mspire-lipidomics 0.1.4

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Files changed (35) hide show
  1. data/.document +5 -0
  2. data/.rspec +1 -0
  3. data/LICENSE +21 -0
  4. data/README.rdoc +18 -0
  5. data/Rakefile +45 -0
  6. data/VERSION +1 -0
  7. data/bin/lipidomic-search.rb +199 -0
  8. data/lib/mspire/lipid/ion/fragment.rb +68 -0
  9. data/lib/mspire/lipid/ion.rb +57 -0
  10. data/lib/mspire/lipid/modification.rb +125 -0
  11. data/lib/mspire/lipid/search/bin.rb +79 -0
  12. data/lib/mspire/lipid/search/db_isobar_group.rb +20 -0
  13. data/lib/mspire/lipid/search/hit.rb +79 -0
  14. data/lib/mspire/lipid/search/probability_distribution.rb +50 -0
  15. data/lib/mspire/lipid/search/query.rb +23 -0
  16. data/lib/mspire/lipid/search.rb +205 -0
  17. data/lib/mspire/lipid.rb +19 -0
  18. data/lib/mspire/lipid_maps.rb +87 -0
  19. data/mspire-lipidomics.gemspec +85 -0
  20. data/scratch/OBConversion_methods.txt +47 -0
  21. data/scratch/atom_methods.txt +145 -0
  22. data/scratch/bond_methods.txt +867 -0
  23. data/scratch/mol_methods.txt +183 -0
  24. data/scratch/split_molecules.rb +93 -0
  25. data/script/find_nearest_lipid.rb +114 -0
  26. data/spec/mspire/lipid/ion_spec.rb +83 -0
  27. data/spec/mspire/lipid/modification_spec.rb +41 -0
  28. data/spec/mspire/lipid/search_spec.rb +79 -0
  29. data/spec/mspire/lipid_maps_spec.rb +64 -0
  30. data/spec/mspire/lipid_spec.rb +16 -0
  31. data/spec/spec_helper.rb +13 -0
  32. data/spec/testfiles/lipidmaps_download.tsv +11 -0
  33. data/spec/testfiles/lipidmaps_programmatic_short.tsv +32 -0
  34. data/spec/testfiles/lipidmaps_sd_download.tsv +11 -0
  35. metadata +162 -0
data/scratch/atom_methods.txt ADDED
@@ -0,0 +1,145 @@
1
+ Visit=
2
+ Visit
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+ duplicate
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+ set_idx
5
+ set_id
6
+ set_hyb
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+ set_atomic_num
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+ set_isotope
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+ set_implicit_valence
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+ increment_implicit_valence
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+ decrement_implicit_valence
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+ set_formal_charge
13
+ set_spin_multiplicity
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+ set_type
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+ set_partial_charge
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+ set_coord_ptr
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+ set_vector
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+ set_residue
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+ set_parent
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+ set_aromatic
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+ unset_aromatic
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+ set_clockwise_stereo
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+ set_anti_clockwise_stereo
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+ set_positive_stereo
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+ set_negative_stereo
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+ 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
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+ get_exact_mass
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+ get_idx
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+ get_index
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+ get_id
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+ get_coordinate_idx
40
+ get_cidx
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+ get_valence
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+ get_hyb
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+ get_implicit_valence
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+ get_hvy_valence
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+ get_hetero_valence
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+ get_type
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+ get_x
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+ get_y
49
+ get_z
50
+ x
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+ y
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+ z
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+ get_coordinate
54
+ get_vector
55
+ get_partial_charge
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+ get_residue
57
+ get_parent
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+ get_new_bond_vector
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+ get_bond
60
+ get_next_atom
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+ begin_bonds
62
+ end_bonds
63
+ begin_bond
64
+ next_bond
65
+ begin_nbr_atom
66
+ next_nbr_atom
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+ 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
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+ hto_methyl
77
+ set_hyb_and_geom
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+ force_no_h
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+ has_no_hforced
80
+ force_impl_h
81
+ has_impl_hforced
82
+ count_free_oxygens
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+ 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
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+ average_bond_angle
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+ bosum
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+ kbosum
92
+ has_residue
93
+ is_hydrogen
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+ is_carbon
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+ is_nitrogen
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+ is_oxygen
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+ is_sulfur
98
+ is_phosphorus
99
+ is_aromatic
100
+ is_in_ring
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+ is_in_ring_size
102
+ is_heteroatom
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+ is_not_cor_h
104
+ is_connected
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+ is_one_three
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+ is_one_four
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+ is_carboxyl_oxygen
108
+ is_phosphate_oxygen
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+ is_sulfate_oxygen
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+ is_nitro_oxygen
111
+ is_amide_nitrogen
112
+ is_polar_hydrogen
113
+ is_non_polar_hydrogen
114
+ is_aromatic_noxide
115
+ is_chiral
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+ is_axial
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+ 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