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Release_2024_09
rdkit/Code/MinimalLib/common.h
Paolo Tosco 802f9d2991 Fix #8027 (#8031) 
* - Fix #8029
- avoid unnecessary rounding errors in the JSON writer
- remove a warning when compiling MinimalLib without SubstructLIbrary support

* changes in response to review

* changes in response to review

---------

Co-authored-by: ptosco <paolo.tosco@novartis.com>
2024-12-19 09:53:20 +01:00

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//
// Copyright (C) 2021 Greg Landrum
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#pragma once
#ifdef __GNUC__
#pragma GCC diagnostic ignored "-Wdeprecated-declarations"
#endif
#include <string>
#include <RDGeneral/versions.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolPickler.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolFileStereochem.h>
#include <RDGeneral/FileParseException.h>
#include <GraphMol/MolDraw2D/MolDraw2DSVG.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <GraphMol/MolInterchange/MolInterchange.h>
#include <GraphMol/Descriptors/Property.h>
#include <GraphMol/Descriptors/MolDescriptors.h>
#include <GraphMol/Fingerprints/Fingerprints.h>
#include <GraphMol/Fingerprints/MorganFingerprints.h>
#include <GraphMol/Fingerprints/AtomPairGenerator.h>
#include <GraphMol/Fingerprints/TopologicalTorsionGenerator.h>
#include <GraphMol/Fingerprints/MorganGenerator.h>
#include <GraphMol/Fingerprints/RDKitFPGenerator.h>
#include <GraphMol/Fingerprints/MACCS.h>
#ifdef RDK_BUILD_AVALON_SUPPORT
#include <External/AvalonTools/AvalonTools.h>
#endif
#include <GraphMol/Depictor/RDDepictor.h>
#include <GraphMol/Depictor/DepictUtils.h>
#include <GraphMol/Conformer.h>
#include <GraphMol/MolAlign/AlignMolecules.h>
#include <GraphMol/Substruct/SubstructUtils.h>
#include <GraphMol/MolTransforms/MolTransforms.h>
#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 <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/ChemReactions/ReactionParser.h>
#include <GraphMol/ChemReactions/SanitizeRxn.h>
#include <GraphMol/RGroupDecomposition/RGroupUtils.h>
#include <RDGeneral/RDLog.h>
#include "common_defs.h"
#include <sstream>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/property_tree/ptree.hpp>
#include <boost/property_tree/json_parser.hpp>
#include <RDGeneral/BoostEndInclude.h>
#ifdef RDK_BUILD_THREADSAFE_SSS
#include <mutex>
#include <atomic>
#endif
#ifndef _MSC_VER
// shutoff some warnings from rapidjson
#if !defined(__clang__) && defined(__GNUC__)
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wclass-memaccess"
#endif
#endif
#include <rapidjson/document.h>
#include <rapidjson/stringbuffer.h>
#include <rapidjson/writer.h>
#ifndef _MSC_VER
#if !defined(__clang__) && defined(__GNUC__)
#pragma GCC diagnostic pop
#endif
#endif
#define GET_JSON_VALUE(doc, drawingDetails, key, type) \
const auto key##It = doc.FindMember(#key); \
if (key##It != doc.MemberEnd()) { \
if (!key##It->value.Is##type()) { \
return "JSON contains '" #key "' field, but its type is not '" #type \
"'"; \
} \
drawingDetails.key = key##It->value.Get##type(); \
}
namespace rj = rapidjson;
namespace RDKit {
namespace MinimalLib {
static constexpr int d_defaultWidth = 250;
static constexpr int d_defaultHeight = 200;
#define LPT_OPT_GET(opt) opt = pt.get(#opt, opt);
#define LPT_OPT_GET2(holder, opt) holder.opt = pt.get(#opt, holder.opt);
RWMol *mol_from_input(const std::string &input,
const std::string &details_json = "") {
auto haveMolBlock = false;
auto haveRDKitJson = false;
if (input.find("M END") != std::string::npos) {
haveMolBlock = true;
} else if (input.find("commonchem") != std::string::npos ||
input.find("rdkitjson") != std::string::npos) {
haveRDKitJson = true;
}
auto haveSmiles = (!haveMolBlock && !haveRDKitJson);
bool sanitize = true;
bool kekulize = true;
bool removeHs = haveSmiles;
bool mergeQueryHs = false;
bool setAromaticity = true;
bool fastFindRings = true;
bool assignChiralTypesFromMolParity = false;
bool assignStereo = true;
bool assignCIPLabels = false;
bool mappedDummiesAreRGroups = false;
bool makeDummiesQueries = false;
RWMol *res = nullptr;
boost::property_tree::ptree pt;
if (!details_json.empty()) {
std::istringstream ss;
ss.str(details_json);
boost::property_tree::read_json(ss, pt);
LPT_OPT_GET(sanitize);
LPT_OPT_GET(kekulize);
LPT_OPT_GET(removeHs);
LPT_OPT_GET(mergeQueryHs);
LPT_OPT_GET(setAromaticity);
LPT_OPT_GET(fastFindRings);
LPT_OPT_GET(assignChiralTypesFromMolParity);
LPT_OPT_GET(assignStereo);
LPT_OPT_GET(assignCIPLabels);
LPT_OPT_GET(mappedDummiesAreRGroups);
LPT_OPT_GET(makeDummiesQueries);
}
try {
// We set default sanitization to false
// as we want to enable partial sanitization
// if required by the user through JSON details
if (haveMolBlock) {
bool strictParsing = false;
LPT_OPT_GET(strictParsing);
res = MolBlockToMol(input, false, false, strictParsing);
} else if (haveRDKitJson) {
auto ps = MolInterchange::defaultJSONParseParameters;
LPT_OPT_GET2(ps, setAromaticBonds);
LPT_OPT_GET2(ps, strictValenceCheck);
LPT_OPT_GET2(ps, parseProperties);
LPT_OPT_GET2(ps, parseConformers);
auto molVect = MolInterchange::JSONDataToMols(input, ps);
if (!molVect.empty()) {
res = new RWMol(*molVect[0]);
}
} else {
SmilesParserParams ps;
ps.sanitize = false;
ps.removeHs = removeHs;
LPT_OPT_GET2(ps, strictCXSMILES);
res = SmilesToMol(input, ps);
}
} catch (...) {
// we really don't want exceptions to be thrown in here
res = nullptr;
}
if (res) {
try {
if (removeHs && !haveSmiles) {
MolOps::RemoveHsParameters removeHsParams;
MolOps::removeHs(*res, removeHsParams, false);
}
if (sanitize) {
unsigned int failedOp;
unsigned int sanitizeOps = MolOps::SANITIZE_ALL;
if (!kekulize) {
sanitizeOps ^= MolOps::SANITIZE_KEKULIZE;
}
if (!setAromaticity) {
sanitizeOps ^= MolOps::SANITIZE_SETAROMATICITY;
}
MolOps::sanitizeMol(*res, failedOp, sanitizeOps);
} else {
res->updatePropertyCache(false);
if (fastFindRings) {
MolOps::fastFindRings(*res);
}
}
if (assignChiralTypesFromMolParity) {
MolOps::assignChiralTypesFromMolParity(*res);
}
if (assignStereo) {
MolOps::assignStereochemistry(*res, true, true, true);
}
if (assignCIPLabels) {
CIPLabeler::assignCIPLabels(*res);
}
if (mergeQueryHs) {
MolOps::mergeQueryHs(*res);
}
if (mappedDummiesAreRGroups) {
relabelMappedDummies(*res);
}
if (makeDummiesQueries) {
auto ps = MolOps::AdjustQueryParameters::noAdjustments();
ps.makeDummiesQueries = true;
MolOps::adjustQueryProperties(*res, &ps);
}
} catch (...) {
delete res;
res = nullptr;
}
}
return res;
}
RWMol *mol_from_input(const std::string &input, const char *details_json) {
std::string json;
if (details_json) {
json = details_json;
}
return mol_from_input(input, json);
}
RWMol *qmol_from_input(const std::string &input,
const std::string &details_json = "") {
RWMol *res = nullptr;
bool removeHs = true;
boost::property_tree::ptree pt;
if (!details_json.empty()) {
// FIX: this should eventually be moved somewhere else
std::istringstream ss;
ss.str(details_json);
boost::property_tree::read_json(ss, pt);
LPT_OPT_GET(removeHs);
}
if (input.find("M END") != std::string::npos) {
bool strictParsing = false;
LPT_OPT_GET(strictParsing);
res = MolBlockToMol(input, false, removeHs, strictParsing);
} else if (input.find("commonchem") != std::string::npos ||
input.find("rdkitjson") != std::string::npos) {
auto ps = MolInterchange::defaultJSONParseParameters;
LPT_OPT_GET2(ps, setAromaticBonds);
LPT_OPT_GET2(ps, strictValenceCheck);
LPT_OPT_GET2(ps, parseProperties);
LPT_OPT_GET2(ps, parseConformers);
auto molVect = MolInterchange::JSONDataToMols(input, ps);
if (!molVect.empty()) {
res = new RWMol(*molVect[0]);
}
} else {
bool mergeHs = false;
LPT_OPT_GET(mergeHs);
res = SmartsToMol(input, 0, mergeHs);
}
return res;
}
RWMol *qmol_from_input(const std::string &input, const char *details_json) {
std::string json;
if (details_json) {
json = details_json;
}
return qmol_from_input(input, json);
}
ChemicalReaction *rxn_from_input(const std::string &input,
const std::string &details_json = "") {
bool useSmiles = false;
bool sanitize = false;
ChemicalReaction *rxn = nullptr;
boost::property_tree::ptree pt;
if (!details_json.empty()) {
std::istringstream ss;
ss.str(details_json);
boost::property_tree::read_json(ss, pt);
LPT_OPT_GET(sanitize);
LPT_OPT_GET(useSmiles);
}
try {
if (input.find("$RXN") != std::string::npos) {
bool removeHs = false;
bool strictParsing = false;
LPT_OPT_GET(removeHs);
LPT_OPT_GET(strictParsing);
rxn = RxnBlockToChemicalReaction(input, false, removeHs, strictParsing);
} else {
rxn = RxnSmartsToChemicalReaction(input, nullptr, useSmiles);
}
} catch (...) {
// we really don't want exceptions to be thrown in here
rxn = nullptr;
}
if (rxn) {
try {
if (sanitize) {
unsigned int failedOp;
unsigned int sanitizeOps = RxnOps::SANITIZE_ALL;
bool adjustReactants = true;
bool mergeQueryHs = true;
LPT_OPT_GET(adjustReactants);
LPT_OPT_GET(mergeQueryHs);
if (!adjustReactants) {
sanitizeOps ^= RxnOps::SANITIZE_ADJUST_REACTANTS;
}
if (!mergeQueryHs) {
sanitizeOps ^= RxnOps::SANITIZE_MERGEHS;
}
RxnOps::sanitizeRxn(*rxn, failedOp, sanitizeOps);
}
} catch (...) {
delete rxn;
rxn = nullptr;
}
}
return rxn;
}
ChemicalReaction *rxn_from_input(const std::string &input,
const char *details_json) {
std::string json;
if (details_json) {
json = details_json;
}
return rxn_from_input(input, json);
}
std::string parse_int_array(const rj::Document &doc, std::vector<int> &intVec,
const std::string &keyName,
const std::string &valueName) {
const auto it = doc.FindMember(keyName.c_str());
if (it != doc.MemberEnd()) {
if (!it->value.IsArray()) {
return "JSON contains '" + keyName + "' field, but it is not an array";
}
for (const auto &val : it->value.GetArray()) {
if (!val.IsInt()) {
return valueName + " should be integers";
}
intVec.push_back(val.GetInt());
}
}
return "";
}
std::string parse_rgba_array(const rj::Value &val, DrawColour &color,
const std::string &keyName) {
if (!val.IsArray() || val.Size() < 3 || val.Size() > 4) {
return "JSON contains '" + keyName +
"' field, but the "
"colors are not R,G,B[,A] arrays";
}
std::vector<double> rgba(4, 1.0);
unsigned int i = 0;
for (const auto &component : val.GetArray()) {
if (!component.IsNumber()) {
return "JSON contains '" + keyName +
"' field, but the "
"R,G,B[,A] arrays contain non-float values";
}
CHECK_INVARIANT(i < 4, "");
rgba[i++] = component.GetDouble();
}
color.r = rgba[0];
color.g = rgba[1];
color.b = rgba[2];
color.a = rgba[3];
return "";
}
std::string parse_highlight_multi_colors(
const rj::Document &doc, std::map<int, std::vector<DrawColour>> &colorMap,
const std::string &keyName, bool &haveMultiColors) {
const auto it = doc.FindMember(keyName.c_str());
haveMultiColors = (it != doc.MemberEnd());
if (!haveMultiColors) {
return "";
}
if (!it->value.IsObject()) {
return "JSON contains '" + keyName + "' field, but it is not an object";
}
for (const auto &entry : it->value.GetObject()) {
int idx = std::atoi(entry.name.GetString());
auto &drawColorVect = colorMap[idx];
if (entry.value.IsArray()) {
const auto &arr = entry.value.GetArray();
if (std::all_of(arr.begin(), arr.end(),
[](const auto &item) { return item.IsArray(); })) {
for (const auto &item : arr) {
DrawColour color;
auto problems = parse_rgba_array(item, color, keyName);
if (!problems.empty()) {
return problems;
}
drawColorVect.push_back(std::move(color));
}
continue;
}
}
return "JSON contains '" + keyName +
"' field, but it is not an array of R,G,B[,A] arrays";
}
return "";
}
std::string parse_highlight_colors(const rj::Document &doc,
std::map<int, DrawColour> &colorMap,
const std::string &keyName) {
const auto it = doc.FindMember(keyName.c_str());
if (it != doc.MemberEnd()) {
if (!it->value.IsObject()) {
return "JSON contains '" + keyName + "' field, but it is not an object";
}
for (const auto &entry : it->value.GetObject()) {
DrawColour color;
auto problems = parse_rgba_array(entry.value, color, keyName);
if (!problems.empty()) {
return problems;
}
int idx = std::atoi(entry.name.GetString());
colorMap[idx] = std::move(color);
}
}
return "";
}
std::string process_details(rj::Document &doc, const std::string &details,
DrawingDetails &drawingDetails) {
doc.Parse(details.c_str());
if (!doc.IsObject()) {
return "Invalid JSON";
}
std::string problems;
problems = parse_int_array(doc, drawingDetails.atomIds, "atoms", "Atom IDs");
if (!problems.empty()) {
return problems;
}
problems = parse_int_array(doc, drawingDetails.bondIds, "bonds", "Bond IDs");
if (!problems.empty()) {
return problems;
}
GET_JSON_VALUE(doc, drawingDetails, width, Int)
GET_JSON_VALUE(doc, drawingDetails, height, Int)
GET_JSON_VALUE(doc, drawingDetails, offsetx, Int)
GET_JSON_VALUE(doc, drawingDetails, offsety, Int)
GET_JSON_VALUE(doc, drawingDetails, panelWidth, Int)
GET_JSON_VALUE(doc, drawingDetails, panelHeight, Int)
GET_JSON_VALUE(doc, drawingDetails, noFreetype, Bool)
GET_JSON_VALUE(doc, drawingDetails, legend, String)
GET_JSON_VALUE(doc, drawingDetails, kekulize, Bool)
GET_JSON_VALUE(doc, drawingDetails, addChiralHs, Bool)
GET_JSON_VALUE(doc, drawingDetails, wedgeBonds, Bool)
GET_JSON_VALUE(doc, drawingDetails, forceCoords, Bool)
GET_JSON_VALUE(doc, drawingDetails, wavyBonds, Bool)
GET_JSON_VALUE(doc, drawingDetails, useMolBlockWedging, Bool)
return "";
}
[[deprecated(
"please use the overload taking DrawingDetails& as parameter")]] std::string
process_details(rj::Document &doc, const std::string &details, int &width,
int &height, int &offsetx, int &offsety, std::string &legend,
std::vector<int> &atomIds, std::vector<int> &bondIds,
bool &kekulize, bool &addChiralHs, bool &wedgeBonds,
bool &forceCoords, bool &wavyBonds) {
DrawingDetails drawingDetails;
auto problems = process_details(doc, details, drawingDetails);
width = drawingDetails.width;
height = drawingDetails.height;
offsetx = drawingDetails.offsetx;
offsety = drawingDetails.offsety;
legend = drawingDetails.legend;
atomIds = drawingDetails.atomIds;
bondIds = drawingDetails.bondIds;
kekulize = drawingDetails.kekulize;
addChiralHs = drawingDetails.addChiralHs;
wedgeBonds = drawingDetails.wedgeBonds;
forceCoords = drawingDetails.forceCoords;
wavyBonds = drawingDetails.wavyBonds;
return problems;
}
std::string process_mol_details(const std::string &details,
MolDrawingDetails &molDrawingDetails) {
rj::Document doc;
auto problems = process_details(doc, details, molDrawingDetails);
if (!problems.empty()) {
return problems;
}
bool haveAtomMultiColors;
problems = parse_highlight_multi_colors(doc, molDrawingDetails.atomMultiMap,
"highlightAtomMultipleColors",
haveAtomMultiColors);
if (!problems.empty()) {
return problems;
}
bool haveBondMultiColors;
problems = parse_highlight_multi_colors(doc, molDrawingDetails.bondMultiMap,
"highlightBondMultipleColors",
haveBondMultiColors);
if (!problems.empty()) {
return problems;
}
if (haveAtomMultiColors || haveBondMultiColors) {
const auto lineWidthMultiplierMapit =
doc.FindMember("highlightLineWidthMultipliers");
if (lineWidthMultiplierMapit != doc.MemberEnd()) {
if (!lineWidthMultiplierMapit->value.IsObject()) {
return "JSON contains 'highlightLineWidthMultipliers' field, but it is not an object";
}
for (const auto &entry : lineWidthMultiplierMapit->value.GetObject()) {
if (!entry.value.IsInt()) {
return "JSON contains 'highlightLineWidthMultipliers' field, but the multipliers"
"are not ints";
}
int idx = std::atoi(entry.name.GetString());
molDrawingDetails.lineWidthMultiplierMap[idx] = entry.value.GetInt();
}
}
} else {
problems = parse_highlight_colors(doc, molDrawingDetails.atomMap,
"highlightAtomColors");
if (!problems.empty()) {
return problems;
}
problems = parse_highlight_colors(doc, molDrawingDetails.bondMap,
"highlightBondColors");
if (!problems.empty()) {
return problems;
}
}
const auto radiiMapit = doc.FindMember("highlightAtomRadii");
if (radiiMapit != doc.MemberEnd()) {
if (!radiiMapit->value.IsObject()) {
return "JSON contains 'highlightAtomRadii' field, but it is not an object";
}
for (const auto &entry : radiiMapit->value.GetObject()) {
if (!entry.value.IsNumber()) {
return "JSON contains 'highlightAtomRadii' field, but the radii"
"are not floats";
}
int idx = std::atoi(entry.name.GetString());
molDrawingDetails.radiiMap[idx] = entry.value.GetDouble();
}
}
return "";
}
[[deprecated(
"please use the overload taking MolDrawingDetails& as parameter")]] std::
string
process_mol_details(const std::string &details, int &width, int &height,
int &offsetx, int &offsety, std::string &legend,
std::vector<int> &atomIds, std::vector<int> &bondIds,
std::map<int, DrawColour> &atomMap,
std::map<int, DrawColour> &bondMap,
std::map<int, double> &radiiMap, bool &kekulize,
bool &addChiralHs, bool &wedgeBonds, bool &forceCoords,
bool &wavyBonds) {
MolDrawingDetails molDrawingDetails;
auto problems = process_mol_details(details, molDrawingDetails);
width = molDrawingDetails.width;
height = molDrawingDetails.height;
offsetx = molDrawingDetails.offsetx;
offsety = molDrawingDetails.offsety;
legend = molDrawingDetails.legend;
atomIds = molDrawingDetails.atomIds;
bondIds = molDrawingDetails.bondIds;
atomMap = molDrawingDetails.atomMap;
bondMap = molDrawingDetails.bondMap;
radiiMap = molDrawingDetails.radiiMap;
kekulize = molDrawingDetails.kekulize;
addChiralHs = molDrawingDetails.addChiralHs;
wedgeBonds = molDrawingDetails.wedgeBonds;
forceCoords = molDrawingDetails.forceCoords;
wavyBonds = molDrawingDetails.wavyBonds;
return problems;
}
std::string process_rxn_details(const std::string &details,
RxnDrawingDetails &rxnDrawingDetails) {
rj::Document doc;
auto problems = process_details(doc, details, rxnDrawingDetails);
if (!problems.empty()) {
return problems;
}
GET_JSON_VALUE(doc, rxnDrawingDetails, highlightByReactant, Bool)
auto highlightColorsReactantsIt = doc.FindMember("highlightColorsReactants");
if (highlightColorsReactantsIt != doc.MemberEnd()) {
if (!highlightColorsReactantsIt->value.IsArray()) {
return "JSON contains 'highlightColorsReactants' field, but it is not an "
"array";
}
for (const auto &rgbaArray : highlightColorsReactantsIt->value.GetArray()) {
DrawColour color;
problems = parse_rgba_array(rgbaArray, color, "highlightColorsReactants");
if (!problems.empty()) {
return problems;
}
rxnDrawingDetails.highlightColorsReactants.push_back(std::move(color));
}
}
return "";
}
[[deprecated(
"please use the overload taking RxnDrawingDetails& as parameter")]] std::
string
process_rxn_details(const std::string &details, int &width, int &height,
int &offsetx, int &offsety, std::string &legend,
std::vector<int> &atomIds, std::vector<int> &bondIds,
bool &kekulize, bool &highlightByReactant,
std::vector<DrawColour> &highlightColorsReactants) {
RxnDrawingDetails rxnDrawingDetails;
auto problems = process_rxn_details(details, rxnDrawingDetails);
width = rxnDrawingDetails.width;
height = rxnDrawingDetails.height;
offsetx = rxnDrawingDetails.offsetx;
offsety = rxnDrawingDetails.offsety;
legend = rxnDrawingDetails.legend;
atomIds = rxnDrawingDetails.atomIds;
bondIds = rxnDrawingDetails.bondIds;
kekulize = rxnDrawingDetails.kekulize;
highlightByReactant = rxnDrawingDetails.highlightByReactant;
highlightColorsReactants = rxnDrawingDetails.highlightColorsReactants;
return problems;
}
std::string molblock_helper(const RWMol &mol, const char *details_json,
bool forceV3000) {
bool includeStereo = true;
bool kekulize = true;
bool useMolBlockWedging = false;
bool addChiralHs = false;
if (details_json && strlen(details_json)) {
boost::property_tree::ptree pt;
std::istringstream ss;
ss.str(details_json);
boost::property_tree::read_json(ss, pt);
LPT_OPT_GET(includeStereo);
LPT_OPT_GET(kekulize);
LPT_OPT_GET(useMolBlockWedging);
LPT_OPT_GET(addChiralHs);
}
const RWMol *molPtr = &mol;
std::unique_ptr<RWMol> molCopy;
if (useMolBlockWedging || addChiralHs) {
molCopy.reset(new RWMol(mol));
molPtr = molCopy.get();
if (useMolBlockWedging) {
RDKit::Chirality::reapplyMolBlockWedging(*molCopy);
}
if (addChiralHs) {
MolDraw2DUtils::prepareMolForDrawing(*molCopy, false, true, false, false,
false);
}
}
return MolToMolBlock(*molPtr, includeStereo, -1, kekulize, forceV3000);
}
void get_sss_json(const ROMol &d_mol, const ROMol &q_mol,
const MatchVectType &match, rj::Value &obj,
rj::Document &doc) {
rj::Value rjAtoms(rj::kArrayType);
for (const auto &pr : match) {
rjAtoms.PushBack(pr.second, doc.GetAllocator());
}
obj.AddMember("atoms", rjAtoms, doc.GetAllocator());
rj::Value rjBonds(rj::kArrayType);
std::vector<int> invMatch(q_mol.getNumAtoms(), -1);
for (const auto &pair : match) {
invMatch[pair.first] = &pair - &match.front();
}
for (const auto qbond : q_mol.bonds()) {
auto beginIdx = invMatch.at(qbond->getBeginAtomIdx());
auto endIdx = invMatch.at(qbond->getEndAtomIdx());
if (beginIdx == -1 || endIdx == -1) {
continue;
}
unsigned int idx1 = match.at(beginIdx).second;
unsigned int idx2 = match.at(endIdx).second;
const auto bond = d_mol.getBondBetweenAtoms(idx1, idx2);
if (bond != nullptr) {
rjBonds.PushBack(bond->getIdx(), doc.GetAllocator());
}
}
obj.AddMember("bonds", rjBonds, doc.GetAllocator());
}
namespace {
class SVGDrawerFromDetails : public DrawerFromDetails {
public:
SVGDrawerFromDetails(int w = -1, int h = -1,
const std::string &details = std::string()) {
init(w, h, details);
}
private:
MolDraw2DSVG &drawer() const {
CHECK_INVARIANT(d_drawer, "d_drawer must not be null");
return *d_drawer;
};
void initDrawer(const DrawingDetails &drawingDetails) {
d_drawer.reset(new MolDraw2DSVG(
drawingDetails.width, drawingDetails.height, drawingDetails.panelWidth,
drawingDetails.panelHeight, drawingDetails.noFreetype));
updateDrawerParamsFromJSON();
}
std::string finalizeDrawing() {
CHECK_INVARIANT(d_drawer, "d_drawer must not be null");
d_drawer->finishDrawing();
return d_drawer->getDrawingText();
}
std::unique_ptr<MolDraw2DSVG> d_drawer;
};
} // end anonymous namespace
std::string mol_to_svg(const ROMol &m, int w = -1, int h = -1,
const std::string &details = "") {
SVGDrawerFromDetails svgDrawer(w, h, details);
return svgDrawer.draw_mol(m);
}
std::string rxn_to_svg(const ChemicalReaction &rxn, int w = -1, int h = -1,
const std::string &details = "") {
SVGDrawerFromDetails svgDrawer(w, h, details);
return svgDrawer.draw_rxn(rxn);
}
std::string get_descriptors(const ROMol &m) {
rj::Document doc;
doc.SetObject();
Descriptors::Properties props;
std::vector<std::string> dns = props.getPropertyNames();
std::vector<double> dvs = props.computeProperties(m);
for (size_t i = 0; i < dns.size(); ++i) {
rj::Value v(dvs[i]);
const auto srt = rj::StringRef(dns[i].c_str());
doc.AddMember(srt, v, doc.GetAllocator());
}
rj::StringBuffer buffer;
rj::Writer<rj::StringBuffer> writer(buffer);
writer.SetMaxDecimalPlaces(5);
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)));
}
bool invertWedgingIfMolHasFlipped(ROMol &mol,
const RDGeom::Transform3D &trans) {
constexpr double FLIP_THRESHOLD = -0.99;
auto zRot = trans.getVal(2, 2);
bool shouldFlip = zRot < FLIP_THRESHOLD;
if (shouldFlip) {
RDKit::Chirality::invertMolBlockWedgingInfo(mol);
}
return shouldFlip;
}
} // namespace
std::unique_ptr<RWMol> do_cleanup(RWMol &mol, const std::string &details_json) {
auto molp = &mol;
return standardize_func(
molp, details_json,
static_cast<RWMol *(*)(const RWMol *,
const MolStandardize::CleanupParameters &)>(
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;
}
std::unique_ptr<ExplicitBitVect> morgan_fp_as_bitvect(
const RWMol &mol, const char *details_json) {
unsigned int radius = 2;
unsigned int nBits = 2048;
bool useCountSimulation = false;
bool useChirality = false;
bool useBondTypes = true;
bool includeRedundantEnvironments = false;
bool onlyNonzeroInvariants = false;
if (details_json && strlen(details_json)) {
// FIX: this should eventually be moved somewhere else
std::istringstream ss;
ss.str(details_json);
boost::property_tree::ptree pt;
boost::property_tree::read_json(ss, pt);
LPT_OPT_GET(radius);
LPT_OPT_GET(nBits);
LPT_OPT_GET(useCountSimulation);
LPT_OPT_GET(useChirality);
LPT_OPT_GET(useBondTypes);
LPT_OPT_GET(includeRedundantEnvironments);
LPT_OPT_GET(onlyNonzeroInvariants);
}
std::unique_ptr<FingerprintGenerator<std::uint32_t>> morganFPGen{
RDKit::MorganFingerprint::getMorganGenerator<std::uint32_t>(
radius, useCountSimulation, useChirality, useBondTypes,
onlyNonzeroInvariants, includeRedundantEnvironments, nullptr, nullptr,
nBits)};
return std::unique_ptr<ExplicitBitVect>(morganFPGen->getFingerprint(mol));
}
std::unique_ptr<ExplicitBitVect> rdkit_fp_as_bitvect(const RWMol &mol,
const char *details_json) {
static const std::vector<std::uint32_t> countBounds{1, 2, 4, 8};
unsigned int minPath = 1;
unsigned int maxPath = 7;
unsigned int nBits = 2048;
unsigned int nBitsPerHash = 2;
bool useHs = true;
bool branchedPaths = true;
bool useBondOrder = true;
bool useCountSimulation = false;
if (details_json && strlen(details_json)) {
// FIX: this should eventually be moved somewhere else
std::istringstream ss;
ss.str(details_json);
boost::property_tree::ptree pt;
boost::property_tree::read_json(ss, pt);
LPT_OPT_GET(minPath);
LPT_OPT_GET(maxPath);
LPT_OPT_GET(nBits);
LPT_OPT_GET(nBitsPerHash);
LPT_OPT_GET(useHs);
LPT_OPT_GET(branchedPaths);
LPT_OPT_GET(useBondOrder);
LPT_OPT_GET(useCountSimulation);
}
std::unique_ptr<FingerprintGenerator<std::uint32_t>> rdkFPGen{
RDKit::RDKitFP::getRDKitFPGenerator<std::uint32_t>(
minPath, maxPath, useHs, branchedPaths, useBondOrder, nullptr,
useCountSimulation, countBounds, nBits, nBitsPerHash)};
return std::unique_ptr<ExplicitBitVect>(rdkFPGen->getFingerprint(mol));
}
std::unique_ptr<ExplicitBitVect> pattern_fp_as_bitvect(
const RWMol &mol, const char *details_json) {
unsigned int nBits = 2048;
bool tautomericFingerprint = false;
if (details_json && strlen(details_json)) {
// FIX: this should eventually be moved somewhere else
std::istringstream ss;
ss.str(details_json);
boost::property_tree::ptree pt;
boost::property_tree::read_json(ss, pt);
LPT_OPT_GET(nBits);
LPT_OPT_GET(tautomericFingerprint);
}
auto fp = PatternFingerprintMol(mol, nBits, nullptr, nullptr,
tautomericFingerprint);
return std::unique_ptr<ExplicitBitVect>{fp};
}
std::unique_ptr<ExplicitBitVect> topological_torsion_fp_as_bitvect(
const RWMol &mol, const char *details_json) {
unsigned int nBits = 2048;
unsigned int torsionAtomCount = 4;
bool useChirality = false;
bool useCountSimulation = true;
if (details_json && strlen(details_json)) {
// FIX: this should eventually be moved somewhere else
std::istringstream ss;
ss.str(details_json);
boost::property_tree::ptree pt;
boost::property_tree::read_json(ss, pt);
LPT_OPT_GET(nBits);
LPT_OPT_GET(torsionAtomCount);
LPT_OPT_GET(useChirality);
LPT_OPT_GET(useCountSimulation);
}
std::unique_ptr<FingerprintGenerator<std::uint64_t>> topoTorsFPGen{
RDKit::TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>(
useChirality, torsionAtomCount, nullptr, useCountSimulation, nBits)};
return std::unique_ptr<ExplicitBitVect>(topoTorsFPGen->getFingerprint(mol));
}
std::unique_ptr<ExplicitBitVect> atom_pair_fp_as_bitvect(
const RWMol &mol, const char *details_json) {
unsigned int nBits = 2048;
unsigned int minLength = 1;
unsigned int maxLength = 30;
bool useChirality = false;
bool use2D = true;
bool useCountSimulation = true;
if (details_json && strlen(details_json)) {
// FIX: this should eventually be moved somewhere else
std::istringstream ss;
ss.str(details_json);
boost::property_tree::ptree pt;
boost::property_tree::read_json(ss, pt);
LPT_OPT_GET(nBits);
LPT_OPT_GET(minLength);
LPT_OPT_GET(maxLength);
LPT_OPT_GET(useChirality);
LPT_OPT_GET(use2D);
LPT_OPT_GET(useCountSimulation);
}
std::unique_ptr<FingerprintGenerator<std::uint32_t>> atomPairFPGen{
RDKit::AtomPair::getAtomPairGenerator<std::uint32_t>(
minLength, maxLength, useChirality, use2D, nullptr,
useCountSimulation, nBits)};
return std::unique_ptr<ExplicitBitVect>(atomPairFPGen->getFingerprint(mol));
}
std::unique_ptr<ExplicitBitVect> maccs_fp_as_bitvect(const RWMol &mol) {
auto fp = MACCSFingerprints::getFingerprintAsBitVect(mol);
return std::unique_ptr<ExplicitBitVect>{fp};
}
#ifdef RDK_BUILD_AVALON_SUPPORT
std::unique_ptr<ExplicitBitVect> avalon_fp_as_bitvect(
const RWMol &mol, const char *details_json) {
unsigned int nBits = 512;
if (details_json && strlen(details_json)) {
// FIX: this should eventually be moved somewhere else
std::istringstream ss;
ss.str(details_json);
boost::property_tree::ptree pt;
boost::property_tree::read_json(ss, pt);
LPT_OPT_GET(nBits);
}
std::unique_ptr<ExplicitBitVect> fp(new ExplicitBitVect(nBits));
AvalonTools::getAvalonFP(mol, *fp, nBits);
return fp;
}
#endif
// If alignOnly is set to true in details_json, original molblock wedging
// information is preserved, and inverted if needed (in case the rigid-body
// alignment required a flip around the Z axis).
// If alignOnly is set to false in details_json or not specified, original
// molblock wedging information is preserved if it only involves the invariant
// core whose coordinates never change, and is cleared in case coordinates were
// changed. If acceptFailure is set to true and no substructure match is found,
// coordinates will be recomputed from scratch, hence molblock wedging
// information will be cleared.
std::string generate_aligned_coords(ROMol &mol, const ROMol &templateMol,
const char *details_json) {
std::string res;
if (!templateMol.getNumConformers()) {
return res;
}
RDDepict::ConstrainedDepictionParams p;
bool useCoordGen = false;
std::string referenceSmarts;
if (details_json && strlen(details_json)) {
std::istringstream ss;
ss.str(details_json);
boost::property_tree::ptree pt;
boost::property_tree::read_json(ss, pt);
LPT_OPT_GET(useCoordGen);
LPT_OPT_GET(referenceSmarts);
LPT_OPT_GET2(p, allowRGroups);
LPT_OPT_GET2(p, acceptFailure);
LPT_OPT_GET2(p, alignOnly);
}
int confId = -1;
MatchVectType match;
#ifdef RDK_BUILD_COORDGEN_SUPPORT
bool oprefer = RDDepict::preferCoordGen;
RDDepict::preferCoordGen = useCoordGen;
#endif
std::unique_ptr<ROMol> refPattern;
if (!referenceSmarts.empty()) {
try {
refPattern.reset(SmartsToMol(referenceSmarts));
} catch (...) {
}
}
try {
match = RDDepict::generateDepictionMatching2DStructure(
mol, templateMol, confId, refPattern.get(), p);
} catch (...) {
}
#ifdef RDK_BUILD_COORDGEN_SUPPORT
RDDepict::preferCoordGen = oprefer;
#endif
if (match.empty()) {
res = (p.acceptFailure ? "{}" : "");
} else {
rj::Document doc;
doc.SetObject();
MinimalLib::get_sss_json(mol, templateMol, match, doc, doc);
rj::StringBuffer buffer;
rj::Writer<rj::StringBuffer> writer(buffer);
doc.Accept(writer);
res = buffer.GetString();
}
return res;
}
void get_mol_frags_details(const std::string &details_json, bool &sanitizeFrags,
bool &copyConformers) {
boost::property_tree::ptree pt;
if (!details_json.empty()) {
std::istringstream ss;
ss.str(details_json);
boost::property_tree::read_json(ss, pt);
LPT_OPT_GET(sanitizeFrags);
LPT_OPT_GET(copyConformers);
}
}
std::string get_mol_frags_mappings(
const std::vector<int> &frags,
const std::vector<std::vector<int>> &fragsMolAtomMapping) {
rj::Document doc;
doc.SetObject();
rj::Value rjFrags(rj::kArrayType);
for (int fragIdx : frags) {
rjFrags.PushBack(fragIdx, doc.GetAllocator());
}
doc.AddMember("frags", rjFrags, doc.GetAllocator());
rj::Value rjFragsMolAtomMapping(rj::kArrayType);
for (const auto &atomIdxVec : fragsMolAtomMapping) {
rj::Value rjAtomIndices(rj::kArrayType);
for (int atomIdx : atomIdxVec) {
rjAtomIndices.PushBack(atomIdx, doc.GetAllocator());
}
rjFragsMolAtomMapping.PushBack(rjAtomIndices, doc.GetAllocator());
}
doc.AddMember("fragsMolAtomMapping", rjFragsMolAtomMapping,
doc.GetAllocator());
rj::StringBuffer buffer;
rj::Writer<rj::StringBuffer> writer(buffer);
doc.Accept(writer);
return buffer.GetString();
}
#ifdef RDK_BUILD_INCHI_SUPPORT
std::string parse_inchi_options(const char *details_json) {
std::string options;
if (details_json && strlen(details_json)) {
boost::property_tree::ptree pt;
std::istringstream ss;
ss.str(details_json);
boost::property_tree::read_json(ss, pt);
LPT_OPT_GET(options);
}
return options;
}
#endif
namespace {
#ifdef RDK_BUILD_THREADSAFE_SSS
std::mutex &getLoggerMutex() {
// create on demand
static std::mutex _mutex;
return _mutex;
}
#endif
class LoggerState {
public:
// this runs only once under mutex lock
LoggerState(const std::string &logName, RDLogger &logger)
: d_logName(logName), d_logger(logger), d_lock(false) {
CHECK_INVARIANT(d_logger, "d_logger must not be null");
// store original logger stream
d_prevDest = d_logger->dp_dest;
// store whether the logger was originally enabled
d_enabled = d_logger->df_enabled;
}
LoggerState(const LoggerState &) = delete;
LoggerState &operator=(const LoggerState &) = delete;
~LoggerState() {}
void resetStream() { setStream(d_prevDest); }
void setTee(std::ostream &ostream) { d_logger->SetTee(ostream); }
void clearTee() { d_logger->ClearTee(); }
void setStream(std::ostream *ostream) {
if (d_logger->dp_dest) {
d_logger->dp_dest->flush();
}
d_logger->dp_dest = ostream;
}
void setEnabled(bool enabled, bool store = false) {
if (store) {
d_enabled = enabled;
}
if (enabled) {
boost::logging::enable_logs(d_logName);
} else if (!d_lock) {
boost::logging::disable_logs(d_logName);
}
}
bool hasLock() { return d_lock; }
bool setLock() {
if (!d_lock) {
d_lock = true;
return true;
}
return false;
}
void releaseLock() {
d_lock = false;
setEnabled(d_enabled);
}
private:
bool d_enabled = false;
std::string d_logName;
RDLogger d_logger;
std::ostream *d_prevDest;
#ifdef RDK_BUILD_THREADSAFE_SSS
std::atomic<bool> d_lock;
#else
bool d_lock;
#endif
};
typedef std::vector<LoggerState *> LoggerStatePtrVector;
class LoggerStateSingletons {
public:
static LoggerStatePtrVector *get(const std::string &logName) {
auto it = instance()->d_map.find(logName);
if (it != instance()->d_map.end()) {
return &it->second;
}
return nullptr;
}
static bool enable(const char *logNameCStr, bool enabled) {
std::string inputLogName(logNameCStr ? logNameCStr : defaultLogName());
auto loggerStates = get(inputLogName);
if (!loggerStates) {
return false;
}
#ifdef RDK_BUILD_THREADSAFE_SSS
std::lock_guard<std::mutex> lock(getLoggerMutex());
#endif
for (auto &loggerState : *loggerStates) {
loggerState->setEnabled(enabled, true);
}
return true;
}
private:
LoggerStateSingletons() {
// this runs only once under mutex lock
// and initializes LoggerState singletons
RDLog::InitLogs();
for (auto &[logName, logger] :
std::vector<std::pair<std::string, RDLogger>>{
{"rdApp.debug", rdDebugLog},
{"rdApp.info", rdInfoLog},
{"rdApp.warning", rdWarningLog},
{"rdApp.error", rdErrorLog},
}) {
d_singletonLoggerStates.emplace_back(new LoggerState(logName, logger));
auto loggerState = d_singletonLoggerStates.back().get();
CHECK_INVARIANT(loggerState, "loggerState must not be nullptr");
d_map[logName].push_back(loggerState);
d_map[defaultLogName()].push_back(loggerState);
}
}
static const char *defaultLogName() {
static const char *DEFAULT_LOG_NAME = "rdApp.*";
return DEFAULT_LOG_NAME;
}
static LoggerStateSingletons *instance() {
// this is called under mutex lock
if (!d_instance) {
d_instance.reset(new LoggerStateSingletons());
}
return d_instance.get();
}
std::vector<std::unique_ptr<LoggerState>> d_singletonLoggerStates;
std::map<std::string, LoggerStatePtrVector> d_map;
static std::unique_ptr<LoggerStateSingletons> d_instance;
};
} // end anonymous namespace
class LogHandle {
public:
~LogHandle() {
#ifdef RDK_BUILD_THREADSAFE_SSS
std::lock_guard<std::mutex> lock(getLoggerMutex());
#endif
close();
}
static bool enableLogging(const char *logNameCStr = nullptr) {
return LoggerStateSingletons::enable(logNameCStr, true);
}
static bool disableLogging(const char *logNameCStr = nullptr) {
return LoggerStateSingletons::enable(logNameCStr, false);
}
void clearBuffer() {
d_stream.str({});
d_stream.clear();
}
std::string getBuffer() {
d_stream.flush();
return d_stream.str();
}
static LogHandle *setLogTee(const char *logNameCStr) {
return setLogCommon(logNameCStr, true);
}
static LogHandle *setLogCapture(const char *logNameCStr) {
return setLogCommon(logNameCStr, false);
}
private:
LogHandle(const std::string &logName, bool isTee)
: d_logName(logName), d_isTee(isTee) {
open();
}
void open() {
// this is called under mutex lock
auto loggerStates = LoggerStateSingletons::get(d_logName);
CHECK_INVARIANT(loggerStates, "loggerStates must not be nullptr");
for (auto &loggerState : *loggerStates) {
CHECK_INVARIANT(loggerState->setLock(), "Failed to acquire lock");
if (d_isTee) {
loggerState->setTee(d_stream);
} else {
loggerState->setStream(&d_stream);
}
loggerState->setEnabled(true);
}
}
void close() {
// this is called under mutex lock
auto loggerStates = LoggerStateSingletons::get(d_logName);
CHECK_INVARIANT(loggerStates, "loggerStates must not be nullptr");
for (const auto &loggerState : *loggerStates) {
if (d_isTee) {
loggerState->clearTee();
} else {
loggerState->resetStream();
}
loggerState->releaseLock();
}
}
// returns nullptr if the requested log does not exist or is already captured
static LogHandle *setLogCommon(const char *logNameCStr, bool isTee) {
if (!logNameCStr) {
return nullptr;
}
std::string logName(logNameCStr);
#ifdef RDK_BUILD_THREADSAFE_SSS
std::lock_guard<std::mutex> lock(getLoggerMutex());
#endif
auto loggerStates = LoggerStateSingletons::get(logName);
if (loggerStates && std::none_of(loggerStates->begin(), loggerStates->end(),
[](const auto &loggerState) {
return loggerState->hasLock();
})) {
return new LogHandle(logName, isTee);
}
return nullptr;
}
std::string d_logName;
bool d_isTee;
std::stringstream d_stream;
};
} // namespace MinimalLib
} // namespace RDKit
#undef LPT_OPT_GET
#undef LPT_OPT_GET2
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