mirror of
https://github.com/schrodinger/pymol-open-source.git
synced 2026-06-04 20:04:21 +08:00
8bf29abf88
* fix isosurface all_states rendering * pdb_hetatm_guess_valences for CIF loading * mutagenesis wizard: improve "apply" performance * fix measurement and alignment object partial PSE loading * some load/save refactoring * keep atom IDs when creating object from selection * when renaming group "A" to "B", then also rename entry "A.X" to "B.X"
1379 lines
42 KiB
C++
1379 lines
42 KiB
C++
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/*
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A* -------------------------------------------------------------------
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B* This file contains source code for the PyMOL computer program
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C* copyright 1998-2006 by Warren Lyford Delano of DeLano Scientific.
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D* -------------------------------------------------------------------
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E* It is unlawful to modify or remove this copyright notice.
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F* -------------------------------------------------------------------
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G* Please see the accompanying LICENSE file for further information.
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H* -------------------------------------------------------------------
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I* Additional authors of this source file include:
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-*
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-*
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-*
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Z* -------------------------------------------------------------------
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*/
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#include"os_python.h"
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#include"os_predef.h"
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#include"os_std.h"
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#include"os_gl.h"
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#include"OOMac.h"
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#include"ObjectAlignment.h"
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#include"Base.h"
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#include"MemoryDebug.h"
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#include"CGO.h"
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#include"Scene.h"
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#include"Setting.h"
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#include"PConv.h"
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#include"main.h"
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#include"Color.h"
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#include"Executive.h"
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#include"OVContext.h"
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#include"Util.h"
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#include"Selector.h"
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#include"Seq.h"
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#include"Seeker.h"
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#include"ShaderMgr.h"
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/*
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just so you don't forget...
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alignment vlas are zero-separated lists of groups of unique atom identifiers
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*/
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static ObjectAlignment *ObjectAlignmentNew(PyMOLGlobals * G);
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static void ObjectAlignmentFree(ObjectAlignment * I);
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void ObjectAlignmentUpdate(ObjectAlignment * I);
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static int GroupOrderKnown(ExecutiveObjectOffset * eoo,
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OVOneToOne * id2eoo,
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int *curVLA,
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int *newVLA,
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int cur_start,
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int new_start, ObjectMolecule * guide, int *action)
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{
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int order_known = false;
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if(guide) {
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int c, id;
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OVreturn_word offset;
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int cur_offset = -1;
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int new_offset = -1;
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/* find lowest offset within the cur group */
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c = cur_start;
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while((id = curVLA[c++])) {
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if(OVreturn_IS_OK(offset = OVOneToOne_GetForward(id2eoo, id))) {
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if(eoo[offset.word].obj == guide) {
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if((cur_offset < 0) || (eoo[offset.word].offset < cur_offset))
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cur_offset = eoo[offset.word].offset;
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}
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}
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}
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/* find lowest offset within the new group */
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c = new_start;
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while((id = newVLA[c++])) {
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if(OVreturn_IS_OK(offset = OVOneToOne_GetForward(id2eoo, id))) {
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if(eoo[offset.word].obj == guide) {
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if((new_offset < 0) || (eoo[offset.word].offset < new_offset))
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new_offset = eoo[offset.word].offset;
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}
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}
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}
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if((new_offset >= 0) && (cur_offset >= 0)) {
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if(new_offset < cur_offset) {
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order_known = true;
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*action = -1;
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} else if(new_offset > cur_offset) {
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order_known = true;
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*action = 1;
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}
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}
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}
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return order_known;
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}
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static int AlignmentFindTag(PyMOLGlobals * G, AtomInfoType * ai, int sele,
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int n_more_plus_one)
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{
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int result = 0; /* default -- no tag */
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AtomInfoType *ai0 = ai;
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while(1) {
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int tag = SelectorIsMember(G, ai0->selEntry, sele);
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if(tag && (ai0->flags & cAtomFlag_guide)) /* use guide atom if present */
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return tag;
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if(result < tag) {
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if(!result)
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result = tag;
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else if(ai0->flags & cAtomFlag_guide) /* residue based and on guide atom */
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result = tag;
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}
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n_more_plus_one--;
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if(n_more_plus_one > 0) {
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ai0++;
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if(!AtomInfoSameResidueP(G, ai, ai0))
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break;
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} else
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break;
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}
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return result;
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}
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int ObjectAlignmentAsStrVLA(PyMOLGlobals * G, ObjectAlignment * I, int state, int format,
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char **str_vla)
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{
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int ok = true;
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ov_size len = 0;
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char *vla = VLAlloc(char, 1000);
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int force_update = false;
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int active_only = false;
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int max_name_len = 12; /* default indentation */
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if(state < 0)
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state = ObjectGetCurrentState(&I->Obj, false);
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if(state < 0)
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state = SceneGetState(G);
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if((state >= 0) && (state < I->NState)) {
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ObjectAlignmentState *oas = I->State + state;
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if(oas->alignVLA) {
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if(state != I->SelectionState) { /* get us a selection for the current state */
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I->ForceState = state;
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force_update = true;
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ObjectAlignmentUpdate(I);
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}
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switch (format) {
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case 0: /* aln */
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UtilConcatVLA(&vla, &len, "CLUSTAL\n\n");
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break;
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}
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{
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int align_sele = SelectorIndexByName(G, I->Obj.Name);
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if(align_sele >= 0) {
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int nRow = 0;
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ov_size nCol = 0;
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CSeqRow *row_vla = NULL, *row;
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char *cons_str = NULL;
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void *hidden = NULL;
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ObjectMolecule *obj;
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if(align_sele < 0) {
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align_sele = ExecutiveGetActiveAlignmentSele(G);
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}
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if(align_sele >= 0) {
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row_vla = VLACalloc(CSeqRow, 10);
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/* first, find out which objects are included in the
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alignment and count the name length */
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while(ExecutiveIterateObjectMolecule(G, &obj, &hidden)) {
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if((obj->Obj.Enabled || !active_only) && (obj->Obj.Name[0] != '_')) {
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int a;
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AtomInfoType *ai = obj->AtomInfo;
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for(a = 0; a < obj->NAtom; a++) {
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if(SelectorIsMember(G, ai->selEntry, align_sele)) {
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int name_len = strlen(obj->Obj.Name);
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if(max_name_len < name_len)
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max_name_len = name_len;
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VLACheck(row_vla, CSeqRow, nRow);
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row = row_vla + nRow;
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row->obj = obj;
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row->nCol = obj->NAtom;
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nRow++;
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break;
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}
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ai++;
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}
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}
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}
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/* next, figure out how many total columns exist */
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{
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int done = false;
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while(!done) {
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int a;
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int min_tag = -1;
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int untagged_col = false;
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done = true;
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for(a = 0; a < nRow; a++) {
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row = row_vla + a;
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while(row->cCol < row->nCol) { /* advance to next tag in each row & find lowest */
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AtomInfoType *ai = row->obj->AtomInfo + row->cCol;
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done = false;
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if(AtomInfoSameResidueP(G, row->last_ai, ai)) {
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row->cCol++;
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} else if(!SeekerGetAbbr(G, ai->resn, 0, 0)) { /* not a known residue type */
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row->cCol++;
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} else {
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int tag =
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AlignmentFindTag(G, ai, align_sele, row->nCol - row->cCol);
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if(tag) { /* we're at a tagged atom... */
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if(min_tag > tag)
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min_tag = tag;
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else if(min_tag < 0)
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min_tag = tag;
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break;
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} else {
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untagged_col = true;
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break;
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}
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}
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}
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if(untagged_col)
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break;
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}
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if(untagged_col) {
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nCol++;
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/* increment all untagged atoms */
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for(a = 0; a < nRow; a++) {
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row = row_vla + a;
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if(row->cCol < row->nCol) {
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AtomInfoType *ai = row->obj->AtomInfo + row->cCol;
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int tag =
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AlignmentFindTag(G, ai, align_sele, row->nCol - row->cCol);
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if(!tag) {
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row->last_ai = ai;
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row->cCol++;
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}
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}
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}
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} else if(min_tag >= 0) {
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/* increment all matching tagged atoms */
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nCol++;
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for(a = 0; a < nRow; a++) {
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row = row_vla + a;
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if(row->cCol < row->nCol) {
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AtomInfoType *ai = row->obj->AtomInfo + row->cCol;
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int tag =
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AlignmentFindTag(G, ai, align_sele, row->nCol - row->cCol);
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if(tag == min_tag) { /* advance past this tag */
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row->cCol++;
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row->last_ai = ai;
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}
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}
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}
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}
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}
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}
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/* allocate storage for the sequence alignment */
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cons_str = Calloc(char, nCol + 1); /* conservation string */
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{
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int a;
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for(a = 0; a < nRow; a++) {
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row = row_vla + a;
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row->txt = Calloc(char, nCol + 1);
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row->len = 0;
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row->last_ai = NULL;
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row->cCol = 0;
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}
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}
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nCol = 0;
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{
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int done = false;
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while(!done) {
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int a;
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int min_tag = -1;
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int untagged_col = false;
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done = true;
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for(a = 0; a < nRow; a++) {
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row = row_vla + a;
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while(row->cCol < row->nCol) { /* advance to next tag in each row & find lowest */
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AtomInfoType *ai = row->obj->AtomInfo + row->cCol;
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done = false;
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if(AtomInfoSameResidueP(G, row->last_ai, ai)) {
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row->cCol++;
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} else if(!SeekerGetAbbr(G, ai->resn, 0, 0)) { /* not a known residue type */
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row->cCol++;
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} else {
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int tag =
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AlignmentFindTag(G, ai, align_sele, row->nCol - row->cCol);
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if(tag) { /* we're at a tagged atom... */
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if(min_tag > tag)
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min_tag = tag;
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else if(min_tag < 0)
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min_tag = tag;
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break;
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} else {
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untagged_col = true;
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break;
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}
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}
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}
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}
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if(untagged_col) {
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/* increment all untagged atoms */
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for(a = 0; a < nRow; a++) {
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row = row_vla + a;
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if(row->cCol < row->nCol) {
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AtomInfoType *ai = row->obj->AtomInfo + row->cCol;
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int tag =
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AlignmentFindTag(G, ai, align_sele, row->nCol - row->cCol);
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if(!tag) {
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if(!AtomInfoSameResidueP(G, row->last_ai, ai)) {
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row->last_ai = ai;
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row->txt[row->len] = SeekerGetAbbr(G, ai->resn, ' ', 'X');
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} else {
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row->txt[row->len] = '-';
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}
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row->len++;
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row->cCol++;
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} else {
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row->txt[row->len] = '-';
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row->len++;
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}
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} else {
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row->txt[row->len] = '-';
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row->len++;
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}
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}
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cons_str[nCol] = ' ';
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nCol++;
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} else if(min_tag >= 0) {
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char cons_abbr = ' ';
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int abbr_cnt = 0;
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/* increment all matching tagged atoms */
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for(a = 0; a < nRow; a++) {
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row = row_vla + a;
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if(row->cCol < row->nCol) {
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AtomInfoType *ai = row->obj->AtomInfo + row->cCol;
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int tag =
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AlignmentFindTag(G, ai, align_sele, row->nCol - row->cCol);
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if(tag == min_tag) { /* advance past this tag */
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char abbr;
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if(!AtomInfoSameResidueP(G, row->last_ai, ai)) {
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row->last_ai = ai;
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abbr = SeekerGetAbbr(G, ai->resn, ' ', 'X');
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if(cons_abbr == ' ')
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cons_abbr = abbr;
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else if(cons_abbr != abbr)
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cons_abbr = 0;
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abbr_cnt++;
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} else {
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abbr = '-';
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cons_abbr = 0;
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}
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row->txt[row->len] = abbr;
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row->len++;
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row->cCol++;
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} else {
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cons_abbr = 0;
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row->txt[row->len] = '-';
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row->len++;
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}
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} else {
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cons_abbr = 0;
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row->txt[row->len] = '-';
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row->len++;
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}
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}
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if(abbr_cnt > 1) {
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if(cons_abbr)
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cons_str[nCol] = '*'; /* aligned and identical */
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else
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cons_str[nCol] = '.'; /* aligned but not identical */
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} else
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cons_str[nCol] = ' ';
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nCol++;
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}
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}
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}
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{
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int block_width = 76 - (max_name_len + 1);
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int done = false;
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ov_size seq_len = 0;
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int a;
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while(!done) {
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done = true;
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for(a = 0; a < nRow; a++) {
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row = row_vla + a;
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UtilNPadVLA(&vla, &len, row->obj->Obj.Name, max_name_len + 1);
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if(seq_len < row->len) {
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UtilNPadVLA(&vla, &len, row->txt + seq_len, block_width);
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}
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UtilConcatVLA(&vla, &len, "\n");
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}
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if(seq_len < nCol) {
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UtilNPadVLA(&vla, &len, "", max_name_len + 1);
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UtilNPadVLA(&vla, &len, cons_str + seq_len, block_width);
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UtilConcatVLA(&vla, &len, "\n");
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}
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seq_len += block_width;
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for(a = 0; a < nRow; a++) {
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row = row_vla + a;
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if(seq_len < row->len) {
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done = false;
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break;
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}
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}
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UtilConcatVLA(&vla, &len, "\n");
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}
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}
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}
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/* free up resources */
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if(row_vla) {
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int a;
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for(a = 0; a < nRow; a++) {
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row = row_vla + a;
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FreeP(row->txt);
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}
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}
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FreeP(cons_str);
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VLAFreeP(row_vla);
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}
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}
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}
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}
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if(force_update) {
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ObjectAlignmentUpdate(I);
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}
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VLASize(vla, char, len + 1);
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vla[len] = 0;
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*str_vla = vla;
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return ok;
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}
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static int *AlignmentMerge(PyMOLGlobals * G, int *curVLA, int *newVLA,
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ObjectMolecule * guide, ObjectMolecule * flush)
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{
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/* curVLA and newVLA must be properly sized and zero terminated... */
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int *result = NULL;
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int n_result = 0;
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{
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ExecutiveObjectOffset *eoo = NULL;
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OVOneToOne *id2eoo = NULL;
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if(ExecutiveGetUniqueIDObjectOffsetVLADict(G, &eoo, &id2eoo)) {
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int n_cur = VLAGetSize(curVLA);
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int n_new = VLAGetSize(newVLA);
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/* now we can take unique IDs to specific atoms */
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/* first, go through and eliminate old matching atoms between guide and flush (if any) */
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{
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int cur_start = 0;
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while(cur_start < n_cur) {
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while((cur_start < n_cur) && !curVLA[cur_start]) {
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cur_start++;
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}
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{
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int other_seen = false;
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int flush_seen = false;
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ObjectMolecule *obj;
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{
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int cur = cur_start;
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int id;
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while((id = curVLA[cur])) {
|
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OVreturn_word offset;
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if(OVreturn_IS_OK(offset = OVOneToOne_GetForward(id2eoo, id))) {
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obj = eoo[offset.word].obj;
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if(obj == flush) {
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flush_seen = true;
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} else {
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other_seen++;
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}
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}
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cur++;
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}
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}
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|
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if(flush_seen) { /* eliminate flush atoms */
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int cur = cur_start;
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int id;
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while((id = curVLA[cur])) {
|
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OVreturn_word offset;
|
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if(OVreturn_IS_OK(offset = OVOneToOne_GetForward(id2eoo, id))) {
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obj = eoo[offset.word].obj;
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if(obj == flush) {
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int tmp = cur;
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while(curVLA[tmp]) {
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curVLA[tmp] = curVLA[tmp + 1];
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tmp++;
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}
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}
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}
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cur++;
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}
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}
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|
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if(other_seen < 2) { /* eliminate orphaned atoms */
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int cur = cur_start;
|
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while(curVLA[cur])
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curVLA[cur++] = 0;
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}
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|
|
while(curVLA[cur_start])
|
|
cur_start++;
|
|
while((cur_start < n_cur) && !curVLA[cur_start]) {
|
|
cur_start++;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
/* now combine the alignments */
|
|
|
|
{
|
|
OVOneToAny *used = OVOneToAny_New(G->Context->heap);
|
|
OVOneToAny *active = OVOneToAny_New(G->Context->heap);
|
|
int cur_start = 0;
|
|
int new_start = 0;
|
|
|
|
result = VLAlloc(int, ((n_cur < n_new) ? n_new : n_cur));
|
|
|
|
while((cur_start < n_cur) || (new_start < n_new)) {
|
|
|
|
int action; /* -1 = insert new, 0 = merge, 1 = insert cur */
|
|
|
|
/* make sure both lists are queued up on the next identifier */
|
|
|
|
while((cur_start < n_cur) && !curVLA[cur_start])
|
|
cur_start++;
|
|
while((new_start < n_new) && !newVLA[new_start])
|
|
new_start++;
|
|
|
|
if(newVLA[new_start]) { /* default is to insert new first... */
|
|
action = -1;
|
|
} else {
|
|
action = 1;
|
|
}
|
|
|
|
if((cur_start < n_cur) && (new_start < n_new) &&
|
|
curVLA[cur_start] && newVLA[new_start]) {
|
|
/* both lists active */
|
|
|
|
int c, id;
|
|
int overlapping = false;
|
|
|
|
OVOneToAny_Reset(active);
|
|
c = cur_start;
|
|
while((id = curVLA[c++])) { /* record active atoms */
|
|
OVOneToAny_SetKey(active, id, 1);
|
|
}
|
|
|
|
c = new_start;
|
|
while((id = newVLA[c++])) { /* see if there are any matches */
|
|
if(OVreturn_IS_OK(OVOneToAny_GetKey(active, id))) {
|
|
overlapping = true;
|
|
break;
|
|
}
|
|
}
|
|
|
|
if(overlapping) {
|
|
/* overlapping, so merge */
|
|
action = 0;
|
|
|
|
} else {
|
|
/* non-overlapping, so we need to figure out which goes first... */
|
|
if(!GroupOrderKnown(eoo, id2eoo, curVLA, newVLA,
|
|
cur_start, new_start, guide, &action)) {
|
|
int c, id;
|
|
OVreturn_word offset;
|
|
ObjectMolecule *obj, *last_obj = NULL;
|
|
c = cur_start;
|
|
while((id = curVLA[c++])) {
|
|
|
|
if(OVreturn_IS_OK(offset = OVOneToOne_GetForward(id2eoo, id))) {
|
|
obj = eoo[offset.word].obj;
|
|
if(obj != last_obj) {
|
|
if(GroupOrderKnown(eoo, id2eoo, curVLA, newVLA,
|
|
cur_start, new_start, obj, &action))
|
|
break;
|
|
else
|
|
last_obj = obj;
|
|
}
|
|
}
|
|
}
|
|
|
|
/* if order isn't set by now, then it doesn't matter...
|
|
so group new will go in first */
|
|
}
|
|
}
|
|
}
|
|
|
|
/* check assumptions */
|
|
|
|
if((action < 1) && !(new_start < n_new))
|
|
action = 1;
|
|
else if((action > (-1)) && !(cur_start < n_cur))
|
|
action = -1;
|
|
|
|
/* take action */
|
|
|
|
{
|
|
int id;
|
|
|
|
switch (action) {
|
|
case -1: /* insert new */
|
|
if(new_start < n_new) {
|
|
while((id = newVLA[new_start])) {
|
|
if(OVOneToAny_GetKey(used, id).status == OVstatus_NOT_FOUND) {
|
|
if(OVreturn_IS_OK(OVOneToAny_SetKey(used, id, 1))) {
|
|
VLACheck(result, int, n_result);
|
|
result[n_result] = id;
|
|
n_result++;
|
|
}
|
|
}
|
|
new_start++;
|
|
}
|
|
while((new_start < n_new) && (!newVLA[new_start]))
|
|
new_start++;
|
|
}
|
|
VLACheck(result, int, n_result);
|
|
result[n_result] = 0;
|
|
n_result++;
|
|
break;
|
|
case 0: /* merge, with cur going first */
|
|
if(new_start < n_new) {
|
|
while((id = newVLA[new_start])) {
|
|
if(OVOneToAny_GetKey(used, id).status == OVstatus_NOT_FOUND) {
|
|
if(OVreturn_IS_OK(OVOneToAny_SetKey(used, id, 1))) {
|
|
VLACheck(result, int, n_result);
|
|
result[n_result] = id;
|
|
n_result++;
|
|
}
|
|
}
|
|
new_start++;
|
|
}
|
|
while((new_start < n_new) && (!newVLA[new_start]))
|
|
new_start++;
|
|
}
|
|
if(cur_start < n_cur) {
|
|
while((id = curVLA[cur_start])) {
|
|
if(OVOneToAny_GetKey(used, id).status == OVstatus_NOT_FOUND) {
|
|
if(OVreturn_IS_OK(OVOneToAny_SetKey(used, id, 1))) {
|
|
VLACheck(result, int, n_result);
|
|
result[n_result] = id;
|
|
n_result++;
|
|
}
|
|
}
|
|
cur_start++;
|
|
}
|
|
while((cur_start < n_cur) && (!curVLA[cur_start]))
|
|
cur_start++;
|
|
}
|
|
VLACheck(result, int, n_result);
|
|
result[n_result] = 0;
|
|
n_result++;
|
|
break;
|
|
case 1: /* insert cur */
|
|
if(cur_start < n_cur) {
|
|
while((id = curVLA[cur_start])) {
|
|
if(OVOneToAny_GetKey(used, id).status == OVstatus_NOT_FOUND) {
|
|
if(OVreturn_IS_OK(OVOneToAny_SetKey(used, id, 1))) {
|
|
VLACheck(result, int, n_result);
|
|
result[n_result] = id;
|
|
n_result++;
|
|
}
|
|
}
|
|
cur_start++;
|
|
}
|
|
while((cur_start < n_cur) && (!curVLA[cur_start]))
|
|
cur_start++;
|
|
VLACheck(result, int, n_result);
|
|
result[n_result] = 0;
|
|
n_result++;
|
|
}
|
|
break;
|
|
}
|
|
}
|
|
}
|
|
OVOneToAny_DEL_AUTO_NULL(active);
|
|
OVOneToAny_DEL_AUTO_NULL(used);
|
|
}
|
|
}
|
|
OVOneToOne_DEL_AUTO_NULL(id2eoo);
|
|
VLAFreeP(eoo);
|
|
}
|
|
if(result && n_result && (!result[n_result - 1])) {
|
|
VLACheck(result, int, n_result);
|
|
result[n_result] = 0;
|
|
n_result++;
|
|
}
|
|
VLASize(result, int, n_result);
|
|
return result;
|
|
}
|
|
|
|
#ifndef _PYMOL_NOPY
|
|
static PyObject *ObjectAlignmentStateAsPyList(ObjectAlignmentState * I)
|
|
{
|
|
PyObject *result = NULL;
|
|
|
|
result = PyList_New(2);
|
|
if(I->alignVLA) {
|
|
PyList_SetItem(result, 0, PConvIntVLAToPyList(I->alignVLA));
|
|
} else {
|
|
PyList_SetItem(result, 0, PConvAutoNone(NULL));
|
|
}
|
|
PyList_SetItem(result, 1, PyString_FromString(I->guide));
|
|
return (PConvAutoNone(result));
|
|
}
|
|
|
|
static PyObject *ObjectAlignmentAllStatesAsPyList(ObjectAlignment * I)
|
|
{
|
|
|
|
PyObject *result = NULL;
|
|
int a;
|
|
result = PyList_New(I->NState);
|
|
for(a = 0; a < I->NState; a++) {
|
|
PyList_SetItem(result, a, ObjectAlignmentStateAsPyList(I->State + a));
|
|
}
|
|
return (PConvAutoNone(result));
|
|
|
|
}
|
|
|
|
static int ObjectAlignmentStateFromPyList(PyMOLGlobals * G, ObjectAlignmentState * I,
|
|
PyObject * list, int version)
|
|
{
|
|
int ok = true;
|
|
int ll = 0;
|
|
if(ok)
|
|
ok = (list != NULL);
|
|
if(ok)
|
|
ok = PyList_Check(list);
|
|
if(ok)
|
|
ll = PyList_Size(list);
|
|
/* TO SUPPORT BACKWARDS COMPATIBILITY...
|
|
Always check ll when adding new PyList_GetItem's */
|
|
if(ok && (ll > 1)) {
|
|
PConvPyListToIntVLA(PyList_GetItem(list, 0), &I->alignVLA);
|
|
strcpy(I->guide, PyString_AsString(PyList_GetItem(list, 1)));
|
|
|
|
for (auto it = I->alignVLA, it_end = I->alignVLA + VLAGetSize(I->alignVLA);
|
|
it != it_end; ++it) {
|
|
if (*it)
|
|
*it = SettingUniqueConvertOldSessionID(G, *it);
|
|
}
|
|
}
|
|
return (ok);
|
|
}
|
|
|
|
static int ObjectAlignmentAllStatesFromPyList(ObjectAlignment * I, PyObject * list,
|
|
int version)
|
|
{
|
|
int ok = true;
|
|
int a;
|
|
VLACheck(I->State, ObjectAlignmentState, I->NState);
|
|
if(ok)
|
|
ok = PyList_Check(list);
|
|
if(ok) {
|
|
for(a = 0; a < I->NState; a++) {
|
|
ok =
|
|
ObjectAlignmentStateFromPyList(I->Obj.G, I->State + a, PyList_GetItem(list, a),
|
|
version);
|
|
if(!ok)
|
|
break;
|
|
}
|
|
}
|
|
return (ok);
|
|
}
|
|
#endif
|
|
|
|
int ObjectAlignmentNewFromPyList(PyMOLGlobals * G, PyObject * list,
|
|
ObjectAlignment ** result, int version)
|
|
{
|
|
#ifdef _PYMOL_NOPY
|
|
return 0;
|
|
#else
|
|
|
|
int ok = true;
|
|
ObjectAlignment *I = NULL;
|
|
(*result) = NULL;
|
|
if(ok)
|
|
ok = (list != Py_None);
|
|
if(ok)
|
|
ok = PyList_Check(list);
|
|
|
|
I = ObjectAlignmentNew(G);
|
|
if(ok)
|
|
ok = (I != NULL);
|
|
|
|
if(ok)
|
|
ok = ObjectFromPyList(G, PyList_GetItem(list, 0), &I->Obj);
|
|
if(ok)
|
|
ok = PConvPyIntToInt(PyList_GetItem(list, 1), &I->NState);
|
|
if(ok)
|
|
ok = ObjectAlignmentAllStatesFromPyList(I, PyList_GetItem(list, 2), version);
|
|
if(ok) {
|
|
(*result) = I;
|
|
ObjectAlignmentRecomputeExtent(I);
|
|
} else {
|
|
/* cleanup? */
|
|
}
|
|
return (ok);
|
|
#endif
|
|
}
|
|
|
|
PyObject *ObjectAlignmentAsPyList(ObjectAlignment * I)
|
|
{
|
|
#ifdef _PYMOL_NOPY
|
|
return NULL;
|
|
#else
|
|
|
|
PyObject *result = NULL;
|
|
|
|
result = PyList_New(3);
|
|
PyList_SetItem(result, 0, ObjectAsPyList(&I->Obj));
|
|
PyList_SetItem(result, 1, PyInt_FromLong(I->NState));
|
|
PyList_SetItem(result, 2, ObjectAlignmentAllStatesAsPyList(I));
|
|
|
|
return (PConvAutoNone(result));
|
|
#endif
|
|
}
|
|
|
|
|
|
/*========================================================================*/
|
|
|
|
static void ObjectAlignmentFree(ObjectAlignment * I)
|
|
{
|
|
int a;
|
|
for(a = 0; a < I->NState; a++) {
|
|
if(I->State[a].shaderCGO)
|
|
CGOFree(I->State[a].shaderCGO);
|
|
if(I->State[a].std)
|
|
CGOFree(I->State[a].std);
|
|
if(I->State[a].ray)
|
|
CGOFree(I->State[a].ray);
|
|
VLAFreeP(I->State[a].alignVLA);
|
|
OVOneToAny_DEL_AUTO_NULL(I->State[a].id2tag);
|
|
}
|
|
VLAFreeP(I->State);
|
|
ObjectPurge(&I->Obj);
|
|
OOFreeP(I);
|
|
}
|
|
|
|
|
|
/*========================================================================*/
|
|
|
|
void ObjectAlignmentRecomputeExtent(ObjectAlignment * I)
|
|
{
|
|
float mx[3], mn[3];
|
|
int extent_flag = false;
|
|
int a;
|
|
for(a = 0; a < I->NState; a++)
|
|
if(I->State[a].std) {
|
|
if(CGOGetExtent(I->State[a].std, mn, mx)) {
|
|
if(!extent_flag) {
|
|
extent_flag = true;
|
|
copy3f(mx, I->Obj.ExtentMax);
|
|
copy3f(mn, I->Obj.ExtentMin);
|
|
} else {
|
|
max3f(mx, I->Obj.ExtentMax, I->Obj.ExtentMax);
|
|
min3f(mn, I->Obj.ExtentMin, I->Obj.ExtentMin);
|
|
}
|
|
}
|
|
}
|
|
I->Obj.ExtentFlag = extent_flag;
|
|
}
|
|
|
|
|
|
/*========================================================================*/
|
|
void ObjectAlignmentUpdate(ObjectAlignment * I)
|
|
{
|
|
PyMOLGlobals *G = I->Obj.G;
|
|
int update_needed = false;
|
|
short use_shader = SettingGetGlobal_b(G, cSetting_alignment_as_cylinders) &&
|
|
SettingGetGlobal_b(G, cSetting_render_as_cylinders) &&
|
|
SettingGetGlobal_b(G, cSetting_use_shaders);
|
|
{
|
|
int a;
|
|
for(a = 0; a < I->NState; a++) {
|
|
ObjectAlignmentState *oas = I->State + a;
|
|
if(!oas->valid || (use_shader && !oas->shaderCGO)){
|
|
update_needed = true;
|
|
}
|
|
}
|
|
}
|
|
if(update_needed) {
|
|
ExecutiveObjectOffset *eoo = NULL;
|
|
OVOneToOne *id2eoo = NULL;
|
|
if(ExecutiveGetUniqueIDObjectOffsetVLADict(G, &eoo, &id2eoo)) {
|
|
int a;
|
|
for(a = 0; a < I->NState; a++) {
|
|
ObjectAlignmentState *oas = I->State + a;
|
|
if(!oas->valid || (use_shader && !oas->shaderCGO)){
|
|
ObjectMolecule *guide_obj = NULL;
|
|
if(oas->guide[0]) {
|
|
guide_obj = ExecutiveFindObjectMoleculeByName(G, oas->guide);
|
|
}
|
|
if(I->SelectionState == a)
|
|
I->SelectionState = -1;
|
|
|
|
if(oas->std) {
|
|
CGOFree(oas->std);
|
|
oas->std = NULL;
|
|
}
|
|
if(oas->ray) {
|
|
CGOFree(oas->ray);
|
|
oas->ray = NULL;
|
|
}
|
|
if(oas->id2tag) {
|
|
OVOneToAny_Reset(oas->id2tag);
|
|
} else {
|
|
oas->id2tag = OVOneToAny_New(G->Context->heap);
|
|
}
|
|
|
|
{
|
|
CGO *cgo = CGONew(G);
|
|
|
|
if(oas->alignVLA) {
|
|
int id, b = 0, c;
|
|
int *vla = oas->alignVLA;
|
|
int n_id = VLAGetSize(vla);
|
|
float mean[3], vert[3], gvert[3];
|
|
int n_coord = 0;
|
|
int tag = SELECTOR_BASE_TAG + 1;
|
|
OVOneToAny *id2tag = oas->id2tag;
|
|
OVreturn_word offset;
|
|
|
|
while(b < n_id) {
|
|
|
|
int gvert_valid;
|
|
while((b < n_id) && (!vla[b]))
|
|
b++;
|
|
|
|
if(!(b < n_id))
|
|
break;
|
|
|
|
c = b;
|
|
n_coord = 0;
|
|
gvert_valid = false;
|
|
zero3f(mean);
|
|
while((id = vla[c++])) {
|
|
if(OVreturn_IS_OK(offset = OVOneToOne_GetForward(id2eoo, id))) {
|
|
if(ObjectMoleculeGetAtomVertex(eoo[offset.word].obj, a,
|
|
eoo[offset.word].offset, vert)) {
|
|
n_coord++;
|
|
add3f(vert, mean, mean);
|
|
if(eoo[offset.word].obj == guide_obj) {
|
|
copy3f(vert, gvert);
|
|
gvert_valid = true;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
if(n_coord > 2) { /* >2 points, then draw to mean or guide vertex */
|
|
float scale = 1.0F / n_coord;
|
|
|
|
scale3f(mean, scale, mean);
|
|
|
|
c = b;
|
|
CGOBegin(cgo, GL_LINES);
|
|
while((id = vla[c++])) {
|
|
if(OVreturn_IS_OK(offset = OVOneToOne_GetForward(id2eoo, id))) {
|
|
if(ObjectMoleculeGetAtomVertex(eoo[offset.word].obj, a,
|
|
eoo[offset.word].offset, vert)) {
|
|
if(gvert_valid) {
|
|
if(eoo[offset.word].obj != guide_obj) {
|
|
CGOVertexv(cgo, gvert);
|
|
CGOVertexv(cgo, vert);
|
|
}
|
|
} else {
|
|
CGOVertexv(cgo, mean);
|
|
CGOVertexv(cgo, vert);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
CGOEnd(cgo);
|
|
} else if(n_coord) { /* if 2 points, then simply draw a line */
|
|
float first[3];
|
|
int first_flag = true;
|
|
c = b;
|
|
CGOBegin(cgo, GL_LINES);
|
|
while((id = vla[c++])) {
|
|
if(OVreturn_IS_OK(offset = OVOneToOne_GetForward(id2eoo, id))) {
|
|
if(ObjectMoleculeGetAtomVertex(eoo[offset.word].obj, a,
|
|
eoo[offset.word].offset, vert)) {
|
|
if(first_flag) {
|
|
copy3f(vert, first);
|
|
first_flag = false;
|
|
} else {
|
|
CGOVertexv(cgo, first);
|
|
CGOVertexv(cgo, vert);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
CGOEnd(cgo);
|
|
}
|
|
/* update the it2tag dictionary */
|
|
|
|
tag++;
|
|
|
|
while((b < n_id) && vla[b]) {
|
|
OVOneToAny_SetKey(id2tag, vla[b], tag);
|
|
b++;
|
|
}
|
|
}
|
|
}
|
|
|
|
CGOStop(cgo);
|
|
|
|
/* simplify if necessary */
|
|
|
|
{
|
|
int est = CGOCheckComplex(cgo);
|
|
{
|
|
CGO *convertcgo = NULL;
|
|
if(cgo){
|
|
if(oas->shaderCGO) {
|
|
CGOFree(oas->shaderCGO);
|
|
oas->shaderCGO = NULL;
|
|
}
|
|
oas->shaderCGO = CGOConvertLinesToShaderCylinders(cgo, 0);
|
|
convertcgo = CGOCombineBeginEnd(cgo, 0);
|
|
CGOFree(cgo);
|
|
cgo = convertcgo;
|
|
}
|
|
}
|
|
if(est) {
|
|
oas->ray = cgo;
|
|
oas->std = CGOSimplify(cgo, est);
|
|
} else
|
|
oas->std = cgo;
|
|
}
|
|
}
|
|
oas->valid = true;
|
|
}
|
|
}
|
|
}
|
|
OVOneToOne_DEL_AUTO_NULL(id2eoo);
|
|
VLAFreeP(eoo);
|
|
}
|
|
if(I->SelectionState < 0) {
|
|
int state = -1;
|
|
if(I->ForceState >= 0) {
|
|
state = I->ForceState;
|
|
I->ForceState = 0;
|
|
}
|
|
if(state < 0)
|
|
state = SettingGet_i(I->Obj.G, NULL, I->Obj.Setting, cSetting_state) - 1;
|
|
if(state < 0)
|
|
state = SceneGetState(G);
|
|
if(state > I->NState)
|
|
state = I->NState - 1;
|
|
if(state < 0)
|
|
state = 0;
|
|
if(state < I->NState) {
|
|
ObjectAlignmentState *oas = I->State + state;
|
|
if(oas->id2tag) {
|
|
SelectorDelete(G, I->Obj.Name);
|
|
SelectorCreateFromTagDict(G, I->Obj.Name, oas->id2tag, false);
|
|
I->SelectionState = state;
|
|
}
|
|
}
|
|
}
|
|
SceneInvalidate(I->Obj.G);
|
|
}
|
|
|
|
|
|
/*========================================================================*/
|
|
|
|
static int ObjectAlignmentGetNState(ObjectAlignment * I)
|
|
{
|
|
return (I->NState);
|
|
}
|
|
|
|
|
|
/*========================================================================*/
|
|
|
|
static void ObjectAlignmentRender(ObjectAlignment * I, RenderInfo * info)
|
|
{
|
|
PyMOLGlobals *G = I->Obj.G;
|
|
int state = info->state;
|
|
CRay *ray = info->ray;
|
|
Picking **pick = info->pick;
|
|
int pass = info->pass;
|
|
ObjectAlignmentState *sobj = NULL;
|
|
int a;
|
|
float *color;
|
|
|
|
ObjectPrepareContext(&I->Obj, ray);
|
|
|
|
color = ColorGet(G, I->Obj.Color);
|
|
|
|
if(!pass) {
|
|
if((I->Obj.visRep & cRepCGOBit)) {
|
|
|
|
if(state < I->NState) {
|
|
sobj = I->State + state;
|
|
}
|
|
if(state < 0) {
|
|
if(I->State) {
|
|
for(a = 0; a < I->NState; a++) {
|
|
sobj = I->State + a;
|
|
if(ray) {
|
|
int try_std = false;
|
|
|
|
if(sobj->ray){
|
|
int ok = CGORenderRay(sobj->ray, ray, color, I->Obj.Setting, NULL);
|
|
if (!ok){
|
|
CGOFree(sobj->ray);
|
|
sobj->ray = NULL;
|
|
try_std = true;
|
|
}
|
|
} else {
|
|
try_std = true;
|
|
}
|
|
if (try_std){
|
|
int ok = CGORenderRay(sobj->std, ray, color, I->Obj.Setting, NULL);
|
|
if (!ok){
|
|
CGOFree(sobj->std);
|
|
sobj->std = NULL;
|
|
}
|
|
}
|
|
} else if(G->HaveGUI && G->ValidContext) {
|
|
if(!info->line_lighting)
|
|
glDisable(GL_LIGHTING);
|
|
SceneResetNormal(G, true);
|
|
if(pick) {
|
|
} else {
|
|
if(sobj->std){
|
|
short use_shader = SettingGetGlobal_b(G, cSetting_alignment_as_cylinders) &&
|
|
SettingGetGlobal_b(G, cSetting_render_as_cylinders) &&
|
|
SettingGetGlobal_b(G, cSetting_use_shaders);
|
|
if (use_shader){
|
|
if (!sobj->shaderCGO){
|
|
ObjectAlignmentUpdate(I);
|
|
}
|
|
if (!sobj->shaderCGO->has_draw_cylinder_buffers){
|
|
CGO *convertcgo = sobj->shaderCGO;
|
|
sobj->shaderCGO = CGOOptimizeGLSLCylindersToVBOIndexedNoColor(convertcgo, 0);
|
|
if (sobj->shaderCGO){
|
|
CGOFree(convertcgo);
|
|
} else {
|
|
sobj->shaderCGO = convertcgo;
|
|
}
|
|
sobj->shaderCGO->use_shader = use_shader;
|
|
}
|
|
{
|
|
CShaderPrg *shaderPrg;
|
|
float line_width = SettingGet_f(G, I->Obj.Setting, NULL, cSetting_line_width);
|
|
float radius = SceneGetLineWidthForCylinders(G, info, line_width);
|
|
shaderPrg = CShaderPrg_Enable_CylinderShader(G);
|
|
CShaderPrg_Set1f(shaderPrg, "uni_radius", radius);
|
|
glVertexAttrib4f(CYLINDER_COLOR, color[0], color[1], color[2], 1.f);
|
|
glVertexAttrib4f(CYLINDER_COLOR2, color[0], color[1], color[2], 1.f);
|
|
CGORenderGL(sobj->shaderCGO, color, NULL, NULL, info, NULL);
|
|
CShaderPrg_Disable(shaderPrg);
|
|
return;
|
|
}
|
|
} else {
|
|
CGORenderGL(sobj->std, color, I->Obj.Setting, NULL, info, NULL);
|
|
}
|
|
}
|
|
}
|
|
glEnable(GL_LIGHTING);
|
|
}
|
|
}
|
|
}
|
|
} else {
|
|
if(!sobj) {
|
|
if(I->NState && SettingGetGlobal_b(G, cSetting_static_singletons))
|
|
sobj = I->State;
|
|
}
|
|
if(ray) {
|
|
int try_std = false;
|
|
if(sobj) {
|
|
if(sobj->ray){
|
|
int ok = CGORenderRay(sobj->ray, ray, color, I->Obj.Setting, NULL);
|
|
if (!ok){
|
|
CGOFree(sobj->ray);
|
|
sobj->ray = NULL;
|
|
try_std = true;
|
|
}
|
|
} else {
|
|
try_std = true;
|
|
}
|
|
if (try_std){
|
|
int ok = CGORenderRay(sobj->std, ray, color, I->Obj.Setting, NULL);
|
|
if (!ok){
|
|
CGOFree(sobj->std);
|
|
sobj->std = NULL;
|
|
}
|
|
}
|
|
}
|
|
} else if(G->HaveGUI && G->ValidContext) {
|
|
if(pick) {
|
|
} else {
|
|
if(!info->line_lighting)
|
|
glDisable(GL_LIGHTING);
|
|
SceneResetNormal(G, true);
|
|
if(sobj) {
|
|
if(sobj->std){
|
|
short use_shader = SettingGetGlobal_b(G, cSetting_alignment_as_cylinders) &&
|
|
SettingGetGlobal_b(G, cSetting_render_as_cylinders) &&
|
|
SettingGetGlobal_b(G, cSetting_use_shaders);
|
|
if (use_shader){
|
|
if (!sobj->shaderCGO){
|
|
ObjectAlignmentUpdate(I);
|
|
}
|
|
if (sobj->shaderCGO && !sobj->shaderCGO->has_draw_cylinder_buffers){
|
|
CGO *convertcgo = sobj->shaderCGO;
|
|
sobj->shaderCGO = CGOOptimizeGLSLCylindersToVBOIndexedNoColor(convertcgo, 0);
|
|
if (sobj->shaderCGO){
|
|
CGOFree(convertcgo);
|
|
} else {
|
|
sobj->shaderCGO = convertcgo;
|
|
}
|
|
sobj->shaderCGO->use_shader = use_shader;
|
|
}
|
|
if (sobj->shaderCGO) {
|
|
CShaderPrg *shaderPrg;
|
|
float linewidth = SettingGet_f(G, I->Obj.Setting, NULL, cSetting_cgo_line_width);
|
|
float lineradius = SettingGet_f(G, I->Obj.Setting, NULL, cSetting_cgo_line_radius);
|
|
float pixel_scale_value = SettingGetGlobal_f(G, cSetting_ray_pixel_scale);
|
|
if (linewidth < 0.f){
|
|
linewidth = 1.f;
|
|
}
|
|
if(pixel_scale_value < 0)
|
|
pixel_scale_value = 1.0F;
|
|
if (lineradius < 0.f){
|
|
lineradius = linewidth * info->vertex_scale * pixel_scale_value / 2.f;
|
|
}
|
|
shaderPrg = CShaderPrg_Enable_CylinderShader(G);
|
|
CShaderPrg_Set1f(shaderPrg, "uni_radius", lineradius);
|
|
glVertexAttrib4f(CYLINDER_COLOR, color[0], color[1], color[2], 1.f);
|
|
glVertexAttrib4f(CYLINDER_COLOR2, color[0], color[1], color[2], 1.f);
|
|
CGORenderGL(sobj->shaderCGO, color, I->Obj.Setting, NULL, info, NULL);
|
|
CShaderPrg_Disable(shaderPrg);
|
|
return;
|
|
}
|
|
} else {
|
|
CGORenderGL(sobj->std, color, I->Obj.Setting, NULL, info, NULL);
|
|
}
|
|
}
|
|
}
|
|
glEnable(GL_LIGHTING);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
static void ObjectAlignmentInvalidate(ObjectAlignment * I, int rep, int level, int state)
|
|
{
|
|
if((rep == cRepAll) || (rep == cRepCGO)) {
|
|
if(state >= 0) {
|
|
if(state < I->NState)
|
|
I->State[state].valid = false;
|
|
} else {
|
|
int a;
|
|
for(a = 0; a < I->NState; a++) {
|
|
I->State[a].valid = false;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
|
|
/*========================================================================*/
|
|
static ObjectAlignment *ObjectAlignmentNew(PyMOLGlobals * G)
|
|
{
|
|
OOAlloc(G, ObjectAlignment);
|
|
|
|
ObjectInit(G, (CObject *) I);
|
|
|
|
I->State = VLACalloc(ObjectAlignmentState, 10); /* auto-zero */
|
|
I->NState = 0;
|
|
I->SelectionState = -1;
|
|
I->ForceState = -1;
|
|
|
|
I->Obj.type = cObjectAlignment;
|
|
I->Obj.fFree = (void (*)(CObject *)) ObjectAlignmentFree;
|
|
I->Obj.fUpdate = (void (*)(CObject *)) ObjectAlignmentUpdate;
|
|
I->Obj.fRender = (void (*)(CObject *, RenderInfo *)) ObjectAlignmentRender;
|
|
I->Obj.fGetNFrame = (int (*)(CObject *)) ObjectAlignmentGetNState;
|
|
I->Obj.fInvalidate = (void (*)(CObject *, int rep, int level, int state))
|
|
ObjectAlignmentInvalidate;
|
|
|
|
return (I);
|
|
}
|
|
|
|
|
|
/*========================================================================*/
|
|
ObjectAlignment *ObjectAlignmentDefine(PyMOLGlobals * G,
|
|
ObjectAlignment * obj,
|
|
int *align_vla,
|
|
int state,
|
|
int merge,
|
|
ObjectMolecule * guide, ObjectMolecule * flush)
|
|
{
|
|
ObjectAlignment *I = NULL;
|
|
|
|
if(obj) {
|
|
if(obj->Obj.type != cObjectAlignment) /* TODO: handle this */
|
|
obj = NULL;
|
|
}
|
|
if(!obj) {
|
|
I = ObjectAlignmentNew(G);
|
|
} else {
|
|
I = obj;
|
|
}
|
|
if(state < 0)
|
|
state = I->NState;
|
|
|
|
if(I->NState <= state) {
|
|
VLACheck(I->State, ObjectAlignmentState, state);
|
|
I->NState = state + 1;
|
|
}
|
|
|
|
{
|
|
ObjectAlignmentState *oas = I->State + state;
|
|
oas->valid = false;
|
|
if(guide) {
|
|
strcpy(oas->guide, guide->Obj.Name);
|
|
}
|
|
if(align_vla) {
|
|
if(merge && oas->alignVLA) {
|
|
int *new_vla = AlignmentMerge(G, oas->alignVLA, align_vla, guide, flush);
|
|
if(new_vla) {
|
|
VLAFreeP(oas->alignVLA);
|
|
oas->alignVLA = new_vla;
|
|
}
|
|
} else {
|
|
int size = VLAGetSize(align_vla);
|
|
if(oas->alignVLA)
|
|
VLAFreeP(oas->alignVLA);
|
|
oas->alignVLA = VLAlloc(int, size);
|
|
UtilCopyMem(oas->alignVLA, align_vla, sizeof(int) * size);
|
|
VLASize(oas->alignVLA, int, size);
|
|
}
|
|
} else {
|
|
VLAFreeP(oas->alignVLA);
|
|
}
|
|
}
|
|
if(I) {
|
|
ObjectAlignmentRecomputeExtent(I);
|
|
}
|
|
SceneChanged(G);
|
|
SceneCountFrames(G);
|
|
return (I);
|
|
}
|