abraham.py

#!/usr/bin/env python
# encoding: utf-8

name = "Abraham Solute Descriptors"
shortDesc = u""
longDesc = u"""

"""
entry(
    index = -3,
    label = "R",
    group = 
"""
1 * R u0
""",
    solute = None,
    shortDesc = u"""""",
    longDesc = 
u"""

""",
)

entry(
    index = -2,
    label = "C",
    group = 
"""
1 * C u0
""",
    solute = None,
    shortDesc = u"""""",
    longDesc = 
u"""

""",
)

entry(
    index = 8,
    label = "Cbf",
    group = 
"""
1 * Cbf u0
""",
    solute = SoluteData(
        S = 0.121,
        B = 0.019,
        E = 0.3,
        L = 0.744,
        A = 0,
    ),
    shortDesc = u"""Platts' fragment 8 fused aromatic""",
    longDesc = 
u"""

""",
)

entry(
    index = -1,
    label = "Css",
    group = 
"""
1 * Cs u0
""",
    solute = None,
    shortDesc = u"""""",
    longDesc = 
u"""

""",
)

entry(
    index = 1,
    label = "CssH3",
    group = 
"""
1 * Cs u0 {2,S} {3,S} {4,S} {5,S}
2   H  u0 {1,S}
3   H  u0 {1,S}
4   H  u0 {1,S}
5   R  u0 {1,S}
""",
    solute = SoluteData(
        S = -0.075,
        B = 0.007,
        E = -0.104,
        L = 0.321,
        A = 0,
    ),
    shortDesc = u"""Platts fragment 1 sp3 CH3""",
    longDesc = 
u"""

""",
)

entry(
    index = 2,
    label = "CssH2",
    group = 
"""
1 * Cs  u0 {2,S} {3,S} {4,S} {5,S}
2   H   u0 {1,S}
3   H   u0 {1,S}
4   R!H u0 {1,S}
5   R!H u0 {1,S}
""",
    solute = SoluteData(
        S = 0,
        B = 0,
        E = 0,
        L = 0.499,
        A = 0,
    ),
    shortDesc = u"""Platts fragment 2 sp3 >CH2""",
    longDesc = 
u"""

""",
)

entry(
    index = 3,
    label = "CssH",
    group = 
"""
1 * Cs  u0 {2,S} {3,S} {4,S} {5,S}
2   H   u0 {1,S}
3   R!H u0 {1,S}
4   R!H u0 {1,S}
5   R!H u0 {1,S}
""",
    solute = SoluteData(
        S = 0.036,
        B = 0.011,
        E = 0.089,
        L = 0.499,
        A = 0,
    ),
    shortDesc = u"""Platts fragment 3 sp3 >CH-""",
    longDesc = 
u"""

""",
)

entry(
    index = 4,
    label = "Css-noH",
    group = 
"""
1 * Cs  u0 {2,S} {3,S} {4,S} {5,S}
2   R!H u0 {1,S}
3   R!H u0 {1,S}
4   R!H u0 {1,S}
5   R!H u0 {1,S}
""",
    solute = SoluteData(
        S = 0.071,
        B = 0.037,
        E = 0.187,
        L = 0.443,
        A = 0,
    ),
    shortDesc = u"""Platts fragment 4 sp3 >C<""",
    longDesc = 
u"""

""",
)

entry(
    index = 0,
    label = "Cds",
    group = 
"""
1 * [Cd,CO] u0
""",
    solute = None,
    shortDesc = u"""""",
    longDesc = 
u"""

""",
)

entry(
    index = 5,
    label = "CdsH2",
    group = 
"""
1 * [Cd,CO] u0 {2,S} {3,S} {4,D}
2   H       u0 {1,S}
3   H       u0 {1,S}
4   R!H     u0 {1,D}
""",
    solute = SoluteData(
        S = -0.085,
        B = 0.019,
        E = -0.045,
        L = 0.244,
        A = 0,
    ),
    shortDesc = u"""Platts' fragment 5 sp2 =CH2""",
    longDesc = 
u"""

""",
)

entry(
    index = 6,
    label = "CdsH",
    group = 
"""
1 * [Cd,CO] u0 {2,S} {3,S} {4,D}
2   H       u0 {1,S}
3   R!H     u0 {1,S}
4   R!H     u0 {1,D}
""",
    solute = SoluteData(
        S = 0.05,
        B = 0.011,
        E = 0.068,
        L = 0.469,
        A = 0,
    ),
    shortDesc = u"""Platts' fragment 6 sp2 =CH-""",
    longDesc = 
u"""

""",
)

entry(
    index = 7,
    label = "Cds-noH",
    group = 
"""
1 * [Cd,CO] u0 {2,S} {3,S} {4,D}
2   R!H     u0 {1,S}
3   R!H     u0 {1,S}
4   R!H     u0 {1,D}
""",
    solute = SoluteData(
        S = 0.101,
        B = 0,
        E = 0.18,
        L = 0.624,
        A = 0,
    ),
    shortDesc = u"""Platts' fragment 7 sp2 =C<""",
    longDesc = 
u"""

""",
)

entry(
    index = 9,
    label = "Ct",
    group = 
"""
1 * Ct u0
""",
    solute = SoluteData(
        S = 0.034,
        B = 0.028,
        E = 0.04,
        L = 0.332,
        A = 0,
    ),
    shortDesc = u"""Platts' fragment 9 sp""",
    longDesc = 
u"""

""",
)

entry(
    index = 10,
    label = "CtOt",
    group = 
"""
1 * Ct u0 {2,T}
2   Ot u0 {1,T}
""",
    solute = SoluteData(
        S = -0.085,
        B = 0.019,
        E = -0.045,
        L = 0.244,
        A = 0,
    ),
    shortDesc = u"""Fake value for C#O that corresponds to its resonance isomer""",
    longDesc = 
u"""

""",
)

entry(
    index = 57,
    label = "Cdd",
    group = 
"""
1 * Cdd u0
""",
    solute = SoluteData(
        S = 0.101,
        B = 0,
        E = 0.18,
        L = 0.624,
        A = 0,
    ),
    shortDesc = u"""Platts' fragment 7 nonfused aromatic =C<""",
    longDesc = 
u"""

""",
)

entry(
    index = -9,
    label = "Cb",
    group = 
"""
1 * Cb u0
""",
    solute = None,
    shortDesc = u"""""",
    longDesc = 
u"""

""",
)


entry(
    index = 37,
    label = "Cbf-noH",
    group = 
"""
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}
""",
    solute = SoluteData(
        S = 0.101,
        B = 0,
        E = 0.18,
        L = 0.624,
        A = 0,
    ),
    shortDesc = u"""same as Platts group 7""",
    longDesc = 
u"""

""",
)

entry(
    index = 38,
    label = "Cb-H",
    group = 
"""
1 * Cb  u0 {2,B} {3,B} {4,S}
2   R!H u0 {1,B}
3   R!H u0 {1,B}
4   H   u0 {1,S}
""",
    solute = SoluteData(
        S = 0.05,
        B = 0.011,
        E = 0.068,
        L = 0.469,
        A = 0,
    ),
    shortDesc = u"""same as Platts group 6""",
    longDesc = 
u"""

""",
)

entry(
    index = 39,
    label = "Cb-noHnoRing",
    group = 
"""
1 * Cb  u0 {2,B} {3,B} {4,S}
2   R!H u0 {1,B}
3   R!H u0 {1,B}
4   R!H u0 {1,S}
""",
    solute = SoluteData(
        S = 0.101,
        B = 0,
        E = 0.18,
        L = 0.624,
        A = 0,
    ),
    shortDesc = u"""same as Platts group 7""",
    longDesc = 
u"""
Cb is attached to a 3rd R group that isn't in the ring,as in phenol.
""",
)

entry(
    index = -4,
    label = "O",
    group = 
"""
1 * [Os,Od,Ot] u0
""",
    solute = None,
    shortDesc = u"""""",
    longDesc = 
u"""

""",
)

entry(
    index = -10,
    label = "Oss",
    group = 
"""
1 * Os u0
""",
    solute = None,
    shortDesc = u"""""",
    longDesc = 
u"""

""",
)

entry(
    index = 26,
    label = "OssH",
    group = 
"""
1 * Os u0 {2,S}
2   H  u0 {1,S}
""",
    solute = SoluteData(
        S = 0.247,
        B = 0.307,
        E = 0.061,
        L = 0.672,
        A = 0,
    ),
    shortDesc = u"""Platts fragment 26 -OH""",
    longDesc = 
u"""

""",
)

entry(
    index = 27,
    label = "Oss-noncyclic",
    group = 
"""
1 * Os  u0 {2,S} {3,S}
2   R!H u0 {1,S}
3   R!H u0 {1,S}
""",
    solute = SoluteData(
        S = 0.185,
        B = 0.211,
        E = 0.014,
        L = 0.36,
        A = 0,
    ),
    shortDesc = u"""Platts fragment 27 noncyclic -O-""",
    longDesc = 
u"""

""",
)

entry(
    index = 30,
    label = "Od",
    group = 
"""
1 * Od u0
""",
    solute = SoluteData(
        S = 0.37,
        B = 0.334,
        E = -0.041,
        L = 0.495,
        A = 0,
    ),
    shortDesc = u"""Platts fragment 30 sp2 =O""",
    longDesc = 
u"""

""",
)

entry(
    index = 30,
    label = "OtCt",
    group = 
"""
1 * Ot u0 {2,T}
2   Ct u0 {1,T}
""",
    solute = SoluteData(
        S = 0.37,
        B = 0.334,
        E = -0.041,
        L = 0.495,
        A = 0,
    ),
    shortDesc = u"""Fake value for C#O that corresponds to resonance isomer""",
    longDesc = 
u"""

""",
)

entry(
    index = -8,
    label = "N",
    group = 
"""
1 * N u0
""",
    solute = None,
    shortDesc = u"""""",
    longDesc = 
u"""

""",
)

entry(
    index = -7,
    label = "N3s",
    group = 
"""
1 * N3s u0
""",
    solute = None,
    shortDesc = u"""""",
    longDesc = 
u"""

""",
)

entry(
    index = 23,
    label = "NO2",
    group = 
"""
1 * N3s u0 {2,S} {3,S} {4,S}
2   R   u0 {1,S}
3   Os  u0 {1,S}
4   Os  u0 {1,S}
""",
    solute = SoluteData(
        S = 0.0,
        B = -0.476,
        E = 0.2,
        L = 0.278,
        A = 0.0,
    ),
    shortDesc = u"""Platts fragment 23 -NO2""",
    longDesc = 
u"""

""",
)

entry(
    index = 46,
    label = "NO2-aromatic",
    group = 
"""
1 * N3s      u0 {2,S} {3,S} {4,S}
2   Os       u0 {1,S}
3   Os       u0 {1,S}
4   [Cb,N3b] u0 {1,S}
""",
    solute = SoluteData(
        S = -0.231,
        B = -0.525,
        E = 0.21,
        L = 0.347,
        A = 0.0,
    ),
    shortDesc = u"""Platts fragment 24""",
    longDesc = 
u"""

""",
)

entry(
    index = 25,
    label = "ONO2",
    group = 
"""
1 * N3s u0 {2,S} {3,S} {4,S}
2   Os  u0 {1,S}
3   Os  u0 {1,S}
4   Os  u0 {1,S}
""",
    solute = SoluteData(
        S = -0.476,
        B = -0.204,
        E = 0.0,
        L = 0.0,
        A = 0.0,
    ),
    shortDesc = u"""Platts fragment 25 nitrate""",
    longDesc = 
u"""

""",
)

entry(
    index = 10,
    label = "N3sH2",
    group = 
"""
1 * N3s u0 {2,S} {3,S}
2   H   u0 {1,S}
3   H   u0 {1,S}
""",
    solute = SoluteData(
        S = 0.175,
        B = 0.481,
        E = 0.085,
        L = 0.781,
        A = 0.0,
    ),
    shortDesc = u"""Platts fragment 10 -NH2-aliphatic""",
    longDesc = 
u"""

""",
)

entry(
    index = 11,
    label = "N3sH2-aromatic",
    group = "OR{N3sH2-Cb, N3sH2-N5ring}",
    solute = SoluteData(
        S = 0.383,
        B = 0.275,
        E = 0.163,
        L = 0.949,
        A = 0.0,
    ),
    shortDesc = u"""Platts fragment 11""",
    longDesc = 
u"""

""",
)

entry(
    index = 40,
    label = "N3sH2-Cb",
    group = 
"""
1 * N3s      u0 {2,S} {3,S} {4,S}
2   H        u0 {1,S}
3   H        u0 {1,S}
4   Cb       u0 {1,S} {5,B} {6,B}
5   [Cb,N3b] u0 {4,B} {7,B}
6   [Cb,N3b] u0 {4,B} {8,B}
7   [Cb,N3b] u0 {5,B} {9,B}
8   [Cb,N3b] u0 {6,B} {9,B}
9   [Cb,N3b] u0 {7,B} {8,B}
""",
    solute = None,
    shortDesc = u"""""",
    longDesc = 
u"""

""",
)

entry(
    index = 41,
    label = "N3sH2-N5ring",
    group = 
"""
1 * N3s      u0 {2,S} {3,S} {4,S}
2   H        u0 {1,S}
3   H        u0 {1,S}
4   N3s      u0 {1,S} {5,S} {6,S}
5   [Cb,N3b] u0 {4,S} {7,B}
6   [Cb,N3b] u0 {4,S} {8,B}
7   [Cb,N3b] u0 {5,B} {8,B}
8   [Cb,N3b] u0 {6,B} {7,B}
""",
    solute = None,
    shortDesc = u"""""",
    longDesc = 
u"""

""",
)

entry(
    index = 12,
    label = "N3sH",
    group = 
"""
1 * N3s u0 {2,S} {3,S} {4,S}
2   H   u0 {1,S}
3   R!H u0 {1,S}
4   R!H u0 {1,S}
""",
    solute = SoluteData(
        S = 0.265,
        B = 0.541,
        E = 0.138,
        L = 0.568,
        A = 0.087,
    ),
    shortDesc = u"""Platts fragment 12 >NH (fragment 5 for A)""",
    longDesc = 
u"""

""",
)

entry(
    index = 43,
    label = "N3sH-aromatic",
    group = 
"""
1 * N3s      u0 {2,S} {3,S} {4,S}
2   H        u0 {1,S}
3   [Cb,N3b] u0 {1,S}
4   [Cb,N3b] u0 {1,S}
""",
    solute = SoluteData(
        S = 0.311,
        B = 0.415,
        E = 0.192,
        L = 0.912,
        A = 0.0,
    ),
    shortDesc = u"""""",
    longDesc = 
u"""

""",
)

entry(
    index = 14,
    label = "N3sH-pyrrole",
    group = 
"""
1 * N3s u0 {2,S} {3,S} {4,S}
2   H   u0 {1,S}
3   Cb  u0 {1,S} {5,B}
4   Cb  u0 {1,S} {6,B}
5   Cb  u0 {3,B} {6,B}
6   Cb  u0 {4,B} {5,B}
""",
    solute = SoluteData(
        S = 0.221,
        B = 0.316,
        E = -0.03,
        L = 1.25,
        A = 0.371,
    ),
    shortDesc = u"""Platts fragment 14 pyrrole (fragment 8 for A)""",
    longDesc = 
u"""

""",
)

entry(
    index = 15,
    label = "N3s-noH",
    group = 
"""
1 * N3s u0 {2,S} {3,S} {4,S}
2   R!H u0 {1,S}
3   R!H u0 {1,S}
4   R!H u0 {1,S}
""",
    solute = SoluteData(
        S = 0.323,
        B = 0.653,
        E = 0.22,
        L = 0.4,
        A = 0.0,
    ),
    shortDesc = u"""Platts fragment 15 >N-""",
    longDesc = 
u"""

""",
)

entry(
    index = 45,
    label = "N3s-noH-aromatic",
    group = 
"""
1 * N3s      u0 {2,S} {3,S} {4,S}
2   R!H      u0 {1,S}
3   [Cb,N3b] u0 {1,S}
4   [Cb,N3b] u0 {1,S}
""",
    solute = SoluteData(
        S = 0.295,
        B = 0.321,
        E = 0.346,
        L = 0.869,
        A = 0.0,
    ),
    shortDesc = u"""""",
    longDesc = 
u"""

""",
)

entry(
    index = 17,
    label = "N3s-noH-pyrrole",
    group = 
"""
1 * N3s u0 {2,S} {3,S} {4,S}
2   R!H u0 {1,S}
3   Cb  u0 {1,S} {5,B}
4   Cb  u0 {1,S} {6,B}
5   Cb  u0 {3,B} {6,B}
6   Cb  u0 {4,B} {5,B}
""",
    solute = SoluteData(
        S = 0.265,
        B = 0.392,
        E = 0.083,
        L = 0.794,
        A = 0.0,
    ),
    shortDesc = u"""Platts fragment 17 pyrrole""",
    longDesc = 
u"""

""",
)

entry(
    index = 18,
    label = "N3d",
    group = 
"""
1 * N3d u0
""",
    solute = SoluteData(
        S = 0.125,
        B = 0.2,
        E = 0.117,
        L = -0.235,
        A = 0.0,
    ),
    shortDesc = u"""Platts fragment 18 =N""",
    longDesc = 
u"""

""",
)

entry(
    index = 21,
    label = "N3t",
    group = 
"""
1 * N3t u0 {2,T}
2   Ct  u0 {1,T}
""",
    solute = SoluteData(
        S = 0.694,
        B = 0.242,
        E = 0.0,
        L = 0.757,
        A = 0.0,
    ),
    shortDesc = u"""Platts fragment 21 N#C-""",
    longDesc = 
u"""

""",
)

entry(
    index = 22,
    label = "N3t-aromatic",
    group = "OR{N3t-Cb, N3t-N5ring}",
    solute = SoluteData(
        S = 0.39,
        B = 0.103,
        E = 0.0,
        L = 0.732,
        A = 0.0,
    ),
    shortDesc = u"""Platts fragment 22""",
    longDesc = 
u"""

""",
)

entry(
    index = 55,
    label = "N3t-Cb",
    group = 
"""
1 * N3t u0 {2,T}
2   Ct  u0 {1,T} {3,S}
3   Cb  u0 {2,S}
""",
    solute = None,
    shortDesc = u"""""",
    longDesc = 
u"""

""",
)

entry(
    index = 56,
    label = "N3t-N5ring",
    group = 
"""
1 * N3t      u0 {2,T}
2   Ct       u0 {1,T} {3,S}
3   N3s      u0 {2,S} {4,S} {5,S}
4   [Cb,N3b] u0 {3,S} {6,B}
5   [Cb,N3b] u0 {3,S} {7,B}
6   [Cb,N3b] u0 {4,B} {7,B}
7   [Cb,N3b] u0 {5,B} {6,B}
""",
    solute = None,
    shortDesc = u"""""",
    longDesc = 
u"""

""",
)

entry(
    index = 19,
    label = "N3b",
    group = 
"""
1 * N3b u0
""",
    solute = SoluteData(
        S = 0.254,
        B = 0.596,
        E = 0.121,
        L = -0.24,
        A = 0,
    ),
    shortDesc = u"""Platts group 19 =N sp2 cyclic""",
    longDesc = 
u"""

""",
)

entry(
    index = 20,
    label = "N3bpyr",
    group = 
"""
1 * N3b u0 {2,B} {6,B}
2   Cb  u0 {1,B} {3,B}
3   Cb  u0 {2,B} {4,B}
4   Cb  u0 {3,B} {5,B}
5   Cb  u0 {4,B} {6,B}
6   Cb  u0 {1,B} {5,B}
""",
    solute = SoluteData(
        S = 0.223,
        B = 0.321,
        E = 0.046,
        L = 0.574,
        A = 0,
    ),
    shortDesc = u"""Platts group 20 pyridine""",
    longDesc = 
u"""

""",
)

entry(
    index = 36,
    label = "S",
    group = 
"""
1 * [S,Ss,Sd,Sa] u0
""",
    solute = SoluteData(
        S = 0.643,
        B = 0.0,
        E = 0.465,
        L = 0.554,
        A = 0,
    ),
    shortDesc = u"""Platts fragment 36 (any other sulfur)""",
    longDesc = 
u"""

""",
)

entry(
    index = 31,
    label = "Ss",
    group = 
"""
1 * Ss u0
""",
    solute = SoluteData(
        S = 0.189,
        B = 0.168,
        E = 0.33,
        L = 1.258,
        A = 0,
    ),
    shortDesc = u"""Platts fragment 31 -S- sp3""",
    longDesc = 
u"""

""",
)

entry(
    index = 32,
    label = "Ss-aromatic",
    group = 
"""
1 * Ss       u0 {2,S} {5,S}
2   Cb       u0 {1,S} {3,B}
3   [Cb,N3b] u0 {2,B} {4,B}
4   [Cb,N3b] u0 {3,B} {5,B}
5   Cb       u0 {1,S} {4,B}
""",
    solute = SoluteData(
        S = 0,
        B = 0.043,
        E = 0.116,
        L = 0.848,
        A = 0,
    ),
    shortDesc = u"""Platts fragment 32 -S- aromatic""",
    longDesc = 
u"""

""",
)

entry(
    index = 33,
    label = "Sd",
    group = 
"""
1 * Sd u0
""",
    solute = SoluteData(
        S = 0.618,
        B = 0.071,
        E = 0.364,
        L = 0.954,
        A = 0,
    ),
    shortDesc = u"""Platts fragment 33 =S sp2""",
    longDesc = 
u"""

""",
)

entry(
    index = 34,
    label = "Sds",
    group = 
"""
1 * Sd u0 {2,S} {3,S}
2   R  u0 {1,S}
3   R  u0 {1,S}
""",
    solute = SoluteData(
        S = 1.065,
        B = 0.448,
        E = 0.413,
        L = 2.196,
        A = 0,
    ),
    shortDesc = u"""Platts fragment 34 >S=""",
    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
            L4: CssH
            L4: Css-noH
        L3: Cds
            L4: CdsH2
            L4: CdsH
            L4: Cds-noH
        L3: Ct
            L4: CtOt
        L3: Cdd
        L3: Cb
            L4: Cb-H
            L4: Cb-noHnoRing
    L2: O
        L3: Oss
            L4: OssH
            L4: Oss-noncyclic
        L3: Od
        L3: OtCt
    L2: N
        L3: N3s
            L4: NO2
                L5: NO2-aromatic
                L5: ONO2
            L4: N3sH2
                L5: N3sH2-aromatic
                    L6: N3sH2-Cb
                    L6: N3sH2-N5ring
            L4: N3sH
                L5: N3sH-aromatic
                    L6: N3sH-pyrrole
            L4: N3s-noH
                L5: N3s-noH-aromatic
                    L6: N3s-noH-pyrrole
        L3: N3d
        L3: N3t
            L4: N3t-aromatic
                L5: N3t-Cb
                L5: N3t-N5ring
        L3: N3b
            L4: N3bpyr
    L2: S
        L3: Ss
            L4: Ss-aromatic
        L3: Sd
            L4: Sds
"""
)