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Avoid code duplication through a templated function and improve JSON parsing of Boolean flags (#8773)

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* - avoid code duplication through a templated function
- enable switching off boolean flags via JSON and not just on as before

* ran clang-format

* change in response to review

---------

Co-authored-by: ptosco <paolo.tosco@novartis.com>
This commit is contained in:
Paolo Tosco
2025-09-16 16:29:04 +02:00
committed by GitHub
parent b693c5d4df
commit 5ed6c56cc8
4 changed files with 105 additions and 32 deletions
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15
Code/GraphMol/SmilesParse/SmilesJSONParsers.cpp
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@@ -9,6 +9,7 @@
//
#define USE_BETTER_ENUMS
#include <RDGeneral/JSONHelpers.h>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/property_tree/ptree.hpp>
#include <boost/property_tree/json_parser.hpp>
@@ -49,19 +50,9 @@ void updateCXSmilesFieldsFromJSON(std::uint32_t &cxSmilesFields,
std::istringstream ss;
ss.str(details_json);
boost::property_tree::read_json(ss, pt);
auto cxSmilesFieldsFromJson =
(+SmilesWrite::CXSmilesFields::CX_NONE)._to_integral();
bool haveCXSmilesFields = false;
for (const auto *key : SmilesWrite::CXSmilesFields::_names()) {
const auto it = pt.find(key);
if (it != pt.not_found()) {
haveCXSmilesFields = true;
if (it->second.get_value<bool>()) {
cxSmilesFieldsFromJson |=
SmilesWrite::CXSmilesFields::_from_string(key)._to_integral();
}
}
}
auto cxSmilesFieldsFromJson =
flagsFromJson<SmilesWrite::CXSmilesFields>(pt, &haveCXSmilesFields);
if (haveCXSmilesFields) {
cxSmilesFields = cxSmilesFieldsFromJson;
}

63
Code/GraphMol/SmilesParse/cxsmiles_test.cpp
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@@ -18,6 +18,7 @@
#include <GraphMol/MarvinParse/MarvinParser.h>
#include <GraphMol/Chirality.h>
#include <GraphMol/SmilesParse/CanonicalizeStereoGroups.h>
#include <GraphMol/SmilesParse/SmilesJSONParsers.h>
#include "SmilesParse.h"
#include "SmilesWrite.h"
#include "SmartsWrite.h"
@@ -1659,4 +1660,64 @@ TEST_CASE("Github #8586: MolFromSmiles loses atom maps if cxsmiles is used") {
dlabel));
CHECK(dlabel == "d");
}
}
}
TEST_CASE("Test CXSmilesFields option parsing from JSON") {
SECTION("Empty JSON string preserves current values") {
std::uint32_t cxSmilesFields =
SmilesWrite::CXSmilesFields::CX_ALL_BUT_COORDS;
unsigned int restoreBondDirs = RestoreBondDirOptionClear;
updateCXSmilesFieldsFromJSON(cxSmilesFields, restoreBondDirs, "{}");
CHECK(cxSmilesFields == SmilesWrite::CXSmilesFields::CX_ALL_BUT_COORDS);
CHECK(restoreBondDirs == RestoreBondDirOptionClear);
}
SECTION("No CXSmilesFields key preserves current values") {
std::uint32_t cxSmilesFields =
SmilesWrite::CXSmilesFields::CX_ALL_BUT_COORDS;
unsigned int restoreBondDirs = RestoreBondDirOptionTrue;
updateCXSmilesFieldsFromJSON(
cxSmilesFields, restoreBondDirs,
"{\"restoreBondDirOption\":\"RestoreBondDirOptionClear\"}");
CHECK(cxSmilesFields == SmilesWrite::CXSmilesFields::CX_ALL_BUT_COORDS);
CHECK(restoreBondDirs == RestoreBondDirOptionClear);
}
SECTION("Multiple CXSmilesFields keys with true value are ORed together") {
std::uint32_t cxSmilesFields = SmilesWrite::CXSmilesFields::CX_ALL;
unsigned int restoreBondDirs = RestoreBondDirOptionClear;
updateCXSmilesFieldsFromJSON(
cxSmilesFields, restoreBondDirs,
"{\"CX_MOLFILE_VALUES\":true,\"CX_COORDS\":true}");
CHECK(cxSmilesFields == (SmilesWrite::CXSmilesFields::CX_MOLFILE_VALUES |
SmilesWrite::CXSmilesFields::CX_COORDS));
CHECK(restoreBondDirs == RestoreBondDirOptionClear);
}
SECTION(
"Multiple CXSmilesFields keys with true value are ORed together; adding unrelated false values makes no difference") {
std::uint32_t cxSmilesFields = SmilesWrite::CXSmilesFields::CX_ALL;
unsigned int restoreBondDirs = RestoreBondDirOptionClear;
updateCXSmilesFieldsFromJSON(
cxSmilesFields, restoreBondDirs,
"{\"CX_MOLFILE_VALUES\":true,\"CX_COORDS\":true,\"CX_ATOM_PROPS\":false,\"CX_BOND_CFG\":false}");
CHECK(cxSmilesFields == (SmilesWrite::CXSmilesFields::CX_MOLFILE_VALUES |
SmilesWrite::CXSmilesFields::CX_COORDS));
CHECK(restoreBondDirs == RestoreBondDirOptionClear);
}
SECTION(
"Multiple CXSmilesFields keys with true value are ORed together, then AND NOTed with ORed false values") {
std::uint32_t cxSmilesFields = SmilesWrite::CXSmilesFields::CX_ALL;
unsigned int restoreBondDirs = RestoreBondDirOptionClear;
updateCXSmilesFieldsFromJSON(cxSmilesFields, restoreBondDirs,
"{\"CX_ALL\":true,\"CX_COORDS\":false}");
CHECK(cxSmilesFields == SmilesWrite::CXSmilesFields::CX_ALL_BUT_COORDS);
CHECK(restoreBondDirs == RestoreBondDirOptionClear);
}
SECTION(
"Multiple CXSmilesFields keys with true value are ORed together, then AND NOTed with ORed false values; order does not matter") {
std::uint32_t cxSmilesFields = SmilesWrite::CXSmilesFields::CX_ALL;
unsigned int restoreBondDirs = RestoreBondDirOptionClear;
updateCXSmilesFieldsFromJSON(cxSmilesFields, restoreBondDirs,
"{\"CX_COORDS\":false,\"CX_ALL\":true}");
CHECK(cxSmilesFields == SmilesWrite::CXSmilesFields::CX_ALL_BUT_COORDS);
CHECK(restoreBondDirs == RestoreBondDirOptionClear);
}
}

23
Code/MinimalLib/JSONParsers.cpp
View File

@@ -13,6 +13,7 @@
#include <GraphMol/MolPickler.h>
#include <GraphMol/FileParsers/PNGParser.h>
#include <GraphMol/SmilesParse/SmilesJSONParsers.h>
#include <RDGeneral/JSONHelpers.h>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/property_tree/ptree.hpp>
#include <boost/property_tree/json_parser.hpp>
@@ -30,16 +31,8 @@ void updatePropertyPickleOptionsFromJSON(unsigned int &propFlags,
boost::property_tree::read_json(ss, pt);
const auto nodeIt = pt.find("propertyFlags");
if (nodeIt != pt.not_found()) {
auto propertyFlagsFromJson =
(+PicklerOps::PropertyPickleOptions::NoProps)._to_integral();
for (const auto *key : PicklerOps::PropertyPickleOptions::_names()) {
if (nodeIt->second.get(key, false)) {
propertyFlagsFromJson |=
PicklerOps::PropertyPickleOptions::_from_string(key)
._to_integral();
}
}
propFlags = propertyFlagsFromJson;
propFlags =
flagsFromJson<PicklerOps::PropertyPickleOptions>(nodeIt->second);
}
}
}
@@ -51,15 +44,7 @@ void updateSanitizeFlagsFromJSON(unsigned int &sanitizeFlags,
boost::property_tree::ptree pt;
ss.str(details_json);
boost::property_tree::read_json(ss, pt);
auto sanitizeFlagsFromJson =
(+MolOps::SanitizeFlags::SANITIZE_NONE)._to_integral();
for (const auto *key : MolOps::SanitizeFlags::_names()) {
if (pt.get(key, false)) {
sanitizeFlagsFromJson |=
MolOps::SanitizeFlags::_from_string(key)._to_integral();
}
}
sanitizeFlags = sanitizeFlagsFromJson;
sanitizeFlags = flagsFromJson<MolOps::SanitizeFlags>(pt);
}
}

36
Code/RDGeneral/JSONHelpers.h Normal file
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@@ -0,0 +1,36 @@
#include <RDGeneral/BoostStartInclude.h>
#include <boost/property_tree/ptree.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include <iostream>
#include <array>
// Convert a JSON object with boolean keys to a bitwise enum flag set.
// The T enum must have been declared as a BETTER_ENUM.
// The JSON object should have keys corresponding to the enum names, and boolean
// values. Example JSON: { "FlagA": true, "FlagB": false, "FlagC": true,
// "FlagD": false } This would set FlagA and FlagC in the resulting flag set,
// then clear FlagB and FlagD. If keysFound is provided and non-null, it will be
// set to true if any of the enum keys were found in the JSON object, false
// otherwise.
template <typename T>
typename T::_integral flagsFromJson(const boost::property_tree::ptree &pt,
bool *keysFound = nullptr) {
std::array<typename T::_integral, 2> flagsByType;
flagsByType.fill(static_cast<T::_integral>(0));
if (keysFound) {
*keysFound = false;
}
for (const auto *key : T::_names()) {
const auto it = pt.find(key);
if (it == pt.not_found()) {
continue;
}
if (keysFound) {
*keysFound = true;
}
auto value = T::_from_string(key)._to_integral();
auto i = static_cast<unsigned int>(it->second.template get_value<bool>());
flagsByType[i] |= value;
}
return (flagsByType[1] & ~flagsByType[0]);
}