rubabel 0.1.0

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Files changed (34) hide show
  1. data/.document +5 -0
  2. data/.rspec +1 -0
  3. data/LICENSE +21 -0
  4. data/README.rdoc +52 -0
  5. data/Rakefile +43 -0
  6. data/VERSION +1 -0
  7. data/lib/rubabel.rb +116 -0
  8. data/lib/rubabel/atom.rb +143 -0
  9. data/lib/rubabel/bond.rb +47 -0
  10. data/lib/rubabel/fingerprint.rb +0 -0
  11. data/lib/rubabel/fragmentation.rb +23 -0
  12. data/lib/rubabel/molecule.rb +305 -0
  13. data/lib/rubabel/molecule_data.rb +0 -0
  14. data/lib/rubabel/pm.rb +38 -0
  15. data/lib/rubabel/smarts.rb +27 -0
  16. data/reference/OBConversion_methods.txt +47 -0
  17. data/reference/arity_method_list.txt +3553 -0
  18. data/reference/arity_method_list_CLASS.txt +337 -0
  19. data/reference/atom_methods.txt +145 -0
  20. data/reference/bond_methods.txt +79 -0
  21. data/reference/get_methods.rb +52 -0
  22. data/reference/mol_methods.txt +183 -0
  23. data/spec/rubabel/atom_spec.rb +49 -0
  24. data/spec/rubabel/bond_spec.rb +19 -0
  25. data/spec/rubabel/molecule_spec.rb +91 -0
  26. data/spec/rubabel_spec.rb +67 -0
  27. data/spec/spec_helper.rb +12 -0
  28. data/spec/testfiles/7-oxocholesterol-d7.mol +97 -0
  29. data/spec/testfiles/7-oxocholesterol-d7.sdf +155 -0
  30. data/spec/testfiles/Samples.sdf +2441 -0
  31. data/spec/testfiles/cholesterol.mol +74 -0
  32. data/spec/testfiles/cholesterol.sdf +132 -0
  33. data/spec/testfiles/two.sdf +287 -0
  34. metadata +130 -0
data/reference/arity_method_list_CLASS.txt ADDED
@@ -0,0 +1,337 @@
1
+ ************************************************************
2
+ OpenBabel
3
+ ************************************************************
4
+ to_angle_data: -1
5
+ to_atom_class_data: -1
6
+ to_chiral_data: -1
7
+ to_comment_data: -1
8
+ to_conformer_data: -1
9
+ to_external_bond_data: -1
10
+ to_grid_data: -1
11
+ to_matrix_data: -1
12
+ to_nasa_thermo_data: -1
13
+ to_pair_data: -1
14
+ to_rate_data: -1
15
+ to_rotamer_list: -1
16
+ to_rotation_data: -1
17
+ to_serial_nums: -1
18
+ to_set_data: -1
19
+ to_symmetry_data: -1
20
+ to_torsion_data: -1
21
+ to_unit_cell: -1
22
+ to_vector_data: -1
23
+ to_vibration_data: -1
24
+ to_virtual_bond: -1
25
+ double_multiply: -1
26
+ double_add: -1
27
+ double_modulus: -1
28
+ rotate_coords: -1
29
+ calc_rms: -1
30
+ <<: -1
31
+ +: -1
32
+ -: -1
33
+ /: -1
34
+ *: -1
35
+ dot: -1
36
+ cross: -1
37
+ vector_angle: -1
38
+ calc_torsion_angle: -1
39
+ point_2plane_signed: -1
40
+ point_2plane: -1
41
+ point_2plane_angle: -1
42
+ point_2line: -1
43
+ VZero: 0
44
+ VX: 0
45
+ VY: 0
46
+ VZ: 0
47
+ obrelease_version: -1
48
+ obErrorLog: 0
49
+ obErrorLog=: 1
50
+ Residue: 0
51
+ Residue=: 1
52
+ ElemDesc: 0
53
+ ElemDesc=: 1
54
+ ResNo: 0
55
+ ResNo=: 1
56
+ ElemNo: 0
57
+ ElemNo=: 1
58
+ throw_error: -1
59
+ cartesian_to_internal: -1
60
+ internal_to_cartesian: -1
61
+ new_extension: -1
62
+ etab: 0
63
+ etab=: 1
64
+ ttab: 0
65
+ ttab=: 1
66
+ isotab: 0
67
+ isotab=: 1
68
+ aromtyper: 0
69
+ aromtyper=: 1
70
+ atomtyper: 0
71
+ atomtyper=: 1
72
+ chainsparser: 0
73
+ chainsparser=: 1
74
+ resdat: 0
75
+ resdat=: 1
76
+ NoId: 0
77
+ get_rmat: -1
78
+ ob_make_rmat: -1
79
+ qtrfit: -1
80
+ superimpose: -1
81
+ compare_ring_size: -1
82
+ smarts_lex_replace: -1
83
+ AliasDataType: 0
84
+ tanimoto: -1
85
+ ***[OpenBabel::VectorUnsignedInt NO METHODS]***
86
+ ***[OpenBabel::VectorInt NO METHODS]***
87
+ ***[OpenBabel::Iterator NO METHODS]***
88
+ ***[OpenBabel::ConstIterator NO METHODS]***
89
+ ***[OpenBabel::GCVALUE NO METHODS]***
90
+ ***[OpenBabel::OBTorsion NO METHODS]***
91
+ ***[OpenBabel::OBSymmetryData NO METHODS]***
92
+ ***[OpenBabel::OBConformerData NO METHODS]***
93
+ ***[OpenBabel::OBUnitCell NO METHODS]***
94
+ ***[OpenBabel::OBRingData NO METHODS]***
95
+ ***[OpenBabel::OBVirtualBond NO METHODS]***
96
+ ***[OpenBabel::OBSetData NO METHODS]***
97
+ ***[OpenBabel::OBPairData NO METHODS]***
98
+ ***[OpenBabel::OBExternalBondData NO METHODS]***
99
+ ***[OpenBabel::OBExternalBond NO METHODS]***
100
+ ***[OpenBabel::OBCommentData NO METHODS]***
101
+ ************************************************************
102
+ OpenBabel::OBAtom
103
+ ************************************************************
104
+ class_description: -1
105
+ ***[OpenBabel::OBInternalCoord NO METHODS]***
106
+ ***[OpenBabel::LineSearchType NO METHODS]***
107
+ ************************************************************
108
+ OpenBabel::OBDescriptor
109
+ ************************************************************
110
+ default: -1
111
+ find_type: -1
112
+ filter_compare: -1
113
+ add_properties: -1
114
+ delete_properties: -1
115
+ get_values: -1
116
+ get_identifier: -1
117
+ get_plugin: -1
118
+ list_as_vector: -1
119
+ list: -1
120
+ list_as_string: -1
121
+ first_line: -1
122
+ begin: -1
123
+ end: -1
124
+ ***[OpenBabel::FastSearchIndexer NO METHODS]***
125
+ ***[OpenBabel::FastSearch NO METHODS]***
126
+ ***[OpenBabel::FptIndexHeader NO METHODS]***
127
+ ************************************************************
128
+ OpenBabel::OBFingerprint
129
+ ************************************************************
130
+ default: -1
131
+ find_type: -1
132
+ tanimoto: -1
133
+ getbitsperint: -1
134
+ find_fingerprint: -1
135
+ get_plugin: -1
136
+ list_as_vector: -1
137
+ list: -1
138
+ list_as_string: -1
139
+ first_line: -1
140
+ begin: -1
141
+ end: -1
142
+ ***[OpenBabel::OBAtomClassData NO METHODS]***
143
+ ************************************************************
144
+ OpenBabel::AliasData
145
+ ************************************************************
146
+ revert_to_alias_form: -1
147
+ ***[OpenBabel::OBMolRingIter NO METHODS]***
148
+ ***[OpenBabel::OBMolPairIter NO METHODS]***
149
+ ***[OpenBabel::OBMolTorsionIter NO METHODS]***
150
+ ***[OpenBabel::OBMolAngleIter NO METHODS]***
151
+ ***[OpenBabel::OBResidueAtomIter NO METHODS]***
152
+ ***[OpenBabel::OBResidueIter NO METHODS]***
153
+ ***[OpenBabel::OBAtomBondIter NO METHODS]***
154
+ ***[OpenBabel::OBAtomAtomIter NO METHODS]***
155
+ ***[OpenBabel::OBMolBondIter NO METHODS]***
156
+ ***[OpenBabel::OBMolBondBFSIter NO METHODS]***
157
+ ***[OpenBabel::OBMolAtomBFSIter NO METHODS]***
158
+ ***[OpenBabel::OBMolAtomDFSIter NO METHODS]***
159
+ ***[OpenBabel::OBMolAtomIter NO METHODS]***
160
+ ***[OpenBabel::OBRotamerList NO METHODS]***
161
+ ***[OpenBabel::OBRotorKeys NO METHODS]***
162
+ ***[OpenBabel::RotorDigit NO METHODS]***
163
+ ***[OpenBabel::OBRotorList NO METHODS]***
164
+ ***[OpenBabel::OBRotor NO METHODS]***
165
+ ***[OpenBabel::OBRotorRules NO METHODS]***
166
+ ***[OpenBabel::OBRotorRule NO METHODS]***
167
+ ***[OpenBabel::OBBitVec NO METHODS]***
168
+ ************************************************************
169
+ OpenBabel::OBOp
170
+ ************************************************************
171
+ default: -1
172
+ find_type: -1
173
+ op_options: -1
174
+ do_ops: -1
175
+ get_plugin: -1
176
+ list_as_vector: -1
177
+ list: -1
178
+ list_as_string: -1
179
+ first_line: -1
180
+ begin: -1
181
+ end: -1
182
+ ************************************************************
183
+ OpenBabel::OBBuilder
184
+ ************************************************************
185
+ get_new_bond_vector: -1
186
+ connect: -1
187
+ swap: -1
188
+ correct_stereo_bonds: -1
189
+ correct_stereo_atoms: -1
190
+ is_spiro_atom: -1
191
+ get_fragment: -1
192
+ add_nbrs: -1
193
+ ************************************************************
194
+ OpenBabel::OBForceField
195
+ ************************************************************
196
+ default: -1
197
+ find_type: -1
198
+ find_force_field: -1
199
+ ignore_calculation: -1
200
+ vector_bond_derivative: -1
201
+ vector_distance_derivative: -1
202
+ vector_length_derivative: -1
203
+ vector_angle_derivative: -1
204
+ vector_oopderivative: -1
205
+ vector_torsion_derivative: -1
206
+ vector_subtract: -1
207
+ vector_add: -1
208
+ vector_divide: -1
209
+ vector_multiply: -1
210
+ vector_self_multiply: -1
211
+ vector_normalize: -1
212
+ vector_copy: -1
213
+ vector_length: -1
214
+ vector_distance: -1
215
+ vector_angle: -1
216
+ vector_torsion: -1
217
+ vector_oop: -1
218
+ vector_clear: -1
219
+ vector_dot: -1
220
+ vector_cross: -1
221
+ print_vector: -1
222
+ get_plugin: -1
223
+ list_as_vector: -1
224
+ list: -1
225
+ list_as_string: -1
226
+ first_line: -1
227
+ begin: -1
228
+ end: -1
229
+ ***[OpenBabel::OBFFConstraints NO METHODS]***
230
+ ***[OpenBabel::OBFFConstraint NO METHODS]***
231
+ ***[OpenBabel::OBFFCalculation4 NO METHODS]***
232
+ ***[OpenBabel::OBFFCalculation3 NO METHODS]***
233
+ ***[OpenBabel::OBFFCalculation2 NO METHODS]***
234
+ ***[OpenBabel::OBFFParameter NO METHODS]***
235
+ ***[OpenBabel::OBSSMatch NO METHODS]***
236
+ ***[OpenBabel::OBSmartsMatcher NO METHODS]***
237
+ ***[OpenBabel::OBSmartsPattern NO METHODS]***
238
+ ***[OpenBabel::OBRTree NO METHODS]***
239
+ ***[OpenBabel::OBRingSearch NO METHODS]***
240
+ ***[OpenBabel::OBRing NO METHODS]***
241
+ ************************************************************
242
+ OpenBabel::OBMol
243
+ ************************************************************
244
+ class_description: -1
245
+ ************************************************************
246
+ OpenBabel::OBBond
247
+ ************************************************************
248
+ class_description: -1
249
+ ************************************************************
250
+ OpenBabel::OBResidue
251
+ ************************************************************
252
+ class_description: -1
253
+ ************************************************************
254
+ OpenBabel::OBConversion
255
+ ************************************************************
256
+ register_format: -1
257
+ find_format: -1
258
+ format_from_ext: -1
259
+ format_from_mime: -1
260
+ get_next_format: -1
261
+ description: -1
262
+ register_option_param: -1
263
+ get_option_params: -1
264
+ get_default_format: -1
265
+ ************************************************************
266
+ OpenBabel::OBFormat
267
+ ************************************************************
268
+ default: -1
269
+ find_type: -1
270
+ format_from_mime: -1
271
+ get_plugin: -1
272
+ list_as_vector: -1
273
+ list: -1
274
+ list_as_string: -1
275
+ first_line: -1
276
+ begin: -1
277
+ end: -1
278
+ ***[OpenBabel::ObLogBuf NO METHODS]***
279
+ ***[OpenBabel::OBMessageHandler NO METHODS]***
280
+ ***[OpenBabel::OBError NO METHODS]***
281
+ ***[OpenBabel::Stringbuf NO METHODS]***
282
+ ************************************************************
283
+ OpenBabel::OBPlugin
284
+ ************************************************************
285
+ get_plugin: -1
286
+ list_as_vector: -1
287
+ list: -1
288
+ list_as_string: -1
289
+ first_line: -1
290
+ begin: -1
291
+ end: -1
292
+ ***[OpenBabel::CharPtrLess NO METHODS]***
293
+ ***[OpenBabel::Dummy NO METHODS]***
294
+ ***[OpenBabel::OBGridData NO METHODS]***
295
+ ***[OpenBabel::OBMatrixData NO METHODS]***
296
+ ***[OpenBabel::OBVectorData NO METHODS]***
297
+ ***[OpenBabel::OBRotationData NO METHODS]***
298
+ ***[OpenBabel::OBElectronicTransitionData NO METHODS]***
299
+ ***[OpenBabel::OBOrbitalData NO METHODS]***
300
+ ***[OpenBabel::OBOrbital NO METHODS]***
301
+ ***[OpenBabel::OBDOSData NO METHODS]***
302
+ ***[OpenBabel::OBVibrationData NO METHODS]***
303
+ ***[OpenBabel::OBSerialNums NO METHODS]***
304
+ ***[OpenBabel::OBChiralData NO METHODS]***
305
+ ***[OpenBabel::OBAngleData NO METHODS]***
306
+ ***[OpenBabel::OBAngle NO METHODS]***
307
+ ***[OpenBabel::OBTorsionData NO METHODS]***
308
+ ************************************************************
309
+ OpenBabel::OBBase
310
+ ************************************************************
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+ class_description: -1
312
+ ***[OpenBabel::OBGenericData NO METHODS]***
313
+ ************************************************************
314
+ OpenBabel::Matrix3x3
315
+ ************************************************************
316
+ jacobi: -1
317
+ ***[OpenBabel::Vector3 NO METHODS]***
318
+ ***[OpenBabel::OBSqrtTbl NO METHODS]***
319
+ ***[OpenBabel::OBStopwatch NO METHODS]***
320
+ ***[OpenBabel::OBRandom NO METHODS]***
321
+ ***[OpenBabel::DoubleType NO METHODS]***
322
+ ***[OpenBabel::OBResidueData NO METHODS]***
323
+ ***[OpenBabel::OBTypeTable NO METHODS]***
324
+ ***[OpenBabel::OBIsotopeTable NO METHODS]***
325
+ ***[OpenBabel::OBElementTable NO METHODS]***
326
+ ***[OpenBabel::OBElement NO METHODS]***
327
+ ***[OpenBabel::OBGlobalDataBase NO METHODS]***
328
+ ***[OpenBabel::VectorpOBGenericData NO METHODS]***
329
+ ***[OpenBabel::VectorpOBRing NO METHODS]***
330
+ ***[OpenBabel::VectorOBRing NO METHODS]***
331
+ ***[OpenBabel::VectorOBResidue NO METHODS]***
332
+ ***[OpenBabel::VectorOBBond NO METHODS]***
333
+ ***[OpenBabel::VectorOBMol NO METHODS]***
334
+ ***[OpenBabel::VectorVector3 NO METHODS]***
335
+ ***[OpenBabel::VectorString NO METHODS]***
336
+ ***[OpenBabel::VectorDouble NO METHODS]***
337
+ ***[OpenBabel::VectorVInt NO METHODS]***
data/reference/atom_methods.txt ADDED
@@ -0,0 +1,145 @@
1
+ Visit=
2
+ Visit
3
+ duplicate
4
+ set_idx
5
+ set_id
6
+ set_hyb
7
+ set_atomic_num
8
+ set_isotope
9
+ set_implicit_valence
10
+ increment_implicit_valence
11
+ decrement_implicit_valence
12
+ set_formal_charge
13
+ set_spin_multiplicity
14
+ set_type
15
+ set_partial_charge
16
+ set_coord_ptr
17
+ set_vector
18
+ set_residue
19
+ set_parent
20
+ set_aromatic
21
+ unset_aromatic
22
+ set_clockwise_stereo
23
+ set_anti_clockwise_stereo
24
+ set_positive_stereo
25
+ set_negative_stereo
26
+ unset_stereo
27
+ set_in_ring
28
+ set_chiral
29
+ clear_coord_ptr
30
+ get_formal_charge
31
+ get_atomic_num
32
+ get_isotope
33
+ get_spin_multiplicity
34
+ get_atomic_mass
35
+ get_exact_mass
36
+ get_idx
37
+ get_index
38
+ get_id
39
+ get_coordinate_idx
40
+ get_cidx
41
+ get_valence
42
+ get_hyb
43
+ get_implicit_valence
44
+ get_hvy_valence
45
+ get_hetero_valence
46
+ get_type
47
+ get_x
48
+ get_y
49
+ get_z
50
+ x
51
+ y
52
+ z
53
+ get_coordinate
54
+ get_vector
55
+ get_partial_charge
56
+ get_residue
57
+ get_parent
58
+ get_new_bond_vector
59
+ get_bond
60
+ get_next_atom
61
+ begin_bonds
62
+ end_bonds
63
+ begin_bond
64
+ next_bond
65
+ begin_nbr_atom
66
+ next_nbr_atom
67
+ get_distance
68
+ get_angle
69
+ new_residue
70
+ add_residue
71
+ delete_residue
72
+ add_bond
73
+ insert_bond
74
+ delete_bond
75
+ clear_bond
76
+ hto_methyl
77
+ set_hyb_and_geom
78
+ force_no_h
79
+ has_no_hforced
80
+ force_impl_h
81
+ has_impl_hforced
82
+ count_free_oxygens
83
+ implicit_hydrogen_count
84
+ explicit_hydrogen_count
85
+ member_of_ring_count
86
+ member_of_ring_size
87
+ count_ring_bonds
88
+ smallest_bond_angle
89
+ average_bond_angle
90
+ bosum
91
+ kbosum
92
+ has_residue
93
+ is_hydrogen
94
+ is_carbon
95
+ is_nitrogen
96
+ is_oxygen
97
+ is_sulfur
98
+ is_phosphorus
99
+ is_aromatic
100
+ is_in_ring
101
+ is_in_ring_size
102
+ is_heteroatom
103
+ is_not_cor_h
104
+ is_connected
105
+ is_one_three
106
+ is_one_four
107
+ is_carboxyl_oxygen
108
+ is_phosphate_oxygen
109
+ is_sulfate_oxygen
110
+ is_nitro_oxygen
111
+ is_amide_nitrogen
112
+ is_polar_hydrogen
113
+ is_non_polar_hydrogen
114
+ is_aromatic_noxide
115
+ is_chiral
116
+ is_axial
117
+ is_clockwise
118
+ is_anti_clockwise
119
+ is_positive_stereo
120
+ is_negative_stereo
121
+ has_chirality_specified
122
+ has_chiral_volume
123
+ is_hbond_acceptor
124
+ is_hbond_donor
125
+ is_hbond_donor_h
126
+ has_alpha_beta_unsat
127
+ has_bond_of_order
128
+ count_bonds_of_order
129
+ has_non_single_bond
130
+ has_single_bond
131
+ has_double_bond
132
+ has_aromatic_bond
133
+ matches_smarts
134
+ clear
135
+ do_transformations
136
+ get_title
137
+ set_title
138
+ has_data
139
+ delete_data
140
+ clone_data
141
+ data_size
142
+ get_all_data
143
+ get_data
144
+ begin_data
145
+ end_data