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valence.py
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#!/usr/bin/python
##################################################################
#
# Title: valence.py
# Description: Assignment of valence parameters for
# the AMOEBA force field
#
# Copyright: Copyright (c) Johnny C. Wu,
# Gaurav Chattree, & Pengyu Ren 2010-2011
#
# Poltype is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 3
# as published by the Free Software Foundation.
#
# Poltype is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Force Field X; if not, write to:
# Free Software Foundation, Inc.
# 59 Temple Place, Suite 330
# Boston, MA 02111-1307 USA
#
##################################################################
import openbabel
import math
radian = 57.29577951308232088
class Valence:
def __init__(self,output_format):
self.sp = openbabel.OBSmartsPattern()
#for tinker4 format, set o_f to 4, for tinker5 format, set o_f to 5
self.o_f = output_format
self.missed_torsions = []
def setidxtoclass(self, symmclass):
self.idxtoclass = symmclass
def get_mt(self):
return self.missed_torsions
def vdwguess(self, mol):
#self.idxToClassInit(xyzfname)
found = []
vals = []
dfltrad = 1.0
dflteps = .1
dfltred = 0
#many of these can be merged
vdwparamvals3 = dict({ \
#37 C "Ethanol CH3" Same as Ethane CH3
'[CH3]' : [3.820, .1010], \
#24 C "Ethane CH3"
#'[CH3]' : [3.820, .1010], \
#38 H "Ethanol H3C"
'[#1][C;D4][OH]' : [2.960, .0240, .92], \
#60 C "Formic Acid C=O" (check) (should it be [C]~[*;D2]?)
'[CH](=O)' : [3.780, .1060], \
'C(S)' : [3.780, .1060], \
})
vdwparamvals2 = dict({ \
#21 N "Dinitrogen N2"
'[#7]([#7])' : [3.71, .08, .99], \
#22 C "Methane CH4"
'[CH4]' : [3.780, .1010], \
#23 H "Methane H4C"
'[#1]([CH4])' : [2.900, .022, .9], \
#Ren, 2011 JCTC "Terminal H3C"
'[#1][CH3]' : [2.960, .0240, .92], \
#25 H "Ethane H3C"
'[#1][CH3][CH3]' : [2.960, .0240, .94], \
#26 C "Alkane -CH2-" (not needed, same as 37)
#'[C;H2]' : [3.820, .1010], \
#27 H "Alkane -H2C-"
'[#1]([CH2])' : [2.98, .024, .94], \
#28 C "Alkane >CH-"
'[CH1]' : [3.65, .1010], \
#29 H "Alkane -HC<"
'[#1]([CH1;D4])' : [2.98, .024, .94], \
#30 C "Alkane >C<"
'[CH0;D4]' : [3.6, .104], \
#31 OW "Water O"
'[O;D2;H2]' : [3.405, .110], \
#32 HW "Water H2O"
'[#1]([O;D2;H2])' : [2.655, 0.0135, .91], \
#33 C "Methanol CH3"
'[CH3]([OH1])' : [3.760, .1010], \
#34 H "Methanol H3C" (check) !!!
'[#1][C;D4][OH]' : [2.870, .024, .91], \
#35 O "Methanol O (check)
'[O;D2][#6]' : [3.405, .1100], \
#36 H "Methanol HO"
'[#1][O;D2][#6]' : [2.655, .0135, .91], \
#39 H "Propanol Me-CH2" (check) (should this be moved, compare wtih #47); in amoeba_new_v2, this is used for HC2-XH in propanol and propylamine. But #47 or #34 is better. For the other H2C-Ch3, this is fine. Not sureif polytype distinguish different CH2 (probably did but we may combined them).
'[#1]([CH2]([CH3]))' : [2.980, .0240, .92], \
#I fee like assigning 39 to atom #96 isn't correct, should have assigned it 47,
#to separate the two i put N in a ring.
'[#1]([CH3]([N;R]))' : [2.980, .0240, .92], \
#76 C "Benzene C"
'c' : [3.800, .0890], \
#77 H "Benzene HC"
'[#1](c)' : [2.980, .0260, .92], \
#47 H "Ethyl Amine H2C" (check) (should this be moved, compare to #39); this should also be the one assigned to methyl amine.
'[#1][C;D4][N,c;D3]' : [2.880, 0.0240, .91], \
})
vdwparamvals1 = dict({ \
#1 He "Helium Atom He"
'[#2]' : [2.99, .0080], \
#2 Ne "Neon Atom Ne"
'[#10]' : [3.150, 0.073], \
#3 Ar "Argon Atom Ar"
'[#18]' : [3.820, 0.26], \
#4 Kr "Krypton Atom Kr"
'[#36]' : [4.090, .359], \
#5 Xe "Xenon Atom Xe"
'[#54]' : [4.370, 0.498], \
#6 Li+ "Lithium Ion Li+" (check) (check all with ;v0, is it really needed?)
'[#3;v0;+]' : [2.380, 0.08], \
#7 Na+ "Sodium Ion Na+"
'[#11;v0;+]' : [3.020, 0.26], \
#8 K+ "Potassium Ion K+"
'[#19;v0;+]' : [3.710, .35], \
#9 Rb+ "Rubidium Ion Rb+"
'[#37;v0;+]' : [4.140, .440], \
#10 Cs+ "Cesium Ion Cs+"
'[#55;v0;+]' : [4.37, .53], \
#11 Mg+ "Magnesium Ion Mg+2"
'[#12;v0;++]' : [2.55, .85], \
#12 Ca+ "Calcium Ion Ca+2"
'[#20;v0;++]' : [3.15, 1.6], \
#13 F- "Fluoride Ion F-"
'[#9;v0;-]' : [3.4, 0.25], \
#14 Cl- "Chloride Ion Cl-"
'[#17;v0;-]' : [4.13, .34], \
#15 Br- "Bromide Ion Br-"
'[#35;v0;-]' : [4.38, .43], \
'[#35]' : [3.98, .43], \
#16 I- "Iodide Ion I-"
'[#53;v0;-]' : [4.66, .52], \
#17 B "Tetrafluoroborate B"
'[#5]([#9])([#9])([#9])([#9])' : [3.9, .1], \
'[#5]' : [3.9, .1], \
#18 F "Tetrafluoroborate F"
'[#9]([#5]([#9])([#9])([#9]))' : [3.22, .12], \
#19 P "Hexafluorophosphate P"
'[#15]([#9])([#9])([#9])([#9])([#9])([#9])' : [4.53, .35], \
#20 F "Hexafluorophosphate F"
'[#9]([#15]([#9])([#9])([#9])([#9])([#9]))' : [3.22, .12], \
#40 C "isoPropanol >CH-"
'[CH1]([CH3])([CH3])([OH1])' : [3.650, .1010], \
#41 H "Methyl Ether H3C"
'[#1]([CH3]([O]([CH2,CH3,c])))' : [2.89, .024, .91], \
#42 N "Ammonia N"
'[NH3]' : [3.71, .1050], \
#43 H "Ammonia H3N"
#'[#1]([N;D3;H3])' : [2.700, .0200, .91], \
'[#1]([N;D3])' : [2.700, .0200, .91], \
#44 M "Amine Lone Pair" (needs_work)
#45 N "Ammonium Ion N+"
'[#7;D4]' : [3.71, .1050], \
#46 H "Ammonium Ion H4N+"
'[#1]([N;D4])' : [2.48, .0115, .90], \
#48 N "Ethyl Amine N"
'[N]([C]([#1]))' : [3.71, .1050], \
#49 H "Ethyl Amine H2N"
'[#1]([N;D3]([C]([#1])))' : [2.7, .02, .91], \
'[#1]([n;D3])' : [2.59, .0200, .91], \
#50 H "Pyrrolidine C-CH2-C" (check)
'[#1]([CH2]([CH2]([N])))' : [2.96, .0220, .92], \
'[#1]([CH2]([N]))' : [2.96, .0220, .92], \
#51 C "Formamide C=O" (check)
'[C](=O)([N,c])' : [3.820, .1060], \
#52 H "Formamide HCO"
'[#1](C(=O)(N))' : [2.800, 0.0260, .91], \
#53 O "Formamide O"
'[O](=C)' : [3.300, .1120], \
#54 N "Formamide N"
'[N](C=O)' : [3.710, .1100], \
#55 H "Formamide H2N"
'[#1]([N](C=O))' : [2.590, .0220, .90], \
#56 H "Acetamide H3C"
'[#1]([CH3](C(=O)(N)))' : [2.950, .0260, .91], \
#57 H "NMeFormamide H3C" (check) (maybe i should change [CH3] -> [C])
'[#1]([CH3](N(C(=O))))' : [2.930, .0260, .91], \
#58 O "Formic Acid OH"
'[OH1](C=O)' : [3.405, .1100], \
#59 H "Formic Acid HO"
'[#1]([OH1](C=O))' : [2.655, .0150, .91], \
#61 H "Formic Acid HC=O"
'[#1](C=O)' : [2.920, .0300, .92], \
#62 H "Acetic Acid H3C"
'[#1]([CH3](C=O))' : [2.980, .0240, .94], \
#63 S "Hydrogen Sulfide S"
'[SH2]' : [4.005, .3550], \
#64 H "Hydrogen Sulfide H2S" (not needed, same as 67)
#'[#1]([S;H2])' : [2.770, .0240, .96], \
#65 H "Methyl Sulfide H3C"
'[#1]([C][S;D2])' : [2.870, .0330, .90], \
#66 S "Methyl Sulfide S"
'[SH]C' : [4.005, .3550], \
#67 H "Methyl Sulfide HS"
'[#1][#16;D2]' : [2.770, .0240, .96], \
#68 C "Ethyl Sulfide CH3"
'[CH3]([CH2](S))' : [3.820, .1040], \
#69 H "Ethyl Sulfide H3C"
'[#1]([CH3]([CH2](S)))' : [2.980, .0240, .92], \
#70 H "Methyl Sulfonate H3C"
'[#1]([C](S(=O)(=O)([O-])))' : [2.910, .0330, .90], \
#71 S "Methyl Sulfonate SO3-"
'S(=O)(=O)([O-])' : [3.910, .3850], \
#72 O "Methyl Sulfonate SO3-" (check)
#'[O-](S(=O)(=O))' : [3.510, .1120], \
'[O;D1](~S)' : [3.510, .1120], \
#73 C "Tricyanomethide >C-"
'[C](C#N)(C#N)(C#N)' : [3.820, .1060], \
#74 C "Tricyanomethide CN"
'[C](#N)(C(C#N)(C#N))' : [3.820, .1060], \
#75 N "Tricyanomethide CN"
'[N](#C(C(C#N)(C#N)))' : [3.690, .1100], \
#78 C "Ethylbenzene C1-CH2"
'[cH0]' : [3.800, .0910], \
'c([cH0])' : [3.800, .0910], \
'c(c([cH0]))' : [3.800, .0910], \
'c(c(c([cH0])))' : [3.800, .0910], \
#79 H "Ethylbenzene H2" (not needed, same values as 77)
#'[#1](c(cH0))' : [2.890, .0260, .92], \
#'[#1](c(c(cH0)))'
#'[#1](c(c(c(cH0))))'
#80 N "Imidazole NH" (merged with 89 to make a less specific smarts string)
#'n([#1])' : [3.710, .1050], \
'n' : [3.710, .1050], \
#81 C "Imidazole N-C-N"
'c(n)' : [3.780, .1010], \
#82 H "Imidazole HC"
'[#1](c(n))' : [3.00, .0240, .94], \
#83 C "Indole C1" (check)
'cnccccc' : [3.800, .1010], \
'ccncccc' : [3.800, .1010], \
'cccnccc' : [3.800, .1010], \
'ccccncc' : [3.800, .1010], \
#84 C "3-Ethylindole CH2" (check)
'[CH2](cnccccc)([CH3])' : [3.820, .1040], \
'[CH2](ccncccc)([CH3])' : [3.820, .1040], \
'[CH2](cccnccc)([CH3])' : [3.820, .1040], \
'[CH2](ccccncc)([CH3])' : [3.820, .1040], \
'[CH3]([CH2](cnccccc))' : [3.820, .1040], \
'[CH3]([CH2](ccncccc))' : [3.820, .1040], \
'[CH3]([CH2](cccnccc))' : [3.820, .1040], \
'[CH3]([CH2](ccccncc))' : [3.820, .1040], \
#85 O "3-Formylindole O=C" (check) (can the top 4 be reduced to the last 1
# since 85 is the only one like this?)
#'O(=C(cnccccc))' : [3.300, .1140], \
#'O(=C(ccncccc))' : [3.300, .1140], \
#'O(=C(cccnccc))' : [3.300, .1140], \
#'O(=C(ccccncc))' : [3.300, .1140], \
'O(=C(c))' : [3.300, .1140], \
# Carboxylate ion O-
'[OD1]~C~[OD1]' : [3.450, .1120], \
#86 N "Benzamidine N"
'N(~C(c))' : [3.710, .1100], \
#87 H "Benzamidine HN"
'[#1](N(~C(c)))' : [2.590, .0220, 0.90], \
#88 C "Benzamidine N-C-N"
'C(N)(=N)(c)' : [3.650, .1010], \
#89 N "Pyridinium N" (not needed, same as 80)
#'[n;+](c)' : [3.710, .1050], \
#90 H "Pyridinium HN" (check) (could merge with 43)
'[#1]([n;+])' : [2.43, .0200, .91], \
})
vdwvals1 = dict({ \
'[#1](c)' : [2.980, .026, .92], \
# HC+
'[#1][#6;D3]' : [2.583, .0260, .92], \
'[#1]([#6;D4]([!#1])([#1])([#1]))' : [2.96, .024, .92], \
'[#1]([#6;D4]([!#1])([!#1])([#1]))' : [2.98, .024, .94], \
'[#1]([#6]([!#1])([!#1])([!#1]))' : [2.98, .024, .94], \
# HN+
'[#1]([#7]([#6]=[#8]))' : [2.59, .022, .90], \
# HO+
'[#1][#8;D3]' : [2.398, .0150, .91], \
'[#1]([#8;D2]([#6;D4]([#6,#1])([#6,#1])([#6,#1])))' : [2.665, .0135, .91], \
'[#1]([#8;D2]([#6;D3]([#6,#1])([#6,#1])))' : [2.665, .0135, .91], \
'[#1]([#8;D2]([#6;D2]([#6])))' : [2.665, .0135, .91], \
# HP+
'[#1][#15;D4]' : [2.682, .0260, .92], \
# HS+
'[#1][#16;D3]' : [2.49, 0.024, .96], \
# C+ ion
'[#6;D3]([*])([*])([*])' : [3.42, .101], \
'c' : [3.8, .091], \
'[#6;D3](=[#8])' : [3.82, .106], \
'[#6;D4]([!#1])([!#1])([!#1])([#1])' : [3.65, .101], \
'[#7;D3]([#6]=[#8])' : [3.71, .11], \
'[#8;D1](~[#16])' : [3.51, .112], \
'[#8;D2](~[#15])' : [3.405, .112], \
# [O-][*] ion (single bond, valence 1)
'[#8;D1][*]' : [3.63, .112], \
# [S-][*] ion
'[#16;D1][*]' : [4.406, .3550], \
})
vdwvals2 = dict({ \
'[#1]([#6])' : [2.78, .026, 0.91], \
'[#1]([#7])' : [2.7, 0.02, .91], \
'[#1]([#8])' : [2.665, 0.015, 0.91], \
'[#1]([#16])' : [2.77, 0.024, .96], \
'c' : [3.8, .091], \
'[#7;D3]' : [3.71, .105], \
'[#7;D2]' : [3.71, .11], \
'[#8;D1]=[#6]' : [3.3, .112], \
'[#8;D1]=[#7]' : [3.3, .112], \
'[#8;D1]=[#15]' : [3.36, .112], \
'[#9;v0]' : [3.4, .25] \
})
vdwvals3 = dict({ \
'[#6;D3]([*])([*])(=[*])' : [3.8, .089], \
'[#8;D1]' : [3.3, .112], \
'[#8;D2]' : [3.405, .11], \
})
vdwvals4 = dict({ \
'[#1]' : [2.98,.026,.92], \
'[#5]' : [3.9, .1], \
'[#6]' : [3.82, .101], \
'[#7]' : [3.71, .105], \
'[#8]' : [3.405, .11], \
#'[#9]' : [3.22, .12], \
'[#9]' : [3.22, .13], \
'[#11]' : [3.02, .26], \
'[#12]' : [2.55, .85], \
'[#15]' : [4.45, .39], \
'[#16]' : [4.005, .355], \
#'[#17]' : [3.73, .34], \
#'[#17]' : [3.73, .24], \
'[#17]' : [3.898, .413], \
'[#19]' : [3.71, .35], \
'[#20]' : [3.15, 1.6], \
#'[#35]' : [3.98, .43], \
'[#35]' : [3.83, .83], \
'[#53]' : [4.21, .52] \
})
vdwvals5 = dict({ \
'*' : [dfltrad, dflteps, dfltred], \
})
vals.append(vdwvals5)
vals.append(vdwvals4)
vals.append(vdwvals3)
vals.append(vdwvals2)
vals.append(vdwvals1)
vals.append(vdwparamvals3)
vals.append(vdwparamvals2)
vals.append(vdwparamvals1)
d = dict()
for v in vals:
for skey in iter(v):
openbabel.OBSmartsPattern.Init(self.sp,skey)
self.sp.Match(mol)
for ia in self.sp.GetMapList():
#key1 = '%d ' % idxtoclass.get(ia[0])
key1 = self.idxtoclass[ia[0] - 1]
if(len(v[skey]) == 3):
key2 = 'vdw%10d%8.4f%9.4f%6.3f' % (key1, v[skey][0], v[skey][1], v[skey][2])
else:
key2 = 'vdw%10d%8.4f%9.4f' % (key1, v[skey][0], v[skey][1])
d.update({key1 : key2})
#if key1 not in found:
#found.append(key1)
#if(v[skey][2] != dfltred):
#key2 = "vdw\t\t" + key1 + "\t\t\t" + '%f %f %f' % (v[skey][0], v[skey][1], v[skey][2])
#key2 = 'vdw%10d%8.3f%9.3f%6.2f' % (key1, v[skey][0], v[skey][1], v[skey][2])
#else:
#key2 = "vdw\t\t" + key1 + "\t\t\t" + '%f %f' % (v[skey][0], v[skey][1])
#print "lol"
#addToOutString(key2)
x = []
for v in dict.itervalues(d):
x.append(v)
return x
def bondguess(self, mol):
found = []
vals = []
defaultBConstVal = 350
bondparamvals3 = dict({ \
#76 76
'cc' : [610.9, 1.3820], \
#37 38
'[C]-[#1]' : [385.0, 1.112], \
#37 78
'[C](c)' : [453.2, 1.499], \
})
bondparamvals2 = dict({ \
#34 37 (check) (does this need to be moved)
'[#1]-[C]([OH1])' : [385.0, 1.1120], \
#37 37
'[C]-[C]' : [453.0, 1.5247], \
#35 37
'[O]-[C]' : [465.1, 1.4130], \
#37 48
'[C]-[N]' : [381.3, 1.4655], \
#51 53
'[C]=[O]' : [601.8, 1.2183], \
#53 60
'[O](=C)' : [705.0, 1.2255], \
#80 83 (not needed, same as 76-89)
#'nc' : [653.9, 1.355], \
#81 81
'c(c(n))(n)' : [539.6, 1.3520], \
#51 61 (less specific than 51-52)
'[C](-[#1])(=[O])' : [314.4, 1.0907], \
#60 66
'[C]-[S]' : [235.8, 1.8250], \
'[#16]~[C]' : [235.8, 1.8250], \
#63 64
'[S]-[#1]' : [278.4, 1.3420], \
#76 77
'c([#1])' : [370.5, 1.0790], \
#76 89
'cn' : [653.9, 1.355], \
#37 47
'[C](-[#1])(N)' : [385.0, 1.0860], \
#37 81
'[C](c(n))' : [453.2, 1.493], \
})
bondparamvals1 = dict({ \
#17 18
'[#5]-[#9]' : [320.0, 1.39], \
#19 20
'[#15]-[#9]' : [350.0, 1.626], \
#21 21
'[#7]-[#7]' : [1613.0, 1.0980], \
#22 23
'[CH4]-[#1]' : [395.5, 1.0835], \
#24 24
'[CH3]-[CH3]' : [323.0, 1.5247], \
#24 25
'[CH3]-[#1]' : [341.0, 1.1020], \
#24 26
'[CH3]-[CH2]' : [323.0, 1.5247], \
#24 28
'[CH3]-[CH1]' : [323.0, 1.5247], \
#26 26 '[CH2]-[CH2]' : [323.0, 1.5247], \
#26 27
'[CH2]-[#1]' : [341.0, 1.1120], \
#28 29
'[CH1]-[#1]' : [341.0, 1.1120], \
#30 78
'[CHO](c)' : [453.2, 1.4950], \
#(check) these are probably unnecessary because a 'c' only has a total of 3 bonds
#'[CHO](c([cH0]))' : [453.2, 1.4950], \
#'[CHO](c(c([cH0])))' : [453.2, 1.4950], \
#'[CHO](c(c(c[cH0])))' : [453.2, 1.4950], \
#31 32
'[OH2]-[#1]' : [529.6, .9572], \
#33 34
'[CH3](-[#1])([OH1])' : [385.0, 1.1120], \
#33 35
'[CH3](-[OH1])' : [500.1, 1.4130], \
#34 40
'[#1]-[CH1]([CH3])([CH3])([OH1])' : [341.0, 1.1120], \
#35 36
'[O](-[#1])([#6])' : [615.9, .9670], \
#35 40
'[O]-[CH1]([CH3])([CH3])' : [410.1, 1.4130], \
#35 78
'[O](c)' : [676.6, 1.3550], \
#37 39 (not needed, same as 37-38)
#'[C]-[#1]' : [385.0, 1.112], \
#37 40 (check) (why did i include the OH1 ??)
'[C][CH1]' : [323.0, 1.5247], \
#37 41
'[C](-[#1])([O]([CH2,CH3,c]))' : [378.0, 1.1120], \
#37 50 (check)
'[CH2]([#1])([N]([CH2]))([CH2])' : [2.96, .0220, .92], \
'[CH2]([#1])([CH2])([N]([CH2]))' : [2.96, .0220, .92], \
#37 51
'[C]-[C](=[O])' : [345.3, 1.5090], \
#37 54
'[C]-[N](C=O)' : [374.8, 1.4460], \
#37 56 (not needed, same as 37-62)
#'[C](-[#1])(C(=O)(N))' : [341.0, 1.1120], \
#37 57
'[C](-[#1])(N(C=O))' : [341.0, 1.1120], \
#37 60
#'[C]-[C](=[O])' : [345.3, 1.5090], \ (not needed, same as 37-51)
'[C]-[C](-[S])' : [345.3, 1.5090], \
#37 62
'[C](-[#1])(C=O)' : [341.0, 1.1120], \
#37 70
'[C](-[#1])(S(=O)(=O)([O-]))' : [341.0, 1.1120], \
#37 71
'[C]-[S](=O)(=O)([O-])' : [220.0, 1.8015], \
#38 84
'[#1]-[C](cnccccc)' : [341.0, 1.112], \
'[#1]-[C](ccncccc)' : [341.0, 1.112], \
'[#1]-[C](cccnccc)' : [341.0, 1.112], \
'[#1]-[C](ccccncc)' : [341.0, 1.112], \
#42 43
'[NH3]-[#1]' : [461.9, 1.015], \
#42 44 (needs_work)
#43 80 (needs_work) (two possible bond values, chose 2nd one)
'[#1](n)' : [467.6, 1.030], \
#44 48 (needs_work)
#44 80 (needs_work)
#45 46
'[N;D4;H4;+]-[#1]' : [461.9, 1.015], \
#48 49
'[N](-[#1])([C]([#1]))' : [515.9, 1.01], \
#51 52
'[C](-[#1])(=[O])([N])' : [356.4, 1.1004], \
#51 54
'[C](-[N])(=[O])' : [482.0, 1.3639], \
#51 83 (check) (could possibly combine with the other bonds with these values)
'[C](cnccccc)(=O)' : [345.3, 1.5090], \
'[C](ccncccc)(=O)' : [345.3, 1.5090], \
'[C](cccnccc)(=O)' : [345.3, 1.5090], \
'[C](ccccncc)(=O)' : [345.3, 1.5090], \
#51 85
'[C](=O)(cnccccc)' : [705.0, 1.2053], \
'[C](=O)(ccncccc)' : [705.0, 1.2053], \
'[C](=O)(cccnccc)' : [705.0, 1.2053], \
'[C](=O)(ccccncc)' : [705.0, 1.2053], \
#54 55
'[N](-[#1])(C=O)' : [542.0, 1.0034], \
#58 59
'[OH1](-[#1])(C=O)' : [514.4, .9737], \
#58 60 (check) (check all those involving #60)
'[OH1](C=O)' : [431.6, 1.3498], \
#60 61 (not needed, same as 51-61)
#60 65
'[C](-[#1])([S])' : [395.5, 1.085], \
#60 68
'[C]([S])([CH3])' : [323.0, 1.5247], \
#66 67
'[S](-[#1])([C])' : [315.4, 1.3320], \
#68 69
'[CH3](-[#1])([CH2]([S]))' : [341.0, 1.112], \
#71 72 (check)
'[S]~[O;D1]' : [570.0, 1.4780], \
#73 74
'[C]-[C](#N)' : [420.0, 1.4065], \
#74 75
'C(#N)(C)' : [1110.0, 1.153], \
#77 83
'[#1](cnccccc)' : [370.5, 1.1010], \
'[#1](ccncccc)' : [370.5, 1.1010], \
'[#1](cccnccc)' : [370.5, 1.1010], \
'[#1](ccccncc)' : [370.5, 1.1010], \
#78 78
'c(c([OH]))' : [610.9, 1.365], \
'c(c(c([OH])))' : [610.9, 1.365], \
'c(c(c(c([OH]))))' : [610.9, 1.365], \
#78 78
'c(c([CH3;CH2]))' : [610.9, 1.365], \
'c(c(c([CH3;CH2])))' : [610.9, 1.365], \
'c(c(c(c([CH3;CH2]))))' : [610.9, 1.365], \
#cc benzamidine
'c(c(~C(~N([#1])([#1]))(~N([#1])([#1]))))' : [472.0, 1.3887], \
'c(c(c(~C(~N([#1])([#1]))(~N([#1])([#1])))))' : [472.0, 1.3887], \
'c(c(c(c(~C(~N([#1])([#1]))(~N([#1])([#1]))))))' : [472.0, 1.3887], \
#78 79
'c([#1])(c([OH]))' : [409.5, 1.080], \
'c([#1])(c(c([OH])))' : [409.5, 1.080], \
'c([#1])(c(c(c([OH]))))' : [409.5, 1.080], \
#78 79
'c([#1])(c([CH3;CH2]))' : [409.5, 1.080], \
'c([#1])(c(c([CH3;CH2])))' : [409.5, 1.080], \
'c([#1])(c(c(c([CH3;CH2]))))' : [409.5, 1.080], \
#78 79
# 'c([#1])([cH0])' : [409.5, 1.080], \
# 'c([#1])(c([cH0]))' : [409.5, 1.080], \
# 'c([#1])(c(c([cH0])))' : [409.5, 1.080], \
#78 88
'c([C](N)(=N))' : [323.0, 1.525], \
#80 81 (check) (everything in the 80s should be checked)
'nc(n)' : [653.9, 1.345], \
#81 82
'c([#1])(n)' : [370.5, 1.0810], \
#83 83
'cc(ncccc)' : [471.9, 1.3887], \
'cc(cnccc)' : [471.9, 1.3887], \
'cc(ccncc)' : [471.9, 1.3887], \
#83 84
'c([CH2])(nccccc)' : [345.3, 1.5090], \
'c([CH2])(cncccc)' : [345.3, 1.5090], \
'c([CH2])(ccnccc)' : [345.3, 1.5090], \
'c([CH2])(cccncc)' : [345.3, 1.5090], \
#84 84
'[CH3]([CH2])(nccccc)' : [323.0, 1.5247], \
'[CH3]([CH2])(cncccc)' : [323.0, 1.5247], \
'[CH3]([CH2])(ccnccc)' : [323.0, 1.5247], \
'[CH3]([CH2])(cccncc)' : [323.0, 1.5247], \
#86 87
'N(-[#1])(~C(~N)(~c))' : [487.0, 1.028], \
#86 88
'N(~C(~N)(~c))' : [491.4, 1.3250], \
#89 90 (not needed, same as 43-80)
#'n([#1])' : [467.6, 1.030], \
})
bondvals1 = dict({ \
'[#1]~[#6;D3]' : [410], \
'[#6;D4]~[#6]' : [385], \
'[#6]~[#6;D4]' : [385], \
'[#6;D4]~[#7]' : [400], \
'[#6]~[#8;D1]' : [680], \
'[#6]~[#8;D2]' : [465], \
'[#6;D3]~[#6;D3]' : [680], \
'[#6;D3]~[#7;D2]' : [435], \
'[#6;D3]~[#7;D3]' : [250], \
'[#7;D1]~[#7]' : [1613], \
'[#7;D2]~[#7;D2]' : [950], \
'[#7]~[#8;D1]' : [900], \
'[#8;D2]~[#15]' : [450], \
'[#8;D1]~[#15]' : [775] \
})
bondvals2 = dict({ \
'[#1]~[#6]' : [400], \
'[#1]~[#7]' : [520], \
'[#1]~[#8]' : [560], \
'[#1]~[#9]' : [500], \
'[#1]~[#14]' : [200], \
'[#1]~[#15]' : [230], \
'[#1]~[#16]' : [260], \
'[#6]~[#6]' : [350], \
'[#6]~[#7]' : [450], \
'[#6]~[#8]' : [465], \
'[#6]~[#9]' : [350], \
'[#6]~[#14]' : [350], \
'[#6]~[#15]' : [350], \
'[#6]~[#16]' : [216], \
'[#6]~[#17]' : [350], \
'[#7]~[#7]' : [850], \
'[#7]~[#8]' : [750], \
'[#7]~[#14]' : [450], \
'[#7]~[#15]' : [500], \
'[#7]~[#16]' : [550], \
'[#8]~[#8]' : [750], \
'[#8]~[#14]' : [500], \
'[#8]~[#15]' : [450], \
'[#8]~[#16]' : [606], \
'[#8]~[#17]' : [500], \
'[#14]~[#14]' : [400], \
'[#14]~[#15]' : [450], \
'[#14]~[#16]' : [500], \
'[#14]~[#17]' : [650], \
'[#16]~[#16]' : [188] \
})
bondvals3 = dict({ \
'[#1]~[*]' : [300], \
'[#6]~[*]' : [450], \
'[#7]~[*]' : [600], \
'[#8]~[*]' : [600], \
'[#14]~[*]' : [450], \
'[#16]~[*]' : [250], \
'[#17]~[*]' : [300] \
})
bondvals4 = dict({ \
'[*]~[*]' : [defaultBConstVal], \
})
vals.append(bondvals4)
vals.append(bondvals3)
vals.append(bondvals2)
vals.append(bondvals1)
vals.append(bondparamvals3)
vals.append(bondparamvals2)
vals.append(bondparamvals1)
d = dict()
for v in vals:
for skey in iter(v):
openbabel.OBSmartsPattern.Init(self.sp,skey)
self.sp.Match(mol)
for ia in self.sp.GetMapList():
sortedlist = [self.idxtoclass[ia[0] - 1], self.idxtoclass[ia[1] - 1]]
sortedlist.sort()
key1 = sortedlist
key1string = '%d %d ' % (key1[0], key1[1])
# if(len(v[skey]) == 2):
blen = mol.GetBond(ia[0],ia[1]).GetLength()
key2 = 'bond%9d%6d%11.4f%10.4f' % (key1[0], key1[1], v[skey][0], blen)
# else:
# key2 = '#bond%10s%10.6f %s' % (key1string,v[skey][0],"error, parameter not found in amoeba parameters, resorted to tinker's analyze.x parameters")
d.update({key1string : key2})
x = []
for v in dict.itervalues(d):
x.append(v)
sortedtuple = sorted(d.iteritems(),
key=lambda(k,v): (k.split()[0],k.split()[1]))
x = [ t[1] for t in sortedtuple ]
return x
def angguess(self, mol):
found = []
vals = []
#dict = ({'[atom a][atom b][atom c]' : angle bend force constant})
angparamvals3 = dict({ \
#38 37 38 (check) (not sure if this is too vague)
'[#1][C][#1]' : [40.57, 107.6, 107.8, 109.47], \
})
angparamvals2 = dict({ \
#24 24 25
'[CH3][CH3][#1]' : [42.44, 109.80, 109.310, 110.70], \
#25 24 25
'[#1][CH3][#1]' : [39.57, 107.60, 107.8, 109.47], \
#25 24 26
'[#1][CH3][CH2]' : [42.44, 109.80, 109.310, 110.70], \
#25 24 28
'[#1][CH3][CH1]' : [42.0, 110.70], \
#24 26 26
'[CH3][CH2][CH2]' : [48.2, 109.5, 110.2, 111.0], \
#24 26 27
'[CH3][CH2][#1]' : [42.44, 109.8, 109.31, 110.7], \
#26 26 27
'[CH2][CH2][#1]' : [42.44, 109.8, 109.31, 110.7], \
#27 26 27
'[#1][CH2][#1]' : [39.57, 107.6, 107.8, 109.47], \
#24 28 24
'[CH3][CH1][CH3]' : [48.2, 109.5, 110.2, 111.0], \
#24 28 29
'[CH3][CH1][#1]' : [42.0, 112.8], \
#37 37 37
'[C][CH2][C]' : [48.2, 109.5, 110.2, 111.0], \
#37 37 38
'[C][C][#1]' : [45.44, 109.8, 109.310, 110.7], \
#37 37 39 (not needed, same as 37 37 38)
#'[C][CH3][#1]'
#37 37 47 (check) (should be moved, less specific than 37 37 50)
'[C][CH2]([#1])([N,c])' : [42.44, 109.8, 109.31, 110.7], \
#34 37 37
'[#1][CH2]([C])([OH1])' : [45.44, 109.8, 109.31, 110.7], \
#38 37 78 (check)
'[#1][C][c]' : [39.57, 109.5], \
#37 48 37
'[C][N][C]' : [51.8, 107.2, 108.2], \
#76 76 76
'ccc' : [63.31, 120], \
#37 81 80
'[C]cn' : [35.97, 122.0], \
})
angparamvals1 = dict({ \
#18 17 18
'[#9][#5][#9]' : [65.0, 109.47], \
#20 19 20 (needs_work) (possible mistake in forcefield)
'[#9][#15][#9]' : [40.0, 180], \
#23 22 23
'[#1][CH4][#1]' : [29.57, 109.470], \
#32 31 32
'[#1][O][#1]' : [34.05, 108.5], \
#34 33 34
'[#1][CH3]([#1])([OH1])' : [45.57, 107.6, 107.8, 109.47], \
#34 33 35
'[#1][CH3][OH1]' : [60.99, 110.0, 108.9, 108.7], \
#33 35 36 (check) (might not be needed, same as 36-35-37)
'[CH3][O][#1]' : [64.96, 106.8], \
#36 35 37
'[#1][O][C]' : [64.96, 106.8], \
#36 35 40 (check) (make more general?)
'[#1][O][CH1]([CH3])([CH3])' : [53.96, 106.8], \
#36 35 78
'[#1][O][c]' : [25.9, 109.0], \
#37 35 37
'[C][O][C]' : [88.5, 106.0], \
#34 37 34 (check)
'[#1][C]([#1])([OH1])' : [40.57, 107.6, 107.8, 109.47], \
#'[#1][C][#1]' : [40.57, 107.6, 107.8, 109.47], \
#34 37 35
'[#1][C][O]' : [60.99, 110.0, 108.9, 108.7], \
#35 37 37
'[O][CH2][C]' : [65.71, 107.5, 107.0, 107.9], \
#35 37 41
'[O]([C])([#1])([CH2,CH3,c])' : [70.0, 110.0, 108.9, 108.7], \
#37 37 48 (check) (should be moved, less specific than 37 37 54)
'[C][CH2][N]' : [56.11, 109.47, 108.0, 111.0], \