openbabel-ruby 3.1.1.2-x86_64-linux

data/lib/openbabel/3.1.0/data/3.1.1/mmffvdw.par

@@ -0,0 +1,105 @@
+*
+*                Copyright (c) Merck and Co., Inc., 1994
+*                         All Rights Reserved
+*
+*  power      B       Beta     DARAD      DAEPS
+*  0.25      0.2       12.       0.8        0.5      
+*
+*  type  alpha-i     N-i       A-i       G-i DA Symb   Origin
+*------------------------------------------------------------
+    1     1.050     2.490     3.890     1.282 - CR     E94
+    2     1.350     2.490     3.890     1.282 - C=C    E94
+    3     1.100     2.490     3.890     1.282 - C=O    E94
+    4     1.300     2.490     3.890     1.282 - CSP    E94
+    5     0.250     0.800     4.200     1.209 - HC     C94
+    6     0.70      3.150     3.890     1.282 A OR     C94
+    7     0.65      3.150     3.890     1.282 A O=C    C94
+    8     1.15      2.820     3.890     1.282 A NR     C94
+    9     0.90      2.820     3.890     1.282 A N=C    C94
+   10     1.000     2.820     3.890     1.282 A NC=O   E94
+   11     0.35      3.480     3.890     1.282 A F      C94
+   12     2.300     5.100     3.320     1.345 A CL     E94
+   13     3.400     6.000     3.190     1.359 A BR     E94
+   14     5.500     6.950     3.080     1.404 A I      E94
+   15     3.00      4.800     3.320     1.345 A S      C94
+   16     3.900     4.800     3.320     1.345 A S=C    E94
+   17     2.700     4.800     3.320     1.345 - SO     E94
+   18     2.100     4.800     3.320     1.345 - SO2    E94
+   19     4.500     4.200     3.320     1.345 - SI     E94
+   20     1.050     2.490     3.890     1.282 - CR3R   E94
+   21     0.150     0.800     4.200     1.209 D HOR    C94
+   22     1.100     2.490     3.890     1.282 - CR3R   E94
+   23     0.150     0.800     4.200     1.209 D HNR    C94
+   24     0.150     0.800     4.200     1.209 D HOCO   C94
+   25     1.600     4.500     3.320     1.345 - PO4    E94
+   26     3.600     4.500     3.320     1.345 A P      E94
+   27     0.150     0.800     4.200     1.209 D HN=C   C94
+   28     0.150     0.800     4.200     1.209 D HNCO   C94
+   29     0.150     0.800     4.200     1.209 D HOCC   C94
+   30     1.350     2.490     3.890     1.282 - CE4R   E94
+   31     0.150     0.800     4.200     1.209 D HOH    C94
+   32     0.75      3.150     3.890     1.282 A O2CM   C94
+   33     0.150     0.800     4.200     1.209 D HOS    C94
+   34     1.00      2.820     3.890     1.282 - NR+    C94
+   35     1.50      3.150     3.890     1.282 A OM     X94
+   36     0.150     0.800     4.200     1.209 D HNR+   C94
+   37     1.350     2.490     3.890     1.282 - CB     E94
+   38     0.85      2.820     3.890     1.282 A NPYD   C94
+   39     1.10      2.820     3.890     1.282 - NPYL   C94
+   40     1.00      2.820     3.890     1.282 A NC=C   E94
+   41     1.100     2.490     3.890     1.282 - CO2M   C94
+   42     1.000     2.820     3.890     1.282 A NSP    E94
+   43     1.000     2.820     3.890     1.282 A NSO2   E94
+   44     3.00      4.800     3.320     1.345 A STHI   C94
+   45     1.150     2.820     3.890     1.282 - NO2    E94
+   46     1.300     2.820     3.890     1.282 - N=O    E94
+   47     1.000     2.820     3.890     1.282 A NAZT   X94
+   48     1.200     2.820     3.890     1.282 A NSO    X94
+   49     1.00      3.150     3.890     1.282 - O+     X94
+   50     0.150     0.800     4.200     1.209 D HO+    C94
+   51     0.400     3.150     3.890     1.282 - O=+    E94
+   52     0.150     0.800     4.200     1.209 D HO=+   C94
+   53     1.000     2.820     3.890     1.282 - =N=    X94
+   54     1.30      2.820     3.890     1.282 - N+=C   C94
+   55     0.80      2.820     3.890     1.282 - NCN+   E94
+   56     0.80      2.820     3.890     1.282 - NGD+   E94
+   57     1.000     2.490     3.890     1.282 - CNN+   E94
+   58     0.80      2.820     3.890     1.282 - NPD+   E94
+   59     0.65      3.150     3.890     1.282 A OFUR   C94
+   60     1.800     2.490     3.890     1.282 A C%-    E94
+   61     0.800     2.820     3.890     1.282 A NR%    E94
+   62     1.300     2.820     3.890     1.282 A NM     X94
+   63     1.350     2.490     3.890     1.282 - C5A    E94
+   64     1.350     2.490     3.890     1.282 - C5B    E94
+   65     1.000     2.820     3.890     1.282 A N5A    E94
+   66     0.75      2.820     3.890     1.282 A N5B    C94
+   67     0.950     2.82      3.890     1.282 A N2OX   X94
+   68     0.90      2.82      3.890     1.282 A N3OX   C94
+   69     0.950     2.82      3.890     1.282 A NPOX   C94
+   70     0.87      3.150     3.890     1.282 A OH2    C94
+   71     0.150     0.800     4.200     1.209 D HS     C94
+   72     4.000     4.800     3.320     1.345 A SM     X94
+   73     3.000     4.800     3.320     1.345 - SMO2   X94
+   74     3.000     4.800     3.320     1.345 - =S=O   X94
+   75     4.000     4.500     3.320     1.345 A -P=C   X94
+   76     1.200     2.820     3.890     1.282 A N5M    X94
+   77     1.500     5.100     3.320     1.345 A CLO4   X94
+   78     1.350     2.490     3.890     1.282 - C5     X94
+   79     1.000     2.820     3.890     1.282 A N5     X94
+   80     1.000     2.490     3.890     1.282 - CIM+   C94
+   81     0.80      2.820     3.890     1.282 - NIM+   C94
+   82     0.950     2.82      3.890     1.282 A N5OX   X94
+   87     0.45      6.        4.        1.4   - FE+2   X94
+   88     0.55      6.        4.        1.4   - FE+3   X94
+   89     1.4       3.48      3.890     1.282 A F-     X94
+   90     4.5       5.100     3.320     1.345 A CL-    X94
+   91     6.0       6.000     3.190     1.359 A BR-    X94
+   92     0.15      2.        4.        1.3   - LI+    X94
+   93     0.4       3.5       4.        1.3   - NA+    X94
+   94     1.0       5.        4.        1.3   - K+     X94
+   95     0.43      6.        4.        1.4   - ZN+2   X94
+   96     0.9       5.        4.        1.4   - CA+2   X94
+   97     0.35      6.        4.        1.4   - CU+1   X94
+   98     0.40      6.        4.        1.4   - CU+2   X94
+   99     0.35      3.5       4.        1.3   - MG+2   X94
+$

data/lib/openbabel/3.1.0/data/3.1.1/mpC.txt

@@ -0,0 +1,177 @@
+#######################################################################
+# An Open Notebook Science Project: Celcius Melting Point Model                                                              
+# This model and the data upon which it is built is released under a CC0 license                                                                                             
+######################################################################
+# mpC Atomic Contributions
+# Authors: Jean-Claude Bradley, Evan M. Curtin, William J. Griffiths, Andrew S.I.D. Lang, Antony J. Williams 
+# ref. ONSMP011 http://onschallenge.wikispaces.com/MeltingPointModel011
+######################################################################
+;hydrogen	
+[*]	0
+[#6]	-11.2891
+[#1]	0
+[#5]	-8.0352
+[#14]	-36.0534
+[#15]	0
+[#16]	0
+[#50]	0
+[#7]	32.1543
+[O][CX4]	7.3289
+[O]c	22.9132
+[O][#5]	48.0277
+[O][#14]	0
+[O][#15]	26.5074
+[O][#33]	0
+[O][#50]	0
+[O][#7]	42.6169
+[O]C=[#6]	0
+[O]C=[#7]	0
+[O]C=O	44.4787
+[O]C=S	0
+[O]O	24.8303
+[O]S	40.0567
+;heavy	
+[*]	0
+[#9-0]	-15.2212
+[#17-0]	-8.2654
+[#35-0]	0
+[#53-0]	14.7222
+[#9-*]	0
+[#17-*]	0
+[#35-*]	0
+[#53-*]	0
+[#53+*]	0
+[B,Si,Ga,Ge,As,Se,Sn,Te,Pb,Nc,Nr,Kr,Xe,Rn]	17.7551
+[Fe,Cu,Zn,Tc,Cd,Pt,Au,Hg]	0
+[#6]	34.2188
+[CH4]	0
+[CH2](C)C	0
+[CH](C)(C)C	0
+[C](C)(C)(C)C	40.6006
+[CH3][O,N,F,Cl,Br,#15,#16,#53;!a]	0
+[CH2X4][O,N,F,Cl,Br,#15,#16,#53;!a]	0
+[CHX4][O,N,F,Cl,Br,#15,#16,#53;!a]	0
+[CH0X4][O,N,F,Cl,Br,#15,#16,#53;!a]	32.9369
+[C]=[A!#6]	20.7267
+[CH2]=C	-14.8687
+[CH1](=C)A	15.5201
+[CH0](=C)(A)A	18.94
+[C](=C)=C	0
+[CX2]#A	8.0103
+[CH3]c	0
+[CH3][a!#6]	0
+[CH2X4]a	0
+[CHX4]a	0
+[CH0X4]a	28.8598
+[c][#5,#14,#15,#33,#34,#50,#80]	27.9572
+[c][#9]	19.6289
+[c][#17]	25.3437
+[c][#35]	26.479
+[c][#53]	10.0405
+[cH]	11.6743
+[c](:a)(:a):a	22.2839
+[c](:a)(:a)-a	18.3672
+[c](:a)(:a)-C	17.1777
+[c](:a)(:a)-N	20.7165
+[c](:a)(:a)-O	18.4476
+[c](:a)(:a)-S	17.1867
+[c](:a)(:a)=C	31.1712
+[c](:a)(:a)=N	43.4894
+[c](:a)(:a)=O	35.4438
+[C](=C)(a)A	18.5955
+[C](=C)(c)a	16.8983
+[CH](=C)a	26.0819
+[C]=c	0
+[CX4][!#6;!#7;!#8;!#9;!#15;!#16;!#17;!#35;!#53;!#1]	0
+[CX4][!#6;!#7;!#8;!#9;!#15;!#16;!#17;!#35;!#53]	21.9141
+[#7]	0
+[N](-*)(-*)-*	13.9251
+[N](-*)=*	7.7621
+[N]#*	0
+[N](-*)(=*)=*	19.467
+[N](=*)#*	0
+[N]1(-*)-*-*1	0
+[NH](-*)-*	-4.975
+[NH]1-*-*1	0
+[NH]=*	-22.2462
+[NH2]-*	-21.349
+[N+](-*)(-*)(-*)-*	0
+[N+](-*)(-*)=*	0
+[N+](-*)#*	0
+[NH+](-*)(-*)-*	0
+[NH+](-*)=*	0
+[NH2+](-*)-*	0
+[NH2+]=*	0
+[NH3+]-*	0
+[n](:*):*	0
+[n](:*)(:*):*	0
+[n](-*)(:*):*	0
+[n](=*)(:*):*	0
+[nH](:*):*	0
+[n+](:*)(:*):*	0
+[n+](-*)(:*):*	0
+[nH+](:*):*	0
+[NH2+0]a	-34.4811
+[NH+0](a)a	0
+[NH+0]=a	-32.8638
+[N+0](=a)a	0
+[N+0](a)(a)a	0
+[N+0]#A	13.9377
+[NH3+*]	0
+[NH2+*]	0
+[NH+*]	0
+[n+0]	15.8908
+[n+*]	0
+[NH0+*](A)(A)(A)A	96.6851
+[NH0+*](=A)(A)a	0
+[NH0+*](=[#6])=[#7]	0
+[N+*]#A	0
+[N-*]	0
+[N+*](=[N-*])=N	0
+[#8]	0
+[O](-*)-*	0
+[O]1-*-*1	0
+[O]=*	10.3334
+[OH]-*	0
+[O-]-*	0
+[o](:*):*	0
+[o]	0
+[OH]	0
+[OH2]	0
+[O](C)C	-8.9495
+[OH0](C)[A!#6]	-6.6031
+[OH0]([A!#6])[A!#6]	0
+[O]([A;!#1])a	0
+[O](a)a	0
+[O]=[#8]	0
+[O]=[#7]	0
+[OX1-*][#7]	0
+[OX1-*][#16]	0
+[OX1-*][#15;#33;#43;#53]	0
+[O]=c	0
+[O]=[CH0](C)[A;!6]	0
+[O]=[CH]N	0
+[O]=[CH]O	-27.6702
+[O]=[CH2]	0
+[O]=[CX2]=O	0
+[O]=[CH]c	8.544
+[O]=C(c)c	4.8169
+[O]=[CH0](C)[a!#6]	0
+[O]=C([a!#6])[a!#6]	0
+[O-1]C(=O)	0
+[#15]	0
+[P](-*)(-*)-*	0
+[P](-*)=*	0
+[P](-*)(-*)(-*)=*	11.6943
+[PH](-*)(-*)=*	0
+[S](-*)-*	0
+[S]=*	0
+[S](-*)(-*)=*	0
+[S](-*)(-*)(=*)=*	0
+[SH]-*	0
+[s](:*):*	0
+[s](=*)(:*):*	0
+[S-0]	8.9702
+[S-*]	0
+[S+*]	0
+[s]	0

data/lib/openbabel/3.1.0/data/3.1.1/mr.txt

@@ -0,0 +1,168 @@
+######################################################################
+# Copyright OELIB:          OpenEye Scientific Software, Santa Fe,      
+#                           U.S.A., 1999,2000,2001                      
+# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of  
+#                           Tuebingen, Germany, 2001,2002,2003,2004,2005
+# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany,        
+#                           2003,2004,2005                              
+#                                                                       
+# Authors: Stephen Jelfs                                                                       
+#          Joerg Kurt Wegner, me@cheminformatics.eu         
+#                                                                       
+# This program is free software; you can redistribute it and/or modify  
+# it under the terms of the GNU General Public License as published by  
+# the Free Software Foundation version 2 of the License.                
+#                                                                       
+# This program 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.                          
+######################################################################
+# MR Atomic Contributions
+# ref. Wildman, S.A. and Crippen, G.M., J. Chem. Inf. Comput. 
+#   Sci., 1999, 39, 868-873.
+# Table below is adapted from above ref. 
+######################################################################
+;hydrogen
+[*]	1.112
+[#6]	1.057
+[#1]	1.057
+[O][CX4]	1.395
+[O]c	1.395
+[O][#5]	1.395
+[O][#14]	1.395
+[O][#15]	1.395
+[O][#33]	1.395
+[O][#50]	1.395
+[#5]	1.395
+[#14]	1.395
+[#15]	1.395
+[#16]	1.395
+[#50]	1.395
+[#7]	0.9627
+[O][#7]	0.9627
+[O]C=[#6]	1.805
+[O]C=[#7]	1.805
+[O]C=O	1.805
+[O]C=S	1.805
+[O]O	1.805
+[O]S	1.805
+;heavy
+[*]	0
+[#6]	3.243
+[CH4]	2.503
+[CH3]C	2.503
+[CH2](C)C	2.503
+[CH](C)(C)C	2.433
+[C](C)(C)(C)C	2.433
+[CH3][O,N,F,Cl,Br,#15,#16,#53;!a]	2.753
+[CH2X4][O,N,F,Cl,Br,#15,#16,#53;!a]	2.753
+[CHX4][O,N,F,Cl,Br,#15,#16,#53;!a]	2.731
+[CH0X4][O,N,F,Cl,Br,#15,#16,#53;!a]	2.731
+[C]=[A!#6]	5.007
+[CH2]=C	3.513
+[CH1](=C)A	3.513
+[CH0](=C)(A)A	3.513
+[C](=C)=C	3.513
+[CX2]#A	3.888
+[CH3]c	2.464
+[CH3][a!#6]	2.412
+[CH2X4]a	2.488
+[CHX4]a	2.582
+[CH0X4]a	2.576
+[c][#5,#14,#15,#33,#34,#50,#80]	4.041
+[c][#9]	3.257
+[c][#17]	3.564
+[c][#35]	3.18
+[c][#53]	3.104
+[cH]	3.35
+[c](:a)(:a):a	4.346
+[c](:a)(:a)-a	3.904
+[c](:a)(:a)-C	3.509
+[c](:a)(:a)-N	4.067
+[c](:a)(:a)-O	3.853
+[c](:a)(:a)-S	2.673
+[c](:a)(:a)=C	3.135
+[c](:a)(:a)=N	3.135
+[c](:a)(:a)=O	3.135
+[C](=C)(a)A	4.305
+[C](=C)(c)a	4.305
+[CH](=C)a	4.305
+[C]=c	4.305
+[CX4][!#6;!#7;!#8;!#9;!#15;!#16;!#17;!#35;!#53]	2.693
+[#7]	2.134
+[NH2+0]A	2.262
+[NH+0](A)A	2.173
+[NH2+0]a	2.827
+[NH+0](A)a	3
+[NH+0](a)a	3
+[NH+0]=A	1.757
+[NH+0]=a	1.757
+[N+0](=A)A	2.428
+[N+0](=A)a	2.428
+[N+0](=a)A	2.428
+[N+0](=a)a	2.428
+[N+0](A)(A)A	1.839
+[N+0](a)(A)A	2.819
+[N+0](a)(a)A	2.819
+[N+0](a)(a)a	2.819
+[N+0]#A	1.725
+[NH3+*]	2.134
+[NH2+*]	2.134
+[NH+*]	2.134
+[n+0]	2.202
+[n+*]	2.134
+[NH0+*](A)(A)(A)A	0.2604
+[NH0+*](=A)(A)A	0.2604
+[NH0+*](=A)(A)a	0.2604
+[NH0+*](=[#6])=[#7]	0.2604
+[N+*]#A	3.359
+[N-*]	3.359
+[N+*](=[N-*])=N	3.359
+[#8]	0.6865
+[o]	1.08
+[OH]	0.8238
+[OH2]	0.8238
+[O](C)C	1.085
+[OH0](C)[A!#6]	1.085
+[OH0]([A!#6])[A!#6]	1.085
+[O](A)a	1.182
+[O](a)a	1.182
+[O]=[#8]	3.367
+[O]=[#7]	3.367
+[OX1-*][#7]	3.367
+[OX1-*][#16]	0.7774
+[OX1-*][#15;#33;#43;#53]	0
+[O]=c	3.135
+[O]=[CH]C	0
+[O]=C(C)C	0
+[O]=[CH0](C)[A;!6]	0
+[O]=[CH]N	0
+[O]=[CH]O	0
+[O]=[CH2]	0
+[O]=[CX2]=O	0
+[O]=[CH]c	0.2215
+[O]=C(C)c	0.2215
+[O]=C(c)c	0.2215
+[O]=[CH0](c)[a!#6]	0.2215
+[O]=[CH0](c)[A!#6]	0.2215
+[O]=[CH0](C)[a!#6]	0.2215
+[O]=C([A!#6])[A!#6]	0.389
+[O]=C([A!#6])[a!#6]	0.389
+[O]=C([a!#6])[a!#6]	0.389
+[O-1]C(=O)	0.6865
+[#9-0]	1.108
+[#17-0]	5.853
+[#35-0]	8.927
+[#53-0]	14.02
+[#9-*]	1.108
+[#17-*]	5.853
+[#35-*]	8.927
+[#53-*]	14.02
+[#53+*]	14.02
+[#15]	6.920
+[S-0]	7.591
+[S-*]	7.365
+[S+*]	7.365
+[s]	6.691
+[B,Si,Ga,Ge,As,Se,Sn,Te,Pb,Nc,Nr,Kr,Xe,Rn]	5.754

data/lib/openbabel/3.1.0/data/3.1.1/patterns.txt

@@ -0,0 +1,76 @@
+#Comments after SMARTS
+##############################################################################
+#                                                                            #
+#                       Open Babel file: patterns.txt                        #
+#                                                                            #
+#  Copyright (c) 2005 Chris Morley                                           #
+#  Part of the Open Babel package, under the GNU General Public License (GPL)#
+#                                                                            #
+# Functional groups for molecular fingerprinting based on Checkmol:          #
+#   http://merian.pch.univie.ac.at/~nhaider/cheminf/fgtable.pdf              #
+# (Numbers 200+ are from Chris Swain)                                        #
+# SMARTS Patterns are used by finger3.cpp:PatternFP                          #
+# Format of each line is a SMARTS pattern, then optionally                   #
+#   followed by a tab character and a pattern number and/or description      #
+#   (everything after the tab will be ignored by the code)                   #
+# A file of this format needs the same first line as this one.               #
+# An alternative format, as in SMARTS_InteLigand.txt, can also be used       #
+#                                                                            #
+#  INCOMPLETE!! Really only useful to test the fingerprint FP3               #
+##############################################################################
+[+]	1	cation
+[-]	2	anion
+[#6][CX3](=O)	3 aldehyde or ketone
+[CX3H1](=O)[#6]	4 aldehyde
+[#6][CX3](=O)[#6]	5 ketone
+[#6][CX3](=S)	6 thioaldehyde or thioketone
+[CX3H1](=S)	7 thioaldehyde
+[#6]C(=[S])[#6]	8 thioketone
+[CX3]=N([#6,#1])[#6,#1]	9 imine
+[#6,#1]C([#6,#1])=[N][N]([#6,#1])[#6,#1]	10 hydrazone
+[#6,#1]C([#6,#1])=[N][N]([#6,#1])C(=[O])[N]([#6,#1])[#6,#1]	11 semicarbazone
+[#6,#1]C([#6,#1])=[N][N]([#6,#1])C(=[S])[N]([#6,#1])[#6,#1]	12 thiosemicarbazone
+[#6,#1]C([#6,#1])=[N][OH]	13 oxime
+[#6,#1]C([#6,#1])=[N][O][#6]	14 oxime ether
+[CX3]=C=O	15 ketene
+[CX3]=C=O	16 keten acetyl derivative***
+[#6,#1]C([#6,#1])([OH])([OH])	17 carbonyl hydrate
+[#6,#1]C([#6,#1])([OH])(O[#6])	18 hemiacetal
+[#6,#1]C([#6,#1])(O[#6])(O[#6])	19 acetal
+[#6,#1]C([#6,#1])(N([#6,#1])[#6,#1])(O[#6])	20 hemiaminal	
+[#6,#1]C([#6,#1])(N([#6,#1])[#6,#1])(N([#6,#1])[#6,#1])	21 aminal	
+[#6,#1]C([#6,#1])(N([#6,#1])[#6,#1])([S][#6])	22 thiohemiaminal	
+[#6,#1]C([#6,#1])([S][#6])([S][#6])	23 thioacetal
+[#6,#1]C([#6,#1])=C([#6,#1])N([#6,#1])[#6,#1]	24 enamine
+[#6,#1]C([#6,#1])=C([#6,#1])[OH]	25 enol
+[#6,#1]C([#6,#1])=C([#6,#1])O[#6]	26 enol ether
+[#6][OH]	27 hydroxy compound
+C[OH]	28 alcohol
+[#6][CH2][OH]	29 primary alcohol   
+[#6][CH]([#6])[OH]	30 secondary alcohol   
+[#6][C]([#6])([#6])[OH]	31 tertiary alcohol   
+[#6,#1]C([#6,#1])([OH])C([#6,#1])([#6,#1])[OH]	32 1,2-diol
+[#6,#1]C([#6,#1])([OH])C([#6,#1])([#6,#1])[NH2]	33 1,2-aminoalcohol
+c[OH]	34 phenol
+[OH]cc[OH]	35 1,2-diphenol
+[OH]C=C[OH]	36 enediol
+[#6]O[#6]	37 ether
+COC	38 dialkyl ether
+cOC	39 alkylaryl ether
+cOc	40 diaryl ether
+[#6]S[#6]	41 thioether
+[#6]SS[#6]	42 disulfide
+[#6]OO[#6]	43 peroxide
+[#6]O[OH]	44 hydroperoxide
+[a]	200 aryl
+[!#6;$([N,O,S,F,Cl,Br,I,P])]	201 heteroatom
+[!#6;!$([+0]);!$([F,Cl,Br,I]);!$([o,s,nX3]);!$([Nv5,Pv5,Sv4,Sv6])]	202 HBA
+[$([N,O;!H0]),$(N(C)(C)C)]	203 HBD
+[R]	204 Ring
+[$([$([C;$(C=[$([O;D1;$(O=C)])])]);$(C[$([O;$([H1&-0,H0&-1])])]);$(C[#6,#1])])]	205 carboxylic acid
+[$([$([C;$(C=[$([O;D1;$(O=C)])])]);$(C(=O)O[#6]);$(C[#6,#1])])]	206 ester
+[$([N;+0,+1;$(N(=O)~[O;H0;-0,-1])])]	207 nitro
+[$([C;$(C#[N;D1])])]	208 nitrile
+[$([N;!$(N*=[!#6])]);$(N[$([a])]);!$(N~[!#6])]	209 aniline
+[$([N;$(N[$([$([C;$(C=[$([O;D1;$(O=C)])])]);$(C(=O)(N)N)])])])]	210 urea
+

data/lib/openbabel/3.1.0/data/3.1.1/phmodel.txt

@@ -0,0 +1,180 @@
+##############################################################################
+#                                                                            #
+#                   Open Babel file: phmodel.txt                             #
+#                                                                            #
+#  Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc.              #
+#  Some portions Copyright (c) 2001-2003 by Geoffrey R. Hutchison            #
+#  Part of the Open Babel package, under the GNU General Public License (GPL)#
+#                                                                            #
+#  pH model data (used by phmodel.cpp:OBPhModel)                             #
+#                                                                            #
+# TRANSFORM: chemical transforms can be used to modify formal charges, bond  #
+#            orders, and to delete atoms (i.e hydrogens). Changes are applied#
+#        to vector bound atoms (use the [:#] SMARTS notation) and bonds      #
+#            between vector bound atoms.                                     #
+# SEEDCHARGE: used to seed partial charges.  Seed partial charges            #
+#             are used as initial values in Gasteiger charge calculation     #
+#                                                                            #
+##############################################################################
+
+#carboxylic acid							# pKa
+#TRANSFORM O=CO[#1:1] >> O=CO						4.0 # pKa from acid (AH)
+TRANSFORM O=C[OD1-0:1] >> O=C[O-:1]					4.0 # pKa from acid (AH)
+
+#uncomment for vinylogous carboxylic acids (e.g. ascorbic acid)
+TRANSFORM [O:1]=[C:2][C:3]=[C:4][O:5] >> [O:1]=[C:2][C:3]=[C:4][O-:5]   4.0 # pKa from acid (AH)
+
+#charged amine
+TRANSFORM [N^3;!$(N~[!#6;!#1]):1] >> [N+:1]				10.0 # pKa from conjugated acid (BH+)
+
+#imidazole: note pKa=7.0
+#if you uncomment this, also uncomment the seedcharge statement below
+TRANSFORM [nD2:1]1c[nH]cc1 >> [n+:1]1c[nH]cc1				7.0
+
+#imine
+TRANSFORM [ND3+0:1]=[#6] >> [ND3+:1]=[#6]				4.0 # pKa from conjugated acid (BH+)
+
+#tetrazole
+TRANSFORM [nD2:1]([#1:2])1[nD2-0][nD2-0][nD2-0]c1 >> [n-:1]1nnnc1	4.89 #pKa from acid (AH)
+TRANSFORM [nD2-0]1[nD2:1]([#1:2])[nD2-0][nD2-0]c1 >> n1[n-:1]nnc1	4.89 #pKa from acid (AH)
+TRANSFORM [nD2-0:1]1[nD2-0][nD2-0][nD2-0]c1 >> [n-:1]1nnnc1		4.89 #pKa from acid (AH)
+
+#azide (always apply these transformations)
+TRANSFORM [ND1:1]~[ND2:2]~[ND1:3] >> [N-:1]=[N+:2]=[N-:3] 1E+10	    # azide ion
+TRANSFORM [ND1:1]~[ND2:2]~[ND1:3]~* >> [N-:1]=[N+:2]=[N:3]-* 1E+10   # azide group
+TRANSFORM [NH2:1]~[NH1:2]~[NH1:3]~* >> [N-:1]=[N+:2]=[N:3]-* 1E+10	# azide group
+TRANSFORM [NH1:1]~[ND2:2]~[NH1:3]~* >> [N-:1]=[N+:2]=[N:3]-* 1E+10	# azide group
+
+#nitro group (-NO2)
+TRANSFORM [O:1]=[N:2]-[O:3] >> [O:1]=[N+:2]-[O-:3]  1E+10
+TRANSFORM [O:1]-[N:2]-[O:3] >> [O:1]=[N+:2]-[O-:3]  1E+10
+
+#hydroxamic acid
+#TRANSFORM O=CN[OD1-0:1][#1:2] >> O=CN[O-:1]				8.0
+TRANSFORM O=CN[OD1-0:1]     >> O=CN[O-:1]				8.0
+
+#sulfinic acid
+TRANSFORM [SD3](=O)[OD1:1]   >> [SD3](=O)[O-:1]				2.0
+TRANSFORM [SD3](=O)[O:1][#1:2] >> [SD3](=O)[O-:1]			2.0
+
+#sulfonic acid
+TRANSFORM [SD4]([!D1])(=O)(=O)[OD1:1] >> [SD4]([!D1])(=O)(=O)[O-:1]	-2.6
+TRANSFORM [SD4]([!D1])(=O)(=O)[O:1][#1:2] >> [SD4]([!D1])(=O)(=O)[O-:1]	-2.6
+#sulfuric acid (same as sulfonic acid...)
+#TRANSFORM [SD4]([!D1])(=O)(=O)[OD1:1] >> [SD4]([!D1])(=O)(=O)[O-:1]
+#TRANSFORM [SD4]([!D1])(=O)(=O)[O:1][#1:2] >> [SD4]([!D1])(=O)(=O)[O-:1]
+
+#guanidine or amidine
+TRANSFORM [#6^2+0:1](=[N^2+0:2])(~[N^2:3])* >> [#6:1](=[N+1:2])(~[N:3])*		12.5
+
+#phosphate ester
+TRANSFORM [PD4](=O)([OD2])([OD2])[OD1:1] >> [PD4](=O)([OD2])([OD2])[O-:1]	2.0
+#TRANSFORM [PD4](=O)([OD2])([OD2])[OD1:1][#1:2] >> [PD4](=O)([OD2])([OD2])[O-:1]	2.0
+
+# phosphonate
+TRANSFORM [PD4](=O)([OD2])([!#8])[OD1:1] >> [PD4](=O)([OD2])([!#8])[O-:1]	2.2
+# http://research.chem.psu.edu/brpgroup/pKa_compilation.pdf
+
+#phosphoric acid
+#TRANSFORM O=P([!D1])([O:1][#1:2])[O:3][#1:4] >> O=P([*D2,*D3])([O:1])[O:3]	2.12
+TRANSFORM O=P([!D1])([O:1][#1:2])[OD1]       >> O=P([!D1])([O:1])O		2.12
+TRANSFORM O=P([*D2,*D3])([OD1:1])[OD1:2] >> O=P([*D2,*D3])([O-:1])[O-:2]	2.12
+#phosphate
+
+#
+#	Amino acids
+#									pKa sidechain
+# aspartic acid
+#TRANSFORM O=CC(N)CC(=O)O[#1:1] >> O=CC(N)CC(=O)O			3.8
+TRANSFORM O=C(O)C(N)CC(=O)[OD1:1] >> O=C(O)C(N)CC(=O)[O-:1]		3.8 
+TRANSFORM O=C(NCC=O)C(N)CC(=O)[OD1:1] >> O=C(NCC=O)C(N)CC(=O)[O-:1]     3.8 
+
+# glutamic acid
+#TRANSFORM O=CC(N)CCC(=O)O[#1:1] >> O=CC(N)CCC(=O)O		        4.3
+TRANSFORM O=C(O)C(N)CCC(=O)[OD1:1] >> O=C(O)C(N)CCC(=O)[O-:1]		5.0
+TRANSFORM O=C(NCC=O)C(N)CCC(=O)[OD1:1] >> O=C(NCC=O)C(N)CCC(=O)[O-:1]	5.0
+
+# arginine
+TRANSFORM O=C(O)C(N)CCCNC(N)=[N:1] >> O=C(O)C(N)CCCNC(N)=[N+:1] 	12.0
+TRANSFORM O=C(NCC=O)C(N)CCCNC(N)=[N:1] >> O=C(NCC=O)C(N)CCCNC(N)=[N+:1] 12.0
+
+# lysine
+TRANSFORM O=C(O)C(N)CCCC[N:1] >> O=C(O)C(N)CCCC[N+:1] 			10.5
+TRANSFORM O=C(NCC=O)C(N)CCCC[N:1] >> O=C(NCC=O)C(N)CCCC[N+:1] 	        10.5
+
+# histidine
+TRANSFORM O=C(O)C(N)Cc1[nH0:1]c[nH]c1  >> O=C(O)C(N)Cc1[n+:1]c[nH]c1            6.08
+TRANSFORM O=C(O)C(N)Cc1[nH]c[nH0:1]c1  >> O=C(O)C(N)Cc1[nH]c[n+:1]c1            6.08
+TRANSFORM O=C(NCC=O)C(N)Cc1[nH0:1]c[nH]c1  >> O=C(NCC=O)C(N)Cc1[n+:1]c[nH]c1    6.08
+
+# cysteine
+TRANSFORM O=C(O)C(N)C[S:1]  >> O=C(O)C(N)C[S-:1]			 8.28
+TRANSFORM O=C(NCC=O)C(N)C[S:1]  >> O=C(NCC=O)C(N)C[S-:1]		 8.28
+
+# tyrosine
+TRANSFORM O=C(O)C(N)Cc1ccc([O:1])cc1  >> O=C(O)C(N)Cc1ccc([O-:1])cc1	        10.1
+TRANSFORM O=C(NCC=O)C(N)Cc1ccc([O:1])cc1  >> O=C(NCC=O)C(N)Cc1ccc([O-:1])cc1    10.1
+
+# old:
+# histidine
+#TRANSFORM [nD2:1]1c[nD2]cc1 >> [n+:1]1c[nD2]cc1
+# uncomment for tryptophan
+# TRANSFORM [nD2:1]1cccc1 >> [n+:1]1cccc1
+#, histidine pKa=6.0
+
+
+#
+#	Seeding partial charges for gasteiger calculation
+#
+#default charges
+SEEDCHARGE [#6+]	1.0
+SEEDCHARGE [#6-]	-1.0
+SEEDCHARGE [#7+]	1.0
+SEEDCHARGE [#7-]	-1.0
+SEEDCHARGE [#8+]	1.0
+SEEDCHARGE [#8-]	-1.0
+SEEDCHARGE [#15+]	1.0
+SEEDCHARGE [#15-]	-1.0
+SEEDCHARGE [#16+]	1.0
+SEEDCHARGE [#16-]	-1.0
+
+#charges spread over multiple atoms
+#carboxylic acid
+SEEDCHARGE	C(=O)[O-]		0.0	-0.5	-0.5
+
+#amines
+SEEDCHARGE	[N+]		1.0
+#tetrazole
+SEEDCHARGE	[nD2]1[nD2][nD2][nD2]c1	-0.2	-0.2	-0.2   -0.2    -0.2
+
+#sulfinic
+SEEDCHARGE	[SD3](=O)[O-]		0.0	-0.5	-0.5
+#sulfuric acid
+SEEDCHARGE	[SD4](=O)(=O)([O-])[OH1]	0.0	-0.33	-0.33	-0.33	0.0
+#sulfonic acid
+SEEDCHARGE	[SD4]([D2])(~[OD1])(~[OD1])~[OD1]	0.0	0.0	-0.33	-0.33	-0.33
+
+#guanidine
+SEEDCHARGE	[#7^2]~[C^2](~[N^2])~[N^2]	0.33	0.0	0.33	0.33
+
+#amidine
+SEEDCHARGE	[#6]~[C^2](~[N^2])~[N^2]	0.0	0.0	0.5	0.5
+
+#phosphoate ester
+SEEDCHARGE	[PD4](=O)([OD2])([OD2])[OD1]	0.0	-0.5	0.0	0.0	-0.5
+#phosphoric acid
+SEEDCHARGE	O=P([!D1])([O-])[O-]	-0.66	0.0	0.0	-0.66	-0.66
+
+
+#phosphuric acid
+SEEDCHARGE	P(=O)(=O)([O-])[O-]	0.0	0.0	0.0     -0.5	-0.5
+#phosphonic acid
+SEEDCHARGE	[#6]P(~[OD1])(~[OD1])~[OD1]	0.0	0.0	-0.33  -0.33 -0.33
+
+#hydroxamic acid
+SEEDCHARGE	O=C[N;!$(N(C=O)C=O)][OD1]	-0.5	0.0	0.0	-0.5
+SEEDCHARGE	O=CN([OD1])NC=O		-0.33	0.0	0.0	-0.33	0.0 0.0	-0.33
+
+#imidazole: note pKa=7.0, histidine pKa=6.0
+#if you uncomment this, also uncomment the transform statement above
+SEEDCHARGE	[n+H]1c[nH]cc1		0.5	0.0	0.5	0.0	0.0