NCBI C++ ToolKit
structure_set.cpp

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1 /* $Id: structure_set.cpp 97253 2022-06-29 17:35:29Z dzhang $
2 * ===========================================================================
3 *
4 * PUBLIC DOMAIN NOTICE
5 * National Center for Biotechnology Information
6 *
7 * This software/database is a "United States Government Work" under the
8 * terms of the United States Copyright Act. It was written as part of
9 * the author's official duties as a United States Government employee and
10 * thus cannot be copyrighted. This software/database is freely available
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22 * Please cite the author in any work or product based on this material.
23 *
24 * ===========================================================================
25 *
26 * Authors: Paul Thiessen
27 *
28 * File Description:
29 * Classes to hold sets of structure data
30 *
31 * ===========================================================================
32 */
33 
34 #include <ncbi_pch.hpp>
35 #include <corelib/ncbistd.hpp>
36 #include <corelib/ncbistre.hpp>
37 #include <corelib/ncbi_limits.h>
38 #include <corelib/ncbistl.hpp>
39 
40 #include <deque>
41 
55 #include <objects/mmdb3/Move.hpp>
71 
73 
74 #include "structure_set.hpp"
75 #include "data_manager.hpp"
76 #include "coord_set.hpp"
77 #include "chemical_graph.hpp"
78 #include "atom_set.hpp"
79 #include "opengl_renderer.hpp"
80 #include "show_hide_manager.hpp"
81 #include "style_manager.hpp"
82 #include "sequence_set.hpp"
83 #include "alignment_set.hpp"
84 #include "alignment_manager.hpp"
85 #include "messenger.hpp"
87 #include "cn3d_tools.hpp"
88 #include "molecule_identifier.hpp"
89 #include "cn3d_cache.hpp"
90 #include "molecule.hpp"
91 #include "residue.hpp"
92 #include "show_hide_dialog.hpp"
93 
96 
97 
98 BEGIN_SCOPE(Cn3D)
99 
100 const unsigned int
109  StructureSet::eCDDData = 0x100,
110  StructureSet::eOtherData = 0x200;
111 
112 const unsigned int
118 
119 StructureSet::StructureSet(CNcbi_mime_asn1 *mime, unsigned int structureLimit, OpenGLRenderer *r) :
120  StructureBase(NULL), renderer(r)
121 {
122  dataManager = new ASNDataManager(mime);
123  Load(structureLimit);
124 }
125 
126 StructureSet::StructureSet(CCdd *cdd, unsigned int structureLimit, OpenGLRenderer *r) :
127  StructureBase(NULL), renderer(r)
128 {
129  dataManager = new ASNDataManager(cdd);
130  Load(structureLimit);
131 }
132 
134 {
135  sequenceSet = new SequenceSet(this, *(dataManager->GetSequences()));
136 
137  if (objects.size() > 1)
138  ERRORMSG("LoadSequencesForSingleStructure() called, but there is > 1 structure");
139  if (objects.size() != 1) return;
140 
141  // look for biopolymer molecules
142  ChemicalGraph::MoleculeMap::const_iterator m, me = objects.front()->graph->molecules.end();
143  SequenceSet::SequenceList::const_iterator s, se = sequenceSet->sequences.end();
144  for (m=objects.front()->graph->molecules.begin(); m!=me; ++m) {
145  if (!m->second->IsProtein() && !m->second->IsNucleotide()) continue;
146 
147  // find matching sequence for each biopolymer
148  for (s=sequenceSet->sequences.begin(); s!=se; ++s) {
149  if ((*s)->molecule != NULL) continue; // skip already-matched sequences
150 
151  if (m->second->identifier == (*s)->identifier) {
152 
153  // verify length
154  if (m->second->residues.size() != (*s)->Length()) {
155  ERRORMSG(
156  "LoadSequencesForSingleStructure() - length mismatch between sequence gi "
157  << "and matching molecule " << m->second->identifier->ToString());
158  continue;
159  }
160  TRACEMSG("matched sequence " << " gi " << (*s)->identifier->gi << " with object "
161  << objects.front()->GetPDBID() << " moleculeID " << m->second->id);
162 
163  (const_cast<Molecule*>(m->second))->sequence = *s;
164  (const_cast<Sequence*>(*s))->molecule = m->second;
165  break;
166  }
167  }
168  if (s == se)
169  ERRORMSG("LoadSequencesForSingleStructure() - can't find sequence for molecule "
170  << m->second->identifier->ToString());
171  }
172 }
173 
174 bool StructureSet::LoadMaster(int masterMMDBID)
175 {
176  if (objects.size() > 0) return false;
177  TRACEMSG("loading master " << masterMMDBID);
178 
180  objects.push_back(new StructureObject(this, *(dataManager->GetMasterStructure()), true));
181  if (masterMMDBID != MoleculeIdentifier::VALUE_NOT_SET && objects.front()->mmdbID != masterMMDBID)
182  ERRORMSG("StructureSet::LoadMaster() - mismatched master MMDB ID");
183  } else if (masterMMDBID != MoleculeIdentifier::VALUE_NOT_SET && dataManager->GetStructureList()) {
184  ASNDataManager::BiostrucList::const_iterator b, be = dataManager->GetStructureList()->end();
185  for (b=dataManager->GetStructureList()->begin(); b!=be; ++b) {
186  if ((*b)->GetId().front()->IsMmdb_id() &&
187  (*b)->GetId().front()->GetMmdb_id().Get() == masterMMDBID) {
188  objects.push_back(new StructureObject(this, **b, true));
189  usedStructures[b->GetPointer()] = true;
190  break;
191  }
192  }
193  }
194  if (masterMMDBID != MoleculeIdentifier::VALUE_NOT_SET && objects.size() == 0) {
195  CRef < CBiostruc > biostruc;
196  if (LoadStructureViaCache(NStr::IntToString(masterMMDBID), dataManager->GetBiostrucModelType(), 0, biostruc, NULL))
197  objects.push_back(new StructureObject(this, *biostruc, true));
198  }
199  return (objects.size() > 0);
200 }
201 
203  const StructureObject *obj, const Sequence **seqHandle)
204 {
205  ChemicalGraph::MoleculeMap::const_iterator m, me = obj->graph->molecules.end();
206  for (m=obj->graph->molecules.begin(); m!=me; ++m) {
207  if (!(m->second->IsProtein() || m->second->IsNucleotide())) continue;
208 
209  if (m->second->identifier == seq->identifier) {
210 
211  // verify length
212  if (m->second->residues.size() != seq->Length()) {
213  ERRORMSG(
214  "MatchSequenceToMoleculeInObject() - length mismatch between sequence gi "
215  << "and matching molecule " << m->second->identifier->ToString());
216  continue;
217  }
218  TRACEMSG("matched sequence " << " gi " << seq->identifier->gi << " with object "
219  << obj->GetPDBID() << " moleculeID " << m->second->id);
220 
221  // sanity check
222  if (m->second->sequence) {
223  ERRORMSG("Molecule " << m->second->identifier->ToString()
224  << " already has an associated sequence");
225  continue;
226  }
227 
228  // automatically duplicate Sequence if it's already associated with a molecule
229  if (seq->molecule) {
230  TRACEMSG("duplicating sequence " << seq->identifier->ToString());
231  SequenceSet *seqSetMod = const_cast<SequenceSet*>(sequenceSet);
232  CBioseq& bioseqMod = const_cast<CBioseq&>(seq->bioseqASN.GetObject());
233  seq = new Sequence(seqSetMod, bioseqMod);
234  seqSetMod->sequences.push_back(seq);
235  // update Sequence handle, which should be a handle to a MasterDependentAlignment dependent,
236  // so that this new Sequence* is correctly loaded into the BlockMultipleAlignment
237  if (seqHandle) *seqHandle = seq;
238  }
239 
240  // do the cross-match
241  (const_cast<Molecule*>(m->second))->sequence = seq;
242  (const_cast<Sequence*>(seq))->molecule = m->second;
243  break;
244  }
245  }
246  return (m != me);
247 }
248 
249 static void SetStructureRowFlags(const AlignmentSet *alignmentSet, unsigned int *structureLimit,
250  vector < bool > *dontLoadRowStructure)
251 {
252  vector < string > titles;
253  vector < unsigned int > rows;
254 
255  // find dependent rows with associated structure
256  AlignmentSet::AlignmentList::const_iterator l, le = alignmentSet->alignments.end();
257  unsigned int row;
258  for (l=alignmentSet->alignments.begin(), row=0; l!=le; ++l, ++row) {
259  if ((*l)->dependent->identifier->mmdbID != MoleculeIdentifier::VALUE_NOT_SET) {
260  titles.push_back((*l)->dependent->identifier->ToString());
261  rows.push_back(row);
262  }
263  }
264 
265  if (*structureLimit - 1 >= titles.size()) return;
266 
267  // let user select which dependents to load
268  wxString *items = new wxString[titles.size()];
269  vector < bool > itemsOn(titles.size(), false);
270  for (row=0; row<titles.size(); ++row) {
271  items[row] = titles[row].c_str();
272  if (row < *structureLimit - 1) // by default, first N-1 are selected
273  itemsOn[row] = true;
274  }
275  ShowHideDialog dialog(items, &itemsOn, NULL, true, NULL, -1, "Choose structures:");
276 
277  if (dialog.ShowModal() == wxOK) {
278  // figure out which rows the user selected, and adjust structureLimit accordingly
279  *structureLimit = 1; // master always visible
280  for (row=0; row<itemsOn.size(); ++row) {
281  if (itemsOn[row])
282  (*structureLimit)++; // structure should be loaded
283  else
284  (*dontLoadRowStructure)[rows[row]] = true; // structure should not be loaded
285  }
286  }
287 
288  delete[] items;
289 }
290 
291 void StructureSet::LoadAlignmentsAndStructures(unsigned int structureLimit)
292 {
293  // try to determine the master structure
294  int masterMMDBID = MoleculeIdentifier::VALUE_NOT_SET;
295  // explicit master structure
297  dataManager->GetMasterStructure()->GetId().front()->IsMmdb_id())
298  masterMMDBID = dataManager->GetMasterStructure()->GetId().front()->GetMmdb_id().Get();
299  // master of structure alignments
300  else if (dataManager->GetStructureAlignments() &&
301  dataManager->GetStructureAlignments()->IsSetId() &&
302  dataManager->GetStructureAlignments()->GetId().front()->IsMmdb_id())
303  masterMMDBID = dataManager->GetStructureAlignments()->GetId().front()->GetMmdb_id().Get();
304  // SPECIAL CASE: if there's no explicit master structure, but there is a structure
305  // list that contains a single structure, then assume that it is the master structure
306  else if (dataManager->GetStructureList() &&
307  dataManager->GetStructureList()->size() == 1 &&
308  dataManager->GetStructureList()->front()->GetId().front()->IsMmdb_id())
309  masterMMDBID = dataManager->GetStructureList()->front()->GetId().front()->GetMmdb_id().Get();
310 
311  // assume data manager has already screened the alignment list
313  typedef list < CRef < CSeq_align > > SeqAlignList;
314  const SeqAlignList& seqAligns = alignments->front()->GetData().GetAlign();
315 
316  // we need to determine the identity of the master sequence; most rigorous way is to look
317  // for a Seq-id that is present in all pairwise alignments
318  const Sequence *seq1 = NULL, *seq2 = NULL, *master = NULL;
319  bool seq1PresentInAll = true, seq2PresentInAll = true;
320 
321  // first, find sequences for first pairwise alignment
322  const CSeq_id& frontSid = seqAligns.front()->GetSegs().IsDendiag() ?
323  seqAligns.front()->GetSegs().GetDendiag().front()->GetIds().front().GetObject() :
324  seqAligns.front()->GetSegs().GetDenseg().GetIds().front().GetObject();
325  const CSeq_id& backSid = seqAligns.front()->GetSegs().IsDendiag() ?
326  seqAligns.front()->GetSegs().GetDendiag().front()->GetIds().back().GetObject() :
327  seqAligns.front()->GetSegs().GetDenseg().GetIds().back().GetObject();
328  SequenceSet::SequenceList::const_iterator s, se = sequenceSet->sequences.end();
329  for (s=sequenceSet->sequences.begin(); s!=se; ++s) {
330  if ((*s)->identifier->MatchesSeqId(frontSid)) seq1 = *s;
331  if ((*s)->identifier->MatchesSeqId(backSid)) seq2 = *s;
332  if (seq1 && seq2) break;
333  }
334  if (!(seq1 && seq2)) {
335  ERRORMSG("Can't match first pair of Seq-ids to Sequences");
336  return;
337  }
338 
339  // now, make sure one of these sequences is present in all the other pairwise alignments
340  SeqAlignList::const_iterator a = seqAligns.begin(), ae = seqAligns.end();
341  for (++a; a!=ae; ++a) {
342  const CSeq_id& frontSid2 = (*a)->GetSegs().IsDendiag() ?
343  (*a)->GetSegs().GetDendiag().front()->GetIds().front().GetObject() :
344  (*a)->GetSegs().GetDenseg().GetIds().front().GetObject();
345  const CSeq_id& backSid2 = (*a)->GetSegs().IsDendiag() ?
346  (*a)->GetSegs().GetDendiag().front()->GetIds().back().GetObject() :
347  (*a)->GetSegs().GetDenseg().GetIds().back().GetObject();
348  if (!seq1->identifier->MatchesSeqId(frontSid2) && !seq1->identifier->MatchesSeqId(backSid2))
349  seq1PresentInAll = false;
350  if (!seq2->identifier->MatchesSeqId(frontSid2) && !seq2->identifier->MatchesSeqId(backSid2))
351  seq2PresentInAll = false;
352  }
353  if (!seq1PresentInAll && !seq2PresentInAll) {
354  ERRORMSG("All pairwise sequence alignments must have a common master sequence");
355  return;
356  } else if (seq1PresentInAll && !seq2PresentInAll)
357  master = seq1;
358  else if (seq2PresentInAll && !seq1PresentInAll)
359  master = seq2;
360  else if (seq1PresentInAll && seq2PresentInAll && seq1 == seq2)
361  master = seq1;
362 
363  // if still ambiguous, see if master3d is set in CDD data
364  if (!master && dataManager->GetCDDMaster3d()) {
366  master = seq1;
367  else if (seq2->identifier->MatchesSeqId(*(dataManager->GetCDDMaster3d())))
368  master = seq2;
369  else
370  ERRORMSG("Unable to match CDD's master3d with either sequence in first pairwise alignment");
371  }
372 
373  // if still ambiguous, try to use master structure info to find master sequence
374  if (!master && masterMMDBID != MoleculeIdentifier::VALUE_NOT_SET) {
375  // load master - has side affect of matching gi's with PDB/molecule ID during graph evaluation
376  if (structureLimit > 0)
377  LoadMaster(masterMMDBID);
378 
379  // see if there's a sequence in the master structure that matches
381  seq1->identifier->mmdbID != seq2->identifier->mmdbID) {
382  if (masterMMDBID == seq1->identifier->mmdbID)
383  master = seq1;
384  else if (masterMMDBID == seq2->identifier->mmdbID)
385  master = seq2;
386  else {
387  ERRORMSG("Structure master does not contain either sequence in first pairwise alignment");
388  return;
389  }
390  }
391  }
392 
393  // if still ambiguous, just use the first one
394  if (!master) {
395  WARNINGMSG("Ambiguous master; using " << seq1->identifier->ToString());
396  master = seq1;
397  }
398 
399  TRACEMSG("determined that master sequence is " << master->identifier->ToString());
400 
401  // load alignments now that we know the identity of the master
402  alignmentSet = new AlignmentSet(this, master, *(dataManager->GetSequenceAlignments()));
403 
404  // check mmdb id's and load master if not already present (and if master has structure)
405  if (masterMMDBID == MoleculeIdentifier::VALUE_NOT_SET) {
406  masterMMDBID = master->identifier->mmdbID;
407  } else if (master->identifier->mmdbID != MoleculeIdentifier::VALUE_NOT_SET &&
408  master->identifier->mmdbID != masterMMDBID) {
409  ERRORMSG("master structure (" << masterMMDBID <<
410  ") disagrees with master sequence (apparently from " << master->identifier->mmdbID << ')');
411  return;
412  }
413  if (objects.size() == 0 && structureLimit > 0 && masterMMDBID != MoleculeIdentifier::VALUE_NOT_SET &&
414  master->identifier->GetLabel() != "consensus") // special case for looking at "raw" CD's
415  LoadMaster(masterMMDBID);
416 
417  // cross-match master sequence and structure
418  if (objects.size() == 1 && !MatchSequenceToMoleculeInObject(master, objects.front())) {
419  ERRORMSG("MatchSequenceToMoleculeInObject() - can't find molecule in object, sequence identifers don't match."
420  << objects.front()->GetPDBID() << " to match master sequence "
421  << master->identifier->ToString());
422  return;
423  }
424 
425  // IFF there's a master structure, then also load dependent structures and cross-match sequences
426  if (objects.size() == 1 && structureLimit > 1) {
427  ASNDataManager::BiostrucList::const_iterator b, be;
429  int row;
430  vector < bool > loadedStructureForDependentRow(alignmentSet->alignments.size(), false);
431 
432  // first, load each remaining dependent structure, and for each one, find the first dependent
433  // sequence that matches it (and that doesn't already have structure)
434  AlignmentSet::AlignmentList::const_iterator l, le = alignmentSet->alignments.end();
435  if (dataManager->GetStructureList()) {
436  for (b=dataManager->GetStructureList()->begin(); b!=be && objects.size()<structureLimit; ++b) {
437 
438  // load structure
439  if (usedStructures.find(b->GetPointer()) != usedStructures.end()) continue;
440  StructureObject *object = new StructureObject(this, **b, false);
441  objects.push_back(object);
443  object->SetTransformToMaster(
444  *(dataManager->GetStructureAlignments()), master->identifier->mmdbID);
445  usedStructures[b->GetPointer()] = true;
446 
447  // find matching unstructured dependent sequence
448  for (l=alignmentSet->alignments.begin(), row=0; l!=le; ++l, ++row) {
449  if (loadedStructureForDependentRow[row]) continue;
450  if (MatchSequenceToMoleculeInObject((*l)->dependent, object,
451  &((const_cast<MasterDependentAlignment*>(*l))->dependent))) {
452  loadedStructureForDependentRow[row] = true;
453  break;
454  }
455  }
456  if (l == le)
457  ERRORMSG("Warning: Structure " << object->GetPDBID()
458  << " doesn't have a matching dependent sequence in the multiple alignment");
459  }
460  }
461 
462  // now loop through dependent rows of the alignment; if the dependent
463  // sequence has an MMDB ID but no structure yet, then load it.
464  if (objects.size() < structureLimit && (dataManager->IsCDD() || dataManager->IsGeneralMime())) {
465 
466  // for CDD's, ask user which structures to load if structureLimit is low
467  if (dataManager->IsCDD())
468  SetStructureRowFlags(alignmentSet, &structureLimit, &loadedStructureForDependentRow);
469 
470  for (l=alignmentSet->alignments.begin(), row=0; l!=le && objects.size()<structureLimit; ++l, ++row) {
471 
472  if ((*l)->dependent->identifier->mmdbID != MoleculeIdentifier::VALUE_NOT_SET &&
473  !loadedStructureForDependentRow[row]) {
474 
475  // first check the biostruc list to see if this structure is present already
476  CRef < CBiostruc > biostruc;
477  if (dataManager->GetStructureList()) {
478  for (b=dataManager->GetStructureList()->begin(); b!=be ; ++b) {
479  if ((*b)->GetId().front()->IsMmdb_id() &&
480  (*b)->GetId().front()->GetMmdb_id().Get() == (*l)->dependent->identifier->mmdbID) {
481  biostruc = *b;
482  break;
483  }
484  }
485  }
486 
487  // if not in list, load Biostruc via HTTP/cache
488  if (biostruc.Empty()) {
489  if (!LoadStructureViaCache(NStr::IntToString((*l)->dependent->identifier->mmdbID),
490  dataManager->GetBiostrucModelType(), 0, biostruc, NULL)) {
491  ERRORMSG("Failed to load MMDB #" << (*l)->dependent->identifier->mmdbID);
492  continue;
493  }
494  }
495 
496  // create StructureObject and cross-match
497  StructureObject *object = new StructureObject(this, *biostruc, false);
498  objects.push_back(object);
500  object->SetTransformToMaster(
501  *(dataManager->GetStructureAlignments()), master->identifier->mmdbID);
502  if (!MatchSequenceToMoleculeInObject((*l)->dependent, object,
503  &((const_cast<MasterDependentAlignment*>(*l))->dependent)))
504  ERRORMSG("Failed to match any molecule in structure " << object->GetPDBID()
505  << " with sequence " << (*l)->dependent->identifier->ToString());
506  loadedStructureForDependentRow[row] = true;
507  }
508  }
509  }
510  }
511 }
512 
513 void StructureSet::Load(unsigned int structureLimit)
514 {
515  // member data initialization
518  sequenceSet = NULL;
519  alignmentSet = NULL;
521  nDomains = 0;
522  isAlphaOnly = false;
523  parentSet = this;
525  styleManager = new StyleManager(this);
526  havePrevPickedAtomCoord = false;
527  hasUserStyle = false;
528 
529  // if this is a single structure, then there should be one sequence per biopolymer
531  const CBiostruc *masterBiostruc = dataManager->GetMasterStructure();
532  if (!masterBiostruc && dataManager->GetStructureList() && dataManager->GetStructureList()->size() == 1)
533  masterBiostruc = dataManager->GetStructureList()->front().GetPointer();
534  if (masterBiostruc)
535  objects.push_back(new StructureObject(this, *masterBiostruc, true));
536  if (dataManager->GetSequences())
538  }
539 
540  // multiple structure: should have exactly one sequence per structure (plus unstructured sequences)
541  else {
543  ERRORMSG("Data interpreted as multiple alignment, "
544  "but missing sequences and/or sequence alignments");
545  return;
546  }
547  sequenceSet = new SequenceSet(this, *(dataManager->GetSequences()));
548  LoadAlignmentsAndStructures(structureLimit);
549  }
550 
551  // find center of coordinates
552  SetCenter();
553 
554  // create alignment manager
555  if (sequenceSet) {
556  if (dataManager->GetUpdates())
557  // if updates present, alignment manager will load those into update viewer
559  else
561  }
562 
563  VerifyFrameMap();
564 
565  // load style dictionary and user annotations
567  if (styles) {
568  if (!styleManager->LoadFromASNStyleDictionary(*styles) ||
570  ERRORMSG("Error loading style dictionary");
571  dataManager->RemoveStyleDictionary(); // remove now; recreated with current settings upon save
572  hasUserStyle = true;
573  }
574 
576  if (annots) {
577  if (!styleManager->LoadFromASNUserAnnotations(*annots) ||
579  ERRORMSG("Error loading user annotations or camera settings");
580  dataManager->RemoveUserAnnotations(); // remove now; recreated with current settings upon save
581  }
582 
583  // setup show/hide items
585 
586  // alignments always start with aligned domains only
587  if (alignmentSet)
589 
591 }
592 
594 {
595  delete dataManager;
596  delete showHideManager;
597  delete styleManager;
599 
602 }
603 
604 bool StructureSet::AddBiostrucToASN(ncbi::objects::CBiostruc *biostruc)
605 {
606  bool added = dataManager->AddBiostrucToASN(biostruc);
607  if (added && objects.size() == 1)
608  InitStructureAlignments(objects.front()->mmdbID);
609  return added;
610 }
611 
612 static const int NO_DOMAIN = -1, MULTI_DOMAIN = 0;
613 
615 {
616  // create or empty the Biostruc-annot-set that will contain these alignments
617  // in the asn data, erasing any structure alignments currently stored there
618  CBiostruc_annot_set *structureAlignments = dataManager->GetStructureAlignments();
619  if (structureAlignments) {
620  structureAlignments->SetId().clear();
621  structureAlignments->SetDescr().clear();
622  structureAlignments->SetFeatures().clear();
623  } else {
624  structureAlignments = new CBiostruc_annot_set();
625  dataManager->SetStructureAlignments(structureAlignments);
626  }
627 
628  // set up the skeleton of the new Biostruc-annot-set
629  // new Mmdb-id
630  structureAlignments->SetId().resize(1);
631  structureAlignments->SetId().front().Reset(new CBiostruc_id());
632  CMmdb_id *mid = new CMmdb_id(masterMMDBID);
633  structureAlignments->SetId().front().GetObject().SetMmdb_id(*mid);
634  // new Biostruc-feature-set
636  featSet->SetId().Set(NO_DOMAIN);
637  featSet->SetFeatures(); // just create an empty list
638  structureAlignments->SetFeatures().resize(1, featSet);
639 
640  // flag a change in data
642 }
643 
645  int masterDomainID, int dependentDomainID)
646 {
647  CBiostruc_annot_set *structureAlignments = dataManager->GetStructureAlignments();
648  if (!structureAlignments) {
649  WARNINGMSG("StructureSet::AddStructureAlignment() - creating new structure alignment list");
650  InitStructureAlignments(objects.front()->mmdbID);
651  structureAlignments = dataManager->GetStructureAlignments();
652  }
653 
654  // check master domain ID, to see if alignments have crossed master's domain boundaries
655  int *currentMasterDomainID = &(structureAlignments->SetFeatures().front().GetObject().SetId().Set());
656  if (*currentMasterDomainID == NO_DOMAIN)
657  *currentMasterDomainID = masterDomainID;
658  else if ((*currentMasterDomainID % 100) != (masterDomainID % 100))
659  *currentMasterDomainID = (*currentMasterDomainID / 100) * 100;
660 
661  // check to see if this dependent domain already has an alignment; if so, increment alignment #
662  CBiostruc_feature_set::TFeatures::const_iterator
663  f, fe = structureAlignments->GetFeatures().front().GetObject().GetFeatures().end();
664  for (f=structureAlignments->GetFeatures().front().GetObject().GetFeatures().begin(); f!=fe; ++f) {
665  if ((f->GetObject().GetId().Get() / 10) == (dependentDomainID / 10))
666  ++dependentDomainID;
667  }
668  CBiostruc_feature_id id(dependentDomainID);
669  feature->SetId(id);
670 
671  CRef<CBiostruc_feature> featureRef(feature);
672  structureAlignments->SetFeatures().front().GetObject().SetFeatures().resize(
673  structureAlignments->GetFeatures().front().GetObject().GetFeatures().size() + 1, featureRef);
674 
675  // flag a change in data
677 }
678 
680 {
682  // flag a change in data
684 }
685 
687 {
689  if (!seqAnnots) {
690  ERRORMSG("StructureSet::ReplaceAlignmentSet() - "
691  << "can't figure out where in the asn the alignments are to go");
692  return;
693  }
694 
695  // update the AlignmentSet
696  if (alignmentSet)
697  delete alignmentSet;
698  alignmentSet = newAlignmentSet;
699 
700  // update the asn alignments
701  seqAnnots->resize(alignmentSet->newAsnAlignmentData->size());
702  ASNDataManager::SeqAnnotList::iterator o = seqAnnots->begin();
703  ASNDataManager::SeqAnnotList::iterator n, ne = alignmentSet->newAsnAlignmentData->end();
704  for (n=alignmentSet->newAsnAlignmentData->begin(); n!=ne; ++n, ++o)
705  o->Reset(n->GetPointer()); // copy each Seq-annot CRef
706 
707  // don't set data PSSM/row order flags here; done by AlignmentManager::SavePairwiseFromMultiple()
709 }
710 
711 void StructureSet::ReplaceUpdates(ncbi::objects::CCdd::TPending& newUpdates)
712 {
713  dataManager->ReplaceUpdates(newUpdates);
714 }
715 
717 {
718  ASNDataManager::SequenceList updateSequences;
719  if (alignmentManager) alignmentManager->GetUpdateSequences(&updateSequences);
721 }
722 
724 {
725  return dataManager->MonitorAlignments();
726 }
727 
728 bool StructureSet::SaveASNData(const char *filename, bool doBinary, unsigned int *changeFlags)
729 {
730  // force a save of any edits to alignment and updates first (it's okay if this has already been done)
732  /*if (dataManager->HasDataChanged())*/ RemoveUnusedSequences();
733 
734  // create and temporarily attach a style dictionary, and annotation set + camera info
735  // to the data (and then remove it again, so it's never out of date)
737  dataManager->SetStyleDictionary(*styleDictionary);
739  if (!styleManager->SaveToASNUserAnnotations(userAnnotations.GetPointer()) ||
740  (objects.size() >= 1 && !renderer->SaveToASNViewSettings(userAnnotations.GetPointer()))) {
741  ERRORMSG("StructureSet::SaveASNData() - error creating user annotations blob");
742  return false;
743  }
744  if (userAnnotations->IsSetAnnotations() || userAnnotations->IsSetView())
745  dataManager->SetUserAnnotations(*userAnnotations);
746 
747  string err;
748  bool writeOK = MonitorAlignments();
749  if (!writeOK)
750  err = "MonitorAlignments() returned error, no file written";
751  else
752  writeOK = dataManager->WriteDataToFile(filename, doBinary, &err, eFNP_Replace);
753 
754  // remove style dictionary and annotations from asn
757 
758  if (writeOK) {
759  *changeFlags = dataManager->GetDataChanged();
761  } else {
762  ERRORMSG("Write failed: " << err);
763  }
764  return writeOK;
765 }
766 
767 // because the frame map (for each frame, a list of diplay lists) is complicated
768 // to create, this just verifies that all display lists occur exactly once
769 // in the map. Also, make sure that total # display lists in all frames adds up.
771 {
772  TRACEMSG("# display lists: " << (lastDisplayList - OpenGLRenderer::FIRST_LIST + 1));
773  for (unsigned int l=OpenGLRenderer::FIRST_LIST; l<=lastDisplayList; ++l) {
774  bool found = false;
775  for (unsigned int f=0; f<frameMap.size(); ++f) {
776  DisplayLists::const_iterator d, de=frameMap[f].end();
777  for (d=frameMap[f].begin(); d!=de; ++d) {
778  if (*d == l) {
779  if (!found)
780  found = true;
781  else
782  ERRORMSG("frameMap: repeated display list " << l);
783  }
784  }
785  }
786  if (!found)
787  ERRORMSG("display list " << l << " not in frameMap");
788  }
789 
790  unsigned int nLists = 0;
791  for (unsigned int f=0; f<frameMap.size(); ++f) {
792  DisplayLists::const_iterator d, de=frameMap[f].end();
793  for (d=frameMap[f].begin(); d!=de; ++d) ++nLists;
794  }
795  if (nLists != lastDisplayList)
796  ERRORMSG("frameMap has too many display lists");
797 }
798 
799 void StructureSet::SetCenter(const Vector *given)
800 {
801  Vector siteSum;
802  int nAtoms = 0;
803  double dist;
804  maxDistFromCenter = 0.0;
805 
806  // set new center if given one
807  if (given) center = *given;
808 
809  // loop trough all atoms twice - once to get average center, then once to
810  // find max distance from this center
811  for (int i=0; i<2; ++i) {
812  if (given && i==0) continue; // skip center calculation if given one
813  ObjectList::const_iterator o, oe=objects.end();
814  for (o=objects.begin(); o!=oe; ++o) {
815  StructureObject::CoordSetList::const_iterator c, ce=(*o)->coordSets.end();
816  for (c=(*o)->coordSets.begin(); c!=ce; ++c) {
817  AtomSet::AtomMap::const_iterator a, ae=(*c)->atomSet->atomMap.end();
818  for (a=(*c)->atomSet->atomMap.begin(); a!=ae; ++a) {
819  Vector site(a->second.front()->site);
820  if ((*o)->IsDependent() && (*o)->transformToMaster)
821  ApplyTransformation(&site, *((*o)->transformToMaster));
822  if (i==0) {
823  siteSum += site;
824  ++nAtoms;
825  } else {
826  dist = (site - center).length();
827  if (dist > maxDistFromCenter)
828  maxDistFromCenter = dist;
829  }
830  }
831  }
832  }
833  if (i==0) {
834  if (nAtoms == 0) {
835  center.Set(0.0, 0.0, 0.0);
836  break;
837  }
838  center = siteSum / nAtoms;
839  }
840  }
841  TRACEMSG("center: " << center << ", maxDistFromCenter " << maxDistFromCenter);
843 }
844 
846 {
847  if (objects.size() != 1)
848  return;
849 
850  TRACEMSG("Computing structure view...");
851  Vector alphaCenter;
852  double alphaRadius = 0.0;
853  int nAlphas = 0;
854 
855  // loop through twice - once to get average center, then once to
856  // find max distance from this center
857  for (int i=0; i<2; ++i) {
858 
859  // find all biopolymer alpha residues
860  ChemicalGraph::MoleculeMap::const_iterator m, me = objects.front()->graph->molecules.end();
861  for (m=objects.front()->graph->molecules.begin(); m!=me; ++m) {
862  if (!m->second->IsBiopolymer())
863  continue;
864  Molecule::ResidueMap::const_iterator r, re = m->second->residues.end();
865  for (r=m->second->residues.begin(); r!=re; ++r) {
866  if (r->second->alphaID == Residue::NO_ALPHA_ID) continue;
867  AtomPntr ap(m->second->id, r->first, r->second->alphaID);
868  const AtomCoord* atom = objects.front()->coordSets.front()->atomSet->GetAtom(ap, true, true);
869  if (atom) {
870  if (i == 0) {
871  alphaCenter += atom->site;
872  ++nAlphas;
873  } else {
874  double dist = (atom->site - alphaCenter).length();
875  if (dist > alphaRadius)
876  alphaRadius = dist;
877  }
878  }
879  }
880  }
881 
882  if (i == 0) {
883  if (nAlphas == 0)
884  return;
885  alphaCenter /= nAlphas;
886  }
887  }
888 
889  renderer->CenterView(alphaCenter, alphaRadius);
890  TRACEMSG("Centered view at " << alphaCenter << " radius " << alphaRadius);
891 }
892 
894 {
896  if (!alignment || !alignment->GetSequenceOfRow(0)) // || !alignment->GetSequenceOfRow(0))
897  return false; // no alignment
898  const Molecule *masterMolecule = alignment->GetSequenceOfRow(0)->molecule;
899  if (!masterMolecule) return false; // no structured master
900  const StructureObject *masterObject;
901  if (!masterMolecule->GetParentOfType(&masterObject)) return false;
902 
903  // get coords of all aligned c-alphas
904  deque < Vector > coords;
905  Molecule::ResidueMap::const_iterator r, re = masterMolecule->residues.end();
906  for (r=masterMolecule->residues.begin(); r!=re; ++r) {
907  if (!alignment->IsAligned(0U, r->first - 1)) continue;
908  if (r->second->alphaID == Residue::NO_ALPHA_ID) continue;
909  AtomPntr ap(masterMolecule->id, r->first, r->second->alphaID);
910  const AtomCoord* atom = masterObject->coordSets.front()->atomSet->GetAtom(ap, true, true);
911  if (atom) coords.push_back(atom->site);
912  }
913  if (coords.size() == 0)
914  return false;
915 
916  // calculate center
917  unsigned int i;
918  Vector alignedCenter;
919  for (i=0; i<coords.size(); ++i) alignedCenter += coords[i];
920  alignedCenter /= coords.size();
921 
922  // find radius
923  double radius = 0.0, d;
924  for (i=0; i<coords.size(); ++i) {
925  d = (coords[i] - alignedCenter).length();
926  if (d > radius) radius = d;
927  }
928 
929  // set view
930  renderer->CenterView(alignedCenter, radius);
931  TRACEMSG("Centered view at " << alignedCenter << " radius " << radius);
932  return true;
933 }
934 
935 bool StructureSet::Draw(const AtomSet *atomSet) const
936 {
937  TRACEMSG("drawing StructureSet");
938  if (!styleManager->CheckGlobalStyleSettings()) return false;
939  return true;
940 }
941 
942 unsigned int StructureSet::CreateName(const Residue *residue, int atomID)
943 {
944  ++lastAtomName;
945  nameMap[lastAtomName] = make_pair(residue, atomID);
946  return lastAtomName;
947 }
948 
949 bool StructureSet::GetAtomFromName(unsigned int name, const Residue **residue, int *atomID) const
950 {
951  NameMap::const_iterator i = nameMap.find(name);
952  if (i == nameMap.end()) return false;
953  *residue = i->second.first;
954  *atomID = i->second.second;
955  return true;
956 }
957 
958 void StructureSet::SelectedAtom(unsigned int name, bool setCenter)
959 {
960  const Residue *residue;
961  int atomID;
962 
963  if (name == OpenGLRenderer::NO_NAME || !GetAtomFromName(name, &residue, &atomID)) {
964  INFOMSG("nothing selected");
965  return;
966  }
967 
968  // add highlight
969  const Molecule *molecule;
970  if (!residue->GetParentOfType(&molecule)) return;
971  GlobalMessenger()->ToggleHighlight(molecule, residue->id, true);
972  wxString molresid;
973  if (molecule->IsHeterogen() || molecule->IsSolvent()) {
974  const StructureObject *object;
975  if (molecule->GetParentOfType(&object)) {
976  // assume hets/solvents are single residue
977  if (object->GetPDBID().size() > 0)
978  molresid.Printf("%s heterogen/solvent molecule %i", object->GetPDBID().c_str(), molecule->id);
979  else
980  molresid = molecule->identifier->ToString().c_str();
981  }
982  } else
983  molresid.Printf("chain %s residue %i", molecule->identifier->ToString().c_str(), residue->id);
984  INFOMSG("selected " << molresid.c_str() << " (PDB: " << residue->nameGraph << ' ' << residue->namePDB
985  << ") atom " << atomID << " (PDB: " << residue->GetAtomInfo(atomID)->name << ')');
986 
987  // get coordinate of picked atom, in coordinates of master frame
988  const StructureObject *object;
989  if (!molecule->GetParentOfType(&object)) return;
990  object->coordSets.front()->atomSet->SetActiveEnsemble(NULL); // don't actually know which alternate...
991  const AtomCoord *pickedAtom = object->coordSets.front()->atomSet->
992  GetAtom(AtomPntr(molecule->id, residue->id, atomID));
993  if (!pickedAtom) {
994  WARNINGMSG("Can't get coordinates for this atom (in the first coordinate set)");
995  return;
996  }
997  Vector pickedAtomCoord = pickedAtom->site;
998  if (object->IsDependent() && object->transformToMaster)
999  ApplyTransformation(&pickedAtomCoord, *(object->transformToMaster));
1000 
1001  // print out distance to previous picked atom
1003  INFOMSG("distance to previously selected atom: " << setprecision(3) <<
1004  (pickedAtomCoord - prevPickedAtomCoord).length() << setprecision(6) << " A");
1005  prevPickedAtomCoord = pickedAtomCoord;
1006  havePrevPickedAtomCoord = true;
1007 
1008  // if indicated, use atom site as rotation center; use coordinate from first CoordSet, default altConf
1009  if (setCenter) {
1010  INFOMSG("rotating about " << object->GetPDBID()
1011  << " molecule " << molecule->id << " residue " << residue->id << ", atom " << atomID);
1012  rotationCenter = pickedAtomCoord;
1013  }
1014 }
1015 
1016 void StructureSet::SelectByDistance(double cutoff, unsigned int options) const
1017 {
1018  StructureObject::ResidueMap residuesToHighlight;
1019 
1020  // add residues to highlight to master list, based on proximities within objects
1021  ObjectList::const_iterator o, oe = objects.end();
1022  for (o=objects.begin(); o!=oe; ++o)
1023  (*o)->SelectByDistance(cutoff, options, &residuesToHighlight);
1024 
1025  // now actually add highlights for new selected residues
1026  StructureObject::ResidueMap::const_iterator r, re = residuesToHighlight.end();
1027  for (r=residuesToHighlight.begin(); r!=re; ++r)
1028  if (!GlobalMessenger()->IsHighlighted(r->second, r->first->id))
1029  GlobalMessenger()->ToggleHighlight(r->second, r->first->id, false);
1030 }
1031 
1032 const Sequence * StructureSet::FindOrCreateSequence(ncbi::objects::CBioseq& bioseq)
1033 {
1034  // see if we have this sequence already
1035  const Sequence *seq = sequenceSet->FindMatchingSequence(bioseq.GetId());
1036  if (seq)
1037  return seq;
1038 
1039  // if not, add new Sequence to SequenceSet
1040  SequenceSet *modifiableSet = const_cast<SequenceSet*>(sequenceSet);
1041  seq = new Sequence(modifiableSet, bioseq);
1042  if (!seq->identifier) {
1043  ERRORMSG("StructureSet::FindOrCreateSequence() - identifier conflict, no new sequence created");
1044  delete seq;
1045  return NULL;
1046  }
1047  modifiableSet->sequences.push_back(seq);
1048 
1049  // add asn sequence to asn data
1050  if (dataManager->GetSequences()) {
1051  CSeq_entry *se = new CSeq_entry();
1052  se->SetSeq(bioseq);
1053  dataManager->GetSequences()->push_back(CRef<CSeq_entry>(se));
1054  } else
1055  ERRORMSG("StructureSet::FindOrCreateSequence() - no sequence list in asn data");
1057 
1058  return seq;
1059 }
1060 
1061 void StructureSet::RejectAndPurgeSequence(const Sequence *reject, string reason, bool purge)
1062 {
1063  if (!dataManager->IsCDD() || !reject || reason.size() == 0) return;
1064 
1065  CReject_id *rejectID = new CReject_id();
1066  rejectID->SetIds() = reject->bioseqASN->GetId(); // copy Seq-id lists
1067 
1068  CUpdate_comment *comment = new CUpdate_comment();
1069  comment->SetComment(reason);
1070  rejectID->SetDescription().push_back(CRef < CUpdate_comment > (comment));
1071 
1072  dataManager->AddReject(rejectID);
1073 
1074  if (purge)
1075  alignmentManager->PurgeSequence(reject->identifier);
1076 }
1077 
1079 {
1080  return dataManager->GetRejects();
1081 }
1082 
1084 {
1085  const RejectList *rejects = GetRejects();
1086  if (!rejects) {
1087  INFOMSG("No rejects in this CD");
1088  return;
1089  }
1090 
1091  INFOMSG("Rejects:");
1092  RejectList::const_iterator r, re = rejects->end();
1093  for (r=rejects->begin(); r!=re; ++r) {
1094  string idstr;
1095  CReject_id::TIds::const_iterator i, ie = (*r)->GetIds().end();
1096  for (i=(*r)->GetIds().begin(); i!=ie; ++i)
1097  idstr += (*i)->AsFastaString() + ", ";
1098  INFOMSG(idstr << "Reason: " <<
1099  (((*r)->IsSetDescription() && (*r)->GetDescription().front()->IsComment()) ?
1100  (*r)->GetDescription().front()->GetComment() : string("none given")));
1101  }
1102 }
1103 
1105 {
1106  if (!dataManager->ConvertMimeDataToCDD(cddName))
1107  return false;
1108 
1109  // make sure all structured sequences have MMDB annot tags
1110  SequenceSet::SequenceList::const_iterator s, se = sequenceSet->sequences.end();
1111  for (s=sequenceSet->sequences.begin(); s!=se; ++s) {
1112  if ((*s)->molecule) {
1113  if ((*s)->identifier->mmdbID == MoleculeIdentifier::VALUE_NOT_SET) {
1114  ERRORMSG("sequence " << (*s)->identifier->ToString()
1115  << " has associated molecule but no MMDB id");
1116  return false;
1117  }
1118  (*s)->AddMMDBAnnotTag((*s)->identifier->mmdbID);
1119  }
1120  }
1121 
1122  return true;
1123 }
1124 
1125 // trivial methods...
1128 void StructureSet::SetDataChanged(unsigned int what) const { dataManager->SetDataChanged(what); }
1129 bool StructureSet::IsCDD(void) const { return dataManager->IsCDD(); }
1130 bool StructureSet::IsCDDInMime(void) const { return dataManager->IsCDDInMime(); }
1131 const string& StructureSet::GetCDDName(void) const { return dataManager->GetCDDName(); }
1132 bool StructureSet::SetCDDName(const string& name) { return dataManager->SetCDDName(name); }
1133 const string& StructureSet::GetCDDDescription(void) const { return dataManager->GetCDDDescription(); }
1134 bool StructureSet::SetCDDDescription(const string& descr) { return dataManager->SetCDDDescription(descr); }
1137 ncbi::objects::CCdd_descr_set * StructureSet::GetCDDDescrSet(void) { return dataManager->GetCDDDescrSet(); }
1138 ncbi::objects::CAlign_annot_set * StructureSet::GetCDDAnnotSet(void) { return dataManager->GetCDDAnnotSet(); }
1139 
1141 
1142 
1143 ///// StructureObject stuff /////
1144 
1145 const int StructureObject::NO_MMDB_ID = -1;
1147 
1148 StructureObject::StructureObject(StructureBase *parent, const CBiostruc& biostruc, bool master) :
1149  StructureBase(parent), isMaster(master), mmdbID(NO_MMDB_ID), transformToMaster(NULL),
1150  minTemperature(NO_TEMPERATURE), maxTemperature(NO_TEMPERATURE)
1151 {
1152  // set numerical id simply based on # objects in parentSet
1153  id = parentSet->objects.size() + 1;
1154 
1155  // get MMDB id
1156  CBiostruc::TId::const_iterator j, je=biostruc.GetId().end();
1157  for (j=biostruc.GetId().begin(); j!=je; ++j) {
1158  if (j->GetObject().IsMmdb_id()) {
1159  mmdbID = j->GetObject().GetMmdb_id().Get();
1160  break;
1161  }
1162  }
1163  TRACEMSG("MMDB id " << mmdbID);
1164 
1165  // get PDB id
1166  if (biostruc.IsSetDescr()) {
1167  CBiostruc::TDescr::const_iterator k, ke=biostruc.GetDescr().end();
1168  for (k=biostruc.GetDescr().begin(); k!=ke; ++k) {
1169  if (k->GetObject().IsName()) {
1170  pdbIDs.push_back(k->GetObject().GetName());
1171  TRACEMSG("PDB id " << pdbIDs.back());
1172  }
1173  }
1174  }
1175 
1176  // get atom and feature spatial coordinates
1177  if (biostruc.IsSetModel()) {
1178  // iterate SEQUENCE OF Biostruc-model
1179  CBiostruc::TModel::const_iterator i, ie=biostruc.GetModel().end();
1180  for (i=biostruc.GetModel().begin(); i!=ie; ++i) {
1181 
1182  // don't know how to deal with these...
1183  if (i->GetObject().GetType() == eModel_type_ncbi_vector ||
1184  i->GetObject().GetType() == eModel_type_other) continue;
1185 
1186  // otherwise, assume all models in this set are of same type
1187  if (i->GetObject().GetType() == eModel_type_ncbi_backbone)
1188  parentSet->isAlphaOnly = true;
1189  else
1190  parentSet->isAlphaOnly = false;
1191 
1192  // load each Biostruc-model into a CoordSet
1193  if (i->GetObject().IsSetModel_coordinates()) {
1194  CoordSet *coordSet =
1195  new CoordSet(this, i->GetObject().GetModel_coordinates());
1196  coordSets.push_back(coordSet);
1197  }
1198  }
1199  }
1200 
1201  TRACEMSG("temperature range: " << minTemperature << " to " << maxTemperature);
1202 
1203  // get graph - must be done after atom coordinates are loaded, so we can
1204  // avoid storing graph nodes for atoms not present in the model
1205  graph = new ChemicalGraph(this, biostruc.GetChemical_graph(), biostruc.GetFeatures());
1206 }
1207 
1209 {
1210  string s;
1211  for (unsigned int i=0; i<pdbIDs.size(); ++i) {
1212  if (i > 0)
1213  s += separator;
1214  s += pdbIDs[i];
1215  }
1216  return s;
1217 }
1218 
1219 
1220 
1222 {
1223  CBiostruc_annot_set::TFeatures::const_iterator f1, f1e=annot.GetFeatures().end();
1224  for (f1=annot.GetFeatures().begin(); f1!=f1e; ++f1) {
1225  CBiostruc_feature_set::TFeatures::const_iterator f2, f2e=f1->GetObject().GetFeatures().end();
1226  for (f2=f1->GetObject().GetFeatures().begin(); f2!=f2e; ++f2) {
1227 
1228  // skip if already used
1229  if (f2->GetObject().IsSetId() &&
1230  parentSet->usedFeatures.find(f2->GetObject().GetId().Get()) !=
1231  parentSet->usedFeatures.end())
1232  continue;
1233 
1234  // look for alignment feature
1235  if (f2->GetObject().IsSetType() &&
1236  f2->GetObject().GetType() == CBiostruc_feature::eType_alignment &&
1237  f2->GetObject().IsSetLocation() &&
1238  f2->GetObject().GetLocation().IsAlignment()) {
1239  const CChem_graph_alignment& graphAlign =
1240  f2->GetObject().GetLocation().GetAlignment();
1241 
1242  // find transform alignment of this object with master
1243  if (graphAlign.GetDimension() == 2 &&
1244  graphAlign.GetBiostruc_ids().size() == 2 &&
1245  graphAlign.IsSetTransform() &&
1246  graphAlign.GetTransform().size() == 1 &&
1247  graphAlign.GetBiostruc_ids().front().GetObject().IsMmdb_id() &&
1248  graphAlign.GetBiostruc_ids().front().GetObject().GetMmdb_id().Get() == masterMMDBID &&
1249  graphAlign.GetBiostruc_ids().back().GetObject().IsMmdb_id() &&
1250  graphAlign.GetBiostruc_ids().back().GetObject().GetMmdb_id().Get() == mmdbID) {
1251 
1252  // mark feature as used
1253  if (f2->GetObject().IsSetId())
1254  parentSet->usedFeatures[f2->GetObject().GetId().Get()] = true;
1255  TRACEMSG("got transform for " << GetPDBID() << "->master");
1256 
1257  // unpack transform into matrix, moves in reverse order;
1258  Matrix xform;
1259  transformToMaster = new Matrix();
1260  CTransform::TMoves::const_iterator
1261  m, me=graphAlign.GetTransform().front().GetObject().GetMoves().end();
1262  for (m=graphAlign.GetTransform().front().GetObject().GetMoves().begin(); m!=me; ++m) {
1263  Matrix xmat;
1264  double scale;
1265  if (m->GetObject().IsTranslate()) {
1266  const CTrans_matrix& trans = m->GetObject().GetTranslate();
1267  scale = 1.0 / trans.GetScale_factor();
1268  SetTranslationMatrix(&xmat,
1269  Vector(scale * trans.GetTran_1(),
1270  scale * trans.GetTran_2(),
1271  scale * trans.GetTran_3()));
1272  } else { // rotate
1273  const CRot_matrix& rot = m->GetObject().GetRotate();
1274  scale = 1.0 / rot.GetScale_factor();
1275  xmat.m[0]=scale*rot.GetRot_11(); xmat.m[1]=scale*rot.GetRot_21(); xmat.m[2]= scale*rot.GetRot_31(); xmat.m[3]=0;
1276  xmat.m[4]=scale*rot.GetRot_12(); xmat.m[5]=scale*rot.GetRot_22(); xmat.m[6]= scale*rot.GetRot_32(); xmat.m[7]=0;
1277  xmat.m[8]=scale*rot.GetRot_13(); xmat.m[9]=scale*rot.GetRot_23(); xmat.m[10]=scale*rot.GetRot_33(); xmat.m[11]=0;
1278  xmat.m[12]=0; xmat.m[13]=0; xmat.m[14]=0; xmat.m[15]=1;
1279  }
1280  ComposeInto(transformToMaster, xmat, xform);
1281  xform = *transformToMaster;
1282  }
1283  return true;
1284  }
1285  }
1286  }
1287  }
1288 
1289  WARNINGMSG("Can't get structure alignment for dependent " << GetPDBID()
1290  << " with master " << masterMMDBID << ";\nwill likely require manual realignment");
1291  return false;
1292 }
1293 
1294 static void AddDomain(int *domain, const Molecule *molecule, const Block::Range *range)
1295 {
1296  const StructureObject *object;
1297  if (!molecule->GetParentOfType(&object)) return;
1298  for (int l=range->from; l<=range->to; ++l) {
1299  if (molecule->residueDomains[l] != Molecule::NO_DOMAIN_SET) {
1300  if (*domain == NO_DOMAIN)
1301  *domain = object->domainID2MMDB.find(molecule->residueDomains[l])->second;
1302  else if (*domain != MULTI_DOMAIN &&
1303  *domain != object->domainID2MMDB.find(molecule->residueDomains[l])->second)
1304  *domain = MULTI_DOMAIN;
1305  }
1306  }
1307 }
1308 
1310  const Vector * const *masterCoords, const Vector * const *dependentCoords,
1311  const double *weights, int dependentRow)
1312 {
1313  Vector masterCOM, dependentCOM; // centers of mass for master, dependent
1314  Matrix dependentRotation; // rotation to align dependent with master
1316 
1317  // do the fit
1318  RigidBodyFit(nCoords, masterCoords, dependentCoords, weights, masterCOM, dependentCOM, dependentRotation);
1319 
1320  // apply the resulting transform elements from the fit to this object's transform Matrix
1321  Matrix single, combined;
1322  SetTranslationMatrix(&single, -dependentCOM);
1323  ComposeInto(transformToMaster, dependentRotation, single);
1324  combined = *transformToMaster;
1325  SetTranslationMatrix(&single, masterCOM);
1326  ComposeInto(transformToMaster, single, combined);
1327 
1328  // print out RMSD
1329  INFOMSG("RMSD of alpha coordinates used to align master structure and " << GetPDBID() << ": "
1330  << setprecision(3) << ComputeRMSD(nCoords, masterCoords, dependentCoords, transformToMaster) << setprecision(6) << " A");
1331 
1332  // create a new Biostruc-feature that contains this alignment
1333  CBiostruc_feature *feature = new CBiostruc_feature();
1336  feature->SetLocation(*location);
1337  CChem_graph_alignment *graphAlignment = new CChem_graph_alignment();
1338  location.GetObject().SetAlignment(*graphAlignment);
1339 
1340  // fill out the Chem-graph-alignment
1341  graphAlignment->SetDimension(2);
1342  CMmdb_id
1343  *masterMID = new CMmdb_id(parentSet->objects.front()->mmdbID),
1344  *dependentMID = new CMmdb_id(mmdbID);
1345  CBiostruc_id
1346  *masterBID = new CBiostruc_id(),
1347  *dependentBID = new CBiostruc_id();
1348  masterBID->SetMmdb_id(*masterMID);
1349  dependentBID->SetMmdb_id(*dependentMID);
1350  graphAlignment->SetBiostruc_ids().resize(2);
1351  graphAlignment->SetBiostruc_ids().front().Reset(masterBID);
1352  graphAlignment->SetBiostruc_ids().back().Reset(dependentBID);
1353  graphAlignment->SetAlignment().resize(2);
1354 
1355  // fill out sequence alignment intervals, tracking domains in alignment
1357  int masterDomain = NO_DOMAIN, dependentDomain = NO_DOMAIN;
1358  const Molecule
1359  *masterMolecule = multiple->GetSequenceOfRow(0)->molecule,
1360  *dependentMolecule = multiple->GetSequenceOfRow(dependentRow)->molecule;
1362  multiple->GetUngappedAlignedBlocks(&blocks);
1363  if (blocks.size() > 0) {
1365  *masterCGPs = new CChem_graph_pntrs(),
1366  *dependentCGPs = new CChem_graph_pntrs();
1367  graphAlignment->SetAlignment().front().Reset(masterCGPs);
1368  graphAlignment->SetAlignment().back().Reset(dependentCGPs);
1370  *masterRPs = new CResidue_pntrs(),
1371  *dependentRPs = new CResidue_pntrs();
1372  masterCGPs->SetResidues(*masterRPs);
1373  dependentCGPs->SetResidues(*dependentRPs);
1374 
1375  masterRPs->SetInterval().resize(blocks.size());
1376  dependentRPs->SetInterval().resize(blocks.size());
1377  BlockMultipleAlignment::UngappedAlignedBlockList::const_iterator b, be = blocks.end();
1378  CResidue_pntrs::TInterval::iterator
1379  mi = masterRPs->SetInterval().begin(),
1380  si = dependentRPs->SetInterval().begin();
1381  for (b=blocks.begin(); b!=be; ++b, ++mi, ++si) {
1383  *masterRIP = new CResidue_interval_pntr(),
1384  *dependentRIP = new CResidue_interval_pntr();
1385  mi->Reset(masterRIP);
1386  si->Reset(dependentRIP);
1387 
1388  masterRIP->SetMolecule_id().Set(masterMolecule->id);
1389  dependentRIP->SetMolecule_id().Set(dependentMolecule->id);
1390 
1391  const Block::Range *range = (*b)->GetRangeOfRow(0);
1392  masterRIP->SetFrom().Set(range->from + 1); // +1 to convert seqLoc to residueID
1393  masterRIP->SetTo().Set(range->to + 1);
1394  AddDomain(&masterDomain, masterMolecule, range);
1395 
1396  range = (*b)->GetRangeOfRow(dependentRow);
1397  dependentRIP->SetFrom().Set(range->from + 1);
1398  dependentRIP->SetTo().Set(range->to + 1);
1399  AddDomain(&dependentDomain, dependentMolecule, range);
1400  }
1401  }
1402 
1403  // fill out structure alignment transform
1404  CTransform *xform = new CTransform();
1405  graphAlignment->SetTransform().resize(1);
1406  graphAlignment->SetTransform().front().Reset(xform);
1407  xform->SetId(1);
1408  xform->SetMoves().resize(3);
1409  CTransform::TMoves::iterator m = xform->SetMoves().begin();
1410  for (int i=0; i<3; ++i, ++m) {
1411  CMove *move = new CMove();
1412  m->Reset(move);
1413  static const int scaleFactor = 100000;
1414  if (i == 0) { // translate dependent so its COM is at origin
1415  CTrans_matrix *trans = new CTrans_matrix();
1416  move->SetTranslate(*trans);
1417  trans->SetScale_factor(scaleFactor);
1418  trans->SetTran_1((int)(-(dependentCOM.x * scaleFactor)));
1419  trans->SetTran_2((int)(-(dependentCOM.y * scaleFactor)));
1420  trans->SetTran_3((int)(-(dependentCOM.z * scaleFactor)));
1421  } else if (i == 1) {
1422  CRot_matrix *rot = new CRot_matrix();
1423  move->SetRotate(*rot);
1424  rot->SetScale_factor(scaleFactor);
1425  rot->SetRot_11((int)(dependentRotation[0] * scaleFactor));
1426  rot->SetRot_12((int)(dependentRotation[4] * scaleFactor));
1427  rot->SetRot_13((int)(dependentRotation[8] * scaleFactor));
1428  rot->SetRot_21((int)(dependentRotation[1] * scaleFactor));
1429  rot->SetRot_22((int)(dependentRotation[5] * scaleFactor));
1430  rot->SetRot_23((int)(dependentRotation[9] * scaleFactor));
1431  rot->SetRot_31((int)(dependentRotation[2] * scaleFactor));
1432  rot->SetRot_32((int)(dependentRotation[6] * scaleFactor));
1433  rot->SetRot_33((int)(dependentRotation[10] * scaleFactor));
1434  } else if (i == 2) { // translate dependent so its COM is at COM of master
1435  CTrans_matrix *trans = new CTrans_matrix();
1436  move->SetTranslate(*trans);
1437  trans->SetScale_factor(scaleFactor);
1438  trans->SetTran_1((int)(masterCOM.x * scaleFactor));
1439  trans->SetTran_2((int)(masterCOM.y * scaleFactor));
1440  trans->SetTran_3((int)(masterCOM.z * scaleFactor));
1441  }
1442  }
1443 
1444  // store the new alignment in the Biostruc-annot-set,
1445  // setting the feature id depending on the aligned domain(s)
1446  if (masterDomain == NO_DOMAIN) masterDomain = 0; // can happen if single domain chain
1447  if (dependentDomain == NO_DOMAIN) dependentDomain = 0;
1448  const StructureObject *masterObject;
1449  if (!masterMolecule->GetParentOfType(&masterObject)) return;
1450  int
1451  masterDomainID = masterObject->mmdbID*10000 + masterMolecule->id*100 + masterDomain,
1452  dependentDomainID = mmdbID*100000 + dependentMolecule->id*1000 + dependentDomain*10 + 1;
1453  parentSet->AddStructureAlignment(feature, masterDomainID, dependentDomainID);
1454 
1455  // for backward-compatibility with Cn3D 3.5, need name to encode chain/domain
1456  CNcbiOstrstream oss;
1457  oss << masterMolecule->identifier->pdbID << masterMolecule->identifier->pdbChain << masterDomain << ' '
1458  << dependentMolecule->identifier->pdbID << dependentMolecule->identifier->pdbChain << dependentDomain << ' '
1459  << "Structure alignment of dependent " << multiple->GetSequenceOfRow(dependentRow)->identifier->ToString()
1460  << " with master " << multiple->GetSequenceOfRow(0)->identifier->ToString()
1461  << ", as computed by Cn3D";
1462 
1463  feature->SetName((string) CNcbiOstrstreamToString(oss));
1464 }
1465 
1466 void StructureObject::SelectByDistance(double cutoff, unsigned int options,
1467  ResidueMap *selectedResidues) const
1468 {
1469  // first make a list of coordinates of atoms in selected residues,
1470  typedef vector < const AtomCoord * > CoordList;
1471  CoordList highlightedAtoms;
1472  typedef map < const Molecule * , bool > MoleculeList;
1473  MoleculeList moleculesWithHighlights;
1474 
1475  ChemicalGraph::MoleculeMap::const_iterator m, me = graph->molecules.end();
1476  for (m=graph->molecules.begin(); m!=me; ++m) {
1477  Molecule::ResidueMap::const_iterator r, re = m->second->residues.end();
1478  for (r=m->second->residues.begin(); r!=re; ++r) {
1479 
1480  if (GlobalMessenger()->IsHighlighted(m->second, r->second->id)) {
1481  const Residue::AtomInfoMap& atomInfos = r->second->GetAtomInfos();
1482  Residue::AtomInfoMap::const_iterator a, ae = atomInfos.end();
1483  for (a=atomInfos.begin(); a!=ae; ++a) {
1484  const AtomCoord *atomCoord = coordSets.front()->atomSet->
1485  GetAtom(AtomPntr(m->second->id, r->second->id, a->first), true, true);
1486  if (atomCoord) highlightedAtoms.push_back(atomCoord);
1487  }
1488  moleculesWithHighlights[m->second] = true;
1489  }
1490  }
1491  }
1492  if (highlightedAtoms.size() == 0) return;
1493 
1494  // now make a list of unselected residues to check for proximity
1495  typedef vector < const Residue * > ResidueList;
1496  ResidueList unhighlightedResidues;
1497 
1498  for (m=graph->molecules.begin(); m!=me; ++m) {
1499  Molecule::ResidueMap::const_iterator r, re = m->second->residues.end();
1500 
1501  if ((options & StructureSet::eSelectOtherMoleculesOnly) &&
1502  moleculesWithHighlights.find(m->second) != moleculesWithHighlights.end())
1503  continue;
1504 
1505  for (r=m->second->residues.begin(); r!=re; ++r) {
1506 
1507  if (!GlobalMessenger()->IsHighlighted(m->second, r->second->id) &&
1508  (((options & StructureSet::eSelectProtein) && m->second->IsProtein()) ||
1509  ((options & StructureSet::eSelectNucleotide) && m->second->IsNucleotide()) ||
1510  ((options & StructureSet::eSelectHeterogen) && m->second->IsHeterogen()) ||
1511  ((options & StructureSet::eSelectSolvent) && m->second->IsSolvent())))
1512  unhighlightedResidues.push_back(r->second);
1513  }
1514  }
1515  if (unhighlightedResidues.size() == 0) return;
1516 
1517  // now check all unhighlighted residues, to see if any atoms are within cutoff distance
1518  // of any highlighted atoms; if so, add to residue selection list
1519  CoordList::const_iterator h, he = highlightedAtoms.end();
1520  ResidueList::const_iterator u, ue = unhighlightedResidues.end();
1521  for (u=unhighlightedResidues.begin(); u!=ue; ++u) {
1522  const Molecule *molecule;
1523  if (!(*u)->GetParentOfType(&molecule)) continue;
1524 
1525  const Residue::AtomInfoMap& atomInfos = (*u)->GetAtomInfos();
1526  Residue::AtomInfoMap::const_iterator a, ae = atomInfos.end();
1527  for (a=atomInfos.begin(); a!=ae; ++a) {
1528  const AtomCoord *uAtomCoord = coordSets.front()->atomSet->
1529  GetAtom(AtomPntr(molecule->id, (*u)->id, a->first), true, true);
1530  if (!uAtomCoord) continue;
1531 
1532  // for each unhighlighted atom, check for proximity to a highlighted atom
1533  for (h=highlightedAtoms.begin(); h!=he; ++h) {
1534  if ((uAtomCoord->site - (*h)->site).length() <= cutoff)
1535  break;
1536  }
1537  if (h != he)
1538  break;
1539  }
1540 
1541  // if any atom of this residue is near a highlighted atom, add to selection list
1542  if (a != ae)
1543  (*selectedResidues)[*u] = molecule;
1544  }
1545 }
1546 
1547 END_SCOPE(Cn3D)
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
list< const CSeq_align * > SeqAlignList
bool HasDataChanged(void) const
bool GetCDDNotes(TextLines *lines) const
void SetUserAnnotations(ncbi::objects::CCn3d_user_annotations &annots)
bool SetCDDDescription(const std::string &descr)
const ncbi::objects::CBiostruc * GetMasterStructure(void) const
void ReplaceUpdates(UpdateAlignList &newUpdates)
void SetStyleDictionary(ncbi::objects::CCn3d_style_dictionary &styles)
void SetDataUnchanged(void) const
bool SetCDDNotes(const TextLines &lines)
const ncbi::objects::CCn3d_user_annotations * GetUserAnnotations(void) const
const UpdateAlignList * GetUpdates(void) const
unsigned int GetDataChanged(void) const
bool ConvertMimeDataToCDD(const std::string &cddName)
ncbi::objects::CAlign_annot_set * GetCDDAnnotSet(void)
std::list< const Sequence * > SequenceList
bool WriteDataToFile(const char *filename, bool isBinary, std::string *err, ncbi::EFixNonPrint fixNonPrint=ncbi::eFNP_Default) const
void SetStructureAlignments(ncbi::objects::CBiostruc_annot_set *structureAlignments)
ncbi::objects::EModel_type GetBiostrucModelType(void) const
bool AddBiostrucToASN(ncbi::objects::CBiostruc *biostruc)
SeqAnnotList * GetSequenceAlignments(void) const
bool IsSingleStructure(void) const
const ncbi::objects::CSeq_id * GetCDDMaster3d(void) const
const ncbi::objects::CCn3d_style_dictionary * GetStyleDictionary(void) const
void RemoveUserAnnotations(void)
bool IsCDDInMime(void) const
bool SetCDDName(const std::string &name)
void SetDataChanged(unsigned int what) const
const std::string & GetCDDName(void) const
const std::string & GetCDDDescription(void) const
void AddReject(ncbi::objects::CReject_id *reject)
ncbi::objects::CBiostruc_annot_set * GetStructureAlignments(void) const
const BiostrucList * GetStructureList(void) const
void RemoveStyleDictionary(void)
bool MonitorAlignments(void) const
ncbi::objects::CCdd_descr_set * GetCDDDescrSet(void)
const StructureSet::RejectList * GetRejects(void) const
std::list< ncbi::CRef< ncbi::objects::CSeq_annot > > SeqAnnotList
SeqEntryList * GetSequences(void) const
bool IsGeneralMime(void) const
bool IsCDD(void) const
void RemoveUnusedSequences(const AlignmentSet *alignmentSet, const SequenceList &updateSequences)
SeqAnnotList * GetOrCreateSequenceAlignments(void)
void PurgeSequence(const MoleculeIdentifier *identifier)
void GetUpdateSequences(std::list< const Sequence * > *updateSequences) const
const BlockMultipleAlignment * GetCurrentMultipleAlignment(void) const
AlignmentList alignments
SeqAnnotList * newAsnAlignmentData
const Sequence * master
Vector site
Definition: atom_set.hpp:62
std::vector< const UngappedAlignedBlock * > UngappedAlignedBlockList
const Sequence * GetSequenceOfRow(unsigned int row) const
void GetUngappedAlignedBlocks(UngappedAlignedBlockList *blocks) const
bool IsAligned(unsigned int row, unsigned int seqIndex) const
CBiostruc_annot_set –.
CBiostruc_feature_id –.
CBiostruc_feature_set –.
CBiostruc_feature –.
CBiostruc_id –.
Definition: Biostruc_id.hpp:66
Definition: Cdd.hpp:51
CChem_graph_alignment –.
CChem_graph_pntrs –.
CCn3d_style_dictionary –.
CCn3d_user_annotations –.
CMmdb_id –.
Definition: Mmdb_id.hpp:66
CMove –.
Definition: Move.hpp:66
CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:
Definition: ncbistre.hpp:802
CReject_id –.
Definition: Reject_id.hpp:66
CResidue_interval_pntr –.
CResidue_pntrs –.
CRot_matrix –.
Definition: Rot_matrix.hpp:66
Definition: Seq_entry.hpp:56
CTrans_matrix –.
CTransform –.
Definition: Transform.hpp:66
CUpdate_comment –.
MoleculeMap molecules
double m[16]
void SequenceWindowsSave(bool prompt)
Definition: messenger.cpp:183
bool RemoveAllHighlights(bool postRedraws)
Definition: messenger.cpp:393
void ToggleHighlight(const Molecule *molecule, int residueID, bool scrollViewersTo=false)
Definition: messenger.cpp:380
bool MatchesSeqId(const ncbi::objects::CSeq_id &sid) const
static void ClearIdentifiers(void)
static const int VALUE_NOT_SET
bool HasStructure(void) const
std::string ToString(void) const
std::vector< int > residueDomains
Definition: molecule.hpp:105
int id
Definition: molecule.hpp:84
static const int NO_DOMAIN_SET
Definition: molecule.hpp:98
bool IsHeterogen(void) const
Definition: molecule.hpp:119
const MoleculeIdentifier * identifier
Definition: molecule.hpp:86
bool IsSolvent(void) const
Definition: molecule.hpp:118
ResidueMap residues
Definition: molecule.hpp:89
void CenterView(const Vector &viewCenter, double radius)
bool LoadFromASNViewSettings(const ncbi::objects::CCn3d_user_annotations &annotations)
static const unsigned int NO_NAME
bool SaveToASNViewSettings(ncbi::objects::CCn3d_user_annotations *annotations)
static const unsigned int FIRST_LIST
static const unsigned int NO_LIST
std::string namePDB
Definition: residue.hpp:74
int id
Definition: residue.hpp:69
const AtomInfo * GetAtomInfo(int aID) const
Definition: residue.hpp:128
static const int NO_ALPHA_ID
Definition: residue.hpp:75
std::map< int, const AtomInfo * > AtomInfoMap
Definition: residue.hpp:115
std::string nameGraph
Definition: residue.hpp:73
const Sequence * FindMatchingSequence(const ncbi::objects::CBioseq::TId &ids) const
SequenceList sequences
Definition: cav_seqset.hpp:73
const Molecule * molecule
const MoleculeIdentifier * identifier
unsigned int Length(void) const
CConstRef< objects::CBioseq > bioseqASN
Definition: cav_seqset.hpp:90
void ConstructShowHideArray(const StructureSet *structureSet)
void ShowAlignedOrAnnotatedDomains(const StructureSet *set)
StructureSet * parentSet
bool GetParentOfType(const T **ptr, bool warnIfNotFound=true) const
bool SetTransformToMaster(const ncbi::objects::CBiostruc_annot_set &annot, int masterMMDBID)
void RealignStructure(int nCoords, const Vector *const *masterCoords, const Vector *const *dependentCoords, const double *weights, int dependentRow)
void SelectByDistance(double cutoff, unsigned int options, ResidueMap *selectedResidues) const
StructureObject(StructureBase *parent, const ncbi::objects::CBiostruc &biostruc, bool isMaster)
static const double NO_TEMPERATURE
std::vector< std::string > pdbIDs
CoordSetList coordSets
Matrix * transformToMaster
std::string GetPDBID(char separator='_') const
const ChemicalGraph * graph
DomainIDMap domainID2MMDB
std::map< const Residue *, const Molecule * > ResidueMap
bool IsDependent(void) const
static const int NO_MMDB_ID
bool IsCDDInMime(void) const
FrameMap frameMap
bool AddBiostrucToASN(ncbi::objects::CBiostruc *biostruc)
const AlignmentSet * alignmentSet
bool IsCDD(void) const
static const unsigned int eRowOrderData
std::vector< std::string > TextLines
const RejectList * GetRejects(void) const
void ShowRejects(void) const
std::map< const ncbi::objects::CBiostruc *, bool > usedStructures
bool Draw(const AtomSet *atomSet) const
void SetCenter(const Vector *setTo=NULL)
static const unsigned int eUserAnnotationData
void SelectByDistance(double cutoff, unsigned int options) const
void InitStructureAlignments(int masterMMDBID)
ObjectList objects
unsigned int lastDisplayList
const Sequence * FindOrCreateSequence(ncbi::objects::CBioseq &bioseq)
static const unsigned int eAnyAlignmentData
unsigned int lastAtomName
ncbi::objects::CCdd_descr_set * GetCDDDescrSet(void)
const SequenceSet * sequenceSet
bool SetCDDDescription(const std::string &descr)
static const unsigned int eSelectProtein
void RemoveUnusedSequences(void)
static const unsigned int eSequenceData
bool havePrevPickedAtomCoord
void ReplaceAlignmentSet(AlignmentSet *newAlignmentSet)
void LoadAlignmentsAndStructures(unsigned int structureLimit)
static const unsigned int eSelectNucleotide
void CenterViewOnStructure(void)
bool MatchSequenceToMoleculeInObject(const Sequence *seq, const StructureObject *obj, const Sequence **seqHandle=NULL)
static const unsigned int eSelectHeterogen
static const unsigned int eCDDData
bool IsMultiStructure(void) const
bool SaveASNData(const char *filename, bool doBinary, unsigned int *changeFlags)
bool LoadMaster(int masterMMDBID)
bool CenterViewOnAlignedResidues(void)
std::map< int, bool > usedFeatures
bool SetCDDName(const std::string &name)
void SelectedAtom(unsigned int name, bool setCenter)
void AddStructureAlignment(ncbi::objects::CBiostruc_feature *feature, int masterDomainID, int dependentDomainID)
Vector rotationCenter
bool SetCDDNotes(const TextLines &lines)
bool MonitorAlignments(void) const
void RemoveStructureAlignments(void)
Vector prevPickedAtomCoord
AlignmentManager * alignmentManager
void LoadSequencesForSingleStructure(void)
unsigned int CreateName(const Residue *residue, int atomID)
ShowHideManager * showHideManager
bool ConvertMimeDataToCDD(const std::string &cddName)
static const unsigned int eOtherData
bool HasStructuredMaster(void) const
static const unsigned int eUpdateData
static const unsigned int eStructureAlignmentData
void ReplaceUpdates(ncbi::objects::CCdd::TPending &newUpdates)
static const unsigned int eStyleData
void VerifyFrameMap(void) const
const std::string & GetCDDName(void) const
OpenGLRenderer * renderer
void RejectAndPurgeSequence(const Sequence *reject, std::string reason, bool purge)
void SetDataChanged(unsigned int what) const
bool HasDataChanged(void) const
static const unsigned int eSelectSolvent
StructureSet(ncbi::objects::CNcbi_mime_asn1 *mime, unsigned int structureLimit, OpenGLRenderer *r)
void Load(unsigned int structureLimit)
StyleManager * styleManager
ASNDataManager * dataManager
static const unsigned int eSelectOtherMoleculesOnly
ncbi::objects::CAlign_annot_set * GetCDDAnnotSet(void)
const std::string & GetCDDDescription(void) const
double maxDistFromCenter
bool GetAtomFromName(unsigned int name, const Residue **residue, int *atomID) const
static const unsigned int ePSSMData
std::list< ncbi::CRef< ncbi::objects::CReject_id > > RejectList
bool GetCDDNotes(TextLines *lines) const
bool LoadFromASNStyleDictionary(const ncbi::objects::CCn3d_style_dictionary &styleDictionary)
ncbi::objects::CCn3d_style_dictionary * CreateASNStyleDictionary(void) const
bool SaveToASNUserAnnotations(ncbi::objects::CCn3d_user_annotations *annotations) const
bool LoadFromASNUserAnnotations(const ncbi::objects::CCn3d_user_annotations &annotations)
bool CheckGlobalStyleSettings(void)
double y
Definition: vector_math.hpp:47
double x
Definition: vector_math.hpp:47
virtual size_t size() const
Definition: njn_vector.hpp:304
double z
Definition: vector_math.hpp:47
void Set(double xs, double ys, double zs)
Definition: vector_math.hpp:62
Definition: map.hpp:338
CNcbi_mime_asn1 * LoadStructureViaCache(const std::string &uid, ncbi::objects::EModel_type modelType, int assemblyId)
Definition: cn3d_cache.cpp:255
#define TRACEMSG(stream)
Definition: cn3d_tools.hpp:83
#define INFOMSG(stream)
Definition: cn3d_tools.hpp:84
#define WARNINGMSG(stream)
Definition: cn3d_tools.hpp:85
#define ERRORMSG(stream)
Definition: cn3d_tools.hpp:86
Include a standard set of the NCBI C++ Toolkit most basic headers.
static const char si[8][64]
Definition: des.c:146
static const char location[]
Definition: config.c:97
string
Definition: cgiapp.hpp:687
#define NULL
Definition: ncbistd.hpp:225
@ eFNP_Replace
replace with '#' silently
Definition: serialdef.hpp:176
TObjectType * GetPointer(void) THROWS_NONE
Get pointer,.
Definition: ncbiobj.hpp:998
TObjectType & GetObject(void) const
Get object.
Definition: ncbiobj.hpp:1697
bool Empty(void) const THROWS_NONE
Check if CRef is empty – not pointing to any object, which means having a null value.
Definition: ncbiobj.hpp:719
#define kMin_Double
Definition: ncbi_limits.h:207
#define END_SCOPE(ns)
End the previously defined scope.
Definition: ncbistl.hpp:75
#define BEGIN_SCOPE(ns)
Define a new scope.
Definition: ncbistl.hpp:72
static string IntToString(int value, TNumToStringFlags flags=0, int base=10)
Convert int to string.
Definition: ncbistr.hpp:5084
void SetScale_factor(TScale_factor value)
Assign a value to Scale_factor data member.
TBiostruc_ids & SetBiostruc_ids(void)
Assign a value to Biostruc_ids data member.
TAlignment & SetAlignment(void)
Assign a value to Alignment data member.
TRot_23 GetRot_23(void) const
Get the Rot_23 member data.
void SetName(const TName &value)
Assign a value to Name data member.
TInterval & SetInterval(void)
Select the variant.
void SetRot_33(TRot_33 value)
Assign a value to Rot_33 data member.
void SetMolecule_id(const TMolecule_id &value)
Assign a value to Molecule_id data member.
void SetRot_32(TRot_32 value)
Assign a value to Rot_32 data member.
void SetTo(const TTo &value)
Assign a value to To data member.
TRot_22 GetRot_22(void) const
Get the Rot_22 member data.
TTransform & SetTransform(void)
Assign a value to Transform data member.
bool IsSetTransform(void) const
Check if a value has been assigned to Transform data member.
TDimension GetDimension(void) const
Get the Dimension member data.
void SetRot_22(TRot_22 value)
Assign a value to Rot_22 data member.
void SetId(const TId &value)
Assign a value to Id data member.
TTran_1 GetTran_1(void) const
Get the Tran_1 member data.
void SetScale_factor(TScale_factor value)
Assign a value to Scale_factor data member.
TRot_32 GetRot_32(void) const
Get the Rot_32 member data.
TRot_21 GetRot_21(void) const
Get the Rot_21 member data.
const TTransform & GetTransform(void) const
Get the Transform member data.
TRot_13 GetRot_13(void) const
Get the Rot_13 member data.
TTran_2 GetTran_2(void) const
Get the Tran_2 member data.
void SetRot_11(TRot_11 value)
Assign a value to Rot_11 data member.
TScale_factor GetScale_factor(void) const
Get the Scale_factor member data.
void SetTran_2(TTran_2 value)
Assign a value to Tran_2 data member.
void SetRot_21(TRot_21 value)
Assign a value to Rot_21 data member.
TTran_3 GetTran_3(void) const
Get the Tran_3 member data.
void SetId(TId value)
Assign a value to Id data member.
Definition: Transform_.hpp:224
void SetRot_13(TRot_13 value)
Assign a value to Rot_13 data member.
void SetDimension(TDimension value)
Assign a value to Dimension data member.
void SetRot_23(TRot_23 value)
Assign a value to Rot_23 data member.
TRot_12 GetRot_12(void) const
Get the Rot_12 member data.
TMoves & SetMoves(void)
Assign a value to Moves data member.
Definition: Transform_.hpp:261
void SetTran_1(TTran_1 value)
Assign a value to Tran_1 data member.
void SetType(TType value)
Assign a value to Type data member.
const TBiostruc_ids & GetBiostruc_ids(void) const
Get the Biostruc_ids member data.
TScale_factor GetScale_factor(void) const
Get the Scale_factor member data.
void SetTran_3(TTran_3 value)
Assign a value to Tran_3 data member.
TResidues & SetResidues(void)
Select the variant.
TRot_11 GetRot_11(void) const
Get the Rot_11 member data.
void SetRot_31(TRot_31 value)
Assign a value to Rot_31 data member.
void SetFrom(const TFrom &value)
Assign a value to From data member.
TRot_33 GetRot_33(void) const
Get the Rot_33 member data.
TRotate & SetRotate(void)
Select the variant.
Definition: Move_.cpp:108
TTranslate & SetTranslate(void)
Select the variant.
Definition: Move_.cpp:130
const TAlignment & GetAlignment(void) const
Get the Alignment member data.
TRot_31 GetRot_31(void) const
Get the Rot_31 member data.
void SetRot_12(TRot_12 value)
Assign a value to Rot_12 data member.
void SetLocation(TLocation &value)
Assign a value to Location data member.
@ eType_alignment
VAST reserved.
@ eModel_type_ncbi_backbone
Definition: Model_type_.hpp:65
@ eModel_type_ncbi_vector
Definition: Model_type_.hpp:64
@ eModel_type_other
Definition: Model_type_.hpp:68
const TFeatures & GetFeatures(void) const
Get the Features member data.
Definition: Biostruc_.hpp:406
TDescr & SetDescr(void)
Assign a value to Descr data member.
TId & SetId(void)
Assign a value to Id data member.
TFeatures & SetFeatures(void)
Assign a value to Features data member.
const TFeatures & GetFeatures(void) const
Get the Features member data.
TMmdb_id & SetMmdb_id(void)
Select the variant.
const TId & GetId(void) const
Get the Id member data.
Definition: Biostruc_.hpp:326
const TModel & GetModel(void) const
Get the Model member data.
Definition: Biostruc_.hpp:431
const TChemical_graph & GetChemical_graph(void) const
Get the Chemical_graph member data.
Definition: Biostruc_.hpp:376
const TDescr & GetDescr(void) const
Get the Descr member data.
Definition: Biostruc_.hpp:351
bool IsSetDescr(void) const
Check if a value has been assigned to Descr data member.
Definition: Biostruc_.hpp:339
bool IsSetModel(void) const
Check if a value has been assigned to Model data member.
Definition: Biostruc_.hpp:419
TComment & SetComment(void)
Select the variant.
TIds & SetIds(void)
Assign a value to Ids data member.
Definition: Reject_id_.hpp:234
TDescription & SetDescription(void)
Assign a value to Description data member.
Definition: Reject_id_.hpp:209
bool IsSetView(void) const
Check if a value has been assigned to View data member.
bool IsSetAnnotations(void) const
Check if a value has been assigned to Annotations data member.
TSeq & SetSeq(void)
Select the variant.
Definition: Seq_entry_.cpp:108
int i
yy_size_t n
Messenger * GlobalMessenger(void)
Definition: messenger.cpp:73
range(_Ty, _Ty) -> range< _Ty >
unsigned int a
Definition: ncbi_localip.c:102
ESERV_Site site
The NCBI C++/STL use hints.
NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.
bool le(T x_, T y_, T round_)
Definition: njn_approx.hpp:84
bool ne(T x_, T y_, T round_)
Definition: njn_approx.hpp:82
double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)
double f(double x_, const double &y_)
Definition: njn_root.hpp:188
#define row(bind, expected)
Definition: string_bind.c:73
std::string name
Definition: residue.hpp:97
static DP_BlockInfo * blocks
USING_SCOPE(objects)
static const int MULTI_DOMAIN
static void AddDomain(int *domain, const Molecule *molecule, const Block::Range *range)
static void SetStructureRowFlags(const AlignmentSet *alignmentSet, unsigned int *structureLimit, vector< bool > *dontLoadRowStructure)
static const int NO_DOMAIN
USING_NCBI_SCOPE
double ComputeRMSD(int nCoords, const Vector *const *masterCoords, const Vector *const *dependentCoords, const Matrix *transformDependentToMaster)
void ComposeInto(Matrix *C, const Matrix &A, const Matrix &B)
void SetTranslationMatrix(Matrix *m, const Vector &v, int n)
Definition: vector_math.cpp:45
void ApplyTransformation(Vector *v, const Matrix &m)
Definition: vector_math.cpp:91
void RigidBodyFit(int natx, const Vector *const *xref, const Vector *const *xvar, const double *weights, Vector &cgref, Vector &cgvar, Matrix &rotMat)
Modified on Thu Apr 11 15:21:27 2024 by modify_doxy.py rev. 669887