mmagnus /
rna-tools
| @@ 218-275 (lines=58) @@ | ||
| 215 | print(p, '', [i + 1 for i in p], end=' ') |
|
| 216 | print(seq, 'seq_min: ' + seq_min, rms) |
|
| 217 | ||
| 218 | if p_min: # found target sequence |
|
| 219 | # what is this? ;-) |
|
| 220 | index = [0 ,0 ,0] |
|
| 221 | index[0] = p_min.index(0) |
|
| 222 | index[1] = p_min.index(1) |
|
| 223 | index[2] = p_min.index(2) |
|
| 224 | ||
| 225 | # ugly re-set 123 to crazy id ! + 100, so this will |
|
| 226 | # fill up 1 2 3 for the second for |
|
| 227 | rs = other_rnamodel.struc[0].get_residues() |
|
| 228 | for i, r in enumerate(rs): |
|
| 229 | r.id = (' ', index[i] + 253, ' ') # ugly, some random offset |
|
| 230 | ||
| 231 | for i, r in enumerate(other_rnamodel.struc[0].get_residues()): |
|
| 232 | r.id = (' ', index[i] + 1, ' ') |
|
| 233 | if args.debug: print('r', r) |
|
| 234 | ||
| 235 | io = Bio.PDB.PDBIO() |
|
| 236 | sup_min.apply(other_rnamodel.struc.get_atoms()) |
|
| 237 | # if args.debug: print(p_min, [i + 1 for i in p_min]) |
|
| 238 | io.set_structure(other_rnamodel.struc) |
|
| 239 | ||
| 240 | args.save_here = True |
|
| 241 | if args.save_here and save: |
|
| 242 | folder = os.path.basename(self.fpath.replace('.pdb', '_' + args.folder_prefix + '_aligned')) |
|
| 243 | # print(f) |
|
| 244 | try: |
|
| 245 | os.mkdir(folder) |
|
| 246 | except: |
|
| 247 | pass |
|
| 248 | fout = folder + os.sep + "{:1.2f}".format(rmsd_min) + '-' + os.path.basename(other_rnamodel.fpath)#.replace('.pdb', '-' + str(rms) + '.pdb')) |
|
| 249 | #_s' + suffix + '.pdb')) |
|
| 250 | else: |
|
| 251 | fout = other_rnamodel.fpath.replace('.pdb', '_aligned.pdb')#_s' + suffix + '.pdb') |
|
| 252 | ||
| 253 | if args.debug: print(fout) |
|
| 254 | ||
| 255 | if save: |
|
| 256 | io.save(fout) |
|
| 257 | # ugly set chain to A |
|
| 258 | set_chain_for_struc(fout, 'A', save_file_inplace=True) |
|
| 259 | # and now run this to sort into 1 2 3 |
|
| 260 | ||
| 261 | r = RNAStructure(fout) |
|
| 262 | remarks = r.get_remarks_text() |
|
| 263 | r1 = r.get_res_text('A', 1) |
|
| 264 | r2 = r.get_res_text('A', 2) |
|
| 265 | r3 = r.get_res_text('A', 3) |
|
| 266 | with open(fout, 'w') as f: |
|
| 267 | f.write(remarks) |
|
| 268 | f.write(r1) |
|
| 269 | f.write(r2) |
|
| 270 | f.write(r3) |
|
| 271 | r.reload() |
|
| 272 | r.get_rnapuzzle_ready() |
|
| 273 | if rmsd_min < 1: # !!!!!!!!!!!! ugly |
|
| 274 | r.write() |
|
| 275 | return str(rmsd_min)# + ',s' + seq_min + ',' + os.path.basename(fout) |
|
| 276 | else: |
|
| 277 | # check if number of the same atoms # |
|
| 278 | # if not the same then return -1 # |
|
| @@ 159-216 (lines=58) @@ | ||
| 156 | print(p, '', [i + 1 for i in p], end=' ') |
|
| 157 | print(seq, 'seq_min: ' + seq_min, rms) |
|
| 158 | ||
| 159 | if p_min: # found target sequence |
|
| 160 | # what is this? ;-) |
|
| 161 | index = [0 ,0 ,0] |
|
| 162 | index[0] = p_min.index(0) |
|
| 163 | index[1] = p_min.index(1) |
|
| 164 | index[2] = p_min.index(2) |
|
| 165 | ||
| 166 | # ugly re-set 123 to crazy id ! + 100, so this will |
|
| 167 | # fill up 1 2 3 for the second for |
|
| 168 | rs = other_rnamodel.struc[0].get_residues() |
|
| 169 | for i, r in enumerate(rs): |
|
| 170 | r.id = (' ', index[i] + 253, ' ') # ugly, some random offset |
|
| 171 | ||
| 172 | for i, r in enumerate(other_rnamodel.struc[0].get_residues()): |
|
| 173 | r.id = (' ', index[i] + 1, ' ') |
|
| 174 | if args.debug: print('r', r) |
|
| 175 | ||
| 176 | io = Bio.PDB.PDBIO() |
|
| 177 | sup_min.apply(other_rnamodel.struc.get_atoms()) |
|
| 178 | # if args.debug: print(p_min, [i + 1 for i in p_min]) |
|
| 179 | io.set_structure(other_rnamodel.struc) |
|
| 180 | ||
| 181 | args.save_here = True |
|
| 182 | if args.save_here and save: |
|
| 183 | folder = os.path.basename(self.fpath.replace('.pdb', '_' + args.folder_prefix + '_aligned')) |
|
| 184 | # print(f) |
|
| 185 | try: |
|
| 186 | os.mkdir(folder) |
|
| 187 | except: |
|
| 188 | pass |
|
| 189 | fout = folder + os.sep + "{:1.2f}".format(rmsd_min) + '-' + os.path.basename(other_rnamodel.fpath)#.replace('.pdb', '-' + str(rms) + '.pdb')) |
|
| 190 | #_s' + suffix + '.pdb')) |
|
| 191 | else: |
|
| 192 | fout = other_rnamodel.fpath.replace('.pdb', '_aligned.pdb')#_s' + suffix + '.pdb') |
|
| 193 | ||
| 194 | if args.debug: print(fout) |
|
| 195 | ||
| 196 | if save: |
|
| 197 | io.save(fout) |
|
| 198 | # ugly set chain to A |
|
| 199 | set_chain_for_struc(fout, 'A', save_file_inplace=True) |
|
| 200 | # and now run this to sort into 1 2 3 |
|
| 201 | ||
| 202 | r = RNAStructure(fout) |
|
| 203 | remarks = r.get_remarks_text() |
|
| 204 | r1 = r.get_res_text('A', 1) |
|
| 205 | r2 = r.get_res_text('A', 2) |
|
| 206 | r3 = r.get_res_text('A', 3) |
|
| 207 | with open(fout, 'w') as f: |
|
| 208 | f.write(remarks) |
|
| 209 | f.write(r1) |
|
| 210 | f.write(r2) |
|
| 211 | f.write(r3) |
|
| 212 | r.reload() |
|
| 213 | r.get_rnapuzzle_ready() |
|
| 214 | if rmsd_min < 1: # !!!!!!!!!!!! ugly |
|
| 215 | r.write() |
|
| 216 | return str(rmsd_min)# + ',s' + seq_min + ',' + os.path.basename(fout) |
|
| 217 | else: |
|
| 218 | # check if number of the same atoms # |
|
| 219 | # if not the same then return -1 # |
|
