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Merge commit '52e59ab2e6e569cb8ce57f47b01cdecb291910b9' into main
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@dominik-kopczynski
dominik-kopczynski committed Sep 12, 2023
2 parents f0cb342 + 52e59ab commit 9a642b0
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17 changes: 8 additions & 9 deletions parsers/src/main/goslin/Shorthand2020.g4
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Original file line number Diff line number Diff line change
Expand Up @@ -104,7 +104,7 @@ 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 | 'H' | 'Cys' | 'Phe' | 'SGlu' | 'SCys' | 'BOO' | 'MMAs' | 'SMe' | 'NH' | 'SCG' | special_elements;
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';
Expand Down Expand Up @@ -192,10 +192,13 @@ hg_lpim_number : number;
pl_hg_fa : med;
pl_hg_alk : fatty_acyl_chain;

carbohydrate_group : carbohydrate | carbohydrate carbohydrate_number | carbohydrate_sulfo;
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 : 'Hex' | 'Gal' | 'Glc' | 'Man' | 'Neu' | 'HexNAc' | 'GalNAc' | 'GlcNAc' | 'NeuAc' | 'NeuGc' | 'Kdn' | 'GlcA' | 'Xyl' | 'Fuc' | 'NeuAc2' | 'HexA' | 'OGlcNAc' | 'OGlc';
carbohydrate_sulfo : 'SHex' | 'SHex2' | 'S' ROB '3' APOSTROPH RCB 'Hex' | 'SGal' | 'SGal2' | 'S' ROB '3' APOSTROPH RCB 'Gal2';
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;
Expand All @@ -205,12 +208,8 @@ sl_double : sl_hg_double headgroup_separator lcb sorted_fa_separator fatty_acyl_
sl_hydroxyl : ROB sl_hydroxyl_number RCB;
sl_hydroxyl_number : number;
sl_hg_single : 'SPB' | 'SPBP' | 'LIPC' | 'LSM';
sl_hg_double : acer_hg | sl_hg_double_name | carbohydrate_structural sl_hg_glyco | carbohydrate_isomeric carbohydrate_separator sl_hg_glyco;
carbohydrate_structural : carbohydrates;
carbohydrates : carbohydrate_group | carbohydrate_group carbohydrates;
carbohydrate_isomeric : carbohydrates_isomeric;
sl_hg_double : acer_hg | sl_hg_double_name | carbohydrates sl_hg_glyco;
sl_hg_glyco : 'Cer' | 'IPC';
carbohydrates_isomeric : carbohydrate | carbohydrate carbohydrate_separator carbohydrates_isomeric;
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)';
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2 changes: 1 addition & 1 deletion parsers/src/main/goslin/testfiles/lipid-maps-test.csv
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Expand Up @@ -31236,7 +31236,7 @@
"GD2",
"GT2",
"GM1",
"GM1(12:0)","Gal2GalNAcGlcNeuAcCer 12:0;O2"
"GM1(12:0)","Hex3HexNAcNeuAcCer 12:0;O2"
"GD1b",
"GT1c",
"GD1a",
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18 changes: 9 additions & 9 deletions parsers/src/main/goslin/testfiles/lipid-masses.csv
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Expand Up @@ -143,15 +143,15 @@ SQDG,SQDG 16:0-16:0,C41H78O12S,[M-H]1-,793.514123,-1
SQDG,SQDG 16:0-16:0,C41H78O12S,[M-H]1-,793.514123,-1
Hex3Cer,Hex3Cer 18:1;2/24:1,C60H111NO18,[M+H]1+,1134.787392,1
Hex3Cer,Hex3Cer 18:1;2/24:1,C60H111NO18,[M+H]1+,1134.787392,1
Gal2GalNAcGlcCer,GB4 18:1;2/24:1,C68H124N2O23,[M+H]1+,1337.866765,1
Gal2GalNAcGlcCer,GB4 18:1;2/24:1,C68H124N2O23,[M+H]1+,1337.866765,1
Gal2GalNAcGlcCer,GB4 18:1;2/24:1,C68H124N2O23,[M+H]1+,1337.866765,1
GalGlcNeuAc2Cer,GD3 18:1;2/24:0,C76H137N3O29,[M-H]1-,1554.9265,-1
GalGlcNeuAc2Cer,GD3 18:1;2/24:0,C76H137N3O29,[M-H]1-,1554.9265,-1
GalGlcNeuAcCer,GM3 18:1;2/24:1,C65H118N2O21,[M-H]1-,1261.815433,-1
GalGlcNeuAcCer,GM3 18:1;2/24:1,C65H118N2O21,[M-H]1-,1261.815433,-1
GalNeuAcCer,GM4 18:1;2/24:0;1,C59H110N2O17,[M-H]1-,1117.773175,-1
GalNeuAcCer,GM4 18:1;2/24:0;1,C59H110N2O17,[M-H]1-,1117.773175,-1
Hex3HexNAcCer,GB4 18:1;2/24:1,C68H124N2O23,[M+H]1+,1337.866765,1
Hex3HexNAcCer,GB4 18:1;2/24:1,C68H124N2O23,[M+H]1+,1337.866765,1
Hex3HexNAcCer,GB4 18:1;2/24:1,C68H124N2O23,[M+H]1+,1337.866765,1
Hex2NeuAc2Cer,GD3 18:1;2/24:0,C76H137N3O29,[M-H]1-,1554.9265,-1
Hex2NeuAc2Cer,GD3 18:1;2/24:0,C76H137N3O29,[M-H]1-,1554.9265,-1
Hex2NeuAcCer,GM3 18:1;2/24:1,C65H118N2O21,[M-H]1-,1261.815433,-1
Hex2NeuAcCer,GM3 18:1;2/24:1,C65H118N2O21,[M-H]1-,1261.815433,-1
HexNeuAcCer,GM4 18:1;2/24:0;1,C59H110N2O17,[M-H]1-,1117.773175,-1
HexNeuAcCer,GM4 18:1;2/24:0;1,C59H110N2O17,[M-H]1-,1117.773175,-1
PEt,PEt 16:0-18:1,C39H75O8P,[M+NH4]1+,720.5537822,1
PEt,PEt 16:0-18:1,C39H75O8P,[M+H]1+,703.5272327,1
PEt,PEt 16:0-18:1,C39H75O8P,[M+H]1+,703.5272327,1
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6 changes: 3 additions & 3 deletions parsers/src/main/goslin/testfiles/shorthand-test.csv
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Expand Up @@ -4,7 +4,7 @@ PC O-16:0/O-18:1(9Z),PC O-16:0/O-18:1(9),PC O-16:0/O-18:1,PC O-16:0_O-18:1,PC dO
"Cer 18:0;1OH,3OH/16:0",Cer 18:0;(OH)2/16:0,Cer 18:0;O2/16:0,Cer 18:0;O2/16:0,Cer 34:0;O2,,
"IPC(1) 18:1(8E);3OH,4OH/24:0;2OH",IPC 18:1(8);(OH)2/24:0;OH,IPC 18:1;O3/24:0;O,IPC 18:1;O3/24:0;O,IPC 42:1;O4,,
CerP(1) 18:1(4E);3OH/16:0;2OH,CerP 18:1(4);OH/16:0;OH,CerP 18:1;O2/16:0;O,CerP 18:1;O2/16:0;O,CerP 34:1;O3,C34H68NO7P,
Gal-Gal-Glc-Cer(1) 18:1(4E);3OH/26:1(17Z),Gal-Gal-Glc-Cer 18:1(4);OH/26:1(17),Gal2GlcCer 18:1;O2/26:1,Gal2GlcCer 18:1;O2/26:1,Gal2GlcCer 44:2;O2,C62H115NO18,
Gal-Gal-Glc-Cer(1) 18:1(4E);3OH/26:1(17Z),Gal-Gal-Glc-Cer 18:1(4);OH/26:1(17),Hex3Cer 18:1;O2/26:1,Hex3Cer 18:1;O2/26:1,Hex3Cer 44:2;O2,C62H115NO18,
"PC 16:0/20:2(5Z,13E);[8-12cy5:0;11OH;9oxo];15OH","PC 16:0/20:2(5,13);[cy5:0;OH;oxo];OH",PC 16:0/20:4;O3,PC 16:0_20:4;O3,PC 36:4;O3,,
"PE-N(FA 8:0) 30:5(12Z,15Z,18Z,21Z,24Z)/18:0","PE-N(FA 8:0) 30:5(12,15,18,21,24)/18:0",PE-N(FA 8:0) 30:5/18:0,PE-N(FA 8:0) 30:5_18:0,PE-N(FA) 56:5,C61H110NO9P,
LPC O-16:1(11Z)/0:0,LPC O-16:1(11)/0:0,LPC O-16:1/0:0,LPC O-16:1,LPC O-16:1,,
Expand Down Expand Up @@ -34,8 +34,8 @@ MG 18:0/0:0/0:0,MG 18:0/0:0/0:0,MG 18:0/0:0/0:0,MG 18:0,MG 18:0,C21H42O4,
LPC 20:1(11Z)/0:0,LPC 20:1(11)/0:0,LPC 20:1/0:0,LPC 20:1,LPC 20:1,C28H56NO7P,
"SPB 18:0;1OH,3OH",SPB 18:0;(OH)2,SPB 18:0;O2,SPB 18:0;O2,SPB 18:0;O2,C18H39NO2,
LPIM1 19:1(9Z)/0:0,LPIM1 19:1(9)/0:0,LPIM1 19:1/0:0,LPIM1 19:1,LPIM1 19:1,C34H63O17P,
"Hex-Hex-Cer(1) 17:1(5E);15Me;3OH,4OH/22:0;2OH",Hex-Hex-Cer 17:1(5);Me;(OH)2/22:0;OH,Hex2Cer 18:1;O3/22:0;O,Hex2Cer 18:1;O3/22:0;O,Hex2Cer 40:1;O4,C52H99NO15,
"Glc-Cer(1) 21:0;[13-15cy3:0];3OH,4OH/22:1(16E);2OH;15oxo",Glc-Cer 21:0;[cy3:0];(OH)2/22:1(16);OH;oxo,GlcCer 21:1;O3/22:2;O2,GlcCer 21:1;O3/22:2;O2,GlcCer 43:3;O5,C49H91NO11,
"Gal-Glc-Cer(1) 17:1(5E);15Me;3OH,4OH/22:0;2OH",Gal-Glc-Cer 17:1(5);Me;(OH)2/22:0;OH,Hex2Cer 18:1;O3/22:0;O,Hex2Cer 18:1;O3/22:0;O,Hex2Cer 40:1;O4,C52H99NO15,
"Glc-Cer(1) 21:0;[13-15cy3:0];3OH,4OH/22:1(16E);2OH;15oxo",Glc-Cer 21:0;[cy3:0];(OH)2/22:1(16);OH;oxo,HexCer 21:1;O3/22:2;O2,HexCer 21:1;O3/22:2;O2,HexCer 43:3;O5,C49H91NO11,
FA 8:0;[6-8SScy5:0],FA 8:0;[SScy5:0],FA 8:1;S2,FA 8:1;S2,FA 8:1;S2,C8H14O2S2,
"FA 20:0;[12-15Ocy5:2(12E,13E);13Me,14Me]","FA 20:0;[Ocy5:2(12,13);(Me)2]",FA 22:3;O,FA 22:3;O,FA 22:3;O,C22H38O3,
DG O-16:0/0:0/O-16:1(9Z),DG O-16:0/0:0/O-16:1(9),DG O-16:0/0:0/O-16:1,DG O-16:0_O-16:1,DG dO-32:1,C35H70O3,
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