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#3604 Add api methods to interact with atoms and bonds in s-groups - #3625

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AlexanderSavelyev merged 39 commits into
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3604-sgroups-api
Jun 12, 2026
Merged

#3604 Add api methods to interact with atoms and bonds in s-groups#3625
AlexanderSavelyev merged 39 commits into
masterfrom
3604-sgroups-api

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@even1024

@even1024 even1024 commented Apr 29, 2026

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Generic request

  • PR name follows the pattern #1234 – issue name
  • branch name does not contain '#'
  • base branch (master or release/xx) is correct
  • PR is linked with the issue
  • task status changed to "Code review"
  • code follows product standards
  • regression tests updated

@AlexanderSavelyev AlexanderSavelyev linked an issue Apr 30, 2026 that may be closed by this pull request
Add api methods to interact with atoms and bonds in s-groups #3604
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AlexanderSavelyev
AlexanderSavelyev requested changes May 8, 2026
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Comment thread core/indigo-core/molecule/molecule_sgroups.h Outdated
Comment thread core/indigo-core/molecule/src/molfile_saver.cpp Outdated
Comment thread core/indigo-core/molecule/src/molfile_saver.cpp Outdated
Comment thread api/tests/integration/tests/basic/3604_sgroup_atoms_bonds.py
Comment thread core/indigo-core/layout/src/metalayout.cpp Outdated
AlexanderSavelyev
AlexanderSavelyev requested changes May 8, 2026
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Comment thread api/java/indigo/src/main/java/com/epam/indigo/IndigoObject.java
Comment thread api/dotnet/src/IndigoObject.cs Outdated
AlexanderSavelyev
AlexanderSavelyev requested changes May 12, 2026
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Comment thread api/tests/integration/ref/basic/sgroups_basic.py.out
AlexanderSavelyev
AlexanderSavelyev reviewed May 25, 2026
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Comment thread core/indigo-core/molecule/src/cml_saver.cpp Outdated

if ((sg_child.parent_group != 0) && (sg_child.parent_group == sgroup.original_group))
_addSgroupElement(sg, mol, sg_child);
if (child_entry.write_parent == write_index)

@AlexanderSavelyev AlexanderSavelyev May 25, 2026

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what does this mean?

Comment thread api/tests/integration/tests/formats/ref/macro/sa-mono.cml
AlexanderSavelyev
AlexanderSavelyev requested changes May 25, 2026
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Comment thread core/indigo-core/layout/src/metalayout.cpp Outdated
{
DataSGroup& group = (DataSGroup&)sg;
if (!group.relative)
if (!group.relative && group.display_pos.hasValue())

@AlexanderSavelyev AlexanderSavelyev May 25, 2026

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it should be just write

Comment thread core/indigo-core/common/base_cpp/nullable.h Outdated
}

operator const T&() const
T& get()

@AlexanderSavelyev AlexanderSavelyev May 25, 2026

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make verification on value

Comment thread core/render2d/src/render_internal.cpp Outdated
TextItem& index = _data.textitems[tiIndex];
index.fontsize = FONT_SIZE_ATTR;
bprintf(index.text, "%d", group.multiplier);
bprintf(index.text, "%d", group.multiplier.get());

@AlexanderSavelyev AlexanderSavelyev May 25, 2026

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need to add check

Comment thread core/render2d/src/render_internal.cpp Outdated
{
const Superatom& group = (Superatom&)sgroup;
Vec3f displayPosition = group.display_position;
Vec3f displayPosition = group.display_position.get();

@AlexanderSavelyev AlexanderSavelyev May 25, 2026

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need to add check

AlexanderSavelyev
AlexanderSavelyev requested changes May 25, 2026
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Comment thread core/indigo-core/layout/src/molecule_layout.cpp Outdated
{
DataSGroup& group = (DataSGroup&)sg;
if (!group.relative)
if (!group.relative && group.display_pos.hasValue())

@AlexanderSavelyev AlexanderSavelyev May 25, 2026

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it is write, should not check for value

Comment thread core/indigo-core/molecule/src/cmf_saver.cpp Outdated
@@ -340,7 +340,7 @@ void CmfSaver::_encodeExtSection(Molecule& mol, const Mapping& mapping)
_encodeString(sd.data);
// Pack detached, relative, display_units, and sd.dasp_pos into one byte
if (sd.dasp_pos < 0 || sd.dasp_pos > 9)

@AlexanderSavelyev AlexanderSavelyev May 25, 2026

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add check

Comment thread core/indigo-core/molecule/src/cmf_saver.cpp Outdated
_encodeUIntArray(sm.parent_atoms, *mapping.atom_mapping);
if (sm.multiplier < 0)
throw Error("internal error: SGroup multiplier is negative: %d", sm.multiplier);
throw Error("internal error: SGroup multiplier is negative: %d", sm.multiplier.get());

@AlexanderSavelyev AlexanderSavelyev May 25, 2026

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add check

Comment thread core/indigo-core/molecule/src/cml_saver.cpp Outdated
{
for (i = _mol->sgroups.begin(); i != _mol->sgroups.end(); i = _mol->sgroups.next(i))
auto entries = getOrderedSGroups(_mol->sgroups);
for (auto& entry : entries)

@AlexanderSavelyev AlexanderSavelyev May 25, 2026

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rename to sgroupEntry

Comment thread core/indigo-core/molecule/src/molecule_sgroups.cpp Outdated
std::vector<int> sgs_mapping(pool_end, 0);

// Roots first (parent_group == 0 or not set)
int iw = 1;

@AlexanderSavelyev AlexanderSavelyev May 25, 2026

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rename

Comment thread core/indigo-core/molecule/src/molecule_sgroups.cpp Outdated
{
SGroup& sg = sgroups.getSGroup(i);
int pg = sg.parent_group.hasValue() ? sg.parent_group.get() : 0;
if (pg == 0)

@AlexanderSavelyev AlexanderSavelyev May 25, 2026

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rename

Comment thread core/indigo-core/molecule/src/molecule_sgroups.cpp Outdated
std::set<int> added_indices;

// Add roots first
for (auto& e : all_entries)

@AlexanderSavelyev AlexanderSavelyev May 25, 2026

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rename

Comment thread core/indigo-core/molecule/molecule_sgroups.h Outdated
struct SGroupWriteEntry
{
int pool_idx; // original pool index in mol.sgroups
int write_index; // sequential 1,2,3... for CTFile output

@AlexanderSavelyev AlexanderSavelyev May 25, 2026

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rename write_index to index

Comment thread core/render2d/src/render_internal.cpp
@@ -565,7 +565,7 @@ void MoleculeRenderInternal::_initSGroups(Tree& sgroups, Rect2f parent)
TextItem& ti = _data.textitems[tii];
if (group.tag != ' ')
{

@AlexanderSavelyev AlexanderSavelyev May 25, 2026

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add check

AlexanderSavelyev
AlexanderSavelyev requested changes May 25, 2026
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Comment thread core/indigo-core/molecule/src/molecule_sgroups.cpp Outdated
for (int i : pool_indices)
{
SGroup& sg = sgroups.getSGroup(i);
int key = (sg.index != 0) ? sg.index : sgs_mapping[i];

@AlexanderSavelyev AlexanderSavelyev May 25, 2026

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potential problem

@AlexanderSavelyev AlexanderSavelyev mentioned this pull request May 29, 2026
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@even1024
even1024 force-pushed the 3604-sgroups-api branch from 6061569 to 32b9cac Compare June 9, 2026 01:44
AlexanderSavelyev
AlexanderSavelyev requested changes Jun 9, 2026
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fix tests

@even1024
even1024 force-pushed the 3604-sgroups-api branch from 3bb039d to e84faa7 Compare June 9, 2026 14:04
even1024 added 21 commits June 9, 2026 23:35
@even1024
even1024 force-pushed the 3604-sgroups-api branch from e84faa7 to 852d265 Compare June 9, 2026 20:35
@AlexanderSavelyev
AlexanderSavelyev merged commit 6cc2697 into master Jun 12, 2026
64 checks passed
@AlexanderSavelyev
AlexanderSavelyev deleted the 3604-sgroups-api branch June 12, 2026 08:32
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Add api methods to interact with atoms and bonds in s-groups

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@even1024 @AlexanderSavelyev