-
Notifications
You must be signed in to change notification settings - Fork 1
/
Shorthand2020.g4
279 lines (249 loc) · 14.6 KB
/
Shorthand2020.g4
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
/*
* MIT License
*
* Copyright (c) the authors (listed in global LICENSE file)
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the 'Software'), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:;
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHether IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*/
/* This is a BNF / ANTLR4 grammar for lipid subspecies identifiers following
* Liebisch et al. Volume 61, Issue 12, December 2020, Pages 1539-1555.
*/
grammar Shorthand2020;
/* first rule is always start rule */
lipid : lipid_eof EOF;
lipid_eof : lipid_pure | lipid_pure adduct_info;
lipid_pure : gl | pl | sl | sterol | med; /* glycero lipids, phospho lipids, sphingo lipids, sterol lipids, lipid mediators
/* adduct information */
adduct_info : adduct_sep | adduct_separator adduct_sep;
adduct_sep : SOB 'M' adduct SCB adduct_charge | SOB 'M' adduct_heavy adduct SCB adduct_charge | SOB 'M' adduct_heavy SCB;
adduct_charge : charge_sign | charge charge_sign;
adduct : adduct_set;
adduct_set : adduct_element | adduct_element adduct_set;
adduct_element : element | element number | number element | plus_minus element | plus_minus element number | plus_minus number element;
adduct_heavy : adduct_heavy_component | adduct_heavy adduct_heavy;
adduct_heavy_component : adduct_heavy_element adduct_heavy_number | adduct_heavy_element;
adduct_heavy_element: '[2]H' | '[13]C' | '[15]N' | '[17]O' | '[18]O' | '[32]P' | '[33]S' | '[34]S';
adduct_heavy_number : number;
/* mediators */
med : med_species | med_subspecies;
med_species : med_hg_double headgroup_separator fatty_acyl_chain | med_hg_triple headgroup_separator fatty_acyl_chain;
med_subspecies : med_hg_single headgroup_separator fatty_acyl_chain |
med_hg_double headgroup_separator fatty_acyl_chain2 |
med_hg_triple headgroup_separator fatty_acyl_chain3;
med_hg_single : 'FA' | 'FOH' | 'FAL' | 'CAR' | 'CoA' | 'NAE' | 'NAT' | 'WD' | 'HC' | 'FAHFA';
med_hg_double : 'WE' | 'NA';
med_hg_triple : 'WD';
/* fatty acyl chain */
lcb : fa_pure | ether fa_pure | fatty_acyl_linkage | fatty_alkyl_linkage;
fatty_acyl_chain : fa_pure | ether fa_pure | fatty_acyl_linkage | fatty_alkyl_linkage;
fatty_alkyl_linkage : fatty_linkage_number fatty_acyl_linkage_sign ROB fatty_acyl_chain RCB | fatty_acyl_linkage_sign ROB fatty_acyl_chain RCB;
fatty_acyl_linkage : fatty_linkage_number fatty_acyl_linkage_sign ROB med RCB | fatty_acyl_linkage_sign ROB med RCB;
hydrocarbon_chain : hydrocarbon_number ROB fatty_acyl_chain RCB | ROB fatty_acyl_chain RCB;
fatty_acyl_linkage_sign : 'O' | 'N';
fatty_linkage_number : number;
hydrocarbon_number : number;
fa_pure : fa_pure_structure | fa_pure_structure sn;
sn : ROB 'sn-' sn_pos RCB;
sn_pos : number;
fa_pure_structure : fa_db_only | carbon carbon_db_separator db db_funcgroup_separator func_group | carbon carbon_db_separator db stereo_fa | carbon carbon_db_separator db stereo_fa db_funcgroup_separator func_group;
fa_db_only : carbon carbon_db_separator db;
ether : ether_num ether_type | ether_type;
ether_num : 'm' | 'd' | 't' | 'e';
ether_type: ether_types plasmalogen_separator | ether_types plasmalogen_separator;
ether_types: 'O' | 'P';
carbon : number;
db : db_count | db_count db_positions;
db_count : number;
db_positions : ROB db_position RCB;
db_position : db_single_position | db_position db_position_separator db_position;
db_single_position : db_position_number | db_position_number cistrans;
db_position_number : number;
cistrans : 'E' | 'Z';
stereo_fa : SOB stereo_type_fa SCB;
stereo_type_fa : stereo_number stereo_direction | stereo_direction;
func_group : func_group_entity;
func_group_entity : func_group_entity funcgroup_separator func_group_entity | func_group_data | func_group_data_repetition;
func_group_data_repetition : func_group_data_repetition func_repetition_separator func_group_data_repetition | func_group_data;
func_group_data : func_group_name | func_group_cycle | func_group_pos func_group_ext_name | func_group_pos func_group_ext_name stereo_fg | func_group_ext_count_name func_group_count | func_group_ext_name func_group_count stereo_fg | molecular_func_group | fatty_acyl_linkage | fatty_alkyl_linkage | hydrocarbon_chain;
func_group_pos : func_group_pos_number | func_group_pos_number ring_stereo;
ring_stereo : 'a' | 'b';
func_group_pos_number : number;
func_group_count : number;
stereo_fg : SOB stereo_type_fg SCB;
stereo_type_fg : stereo_number stereo_direction | stereo_direction;
stereo_number : number;
stereo_direction : 'R' | 'S';
molecular_func_group : molecular_func_group_name | molecular_func_group_name func_group_count;
func_group_ext_name : round_open_bracket func_group_name round_close_bracket | func_group_name;
func_group_ext_count_name : round_open_bracket func_group_name round_close_bracket | molecular_func_group_name;
func_group_name : 'Et' | 'Me' | 'Ac' | 'NO2' | 'My' | 'Ep' | 'OO' | 'dMe' | 'OMe' | 'oxy' | 'NH2' | 'OOH' | 'SH' | 'OH' | 'oxo' | 'CN' | 'Ph' | 'Su' | 'COOH' | 'G' | 'T' | 'COG' | 'COT' | carbohydrate_sn | carbohydrate_iso | 'H' | 'Cys' | 'Phe' | 'SGlu' | 'SCys' | 'BOO' | 'MMAs' | 'SMe' | 'NH' | 'SCG' | special_elements;
molecular_func_group_name : elements | special_elements;
elements : 'O' | 'N' | 'P' | 'S' | 'As';
special_elements: 'Br' | 'Cl' | 'F' | 'I';
func_group_cycle : SOB cycle_base SCB | SOB cycle_base funcgroup_separator cycle_func_group_data SCB;
cycle_base : cycle_def | cycle_def carbon_db_separator cycle_db;
cycle_def : cycle_start cycle_separator cycle_end cycle_token cycle_number | cycle_start cycle_separator cycle_end cycle_bridge cycle_token cycle_number | cycle_bridge cycle_token cycle_number | cycle_token cycle_number;
cycle_bridge : cylce_elements;
cylce_elements : cylce_elements cylce_elements | cylce_element;
cylce_element : elements;
cycle_token : 'cy';
cycle_number : number;
cycle_start : number;
cycle_end : number;
cycle_func_group_data : func_group_entity;
cycle_db : cycle_db_cnt | cycle_db_cnt ROB cycle_db_positions RCB;
cycle_db_cnt : number;
cycle_db_positions : cycle_db_position;
cycle_db_position : cycle_db_position db_position_separator cycle_db_position | cycle_db_position_number | cycle_db_position_number cycle_db_position_cis_trans;
cycle_db_position_number : number;
cycle_db_position_cis_trans : cistrans;
fatty_acyl_chain2 : fa2_sorted | fa2_unsorted;
fa2_unsorted : fatty_acyl_chain unsorted_fa_separator fatty_acyl_chain;
fa2_sorted : fatty_acyl_chain sorted_fa_separator fatty_acyl_chain;
fatty_acyl_chain3 : f3_sorted | fa3_unsorted;
f3_sorted : fa2_sorted sorted_fa_separator fatty_acyl_chain;
fa3_unsorted : fa2_unsorted unsorted_fa_separator fatty_acyl_chain;
fatty_acyl_chain4 : f4_sorted | fa4_unsorted;
f4_sorted : fa2_sorted sorted_fa_separator fa2_sorted;
fa4_unsorted : fa2_unsorted unsorted_fa_separator fa2_unsorted;
/* glycero lipids */
gl : gl_species | gl_subpsecies | gl_molecular_species;
gl_species : gl_hg_dt headgroup_separator fatty_acyl_chain;
gl_molecular_species : gl_hg_triple headgroup_separator fa2_unsorted;
gl_subpsecies : gl_hg headgroup_separator fatty_acyl_chain3 |
gl_hg_glycosyl headgroup_separator fatty_acyl_chain2 |
gl_hg_double headgroup_separator fa2_unsorted |
gl_hg_single headgroup_separator fatty_acyl_chain |
gl_hg_glycosyl_single headgroup_separator fatty_acyl_chain;
gl_hg_glycosyl : gl_hg_glycosyl_single | gl_hg_glycosyl_double;
gl_hg_dt : gl_hg_double | gl_hg_glycosyl_double | gl_hg_triple;
gl_hg : gl_hg_single | gl_hg_double | gl_hg_triple;
gl_hg_single : 'MG';
gl_hg_glycosyl_single : 'MGMG' | 'DGMG' | 'SQMG';
gl_hg_double : 'DG';
gl_hg_glycosyl_double : 'MGDG' | 'DGDG' | 'SQDG' | 'SMGDG';
gl_hg_triple : 'TG' | gl_hg_tg_est;
gl_hg_tg_est : 'TG-EST' | 'TG EST' | 'TAG EST' | 'TAG-EST';
pl : pl_species | pl_subspecies | pl_molecular_species | pl_cpa;
pl_species : pl_hg headgroup_separator fatty_acyl_chain;
pl_cpa : pl_cpa_head headgroup_separator fatty_acyl_chain;
pl_cpa_head : 'CPA' | 'cLPA' | 'CLPA';
pl_subspecies : pl_single | pl_double | pl_quadro;
pl_molecular_species : pl_hg_quadro headgroup_separator fa2_unsorted | pl_hg_quadro headgroup_separator fa3_unsorted;
pl_single : pl_hg_single headgroup_separator fatty_acyl_chain;
pl_full : pl_hg_single headgroup_separator fatty_acyl_chain2;
pl_double : pl_full | pl_hg_double_all headgroup_separator fatty_acyl_chain2;
pl_quadro : pl_hg_quadro headgroup_separator fatty_acyl_chain4;
pl_hg : pl_hg_double_all | pl_hg_quadro;
pl_hg_single : 'LPA' | 'LPC' | 'LPE' | 'LPG' | 'LPI' | 'LPS' | hg_lpim | 'LCDPDAG' | 'LDMPE' | 'LMMPE' | 'LPIMIP' | 'LPIN' | 'PE-isoLG';
pl_hg_double_all : pl_hg_double_fa | pl_hg_double | hg_pip;
pl_hg_double_fa : pl_hg_double_fa_hg ROB pl_hg_fa RCB | pl_hg_double_fa_hg ROB pl_hg_alk RCB;
pl_hg_double_fa_hg : 'PS-N' | 'PE-N';
pl_hg_double : 'CDP-DAG' | 'DMPE' | 'MMPE' | 'PA' | 'PC' | 'PE' | 'PEt' | 'PEtOH' | 'PMeOH' | 'PG' | 'PI' | 'PS' | 'LBPA' | 'PGP' | 'PPA' | 'Glc-GP' | '6-Ac-Glc-GP' | hg_pim | 'PnC' | 'PnE' | 'PT' | 'PE-NMe2' | 'PE-NMe' | 'PIMIP' | 'CDPDAG' | 'PS-CAP' | 'PS-MDA' | 'PE-CAP' | 'PE-Glc' | 'PE-GlcA' | 'PE-GlcK' | 'PE-CM' | 'PE-CE' | 'PE-FA' | 'PE-CA' | 'PE-MDA' | 'PE-HNE' | pl_hg_species;
pl_hg_species : hg_PE_PS ROB hg_PE_PS_type RCB;
hg_PE_PS : 'PE-N' | 'PS-N';
hg_PE_PS_type : 'Alk' | 'FA';
pl_hg_quadro : 'BMP' | 'CL' | 'LCL' | 'DLCL';
hg_pip : hg_pip_pure_m | hg_pip_pure_d | hg_pip_pure_t | hg_pip_pure_m ROB hg_pip_m RCB | hg_pip_pure_d ROB hg_pip_d RCB | hg_pip_pure_t ROB hg_pip_t RCB;
hg_pip_pure_m : 'PIP';
hg_pip_pure_d : 'PIP2';
hg_pip_pure_t : 'PIP3';
hg_pip_m : '3' APOSTROPH | '4' APOSTROPH | '5' APOSTROPH;
hg_pip_d : '3' APOSTROPH COMMA '4' APOSTROPH | '4' APOSTROPH COMMA '5' APOSTROPH | '3' APOSTROPH COMMA '5' APOSTROPH;
hg_pip_t : '3' APOSTROPH COMMA '4' APOSTROPH COMMA '5' APOSTROPH;
hg_pim : 'PIM' hg_pim_number;
hg_pim_number : number;
hg_lpim : 'LPIM' hg_lpim_number;
hg_lpim_number : number;
pl_hg_fa : med;
pl_hg_alk : fatty_acyl_chain;
carbohydrates : carbohydrate_type | carbohydrate_type carbohydrates;
carbohydrate_type : carbohydrate_sn_position | carbohydrate_isomeric;
carbohydrate_sn_position : carbohydrate_iso | carbohydrate_iso carbohydrate_number | carbohydrate_iso carbohydrate_number carbohydrate_separator | carbohydrate_sn | carbohydrate_sn carbohydrate_number | carbohydrate_sn carbohydrate_number carbohydrate_separator | carbohydrate_sn carbohydrate_separator;
carbohydrate_isomeric : carbohydrate_iso carbohydrate_separator;
carbohydrate_number : number;
carbohydrate_sn : 'Hex' | 'SHex' | 'SGal' | 'HexNAc' | 'HexA';
carbohydrate_iso : 'Gal' | 'Glc' | 'GalNAc' | 'GlcNAc' | 'S' ROB '3' APOSTROPH RCB 'Hex' | 'S' ROB '3' APOSTROPH RCB 'Gal' | 'Man' | 'Neu' | 'NeuGc' | 'Kdn' | 'GlcA' | 'Xyl' | 'Fuc' | 'OGlcNAc' | 'OGlc' | 'NeuAc';
sl : sl_species | sl_subspecies;
sl_species : sl_hg_double headgroup_separator lcb | acer_species headgroup_separator lcb;
sl_subspecies : sl_single | sl_double;
sl_single : sl_hg_single headgroup_separator lcb | sl_hg_single sl_hydroxyl headgroup_separator lcb | sl_hg_single headgroup_separator lcb '/0:0' | sl_hg_single sl_hydroxyl headgroup_separator lcb '/0:0';
sl_double : sl_hg_double headgroup_separator lcb sorted_fa_separator fatty_acyl_chain | sl_hg_double sl_hydroxyl headgroup_separator lcb sorted_fa_separator fatty_acyl_chain;
sl_hydroxyl : ROB sl_hydroxyl_number RCB;
sl_hydroxyl_number : number;
sl_hg_single : 'SPB' | 'SPBP' | 'LIPC' | 'LSM' | 'LHexCer' | 'LHex2Cer' | 'LHex3Cer';
sl_hg_double : acer_hg | sl_hg_double_name | carbohydrates sl_hg_glyco;
sl_hg_glyco : 'Cer' | 'IPC';
sl_hg_double_name : 'SM' | sl_hg_glyco | 'CerP' | acer_hg | 'SL' | 'LacCer' | 'SHexCer' | 'PI-Cer' | 'EPC' | 'PE-Cer' | 'GIPC' | 'MIPC' | 'M(IP)2C' | glyco_sphingo_lipid | 'S' ROB '3' APOSTROPH RCB 'HexCer' | 'S' ROB '3' APOSTROPH RCB 'GalCer';
acer_hg : acer_hg_pure ROB med RCB;
acer_species : acer_hg_pure | acer_hg_pure '(FA)';
acer_hg_pure : 'ACer';
glyco_sphingo_lipid : 'GA1' | 'Ga1' | 'GA2' | 'Ga2' |
'GB3' | 'Gb3' | 'GB4' | 'Gb4' |
'GD0a' | 'Gd0a' | 'GD1' | 'Gd1' | 'GD2' | 'Gd2' | 'GD3' | 'Gd3' | 'GD1a' | 'Gd1a' | 'GD1b' | 'Gd1b' | 'GD1a-AC' | 'Gd1a-AC' |
'GM1' | 'Gm1' | 'GM2' | 'Gm2' | 'GM3' | 'Gm3' | 'GM4' | 'Gm4' |
'GP1' | 'Gp1' |
'GQ1' | 'Gq1' | 'GQ1b' | 'Gq1b' | 'GQ1-AC' | 'Gq1-AC' |
'GT1' | 'Gt1' | 'GT1b' | 'Gt1b' | 'GT2' | 'Gt2' | 'GT3' | 'Gt3' | 'GT1b-AC' | 'Gt1b-AC' | 'GT3-AC' | 'Gt3-AC';
/*
acer_hg : acer_hg_pure | acer_med '-' acer_hg_pure;
acer_med : med;
*/
/* sterol lipids */
sterol : st | st_ester;
st : st_hg headgroup_separator sterol_definition;
st_ester : st_hg_ester headgroup_separator sterol_ester_definition sorted_fa_separator fatty_acyl_chain | st_hg_ester headgroup_separator fatty_acyl_chain;
sterol_definition : '27:1;O' | '27:2;O' | '28:2;O' | '28:3;O' | '29:2;O' | '30:2;O' | '28:1;O' | '29:1;O' | '27:0;O;S' | '27:1;O;S' | '28:1;O;S' | '28:2;O;S' | '29:1;O;S' | '27:1;O;Hex' | '28:1;O;Hex' | '28:2;O;Hex';
sterol_ester_definition : '27:1' | '27:2' | '28:1' | '28:2' | '28:3' | '29:1' | '29:2' | '30:2';
st_hg : 'ST'; // | 'BA' | 'FC' | 'SG' | 'ASG';
st_hg_ester : 'SE' | 'CE';
/* separators */
SPACE : ' ';
COLON : ':';
SEMICOLON : ';';
DASH : '-';
UNDERSCORE : '_';
SLASH : '/';
BACKSLASH : '\\';
COMMA: ',';
ROB: '(';
RCB: ')';
SOB: '[';
SCB: ']';
APOSTROPH : '\'' | '′';
sorted_fa_separator : SLASH | BACKSLASH | SPACE SLASH SPACE | SPACE BACKSLASH SPACE;
adduct_separator : SPACE;
unsorted_fa_separator : UNDERSCORE | SPACE UNDERSCORE SPACE;
plasmalogen_separator : DASH;
headgroup_separator : SPACE;
carbon_db_separator : COLON;
cycle_separator: DASH;
db_funcgroup_separator : SEMICOLON;
db_position_separator : COMMA;
carbohydrate_separator : DASH;
funcgroup_separator : SEMICOLON;
func_repetition_separator : COMMA;
round_open_bracket : ROB;
round_close_bracket : RCB;
number : digit | digit number;
digit : '0' | '1' | '2' | '3' | '4' | '5' | '6' | '7' | '8' | '9';
element: 'C' | 'H' | 'N' | 'O' | 'P' | 'S' | 'Br' | 'I' | 'F' | 'Cl' | 'As';
charge : '1' | '2' | '3' | '4';
charge_sign : plus_minus;
plus_minus : '-' | '+';