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#2575 - Saving atom to monomer connections to Mol and HELM (#2592)
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@AliaksandrDziarkach
AliaksandrDziarkach authored Oct 31, 2024
1 parent 2596f46 commit 8d80b5b
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Showing 4 changed files with 263 additions and 0 deletions.
1 change: 1 addition & 0 deletions api/tests/integration/ref/formats/ket_to_helm.py.out
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ helm_mixed_base.ket:SUCCEED
helm_mixed_custom.ket:SUCCEED
helm_molecule_2418.ket:SUCCEED
helm_monomer_molecule.ket:SUCCEED
helm_monomer_molecule_direct.ket:SUCCEED
helm_multi_char_rna.ket:SUCCEED
helm_peptide.ket:SUCCEED
helm_rna_without_base.ket:SUCCEED
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1 change: 1 addition & 0 deletions api/tests/integration/tests/formats/ket_to_helm.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@ def find_diff(a, b):
"helm_smiles_sugar": "RNA1{[C(C(CO[*:1])O[*:2])[*:3] |$;;;;_R1;;_R2;_R3$|](A)P}$$$$V2.0",
"helm_molecule_2418": "PEPTIDE1{A}|CHEM1{[C1C=CC=CC=1[*:1] |$;;;;;;_R1$|]}$PEPTIDE1,CHEM1,1:R1-1:R1$$$V2.0",
"helm_chem_rna_hydro": "CHEM1{[MCC]}|RNA1{R(U)P}$CHEM1,RNA1,1:pair-3:pair$$$V2.0",
"helm_monomer_molecule_direct": "PEPTIDE1{A}|CHEM1{[C(=C)N[*:1] |$;;;_R1$|]}$PEPTIDE1,CHEM1,1:R2-1:R1$$$V2.0",
}

for filename in sorted(helm_data.keys()):
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223 changes: 223 additions & 0 deletions api/tests/integration/tests/formats/ref/helm_monomer_molecule_direct.ket
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Original file line number Diff line number Diff line change
@@ -0,0 +1,223 @@
{
"root": {
"nodes": [
{
"$ref": "monomer5635"
},
{
"$ref": "mol0"
}
],
"connections": [
{
"connectionType": "single",
"endpoint1": {
"monomerId": "monomer5635",
"attachmentPointId": "R2"
},
"endpoint2": {
"moleculeId": "mol0",
"atomId": "1"
}
}
],
"templates": [
{
"$ref": "monomerTemplate-A___Alanine"
}
]
},
"mol0": {
"type": "molecule",
"atoms": [
{
"label": "C",
"location": [
22.70380779065583,
-10.331249794220879,
0
]
},
{
"label": "N",
"location": [
23.569833212558642,
-10.831249821106224,
0
]
},
{
"label": "C",
"location": [
21.837782294247205,
-10.831249783853321,
0
]
}
],
"bonds": [
{
"type": 1,
"atoms": [
0,
1
]
},
{
"type": 2,
"atoms": [
0,
2
]
}
],
"stereoFlagPosition": {
"x": 23.569833212558642,
"y": 9.331249794220879,
"z": 0
}
},
"monomer5635": {
"type": "monomer",
"id": "5635",
"position": {
"x": 25.774999999999988,
"y": -10.725000000000009
},
"alias": "A",
"templateId": "A___Alanine"
},
"monomerTemplate-A___Alanine": {
"type": "monomerTemplate",
"atoms": [
{
"label": "N",
"location": [
-1.2549,
-0.392,
0
]
},
{
"label": "C",
"location": [
-0.272,
0.2633,
0
],
"stereoLabel": "abs"
},
{
"label": "C",
"location": [
-0.3103,
1.7393,
0
]
},
{
"label": "C",
"location": [
1.0523,
-0.392,
0
]
},
{
"label": "O",
"location": [
1.0829,
-1.5722,
0
]
},
{
"label": "O",
"location": [
2.0353,
0.2633,
0
]
},
{
"label": "H",
"location": [
-2.3334,
0.0905,
0
]
}
],
"bonds": [
{
"type": 1,
"atoms": [
1,
0
]
},
{
"type": 1,
"atoms": [
1,
2
],
"stereo": 1
},
{
"type": 1,
"atoms": [
1,
3
]
},
{
"type": 2,
"atoms": [
3,
4
]
},
{
"type": 1,
"atoms": [
3,
5
]
},
{
"type": 1,
"atoms": [
0,
6
]
}
],
"class": "AminoAcid",
"classHELM": "PEPTIDE",
"id": "A___Alanine",
"fullName": "Alanine",
"alias": "A",
"attachmentPoints": [
{
"attachmentAtom": 0,
"leavingGroup": {
"atoms": [
6
]
},
"type": "left"
},
{
"attachmentAtom": 3,
"leavingGroup": {
"atoms": [
5
]
},
"type": "right"
}
],
"naturalAnalogShort": "A"
}
}
38 changes: 38 additions & 0 deletions core/indigo-core/molecule/src/sequence_saver.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1319,6 +1319,25 @@ std::string SequenceSaver::saveHELM(KetDocument& document, std::vector<std::dequ
auto& molecules = document.jsonMolecules();
int molecule_idx = 0;
rapidjson::Document json{};
std::map<std::string, std::vector<int>> molecules_connections;
if (molecules.Size() > 0)
{
auto process_ep = [&molecules_connections](const KetConnectionEndPoint& ep) {
if (ep.hasStringProp("moleculeId"))
{
const auto& mol_id = ep.getStringProp("moleculeId");
if (molecules_connections.count(mol_id) == 0)
molecules_connections.try_emplace(mol_id);
if (ep.hasStringProp("atomId"))
molecules_connections.at(mol_id).push_back(std::stoi(ep.getStringProp("atomId")));
}
};
for (const auto& connection : document.nonSequenceConnections())
{
process_ep(connection.ep1());
process_ep(connection.ep2());
}
}
for (rapidjson::SizeType i = 0; i < molecules.Size(); i++)
{
const auto& molecule = molecules[i];
Expand All @@ -1341,6 +1360,7 @@ std::string SequenceSaver::saveHELM(KetDocument& document, std::vector<std::dequ
}
// convert Sup sgroup without name attachment points to rg-labels
auto& sgroups = pbmol->sgroups;
int ap_count = 0;
for (int i = sgroups.begin(); i != sgroups.end(); i = sgroups.next(i))
{
auto& sgroup = sgroups.getSGroup(i);
Expand All @@ -1355,6 +1375,7 @@ std::string SequenceSaver::saveHELM(KetDocument& document, std::vector<std::dequ
static std::string apid_prefix{'R'};
for (int ap_id = sa.attachment_points.begin(); ap_id != sa.attachment_points.end(); ap_id = sa.attachment_points.next(ap_id))
{
ap_count++;
auto& ap = sa.attachment_points.at(ap_id);
std::string apid = apid_prefix + ap.apid.ptr();
atom_to_ap->second.emplace(ap.aidx, apid);
Expand All @@ -1374,6 +1395,23 @@ std::string SequenceSaver::saveHELM(KetDocument& document, std::vector<std::dequ
}
sgroups.remove(i);
}
// check direct monomer to molecule connections without attachment point
if (molecules_connections.count(mol_id) > 0 && ap_count == 0)
{
int ap_idx = 1;
auto res = mol_atom_to_ap.try_emplace(mol_id);
auto& atom_to_ap = res.first;
static std::string apid_prefix{'R'};
for (auto atom_id : molecules_connections.at(mol_id))
{
std::string apid = apid_prefix + std::to_string(ap_idx);
atom_to_ap->second.emplace(atom_id, apid);
// add leaving atom and set it as R-site
auto leaving_atom = pbmol->addAtom(ELEM_RSITE);
pbmol->addBond(atom_id, leaving_atom, BOND_SINGLE);
pbmol->allowRGroupOnRSite(leaving_atom, ap_idx++);
}
}
// generate smiles
std::string smiles;
StringOutput s_out(smiles);
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