Started a database for radical solvation thermo.

These groups are radical corrections to the H bonding 'A' value.
We use them after we calculate solvation thermo for a saturated
structure that we made by saturating radicals with hydrogens.

Author: bslakman

input/solvation/groups/radical.py

@@ -0,0 +1,119 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Radical Groups"
+shortDesc = u"Radical corrections to A"
+longDesc = u"""
+H-bonding parameter A should be modified for when we saturate 
+radical molecules with hydrogens and look up the saturated
+structure.
+"""
+entry(
+    index = 0,
+    label = "R_rad",
+    group = 
+"""
+1 * R u1
+""",
+    solute = None,
+    shortDesc = u"""""",
+    longDesc = 
+u"""
+
+""",
+)
+
+entry(
+    index = 1,
+    label = "O_rad",
+    group = 
+"""
+1 * O u1 p2
+""",
+    solute = None,
+    shortDesc = u"""""",
+    longDesc = 
+u"""
+
+""",
+)
+
+entry(
+    index = 2,
+    label = "ROJ",
+    group = 
+"""
+1 * O u1 p2 c0 {2,S}
+2   R u0 {1,S}
+""",
+    solute = SoluteData(
+        S = 0.0,
+        B = 0.0,
+        E = 0.0,
+        L = 0.0,
+        A = -0.345,
+    ),
+    shortDesc = u"""""",
+    longDesc = 
+u"""
+
+""",
+)
+
+entry(
+    index = 3,
+    label = "ROOJ",
+    group = 
+"""
+1 * O u1 p2 c0 {2,S}
+2   O u0 p2 {1,S} {3,S}
+3   R u0 {2,S}
+""",
+    solute = SoluteData(
+        S = 0.0,
+        B = 0.0,
+        E = 0.0,
+        L = 0.0,
+        A = -0.345,
+    ),
+    shortDesc = u"""""",
+    longDesc = 
+u"""
+
+""",
+)
+
+entry(
+    index = 4,
+    label = "RC(O)OJ",
+    group = 
+"""
+1 * O u1 p2 c0 {2,S}
+2   C u0 p0 {1,S} {3,D} {4,S}
+3   O u0 p2 {2,D}
+4   R u0 {2,S}
+""",
+    solute = SoluteData(
+        S = 0.0,
+        B = 0.0,
+        E = 0.0,
+        L = 0.0,
+        A = -0.243,
+    ),
+    shortDesc = u"""""",
+    longDesc = 
+u"""
+
+""",
+)
+
+tree(
+"""
+L1: R_rad
+    L2: O_rad
+        L3: ROJ
+            L4: RC(O)OJ
+            L4: ROOJ
+"""
+)
+