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Source code changes of the file "layer2/ObjectAlignment.cpp" between
pymol-open-source-2.2.0.tar.gz and pymol-open-source-2.3.0.tar.gz

About: PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.

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ObjectAlignment.cpp  (pymol-open-source-2.2.0):ObjectAlignment.cpp  (pymol-open-source-2.3.0)
skipping to change at line 17 skipping to change at line 17
E* It is unlawful to modify or remove this copyright notice. E* It is unlawful to modify or remove this copyright notice.
F* ------------------------------------------------------------------- F* -------------------------------------------------------------------
G* Please see the accompanying LICENSE file for further information. G* Please see the accompanying LICENSE file for further information.
H* ------------------------------------------------------------------- H* -------------------------------------------------------------------
I* Additional authors of this source file include: I* Additional authors of this source file include:
-* -*
-* -*
-* -*
Z* ------------------------------------------------------------------- Z* -------------------------------------------------------------------
*/ */
#include <set>
#include"os_python.h" #include"os_python.h"
#include"os_predef.h" #include"os_predef.h"
#include"os_std.h" #include"os_std.h"
#include"os_gl.h" #include"os_gl.h"
#include"OOMac.h" #include"OOMac.h"
#include"ObjectAlignment.h" #include"ObjectAlignment.h"
#include"Base.h" #include"Base.h"
#include"MemoryDebug.h" #include"MemoryDebug.h"
skipping to change at line 124 skipping to change at line 127
if(n_more_plus_one > 0) { if(n_more_plus_one > 0) {
ai0++; ai0++;
if(!AtomInfoSameResidueP(G, ai, ai0)) if(!AtomInfoSameResidueP(G, ai, ai0))
break; break;
} else } else
break; break;
} }
return result; return result;
} }
/*
* Get single letter abbreviation for CLUSTAL output.
*
* See also:
* pymol.exporting._resn_to_aa
* AtomInfoKnownNucleicResName
* AtomInfoKnownProteinResName
* SeekerGetAbbr
*/
static char get_abbr(PyMOLGlobals * G, const AtomInfoType * ai) {
const char * resn = LexStr(G, ai->resn);
const char unknown = ((ai->flags & cAtomFlag_polymer)) ? '?' : 0;
if ((ai->flags & cAtomFlag_nucleic)) {
if (resn[0] == 'D') {
++resn;
}
if (strlen(resn) != 1) {
return unknown;
}
return resn[0];
}
return SeekerGetAbbr(G, resn, 0, unknown);
}
int ObjectAlignmentAsStrVLA(PyMOLGlobals * G, ObjectAlignment * I, int state, in t format, int ObjectAlignmentAsStrVLA(PyMOLGlobals * G, ObjectAlignment * I, int state, in t format,
char **str_vla) char **str_vla)
{ {
int ok = true; int ok = true;
ov_size len = 0; ov_size len = 0;
char *vla = VLAlloc(char, 1000); char *vla = VLAlloc(char, 1000);
int force_update = false; int force_update = false;
int active_only = false; int active_only = false;
int max_name_len = 12; /* default indentation */ int max_name_len = 12; /* default indentation */
skipping to change at line 164 skipping to change at line 195
int align_sele = SelectorIndexByName(G, I->Obj.Name); int align_sele = SelectorIndexByName(G, I->Obj.Name);
if(align_sele >= 0) { if(align_sele >= 0) {
int nRow = 0; int nRow = 0;
ov_size nCol = 0; ov_size nCol = 0;
CSeqRow *row_vla = NULL, *row; CSeqRow *row_vla = NULL, *row;
char *cons_str = NULL; char *cons_str = NULL;
void *hidden = NULL; void *hidden = NULL;
ObjectMolecule *obj; ObjectMolecule *obj;
if(align_sele < 0) { {
align_sele = ExecutiveGetActiveAlignmentSele(G);
}
if(align_sele >= 0) {
row_vla = VLACalloc(CSeqRow, 10); row_vla = VLACalloc(CSeqRow, 10);
/* first, find out which objects are included in the /* first, find out which objects are included in the
alignment and count the name length */ alignment and count the name length */
while(ExecutiveIterateObjectMolecule(G, &obj, &hidden)) { while(ExecutiveIterateObjectMolecule(G, &obj, &hidden)) {
if((obj->Obj.Enabled || !active_only) && (obj->Obj.Name[0] != '_') ) { if((obj->Obj.Enabled || !active_only) && (obj->Obj.Name[0] != '_') ) {
int a; int a;
AtomInfoType *ai = obj->AtomInfo; AtomInfoType *ai = obj->AtomInfo;
for(a = 0; a < obj->NAtom; a++) { for(a = 0; a < obj->NAtom; a++) {
skipping to change at line 210 skipping to change at line 238
int min_tag = -1; int min_tag = -1;
int untagged_col = false; int untagged_col = false;
done = true; done = true;
for(a = 0; a < nRow; a++) { for(a = 0; a < nRow; a++) {
row = row_vla + a; row = row_vla + a;
while(row->cCol < row->nCol) { /* advance to next tag i n each row & find lowest */ while(row->cCol < row->nCol) { /* advance to next tag i n each row & find lowest */
AtomInfoType *ai = row->obj->AtomInfo + row->cCol; AtomInfoType *ai = row->obj->AtomInfo + row->cCol;
done = false; done = false;
if(AtomInfoSameResidueP(G, row->last_ai, ai)) { if(AtomInfoSameResidueP(G, row->last_ai, ai)) {
row->cCol++; row->cCol++;
} else if(!SeekerGetAbbr(G, LexStr(G, ai->resn), 0, 0)) { /* not a known residue type */ } else if(!get_abbr(G, ai)) { /* not a polymer residue */
row->cCol++; row->cCol++;
} else { } else {
int tag = int tag =
AlignmentFindTag(G, ai, align_sele, row->nCol - row->cCo l); AlignmentFindTag(G, ai, align_sele, row->nCol - row->cCo l);
if(tag) { /* we're at a tagged atom... */ if(tag) { /* we're at a tagged atom... */
if(min_tag > tag) if(min_tag > tag)
min_tag = tag; min_tag = tag;
else if(min_tag < 0) else if(min_tag < 0)
min_tag = tag; min_tag = tag;
break; break;
skipping to change at line 294 skipping to change at line 322
int min_tag = -1; int min_tag = -1;
int untagged_col = false; int untagged_col = false;
done = true; done = true;
for(a = 0; a < nRow; a++) { for(a = 0; a < nRow; a++) {
row = row_vla + a; row = row_vla + a;
while(row->cCol < row->nCol) { /* advance to next tag i n each row & find lowest */ while(row->cCol < row->nCol) { /* advance to next tag i n each row & find lowest */
AtomInfoType *ai = row->obj->AtomInfo + row->cCol; AtomInfoType *ai = row->obj->AtomInfo + row->cCol;
done = false; done = false;
if(AtomInfoSameResidueP(G, row->last_ai, ai)) { if(AtomInfoSameResidueP(G, row->last_ai, ai)) {
row->cCol++; row->cCol++;
} else if(!SeekerGetAbbr(G, LexStr(G, ai->resn), 0, 0)) { /* not a known residue type */ } else if(!get_abbr(G, ai)) { /* not a polymer residue */
row->cCol++; row->cCol++;
} else { } else {
int tag = int tag =
AlignmentFindTag(G, ai, align_sele, row->nCol - row->cCo l); AlignmentFindTag(G, ai, align_sele, row->nCol - row->cCo l);
if(tag) { /* we're at a tagged atom... */ if(tag) { /* we're at a tagged atom... */
if(min_tag > tag) if(min_tag > tag)
min_tag = tag; min_tag = tag;
else if(min_tag < 0) else if(min_tag < 0)
min_tag = tag; min_tag = tag;
break; break;
skipping to change at line 323 skipping to change at line 351
/* increment all untagged atoms */ /* increment all untagged atoms */
for(a = 0; a < nRow; a++) { for(a = 0; a < nRow; a++) {
row = row_vla + a; row = row_vla + a;
if(row->cCol < row->nCol) { if(row->cCol < row->nCol) {
AtomInfoType *ai = row->obj->AtomInfo + row->cCol; AtomInfoType *ai = row->obj->AtomInfo + row->cCol;
int tag = int tag =
AlignmentFindTag(G, ai, align_sele, row->nCol - row->cCo l); AlignmentFindTag(G, ai, align_sele, row->nCol - row->cCo l);
if(!tag) { if(!tag) {
if(!AtomInfoSameResidueP(G, row->last_ai, ai)) { if(!AtomInfoSameResidueP(G, row->last_ai, ai)) {
row->last_ai = ai; row->last_ai = ai;
row->txt[row->len] = SeekerGetAbbr(G, LexStr(G, ai->re sn), ' ', 'X'); row->txt[row->len] = get_abbr(G, ai);
} else { } else {
row->txt[row->len] = '-'; row->txt[row->len] = '-';
} }
row->len++; row->len++;
row->cCol++; row->cCol++;
} else { } else {
row->txt[row->len] = '-'; row->txt[row->len] = '-';
row->len++; row->len++;
} }
} else { } else {
skipping to change at line 354 skipping to change at line 382
for(a = 0; a < nRow; a++) { for(a = 0; a < nRow; a++) {
row = row_vla + a; row = row_vla + a;
if(row->cCol < row->nCol) { if(row->cCol < row->nCol) {
AtomInfoType *ai = row->obj->AtomInfo + row->cCol; AtomInfoType *ai = row->obj->AtomInfo + row->cCol;
int tag = int tag =
AlignmentFindTag(G, ai, align_sele, row->nCol - row->cCo l); AlignmentFindTag(G, ai, align_sele, row->nCol - row->cCo l);
if(tag == min_tag) { /* advance past this tag */ if(tag == min_tag) { /* advance past this tag */
char abbr; char abbr;
if(!AtomInfoSameResidueP(G, row->last_ai, ai)) { if(!AtomInfoSameResidueP(G, row->last_ai, ai)) {
row->last_ai = ai; row->last_ai = ai;
abbr = SeekerGetAbbr(G, LexStr(G, ai->resn), ' ', 'X') ; abbr = get_abbr(G, ai);
if(cons_abbr == ' ') if(cons_abbr == ' ')
cons_abbr = abbr; cons_abbr = abbr;
else if(cons_abbr != abbr) else if(cons_abbr != abbr)
cons_abbr = 0; cons_abbr = 0;
abbr_cnt++; abbr_cnt++;
} else { } else {
abbr = '-'; abbr = '-';
cons_abbr = 0; cons_abbr = 0;
} }
row->txt[row->len] = abbr; row->txt[row->len] = abbr;
skipping to change at line 461 skipping to change at line 489
/* curVLA and newVLA must be properly sized and zero terminated... */ /* curVLA and newVLA must be properly sized and zero terminated... */
int *result = NULL; int *result = NULL;
int n_result = 0; int n_result = 0;
{ {
{ {
int n_cur = VLAGetSize(curVLA); int n_cur = VLAGetSize(curVLA);
int n_new = VLAGetSize(newVLA); int n_new = VLAGetSize(newVLA);
/* now we can take unique IDs to specific atoms */ // get the set of non-guide objects in the new alignment, they need
// to be flushed (removed) from the current alignment
std::set<const ObjectMolecule*> flushobjects;
if (flush) {
flushobjects.insert(flush);
} else {
for (const int *it = newVLA, *it_end = it + n_new; it != it_end; ++it) {
if (*it) {
auto eoo = ExecutiveUniqueIDAtomDictGet(G, *it);
if (eoo && eoo->obj != guide) {
flushobjects.insert(eoo->obj);
}
}
}
}
/* first, go through and eliminate old matching atoms between guide and fl ush (if any) */ /* first, go through and eliminate old matching atoms between guide and fl ush (if any) */
{ {
int cur_start = 0; int cur_start = 0;
while(cur_start < n_cur) { while(cur_start < n_cur) {
while((cur_start < n_cur) && !curVLA[cur_start]) { while((cur_start < n_cur) && !curVLA[cur_start]) {
cur_start++; cur_start++;
} }
skipping to change at line 484 skipping to change at line 526
int flush_seen = false; int flush_seen = false;
ObjectMolecule *obj; ObjectMolecule *obj;
{ {
int cur = cur_start; int cur = cur_start;
int id; int id;
while((id = curVLA[cur])) { while((id = curVLA[cur])) {
auto eoo = ExecutiveUniqueIDAtomDictGet(G, id); auto eoo = ExecutiveUniqueIDAtomDictGet(G, id);
if (eoo) { if (eoo) {
obj = eoo->obj; obj = eoo->obj;
if(obj == flush) { if(flushobjects.count(obj)) {
flush_seen = true; flush_seen = true;
} else { } else {
other_seen++; other_seen++;
} }
} }
cur++; cur++;
} }
} }
if(flush_seen) { /* eliminate flush atoms */ if(flush_seen) { /* eliminate flush atoms */
int cur = cur_start; int cur = cur_start;
int id; int id;
while((id = curVLA[cur])) { while((id = curVLA[cur])) {
auto eoo = ExecutiveUniqueIDAtomDictGet(G, id); auto eoo = ExecutiveUniqueIDAtomDictGet(G, id);
if (eoo) { if (eoo) {
obj = eoo->obj; obj = eoo->obj;
if(obj == flush) { if(flushobjects.count(obj)) {
int tmp = cur; int tmp = cur;
while(curVLA[tmp]) { while(curVLA[tmp]) {
curVLA[tmp] = curVLA[tmp + 1]; curVLA[tmp] = curVLA[tmp + 1];
tmp++; tmp++;
} }
} }
} }
cur++; cur++;
} }
} }
skipping to change at line 1043 skipping to change at line 1085
return (I->NState); return (I->NState);
} }
/*========================================================================*/ /*========================================================================*/
static void ObjectAlignmentRender(ObjectAlignment * I, RenderInfo * info) static void ObjectAlignmentRender(ObjectAlignment * I, RenderInfo * info)
{ {
PyMOLGlobals *G = I->Obj.G; PyMOLGlobals *G = I->Obj.G;
int state = info->state; int state = info->state;
CRay *ray = info->ray; CRay *ray = info->ray;
Picking **pick = info->pick; auto pick = info->pick;
int pass = info->pass; int pass = info->pass;
ObjectAlignmentState *sobj = NULL; ObjectAlignmentState *sobj = NULL;
const float *color; const float *color;
ObjectPrepareContext(&I->Obj, info); ObjectPrepareContext(&I->Obj, info);
color = ColorGet(G, I->Obj.Color); color = ColorGet(G, I->Obj.Color);
if (pick) if (pick)
return; return;
 End of changes. 11 change blocks. 
12 lines changed or deleted 54 lines changed or added
To the C++ Programs section of the PyMOL source changes report or the top of this page
Mainly generated by pkgdiff using rfcdiff
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