001/* 002 * BioJava development code 003 * 004 * This code may be freely distributed and modified under the 005 * terms of the GNU Lesser General Public Licence. This should 006 * be distributed with the code. If you do not have a copy, 007 * see: 008 * 009 * http://www.gnu.org/copyleft/lesser.html 010 * 011 * Copyright for this code is held jointly by the individual 012 * authors. These should be listed in @author doc comments. 013 * 014 * For more information on the BioJava project and its aims, 015 * or to join the biojava-l mailing list, visit the home page 016 * at: 017 * 018 * http://www.biojava.org/ 019 * 020 */ 021package org.biojava.nbio.structure.io.mmcif.model; 022 023public class Refine { 024 String entry_id; 025 String ls_number_reflns_obs; 026 String ls_number_reflns_all; 027 String pdbx_ls_sigma_I; 028 String pdbx_ls_sigma_F; 029 String pdbx_data_cutoff_high_absF; 030 String pdbx_data_cutoff_low_absF ; 031 String pdbx_data_cutoff_high_rms_absF; 032 String ls_d_res_low ; 033 String ls_d_res_high ; 034 String ls_percent_reflns_obs; 035 String ls_R_factor_obs ; 036 String ls_R_factor_all ; 037 String ls_R_factor_R_work; 038 String ls_R_factor_R_free ; 039 String ls_R_factor_R_free_error; 040 String ls_R_factor_R_free_error_details; 041 String ls_percent_reflns_R_free; 042 String ls_number_reflns_R_free; 043 String ls_number_parameters; 044 String ls_number_restraints; 045 String occupancy_min; 046 String occupancy_max; 047 String B_iso_mean; 048 @CIFLabel(label="aniso_B[1][1]") 049 String aniso_B11; 050 @CIFLabel(label="aniso_B[2][2]") 051 String aniso_B22; 052 @CIFLabel(label="aniso_B[3][3]") 053 String aniso_B33; 054 @CIFLabel(label="aniso_B[1][2]") 055 String aniso_B12; 056 @CIFLabel(label="aniso_B[1][3]") 057 String aniso_B13; 058 @CIFLabel(label="aniso_B[2][3]") 059 String aniso_B23; 060 String solvent_model_details ; 061 String solvent_model_param_ksol; 062 String solvent_model_param_bsol; 063 String pdbx_ls_cross_valid_method; 064 String details; 065 String pdbx_starting_model; 066 String pdbx_method_to_determine_struct; 067 String pdbx_isotropic_thermal_model; 068 String pdbx_stereochemistry_target_values; 069 String pdbx_stereochem_target_val_spec_case; 070 String pdbx_R_Free_selection_details; 071 String pdbx_overall_ESU_R; 072 String pdbx_overall_ESU_R_Free; 073 String overall_SU_ML; 074 String overall_SU_B; 075 String ls_redundancy_reflns_obs; 076 String pdbx_overall_phase_error ; 077 String B_iso_min; 078 String B_iso_max; 079 String correlation_coeff_Fo_to_Fc; 080 String correlation_coeff_Fo_to_Fc_free; 081 String pdbx_solvent_vdw_probe_radii; 082 String pdbx_solvent_ion_probe_radii; 083 String pdbx_solvent_shrinkage_radii; 084 String overall_SU_R_Cruickshank_DPI; 085 String overall_SU_R_free; 086 String ls_wR_factor_R_free; 087 String ls_wR_factor_R_work; 088 String overall_FOM_free_R_set; 089 String overall_FOM_work_R_set; 090 String pdbx_refine_id; 091 String pdbx_diffrn_id; 092 String pdbx_TLS_residual_ADP_flag; 093 String pdbx_overall_SU_R_free_Cruickshank_DPI; 094 String pdbx_overall_SU_R_Blow_DPI; 095 String pdbx_overall_SU_R_free_Blow_DPI; 096 // these 2 fields are present only in some files (e.g. 4lnc, a hybrid X-RAY/NEUTRON DIFFRACTION) 097 String ls_matrix_type; 098 String ls_number_reflns_R_work; 099 100 public Refine(){ 101 //aniso_B = new String[3][3]; 102 } 103 104 public String getEntry_id() { 105 return entry_id; 106 } 107 108 public void setEntry_id(String entry_id) { 109 this.entry_id = entry_id; 110 } 111 112 public String getLs_number_reflns_obs() { 113 return ls_number_reflns_obs; 114 } 115 116 public void setLs_number_reflns_obs(String ls_number_reflns_obs) { 117 this.ls_number_reflns_obs = ls_number_reflns_obs; 118 } 119 120 public String getLs_number_reflns_all() { 121 return ls_number_reflns_all; 122 } 123 124 public void setLs_number_reflns_all(String ls_number_reflns_all) { 125 this.ls_number_reflns_all = ls_number_reflns_all; 126 } 127 128 public String getPdbx_ls_sigma_I() { 129 return pdbx_ls_sigma_I; 130 } 131 132 public void setPdbx_ls_sigma_I(String pdbx_ls_sigma_I) { 133 this.pdbx_ls_sigma_I = pdbx_ls_sigma_I; 134 } 135 136 public String getPdbx_ls_sigma_F() { 137 return pdbx_ls_sigma_F; 138 } 139 140 public void setPdbx_ls_sigma_F(String pdbx_ls_sigma_F) { 141 this.pdbx_ls_sigma_F = pdbx_ls_sigma_F; 142 } 143 144 public String getPdbx_data_cutoff_high_absF() { 145 return pdbx_data_cutoff_high_absF; 146 } 147 148 public void setPdbx_data_cutoff_high_absF(String pdbx_data_cutoff_high_absF) { 149 this.pdbx_data_cutoff_high_absF = pdbx_data_cutoff_high_absF; 150 } 151 152 public String getPdbx_data_cutoff_low_absF() { 153 return pdbx_data_cutoff_low_absF; 154 } 155 156 public void setPdbx_data_cutoff_low_absF(String pdbx_data_cutoff_low_absF) { 157 this.pdbx_data_cutoff_low_absF = pdbx_data_cutoff_low_absF; 158 } 159 160 public String getPdbx_data_cutoff_high_rms_absF() { 161 return pdbx_data_cutoff_high_rms_absF; 162 } 163 164 public void setPdbx_data_cutoff_high_rms_absF( 165 String pdbx_data_cutoff_high_rms_absF) { 166 this.pdbx_data_cutoff_high_rms_absF = pdbx_data_cutoff_high_rms_absF; 167 } 168 169 public String getLs_d_res_low() { 170 return ls_d_res_low; 171 } 172 173 public void setLs_d_res_low(String ls_d_res_low) { 174 this.ls_d_res_low = ls_d_res_low; 175 } 176 177 public String getLs_d_res_high() { 178 return ls_d_res_high; 179 } 180 181 public void setLs_d_res_high(String ls_d_res_high) { 182 this.ls_d_res_high = ls_d_res_high; 183 } 184 185 public String getLs_percent_reflns_obs() { 186 return ls_percent_reflns_obs; 187 } 188 189 public void setLs_percent_reflns_obs(String ls_percent_reflns_obs) { 190 this.ls_percent_reflns_obs = ls_percent_reflns_obs; 191 } 192 193 public String getLs_R_factor_obs() { 194 return ls_R_factor_obs; 195 } 196 197 public void setLs_R_factor_obs(String ls_R_factor_obs) { 198 this.ls_R_factor_obs = ls_R_factor_obs; 199 } 200 201 public String getLs_R_factor_all() { 202 return ls_R_factor_all; 203 } 204 205 public void setLs_R_factor_all(String ls_R_factor_all) { 206 this.ls_R_factor_all = ls_R_factor_all; 207 } 208 209 public String getLs_R_factor_R_work() { 210 return ls_R_factor_R_work; 211 } 212 213 public void setLs_R_factor_R_work(String ls_R_factor_R_work) { 214 this.ls_R_factor_R_work = ls_R_factor_R_work; 215 } 216 217 public String getLs_R_factor_R_free() { 218 return ls_R_factor_R_free; 219 } 220 221 public void setLs_R_factor_R_free(String ls_R_factor_R_free) { 222 this.ls_R_factor_R_free = ls_R_factor_R_free; 223 } 224 225 public String getLs_R_factor_R_free_error() { 226 return ls_R_factor_R_free_error; 227 } 228 229 public void setLs_R_factor_R_free_error(String ls_R_factor_R_free_error) { 230 this.ls_R_factor_R_free_error = ls_R_factor_R_free_error; 231 } 232 233 public String getLs_R_factor_R_free_error_details() { 234 return ls_R_factor_R_free_error_details; 235 } 236 237 public void setLs_R_factor_R_free_error_details( 238 String ls_R_factor_R_free_error_details) { 239 this.ls_R_factor_R_free_error_details = ls_R_factor_R_free_error_details; 240 } 241 242 public String getLs_percent_reflns_R_free() { 243 return ls_percent_reflns_R_free; 244 } 245 246 public void setLs_percent_reflns_R_free(String ls_percent_reflns_R_free) { 247 this.ls_percent_reflns_R_free = ls_percent_reflns_R_free; 248 } 249 250 public String getLs_number_reflns_R_free() { 251 return ls_number_reflns_R_free; 252 } 253 254 public void setLs_number_reflns_R_free(String ls_number_reflns_R_free) { 255 this.ls_number_reflns_R_free = ls_number_reflns_R_free; 256 } 257 258 public String getLs_number_parameters() { 259 return ls_number_parameters; 260 } 261 262 public void setLs_number_parameters(String ls_number_parameters) { 263 this.ls_number_parameters = ls_number_parameters; 264 } 265 266 public String getLs_number_restraints() { 267 return ls_number_restraints; 268 } 269 270 public void setLs_number_restraints(String ls_number_restraints) { 271 this.ls_number_restraints = ls_number_restraints; 272 } 273 274 public String getOccupancy_min() { 275 return occupancy_min; 276 } 277 278 public void setOccupancy_min(String occupancy_min) { 279 this.occupancy_min = occupancy_min; 280 } 281 282 public String getOccupancy_max() { 283 return occupancy_max; 284 } 285 286 public void setOccupancy_max(String occupancy_max) { 287 this.occupancy_max = occupancy_max; 288 } 289 290 public String getB_iso_mean() { 291 return B_iso_mean; 292 } 293 294 public void setB_iso_mean(String b_iso_mean) { 295 B_iso_mean = b_iso_mean; 296 } 297 298 public String getSolvent_model_details() { 299 return solvent_model_details; 300 } 301 302 public void setSolvent_model_details(String solvent_model_details) { 303 this.solvent_model_details = solvent_model_details; 304 } 305 306 public String getSolvent_model_param_ksol() { 307 return solvent_model_param_ksol; 308 } 309 310 public void setSolvent_model_param_ksol(String solvent_model_param_ksol) { 311 this.solvent_model_param_ksol = solvent_model_param_ksol; 312 } 313 314 public String getSolvent_model_param_bsol() { 315 return solvent_model_param_bsol; 316 } 317 318 public void setSolvent_model_param_bsol(String solvent_model_param_bsol) { 319 this.solvent_model_param_bsol = solvent_model_param_bsol; 320 } 321 322 public String getPdbx_ls_cross_valid_method() { 323 return pdbx_ls_cross_valid_method; 324 } 325 326 public void setPdbx_ls_cross_valid_method(String pdbx_ls_cross_valid_method) { 327 this.pdbx_ls_cross_valid_method = pdbx_ls_cross_valid_method; 328 } 329 330 public String getDetails() { 331 return details; 332 } 333 334 public void setDetails(String details) { 335 this.details = details; 336 } 337 338 public String getPdbx_starting_model() { 339 return pdbx_starting_model; 340 } 341 342 public void setPdbx_starting_model(String pdbx_starting_model) { 343 this.pdbx_starting_model = pdbx_starting_model; 344 } 345 346 public String getPdbx_method_to_determine_struct() { 347 return pdbx_method_to_determine_struct; 348 } 349 350 public void setPdbx_method_to_determine_struct( 351 String pdbx_method_to_determine_struct) { 352 this.pdbx_method_to_determine_struct = pdbx_method_to_determine_struct; 353 } 354 355 public String getPdbx_isotropic_thermal_model() { 356 return pdbx_isotropic_thermal_model; 357 } 358 359 public void setPdbx_isotropic_thermal_model(String pdbx_isotropic_thermal_model) { 360 this.pdbx_isotropic_thermal_model = pdbx_isotropic_thermal_model; 361 } 362 363 public String getPdbx_stereochemistry_target_values() { 364 return pdbx_stereochemistry_target_values; 365 } 366 367 public void setPdbx_stereochemistry_target_values( 368 String pdbx_stereochemistry_target_values) { 369 this.pdbx_stereochemistry_target_values = pdbx_stereochemistry_target_values; 370 } 371 372 public String getPdbx_stereochem_target_val_spec_case() { 373 return pdbx_stereochem_target_val_spec_case; 374 } 375 376 public void setPdbx_stereochem_target_val_spec_case( 377 String pdbx_stereochem_target_val_spec_case) { 378 this.pdbx_stereochem_target_val_spec_case = pdbx_stereochem_target_val_spec_case; 379 } 380 381 public String getPdbx_R_Free_selection_details() { 382 return pdbx_R_Free_selection_details; 383 } 384 385 public void setPdbx_R_Free_selection_details( 386 String pdbx_R_Free_selection_details) { 387 this.pdbx_R_Free_selection_details = pdbx_R_Free_selection_details; 388 } 389 390 public String getPdbx_overall_ESU_R() { 391 return pdbx_overall_ESU_R; 392 } 393 394 public void setPdbx_overall_ESU_R(String pdbx_overall_ESU_R) { 395 this.pdbx_overall_ESU_R = pdbx_overall_ESU_R; 396 } 397 398 public String getPdbx_overall_ESU_R_Free() { 399 return pdbx_overall_ESU_R_Free; 400 } 401 402 public void setPdbx_overall_ESU_R_Free(String pdbx_overall_ESU_R_Free) { 403 this.pdbx_overall_ESU_R_Free = pdbx_overall_ESU_R_Free; 404 } 405 406 public String getOverall_SU_ML() { 407 return overall_SU_ML; 408 } 409 410 public void setOverall_SU_ML(String overall_SU_ML) { 411 this.overall_SU_ML = overall_SU_ML; 412 } 413 414 public String getOverall_SU_B() { 415 return overall_SU_B; 416 } 417 418 public void setOverall_SU_B(String overall_SU_B) { 419 this.overall_SU_B = overall_SU_B; 420 } 421 422 public String getPdbx_refine_id() { 423 return pdbx_refine_id; 424 } 425 426 public void setPdbx_refine_id(String pdbx_refine_id) { 427 this.pdbx_refine_id = pdbx_refine_id; 428 } 429 430 public String getLs_redundancy_reflns_obs() { 431 return ls_redundancy_reflns_obs; 432 } 433 434 public void setLs_redundancy_reflns_obs(String ls_redundancy_reflns_obs) { 435 this.ls_redundancy_reflns_obs = ls_redundancy_reflns_obs; 436 } 437 438 public String getPdbx_overall_phase_error() { 439 return pdbx_overall_phase_error; 440 } 441 442 public void setPdbx_overall_phase_error(String pdbx_overall_phase_error) { 443 this.pdbx_overall_phase_error = pdbx_overall_phase_error; 444 } 445 446 public String getB_iso_min() { 447 return B_iso_min; 448 } 449 450 public void setB_iso_min(String b_iso_min) { 451 B_iso_min = b_iso_min; 452 } 453 454 public String getB_iso_max() { 455 return B_iso_max; 456 } 457 458 public void setB_iso_max(String b_iso_max) { 459 B_iso_max = b_iso_max; 460 } 461 462 public String getCorrelation_coeff_Fo_to_Fc() { 463 return correlation_coeff_Fo_to_Fc; 464 } 465 466 public void setCorrelation_coeff_Fo_to_Fc(String correlation_coeff_Fo_to_Fc) { 467 this.correlation_coeff_Fo_to_Fc = correlation_coeff_Fo_to_Fc; 468 } 469 470 public String getCorrelation_coeff_Fo_to_Fc_free() { 471 return correlation_coeff_Fo_to_Fc_free; 472 } 473 474 public void setCorrelation_coeff_Fo_to_Fc_free( 475 String correlation_coeff_Fo_to_Fc_free) { 476 this.correlation_coeff_Fo_to_Fc_free = correlation_coeff_Fo_to_Fc_free; 477 } 478 479 public String getPdbx_solvent_vdw_probe_radii() { 480 return pdbx_solvent_vdw_probe_radii; 481 } 482 483 public void setPdbx_solvent_vdw_probe_radii(String pdbx_solvent_vdw_probe_radii) { 484 this.pdbx_solvent_vdw_probe_radii = pdbx_solvent_vdw_probe_radii; 485 } 486 487 public String getPdbx_solvent_ion_probe_radii() { 488 return pdbx_solvent_ion_probe_radii; 489 } 490 491 public void setPdbx_solvent_ion_probe_radii(String pdbx_solvent_ion_probe_radii) { 492 this.pdbx_solvent_ion_probe_radii = pdbx_solvent_ion_probe_radii; 493 } 494 495 public String getPdbx_solvent_shrinkage_radii() { 496 return pdbx_solvent_shrinkage_radii; 497 } 498 499 public void setPdbx_solvent_shrinkage_radii(String pdbx_solvent_shrinkage_radii) { 500 this.pdbx_solvent_shrinkage_radii = pdbx_solvent_shrinkage_radii; 501 } 502 503 public String getOverall_SU_R_Cruickshank_DPI() { 504 return overall_SU_R_Cruickshank_DPI; 505 } 506 507 public void setOverall_SU_R_Cruickshank_DPI(String overall_SU_R_Cruickshank_DPI) { 508 this.overall_SU_R_Cruickshank_DPI = overall_SU_R_Cruickshank_DPI; 509 } 510 511 public String getOverall_SU_R_free() { 512 return overall_SU_R_free; 513 } 514 515 public void setOverall_SU_R_free(String overall_SU_R_free) { 516 this.overall_SU_R_free = overall_SU_R_free; 517 } 518 519 public String getLs_wR_factor_R_free() { 520 return ls_wR_factor_R_free; 521 } 522 523 public void setLs_wR_factor_R_free(String ls_wR_factor_R_free) { 524 this.ls_wR_factor_R_free = ls_wR_factor_R_free; 525 } 526 527 public String getLs_wR_factor_R_work() { 528 return ls_wR_factor_R_work; 529 } 530 531 public void setLs_wR_factor_R_work(String ls_wR_factor_R_work) { 532 this.ls_wR_factor_R_work = ls_wR_factor_R_work; 533 } 534 535 public String getOverall_FOM_free_R_set() { 536 return overall_FOM_free_R_set; 537 } 538 539 public void setOverall_FOM_free_R_set(String overall_FOM_free_R_set) { 540 this.overall_FOM_free_R_set = overall_FOM_free_R_set; 541 } 542 543 public String getOverall_FOM_work_R_set() { 544 return overall_FOM_work_R_set; 545 } 546 547 public void setOverall_FOM_work_R_set(String overall_FOM_work_R_set) { 548 this.overall_FOM_work_R_set = overall_FOM_work_R_set; 549 } 550 551 public String getPdbx_diffrn_id() { 552 return pdbx_diffrn_id; 553 } 554 555 public void setPdbx_diffrn_id(String pdbx_diffrn_id) { 556 this.pdbx_diffrn_id = pdbx_diffrn_id; 557 } 558 559 public String getPdbx_TLS_residual_ADP_flag() { 560 return pdbx_TLS_residual_ADP_flag; 561 } 562 563 public void setPdbx_TLS_residual_ADP_flag(String pdbx_TLS_residual_ADP_flag) { 564 this.pdbx_TLS_residual_ADP_flag = pdbx_TLS_residual_ADP_flag; 565 } 566 567 public String getPdbx_overall_SU_R_free_Cruickshank_DPI() { 568 return pdbx_overall_SU_R_free_Cruickshank_DPI; 569 } 570 571 public void setPdbx_overall_SU_R_free_Cruickshank_DPI( 572 String pdbx_overall_SU_R_free_Cruickshank_DPI) { 573 this.pdbx_overall_SU_R_free_Cruickshank_DPI = pdbx_overall_SU_R_free_Cruickshank_DPI; 574 } 575 576 public String getPdbx_overall_SU_R_Blow_DPI() { 577 return pdbx_overall_SU_R_Blow_DPI; 578 } 579 580 public void setPdbx_overall_SU_R_Blow_DPI(String pdbx_overall_SU_R_Blow_DPI) { 581 this.pdbx_overall_SU_R_Blow_DPI = pdbx_overall_SU_R_Blow_DPI; 582 } 583 584 public String getPdbx_overall_SU_R_free_Blow_DPI() { 585 return pdbx_overall_SU_R_free_Blow_DPI; 586 } 587 588 public void setPdbx_overall_SU_R_free_Blow_DPI( 589 String pdbx_overall_SU_R_free_Blow_DPI) { 590 this.pdbx_overall_SU_R_free_Blow_DPI = pdbx_overall_SU_R_free_Blow_DPI; 591 } 592 593 public String getLs_matrix_type() { 594 return ls_matrix_type; 595 } 596 597 public void setLs_matrix_type(String ls_matrix_type) { 598 this.ls_matrix_type = ls_matrix_type; 599 } 600 601 public String getLs_number_reflns_R_work() { 602 return ls_number_reflns_R_work; 603 } 604 605 public void setLs_number_reflns_R_work(String ls_number_reflns_R_work) { 606 this.ls_number_reflns_R_work = ls_number_reflns_R_work; 607 } 608 609 public String getAniso_B11() { 610 return aniso_B11; 611 } 612 613 public void setAniso_B11(String aniso_B11) { 614 this.aniso_B11 = aniso_B11; 615 } 616 617 public String getAniso_B22() { 618 return aniso_B22; 619 } 620 621 public void setAniso_B22(String aniso_B22) { 622 this.aniso_B22 = aniso_B22; 623 } 624 625 public String getAniso_B33() { 626 return aniso_B33; 627 } 628 629 public void setAniso_B33(String aniso_B33) { 630 this.aniso_B33 = aniso_B33; 631 } 632 633 public String getAniso_B12() { 634 return aniso_B12; 635 } 636 637 public void setAniso_B12(String aniso_B12) { 638 this.aniso_B12 = aniso_B12; 639 } 640 641 public String getAniso_B13() { 642 return aniso_B13; 643 } 644 645 public void setAniso_B13(String aniso_B13) { 646 this.aniso_B13 = aniso_B13; 647 } 648 649 public String getAniso_B23() { 650 return aniso_B23; 651 } 652 653 public void setAniso_B23(String aniso_B23) { 654 this.aniso_B23 = aniso_B23; 655 } 656 657 658}