Merge pull request #128 from ReactionMechanismGenerator/entryAcessibi…

…lity Entry acessibility
ReactionMechanismGenerator · Sep 15, 2016 · 8dd0154 · 8dd0154
2 parents e6ce739 + a5e92e8
commit 8dd0154
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diff --git a/.travis.yml b/.travis.yml
@@ -34,6 +34,7 @@ install:
 
 script:
   - make test-database
+  - make test
   - cd $TRAVIS_BUILD_DIR
 
 after_success:

diff --git a/input/solvation/groups/abraham.py b/input/solvation/groups/abraham.py
@@ -338,15 +338,16 @@
 """,
 )
 
+
 entry(
     index = 37,
-    label = "Cb-noH",
+    label = "Cbf-noH",
     group = 
 """
-1 * Cb  u0 {2,B} {3,B} {4,B}
+1 * Cbf u0 {2,B} {3,B} {4,B}
 2   R!H u0 {1,B}
-3   R!H u0 {1,B}
-4   R!H u0 {1,B}
+3   R!H  u0 {1,B}
+4   R!H  u0 {1,B}
 """,
     solute = SoluteData(
         S = 0.101,
@@ -1120,37 +1121,38 @@
 
 """,
 )
-
-entry(
-    index = 35,
-    label = "SdsOsOdOd",
-    group = 
-"""
-1 * Sd u0 {2,D} {3,D} {4,S} {5,S}
-2   Od u0 {1,D}
-3   Od u0 {1,D}
-4   Os u0 {1,S}
-5   R  u0 {1,S}
-""",
-    solute = SoluteData(
-        S = -0.505,
-        B = -0.188,
-        E = 0.0,
-        L = 0.0,
-        A = 0.0,
-    ),
-    shortDesc = u"""Platts fragment 35 sulfonate""",
-    longDesc = 
-u"""
-
-""",
-)
+#removed until we have aromatic sulfurs
+# entry(
+#     index = 35,
+#     label = "SdsOsOdOd",
+#     group = 
+# """
+# 1 * Sd u0 {2,D} {3,D} {4,S} {5,S}
+# 2   Od u0 {1,D}
+# 3   Od u0 {1,D}
+# 4   Os u0 {1,S}
+# 5   R  u0 {1,S}
+# """,
+#     solute = SoluteData(
+#         S = -0.505,
+#         B = -0.188,
+#         E = 0.0,
+#         L = 0.0,
+#         A = 0.0,
+#     ),
+#     shortDesc = u"""Platts fragment 35 sulfonate""",
+#     longDesc = 
+# u"""
+
+# """,
+# )
 
 tree(
 """
 L1: R
     L2: C
         L3: Cbf
+            L4: Cbf-noH
         L3: Css
             L4: CssH3
             L4: CssH2
@@ -1164,7 +1166,6 @@
             L4: CtOt
         L3: Cdd
         L3: Cb
-            L4: Cb-noH
             L4: Cb-H
             L4: Cb-noHnoRing
     L2: O
@@ -1200,7 +1201,6 @@
             L4: Ss-aromatic
         L3: Sd
             L4: Sds
-                L5: SdsOsOdOd
 """
 )
 
diff --git a/input/solvation/groups/nonacentered.py b/input/solvation/groups/nonacentered.py
@@ -557,9 +557,9 @@
     label = "OxR3",
     group = 
 """
-1 * Os u0 {2,S} {3,S}
-2   R  u0 {1,S} {3,[S,D,B]}
-3   R  u0 {1,S} {2,[S,D,B]}
+1 * Os  u0 {2,S} {3,S}
+2   R!H u0 {1,S} {3,[S,D,B]}
+3   R!H u0 {1,S} {2,[S,D,B]}
 """,
     solute = None,
     shortDesc = u"""O in a 3 membered ring""",
@@ -574,10 +574,10 @@
     label = "OxR4",
     group = 
 """
-1 * Os u0 {2,S} {4,S}
-2   R  u0 {1,S} {3,[S,D,B]}
-3   R  u0 {2,[S,D,B]} {4,[S,D,B]}
-4   R  u0 {1,S} {3,[S,D,B]}
+1 * Os  u0 {2,S} {4,S}
+2   R!H u0 {1,S} {3,[S,D,B]}
+3   R!H u0 {2,[S,D,B]} {4,[S,D,B]}
+4   R!H u0 {1,S} {3,[S,D,B]}
 """,
     solute = None,
     shortDesc = u"""O in a 4 membered ring""",
@@ -592,11 +592,11 @@
     label = "OxR5",
     group = 
 """
-1 * Os u0 {2,S} {5,S}
-2   R  u0 {1,S} {3,[S,D,B]}
-3   R  u0 {2,[S,D,B]} {4,[S,D,B]}
-4   R  u0 {3,[S,D,B]} {5,[S,D,B]}
-5   R  u0 {1,S} {4,[S,D,B]}
+1 * Os  u0 {2,S} {5,S}
+2   R!H u0 {1,S} {3,[S,D,B]}
+3   R!H u0 {2,[S,D,B]} {4,[S,D,B]}
+4   R!H u0 {3,[S,D,B]} {5,[S,D,B]}
+5   R!H u0 {1,S} {4,[S,D,B]}
 """,
     solute = None,
     shortDesc = u"""O in a 5 membered ring""",
@@ -611,12 +611,12 @@
     label = "OxR6",
     group = 
 """
-1 * Os u0 {2,S} {6,S}
-2   R  u0 {1,S} {3,[S,D,B]}
-3   R  u0 {2,[S,D,B]} {4,[S,D,B]}
-4   R  u0 {3,[S,D,B]} {5,[S,D,B]}
-5   R  u0 {4,[S,D,B]} {6,[S,D,B]}
-6   R  u0 {1,S} {5,[S,D,B]}
+1 * Os  u0 {2,S} {6,S}
+2   R!H u0 {1,S} {3,[S,D,B]}
+3   R!H u0 {2,[S,D,B]} {4,[S,D,B]}
+4   R!H u0 {3,[S,D,B]} {5,[S,D,B]}
+5   R!H u0 {4,[S,D,B]} {6,[S,D,B]}
+6   R!H u0 {1,S} {5,[S,D,B]}
 """,
     solute = None,
     shortDesc = u"""O in a 6 membered ring""",
@@ -631,13 +631,13 @@
     label = "OxR7",
     group = 
 """
-1 * Os u0 {2,S} {7,S}
-2   R  u0 {1,S} {3,[S,D,B]}
-3   R  u0 {2,[S,D,B]} {4,[S,D,B]}
-4   R  u0 {3,[S,D,B]} {5,[S,D,B]}
-5   R  u0 {4,[S,D,B]} {6,[S,D,B]}
-6   R  u0 {5,[S,D,B]} {7,[S,D,B]}
-7   R  u0 {1,S} {6,[S,D,B]}
+1 * Os  u0 {2,S} {7,S}
+2   R!H u0 {1,S} {3,[S,D,B]}
+3   R!H u0 {2,[S,D,B]} {4,[S,D,B]}
+4   R!H u0 {3,[S,D,B]} {5,[S,D,B]}
+5   R!H u0 {4,[S,D,B]} {6,[S,D,B]}
+6   R!H u0 {5,[S,D,B]} {7,[S,D,B]}
+7   R!H u0 {1,S} {6,[S,D,B]}
 """,
     solute = None,
     shortDesc = u"""O in a 7 membered ring""",
@@ -647,29 +647,30 @@
 """,
 )
 
-entry(
-    index = 26,
-    label = "SdOdOdN",
-    group = 
-"""
-1 * Sd u0 {2,D} {3,D} {4,S}
-2   Od u0 {1,D}
-3   Od u0 {1,D}
-4   N  u0 {1,S}
-""",
-    solute = SoluteData(
-        S = -0.569,
-        B = -0.446,
-        E = -0.111,
-        L = 0.0,
-        A = 0.356,
-    ),
-    shortDesc = u"""Platts group 51 sulfonamide -S(O)(O)N- (and fragment 13 for A)""",
-    longDesc = 
-u"""
+#temporarily removed until multivalent Sulfur is implemented
+# entry(
+#     index = 26,
+#     label = "SdOdOdN",
+#     group = 
+# """
+# 1 * Sd u0 {2,D} {3,D} {4,S}
+# 2   Od u0 {1,D}
+# 3   Od u0 {1,D}
+# 4   N  u0 {1,S}
+# """,
+#     solute = SoluteData(
+#         S = -0.569,
+#         B = -0.446,
+#         E = -0.111,
+#         L = 0.0,
+#         A = 0.356,
+#     ),
+#     shortDesc = u"""Platts group 51 sulfonamide -S(O)(O)N- (and fragment 13 for A)""",
+#     longDesc = 
+# u"""
 
-""",
-)
+# """,
+# )
 
 entry(
     index = 30,
@@ -861,21 +862,21 @@
 """
 L1: R
     L2: CO
+        L3: Lac
+            L4: Lac3
+            L4: Lac4
+            L4: Lac5
+            L4: Lac6
         L3: Oss(CdsOd)
-            L4: Lac
-                L5: Lac3
-                L5: Lac4
-                L5: Lac5
-                L5: Lac6
         L3: Oss(CdsOd)Oss
         L3: OssH(CdsOd)
         L3: Cd(Od)Cd=CdCd(Od)
+        L3: Lactam
+            L4: Lactam4
+            L4: Lactam5
+            L4: Lactam6
+            L4: Lactam7        
         L3: Cd(Od)N
-            L4: Lactam
-                L5: Lactam4
-                L5: Lactam5
-                L5: Lactam6
-                L5: Lactam7
             L4: NCd(Od)N
             L4: OsCd(Od)N
             L4: Cd(Od)NCd(Od)
@@ -889,12 +890,11 @@
         L3: OxR5
         L3: OxR6
         L3: OxR7
-    L2: SdOdOdN
     L2: N3sH2-benz
+    L2: N3sHCd(Od)N3sH
     L2: Cd(Od)NH2
     L2: Cd(Od)NHR
         L3: Cd(Od)NH-arom
-    L2: N3sHCd(Od)N3sH
     L2: N3sCd(Od)N3sH
     L2: CdsNdNsNs
 """

diff --git a/input/statmech/groups/groups.py b/input/statmech/groups/groups.py
@@ -929,7 +929,7 @@
     label = "Nitro",
     group = 
 """
-1 * N   u0 {2,D} {3,S} {4,S}
+1 * N5d u0 {2,D} {3,S} {4,S}
 2   O   u0 {1,D}
 3   O   u0 {1,S}
 4   R!H ux {1,S}
@@ -962,10 +962,10 @@
     label = "Nitrates",
     group = 
 """
-1 * N u0 {2,D} {3,S} {4,S}
-2   O u0 {1,D}
-3   O u0 {1,S}
-4   O u0 {1,S}
+1 * N5d u0 {2,D} {3,S} {4,S}
+2   O   u0 {1,D}
+3   O   u0 {1,S}
+4   O   u0 {1,S}
 """,
     statmech = GroupFrequencies(
         frequencies = [
@@ -1377,9 +1377,9 @@
                 L5: Amide_ter
             L4: Nitrile
             L4: Nitroso
-                L5: Nitrites
                 L5: Nitro
                     L6: Nitrates
+                L5: Nitrites
     L2: R!Hx1
         L3: C_R1
             L4: RsCH2r