Indeed, however, you lose the index of the atom in the original molecule you want to create a bond to, due to the index/id reordering that happens upon the fragment::Separate.
I am doing two fragment::separate calls. The first is to remove the sidechain from the protein to create a protein /w vacant site (to be used later), and a sidechain to be deleted. Each OBMol in the resulting vector <OBMol>has had its indexes/ids reordered at this point. THe second OBMol::separate is to split an amino acid into a fragment to be added to the vacant-site protein, and a useless backbone chain. e.g upon deleting Ca-Cb bond from a specific residue within the protein: atom ids: 0 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 after OBMol::separate, 0 8 10 9 1 11 2 3 16 24 17 18 35 36 39 40 41 43 53 45 46 55 44 54 51 42 52 50 49 37 38 56 57 65 60 61 63 74 72 73 68 67 62 70 71 69 66 58 59 75 84 76 77 92 93 94 116 117 120 121 122 131 130 129 123 134 132 133 128 127 126 125 118 119 135 144 136 145 137 138 157 165 158 159 169 170 171 172 176 177 182 178 183 189 188 193 194 187 191 192 195 196 184 190 185 197 203 198 201 202 207 205 206 204 199 200 208 214 209 212 216 217 213 218 215 210 219 223 220 224 221 226 237 227 228 229 250 251 257 252 264 270 269 275 274 268 273 272 277 276 265 271 266 267 278 284 290 291 283 288 289 282 286 287 279 280 281 292 293 300 294 298 295 299 285 253 254 259 258 255 261 260 256 263 262 238 230 231 242 241 232 243 244 233 245 234 236 248 249 235 246 247 239 240 222 225 211 186 179 181 180 174 175 173 160 166 161 167 168 162 163 164 139 147 146 140 149 148 141 150 151 142 152 153 143 155 154 156 124 95 96 109 97 99 102 104 114 105 115 103 113 112 101 100 111 98 110 108 107 106 78 85 79 86 87 80 89 81 82 83 91 90 88 64 48 47 19 20 21 22 31 29 30 28 23 34 33 32 26 27 25 4 5 6 7 15 14 12 I have now lost the index of the atom that I need to use to connect it to a fragment. In the original protein, the Ca atom had the index 294, now after OBMol::separate, it's index is 169. -- View this message in context: http://forums.openbabel.org/Connecting-Molecular-Fragments-from-Separate-OBMol-Structures-C-tp4657054p4657069.html Sent from the openbabel-devel mailing list archive at Nabble.com. ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
