"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "layer3/Seeker.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.

[ To the main PyMOL source changes report ]

Seeker.cpp  (pymol-open-source-2.2.0):Seeker.cpp  (pymol-open-source-2.3.0)
skipping to change at line 120 skipping to change at line 120
atom_vla[n_at++] = at_idx; atom_vla[n_at++] = at_idx;
} }
} }
} }
VLACheck(atom_vla, int, n_at); VLACheck(atom_vla, int, n_at);
atom_vla[n_at] = -1; atom_vla[n_at] = -1;
SeekerBuildSeleFromAtomList(G, row->name, atom_vla, cTempSeekerSele, true) ; SeekerBuildSeleFromAtomList(G, row->name, atom_vla, cTempSeekerSele, true) ;
VLAFreeP(atom_vla); VLAFreeP(atom_vla);
{ {
char *sele_mode_kw; const char *sele_mode_kw;
sele_mode_kw = SceneGetSeleModeKeyword(G); sele_mode_kw = SceneGetSeleModeKeyword(G);
if(logging) if(logging)
SelectorLogSele(G, cTempSeekerSele); SelectorLogSele(G, cTempSeekerSele);
{ {
ExecutiveGetActiveSeleName(G, selName, true, logging); ExecutiveGetActiveSeleName(G, selName, true, logging);
/* selection or deselecting? */ /* selection or deselecting? */
skipping to change at line 190 skipping to change at line 190
int *atom_list; int *atom_list;
char prefix[3] = ""; char prefix[3] = "";
int logging = SettingGetGlobal_i(G, cSetting_logging); int logging = SettingGetGlobal_i(G, cSetting_logging);
if(logging == cPLog_pml) if(logging == cPLog_pml)
strcpy(prefix, "_ "); strcpy(prefix, "_ ");
row = rowVLA + row_num; row = rowVLA + row_num;
col = row->col + col_num; col = row->col + col_num;
if(!col->spacer) if(!col->spacer)
if(ExecutiveFindObjectByName(G, row->name)) { if(ExecutiveFindObjectByName(G, row->name)) {
char *sele_mode_kw; const char *sele_mode_kw;
atom_list = row->atom_lists + col->atom_at; atom_list = row->atom_lists + col->atom_at;
/* build up a selection consisting of residue atoms */ /* build up a selection consisting of residue atoms */
SeekerBuildSeleFromAtomList(G, row->name, atom_list, cTempSeekerSele, tr ue); SeekerBuildSeleFromAtomList(G, row->name, atom_list, cTempSeekerSele, tr ue);
sele_mode_kw = SceneGetSeleModeKeyword(G); sele_mode_kw = SceneGetSeleModeKeyword(G);
if(logging) if(logging)
SelectorLogSele(G, cTempSeekerSele); SelectorLogSele(G, cTempSeekerSele);
skipping to change at line 1025 skipping to change at line 1025
break; break;
} }
if(do_break) if(do_break)
break; break;
} else } else
break; break;
} }
return result; return result;
} }
PyObject *SeekerGetRawAlignment(PyMOLGlobals * G, int align_sele, int active_onl
y)
{
#ifdef _PYMOL_NOPY
return NULL;
#else
PyObject *result = NULL;
int nRow = 0;
int nCol = 0;
CSeqRow *row_vla = NULL, *row;
void *hidden = NULL;
ObjectMolecule *obj;
if(align_sele < 0) {
align_sele = ExecutiveGetActiveAlignmentSele(G);
}
if(align_sele >= 0) {
row_vla = VLACalloc(CSeqRow, 10);
/* first, find out which objects are included in the alignment */
while(ExecutiveIterateObjectMolecule(G, &obj, &hidden)) {
if((obj->Obj.Enabled || !active_only) && (obj->Obj.Name[0] != '_')) {
int a;
AtomInfoType *ai = obj->AtomInfo;
for(a = 0; a < obj->NAtom; a++) {
if(SelectorIsMember(G, ai->selEntry, align_sele)) {
VLACheck(row_vla, CSeqRow, nRow);
row = row_vla + nRow;
row->obj = obj;
row->nCol = obj->NAtom;
nRow++;
break;
}
ai++;
}
}
}
/* next, figure out how many aligned columns exist */
{
int done = false;
while(!done) {
int a;
int min_tag = -1;
done = true;
for(a = 0; a < nRow; a++) {
row = row_vla + a;
while(row->cCol < row->nCol) { /* advance to next tag in each r
ow & find lowest */
AtomInfoType *ai = row->obj->AtomInfo + row->cCol;
int tag = SelectorIsMember(G, ai->selEntry, align_sele);
if(!tag) {
row->cCol++;
} else { /* we're at a tagged atom... */
if(min_tag > tag)
min_tag = tag;
else if(min_tag < 0)
min_tag = tag;
done = false;
break;
}
}
}
if(min_tag >= 0) {
nCol++;
for(a = 0; a < nRow; a++) {
row = row_vla + a;
if(row->cCol < row->nCol) {
AtomInfoType *ai = row->obj->AtomInfo + row->cCol;
int tag = SelectorIsMember(G, ai->selEntry, align_sele);
if(tag == min_tag) { /* advance past this tag */
row->cCol++;
}
}
}
}
}
}
/* now populate the table */
result = PyList_New(nCol);
if(nCol) {
int done = false;
nCol = 0;
{ /* reset start points for our second pass */
int a;
for(a = 0; a < nRow; a++) {
row = row_vla + a;
row->cCol = 0;
}
}
while(!done) {
int a;
int min_tag = -1;
done = true;
for(a = 0; a < nRow; a++) {
row = row_vla + a;
while(row->cCol < row->nCol) { /* advance to next tag in each r
ow & find lowest */
AtomInfoType *ai = row->obj->AtomInfo + row->cCol;
int tag = SelectorIsMember(G, ai->selEntry, align_sele);
if(!tag) {
row->cCol++;
} else { /* we're at a tagged atom... */
if(min_tag > tag)
min_tag = tag;
else if(min_tag < 0)
min_tag = tag;
done = false;
break;
}
}
}
if(min_tag >= 0) {
int n_member = 0;
for(a = 0; a < nRow; a++) {
row = row_vla + a;
if(row->cCol < row->nCol) {
AtomInfoType *ai = row->obj->AtomInfo + row->cCol;
int tag = SelectorIsMember(G, ai->selEntry, align_sele);
if(tag == min_tag) { /* participates */
n_member++;
}
}
}
{
PyObject *column_list = PyList_New(n_member);
n_member = 0;
for(a = 0; a < nRow; a++) {
row = row_vla + a;
if(row->cCol < row->nCol) {
AtomInfoType *ai = row->obj->AtomInfo + row->cCol;
int tag = SelectorIsMember(G, ai->selEntry, align_sele);
if(tag == min_tag) { /* participates */
PyObject *tup = PyTuple_New(2);
PyTuple_SetItem(tup, 0, PyString_FromString(row->obj->Obj.Name
));
PyTuple_SetItem(tup, 1, PyInt_FromLong(row->cCol + 1));
/* +1, for 1-based PyMOL atom "index" */
PyList_SetItem(column_list, n_member, tup);
row->cCol++; /* advance past this tag */
n_member++;
}
}
}
PyList_SetItem(result, nCol, column_list);
}
nCol++;
}
}
}
}
VLAFreeP(row_vla);
return result;
#endif
}
void SeekerUpdate(PyMOLGlobals * G) void SeekerUpdate(PyMOLGlobals * G)
{ {
/* CObject *o = NULL; /* CObject *o = NULL;
int s; */ int s; */
void *hidden = NULL; void *hidden = NULL;
AtomInfoType *ai; AtomInfoType *ai;
ObjectMolecule *obj; ObjectMolecule *obj;
int nRow = 0; int nRow = 0;
int label_mode = 0; int label_mode = 0;
int codes = 0; int codes = 0;
int max_row = 50; int max_row = 50;
int default_color = 0; int default_color = 0;
int align_sele = -1; /* alignment selection */ int align_sele = -1; /* alignment selection */
const int MAXCONSECUTIVEGAPS = 9;
CSeqRow *row_vla, *row, *lab = NULL; CSeqRow *row_vla, *row, *lab = NULL;
row_vla = VLACalloc(CSeqRow, 10); row_vla = VLACalloc(CSeqRow, 10);
/* FIRST PASS: get all the residues represented properly */ /* FIRST PASS: get all the residues represented properly */
label_mode = SettingGetGlobal_i(G, cSetting_seq_view_label_mode); label_mode = SettingGetGlobal_i(G, cSetting_seq_view_label_mode);
align_sele = ExecutiveGetActiveAlignmentSele(G); align_sele = ExecutiveGetActiveAlignmentSele(G);
while(ExecutiveIterateObjectMolecule(G, &obj, &hidden)) { while(ExecutiveIterateObjectMolecule(G, &obj, &hidden)) {
if(obj->Obj.Enabled && (SettingGet_b(G, obj->Obj.Setting, NULL, cSetting_seq _view)) && if(obj->Obj.Enabled && (SettingGet_b(G, obj->Obj.Setting, NULL, cSetting_seq _view)) &&
(obj->Obj.Name[0] != '_')) { (obj->Obj.Name[0] != '_')) {
skipping to change at line 1225 skipping to change at line 1065
int last_spacer = false; int last_spacer = false;
int nCol = 0; int nCol = 0;
int nListEntries = 1; /* first list starts at 1 always... */ int nListEntries = 1; /* first list starts at 1 always... */
int est_col = obj->NAtom / 5 + 1; int est_col = obj->NAtom / 5 + 1;
int est_char = obj->NAtom * 4; int est_char = obj->NAtom * 4;
int first_atom_in_label; int first_atom_in_label;
int missing_color = SettingGet_i(G, obj->Obj.Setting, NULL, cSetting_seq_v iew_fill_color); int missing_color = SettingGet_i(G, obj->Obj.Setting, NULL, cSetting_seq_v iew_fill_color);
CoordSet *cs = obj->DiscreteFlag ? NULL : ObjectMoleculeGetCoordSet(obj, s td::max(0, obj->getState())); CoordSet *cs = obj->DiscreteFlag ? NULL : ObjectMoleculeGetCoordSet(obj, s td::max(0, obj->getState()));
bool atom_in_state; bool atom_in_state;
int gapMode = SettingGet_i(G, obj->Obj.Setting, nullptr, cSetting_seq_view _gap_mode);
int min_pad = -1; int min_pad = -1;
CSeqCol *r1 = NULL, *l1 = NULL; /* *col */ CSeqCol *r1 = NULL, *l1 = NULL; /* *col */
if(nRow >= max_row) if(nRow >= max_row)
break; break;
codes = SettingGet_i(G, obj->Obj.Setting, NULL, cSetting_seq_view_format); codes = SettingGet_i(G, obj->Obj.Setting, NULL, cSetting_seq_view_format);
if(obj->DiscreteFlag && SettingGet_b(G, if(obj->DiscreteFlag && SettingGet_b(G,
obj->Obj.Setting, obj->Obj.Setting,
NULL, cSetting_seq_view_discrete_by_s tate)) NULL, cSetting_seq_view_discrete_by_s tate))
skipping to change at line 1445 skipping to change at line 1286
for (int v = ai->resv; v; v /= 10) { for (int v = ai->resv; v; v /= 10) {
min_pad++; min_pad++;
} }
if (ai->inscode) { if (ai->inscode) {
min_pad++; min_pad++;
} }
} }
atom_in_state = (cs && a < cs->NAtIndex && cs->AtmToIdx[a] >= 0); atom_in_state = (cs && a < cs->NAtIndex && cs->AtmToIdx[a] >= 0);
int gapsNeeded{0};
if(gapMode != GapMode::NONE
&& AtomInfoSameChainP(G, ai, last)
&& (ai->flags & last->flags & cAtomFlag_polymer)
&& align_sele < 0){
gapsNeeded = ai->resv - last->resv - 1;
if(gapsNeeded > 1 && gapMode == GapMode::SINGLE){
gapsNeeded = 1;
}
}
auto push_gap = [&](const char* str)
{
auto str_size = strlen(str);
UtilConcatVLA(&row->txt, &row->len, str);
VLACheck(row->col, CSeqCol, nCol + str_size);
r1 = row->col + nCol;
for(int i = 0; i < str_size; i++){
r1->color = missing_color;
r1->spacer = true;
r1->stop = r1->start + 1;
auto lastStop = r1->stop;
nCol++;
r1 = row->col + nCol;
r1->start = lastStop;
}
};
switch (codes) { switch (codes) {
case 0: /* one letter residue codes */ case 0: /* one letter residue codes */
if(!AtomInfoSameResidueP(G, last, ai)) { if(!AtomInfoSameResidueP(G, last, ai)) {
char abbr[2] = "1"; char abbr[2] = "1";
last = ai; last = ai;
VLACheck(row->col, CSeqCol, nCol); VLACheck(row->col, CSeqCol, nCol);
r1 = row->col + nCol; r1 = row->col + nCol;
r1->start = row->len; r1->start = row->len;
//Only include non-consecutive gaps when not doing alignment
if(gapsNeeded > 0 && gapsNeeded <= MAXCONSECUTIVEGAPS){
for(int g = 0; g < gapsNeeded; ++g){
push_gap("-");
}
}
else if(gapsNeeded > MAXCONSECUTIVEGAPS){
push_gap("---...---");
}
if(obj->DiscreteFlag) if(obj->DiscreteFlag)
r1->state = ai->discrete_state; r1->state = ai->discrete_state;
first_atom_in_label = true; first_atom_in_label = true;
// single letter codes for polymer/solvent // single letter codes for polymer/solvent
if (!(ai->flags & (cAtomFlag_organic | cAtomFlag_inorganic))) { if (!(ai->flags & (cAtomFlag_organic | cAtomFlag_inorganic))) {
abbr[0] = SeekerGetAbbr(G, LexStr(G, ai->resn), 'O', 0); abbr[0] = SeekerGetAbbr(G, LexStr(G, ai->resn), 'O', 0);
} else { } else {
abbr[0] = 0; abbr[0] = 0;
skipping to change at line 1515 skipping to change at line 1396
if(!AtomInfoSameResidueP(G, last, ai)) { if(!AtomInfoSameResidueP(G, last, ai)) {
last = ai; last = ai;
VLACheck(row->col, CSeqCol, nCol); VLACheck(row->col, CSeqCol, nCol);
r1 = row->col + nCol; r1 = row->col + nCol;
r1->start = row->len; r1->start = row->len;
if(obj->DiscreteFlag) if(obj->DiscreteFlag)
r1->state = ai->discrete_state; r1->state = ai->discrete_state;
first_atom_in_label = true; first_atom_in_label = true;
//Only include non-consecutive gaps when not doing alignment
if(gapsNeeded > 0 && gapsNeeded <= MAXCONSECUTIVEGAPS){
for(int g = 0; g < gapsNeeded; ++g){
push_gap("--- ");
}
}
else if(gapsNeeded > MAXCONSECUTIVEGAPS){
push_gap("---...--- ");
}
if(ai->resn) if(ai->resn)
UtilConcatVLA(&row->txt, &row->len, LexStr(G, ai->resn)); UtilConcatVLA(&row->txt, &row->len, LexStr(G, ai->resn));
else else
UtilConcatVLA(&row->txt, &row->len, "''"); UtilConcatVLA(&row->txt, &row->len, "''");
r1->stop = row->len; r1->stop = row->len;
if(!atom_in_state) if(!atom_in_state)
r1->color = missing_color; r1->color = missing_color;
else if(default_color < 0) else if(default_color < 0)
r1->color = SeekerFindColor(G, ai, obj->NAtom - a); r1->color = SeekerFindColor(G, ai, obj->NAtom - a);
skipping to change at line 2011 skipping to change at line 1902
int n_skipped = 0; int n_skipped = 0;
int last_resv = -1; int last_resv = -1;
AtomInfoType *last_ai = NULL; AtomInfoType *last_ai = NULL;
ObjectMolecule *obj; ObjectMolecule *obj;
AtomInfoType *ai; AtomInfoType *ai;
row = lab + 1; row = lab + 1;
nCol = row->nCol; nCol = row->nCol;
obj = row->obj; obj = row->obj;
div = SettingGet_i(G, obj->Obj.Setting, NULL, cSetting_seq_view_label_sp acing); div = SettingGet_i(G, obj->Obj.Setting, NULL, cSetting_seq_view_label_sp acing);
sub = SettingGet_i(G, obj->Obj.Setting, NULL, cSetting_seq_view_label_st art); sub = SettingGet_i(G, obj->Obj.Setting, NULL, cSetting_seq_view_label_st art);
for(b = 0; b < nCol; b++) { for(b = 0; b < nCol; b++) {
CSeqCol *r1 = row->col + b; CSeqCol *r1 = row->col + b;
CSeqCol *l1 = lab->col + b; CSeqCol *l1 = lab->col + b;
ai = NULL; ai = NULL;
if(r1->atom_at) { if(r1->atom_at) {
atom_list = row->atom_lists + r1->atom_at; atom_list = row->atom_lists + r1->atom_at;
if(*atom_list >= 0) if(*atom_list >= 0)
ai = obj->AtomInfo + (*atom_list); /* get first atom in lis t */ ai = obj->AtomInfo + (*atom_list); /* get first atom in lis t */
} }
 End of changes. 9 change blocks. 
168 lines changed or deleted 55 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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