UNPKG

biojs-vis-pdbviewer

Version:

A BioJS 2.0 component to view protein structures

github.com/sillitoe/biojs-vis-pdbviewer

sillitoe/biojs-vis-pdbviewer

260 lines (136 loc) • 10.1 kB
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
#AtSym ElemNo mmType HType formalCharge*12 val Desc Smiles Li 3 92 0 12 0 LITHIUM CATION [LiD0] C 6 22 5 0 4 C IN CYCLOPROPLY [CD4r3] C 6 20 5 0 4 C IN CYCLOBUTYL [CD4r4] C 6 1 5 0 4 ALKYL CARBON [CD4] C 6 30 5 0 4 C=C IN 4-RING $([CD3r4]=C) C 6 2 5 0 4 VINYLIC $([CD3]=C) C 6 41 5 0 4 C IN CO2- ANION [$([CD3]([OD1])[OD1]), $([CD3]([SD1])[SD1])] C 6 57 5 0 4 GUANIDINIUM CARBON $([CD3]([#7D3v3])([#7D3v3])=[#7D3v4&!r600&!$([#7][OD1])]) C 6 57 5 0 4 C IN +N=C-N RESONANCE $([CD3]([#7D3v3])=[#7D3v4&!r600&!$([#7][OD1])]) C 6 3 5 0 4 GUANIDINE CARBON $([CD3](=[#7D3v3])([#7D3v3])[#7D2v3]) C 6 3 5 0 4 GENERAL CARBONYL C $([CD3]=[O,N,P,S]) C 6 80 5 0 4 C IN N-C-N, IM+ ION $([cD3r500]([#7D3v3])=[#7D3v4&!r600&!$([#7][OD1])]) C 6 78 5 0 4 general 5-ring C both alp [$([cD3r500]1[oD2r500,sD2r500,nD3v3r500]aaa1);$([cD3r500]1a[oD2r500,sD2r500,nD3v3r500]aa1)] C 6 63 5 0 4 ALPHA AROM 5-RING C (fur $([cD3r500]:[oD2r500,sD2r500]) C 6 64 5 0 4 BETA AROM 5-RING C (fura $([cD3r500]:a:[oD2r500,sD2r500]) C 6 78 5 0 4 general 5-ring C (imidzol [$([cD3r500]1[nv4r500&!$(n[OD1])]aaa1),$([cr500]1a[nv4r500&!$(n[OD1])]aa1)] C 6 78 5 0 4 general 5-ring C (1,2-dia [$([cD3r500]1[cr500][cr500][nD2r500][nD2r500]1),$([cD3r500]1[cr500][nD2r500][nD2r500][cr500]1)] C 6 63 5 0 4 ALPHA AROM 5-RING C $([cD3r500]:[nD3v3r500]) C 6 64 5 0 4 BETA AROM 5-RING C $([cD3r500]1a[nD3v3r500]aa1) C 6 37 5 0 4 CARBON AS IN BENZENE, PYR [cD3]1ccccc1 C 6 78 5 0 4 GENERAL AROM 5-RING C [cD3r500] C 6 37 5 0 4 AROMATIC C [cD3] C 6 4 5 0 4 ACETYLENIC C $([#6D2]#*) C 6 4 5 0 4 ALLENIC C (also isocyanat $([#6D2](=*)=*) C 6 60 0 0 3 ISONITRILE CARBON $([CD1]#N) N 7 42 0 0 3 N TRIPLE BONDED $([ND1]#*) N 7 47 0 0 2 TERMINAL N, AZIDE $([ND1][ND2]) N 7 53 0 0 4 N TWICE DOUBLE BONDED $([ND2](=*)=*) N 7 9 27 0 3 N=C, IMINES $([ND2]=[#6,#7]) N 7 43 28 0 3 N, SULFONAMIDES (S(O)2-N= $([ND2v3]S([OD1])[OD1]) N 7 46 0 0 3 NITROSO GROUP N $([ND2](=O)[#6,#7]) N 7 48 28 0 2 DIVALENT NITROGEN REPLACI $([ND2][SD4]([OD1])([#6])[#6]) N 7 62 23 -12 2 SULFONAMIDE N- [$([ND2v2][SD4]),$([ND2v2][CD3])] N 7 61 0 0 4 ISONITRILE N $([ND2]#[#6]) N 7 61 0 12 4 diazo N (+1) $([ND2]#[#7]) N 7 38 0 0 3 AROMATIC N, PYRIDINE [nD2r600] N 7 65 0 0 3 ALPHA AROM 5-RING N (thio $([nD2r500]:[sD2]) N 7 66 0 0 3 (BETA) AROM 5-RING N (thi $([nD2r500]:a:[sD2]) N 7 65 0 0 3 ALPHA AROM 5-RING N (fura $([nD2r500]:[oD2]) N 7 66 0 0 3 (BETA) AROM 5-RING N (fur $([nD2r500]:a:[oD2]) N 7 65 0 0 3 ALPHA AROM 5-RING N [$([nD2r500]:[nD3v3])&!$([$(n:[$([nv4])&!$([#7][OD1])]),$(n:a=[$([nv4])&!$([#7][OD1])]),$(n=a:[$([nv4])&!$([#7][OD1])])])] N 7 66 0 0 3 (BETA) AROM 5-RING N [$([nD2r500]:a:[nD3v3])&!$([$(n:[$([nv4])&!$([#7][OD1])]),$(n:a=[$([nv4])&!$([#7][OD1])]),$(n=a:[$([nv4])&!$([#7][OD1])])])] N 7 76 0 -3 2 NEG N IN TETRAZOLE AN [nD2r500][nD2r500][nD2r500][nD2r500] N 7 76 0 -4 2 (NEG N IN TRIAZOLE) [nD2r500]:[nD2r500]:c:[nD2r500] N 7 76 0 -6 2 NEG N IN DIAZOLE $([nD2r500]:[nD2r500]:c:c:c) N 7 79 0 0 3 GENERAL AROM 5-RING N [nD2r500] N 7 45 0 0 4 NITRO GROUP N $([ND3](=O)O) N 7 67 23 0 4 NITROGEN IN N-OXIDE [$([ND3]([OD1])([#6])[#6]),$([ND3]([OD1])=[#6,#7])] N 7 56 36 4 34 GUANIDINIUM N; Q=1/3 [$([ND3v3][#6D3]([#7D3v3&!r600&!$([#7][OD1])])=[#7D3v4&!r600&!$([#7][OD1])]),$([ND3v4]=[#6D3]([#7D3v3&!r600&!$([#7][OD1])])[#7D3v3&!r600&!$([#7][OD1])])] N 7 55 36 6 34 N IN +N=C-N: ; Q=1/2 [$([ND3v4]=[#6D3][#7D3v3]),$([ND3v3][#6D3]=[#7D3v4&!r600&!$([#7][OD1])])] N 7 54 36 12 4 IMINIUM NITROGEN $([ND3v4]=[#6,#7]) N 7 54 36 12 4 AZONIUM NITROGEN $([ND3v4]([H])([#6])=[#7]) N 7 43 28 0 3 N, SULFONAMIDES (and phos [$([ND3]S([OD1])[OD1]),$([ND3]P([OD1])[OD1])] N 7 10 28 0 3 N-C=O, AMIDES $([ND3v3][#6]=O) N 7 43 28 0 3 N, sulfinamide # not implemented: [$([ND3]S[OD1])&!$([ND3]S([OD1])[OD1])] N 7 39 23 0 3 AROMATIC N, PYRROLE (tetr $([nD3v3r500][nD2]=[nD2][nD2]) N 7 10 28 0 3 N-C=S (DELOC LP) $([ND3][#6]=[#16]) N 7 10 28 0 3 N-N=C (DELOC LP) # not implemented??$([ND3][#7]=[#6,#7]) N 7 40 28 0 3 N-C=C (DELOC LP) [$([ND3][#6]=[#6]),$([ND3]c)] N 7 10 28 0 3 N-N=N (DELOC LP) $([ND3v3][#7D2v3]=[#7D2v3]) N 7 40 28 0 3 N-C=N (DELOC LP) $([ND3][#6]=[#7,#15]) N 7 43 28 0 3 NITROGEN ATTACHED TO CYAN $([ND3][CD2][ND1]) N 7 8 23 0 3 AMINE N [$([ND3](-A)(-A)-A),$([ND3](-A)(-A)-n)] N 7 82 0 0 4 N-OXIDE NITROGEN IN GENER $([nD3r500][OD1]) N 7 69 0 0 4 NITROGEN IN N-OXIDE $([nD3][OD1]) N 7 81 36 4 4 GUANIDINIUM N; Q=1/3 $([nD3v3][#6D3]([#7D3v3&!r600])=[#7D3v4&!r600&!$([#7][OD1])]) N 7 81 36 4 4 GUANIDINIUM N; Q=1/3 $([nD3v4]=[#6D3]([#7D3v3&!r600])[#7D3v3&!r600&!$([#7][OD1])]) N 7 81 36 6 4 N IN N-C-N, IM+ ION [$([nD3r500v4]=[cD3][#7D3v3]),$([nD3r500v3][#6D3]=[#7D3v4&!r600&!$([#7][OD1])])] N 7 81 36 12 4 POSITIVE N5B NITROGEN - F $([nD3r500v4]:a:[oD2,sD2]) N 7 58 36 12 4 N PYRIDINIUM ION [nD3r600v4] N 7 39 23 0 3 AROMATIC N, PYRROLE [nD3r500v3] N 7 68 23 0 4 NITROGEN IN N-OXIDE $([ND4][OD1]) N 7 34 36 12 4 N+, QUATERNARY N [ND4] O 8 49 50 12 3 OXONIUM (TRICOORD) O [OD3] O 8 70 31 0 2 OXYGEN IN WATER $([OD2](H)H) O 8 59 0 0 2 AROMATIC O, FURAN [oD2r500] O 8 6 24 0 2 RCO2H $([OD2](H)[#6]=O) O 8 6 21 0 2 RCO2R $([OD2]C=O) O 8 6 29 0 2 ENOL OR PHENOLIC O $([OD2][#6D3][#6D3]) O 8 6 29 0 2 OXYGEN IN -O-C=N MOIETY $([OD2]-[#6D3]=[#7]) O 8 6 33 0 2 DIVALENT O IN SULFATE $([OD2][#16]) O 8 6 24 0 2 DIVALENT O IN PHOSPHATE $([OD2][#15]) O 8 6 31 0 2 OXYGEN IN H2O $([OD2]([H])[H]) O 8 6 21 0 2 O-CSP3 $([#8D2](-*)-*) O 8 51 52 12 3 OXENIUM OXYGEN+ $([OD2]=*) O 8 7 0 0 2 O=S=C $([OD1]=[#16D2]=*) O 8 32 0 -6 12 O, CARBOXYLATE ANION $([OD1][CD3][OD1]) O 8 32 0 0 12 NITRO-GROUP OXYGEN $([OD1][ND3]([#6])[OD1]) O 8 32 0 0 12 NITRO-GROUP IN NITRATE $([OD1][ND3]([OD1])[OD2]) O 8 32 0 -4 12 NITRATE ANION OXYGEN $([OD1][ND3]([OD1])[OD1]) O 8 32 0 0 12 OXIDE ON NITROHGEN [$([OD1]$([#7D3]=,:*)),$([OD1][#7D4])] O 8 32 0 -6 12 SO4(2-) $([OD1][SD4]([OD1])([OD1])[OD1]) O 8 32 0 -4 12 SULFONATES, TERM OX ROSO3 $([OD1][SD4]([OD1])[OD1]) O 8 32 0 0 12 SULFONES, SULFONAMIDES [$([OD1][SD4][OD1,ND2]),$([OD1][SD3]([OD1,ND2])=C)] O 8 32 0 -6 12 THIOSULFINATE O (-1/2) $([OD1][SD3][OD1,SD1]) O 8 32 0 0 12 SINGLE TERM O ON TET S #$([OD1][#16]) O 8 32 0 -6 12 TERMINAL O, O2P GROUP (RO $([OD1][PD4]([OD1,SD1])([!$([OD1,SD1])])[!$([OD1,SD1])]) O 8 32 0 -8 12 TERMINAL O, O3P GROUP ROP $([OD1][PD4]([OD1])([OD1])[OD2,SD2]) O 8 32 0 -9 12 TERMINAL O, PO4(-3) $([OD1][PD4]([OD1])([OD1])[OD1]) O 8 32 0 0 12 TERMINAL O, O-P $([OD1][#15]) O 8 32 0 -3 12 TERMINAL O IN CLO4(-) $([OD1][ClD4]([OD1])([OD1])[OD1]) O 8 7 0 0 2 O=C, GENERIC $([#8D1]=[#6,#7,#16]) O 8 35 21 -12 1 RO- or HO- [OD1] F 9 11 0 0 1 FLUORINE [FD1] F 9 89 0 -12 0 FLUORIDE ANION [FD0] Na 11 93 0 12 0 SODIUM CATION [NaD0] Mg 12 99 0 24 0 DIPOSITIVE MAGNESIUM CATI [MgD0] Si 14 19 5 0 4 SILICON [SiD4] P 15 25 71 0 4 GENERAL TETRACRD P [PD4] P 15 26 71 0 3 TRICOORDINATE P [PD3] P 15 75 71 0 3 P DOUBLY BONDED TO C $([PD2]=C) S 16 18 0 0 4 SULFONAMIDE S [$([SD4]([OD1,ND2])[OD1,ND2]),$([SD3](=C)([OD1,ND2])[OD1,ND2])] S 16 17 71 0 4 SULFOXIDE S (also S(=O)[N $([SD3]([OD1,ND2])([#6,#7D3,#8D2])[#6,#7D3,#8D2]) S 16 73 0 0 3 SULFUR IN SULFINATE $([SD3]([OD1,SD1])[OD1]) S 16 44 0 0 2 S IN THIOPHENE [sD2r500] S 16 15 71 0 2 THIOL, SULFIDE $([SD2](-*)-*) S 16 74 0 0 4 SULFINYL SULFUR, C=S=O $([SD2]([CD3])[OD1]) S 16 72 0 -6 1 THIOCARBOXYLATE S $([SD1][CD3][SD1]) S 16 16 0 0 2 S DOUBLY BONDED TO C $([SD1]=[#6D3]) S 16 72 0 -6 1 TERMINAL SULFUR ON C (P,S $([SD1][#15,#6,#16][OD1]) S 16 72 0 -12 1 TERMINAL SULFUR on alken $([SD1][#6]) S 16 72 0 0 1 TERMINAL SULFUR ON P $([SD1][#15,#16]) Cl 17 12 0 0 1 CHLORINE [ClD1] Cl 17 77 0 0 4 CHLORINE IN CLO4(-) $([ClD4]([OD1])([OD1])([OD1])[OD1]) Cl 17 90 0 -12 0 CHLORIDE ANION [ClD0] K 19 94 0 12 0 POTASSIUM CATION [KD0] Ca 20 96 0 24 0 DIPOSITIVE CALCIUM CATION [CaD0] Fe 26 87 0 24 0 IRON +2 CATION [FeD0+2] Fe 26 88 0 36 0 IRON +3 CATION [FeD0+3] Cu 29 97 0 12 0 MONOPOSITIVE COPPER CATIO [CuD0+1] Cu 29 98 0 24 0 DIPOSITIVE COPPER CATION [CuD0+2] Zn 30 95 0 24 0 DIPOSITIVE ZINC CATION [ZnD0+2] Br 35 13 0 0 1 BROMINE [BrD1] Br 35 91 0 -12 0 BROMIDE ANION [BrD0] I 53 14 0 0 1 IODINE [ID1]