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}