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Add support of R-groups to the CDX loader. #36 #946

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merged 2 commits into from
Dec 22, 2022
Merged

Add support of R-groups to the CDX loader. #36 #946

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2358545
rgroups
even1024 Dec 21, 2022
78922f5
Merge branch 'release/1.9' of https://github.com/epam/Indigo into bug…
even1024 Dec 22, 2022
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3 changes: 3 additions & 0 deletions api/tests/integration/ref/formats/cdx_to_ket.py.out
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@@ -0,0 +1,3 @@
*** CDXML to mol ***
simple_rgrp64.cdx
{"root":{"nodes":[{"$ref":"mol0"},{"$ref":"rg1"}]},"mol0":{"type":"molecule","atoms":[{"label":"C","location":[0.4969991147518158,-0.639666736125946,0.0]},{"type":"rg-label","$refs":["rg-1"],"location":[0.49533283710479739,-0.1623331755399704,0.0]},{"label":"C","location":[0.011334228329360485,-0.6336659789085388,0.0]},{"label":"C","location":[0.009999592788517475,-0.1623331755399704,0.0]}],"bonds":[{"type":1,"atoms":[0,1]},{"type":1,"atoms":[0,2]},{"type":1,"atoms":[1,3]},{"type":1,"atoms":[2,3]}]},"rg1":{"rlogic":{"number":1},"type":"rgroup","atoms":[{"label":"C","location":[27.818666458129884,-13.968999862670899,0.0]},{"label":"C","location":[28.23433494567871,-14.208999633789063,0.0]},{"label":"C","location":[28.649999618530275,-13.968999862670899,0.0]},{"label":"C","location":[29.06566619873047,-14.208999633789063,0.0]},{"label":"Cl","location":[29.481332778930665,-13.968999862670899,0.0]}],"bonds":[{"type":1,"atoms":[0,1]},{"type":1,"atoms":[1,2]},{"type":1,"atoms":[2,3]},{"type":1,"atoms":[3,4]}]}}
28 changes: 28 additions & 0 deletions api/tests/integration/tests/formats/cdx_to_ket.py
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import os
import sys

sys.path.append(
os.path.normpath(
os.path.join(os.path.abspath(__file__), "..", "..", "..", "common")
)
)
from env_indigo import * # noqa

indigo = Indigo()
indigo.setOption("molfile-saving-skip-date", True)

print("*** CDXML to mol ***")

root = joinPathPy("molecules/cdx", __file__)
files = os.listdir(root)
files.sort()
for filename in files:
print(filename)
try:
mol = indigo.loadMoleculeFromFile(os.path.join(root, filename))
print(mol.json())
except IndigoException as e:
print(getIndigoExceptionText(e))
print("*** Try as Query ***")
mol = indigo.loadQueryMoleculeFromFile(os.path.join(root, filename))
print(mol.json())
43 changes: 43 additions & 0 deletions api/tests/integration/tests/formats/molecules/cdx/simple_rgrp64.cdx
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@@ -0,0 +1,43 @@
VmpDRDAxMDAEAwIBAAAAAAAAAAAAAACAAAAAAAMAFQAAAENoZW1EcmF3IEpTIDIu
MC4wLjkEAhAAvVl5ASOP3QJw/bgBHkWEAwEJCAAAAAAAAAAAAAIJCAAAANIEAADb
CQ0IAQABCAcBAAE6BAEAATsEAQAARQQBAAE8BAEAAEoEAQAADAYBAAEPBgEAAQ0G
AQAAQgQBAABDBAEAAEQEAQAADggCAJoCCggIABgAYADIAAMACwgIABgAAADIAAMA
CQgEAACAAgAICAQAmZkBAAcIBACZmQAABggEAAAAAgAFCAQAZmYOAAQIAgC0AAMI
BAAAAHgAIwgBAAUMCAEAACgIAQABKQgBAAEqCAEAATIIAQAAKwgBACgsCAEACi0I
AQABLggBAAACCBAAAAAkAAAAJAAAACQAAAAkAAEDAgAAAAIDAgABAAADMgAIAP//
/////wAAAAAAAP//AAAAAP////8AAAAA//8AAAAA/////wAAAAD/////AAD//wAB
DwAAAAEAGADp/QUAQXJpYWwACHgAAAMAAAEgASAAAAAAC2YIoP+E/4gL4wkYA2cF
JwP8AAIAAAEgASAAAAAAC2YIoAABAAAAZAAAAAEAAQEBAAAAAScPAAEAAQAAAAAA
AAAAAAAAAAACABkBkAAAAAAAQAAAAAAAAAAAAAEAAAAAAAAAAAAAAAAAAAAAtAsC
AAAAtQsUAAAAQ2hlbWljYWwgRm9ybXVsYTogtgsOAAAARXhhY3QgTWFzczogtwsU
AAAATW9sZWN1bGFyIFdlaWdodDoguAsHAAAAbS96OiC5CxYAAABFbGVtZW50YWwg
QW5hbHlzaXM6ILoLEQAAAEJvaWxpbmcgUG9pbnQ6ILsLEQAAAE1lbHRpbmcgUG9p
bnQ6ILwLEQAAAENyaXRpY2FsIFRlbXA6IL0LEQAAAENyaXRpY2FsIFByZXM6IL4L
EAAAAENyaXRpY2FsIFZvbDogvwsQAAAAR2liYnMgRW5lcmd5OiDACwkAAABMb2cg
UDogwQsGAAAATVI6IMILDwAAAEhlbnJ5J3MgTGF3OiDDCxAAAABIZWF0IG9mIEZv
cm06IMQLCAAAAHRQU0E6IMkLAgAAAMoLAgAAAAsMAgABAAoMAQAACQwBAAAMDAUA
AAAoIykBgBwAAAAEAhAAAAAAAAAAAACFqzYDAACSBhIIBAAAAJIGEwgEAIWrNgMW
CAQAAAAkABgIBAAAACQAFAgEAAAAAAAZCAAAEAgCAAEADwgCAAEAEQgBAAEDgAEA
AAAEAhAAvVl5ASOP3QL+14wBtTP0AgoAAgABAASAEAAAAAACCAA9iowBUXjsAgoA
AgACADcEAQABAAAEgBEAAAAAAggAUTh+AYVr7AIKAAIAAwAABAIACQBIBAAANwQB
AAE0BAQAAgAAADEECAAVAAAAFwAAAAaAAAAAAAACCAA0sYEBJc/oAgQCEAC9WXkB
Jc/oAjRxgwG1M/QCIwgBAAACBwIAAAAFBwEAAQAHDgABAAAAGABgAMgAAABSMQkH
DgABAAAAGABgAMgAAABSMQAAAAAEgBMAAAAAAggAKFyMAWbm3QIKAAIABAA3BAEA
AQAABIAUAAAAAAIIAFE4fgEo3N0CCgACAAUANwQBAAEAAAWAFQAAAAoAAgAGAAQG
BAAQAAAABQYEABEAAAAKBgEAAQAABYAWAAAACgACAAcABAYEABAAAAAFBgQAEwAA
AAoGAQABAAAFgBcAAAAKAAIACAAEBgQAEQAAAAUGBAAUAAAACgYBAAEAAAWAGAAA
AAoAAgAJAAQGBAATAAAABQYEABQAAAAKBgEAAQAAAAAKgAIAAAAEAhAAhat9Abhe
JwNw/bgBHkWEAwALEAAeRX4BUfgnAz2KlAFm5joDAQsQAD2KlAFR+CcD12O4AYWr
gwMCCwIAAQADgAQAAAAEAhAAVzOeAR/FMQOZma4Bw0V6AwoAAgALAASABQAAAAAC
CADrEaMBXI9CAwoAAgAMADcEAQABAAAEgAYAAAAAAggAHkWqAa4HTwMKAAIADQA3
BAEAAQAABIAHAAAAAAIIAOsRowEAgFsDCgACAA4ANwQBAAEAAASACAAAAAACCAAe
RaoBUfhnAwoAAgAPADcEAQABAAAEgAkAAAAAAggA6xGjAaNwdAMKAAIAEAACBAIA
EQArBAIAAABIBAAANwQBAAEGgAAAAAAAAggAzoqmAUPUcAMEAhAAVzOeAUPUcAMB
vqYBw0V6AyMIAQAAAgcCAAAABQcBAAEABw4AAQAAABgAYADIAAAAQ2wJBw4AAQAA
ABgAYADIAAAAQ2wAAAAABIAOAAAAAAIIAABAqgG4HjYDCgACABEAAAQCAAwASwQB
AAE3BAEAAQAABYAKAAAACgACABIABAYEAAUAAAAFBgQABgAAAAoGAQABAAAFgAsA
AAAKAAIAEwAEBgQABgAAAAUGBAAHAAAACgYBAAEAAAWADAAAAAoAAgAUAAQGBAAH
AAAABQYEAAgAAAAKBgEAAQAABYANAAAACgACABUABAYEAAgAAAAFBgQACQAAAAoG
AQABAAAFgA8AAAAKAAIAFgAEBgQADgAAAAUGBAAFAAAACgYBAAEAAAAABoAdAAAA
AAIIAJnZigEeRS0DBAIQAIWrfQG4XicDcP24AR5FhAMKAAIACgAHBwIAAAACBwIA
AAAABw4AAQAAABgAYADIAAAAUjEJBw4AAQAAABgAYADIAAAAUjEAAAAAAAAAAAAA
4 changes: 4 additions & 0 deletions core/indigo-core/molecule/molecule_cdxml_loader.h
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Expand Up @@ -132,6 +132,9 @@ namespace indigo
AutoInt enhanced_stereo_group;
AutoInt index;
AutoInt geometry;
AutoInt alt_group_id;
AutoInt rg_index;

bool is_not_list;
std::vector<AutoInt> element_list;
std::unordered_map<int, int> bond_id_to_connection_idx;
Expand Down Expand Up @@ -893,6 +896,7 @@ namespace indigo

void _parseGraphic(CDXElement elem);
void _parseArrow(CDXElement elem);
void _parseAltGroup(CDXElement elem);

void _addAtomsAndBonds(BaseMolecule& mol, const std::vector<int>& atoms, const std::vector<CdxmlBond>& bonds);
void _addBracket(BaseMolecule& mol, const CdxmlBracket& bracket);
Expand Down
108 changes: 84 additions & 24 deletions core/indigo-core/molecule/src/molecule_cdxml_loader.cpp
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Expand Up @@ -152,14 +152,22 @@ void MoleculeCdxmlLoader::_parseCollections(BaseMolecule& mol)
int node_idx = _id_to_node_index.at(node.id);
switch (node.type)
{
case kCDXNodeType_NamedAlternativeGroup:
case kCDXNodeType_Element:
case kCDXNodeType_ElementList:
atoms.push_back(node_idx);
break;
case kCDXNodeType_ExternalConnectionPoint: {
auto& fn = nodes[_fragment_nodes.back()];
if (fn.connections.size() == 0)
fn.ext_connections.push_back(node.id);
if (_fragment_nodes.size())
{
auto& fn = nodes[_fragment_nodes.back()];
if (fn.connections.size() == 0)
fn.ext_connections.push_back(node.id);
}
else
{
// handle free external connection. attachment point?
}
}
break;
case kCDXNodeType_Nickname:
Expand Down Expand Up @@ -366,9 +374,11 @@ void MoleculeCdxmlLoader::_parseCDXMLElements(CDXElement elem, bool no_siblings,

auto arrow_lambda = [this](CDXElement elem) { this->_parseArrow(elem); };

auto altgroup_lambda = [this](CDXElement elem) { this->_parseAltGroup(elem); };

std::unordered_map<std::string, std::function<void(CDXElement elem)>> cdxml_dispatcher = {
{"n", node_lambda}, {"b", bond_lambda}, {"fragment", fragment_lambda}, {"group", group_lambda}, {"bracketedgroup", bracketed_lambda},
{"t", text_lambda}, {"graphic", graphic_lambda}, {"arrow", arrow_lambda}};
{"n", node_lambda}, {"b", bond_lambda}, {"fragment", fragment_lambda}, {"group", group_lambda}, {"bracketedgroup", bracketed_lambda},
{"t", text_lambda}, {"graphic", graphic_lambda}, {"arrow", arrow_lambda}, {"altgroup", altgroup_lambda}};

for (elem; elem.hasContent(); elem = elem.nextSiblingElement())
{
Expand Down Expand Up @@ -416,6 +426,10 @@ void MoleculeCdxmlLoader::_addAtomsAndBonds(BaseMolecule& mol, const std::vector
if (_pmol)
{
atom_idx = _pmol->addAtom(atom.element);

if (atom.type == kCDXNodeType_NamedAlternativeGroup)
mol.allowRGroupOnRSite(atom_idx, atom.rg_index);

_id_to_atom_idx.emplace(atom.id, atom_idx);
mol.setAtomXyz(atom_idx, atom.pos);
_pmol->setAtomCharge_Silent(atom_idx, atom.charge);
Expand Down Expand Up @@ -752,7 +766,11 @@ void MoleculeCdxmlLoader::_parseNode(CdxmlNode& node, CDXElement elem)

auto stereo_lambda = [&node](const std::string& data) { node.stereo = KCIPStereochemistryCharToIndex.at(data.front()); };

auto node_type_lambda = [&node](const std::string& data) { node.type = KNodeTypeNameToInt.at(data); };
auto node_type_lambda = [&node](const std::string& data) {
node.type = KNodeTypeNameToInt.at(data);
if (node.type == kCDXNodeType_NamedAlternativeGroup)
node.element = ELEM_RSITE;
};

auto element_list_lambda = [&node](const std::string& data) {
std::vector<std::string> elements = split(data, ' ');
Expand All @@ -770,25 +788,36 @@ void MoleculeCdxmlLoader::_parseNode(CdxmlNode& node, CDXElement elem)

auto enhanced_stereo_group_lambda = [&node](const std::string& data) { node.enhanced_stereo_group = data; };

std::unordered_map<std::string, std::function<void(const std::string&)>> node_dispatcher = {
{"id", id_lambda},
{"p", pos_lambda},
{"xyz", pos_lambda},
{"NumHydrogens", hydrogens_lambda},
{"Charge", charge_lambda},
{"Isotope", isotope_lambda},
{"Radical", radical_lambda},
{"AS", stereo_lambda},
{"NodeType", node_type_lambda},
{"Element", element_lambda},
{"GenericNickname", label_lambda},
{"ElementList", element_list_lambda},
{"BondOrdering", bond_ordering_lambda},
{"Geometry", geometry_lambda},
{"EnhancedStereoType", enhanced_stereo_type_lambda},
{"EnhancedStereoGroupNum", enhanced_stereo_group_lambda},
};
auto alt_group_id_lambda = [&node](const std::string& data) { node.alt_group_id = data; };

std::unordered_map<std::string, std::function<void(const std::string&)>> node_dispatcher = {{"id", id_lambda},
{"p", pos_lambda},
{"xyz", pos_lambda},
{"NumHydrogens", hydrogens_lambda},
{"Charge", charge_lambda},
{"Isotope", isotope_lambda},
{"Radical", radical_lambda},
{"AS", stereo_lambda},
{"NodeType", node_type_lambda},
{"Element", element_lambda},
{"GenericNickname", label_lambda},
{"ElementList", element_list_lambda},
{"BondOrdering", bond_ordering_lambda},
{"Geometry", geometry_lambda},
{"EnhancedStereoType", enhanced_stereo_type_lambda},
{"EnhancedStereoGroupNum", enhanced_stereo_group_lambda},
{"AltGroupID", alt_group_id_lambda}};
applyDispatcher(elem.firstProperty(), node_dispatcher);
for (auto child_elem = elem.firstChildElement(); child_elem.hasContent(); child_elem = child_elem.nextSiblingElement())
{
if (child_elem.name() == "t")
{
std::string label;
_parseLabel(child_elem, label);
if (label.find("R") == 0)
node.rg_index = label.substr(1);
}
}
}

void MoleculeCdxmlLoader::_addNode(CdxmlNode& node)
Expand Down Expand Up @@ -879,6 +908,37 @@ void MoleculeCdxmlLoader::parseBBox(const std::string& data, Rect2f& bbox)
throw Error("Not enought coordinates for text bounding box");
}

void MoleculeCdxmlLoader::_parseAltGroup(CDXElement elem)
{
std::vector<AutoInt> r_labels;
std::vector<CDXElement> r_fragments;
for (auto r_elem = elem.firstChildElement(); r_elem.hasContent(); r_elem = r_elem.nextSiblingElement())
{
auto el_name = r_elem.name();
if (el_name == "fragment")
r_fragments.push_back(r_elem);
else if (el_name == "t")
{
std::string rl;
_parseLabel(r_elem, rl);
if (rl.find("R") == 0)
r_labels.push_back(rl.substr(1));
}
}

if (r_fragments.size() && r_labels.size())
{
MoleculeCdxmlLoader alt_loader(_scanner, _is_binary);
BaseMolecule& mol = _pmol ? *(BaseMolecule*)_pmol : *(BaseMolecule*)_pqmol;
std::unique_ptr<BaseMolecule> fragment(mol.neu());
alt_loader.stereochemistry_options = stereochemistry_options;
alt_loader.loadMoleculeFromFragment(*fragment.get(), r_fragments.front());
MoleculeRGroups& rgroups = mol.rgroups;
RGroup& rgroup = rgroups.getRGroup(r_labels.front());
rgroup.fragments.add(fragment.release());
}
}

void MoleculeCdxmlLoader::_parseGraphic(CDXElement elem)
{
AutoInt superseded_id = 0;
Expand Down