra_RH_Add_Endocyclic/groups.py | 14 ++++++++------ .../families/Intra_RH_Add_Exocyclic/groups.py | 14 ++++++++------ 2 files changed, 16 insertions(+), 12 deletions(-) diff --git a/input/kinetics/families/Intra_RH_Add_Endocyclic/groups.py b/input/kinetics/families/Intra_RH_Add_Endocyclic/groups.py index eac7abc6cd..2f50f08a2c 100644 --- a/input/kinetics/families/Intra_RH_Add_Endocyclic/groups.py +++ b/input/kinetics/families/Intra_RH_Add_Endocyclic/groups.py @@ -1087,24 +1087,26 @@ entry( index = 182, - label = "radadd_intra_csHNd", + label = "radadd_intra_csHHNd", group = """ -1 *1 Cs u0 {2,S} {3,S} +1 *1 Cs u0 {2,S} {3,S} {4,S} 2 *4 H u0 {1,S} 3 [Cs,O] u0 {1,S} +4 H u0 {1,S} """, kinetics = None, ) entry( index = 183, - label = "radadd_intra_csHDe", + label = "radadd_intra_csHHDe", group = """ -1 *1 Cs u0 {2,S} {3,S} +1 *1 Cs u0 {2,S} {3,S} {4,S} 2 *4 H u0 {1,S} 3 [Cd,Ct,Cb,CO] u0 {1,S} +4 H u0 {1,S} """, kinetics = None, ) @@ -1324,8 +1326,8 @@ L1: radadd_intra L2: radadd_intra_cs L3: radadd_intra_cs2H - L3: radadd_intra_csHNd - L3: radadd_intra_csHDe + L4: radadd_intra_csHHNd + L4: radadd_intra_csHHDe L3: radadd_intra_csNdNd L3: radadd_intra_csNdDe L3: radadd_intra_csDeDe diff --git a/input/kinetics/families/Intra_RH_Add_Exocyclic/groups.py b/input/kinetics/families/Intra_RH_Add_Exocyclic/groups.py index eadb841f4a..2489ef3240 100644 --- a/input/kinetics/families/Intra_RH_Add_Exocyclic/groups.py +++ b/input/kinetics/families/Intra_RH_Add_Exocyclic/groups.py @@ -2556,24 +2556,26 @@ entry( index = 182, - label = "radadd_intra_csHNd", + label = "radadd_intra_csHHNd", group = """ -1 *1 Cs u0 {2,S} {3,S} +1 *1 Cs u0 {2,S} {3,S} {4,S} 2 *4 H u0 {1,S} 3 [Cs,O] u0 {1,S} +4 H u0 {1,S} """, kinetics = None, ) entry( index = 183, - label = "radadd_intra_csHDe", + label = "radadd_intra_csHHDe", group = """ -1 *1 Cs u0 {2,S} {3,S} +1 *1 Cs u0 {2,S} {3,S} {4,S} 2 *4 H u0 {1,S} 3 [Cd,Ct,Cb,CO] u0 {1,S} +4 H u0 {1,S} """, kinetics = None, ) @@ -2886,8 +2888,8 @@ L1: radadd_intra L2: radadd_intra_cs L3: radadd_intra_cs2H - L3: radadd_intra_csHNd - L3: radadd_intra_csHDe + L4: radadd_intra_csHHNd + L4: radadd_intra_csHHDe L3: radadd_intra_csNdNd L3: radadd_intra_csNdDe L3: radadd_intra_csDeDe From 471a8a0846817cf9ff11c082aeab2b5a1d33cfee Mon Sep 17 00:00:00 2001 From: Nathan Yee Date: Mon, 13 Jun 2016 18:38:12 -0400 Subject: [PATCH 11/21] Fix sibling parent/child for intra_substitutionCS_isomerization Moved three groups that had this bug. --- .../families/intra_substitutionCS_isomerization/groups.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/input/kinetics/families/intra_substitutionCS_isomerization/groups.py b/input/kinetics/families/intra_substitutionCS_isomerization/groups.py index 0aa52625c6..e1d9014286 100644 --- a/input/kinetics/families/intra_substitutionCS_isomerization/groups.py +++ b/input/kinetics/families/intra_substitutionCS_isomerization/groups.py @@ -9,6 +9,8 @@ template(reactants=["XSYJ"], products=["XYSJ"], ownReverse=False) +reverse = "Ring_Opening_bySradical" + recipe(actions=[ ['BREAK_BOND', '*1', 'S', '*2'], ['FORM_BOND', '*1', 'S', '*3'], @@ -1595,10 +1597,10 @@ L4: CdsJ-Cd L3: CdsJ-2 L4: CdsJ_C-2 - L4: CdsJ_C-Cs2 - L4: CdsJ_C-Ss2 + L5: CdsJ_C-Cs2 + L5: CdsJ_C-Ss2 + L5: CdsJ_C-Cd2 L4: CdsJ_S-2 - L4: CdsJ_C-Cd2 L3: CsJ L4: CsJ-Cs L5: CsJ-CsHH From 434f98f5df66f9fb7a08aa8bd5639818cea41fee Mon Sep 17 00:00:00 2001 From: Nathan Yee Date: Mon, 13 Jun 2016 18:54:31 -0400 Subject: [PATCH 12/21] Fix sibling parent/child relationships for H_Abstraction Clarified adjlist for one group and moved another to correct parent. --- input/kinetics/families/H_Abstraction/groups.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/input/kinetics/families/H_Abstraction/groups.py b/input/kinetics/families/H_Abstraction/groups.py index f51b15018d..8811730822 100644 --- a/input/kinetics/families/H_Abstraction/groups.py +++ b/input/kinetics/families/H_Abstraction/groups.py @@ -533,10 +533,10 @@ label = "Cd/H/OneDe", group = """ -1 *1 C u0 {2,D} {3,S} {4,S} -2 Cd u0 {1,D} {5,S} -3 *2 H u0 {1,S} -4 [Cd,Ct,Cb,CO,CS,N] u0 {1,S} +1 *1 C u0 {2,D} {3,S} {4,S} +2 Cd u0 {1,D} {5,S} +3 *2 H u0 {1,S} +4 [Cd,Ct,Cb,CO,CS,N3d,N3t,N3b,N5d,N5dd,N5t,N5b] u0 {1,S} 5 R u0 {2,S} """, kinetics = None, @@ -6678,8 +6678,8 @@ L8: O_rad/Cd\Cs_Cd\H2 L8: O_rad/Cd\Cs_Cd\H\Cs L8: O_rad/Cd\Cs_Cd\Cs2 - L6: InChI=1S/NO3/c2-1(3)4 L6: O_rad/OneDeN + L7: InChI=1S/NO3/c2-1(3)4 L3: S_rad L4: S_pri_rad L4: S_sec_rad From f3a5a53af0025148d94b4f338653346343cd9e5c Mon Sep 17 00:00:00 2001 From: Nathan Yee Date: Mon, 13 Jun 2016 19:08:00 -0400 Subject: [PATCH 13/21] Fix sibling parent/child relationships for Cyclic_Ether_Formation Moved 6 groups in the tree --- .../families/Cyclic_Ether_Formation/groups.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/input/kinetics/families/Cyclic_Ether_Formation/groups.py b/input/kinetics/families/Cyclic_Ether_Formation/groups.py index f0eb95faa5..861d6b1f22 100644 --- a/input/kinetics/families/Cyclic_Ether_Formation/groups.py +++ b/input/kinetics/families/Cyclic_Ether_Formation/groups.py @@ -1245,26 +1245,26 @@ L3: R3OOJ L3: R3OOH L4: R3OOH_SS - L4: R3OOH_SSCO + L5: R3OOH_SSCO L4: R3OOH_SD L4: R3OOH_DS L3: R3OOR L4: R3OOR_SS - L4: R3OOR_SSCO + L5: R3OOR_SSCO L4: R3OOR_SD L4: R3OOR_DS L2: R4OO L3: R4OOJ L3: R4OOH L4: R4OOH_SSS - L4: R4OOH_SSSCO + L5: R4OOH_SSSCO L4: R4OOH_SSD L4: R4OOH_SDS L4: R4OOH_DSS L4: R4OOH_DSD L3: R4OOR L4: R4OOR_SSS - L4: R4OOR_SSSCO + L5: R4OOR_SSSCO L4: R4OOR_SSD L4: R4OOR_SDS L4: R4OOR_DSS @@ -1273,7 +1273,7 @@ L3: R5OOJ L3: R5OOH L4: R5OOH_SSSS - L4: R5OOH_SSSSCO + L5: R5OOH_SSSSCO L4: R5OOH_SSSD L4: R5OOH_SSDS L4: R5OOH_SDSS @@ -1282,7 +1282,7 @@ L4: R5OOH_DSDS L3: R5OOR L4: R5OOR_SSSS - L4: R5OOR_SSSSCO + L5: R5OOR_SSSSCO L4: R5OOR_SSSD L4: R5OOR_SSDS L4: R5OOR_SDSS From 28df61ddb937a9839db536e0e15af2035ba54868 Mon Sep 17 00:00:00 2001 From: Nathan Yee Date: Mon, 13 Jun 2016 19:14:44 -0400 Subject: [PATCH 14/21] Redefine one group in intra_H_migration to fix sibling parent/child bug --- input/kinetics/families/intra_H_migration/groups.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/input/kinetics/families/intra_H_migration/groups.py b/input/kinetics/families/intra_H_migration/groups.py index e18400033e..9d2be89dc2 100644 --- a/input/kinetics/families/intra_H_migration/groups.py +++ b/input/kinetics/families/intra_H_migration/groups.py @@ -3046,11 +3046,10 @@ entry( index = 198, - label = "C=S_rad_out", + label = "CS_rad_out", group = """ -1 *1 Cd u1 {2,D} -2 Sd u0 {1,D} +1 *1 CS u1 """, kinetics = None, ) @@ -4126,7 +4125,7 @@ L2: Ct_rad_out L2: Cb_rad_out L2: CO_rad_out - L2: C=S_rad_out + L2: CS_rad_out L2: C_rad_out_single L3: C_rad_out_2H L3: C_rad_out_1H From 1d47b07cc7e42b02c1e647608d591076cbde95a4 Mon Sep 17 00:00:00 2001 From: Nathan Yee Date: Tue, 14 Jun 2016 14:34:39 -0400 Subject: [PATCH 15/21] Fix groups in R_Addition_Multiple_Bond Based on the name and other groups on the same level, it looks like Ct-Cd_Ct-Cs was written with the incorrect AdjList. Also changed one instance of Cd=Sd to CS, which makes it accessible. --- .../families/R_Addition_MultipleBond/groups.py | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) diff --git a/input/kinetics/families/R_Addition_MultipleBond/groups.py b/input/kinetics/families/R_Addition_MultipleBond/groups.py index c8db130859..9b198b8930 100644 --- a/input/kinetics/families/R_Addition_MultipleBond/groups.py +++ b/input/kinetics/families/R_Addition_MultipleBond/groups.py @@ -13359,10 +13359,10 @@ label = "Ct-De_Ct-Cs", group = """ -1 *1 Ct u0 {2,T} {3,S} -2 *2 Ct u0 {1,T} {4,S} -3 [Cd,Ct,Cb,CO,N3d,N5d] u0 {1,S} -4 Cs u0 {2,S} +1 *1 Ct u0 {2,T} {3,S} +2 *2 Ct u0 {1,T} {4,S} +3 [Cd,Ct,Cb,CO,CS,N3d,N5d] u0 {1,S} +4 Cs u0 {2,S} """, kinetics = None, ) @@ -13400,9 +13400,8 @@ """ 1 *1 Ct u0 {2,T} {3,S} 2 *2 Ct u0 {1,T} {4,S} -3 Ct u0 {1,S} {5,T} +3 Cd u0 {1,S} 4 Cs u0 {2,S} -5 Ct u0 {3,T} """, kinetics = None, ) @@ -13423,14 +13422,13 @@ entry( index = 867, - label = "Ct-C=S_Ct-Cs", + label = "Ct-CS_Ct-Cs", group = """ 1 *1 Ct u0 {2,T} {3,S} 2 *2 Ct u0 {1,T} {4,S} -3 Cd u0 {1,S} {5,D} +3 CS u0 {1,S} 4 Cs u0 {2,S} -5 Sd u0 {3,D} """, kinetics = None, ) @@ -17657,7 +17655,7 @@ L5: Ct-CO_Ct-Cs L5: Ct-Cd_Ct-Cs L5: Ct-Ct_Ct-Cs - L5: Ct-C=S_Ct-Cs + L5: Ct-CS_Ct-Cs L4: Ct-De_Ct-De L5: Ct-Ct_Ct-Ct L5: Ct-Cd_Ct-Ct From fe0513677cb99a795e99b4b6d21350914f3f1652 Mon Sep 17 00:00:00 2001 From: Nathan Yee Date: Tue, 14 Jun 2016 15:28:27 -0400 Subject: [PATCH 16/21] Fix sibling child/parent bug for R_Addition_MultipleBond Moved two groups Cds-CdH_Cds-TwoDe and Cds-CdCs_Cds-TwoDe in the tree. --- .../R_Addition_MultipleBond/groups.py | 64 +++++++++---------- 1 file changed, 32 insertions(+), 32 deletions(-) diff --git a/input/kinetics/families/R_Addition_MultipleBond/groups.py b/input/kinetics/families/R_Addition_MultipleBond/groups.py index 9b198b8930..3e565be9f7 100644 --- a/input/kinetics/families/R_Addition_MultipleBond/groups.py +++ b/input/kinetics/families/R_Addition_MultipleBond/groups.py @@ -17263,22 +17263,22 @@ L9: Cds-CdH_Cds-COSs L9: Cds-CdH_Cds-CdSs L9: Cds-CdH_Cds-C=SSs - L7: Cds-CdH_Cds-TwoDe - L8: Cds-CdH_Cds-CtCt - L8: Cds-CdH_Cds-CtCb - L8: Cds-CdH_Cds-CtCO - L8: Cds-CdH_Cds-CbCb - L8: Cds-CdH_Cds-CbCO - L8: Cds-CdH_Cds-COCO - L8: Cds-CdH_Cds-CdCt - L8: Cds-CdH_Cds-CdCb - L8: Cds-CdH_Cds-CdCO - L8: Cds-CdH_Cds-CtC=S - L8: Cds-CdH_Cds-CbC=S - L8: Cds-CdH_Cds-COC=S - L8: Cds-CdH_Cds-CdCd - L8: Cds-CdH_Cds-CdC=S - L8: Cds-CdH_Cds-C=SC=S + L8: Cds-CdH_Cds-TwoDe + L9: Cds-CdH_Cds-CtCt + L9: Cds-CdH_Cds-CtCb + L9: Cds-CdH_Cds-CtCO + L9: Cds-CdH_Cds-CbCb + L9: Cds-CdH_Cds-CbCO + L9: Cds-CdH_Cds-COCO + L9: Cds-CdH_Cds-CdCt + L9: Cds-CdH_Cds-CdCb + L9: Cds-CdH_Cds-CdCO + L9: Cds-CdH_Cds-CtC=S + L9: Cds-CdH_Cds-CbC=S + L9: Cds-CdH_Cds-COC=S + L9: Cds-CdH_Cds-CdCd + L9: Cds-CdH_Cds-CdC=S + L9: Cds-CdH_Cds-C=SC=S L6: Cds-C=SH_Cds L5: Cds-OneDeCs_Cds L6: Cds-CtCs_Cds @@ -17422,22 +17422,22 @@ L9: Cds-CdCs_Cds-COSs L9: Cds-CdCs_Cds-CdSs L9: Cds-CdCs_Cds-C=SSs - L7: Cds-CdCs_Cds-TwoDe - L8: Cds-CdCs_Cds-CtCt - L8: Cds-CdCs_Cds-CtCb - L8: Cds-CdCs_Cds-CtCO - L8: Cds-CdCs_Cds-CbCb - L8: Cds-CdCs_Cds-CbCO - L8: Cds-CdCs_Cds-COCO - L8: Cds-CdCs_Cds-CdCt - L8: Cds-CdCs_Cds-CdCb - L8: Cds-CdCs_Cds-CdCO - L8: Cds-CdCs_Cds-CtC=S - L8: Cds-CdCs_Cds-CbC=S - L8: Cds-CdCs_Cds-COC=S - L8: Cds-CdCs_Cds-CdCd - L8: Cds-CdCs_Cds-CdC=S - L8: Cds-CdCs_Cds-C=SC=S + L8: Cds-CdCs_Cds-TwoDe + L9: Cds-CdCs_Cds-CtCt + L9: Cds-CdCs_Cds-CtCb + L9: Cds-CdCs_Cds-CtCO + L9: Cds-CdCs_Cds-CbCb + L9: Cds-CdCs_Cds-CbCO + L9: Cds-CdCs_Cds-COCO + L9: Cds-CdCs_Cds-CdCt + L9: Cds-CdCs_Cds-CdCb + L9: Cds-CdCs_Cds-CdCO + L9: Cds-CdCs_Cds-CtC=S + L9: Cds-CdCs_Cds-CbC=S + L9: Cds-CdCs_Cds-COC=S + L9: Cds-CdCs_Cds-CdCd + L9: Cds-CdCs_Cds-CdC=S + L9: Cds-CdCs_Cds-C=SC=S L6: Cds-C=SCs_Cds L5: Cds-OneDeSs_Cds L6: Cds-CtSs_Cds From 129d1e5a96e52044d21af4d087f622e8f344b1c4 Mon Sep 17 00:00:00 2001 From: Nathan Yee Date: Tue, 14 Jun 2016 17:06:05 -0400 Subject: [PATCH 17/21] Clarify some groups in statmech to avoid sibling bug It looks like some of these groups were added before we had enabled lone pairs in the Adjlist. As such they tried to incorperate both triplet/singlet and doublet/quartet in the one node. However, this made the tree fail the sibling child/parent check. For now, I have removed the possibility for singlet bi-rads and doublet tri-rads. Additionally the Nitrites group was just written incorrectly from the start. I have added one extra atom to the Adjlist after consulting with alongd --- input/statmech/groups/groups.py | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/input/statmech/groups/groups.py b/input/statmech/groups/groups.py index f68c96c9e1..c63e7a9847 100644 --- a/input/statmech/groups/groups.py +++ b/input/statmech/groups/groups.py @@ -9,7 +9,7 @@ entry( index = -1, label = "R!H", - group = "OR{R!Hx0, R!Hx1, R!Hx2, R!Hx3}", + group = "OR{R!Hx0, R!Hx1, R!Hx2_trip, R!Hx3_quart}", statmech = None, shortDesc = u"""""", longDesc = @@ -901,7 +901,8 @@ """ 1 * N u0 {2,D} {3,S} 2 O u0 {1,D} -3 O u0 {1,S} +3 O u0 {1,S} {4,S} +4 R u0 {3,S} """, statmech = GroupFrequencies( frequencies = [ @@ -1244,10 +1245,10 @@ entry( index = -1, - label = "R!Hx2", + label = "R!Hx2_trip", group = """ -1 * R!H u[0,2] +1 * R!H u2 """, statmech = None, shortDesc = u"""""", @@ -1329,10 +1330,10 @@ entry( index = -1, - label = "R!Hx3", + label = "R!Hx3_quart", group = """ -1 * R!H u[1,3] +1 * R!H u3 """, statmech = None, shortDesc = u"""""", @@ -1391,12 +1392,12 @@ L4: RsCrsR2 L3: O_R1 L4: Oxy - L2: R!Hx2 + L2: R!Hx2_trip L3: C_R2 L4: RsCHrr L4: RdCrr L4: RsCrrsR - L2: R!Hx3 + L2: R!Hx3_quart """ ) From a5d14ffbbfde244235facc140843163d5f5ca678 Mon Sep 17 00:00:00 2001 From: Nathan Yee Date: Tue, 14 Jun 2016 17:28:16 -0400 Subject: [PATCH 18/21] Moved four groups to fix sibling child/parent in statmech In addition to moving them, I changed the atomTypes on a few to make them more explicit. --- input/statmech/groups/groups.py | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/input/statmech/groups/groups.py b/input/statmech/groups/groups.py index c63e7a9847..e5deaea39f 100644 --- a/input/statmech/groups/groups.py +++ b/input/statmech/groups/groups.py @@ -618,7 +618,7 @@ group = """ 1 * N u0 {2,S} {5,S} {6,S} -2 C u0 {1,S} {3,S} {4,D} +2 CO u0 {1,S} {3,S} {4,D} 3 C u0 {2,S} 4 O u0 {2,D} 5 H u0 {1,S} @@ -660,7 +660,7 @@ group = """ 1 * N u0 {2,S} {5,S} {6,S} -2 C u0 {1,S} {3,S} {4,D} +2 CO u0 {1,S} {3,S} {4,D} 3 C u0 {2,S} 4 O u0 {2,D} 5 C u0 {1,S} @@ -694,7 +694,7 @@ group = """ 1 * N u0 {2,S} {5,S} {6,S} -2 C u0 {1,S} {3,S} {4,D} +2 CO u0 {1,S} {3,S} {4,D} 3 C u0 {2,S} 4 O u0 {2,D} 5 C u0 {1,S} @@ -729,10 +729,10 @@ """ 1 * N u0 {2,S} {3,S} {6,S} 2 H u0 {1,S} -3 C u0 {1,S} {4,D} {5,S} +3 CO u0 {1,S} {4,D} {5,S} 4 O u0 {3,D} 5 R u0 {3,S} -6 C u0 {1,S} {7,D} {8,S} +6 CO u0 {1,S} {7,D} {8,S} 7 O u0 {6,D} 8 R u0 {6,S} """, @@ -1369,13 +1369,13 @@ L4: COOC L4: Peroxy L3: N_R0 - L4: Amide_pri - L4: Amide_sec - L4: Amide_ter - L4: Imide L4: Amine_pri + L5: Amide_pri L4: Amine_sec + L5: Amide_sec + L5: Imide L4: Amine_ter + L5: Amide_ter L4: Nitrile L4: Nitroso L5: Nitrites From d20fd02c5eef09794763c1334cc9b09a3b028de6 Mon Sep 17 00:00:00 2001 From: Nathan Yee Date: Tue, 14 Jun 2016 18:08:14 -0400 Subject: [PATCH 19/21] Move a groups to fix sibling bug in transport --- input/transport/groups/nonring.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/input/transport/groups/nonring.py b/input/transport/groups/nonring.py index c04da675cf..77a4db7202 100644 --- a/input/transport/groups/nonring.py +++ b/input/transport/groups/nonring.py @@ -617,8 +617,8 @@ L3: CdH2R L3: CdR3 L4: Ketone_Ccentered - L4: Acid_Ccentered - L4: Ester_Ccentered + L5: Acid_Ccentered + L5: Ester_Ccentered L3: CdHR2 L4: Aldehyde_Ccentered L3: CddR2 @@ -632,9 +632,9 @@ L4: Ester_Ocentered1 L3: Od L4: Ketone_Ocentered + L5: Acid_Ocentered2 + L5: Ester_Ocentered2 L4: Aldehyde_Ocentered - L4: Acid_Ocentered2 - L4: Ester_Ocentered2 L2: S_centered L3: Thiol L3: Thioether From a48a1f4f7ab3cd332992c4f40138e201c5873ada Mon Sep 17 00:00:00 2001 From: Nathan Yee Date: Wed, 15 Jun 2016 14:42:39 -0400 Subject: [PATCH 20/21] Add sibling check for transport, kinetic families, solvation, statmech and solvation --- testing/databaseTest.py | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/testing/databaseTest.py b/testing/databaseTest.py index 5166794ed9..b1065be6fc 100644 --- a/testing/databaseTest.py +++ b/testing/databaseTest.py @@ -129,6 +129,12 @@ def test_solvation(self): test.description = test_name self.compat_func_name = test_name yield test, group_name + + test = lambda x: self.general_checkSiblingsForParents(group_name, group) + test_name = "Solvation groups {0}: sibling relationships are correct?".format(group_name) + test.description = test_name + self.compat_func_name = test_name + yield test, group_name def test_statmech(self): for group_name, group in self.database.statmech.groups.iteritems(): @@ -150,6 +156,12 @@ def test_statmech(self): self.compat_func_name = test_name yield test, group_name + test = lambda x: self.general_checkSiblingsForParents(group_name, group) + test_name = "Statmech groups {0}: sibling relationships are correct?".format(group_name) + test.description = test_name + self.compat_func_name = test_name + yield test, group_name + def test_transport(self): for group_name, group in self.database.transport.groups.iteritems(): test = lambda x: self.general_checkNodesFoundInTree(group_name, group) @@ -169,6 +181,12 @@ def test_transport(self): test.description = test_name self.compat_func_name = test_name yield test, group_name + + test = lambda x: self.general_checkSiblingsForParents(group_name, group) + test_name = "Transport groups {0}: sibling relationships are correct?".format(group_name) + test.description = test_name + self.compat_func_name = test_name + yield test, group_name # These are the actual tests, that don't start with a "test_" name: def kinetics_checkCorrectNumberofNodesInRules(self, family_name): @@ -259,6 +277,26 @@ def kinetics_checkChildParentRelationships(self, family_name): nose.tools.assert_true(family.matchNodeToChild(ancestorNode, childNode), "In {family} family, group {ancestor} is not a proper ancestor of its child {child}.".format(family=family_name, ancestor=ancestorNode, child=nodeName)) + def kinetics__checkSiblingsForParents(self, family_name): + """ + This test checks that siblings in a tree are not actually parent/child + """ + from rmgpy.data.base import Database + originalFamily = self.database.kinetics.families[family_name] + family = Database() + family.entries = originalFamily.groups.entries + for nodeName, node in family.entries.iteritems(): + #Some families also construct a 2-level trees (root with all entries down one level) + #We don't care about this tree as it is not used in searching, so we ignore products + if node in family.forwardTemplate.products: continue + for index, child1 in enumerate(node.children): + for child2 in node.children[index+1:]: + #Don't check a node against itself + if child1 is child2: continue + nose.tools.assert_false(family.matchNodeToChild(child1, child2), + "In {0} group, node {1} is written as a sibling of {2}, when it is actually a parent.".format(group_name, child1, child2)) + + def kinetics_checkAdjlistsNonidentical(self, database): """ This test checks whether adjacency lists of reactants in a KineticsDepository or KineticsLibrary database object are nonidentical. From 253b662facd35b061ac562d1549acb4b4b2f5c71 Mon Sep 17 00:00:00 2001 From: Nathan Yee Date: Wed, 15 Jun 2016 18:29:31 -0400 Subject: [PATCH 21/21] Fix bug with sibling check Previously only checked siblings in one directions, now the test checks in both directions --- testing/databaseTest.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/testing/databaseTest.py b/testing/databaseTest.py index b1065be6fc..a9fc1013cc 100644 --- a/testing/databaseTest.py +++ b/testing/databaseTest.py @@ -295,7 +295,8 @@ def kinetics__checkSiblingsForParents(self, family_name): if child1 is child2: continue nose.tools.assert_false(family.matchNodeToChild(child1, child2), "In {0} group, node {1} is written as a sibling of {2}, when it is actually a parent.".format(group_name, child1, child2)) - + nose.tools.assert_false(family.matchNodeToChild(child2, child1), + "In {0} group, node {1} is written as a sibling of {2}, when it is actually a parent.".format(group_name, child2, child1)) def kinetics_checkAdjlistsNonidentical(self, database): """ @@ -406,6 +407,7 @@ def general_checkSiblingsForParents(self, group_name, group): if child1 is child2: continue nose.tools.assert_false(group.matchNodeToChild(child1, child2), "In {0} group, node {1} is written as a sibling of {2}, when it is actually a parent.".format(group_name, child1, child2)) - + nose.tools.assert_false(group.matchNodeToChild(child2, child1), + "In {0} group, node {1} is written as a sibling of {2}, when it is actually a parent.".format(group_name, child2, child1)) if __name__ == '__main__': nose.run(argv=[__file__, '-v', '--nologcapture'], defaultTest=__name__)