mspire-lipidomics 0.1.4
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- data/.document +5 -0
- data/.rspec +1 -0
- data/LICENSE +21 -0
- data/README.rdoc +18 -0
- data/Rakefile +45 -0
- data/VERSION +1 -0
- data/bin/lipidomic-search.rb +199 -0
- data/lib/mspire/lipid/ion/fragment.rb +68 -0
- data/lib/mspire/lipid/ion.rb +57 -0
- data/lib/mspire/lipid/modification.rb +125 -0
- data/lib/mspire/lipid/search/bin.rb +79 -0
- data/lib/mspire/lipid/search/db_isobar_group.rb +20 -0
- data/lib/mspire/lipid/search/hit.rb +79 -0
- data/lib/mspire/lipid/search/probability_distribution.rb +50 -0
- data/lib/mspire/lipid/search/query.rb +23 -0
- data/lib/mspire/lipid/search.rb +205 -0
- data/lib/mspire/lipid.rb +19 -0
- data/lib/mspire/lipid_maps.rb +87 -0
- data/mspire-lipidomics.gemspec +85 -0
- data/scratch/OBConversion_methods.txt +47 -0
- data/scratch/atom_methods.txt +145 -0
- data/scratch/bond_methods.txt +867 -0
- data/scratch/mol_methods.txt +183 -0
- data/scratch/split_molecules.rb +93 -0
- data/script/find_nearest_lipid.rb +114 -0
- data/spec/mspire/lipid/ion_spec.rb +83 -0
- data/spec/mspire/lipid/modification_spec.rb +41 -0
- data/spec/mspire/lipid/search_spec.rb +79 -0
- data/spec/mspire/lipid_maps_spec.rb +64 -0
- data/spec/mspire/lipid_spec.rb +16 -0
- data/spec/spec_helper.rb +13 -0
- data/spec/testfiles/lipidmaps_download.tsv +11 -0
- data/spec/testfiles/lipidmaps_programmatic_short.tsv +32 -0
- data/spec/testfiles/lipidmaps_sd_download.tsv +11 -0
- metadata +162 -0
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get_idx
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get_id
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get_bo
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get_bond_order
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get_flags
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get_begin_atom_idx
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get_end_atom_idx
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get_begin_atom
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get_end_atom
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get_nbr_atom
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get_parent
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get_equib_length
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get_length
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get_nbr_atom_idx
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find_smallest_ring
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is_aromatic
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clear
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do_transformations
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get_title
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set_title
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has_data
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delete_data
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clone_data
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data_size
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get_all_data
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get_data
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begin_data
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unset_kekule
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get_idx
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get_id
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get_bo
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get_flags
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get_begin_atom_idx
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get_begin_atom
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get_length
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find_smallest_ring
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clear
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do_transformations
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get_title
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set_title
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has_data
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delete_data
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clone_data
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data_size
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get_all_data
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get_data
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unset_kekule
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get_idx
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get_id
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get_bo
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get_flags
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get_length
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find_smallest_ring
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clear
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do_transformations
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get_title
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set_title
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has_data
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delete_data
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clone_data
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data_size
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get_all_data
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get_data
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begin_data
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end_data
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Visit=
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set_begin
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set_parent
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set_length
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set
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set_hash
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set_up
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set_down
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set_in_ring
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set_closure
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unset_hash
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unset_wedge
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unset_up
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unset_down
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unset_aromatic
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unset_kekule
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get_idx
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get_id
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get_bo
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get_bond_order
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get_flags
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get_begin_atom_idx
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get_begin_atom
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get_nbr_atom
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get_parent
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get_equib_length
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get_length
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get_nbr_atom_idx
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find_smallest_ring
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is_aromatic
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clear
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do_transformations
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get_title
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set_title
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has_data
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delete_data
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clone_data
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data_size
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get_all_data
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get_data
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begin_data
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set_begin
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set_length
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set
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set_aromatic
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set_wedge
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set_hash
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set_up
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set_down
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set_in_ring
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set_closure
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unset_hash
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unset_wedge
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unset_up
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unset_down
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unset_aromatic
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unset_kekule
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get_idx
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get_id
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get_bo
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get_bond_order
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get_flags
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get_begin_atom_idx
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get_end_atom_idx
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get_begin_atom
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get_end_atom
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get_nbr_atom
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get_parent
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get_equib_length
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get_length
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get_nbr_atom_idx
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find_smallest_ring
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is_aromatic
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|
+
is_in_ring
|
|
358
|
+
is_rotor
|
|
359
|
+
is_amide
|
|
360
|
+
is_primary_amide
|
|
361
|
+
is_secondary_amide
|
|
362
|
+
is_tertiary_amide
|
|
363
|
+
is_ester
|
|
364
|
+
is_carbonyl
|
|
365
|
+
is_single
|
|
366
|
+
is_double
|
|
367
|
+
is_triple
|
|
368
|
+
is_ksingle
|
|
369
|
+
is_kdouble
|
|
370
|
+
is_ktriple
|
|
371
|
+
is_closure
|
|
372
|
+
is_up
|
|
373
|
+
is_down
|
|
374
|
+
is_wedge
|
|
375
|
+
is_hash
|
|
376
|
+
is_wedge_or_hash
|
|
377
|
+
is_cis_or_trans
|
|
378
|
+
is_double_bond_geometry
|
|
379
|
+
clear
|
|
380
|
+
do_transformations
|
|
381
|
+
get_title
|
|
382
|
+
set_title
|
|
383
|
+
has_data
|
|
384
|
+
delete_data
|
|
385
|
+
clone_data
|
|
386
|
+
data_size
|
|
387
|
+
get_all_data
|
|
388
|
+
get_data
|
|
389
|
+
begin_data
|
|
390
|
+
end_data
|
|
391
|
+
Visit=
|
|
392
|
+
Visit
|
|
393
|
+
set_idx
|
|
394
|
+
set_id
|
|
395
|
+
set_bo
|
|
396
|
+
set_bond_order
|
|
397
|
+
set_begin
|
|
398
|
+
set_end
|
|
399
|
+
set_parent
|
|
400
|
+
set_length
|
|
401
|
+
set
|
|
402
|
+
set_ksingle
|
|
403
|
+
set_kdouble
|
|
404
|
+
set_ktriple
|
|
405
|
+
set_aromatic
|
|
406
|
+
set_wedge
|
|
407
|
+
set_hash
|
|
408
|
+
set_wedge_or_hash
|
|
409
|
+
set_up
|
|
410
|
+
set_down
|
|
411
|
+
set_in_ring
|
|
412
|
+
set_closure
|
|
413
|
+
unset_hash
|
|
414
|
+
unset_wedge
|
|
415
|
+
unset_up
|
|
416
|
+
unset_down
|
|
417
|
+
unset_aromatic
|
|
418
|
+
unset_kekule
|
|
419
|
+
get_idx
|
|
420
|
+
get_id
|
|
421
|
+
get_bo
|
|
422
|
+
get_bond_order
|
|
423
|
+
get_flags
|
|
424
|
+
get_begin_atom_idx
|
|
425
|
+
get_end_atom_idx
|
|
426
|
+
get_begin_atom
|
|
427
|
+
get_end_atom
|
|
428
|
+
get_nbr_atom
|
|
429
|
+
get_parent
|
|
430
|
+
get_equib_length
|
|
431
|
+
get_length
|
|
432
|
+
get_nbr_atom_idx
|
|
433
|
+
find_smallest_ring
|
|
434
|
+
is_aromatic
|
|
435
|
+
is_in_ring
|
|
436
|
+
is_rotor
|
|
437
|
+
is_amide
|
|
438
|
+
is_primary_amide
|
|
439
|
+
is_secondary_amide
|
|
440
|
+
is_tertiary_amide
|
|
441
|
+
is_ester
|
|
442
|
+
is_carbonyl
|
|
443
|
+
is_single
|
|
444
|
+
is_double
|
|
445
|
+
is_triple
|
|
446
|
+
is_ksingle
|
|
447
|
+
is_kdouble
|
|
448
|
+
is_ktriple
|
|
449
|
+
is_closure
|
|
450
|
+
is_up
|
|
451
|
+
is_down
|
|
452
|
+
is_wedge
|
|
453
|
+
is_hash
|
|
454
|
+
is_wedge_or_hash
|
|
455
|
+
is_cis_or_trans
|
|
456
|
+
is_double_bond_geometry
|
|
457
|
+
clear
|
|
458
|
+
do_transformations
|
|
459
|
+
get_title
|
|
460
|
+
set_title
|
|
461
|
+
has_data
|
|
462
|
+
delete_data
|
|
463
|
+
clone_data
|
|
464
|
+
data_size
|
|
465
|
+
get_all_data
|
|
466
|
+
get_data
|
|
467
|
+
begin_data
|
|
468
|
+
end_data
|
|
469
|
+
Visit=
|
|
470
|
+
Visit
|
|
471
|
+
set_idx
|
|
472
|
+
set_id
|
|
473
|
+
set_bo
|
|
474
|
+
set_bond_order
|
|
475
|
+
set_begin
|
|
476
|
+
set_end
|
|
477
|
+
set_parent
|
|
478
|
+
set_length
|
|
479
|
+
set
|
|
480
|
+
set_ksingle
|
|
481
|
+
set_kdouble
|
|
482
|
+
set_ktriple
|
|
483
|
+
set_aromatic
|
|
484
|
+
set_wedge
|
|
485
|
+
set_hash
|
|
486
|
+
set_wedge_or_hash
|
|
487
|
+
set_up
|
|
488
|
+
set_down
|
|
489
|
+
set_in_ring
|
|
490
|
+
set_closure
|
|
491
|
+
unset_hash
|
|
492
|
+
unset_wedge
|
|
493
|
+
unset_up
|
|
494
|
+
unset_down
|
|
495
|
+
unset_aromatic
|
|
496
|
+
unset_kekule
|
|
497
|
+
get_idx
|
|
498
|
+
get_id
|
|
499
|
+
get_bo
|
|
500
|
+
get_bond_order
|
|
501
|
+
get_flags
|
|
502
|
+
get_begin_atom_idx
|
|
503
|
+
get_end_atom_idx
|
|
504
|
+
get_begin_atom
|
|
505
|
+
get_end_atom
|
|
506
|
+
get_nbr_atom
|
|
507
|
+
get_parent
|
|
508
|
+
get_equib_length
|
|
509
|
+
get_length
|
|
510
|
+
get_nbr_atom_idx
|
|
511
|
+
find_smallest_ring
|
|
512
|
+
is_aromatic
|
|
513
|
+
is_in_ring
|
|
514
|
+
is_rotor
|
|
515
|
+
is_amide
|
|
516
|
+
is_primary_amide
|
|
517
|
+
is_secondary_amide
|
|
518
|
+
is_tertiary_amide
|
|
519
|
+
is_ester
|
|
520
|
+
is_carbonyl
|
|
521
|
+
is_single
|
|
522
|
+
is_double
|
|
523
|
+
is_triple
|
|
524
|
+
is_ksingle
|
|
525
|
+
is_kdouble
|
|
526
|
+
is_ktriple
|
|
527
|
+
is_closure
|
|
528
|
+
is_up
|
|
529
|
+
is_down
|
|
530
|
+
is_wedge
|
|
531
|
+
is_hash
|
|
532
|
+
is_wedge_or_hash
|
|
533
|
+
is_cis_or_trans
|
|
534
|
+
is_double_bond_geometry
|
|
535
|
+
clear
|
|
536
|
+
do_transformations
|
|
537
|
+
get_title
|
|
538
|
+
set_title
|
|
539
|
+
has_data
|
|
540
|
+
delete_data
|
|
541
|
+
clone_data
|
|
542
|
+
data_size
|
|
543
|
+
get_all_data
|
|
544
|
+
get_data
|
|
545
|
+
begin_data
|
|
546
|
+
end_data
|
|
547
|
+
Visit=
|
|
548
|
+
Visit
|
|
549
|
+
set_idx
|
|
550
|
+
set_id
|
|
551
|
+
set_bo
|
|
552
|
+
set_bond_order
|
|
553
|
+
set_begin
|
|
554
|
+
set_end
|
|
555
|
+
set_parent
|
|
556
|
+
set_length
|
|
557
|
+
set
|
|
558
|
+
set_ksingle
|
|
559
|
+
set_kdouble
|
|
560
|
+
set_ktriple
|
|
561
|
+
set_aromatic
|
|
562
|
+
set_wedge
|
|
563
|
+
set_hash
|
|
564
|
+
set_wedge_or_hash
|
|
565
|
+
set_up
|
|
566
|
+
set_down
|
|
567
|
+
set_in_ring
|
|
568
|
+
set_closure
|
|
569
|
+
unset_hash
|
|
570
|
+
unset_wedge
|
|
571
|
+
unset_up
|
|
572
|
+
unset_down
|
|
573
|
+
unset_aromatic
|
|
574
|
+
unset_kekule
|
|
575
|
+
get_idx
|
|
576
|
+
get_id
|
|
577
|
+
get_bo
|
|
578
|
+
get_bond_order
|
|
579
|
+
get_flags
|
|
580
|
+
get_begin_atom_idx
|
|
581
|
+
get_end_atom_idx
|
|
582
|
+
get_begin_atom
|
|
583
|
+
get_end_atom
|
|
584
|
+
get_nbr_atom
|
|
585
|
+
get_parent
|
|
586
|
+
get_equib_length
|
|
587
|
+
get_length
|
|
588
|
+
get_nbr_atom_idx
|
|
589
|
+
find_smallest_ring
|
|
590
|
+
is_aromatic
|
|
591
|
+
is_in_ring
|
|
592
|
+
is_rotor
|
|
593
|
+
is_amide
|
|
594
|
+
is_primary_amide
|
|
595
|
+
is_secondary_amide
|
|
596
|
+
is_tertiary_amide
|
|
597
|
+
is_ester
|
|
598
|
+
is_carbonyl
|
|
599
|
+
is_single
|
|
600
|
+
is_double
|
|
601
|
+
is_triple
|
|
602
|
+
is_ksingle
|
|
603
|
+
is_kdouble
|
|
604
|
+
is_ktriple
|
|
605
|
+
is_closure
|
|
606
|
+
is_up
|
|
607
|
+
is_down
|
|
608
|
+
is_wedge
|
|
609
|
+
is_hash
|
|
610
|
+
is_wedge_or_hash
|
|
611
|
+
is_cis_or_trans
|
|
612
|
+
is_double_bond_geometry
|
|
613
|
+
clear
|
|
614
|
+
do_transformations
|
|
615
|
+
get_title
|
|
616
|
+
set_title
|
|
617
|
+
has_data
|
|
618
|
+
delete_data
|
|
619
|
+
clone_data
|
|
620
|
+
data_size
|
|
621
|
+
get_all_data
|
|
622
|
+
get_data
|
|
623
|
+
begin_data
|
|
624
|
+
end_data
|
|
625
|
+
Visit=
|
|
626
|
+
Visit
|
|
627
|
+
set_idx
|
|
628
|
+
set_id
|
|
629
|
+
set_bo
|
|
630
|
+
set_bond_order
|
|
631
|
+
set_begin
|
|
632
|
+
set_end
|
|
633
|
+
set_parent
|
|
634
|
+
set_length
|
|
635
|
+
set
|
|
636
|
+
set_ksingle
|
|
637
|
+
set_kdouble
|
|
638
|
+
set_ktriple
|
|
639
|
+
set_aromatic
|
|
640
|
+
set_wedge
|
|
641
|
+
set_hash
|
|
642
|
+
set_wedge_or_hash
|
|
643
|
+
set_up
|
|
644
|
+
set_down
|
|
645
|
+
set_in_ring
|
|
646
|
+
set_closure
|
|
647
|
+
unset_hash
|
|
648
|
+
unset_wedge
|
|
649
|
+
unset_up
|
|
650
|
+
unset_down
|
|
651
|
+
unset_aromatic
|
|
652
|
+
unset_kekule
|
|
653
|
+
get_idx
|
|
654
|
+
get_id
|
|
655
|
+
get_bo
|
|
656
|
+
get_bond_order
|
|
657
|
+
get_flags
|
|
658
|
+
get_begin_atom_idx
|
|
659
|
+
get_end_atom_idx
|
|
660
|
+
get_begin_atom
|
|
661
|
+
get_end_atom
|
|
662
|
+
get_nbr_atom
|
|
663
|
+
get_parent
|
|
664
|
+
get_equib_length
|
|
665
|
+
get_length
|
|
666
|
+
get_nbr_atom_idx
|
|
667
|
+
find_smallest_ring
|
|
668
|
+
is_aromatic
|
|
669
|
+
is_in_ring
|
|
670
|
+
is_rotor
|
|
671
|
+
is_amide
|
|
672
|
+
is_primary_amide
|
|
673
|
+
is_secondary_amide
|
|
674
|
+
is_tertiary_amide
|
|
675
|
+
is_ester
|
|
676
|
+
is_carbonyl
|
|
677
|
+
is_single
|
|
678
|
+
is_double
|
|
679
|
+
is_triple
|
|
680
|
+
is_ksingle
|
|
681
|
+
is_kdouble
|
|
682
|
+
is_ktriple
|
|
683
|
+
is_closure
|
|
684
|
+
is_up
|
|
685
|
+
is_down
|
|
686
|
+
is_wedge
|
|
687
|
+
is_hash
|
|
688
|
+
is_wedge_or_hash
|
|
689
|
+
is_cis_or_trans
|
|
690
|
+
is_double_bond_geometry
|
|
691
|
+
clear
|
|
692
|
+
do_transformations
|
|
693
|
+
get_title
|
|
694
|
+
set_title
|
|
695
|
+
has_data
|
|
696
|
+
delete_data
|
|
697
|
+
clone_data
|
|
698
|
+
data_size
|
|
699
|
+
get_all_data
|
|
700
|
+
get_data
|
|
701
|
+
begin_data
|
|
702
|
+
end_data
|
|
703
|
+
Visit=
|
|
704
|
+
Visit
|
|
705
|
+
set_idx
|
|
706
|
+
set_id
|
|
707
|
+
set_bo
|
|
708
|
+
set_bond_order
|
|
709
|
+
set_begin
|
|
710
|
+
set_end
|
|
711
|
+
set_parent
|
|
712
|
+
set_length
|
|
713
|
+
set
|
|
714
|
+
set_ksingle
|
|
715
|
+
set_kdouble
|
|
716
|
+
set_ktriple
|
|
717
|
+
set_aromatic
|
|
718
|
+
set_wedge
|
|
719
|
+
set_hash
|
|
720
|
+
set_wedge_or_hash
|
|
721
|
+
set_up
|
|
722
|
+
set_down
|
|
723
|
+
set_in_ring
|
|
724
|
+
set_closure
|
|
725
|
+
unset_hash
|
|
726
|
+
unset_wedge
|
|
727
|
+
unset_up
|
|
728
|
+
unset_down
|
|
729
|
+
unset_aromatic
|
|
730
|
+
unset_kekule
|
|
731
|
+
get_idx
|
|
732
|
+
get_id
|
|
733
|
+
get_bo
|
|
734
|
+
get_bond_order
|
|
735
|
+
get_flags
|
|
736
|
+
get_begin_atom_idx
|
|
737
|
+
get_end_atom_idx
|
|
738
|
+
get_begin_atom
|
|
739
|
+
get_end_atom
|
|
740
|
+
get_nbr_atom
|
|
741
|
+
get_parent
|
|
742
|
+
get_equib_length
|
|
743
|
+
get_length
|
|
744
|
+
get_nbr_atom_idx
|
|
745
|
+
find_smallest_ring
|
|
746
|
+
is_aromatic
|
|
747
|
+
is_in_ring
|
|
748
|
+
is_rotor
|
|
749
|
+
is_amide
|
|
750
|
+
is_primary_amide
|
|
751
|
+
is_secondary_amide
|
|
752
|
+
is_tertiary_amide
|
|
753
|
+
is_ester
|
|
754
|
+
is_carbonyl
|
|
755
|
+
is_single
|
|
756
|
+
is_double
|
|
757
|
+
is_triple
|
|
758
|
+
is_ksingle
|
|
759
|
+
is_kdouble
|
|
760
|
+
is_ktriple
|
|
761
|
+
is_closure
|
|
762
|
+
is_up
|
|
763
|
+
is_down
|
|
764
|
+
is_wedge
|
|
765
|
+
is_hash
|
|
766
|
+
is_wedge_or_hash
|
|
767
|
+
is_cis_or_trans
|
|
768
|
+
is_double_bond_geometry
|
|
769
|
+
clear
|
|
770
|
+
do_transformations
|
|
771
|
+
get_title
|
|
772
|
+
set_title
|
|
773
|
+
has_data
|
|
774
|
+
delete_data
|
|
775
|
+
clone_data
|
|
776
|
+
data_size
|
|
777
|
+
get_all_data
|
|
778
|
+
get_data
|
|
779
|
+
begin_data
|
|
780
|
+
end_data
|
|
781
|
+
Visit=
|
|
782
|
+
Visit
|
|
783
|
+
set_idx
|
|
784
|
+
set_id
|
|
785
|
+
set_bo
|
|
786
|
+
set_bond_order
|
|
787
|
+
set_begin
|
|
788
|
+
set_end
|
|
789
|
+
set_parent
|
|
790
|
+
set_length
|
|
791
|
+
set
|
|
792
|
+
set_ksingle
|
|
793
|
+
set_kdouble
|
|
794
|
+
set_ktriple
|
|
795
|
+
set_aromatic
|
|
796
|
+
set_wedge
|
|
797
|
+
set_hash
|
|
798
|
+
set_wedge_or_hash
|
|
799
|
+
set_up
|
|
800
|
+
set_down
|
|
801
|
+
set_in_ring
|
|
802
|
+
set_closure
|
|
803
|
+
unset_hash
|
|
804
|
+
unset_wedge
|
|
805
|
+
unset_up
|
|
806
|
+
unset_down
|
|
807
|
+
unset_aromatic
|
|
808
|
+
unset_kekule
|
|
809
|
+
get_idx
|
|
810
|
+
get_id
|
|
811
|
+
get_bo
|
|
812
|
+
get_bond_order
|
|
813
|
+
get_flags
|
|
814
|
+
get_begin_atom_idx
|
|
815
|
+
get_end_atom_idx
|
|
816
|
+
get_begin_atom
|
|
817
|
+
get_end_atom
|
|
818
|
+
get_nbr_atom
|
|
819
|
+
get_parent
|
|
820
|
+
get_equib_length
|
|
821
|
+
get_length
|
|
822
|
+
get_nbr_atom_idx
|
|
823
|
+
find_smallest_ring
|
|
824
|
+
is_aromatic
|
|
825
|
+
is_in_ring
|
|
826
|
+
is_rotor
|
|
827
|
+
is_amide
|
|
828
|
+
is_primary_amide
|
|
829
|
+
is_secondary_amide
|
|
830
|
+
is_tertiary_amide
|
|
831
|
+
is_ester
|
|
832
|
+
is_carbonyl
|
|
833
|
+
is_single
|
|
834
|
+
is_double
|
|
835
|
+
is_triple
|
|
836
|
+
is_ksingle
|
|
837
|
+
is_kdouble
|
|
838
|
+
is_ktriple
|
|
839
|
+
is_closure
|
|
840
|
+
is_up
|
|
841
|
+
is_down
|
|
842
|
+
is_wedge
|
|
843
|
+
is_hash
|
|
844
|
+
is_wedge_or_hash
|
|
845
|
+
is_cis_or_trans
|
|
846
|
+
is_double_bond_geometry
|
|
847
|
+
clear
|
|
848
|
+
do_transformations
|
|
849
|
+
get_title
|
|
850
|
+
set_title
|
|
851
|
+
has_data
|
|
852
|
+
delete_data
|
|
853
|
+
clone_data
|
|
854
|
+
data_size
|
|
855
|
+
get_all_data
|
|
856
|
+
get_data
|
|
857
|
+
begin_data
|
|
858
|
+
end_data
|
|
859
|
+
to_i
|
|
860
|
+
to_f
|
|
861
|
+
to_a
|
|
862
|
+
&
|
|
863
|
+
|
|
|
864
|
+
^
|
|
865
|
+
to_r
|
|
866
|
+
rationalize
|
|
867
|
+
to_c
|