openbabel-ruby 3.1.1.2-arm64-darwin

data/lib/openbabel/3.2.0/data/3.1.1/bondtyp.txt

@@ -0,0 +1,113 @@
+##############################################################################
+#                                                                            #
+#    Open Babel file: bondtyp.txt                                            #
+#                                                                            #
+#  Copyright (c) 2002-2005 by Geoffrey R Hutchison                           #
+#  Part of the Open Babel package, under the GNU General Public License (GPL)#
+#                                                                            #
+# Used by bondtyper.cpp::OBBondTyper (and thus OBMol::PerceiveBondOrders()   #
+#                                                                            #
+# List of functional groups with double, triple (etc.) bond orders           #
+# Pattern       Atom1 Atom2 Bond Order (repeat as needed)                    #
+# * = Any atom (for setting non-multiple bonds)                              #
+#                                                                            #
+# NOTE: These are applied in order, first to last.                           #
+#     So it's generally better to have a long (specifc) SMARTS first.        #
+#     (all bonds must be single bonds to match)                              #
+#                                                                            #
+##############################################################################
+
+# Porphyrin / phthalocyanine (3 patterns for three separate bonding motifs)
+# this one has explicit bonds to all four nitrogens (e.g., metal bond or hydrogens)
+# X2,X3 is needed to avoid mis-typing coproporphyrinogen
+#0        1    2       3   4   5  6        7     8      9  10  11  12       13   14     15 16   17  18       19  20       21 22  23
+[X2,X3]1[#6]([#7D3]2)[#6][#6][#6]2[X2,X3][#6]([#7D3]3)[#6][#6][#6]3[X2,X3][#6]([#7D3]4)[#6][#6][#6]4[X2,X3][#6]([#7D3]5)[#6][#6][#6]51	0 1 2 1 2 1 1 3 1 3 4 2 4 5 1 5 2 1 5 6 2 6 7 1 7 8 2 7 9 1 9 10 2 10 11 1 11 8 1 11 12 2 12 13 1 13 14 1 13 15 2 15 16 1 16 17 2 17 14 1 17 18 1 18 19 2 19 20 1 19 21 1 21 22 2 22 23 1 23 20 2
+
+# this one has explicit bonds to two nitrogens (12 and 14)
+#0        1    2       3   4   5  6        7    8     9  10  11  12       13   14     15 16   17  18      19  20    21 22  23
+[X2,X3]1[#6]([#7D3]2)[#6][#6][#6]2[X2,X3][#6]([#7]3)[#6][#6][#6]3[X2,X3][#6]([#7D3]4)[#6][#6][#6]4[X2,X3][#6]([#7]5)[#6][#6][#6]51	0 1 2 1 2 1 1 3 1 3 4 2 4 5 1 5 2 1 5 6 2 6 7 1 7 8 2 7 9 1 9 10 2 10 11 1 11 8 1 11 12 2 12 13 1 13 14 1 13 15 2 15 16 1 16 17 2 17 14 1 17 18 1 18 19 2 19 20 1 19 21 1 21 22 2 22 23 1 23 20 2
+
+# and this one doesn't have any explicit bonds to the nitrogens
+#0        1    2     3   4   5  6        7    8     9  10  11  12      13   14   15  16  17 18        19   20    21 22  23
+[X2,X3]1[#6]([#7]2)[#6][#6][#6]2[X2,X3][#6]([#7]3)[#6][#6][#6]3[X2,X3][#6]([#7]4)[#6][#6][#6]4[X2,X3][#6]([#7]5)[#6][#6][#6]51	0 1 2 1 2 1 1 3 1 3 4 2 4 5 1 5 2 1 5 6 2 6 7 1 7 8 2 7 9 1 9 10 2 10 11 1 11 8 1 11 12 2 12 13 1 13 14 1 13 15 2 15 16 1 16 17 2 17 14 1 17 18 1 18 19 2 19 20 1 19 21 1 21 22 2 22 23 1 23 20 2
+
+# Azide
+[#7D2][#7D2^1][#7D1]		0 1 2 1 2 2
+# Nitro
+[#8D1][#7D3^2]([#8D1])*		0 1 2 1 2 2 1 3 1
+
+# Sulfones
+[#16D4]([#8D1])([#8D1])([*!#8])([*!#8]) 	0 1 2 0 2 2 0 3 1 0 4 1
+# Sulfates
+[#16D4]([#8D1])([#8D1])([#8-,#8D1])([#8-,#8D1])	0 1 2 0 2 2 0 3 1 0 4 1
+# Thiosulfates
+[#16D4]([#16D1])([#8D1])([#8-,#8])([#8-,#8])	0 1 2 0 2 2 0 3 1 0 4 1
+# Sulfoxides
+[#16D3]([#8D1])([*!#8])([*!#8])			0 1 2 0 2 1 0 3 1
+# Sulfite
+[#16D3]([#8D1])([#8D1-])([#8D1-])		0 1 2 0 2 1 0 3 1
+# Sulfur trioxide
+[#16D3^2]([#8D1])([#8D1])([#8D1])                      0 1 2 0 2 2 0 3 2
+# Sulfites
+[#16D3]([#8D1])([#8])([#8])			0 1 2 0 2 1 0 3 1
+# Disulfur monoxide
+[#16D2]([#8D1])([#16D1])			0 1 2 0 2 2
+# Sulfmonoxides
+[#16D2]([#8D1])([*!#8])				0 1 2 0 2 1
+# Sulfur dioxide
+[#16D2]([#8D1])([#8D1])				0 1 2 0 2 2
+
+#Phosphite
+[#15D3]([#8D1])([#8D1])([#8D2])		0 1 2 0 2 2 0 3 1
+
+#oxophosphane
+#[#15D2]([#8D1])([#1])      0 1 2 0 2 1
+
+#Nitrosyl Hydride
+[#7D2]([#8D1])([#1])		0 1 2 0 2 1
+
+# Phosphone
+[#15D4]([#8D1])(*)(*)(*)	0 1 2 0 2 1 0 3 1 0 4 1
+
+
+# Carboxylic Acid, ester, etc.
+[#6D3^2]([#8D1])([#8])*		0 1 2 0 2 1 0 3 1
+# Carbon dioxide
+[#8D1][#6D2^1][#8D1]		0 1 2 1 2 2
+# Amide C(=O)N  - no negative charge on O (2aix_u1k.sdf)
+[#6D3^2]([#8D1;!-])([#7])*		0 1 2 0 2 1 0 3 1
+# Seleninic acid Se(=O)OH
+[#34D3^2]([#8D1])([#8])*		0 1 2 0 2 1 0 3 1
+# Thioacid / Thioester C(=O)S
+[#6D3^2]([#8D1])([#16])*		0 1 2 0 2 1 0 3 1
+# dithioacid / dithioester C(=S)S
+[#6D3^2]([#16D1])([#16])*		0 1 2 0 2 1 0 3 1
+# thioamide C(=S)N
+# avoid aromatics (pdb_ligands_sdf/1yry_msg.sdf)
+[CD3^2]([#16D1])([N])*		0 1 2 0 2 1 0 3 1
+
+# allene C=C=C
+# (this is problematic -- need to make sure the center carbon is sp)
+[#6^2][#6D2^1][#6^2]		0 1 2 1 2 2
+# ene-one C=C=O
+[#6^2][#6D2^1][#8D1]		0 1 2 1 2 2  
+
+# isonitrile / isocyano
+[#6D1][#7D2^1]*  0 1 3 1 2 1
+
+# if three N are present in R-N-guanidine-ish, prefer double bond to the
+#  non-terminal N (i.e. D2 if present)
+[#6D3^2;!R]([#7D2;!R])([#7D1;!R])~[#7D1;!R] 0 1 2 0 2 1 0 3 1
+# guanidinium and amidine -C(=NH)NH2 without hydrogens
+[#6D3^2;!R]([#7D1H0;!R])([#7;!R])*	0 1 2 0 2 1 0 3 1
+# and also with hydrogens
+# (this can normally be figured out, but is needed to avoid matching the next SMARTS)
+[#6D3^2;!R]([#7D2H1;!R])([#7;!R])*	0 1 2 0 2 1 0 3 1
+# and also with more hydrogens than normal (protonated)
+[#6D3^2;!R]([#7D3H2;!R])([#7;!R])*	0 1 2 0 2 1 0 3 1
+
+# Schiff base, protonated
+[#6D3^2;!R]([#1,#6])([#1,#6])[#7D3^2;!R]([#1])[#6]	0 1 1 0 2 1 0 3 2 3 4 1 3 5 1
+
+### other potential functional groups that may (or may not) be useful to add
+# imidines ( N=C/N\C=N

data/lib/openbabel/3.2.0/data/3.1.1/eem.txt

@@ -0,0 +1,22 @@
+kappa	0.529176
+H	*	0.20606	1.31942
+Li	*	0.36237	0.65932
+B	*	0.36237	0.65932
+C	*	0.36237	0.65932
+N	*	0.49279	0.69038
+O	*	0.73013	1.08856
+F	*	0.72052	1.45328
+Na	*	0.36237	0.65932
+Mg	*	0.36237	0.65932
+Si	*	0.36237	0.65932
+P	*	0.36237	0.65932
+S	*	0.62020	0.41280
+Cl	*	0.36237	0.65932
+K	*	0.36237	0.65932
+Ca	*	0.36237	0.65932
+Fe	*	0.36237	0.65932
+Cu	*	0.36237	0.65932
+Zn	*	0.36237	0.65932
+Br	*	0.70052	1.09108
+I	*	0.68052	0.61328
+*	*	0.20606	1.31942

data/lib/openbabel/3.2.0/data/3.1.1/eem2015ba.txt

@@ -0,0 +1,18 @@
+kappa 0.23470000
+Br	1	2.46770000	0.64790000
+C	1	2.43240000	0.31920000
+C	2	2.44660000	0.30330000
+C	3	2.29030000	0.53320000
+Cl	1	2.60260000	0.82900000
+F	1	3.51580000	1.93870000
+H	1	2.42380000	0.55860000
+I	1	2.36140000	0.85450000
+N	1	2.59970000	0.36080000
+N	2	2.56910000	0.28930000
+N	3	2.82230000	0.57040000
+O	1	2.66330000	0.38900000
+O	2	2.67290000	0.37700000
+P	1	1.89340000	0.43380000
+P	2	1.95100000	0.35970000
+S	1	2.40470000	0.29550000
+S	2	2.43540000	0.20830000

data/lib/openbabel/3.2.0/data/3.1.1/eem2015bm.txt

@@ -0,0 +1,18 @@
+kappa 0.22120000
+Br	1	2.34390000	0.76870000
+C	1	2.52040000	0.31150000
+C	2	2.49600000	0.28200000
+C	3	2.50810000	0.21010000
+Cl	1	2.49910000	1.00910000
+F	1	3.11060000	1.67910000
+H	1	2.37700000	0.71380000
+I	1	2.27430000	0.74980000
+N	1	2.61080000	0.34590000
+N	2	2.58320000	0.38360000
+N	3	2.55440000	0.93730000
+O	1	2.63710000	0.40760000
+O	2	2.63610000	0.46120000
+P	1	2.42480000	0.16460000
+P	2	2.14460000	0.40450000
+S	1	2.41210000	0.31250000
+S	2	2.46260000	0.20700000

data/lib/openbabel/3.2.0/data/3.1.1/eem2015bn.txt

@@ -0,0 +1,18 @@
+kappa 0.25090000
+Br	1	2.42440000	0.75110000
+C	1	2.49920000	0.32200000
+C	2	2.50650000	0.31730000
+C	3	2.46170000	0.34890000
+Cl	1	2.51040000	0.83640000
+F	1	3.00280000	1.24330000
+H	1	2.38640000	0.65810000
+I	1	2.32720000	0.93030000
+N	1	2.58910000	0.40720000
+N	2	2.55680000	0.29490000
+N	3	2.53480000	0.40250000
+O	1	2.63420000	0.40410000
+O	2	2.65880000	0.42320000
+P	1	2.38980000	0.19020000
+P	2	2.20980000	0.32810000
+S	1	2.45060000	0.24040000
+S	2	2.48840000	0.20430000

data/lib/openbabel/3.2.0/data/3.1.1/eem2015ha.txt

@@ -0,0 +1,18 @@
+kappa 0.19760000
+Br	1	2.47030000	0.53870000
+C	1	2.42460000	0.27570000
+C	2	2.44350000	0.25400000
+C	3	2.31210000	0.42930000
+Cl	1	2.60370000	0.68220000
+F	1	3.54390000	1.71380000
+H	1	2.42640000	0.50540000
+I	1	2.35920000	0.74760000
+N	1	2.59980000	0.29790000
+N	2	2.56820000	0.24540000
+N	3	3.16550000	0.81880000
+O	1	2.65750000	0.32740000
+O	2	2.66330000	0.31630000
+P	1	1.92710000	0.37950000
+P	2	1.84280000	0.34420000
+S	1	2.39530000	0.27310000
+S	2	2.43130000	0.17920000

data/lib/openbabel/3.2.0/data/3.1.1/eem2015hm.txt

@@ -0,0 +1,18 @@
+kappa 0.20020000
+Br	1	2.34280000	0.78160000
+C	1	2.50140000	0.27230000
+C	2	2.48850000	0.24660000
+C	3	2.51540000	0.23820000
+Cl	1	2.52590000	0.87310000
+F	1	3.01860000	1.11320000
+H	1	2.37510000	0.66210000
+I	1	2.28840000	0.64130000
+N	1	2.61000000	0.30600000
+N	2	2.56570000	0.29110000
+N	3	2.60770000	0.75790000
+O	1	2.63700000	0.34440000
+O	2	2.64810000	0.39920000
+P	1	2.40710000	0.15080000
+P	2	2.16540000	0.32590000
+S	1	2.42020000	0.25020000
+S	2	2.46420000	0.18340000

data/lib/openbabel/3.2.0/data/3.1.1/eem2015hn.txt

@@ -0,0 +1,18 @@
+kappa 0.23990000
+Br	1	2.44000000	0.65270000
+C	1	2.48870000	0.30540000
+C	2	2.49750000	0.29610000
+C	3	2.46130000	0.31760000
+Cl	1	2.52250000	0.79330000
+F	1	3.02110000	1.19770000
+H	1	2.39150000	0.62770000
+I	1	2.32740000	0.92110000
+N	1	2.59430000	0.39200000
+N	2	2.55000000	0.27810000
+N	3	2.53340000	0.37180000
+O	1	2.63990000	0.39450000
+O	2	2.65050000	0.38190000
+P	1	2.39290000	0.17320000
+P	2	2.17410000	0.31920000
+S	1	2.44710000	0.23960000
+S	2	2.49060000	0.19500000

data/lib/openbabel/3.2.0/data/3.1.1/eqeqIonizations.txt

@@ -0,0 +1,100 @@
+#
+# Open Babel file: eqeqIonizations.txt
+#
+# Additional ionization energies for elements used by EQeq.
+# Also contains common metal ion charges and electron affinities.
+#
+# Note that some of this information is redundant with OBElementTable. TODO fix.
+#
+# Parameters:
+#   Num: Atomic number
+#   Symbol: Element symbol
+#   Charge: Common charge of ionized metals (0 if nonmetal)
+#   Affinity: Element electron affinity
+#   Ionizations: Nth ionization of atom (-1 if does not exist)
+#
+# Num   Symbol  Charge  Affinity Ionizations
+1	H	0	0.7542	13.598	-1	-1	-1	-1	-1	-1	-1
+2	He	0	0	24.587	54.416	-1	-1	-1	-1	-1	-1
+3	Li	1	0.61805	5.392	75.638	122.451	-1	-1	-1	-1	-1
+4	Be	2	0	9.322	18.211	153.893	217.713	-1	-1	-1	-1
+5	B	0	0.27972	8.298	25.154	37.93	259.368	340.217	-1	-1	-1
+6	C	0	1.26212	11.26	24.383	47.887	64.492	392.077	489.981	-1	-1
+7	N	0	-0.07	14.534	29.601	47.448	77.472	97.888	552.057	667.029	-1
+8	O	0	1.46111	13.618	35.116	54.934	77.412	113.896	138.116	739.315	871.387
+9	F	0	3.40119	17.422	34.97	62.707	87.138	114.24	157.161	185.182	953.886
+10	Ne	0	0	21.564	40.962	63.45	97.11	126.21	157.93	207.27	239.09
+11	Na	1	0.54793	5.139	47.286	71.64	98.91	138.39	172.15	208.47	264.18
+12	Mg	2	0	7.646	15.035	80.143	109.24	141.26	186.5	224.94	265.9
+13	Al	3	0.43283	5.986	18.828	28.447	119.99	153.71	190.47	241.43	284.59
+14	Si	0	1.38952	8.151	16.345	33.492	45.141	166.77	205.05	246.52	303.17
+15	P	0	0.7465	10.458	19.725	30.18	51.37	65.023	220.43	263.22	309.41
+16	S	0	2.0771	10.36	23.33	34.83	47.3	72.68	88.049	280.93	328.23
+17	Cl	0	3.61272	12.967	23.81	39.61	53.46	67.8	97.03	114.193	348.28
+18	Ar	0	0	15.759	27.629	40.74	59.81	75.02	91.007	124.319	143.456
+19	K	1	0.50146	4.341	31.625	45.72	60.91	82.66	100	117.56	154.86
+20	Ca	2	0.02455	6.113	11.871	50.908	67.1	84.41	108.78	127.7	147.24
+21	Sc	3	0.188	6.54	12.8	24.76	73.47	91.66	111.1	138	158.7
+22	Ti	3	0.084	6.82	13.58	27.491	43.266	99.22	119.36	140.8	168.5
+23	V	3	0.525	6.74	14.65	29.31	46.707	65.23	128.12	150.17	173.7
+24	Cr	2	0.67584	6.766	16.5	30.96	49.1	69.3	90.56	161.1	184.7
+25	Mn	2	0	7.435	15.64	33.667	51.2	72.4	95	119.27	196.46
+26	Fe	3	0.151	7.87	16.18	30.651	54.8	75	99	125	151.06
+27	Co	2	0.6633	7.86	17.06	33.5	51.3	79.5	102	129	157
+28	Ni	2	1.15716	7.635	18.168	35.17	54.9	75.5	108	133	162
+29	Cu	2	1.23578	7.726	20.292	36.83	55.2	79.9	103	139	166
+30	Zn	2	0	9.394	17.964	39.722	59.4	82.6	108	134	174
+31	Ga	3	0.41	5.999	20.51	30.71	64	-1	-1	-1	-1
+32	Ge	4	1.23271	7.899	15.934	34.22	45.71	93.5	-1	-1	-1
+33	As	0	0.814	9.81	18.633	28.351	50.13	62.63	127.6	-1	-1
+34	Se	0	2.0207	9.752	21.19	30.82	42.944	68.3	81.7	155.4	-1
+35	Br	0	3.36359	11.814	21.8	36	47.3	59.7	88.6	103	192.8
+36	Kr	0	0	13.999	24.359	36.95	52.5	64.7	18.5	111	126
+37	Rb	1	0.48592	4.177	27.28	40	52.6	71	84.4	99.2	136
+38	Sr	2	0.05206	5.695	11.03	43.6	57	71.6	90.8	106	122.3
+39	Y	3	0.307	6.38	12.24	20.52	61.8	77	93	116	129
+40	Zr	4	0.426	6.84	13.13	22.99	34.34	81.5	-1	-1	-1
+41	Nb	5	0.893	6.88	14.32	25.04	38.3	50.55	102.6	125	-1
+42	Mo	6	0.7472	7.099	16.15	27.16	46.4	61.2	68	126.8	153
+43	Tc	7	0.55	7.28	15.26	29.54	-1	-1	-1	-1	-1
+44	Ru	3	1.04638	7.37	16.76	28.47	-1	-1	-1	-1	-1
+45	Rh	3	1.14289	7.46	18.08	31.06	-1	-1	-1	-1	-1
+46	Pd	2	0.56214	8.34	19.43	32.93	-1	-1	-1	-1	-1
+47	Ag	1	1.30447	7.576	21.49	34.83	-1	-1	-1	-1	-1
+48	Cd	2	0	8.993	16.908	37.48	-1	-1	-1	-1	-1
+49	In	3	0.404	5.786	18.869	28.03	54	-1	-1	-1	-1
+50	Sn	4	1.11207	7.344	14.632	30.502	40.734	72.28	-1	-1	-1
+51	Sb	3	1.0474	8.641	16.53	25.3	44.2	56	108	-1	-1
+52	Te	0	1.97088	9.009	18.6	27.96	37.41	58.75	70.7	137	-1
+53	I	0	3.05904	10.451	19.131	33	-1	-1	-1	-1	-1
+54	Xe	0	0	12.13	21.21	32.1	-1	-1	-1	-1	-1
+55	Cs	1	0.47163	3.894	25.1	-1	-1	-1	-1	-1	-1
+56	Ba	2	0.14462	5.212	10.004	-1	-1	-1	-1	-1	-1
+57	La	3	0.47	5.577	11.06	19.175	-1	-1	-1	-1	-1
+58	Ce	3	0.7	5.47	10.85	20.2	36.72	-1	-1	-1	-1
+59	Pr	3	0.5	5.42	10.55	21.62	38.95	57.45	-1	-1	-1
+60	Nd	3	0.5	5.49	10.72	-1	-1	-1	-1	-1	-1
+61	Pm	3	0.5	5.55	10.9	-1	-1	-1	-1	-1	-1
+62	Sm	3	0.5	5.63	11.07	-1	-1	-1	-1	-1	-1
+63	Eu	3	0.5	5.67	11.25	-1	-1	-1	-1	-1	-1
+64	Gd	3	0.5	6.14	12.1	-1	-1	-1	-1	-1	-1
+65	Tb	3	0.5	5.85	11.52	-1	-1	-1	-1	-1	-1
+66	Dy	3	0.5	5.93	11.67	-1	-1	-1	-1	-1	-1
+67	Ho	3	0.5	6.02	11.8	-1	-1	-1	-1	-1	-1
+68	Er	3	0.5	6.1	11.93	-1	-1	-1	-1	-1	-1
+69	Tm	3	0.5	6.18	12.05	23.71	-1	-1	-1	-1	-1
+70	Yb	3	0.5	6.254	12.17	25.2	-1	-1	-1	-1	-1
+71	Lu	3	0.5	5.426	13.9	-1	-1	-1	-1	-1	-1
+72	Hf	4	0	7	14.9	23.3	33.3	-1	-1	-1	-1
+73	Ta	5	0.322	7.89	-1	-1	-1	-1	-1	-1	-1
+74	W	6	0.815	7.98	-1	-1	-1	-1	-1	-1	-1
+75	Re	7	0.015	7.88	-1	-1	-1	-1	-1	-1	-1
+76	Os	4	1.0778	8.7	-1	-1	-1	-1	-1	-1	-1
+77	Ir	4	1.56436	9.1	-1	-1	-1	-1	-1	-1	-1
+78	Pt	4	2.1251	9	18.563	-1	-1	-1	-1	-1	-1
+79	Au	3	2.30861	9.225	20.5	-1	-1	-1	-1	-1	-1
+80	Hg	2	0	10.437	18.756	34.2	-1	-1	-1	-1	-1
+81	Tl	1	0.377	6.108	20.428	29.83	-1	-1	-1	-1	-1
+82	Pb	2	0.364	7.416	15.032	31.937	42.32	68.8	-1	-1	-1
+83	Bi	3	0.94236	7.289	16.69	25.56	45.3	56	88.3	-1	-1
+84	Po	2	1.9	8.42	-1	-1	-1	-1	-1	-1	-1