openbabel-ruby 3.1.1.2-x86_64-linux

data/lib/openbabel/3.4.0/data/3.1.1/plugindefines.txt

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+# Data file for OBDefinable class.
+# A # in the first column or a # followed by whitespace introduces a comment and
+#   the rest of the characters on a line are ignored.
+# White space is trimmed from the front and back of the line.
+#   
+# There can be any number of lines containing only whitespace and 
+#   comment between objects, but none within an object.
+# Lines which have "\n" at the end have this replaced by a new line
+#   character and the next line is concatenated.
+
+#SmartsDescriptor
+#nHal             # name of descriptor. Use for example --filter "nHal<3" 
+#[F,Cl,Br,I,At]   # SMARTS defining the descriptor
+#Number of halogen atoms\n      #This comment has two lines because of \n at the end.
+#count fluorine, chlorine, etc. #When listing plugins, use verbose option to see lines after the first
+
+#OpTransform      # Description() for the class includes a line "OpTransform is definable"
+#tautomers        # ID. Commandline option to invoke is --tautomers
+#tautomers.txt    # Datafile containing transforms. If filename is * the data follows later in the entry.
+#Replace tautomers with their standard forms. Not reliable at present. # An explanatory description.
+
+#OpTransform
+#nodative        # ID. Commandline option to invoke is --nodative
+#*               # There is no datafile; the transforms are at the end of the entry
+#Replace [N+]([O-])=O by N(=O)=O
+#TRANSFORM [N+:1](=O)[O-:2] >> [N:1](=O)=[O:2]
+
+CompoundFilter
+L5                           # ID
+HBD<5 HBA1<10 MW<500 logP<5  # definition in terms of other descriptors or properties
+Lipinski Rule of Five        # description
+
+PatternFP
+MACCS          # ID of this fingerprint type
+MACCS.txt      # File containing the SMARTS patterns
+
+SmartsDescriptor
+sbonds
+*-*
+Number of single bonds
+
+SmartsDescriptor
+dbonds
+*=*
+Number of double bonds
+
+SmartsDescriptor
+tbonds
+*#*
+Number of triple bonds
+
+SmartsDescriptor
+abonds
+*:*
+Number of aromatic bonds
+
+SmartsDescriptor
+bonds
+*~*
+Number of bonds\n
+Add or remove hydrogens to count total or bonds between heavy atoms
+
+SmartsDescriptor
+atoms
+*
+Number of atoms\n
+Add or remove hydrogens to count total or heavy atoms
+
+OBGroupContrib
+MP        # name of descriptor
+mpC.txt   # data file
+Melting point\n    # brief description
+This is a melting point descriptor developed\n   # longer description
+by Andy Lang. For details see:\n
+ http://onschallenge.wikispaces.com/MeltingPointModel011

data/lib/openbabel/3.4.0/data/3.1.1/psa.txt

@@ -0,0 +1,68 @@
+######################################################################
+# 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.                          
+######################################################################
+# Atomic Contributions to Polar Surface Area PSA
+# ref. Ertl P., Rohde R., Selzer P., J. Med. Chem. 2000, 43, 3714-3717
+######################################################################
+;heavy
+[*]	0.00
+[N](-*)(-*)-*	3.24
+[N](-*)=*	12.36
+[N]#*	23.79
+[N](-*)(=*)=*	11.68
+[N](=*)#*	13.60
+[N]1(-*)-*-*1	3.01
+[NH](-*)-*	12.03
+[NH]1-*-*1	21.94
+[NH]=*	23.85
+[NH2]-*	26.02
+[N+](-*)(-*)(-*)-*	0.00
+[N+](-*)(-*)=*	3.01
+[N+](-*)#*	4.36
+[NH+](-*)(-*)-*	4.44
+[NH+](-*)=*	13.97
+[NH2+](-*)-*	16.61
+[NH2+]=*	25.59
+[NH3+]-*	27.64
+[n](:*):*	12.89
+[n](:*)(:*):*	4.41
+[n](-*)(:*):*	4.93
+[n](=*)(:*):*	8.39
+[nH](:*):*	15.79
+[n+](:*)(:*):*	4.10
+[n+](-*)(:*):*	3.88
+[nH+](:*):*	14.14
+[O](-*)-*	9.23
+[O]1-*-*1	12.53
+[O]=*	17.07
+[OH]-*	20.23
+[O-]-*	23.06
+[o](:*):*	13.14
+[S](-*)-*	25.30
+[S]=*	32.09
+[S](-*)(-*)=*	19.21
+[S](-*)(-*)(=*)=*	8.38
+[SH]-*	38.80
+[s](:*):*	28.24
+[s](=*)(:*):*	21.70
+[P](-*)(-*)-*	13.59
+[P](-*)=*	34.14
+[P](-*)(-*)(-*)=*	9.81
+[PH](-*)(-*)=*	23.47

data/lib/openbabel/3.4.0/data/3.1.1/qeq.txt

@@ -0,0 +1,116 @@
+#
+# Open Babel file: qeq.txt
+#
+# Charge parameters for the QEq and QTPIE methods
+# Used by QEqCharges and QTPIECharges, which are daughters of OBChargeModel
+#
+# Parameters:
+#
+#   Elt: Element symbol
+#   Eneg: Atomic electronegativity (Volts)
+#   Hard: Atomic (chemical) hardness (Volts/e)
+#   Radius: screening radius (Angstrom)
+# Elt   Eneg    Hard    Radius
+H 	4.528 	13.8904  0.8271
+He 	9.66 	29.8400  1.7640
+Li 	3.006 	 4.7720  2.4076
+Be 	4.877 	 8.8860  1.2930
+B 	5.11 	 9.5000  1.2094
+C 	5.343 	10.1260  1.1346
+N 	6.899 	11.7600  0.9770
+O 	8.741 	13.3640  0.8597
+F 	10.874 	14.9480  0.7686
+Ne 	11.04 	21.1000  1.4394
+Na 	2.843 	 4.5920  2.5020
+Mg 	3.951 	 7.3860  1.5555
+Al 	4.06 	 7.1800  1.6002
+Si 	4.168 	 6.9740  1.6474
+P 	5.463 	 8.0000  1.4362
+S 	6.928 	 8.9720  1.2806
+Cl 	8.564 	 9.8920  1.1615
+Ar 	9.465 	12.7100  1.2259
+K 	2.421 	 3.8400  2.9920
+Ca 	3.231 	 5.7600  1.9947
+Sc 	3.395 	 6.1600  1.8651
+Ti 	3.47 	 6.7600  1.6996
+V 	3.65 	 6.8200  1.6846
+Cr 	3.415 	 7.7300  1.4863
+Mn 	3.325 	 8.2100  1.3994
+Fe 	3.76 	 8.2800  1.3876
+Co 	4.105 	 8.3500  1.3760
+Ni 	4.465 	 8.4100  1.3661
+Cu 	4.2 	 8.4400  1.3613
+Zn 	5.106 	 8.5700  1.3406
+Ga 	3.641 	 6.3200  1.8179
+Ge 	4.051 	 6.8760  1.6709
+As 	5.188 	 7.6180  1.5082
+Se 	6.428 	 8.2620  1.3906
+Br 	7.79 	 8.8500  1.2982
+Kr 	8.505 	11.4300  1.0268
+Rb 	2.331 	 3.6920  3.1119
+Sr 	3.024 	 4.8800  2.3544
+Y 	3.83 	 5.6200  2.0444
+Zr 	3.4 	 7.1000  1.6182
+Nb 	3.55 	 6.7600  1.6996
+Mo 	3.465 	 7.5100  1.5299
+Tc 	3.29 	 7.9800  1.4398
+Ru 	3.575 	 8.0300  1.4308
+Rh 	3.975 	 8.0100  1.4344
+Pd 	4.32 	 8.0000  1.4362
+Ag 	4.436 	 6.2680  1.8330
+Cd 	5.034 	 7.9140  1.4518
+In 	3.506 	 5.7920  1.9836
+Sn 	3.987 	 6.2480  1.8389
+Sb 	4.899 	 6.6840  1.7189
+Te 	5.816 	 7.0520  1.6292
+I 	6.822 	 7.5240  1.5270
+Xe 	7.595 	 9.9500  1.1547
+Cs 	2.183 	 3.4220  3.3575
+Ba 	2.814 	 4.7920  2.3976
+La 	2.8355 	 5.4830  2.0954
+Ce 	2.774 	 5.3840  2.1340
+Pr 	2.858 	 5.1280  2.2405
+Nd 	2.8685 	 5.2410  2.1922
+Pm 	2.881 	 5.3460  2.1491
+Sm 	2.9115 	 5.4390  2.1124
+Eu 	2.8785 	 5.5750  2.0609
+Gd 	3.1665 	 5.9490  1.9313
+Tb 	3.018 	 5.6680  2.0270
+Dy 	3.0555 	 5.7430  2.0006
+Ho 	3.127 	 5.7820  1.9871
+Er 	3.1865 	 5.8290  1.9711
+Tm 	3.2514 	 5.8658  1.9587
+Yb 	3.2889 	 5.9300  1.9375
+Lu 	2.9629 	 4.9258  2.3325
+Hf 	3.7 	 6.8000  1.6896
+Ta 	5.1 	 5.7000  2.0157
+W 	4.63 	 6.6200  1.7355
+Re 	3.96 	 7.8400  1.4655
+Os 	5.14 	 7.2600  1.5825
+Ir 	5 	 8.0000  1.4362
+Pt 	4.79 	 8.8600  1.2968
+Au 	4.894 	 5.1720  2.2214
+Hg 	6.27 	 8.3200  1.3809
+Tl 	3.2 	 5.8000  1.9809
+Pb 	3.9 	 7.0600  1.6274
+Bi 	4.69 	 7.4800  1.5360
+Po 	4.21 	 8.4200  1.3645
+At 	4.75 	 9.5000  1.2094
+Rn 	5.37 	10.7400  1.0698
+Fr 	2 	 4.0000  2.8723
+Ra 	2.843 	 4.8680  2.3602
+Ac 	2.835 	 5.6700  2.0263
+Th 	3.175 	 5.8100  1.9775
+Pa 	2.985 	 5.8100  1.9775
+U 	3.341 	 5.7060  2.0135
+Np 	3.549 	 5.4340  2.1143
+Pu 	3.243 	 5.6380  2.0378
+Am 	2.9895 	 6.0070  1.9126
+Cm 	2.8315 	 6.3790  1.8011
+Bk 	3.1935 	 6.0710  1.8925
+Cf 	3.197 	 6.2020  1.8525
+Es 	3.333 	 6.1780  1.8597
+Fm 	3.4 	 6.2000  1.8531
+Md 	3.47 	 6.2200  1.8471
+No 	3.475 	 6.3500  1.8093
+Lr 	3.5 	 6.4000  1.7952