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Add some MolStandardize functionality to the CFFI library (#4062)

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* support CleanupParameters from JSON

* add standardization to cffi

* remove a bunch of repeated code from the new stuff
This commit is contained in:
Greg Landrum
2021-04-22 05:23:25 +02:00
committed by GitHub
parent a96a72219d
commit 158fe71ff2
8 changed files with 308 additions and 31 deletions
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93
Code/MinimalLib/common.h
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@@ -28,6 +28,9 @@
#include <GraphMol/CIPLabeler/CIPLabeler.h>
#include <GraphMol/Abbreviations/Abbreviations.h>
#include <DataStructs/BitOps.h>
#include <GraphMol/MolStandardize/MolStandardize.h>
#include <GraphMol/MolStandardize/Charge.h>
#include <GraphMol/MolStandardize/Tautomer.h>
#include <sstream>
#include <RDGeneral/BoostStartInclude.h>
@@ -298,6 +301,96 @@ std::string get_descriptors(const ROMol &m) {
doc.Accept(writer);
return buffer.GetString();
}
namespace {
template <typename T, typename U>
std::unique_ptr<RWMol> standardize_func(T &mol, const std::string &details_json,
U func) {
MolStandardize::CleanupParameters ps =
MolStandardize::defaultCleanupParameters;
if (!details_json.empty()) {
MolStandardize::updateCleanupParamsFromJSON(ps, details_json);
}
return std::unique_ptr<RWMol>(static_cast<RWMol *>(func(mol, ps)));
}
} // namespace
std::unique_ptr<RWMol> do_cleanup(RWMol &mol, const std::string &details_json) {
return standardize_func(mol, details_json, MolStandardize::cleanup);
}
std::unique_ptr<RWMol> do_normalize(RWMol &mol,
const std::string &details_json) {
auto molp = &mol;
return standardize_func(molp, details_json, MolStandardize::normalize);
}
std::unique_ptr<RWMol> do_reionize(RWMol &mol,
const std::string &details_json) {
auto molp = &mol;
return standardize_func(molp, details_json, MolStandardize::reionize);
}
std::unique_ptr<RWMol> do_canonical_tautomer(RWMol &mol,
const std::string &details_json) {
MolStandardize::CleanupParameters ps =
MolStandardize::defaultCleanupParameters;
if (!details_json.empty()) {
MolStandardize::updateCleanupParamsFromJSON(ps, details_json);
}
MolStandardize::TautomerEnumerator te(ps);
std::unique_ptr<RWMol> res(static_cast<RWMol *>(te.canonicalize(mol)));
return res;
}
std::unique_ptr<RWMol> do_neutralize(RWMol &mol,
const std::string &details_json) {
MolStandardize::CleanupParameters ps =
MolStandardize::defaultCleanupParameters;
if (!details_json.empty()) {
MolStandardize::updateCleanupParamsFromJSON(ps, details_json);
}
MolStandardize::Uncharger uncharger(ps.doCanonical);
std::unique_ptr<RWMol> res(static_cast<RWMol *>(uncharger.uncharge(mol)));
return res;
}
std::unique_ptr<RWMol> do_charge_parent(RWMol &mol,
const std::string &details_json) {
MolStandardize::CleanupParameters ps =
MolStandardize::defaultCleanupParameters;
bool skipStandardize = false;
if (!details_json.empty()) {
MolStandardize::updateCleanupParamsFromJSON(ps, details_json);
boost::property_tree::ptree pt;
std::istringstream ss;
ss.str(details_json);
boost::property_tree::read_json(ss, pt);
LPT_OPT_GET(skipStandardize);
}
std::unique_ptr<RWMol> res(
MolStandardize::chargeParent(mol, ps, skipStandardize));
return res;
}
std::unique_ptr<RWMol> do_fragment_parent(RWMol &mol,
const std::string &details_json) {
MolStandardize::CleanupParameters ps =
MolStandardize::defaultCleanupParameters;
bool skipStandardize = false;
if (!details_json.empty()) {
MolStandardize::updateCleanupParamsFromJSON(ps, details_json);
boost::property_tree::ptree pt;
std::istringstream ss;
ss.str(details_json);
boost::property_tree::read_json(ss, pt);
LPT_OPT_GET(skipStandardize);
}
std::unique_ptr<RWMol> res(
MolStandardize::fragmentParent(mol, ps, skipStandardize));
return res;
}
} // namespace MinimalLib
} // namespace RDKit
#undef LPT_OPT_GET