1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
|
##############################################################################
##############################################################################
##############################################################################
#
# JOELib2 properties
#
# \ slashes should be written as \\
# spaces can be written as \ \, but white spaces are removed at the end of
# lines !!!
# Please use the Unicode expression \u0020 to encode white spaces !!!
#
##############################################################################
#
# Version: $Revision: 1.15 $
# $Date: 2006/07/24 22:29:15 $
# $Author: wegner $
#
##############################################################################
# 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
#
# 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.
##############################################################################
##############################################################################
##############################################################################
# resource locations of data files
##############################################################################
joelib2.data.BasicHybridisationTyper.resourceFile=joelib2/data/plain/hybridisation.txt
joelib2.data.BasicAromaticityTyper.resourceFile=joelib2/data/plain/aromatic.txt
joelib2.data.BasicAromaticityTyper.useAromaticityModel=true
joelib2.data.BasicImplicitValenceTyper.resourceFile=joelib2/data/plain/implicitValence.txt
joelib2.data.BasicAtomTyper.resourceFile=joelib2/data/plain/atomtype.txt
joelib2.data.BasicElementHolder.resourceFile=joelib2/data/plain/element.txt
joelib2.data.BasicIsotopeHolder.resourceFile=joelib2/data/plain/isotope.txt
joelib2.data.BasicProtonationModel.resourceFile=joelib2/data/plain/phmodel.txt
joelib2.data.BasicGroupContributionHolder.resourceDir=joelib2/data/plain
joelib2.data.BasicGroupContributionHolder.contributionExtension=.contributions
joelib2.data.BasicGroupContributionHolder.models=LogP MR PSA
joelib2.feature.ResultFactory.resourceFile=joelib2/data/plain/knownResults.txt
joelib2.process.types.DescriptorStatistic.descriptors2ignore=joelib2/data/plain/desc2ignore.txt
joelib2.process.types.DescriptorBinning.descriptors2ignore=joelib2/data/plain/desc2ignore.txt
##############################################################################
# Database
##############################################################################
wsi.ra.database.DatabaseConnection.location=jdbc:mysql://localhost/test
wsi.ra.database.DatabaseConnection.password=
wsi.ra.database.DatabaseConnection.username=
wsi.ra.database.DatabaseConnection.driver=org.gjt.mm.mysql.Driver
##############################################################################
# 2D rendering options
##############################################################################
joelib2.gui.render2D.Renderer2DModel.bond.length=30.0
joelib2.gui.render2D.Renderer2DModel.bond.distance=6.0
joelib2.gui.render2D.Renderer2DModel.bond.width=2.0
joelib2.gui.render2D.Renderer2DModel.drawNumbers=true
joelib2.gui.render2D.Renderer2DModel.useKekuleStructure=true
joelib2.gui.render2D.Renderer2DModel.showEndCarbons=true
joelib2.gui.render2D.Renderer2DModel.atomColoring=false
joelib2.gui.render2D.Renderer2DModel.drawCarbonAtoms=false
joelib2.gui.render2D.Renderer2DModel.orthoLineOffset=20
joelib2.gui.render2D.Renderer2DModel.arrowOffset=10
joelib2.gui.render2D.Renderer2DModel.arrowSize=5
joelib2.gui.render2D.Renderer2DModel.background.color.r=255
joelib2.gui.render2D.Renderer2DModel.background.color.g=255
joelib2.gui.render2D.Renderer2DModel.background.color.b=255
joelib2.gui.render2D.Renderer2DModel.foreground.color.r=0
joelib2.gui.render2D.Renderer2DModel.foreground.color.g=0
joelib2.gui.render2D.Renderer2DModel.foreground.color.b=0
joelib2.gui.render2D.Renderer2DModel.highlight.color.r=255
joelib2.gui.render2D.Renderer2DModel.highlight.color.g=0
joelib2.gui.render2D.Renderer2DModel.highlight.color.b=0
joelib2.gui.render2D.Renderer2DModel.number.color.r=0
joelib2.gui.render2D.Renderer2DModel.number.color.g=0
joelib2.gui.render2D.Renderer2DModel.number.color.b=255
joelib2.gui.render2D.Renderer2DModel.conjugatedRing.color.r=0
joelib2.gui.render2D.Renderer2DModel.conjugatedRing.color.g=0
joelib2.gui.render2D.Renderer2DModel.conjugatedRing.color.b=0
joelib2.gui.render2D.Renderer2DModel.arrow.color.r=0
joelib2.gui.render2D.Renderer2DModel.arrow.color.g=255
joelib2.gui.render2D.Renderer2DModel.arrow.color.b=0
joelib2.gui.render2D.Renderer2DModel.orthogonalLine.color.r=0
joelib2.gui.render2D.Renderer2DModel.orthogonalLine.color.g=0
joelib2.gui.render2D.Renderer2DModel.orthogonalLine.color.b=255
##############################################################################
# Smiles ARbitrary Target Specification (SMARTS) matcher parameters
##############################################################################
# '*' matches also explicite hydrogens when 'true'
# '*' matches only non-hydrogen (heavy weight) atoms when 'false'
joelib2.smarts.SMARTSParser.anyRecognizesExpliciteHydrogens=false
##############################################################################
# Supported file types
##############################################################################
joelib2.filetypes.1.name = SDF
joelib2.filetypes.2.name = XYZ
joelib2.filetypes.3.name = SMILES
joelib2.filetypes.4.name = TINKER
joelib2.filetypes.5.name = CTX
joelib2.filetypes.6.name = CML
joelib2.filetypes.7.name = POV
joelib2.filetypes.8.name = MOL2
joelib2.filetypes.9.name = PDB
joelib2.filetypes.10.name = MATLAB
joelib2.filetypes.11.name = FLAT
joelib2.filetypes.11.representation = joelib2.io.types.Flat
joelib2.filetypes.12.name = MOLCONNZ
joelib2.filetypes.12.representation = joelib2.io.types.MolconnZ
joelib2.filetypes.13.name = HIN
joelib2.filetypes.14.name = GAUSSIANCART
joelib2.filetypes.15.name = JPEG
joelib2.filetypes.16.name = GIF
joelib2.filetypes.17.name = PPM
# PNG requires another implementation or Marvin
#joelib2.filetypes.18.name = PNG
joelib2.filetypes.18.name = BMP
joelib2.filetypes.19.name = PDF
joelib2.filetypes.20.name = ZIP
joelib2.filetypes.21.name = PREP
joelib2.filetypes.22.name = MOPACOUT
#joelib2.filetypes.16.name = GHEMICAL
# if you want another loader/writer define one
#joelib2.filetypes.1.representation = joelib2.io.types.MDLSD
#joelib2.filetypes.2.representation = joelib2.io.types.XYZ
#joelib2.filetypes.3.representation = joelib2.io.types.Smiles
##############################################################################
# filters
##############################################################################
joelib2.filter.1.name =NOTFilter
joelib2.filter.1.representation =joelib2.process.filter.NOTFilter
joelib2.filter.1.descriptionFile =docs/process/notFilter
joelib2.filter.2.name =ORFilter
joelib2.filter.2.representation =joelib2.process.filter.ORFilter
joelib2.filter.2.descriptionFile =docs/process/orFilter
joelib2.filter.3.name =ANDFilter
joelib2.filter.3.representation =joelib2.process.filter.ANDFilter
joelib2.filter.3.descriptionFile =docs/process/andFilter
joelib2.filter.4.name =HasDataFilter
joelib2.filter.4.representation =joelib2.process.filter.HasDataFilter
joelib2.filter.4.descriptionFile =docs/process/hasDataFilter
joelib2.filter.5.name =DescriptorFilter
joelib2.filter.5.representation =joelib2.process.filter.DescriptorFilter
joelib2.filter.5.descriptionFile =docs/process/descriptorFilter
joelib2.filter.6.name =NativeValueFilter
joelib2.filter.6.representation =joelib2.process.filter.NativeValueFilter
joelib2.filter.6.descriptionFile =docs/process/nativeValueFilter
##############################################################################
# processes
##############################################################################
joelib2.process.1.name =ProcessPipe
joelib2.process.1.representation =joelib2.process.ProcessPipe
joelib2.process.1.descriptionFile =docs/process/processPipe
joelib2.process.2.name =FeatureSelectionWriter
joelib2.process.2.representation =joelib2.process.types.FeatureSelectionWriter
joelib2.process.2.descriptionFile =docs/process/featureSelectionWriter
joelib2.process.3.name =DescriptorStatistic
joelib2.process.3.representation =joelib2.process.types.DescStatistic
joelib2.process.3.descriptionFile =docs/process/descriptorStatistic
################
joelib2.process.4.name =DescriptorBinning
joelib2.process.4.representation =joelib2.process.types.DescBinning
joelib2.process.4.descriptionFile =docs/process/descriptorBinning
joelib2.process.types.DescBinning.numberOfBins=20
################
joelib2.process.5.name =DistanceCalculation
joelib2.process.5.representation =joelib2.process.types.DistanceCalculation
joelib2.process.5.descriptionFile =docs/process/distanceCalculation
##############################################################################
# miscellaneous
##############################################################################
#SD Files
# if set to false aromatic bonds are stored, so this structure can be used
# as QUERY structure. That's only an export feature, internally you can have
# both types by using the kekule bonds or the 'normal/aromatic' bonds.
joelib2.io.types.MDLSD.writeAromaticityAsKekuleSystem=true
#SMILES
joelib2.smiles.SMILESGenerator.assignCisTransInformations=true
joelib2.smiles.SMILESGenerator.assignChiralityInformations=true
joelib2.io.types.Smiles.canonical=false
joelib2.io.types.Smiles.lineStructure=SMILES|TITLE
joelib2.io.types.Smiles.lineStructure.delimiter=|
joelib2.io.types.Smiles.lineStructure.input.delimiter=\u0020\t\n\r
joelib2.io.types.Smiles.lineStructure.output.delimiter=\u0020
# MolconnZ
joelib2.io.types.MolconnZ.parserDefinition=joelib2/data/plain/molconnz350.txt
# Flat
joelib2.io.types.Flat.lineStructure.input.delimiter=\u0020\t\n\r
joelib2.io.types.Flat.lineStructure.output.delimiter=\t
joelib2.io.types.Flat.lineStructure.delimiter=\u0020\t
joelib2.io.types.Flat.lineStructure=TITLE
###########
# CML
# version: 1.0 and 2.0
# ouput: attributearray, array, large, huge
# delimiter: if you comment this line, standard white space will be used
# force.formalCharge: formal charges will be always written, even when they are zero
# partialCharge: write partial atom charge
# hydrogen=joelib2.feature.types.count: write number of implicite+explicite hydrogens
###########
## use slower memory saving preparser for avoiding to load the complete data set into memory
## This flag will be automatically switched 'ON' for CML files in compressed ZIP files !
## The basic convert does not need it, because it uses already another sequential
## SAX reader (forced by a callback)
joelib2.io.types.ChemicalMarkupLanguage.useSlowerMemorySavingPreparser=false
###########
joelib2.io.types.ChemicalMarkupLanguage.output.defaultVersion=2.0
joelib2.io.types.ChemicalMarkupLanguage.defaultDelimiter=\u0020
#joelib2.io.types.ChemicalMarkupLanguage.defaultDelimiter=|
joelib2.io.types.ChemicalMarkupLanguage.output=huge
joelib2.io.types.ChemicalMarkupLanguage.output.force.formalCharge=false
joelib2.io.types.ChemicalMarkupLanguage.output.partialCharge=true
joelib2.io.types.ChemicalMarkupLanguage.output.hydrogenCount=true
joelib2.io.types.ChemicalMarkupLanguage.output.useNamespace=true
joelib2.io.types.ChemicalMarkupLanguage.output.namespace=cml
joelib2.io.types.ChemicalMarkupLanguage.output.xmlDeclaration=http://www.xml-cml.org/schema/cml2/core
joelib2.io.types.ChemicalMarkupLanguage.DTD.resourceDir=joelib2/io/types/cml/data/
###########
## a first step to 'reproducable' descriptor calculation algorithms
joelib2.io.types.ChemicalMarkupLanguage.output.storeChemistryKernelInfo=true
## these informations are not really a CML standard
###########
joelib2.io.types.ChemicalMarkupLanguage.output.symmetryInformations=false
###########
# PovRay
# ouput type can be: stick, sphere, ball_and_stick
joelib2.io.types.POVRay.output=ball_and_stick
joelib2.io.types.POVRay.atomPropertyColoring=false
joelib2.io.types.POVRay.atomProperty=Gasteiger_Marsili
# Image writer
joelib2.gui.render2D.Mol2Image.defaultWidth=500
joelib2.gui.render2D.Mol2Image.defaultHeight=400
# PDF writer
joelib2.io.types.PDF.fontSize=10
joelib2.io.types.PDF.fontOffset=2
joelib2.io.types.PDF.pageBorder=20
joelib2.temporary.directory.windows=C:\\temp
joelib2.temporary.directory.linux=/tmp
joelib2.process.types.DescBinning.descriptors2ignore=joelib2/data/plain/desc2ignore.txt
joelib2.process.types.DescStatistic.descriptors2ignore=joelib2/data/plain/desc2ignore.txt
joelib2.process.types.DescVarianceNorm.descriptors2ignore=joelib2/data/plain/desc2ignore.txt
joelib2.feature.data.MolDesc=joelib2.feature.types.counter.descriptors2ignore=joelib2/data/plain/desc2ignore.txt
joelib2.feature.data.MoleculesDescriptorMatrix.descriptors2ignore=joelib2/data/plain/desc2ignore.txt
joelib2.feature.data.MoleculesDescriptorMatrix.normalizeOnLoad=true
#joelib2.feature.data.MoleculesDescriptorMatrix.normalizeStatFile=../../datasets/test.sdf
##############################################################################
# number output (!!!) format
# import not implemented for locale!=en and/or groupingUsed!=false
##############################################################################
# initialize the number ouput format !
# number of '0' means the minimum number of digits to use
# number of '#' means the maximum number of digits to use
# in the property file you must use \# to quote the #'s
# If not used all digits will be used.
# deviant to the Java standard the exponential terms with E0 are removed.
#wsi.ra.text.DecimalFormatHelper.double.format=0.\#\#\#\#\#E0
# the both following parameters should be used carefully, because
# the import is not implemented correctly !!!
# e.g.: en, de
#wsi.ra.text.DecimalFormatHelper.double.locale=en
#wsi.ra.text.DecimalFormatHelper.double.groupingUsed=false
##############################################################################
# external processes
##############################################################################
joelib2.external.1.name =Title2Data
joelib2.external.1.representation =joelib2.ext.Title2Data
joelib2.external.1.descriptionFile =docs/ext/title2Data
joelib2.external.1.linux =../lib/linux/title2data
joelib2.external.1.windows =..\lib\windows\title2data.exe
joelib2.external.1.argument.1 =MOL_TITLE
##############################################################################
# Features and feature properties
##############################################################################
joelib2.feature.addIfNotExist=true
##############################################
joelib2.feature.0.representation =joelib2.ring.RingFinderSSSR
joelib2.feature.1.representation =joelib2.algo.BFS
joelib2.feature.2.representation =joelib2.algo.DFS
joelib2.feature.3.representation =joelib2.algo.APropertyBFS
joelib2.feature.4.representation =joelib2.feature.types.atomlabel.AtomBondOrderSum
joelib2.feature.5.representation =joelib2.feature.types.atomlabel.AtomElectronAffinity
joelib2.feature.6.representation =joelib2.feature.types.atomlabel.AtomENAllredRochow
joelib2.feature.7.representation =joelib2.feature.types.atomlabel.AtomENPauling
joelib2.feature.8.representation =joelib2.feature.types.atomlabel.AtomENSanderson
joelib2.feature.9.representation =joelib2.feature.types.atomlabel.AtomExplicitHydrogenCount
joelib2.feature.10.representation =joelib2.feature.types.atomlabel.AtomFreeElectronsCount
joelib2.feature.11.representation =joelib2.feature.types.atomlabel.AtomFreeOxygenCount
joelib2.feature.12.representation =joelib2.feature.types.atomlabel.AtomHeavyValence
joelib2.feature.13.representation =joelib2.feature.types.atomlabel.AtomHeteroValence
joelib2.feature.14.representation =joelib2.feature.types.atomlabel.AtomHybridisation
joelib2.feature.15.representation =joelib2.feature.types.atomlabel.AtomImplicitHydrogenCount
joelib2.feature.16.representation =joelib2.feature.types.atomlabel.AtomImplicitValence
joelib2.feature.17.representation =joelib2.feature.types.atomlabel.AtomInAcceptor
joelib2.feature.18.representation =joelib2.feature.types.atomlabel.AtomInAromaticSystem
joelib2.feature.19.representation =joelib2.feature.types.atomlabel.AtomInConjEnvironment
joelib2.feature.20.representation =joelib2.feature.types.atomlabel.AtomInDonAcc
joelib2.feature.21.representation =joelib2.feature.types.atomlabel.AtomInDonor
joelib2.feature.22.representation =joelib2.feature.types.atomlabel.AtomInRing
joelib2.feature.23.representation =joelib2.feature.types.atomlabel.AtomInRingsCount
joelib2.feature.24.representation =joelib2.feature.types.atomlabel.AtomInTerminalCarbon
joelib2.feature.25.representation =joelib2.feature.types.atomlabel.AtomIsAlphaBetaUnsaturated
joelib2.feature.26.representation =joelib2.feature.types.atomlabel.AtomIsAmideNitrogen
joelib2.feature.27.representation =joelib2.feature.types.atomlabel.AtomIsAntiClockwise
joelib2.feature.28.representation =joelib2.feature.types.atomlabel.AtomIsAromaticNOxide
joelib2.feature.29.representation =joelib2.feature.types.atomlabel.AtomIsAxial
joelib2.feature.30.representation =joelib2.feature.types.atomlabel.AtomIsCarbon
joelib2.feature.31.representation =joelib2.feature.types.atomlabel.AtomIsCarboxylOxygen
joelib2.feature.32.representation =joelib2.feature.types.atomlabel.AtomIsChiral
joelib2.feature.33.representation =joelib2.feature.types.atomlabel.AtomIsClockwise
joelib2.feature.34.representation =joelib2.feature.types.atomlabel.AtomIsElectronegative
joelib2.feature.35.representation =joelib2.feature.types.atomlabel.AtomIsHalogen
joelib2.feature.36.representation =joelib2.feature.types.atomlabel.AtomIsHeteroatom
joelib2.feature.37.representation =joelib2.feature.types.atomlabel.AtomIsHydrogen
joelib2.feature.38.representation =joelib2.feature.types.atomlabel.AtomIsNegative
joelib2.feature.39.representation =joelib2.feature.types.atomlabel.AtomIsNitrogen
joelib2.feature.40.representation =joelib2.feature.types.atomlabel.AtomIsNitroOxygen
joelib2.feature.41.representation =joelib2.feature.types.atomlabel.AtomIsNonPolarHydrogen
joelib2.feature.42.representation =joelib2.feature.types.atomlabel.AtomIsOxygen
joelib2.feature.43.representation =joelib2.feature.types.atomlabel.AtomIsPhosphateOxygen
joelib2.feature.44.representation =joelib2.feature.types.atomlabel.AtomIsPhosphorus
joelib2.feature.45.representation =joelib2.feature.types.atomlabel.AtomIsPolarHydrogen
joelib2.feature.46.representation =joelib2.feature.types.atomlabel.AtomIsPositive
joelib2.feature.47.representation =joelib2.feature.types.atomlabel.AtomIsSulfateOxygen
joelib2.feature.48.representation =joelib2.feature.types.atomlabel.AtomIsSulfur
joelib2.feature.49.representation =joelib2.feature.types.atomlabel.AtomIsUnsaturated
joelib2.feature.50.representation =joelib2.feature.types.atomlabel.AtomKekuleBondOrderSum
joelib2.feature.51.representation =joelib2.feature.types.atomlabel.AtomMass
joelib2.feature.52.representation =joelib2.feature.types.atomlabel.AtomPartialCharge
joelib2.feature.53.representation =joelib2.feature.types.atomlabel.AtomType
joelib2.feature.54.representation =joelib2.feature.types.atomlabel.AtomValence
joelib2.feature.55.representation =joelib2.feature.types.atomlabel.AtomValenceSum
joelib2.feature.56.representation =joelib2.feature.types.atomlabel.AtomVanDerWaalsVolume
joelib2.feature.57.representation =joelib2.feature.types.atompair.TopologicalAtomPair
joelib2.feature.58.representation =joelib2.feature.types.bondlabel.BondInAromaticSystem
joelib2.feature.59.representation =joelib2.feature.types.bondlabel.BondInRing
joelib2.feature.60.representation =joelib2.feature.types.bondlabel.BondIsAmide
joelib2.feature.61.representation =joelib2.feature.types.bondlabel.BondIsCarbonyl
joelib2.feature.62.representation =joelib2.feature.types.bondlabel.BondIsClosure
joelib2.feature.63.representation =joelib2.feature.types.bondlabel.BondIsEster
joelib2.feature.64.representation =joelib2.feature.types.bondlabel.BondIsPrimaryAmide
joelib2.feature.65.representation =joelib2.feature.types.bondlabel.BondIsRotor
joelib2.feature.66.representation =joelib2.feature.types.bondlabel.BondKekuleType
joelib2.feature.67.representation =joelib2.feature.types.count.AcidicGroups
joelib2.feature.68.representation =joelib2.feature.types.count.AliphaticOHGroups
joelib2.feature.69.representation =joelib2.feature.types.count.AromaticBonds
joelib2.feature.70.representation =joelib2.feature.types.count.AromaticOHGroups
joelib2.feature.71.representation =joelib2.feature.types.count.BasicGroups
joelib2.feature.72.representation =joelib2.feature.types.count.HBA1
joelib2.feature.73.representation =joelib2.feature.types.count.HBA2
joelib2.feature.74.representation =joelib2.feature.types.count.HBD1
joelib2.feature.75.representation =joelib2.feature.types.count.HBD2
joelib2.feature.76.representation =joelib2.feature.types.count.HeavyBonds
joelib2.feature.77.representation =joelib2.feature.types.count.HeteroCycles
joelib2.feature.78.representation =joelib2.feature.types.count.HydrophobicGroups
joelib2.feature.79.representation =joelib2.feature.types.count.NO2Groups
joelib2.feature.80.representation =joelib2.feature.types.count.NumberOfAtoms
joelib2.feature.81.representation =joelib2.feature.types.count.NumberOfB
joelib2.feature.82.representation =joelib2.feature.types.count.NumberOfBonds
joelib2.feature.83.representation =joelib2.feature.types.count.NumberOfBr
joelib2.feature.84.representation =joelib2.feature.types.count.NumberOfC
joelib2.feature.85.representation =joelib2.feature.types.count.NumberOfCl
joelib2.feature.86.representation =joelib2.feature.types.count.NumberOfF
joelib2.feature.87.representation =joelib2.feature.types.count.NumberOfHal
joelib2.feature.88.representation =joelib2.feature.types.count.NumberOfI
joelib2.feature.89.representation =joelib2.feature.types.count.NumberOfN
joelib2.feature.90.representation =joelib2.feature.types.count.NumberOfO
joelib2.feature.91.representation =joelib2.feature.types.count.NumberOfP
joelib2.feature.92.representation =joelib2.feature.types.count.NumberOfS
joelib2.feature.93.representation =joelib2.feature.types.count.OSOGroups
joelib2.feature.94.representation =joelib2.feature.types.count.SO2Groups
joelib2.feature.95.representation =joelib2.feature.types.count.SOGroups
joelib2.feature.96.representation =joelib2.feature.types.APropertyDistanceMatrix
joelib2.feature.97.representation =joelib2.feature.types.Autocorrelation
joelib2.feature.98.representation =joelib2.feature.types.BCUT
joelib2.feature.99.representation =joelib2.feature.types.BurdenEigenvalues
joelib2.feature.100.representation =joelib2.feature.types.BurdenModifiedEigenvalues
joelib2.feature.101.representation =joelib2.feature.types.ConjElectroTopolState
joelib2.feature.102.representation =joelib2.feature.types.ConjugatedTopologicalDistance
joelib2.feature.103.representation =joelib2.feature.types.DistanceDistanceMatrix
joelib2.feature.104.representation =joelib2.feature.types.DistanceMatrix
joelib2.feature.105.representation =joelib2.feature.types.ElectrogeometricalState
joelib2.feature.106.representation =joelib2.feature.types.ElectrotopologicalState
joelib2.feature.107.representation =joelib2.feature.types.FractionRotatableBonds
joelib2.feature.108.representation =joelib2.feature.types.GeomDistanceMatrix
joelib2.feature.109.representation =joelib2.feature.types.GeometricalDiameter
joelib2.feature.110.representation =joelib2.feature.types.GeometricalRadius
joelib2.feature.111.representation =joelib2.feature.types.GeometricalShapeCoefficient
joelib2.feature.112.representation =joelib2.feature.types.GlobalTopologicalChargeIndex
joelib2.feature.113.representation =joelib2.feature.types.GraphPotentials
joelib2.feature.114.representation =joelib2.feature.types.GraphShapeCoefficient
joelib2.feature.115.representation =joelib2.feature.types.IntrinsicState
joelib2.feature.116.representation =joelib2.feature.types.KierShape1
joelib2.feature.117.representation =joelib2.feature.types.KierShape2
joelib2.feature.118.representation =joelib2.feature.types.KierShape3
joelib2.feature.119.representation =joelib2.feature.types.LogP
joelib2.feature.120.representation =joelib2.feature.types.MolarRefractivity
joelib2.feature.121.representation =joelib2.feature.types.MolecularWeight
joelib2.feature.122.representation =joelib2.feature.types.PolarSurfaceArea
j##############################################
joelib2.feature.123.representation =joelib2.feature.types.RadialDistributionFunction
joelib2.feature.types.RadialDistributionFunction.minSphericalVolume = 0.2
joelib2.feature.types.RadialDistributionFunction.maxSphericalVolume = 10.0
joelib2.feature.types.RadialDistributionFunction.sphericalVolumeResolution = 0.05
joelib2.feature.types.RadialDistributionFunction.smoothingFactor = 25
##############################################
joelib2.feature.124.representation =joelib2.feature.types.RotatableBonds
joelib2.feature.125.representation =joelib2.feature.types.SMILESMolecule
joelib2.feature.126.representation =joelib2.feature.types.SSKey3DS
joelib2.feature.127.representation =joelib2.feature.types.TopologicalDiameter
joelib2.feature.128.representation =joelib2.feature.types.TopologicalRadius
joelib2.feature.129.representation =joelib2.feature.types.WeightedBurdenEigenvalues
joelib2.feature.130.representation =joelib2.feature.types.WeightedBurdenModifiedEigenvalues
joelib2.feature.131.representation =joelib2.feature.types.ZagrebIndex1
joelib2.feature.132.representation =joelib2.feature.types.MoleculeHashcode
joelib2.feature.133.representation =joelib2.feature.types.CharacteristicPolynomialCoefficients
joelib2.feature.134.representation =joelib2.feature.types.CharacteristicPolynomial
#joelib2.feature.135.representation =joelib2.feature.types.cfm.CompressedFeatureMatrix
#joelib2.feature.136.representation =
#joelib2.feature.137.representation =
#joelib2.feature.138.representation =
#joelib2.feature.139.representation =
#joelib2.feature.140.representation =
#joelib2.feature.141.representation =
##############################################################################
# End of JOELib2 properties definitions
##############################################################################
##############################################################################
# Start of JTextTools definitions
##############################################################################
jtt.docbook.DocBookEquations.latex=/usr/bin/latex
jtt.docbook.DocBookEquations.dvips=/usr/bin/dvips
jtt.docbook.DocBookEquations.convert=/usr/bin/convert
#jtt.docbook.DocBookEquations.latex=C:/Programme/latex/texmf/miktex/bin/latex.exe
#jtt.docbook.DocBookEquations.dvips=C:/Programme/latex/texmf/miktex/bin/dvips.exe
#jtt.docbook.DocBookEquations.convert=C:/Programme/ImageMagick/convert.exe
jtt.docbook.DocBookEquations.fontSize=12
jtt.docbook.DocBookEquations.bold=true
jtt.docbook.DocBookEquations.large=true
jtt.docbook.DocBookEquations.fileExtension=sgml
jtt.docbook.DocBookMolecules.fileExtension=sgml
jtt.docbook.Jade.jade=/usr/bin/jade
#jtt.docbook.Jade.jade=C:/cygwin/usr/share/sgml/docbook/jade121/jade
jtt.docbook.Jade.DSSSL.rtf=/usr/share/sgml/docbook/dsssl-stylesheets-1.77/print/docbook.dsl
jtt.docbook.Jade.DSSSL.html=/usr/share/sgml/docbook/dsssl-stylesheets-1.77/html/docbook.dsl
jtt.docbook.Jade.SGML.catalg.files=/usr/share/sgml/docbook_4.2/docbook.cat:/usr/share/sgml/jade_dsl/catalog
jtt.docbook.Jade.index=true
jtt.docbook.DocBookArticles.version=XML V4.2
jtt.docbook.DocBookArticles.fileExtension=sgml
jtt.docbook.DocBookArticles.DTD=/usr/share/sgml/docbook_4.2/docbook.dtd
##############################################################################
# End of JTextTools definitions
##############################################################################
|
