Added API degradation relevant kinetic families

input/kinetics/families/HOCK_rearrangement/groups.py

@@ -0,0 +1,50 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "HOCK_rearrangement/groups"
+shortDesc = u""
+longDesc = u"""
+he Hock fragmentation (or rearrangement) is a well-known reaction for benzylic, allylic and dienylic hydroperoxides. 
+This family describes reactions of the sort:
+CC-OOH + [H+] <=>  CC-O[OH2+] <=RDS=> C-O-[C+] + H2O <=> C-O-C-[OH2+] <=> C-[OH+]-C-OH <=> C-OH + C=O
+overall taken as:
+CC-OOH <=> C-OH + C=O
+atom labels:
+C(*1)C(*2)-O(*3)O(*4)H <=> C(*1)-O(*4)H + C(*2)=O(*3)
+"""
+
+template(reactants=["CC-OOH"], products=["COH", "C=O"], ownReverse=False)
+
+reverse = "reverse_HOCK"
+
+reversible = True
+
+only_forward = True
+
+recipe(actions=[
+    ['BREAK_BOND', '*1', 1, '*2'],
+    ['BREAK_BOND', '*3', 1, '*4'],
+    ['FORM_BOND', '*1', 1, '*4'],
+    ['CHANGE_BOND', '*2', 1, '*3'],
+])
+
+entry(
+    index = 0,
+    label = "CC-OOH",
+    group =
+"""
+1     R!H u0 p0 c0 {2,D}
+2  *1 C   u0 p0 c0 {1,D} {3,S}
+3  *2 C   u0 p0 c0 {2,S} {4,S}
+4  *3 O   u0 p2 c0 {3,S} {5,S}
+5  *4 O   u0 p2 c0 {4,S} {6,S}
+6     H   u0 p0 c0 {5,S}
+""",
+    kinetics = None,
+)
+
+tree(
+"""
+L1: CC-OOH
+"""
+)

input/kinetics/families/HOCK_rearrangement/rules.py

@@ -0,0 +1,22 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "HOCK_rearrangement/rules"
+shortDesc = u""
+longDesc = u"""
+"""
+
+entry(
+    index = 0,
+    label = "CC-OOH",
+    kinetics = ArrheniusEP(
+        A = (3e+6, 's^-1'),
+        n = 0,
+        alpha = 0,
+        E0 = (8, 'kcal/mol'),
+        Tmin = (300, 'K'),
+        Tmax = (1500, 'K'),
+    ),
+    rank = 0,
+    shortDesc = u"""Default""",
+)

input/kinetics/families/HOCK_rearrangement/training/reactions.py

@@ -0,0 +1,9 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "HOCK_rearrangement/training"
+shortDesc = u"Reaction kinetics used to generate rate rules"
+longDesc = u"""
+Put kinetic parameters for specific reactions in this file to use as a
+training set for generating rate rules to populate this kinetics family.
+"""

input/kinetics/families/acetal_hydrolysis/groups.py

@@ -0,0 +1,131 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "acetal_hydrolysis/groups"
+shortDesc = u""
+longDesc = u"""
+This family describes hydrolysis of an acetal species (two esters), R1C(OR2)OR3.
+The reaction is acid-catalyzed, the template here does not consider a pH effect.
+R1C(OR2)OR3 + H2O <=> R1C(OR2)OH + R3OH
+
+atom labels:
+
+R1_C_(O_R2)_O[*1]_R3[*2] + H[*3]_O[*4]_H <=> R1_C_(O_R2)_O[*1]_H[*3] + R3[*2]_O[*4]_H
+
+Some rate data is available here: https://doi.org/10.1021/ja00406a036
+"""
+
+template(reactants=["acetal", "H2O"], products=["hemiacetal", "alcohol"], ownReverse=False)
+
+reverse = "alcohol_hemiacetal_condensation"
+
+reversible = True
+
+only_forward = True
+
+recipe(actions=[
+    ['BREAK_BOND', '*1', 1, '*2'],
+    ['BREAK_BOND', '*3', 1, '*4'],
+    ['FORM_BOND', '*1', 1, '*3'],
+    ['FORM_BOND', '*2', 1, '*4'],
+])
+
+entry(
+    index=0,
+    label="acetal",
+    group=
+"""
+1     Cs u0 p0 c0 {2,S} {3,S} {4,S}
+2  *1 O  u0 p2 c0 {1,S} {5,S}
+3     O  u0 p2 c0 {1,S} {6,S}
+4     H  u0 p0 c0 {1,S}
+5  *2 R!H ux px cx {2,S}
+6     R!H ux px cx {3,S}
+""",
+    kinetics=None,
+)
+
+entry(
+    index=1,
+    label="H2O",
+    group=
+"""
+1 *4 O u0 p2 c0 {2,S} {3,S}
+2 *3 H u0 p0 c0 {1,S}
+3    H u0 p0 c0 {1,S}
+""",
+    kinetics=None,
+)
+
+entry(
+    index=2,
+    label="erythromycin_functional",
+    group=
+"""
+1  C u0 p0 c0 {2,S} {17,S} {18,S} {19,S}
+2  *2 C u0 p0 c0 {1,S} {3,S} {14,S} {20,S}
+3  *1 O u0 p2 c0 {2,S} {4,S}
+4  Cs u0 p0 c0 {3,S} {5,S} {12,S} {21,S}
+5  O u0 p2 c0 {4,S} {6,S}
+6  C u0 p0 c0 {5,S} {7,S} {22,S} {23,S}
+7  C u0 p0 c0 {6,S} {8,S} {24,S} {25,S}
+8  C u0 p0 c0 {7,S} {9,S} {12,S} {26,S}
+9  N u0 p1 c0 {8,S} {10,S} {11,S}
+10 C u0 p0 c0 {9,S} {27,S} {28,S} {29,S}
+11 C u0 p0 c0 {9,S} {30,S} {31,S} {32,S}
+12 C u0 p0 c0 {4,S} {8,S} {13,S} {33,S}
+13 O u0 p2 c0 {12,S} {34,S}
+14 C u0 p0 c0 {2,S} {15,S} {16,S} {35,S}
+15 O u0 p2 c0 {14,S} {36,S}
+16 C u0 p0 c0 {14,S} {37,S} {38,S} {39,S}
+17 H u0 p0 c0 {1,S}
+18 H u0 p0 c0 {1,S}
+19 H u0 p0 c0 {1,S}
+20 H u0 p0 c0 {2,S}
+21 H u0 p0 c0 {4,S}
+22 H u0 p0 c0 {6,S}
+23 H u0 p0 c0 {6,S}
+24 H u0 p0 c0 {7,S}
+25 H u0 p0 c0 {7,S}
+26 H u0 p0 c0 {8,S}
+27 H u0 p0 c0 {10,S}
+28 H u0 p0 c0 {10,S}
+29 H u0 p0 c0 {10,S}
+30 H u0 p0 c0 {11,S}
+31 H u0 p0 c0 {11,S}
+32 H u0 p0 c0 {11,S}
+33 H u0 p0 c0 {12,S}
+34 H u0 p0 c0 {13,S}
+35 H u0 p0 c0 {14,S}
+36 H u0 p0 c0 {15,S}
+37 H u0 p0 c0 {16,S}
+38 H u0 p0 c0 {16,S}
+39 H u0 p0 c0 {16,S}
+""",
+    kinetics=None,
+)
+
+entry(
+    index=3,
+    label="Cbdt_acetal",
+    group=
+"""
+1    Cs         u0 p0 c0 {2,S} {3,S} {4,S} {7,S}
+2 *1 O          u0 p2 c0 {1,S} {5,S}
+3    O          u0 p2 c0 {1,S} {6,S}
+4    H          u0 p0 c0 {1,S}
+5 *2 R!H        ux px cx {2,S}
+6    R!H        ux px cx {3,S}
+7    [Cb,Cd,Ct] ux px cx {1,S}
+""",
+    kinetics=None,
+)
+
+tree(
+"""
+L1: acetal
+  L2: erythromycin_functional
+  L2: Cbdt_acetal
+L1: H2O
+"""
+)

input/kinetics/families/acetal_hydrolysis/rules.py

@@ -0,0 +1,16 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "acetal_hydrolysis/rules"
+shortDesc = u""
+longDesc = u"""
+
+"""
+
+entry(
+    index=0,
+    label="acetal;H2O",
+    kinetics=ArrheniusEP(A=(10, 'cm^3/(mol*s)'), n=0, alpha=0, E0=(0, 'kcal/mol')),
+    rank=0,
+    shortDesc=u"""Default""",
+)