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rdkit/Code/GraphMol/MarvinParse/MarvinParser.cpp
Greg Landrum e35f7db009 Cleanup/get atoms and bonds (#9243)
2026-04-18 05:22:09 +02:00

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//
// Copyright (C) 2022-2023 Tad Hurst, Greg Landrum and other RDKit contributors
//
// @@ 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.
//
// this file parses MRV file for molecules and reactions
#include <string>
#include <exception>
#include <fstream>
#include <vector>
#include <sstream>
#include <iomanip>
#include <cfloat>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolSGroupParsing.h>
#include <GraphMol/FileParsers/MolFileStereochem.h>
#include "MarvinParser.h"
#include "MarvinDefs.h"
#include <GraphMol/Conformer.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/Atropisomers.h>
#include <GraphMol/Chirality.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/StereoGroup.h>
#include <GraphMol/SubstanceGroup.h>
#include "MarvinParser.h"
#include <RDGeneral/StreamOps.h>
#include <RDGeneral/FileParseException.h>
#include <RDGeneral/BadFileException.h>
#include <RDGeneral/LocaleSwitcher.h>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/algorithm/string.hpp>
#include <RDGeneral/BoostEndInclude.h>
namespace RDKit {
namespace v2 {
namespace MarvinParser {
/*
Imports the Marvin-specific dialect of CML (Chemical Markup Language) and
converts it to datastructures that are compatible with Molfile, RXNfile, and
Molfile complemented with canvas objects.
*/
class MarvinCMLReader {
public:
MarvinCMLReader() {};
~MarvinCMLReader() {};
std::unique_ptr<RWMol> parseMolecule(boost::property_tree::ptree molTree,
bool sanitize = false,
bool removeHs = false) {
boost::property_tree::ptree molSection;
try {
molSection = molTree.get_child("cml.MDocument.MChemicalStruct.molecule");
} catch (const std::exception &) {
try {
molSection = molTree.get_child("cml.MDocument");
return std::make_unique<RWMol>();
} catch (const std::exception &) {
try {
molSection = molTree.get_child("cml");
return std::make_unique<RWMol>();
} catch (const std::exception &) {
throw FileParseException("Expected \"molecule\" in MRV file");
}
}
}
std::unique_ptr<MarvinMol> marvinMol{
(MarvinMol *)parseMarvinMolecule(molSection)};
marvinMol->prepSgroupsForRDKit();
return parseMolecule(marvinMol.get(), sanitize, removeHs);
}
std::unique_ptr<ChemicalReaction> parseReaction(
boost::property_tree::ptree rxnTree,
boost::property_tree::ptree documentTree, bool sanitize = false,
bool removeHs = false) {
std::unique_ptr<ChemicalReaction> rxn{new ChemicalReaction()};
rxnTree = rxnTree.get_child("cml.MDocument.MChemicalStruct.reaction");
std::unique_ptr<MarvinReaction> marvinReaction{
parseMarvinReaction(rxnTree, documentTree)};
marvinReaction->prepSgroupsForRDKit();
// get each reactant
for (auto &mol : marvinReaction->reactants) {
rxn->addReactantTemplate(
ROMOL_SPTR(parseMolecule(mol.get(), sanitize, removeHs)));
}
// get each agent
for (auto &mol : marvinReaction->agents) {
rxn->addAgentTemplate(
ROMOL_SPTR(parseMolecule(mol.get(), sanitize, removeHs)));
}
// get each product
for (auto &mol : marvinReaction->products) {
rxn->addProductTemplate(
ROMOL_SPTR(parseMolecule(mol.get(), sanitize, removeHs)));
}
// convert atoms to queries:
for (auto mol : rxn->getReactants()) {
for (auto atom : mol->atoms()) {
QueryOps::replaceAtomWithQueryAtom(static_cast<RWMol *>(mol.get()),
atom);
}
}
for (auto mol : rxn->getProducts()) {
for (auto atom : mol->atoms()) {
QueryOps::replaceAtomWithQueryAtom(static_cast<RWMol *>(mol.get()),
atom);
}
}
marvinReaction->prepSgroupsForRDKit();
return rxn;
}
Atom *molAtomFromMarvinAtom(const MarvinAtom *marvinAtom,
const MarvinMolBase *marvinMolBase) {
PRECONDITION(marvinAtom, "bad marvin atom");
PRECONDITION(marvinMolBase, "bad marvin mol");
Atom *res = nullptr;
try {
std::string symb = marvinAtom->elementType;
boost::trim(symb);
if (symb == "*") {
auto *query = new QueryAtom(0); // wHAT IS AUTO *
res = query;
query->setQuery(makeAtomNullQuery());
query->setProp(common_properties::dummyLabel, "*");
// queries have no implicit Hs:
res->setNoImplicit(true);
} else if (symb == "R") {
// It must have an rgroupRef/>
if (marvinAtom->rgroupRef < 0) {
throw FileParseException(
"Expected an R group atom to have an rgroupRef designation");
}
auto *query = new QueryAtom(0); // wHAT IS AUTO *
res = query;
query->setProp(common_properties::_MolFileRLabel,
marvinAtom->rgroupRef);
std::string dLabel = "R" + std::to_string(marvinAtom->rgroupRef);
query->setProp(common_properties::dummyLabel, dLabel);
if (marvinAtom->mrvAlias != "") {
query->setProp(common_properties::molFileAlias, marvinAtom->mrvAlias);
}
query->setQuery(makeAtomNullQuery());
query->setIsotope(marvinAtom->rgroupRef);
query->setProp(common_properties::_MolFileRLabel,
static_cast<unsigned int>(marvinAtom->rgroupRef));
}
else if (symb.size() <= 2) {
// must be a regular atom
if (symb.size() == 2 && symb[1] >= 'A' && symb[1] <= 'Z') {
symb[1] = static_cast<char>(tolower(symb[1]));
}
res = new Atom();
try {
res->setAtomicNum(PeriodicTable::getTable()->getAtomicNumber(symb));
} catch (const Invar::Invariant &e) {
delete res;
res = nullptr;
throw FileParseException(e.what());
}
} else {
throw FileParseException("Unrecognized atom type in MRV file");
}
// res->setPos(marvinAtom.x2,marvinAtom->y2,0.0);
if (marvinAtom->formalCharge != 0) {
res->setFormalCharge(marvinAtom->formalCharge);
}
if (marvinAtom->isotope != 0) {
res->setIsotope(marvinAtom->isotope);
}
// mrvValence and hydrogenCount both set the number of explicit hydrogens
// if both are present, they must agreee
if (marvinAtom->hydrogenCount >= 0) {
res->setNumExplicitHs(marvinAtom->hydrogenCount);
}
if (marvinAtom->mrvValence >= 0) {
int explicitValence = marvinMolBase->getExplicitValence(*marvinAtom);
// if (explicitValence > marvinAtom->mrvValence)
// throw FileParseException("atom has specified valence (" +
// std::to_string(marvinAtom->mrvValence) + ") smaller than the drawn
// valence");
int hCount = marvinAtom->mrvValence - explicitValence;
if (hCount >= 0) {
if (marvinAtom->hydrogenCount >= 0) {
if (marvinAtom->hydrogenCount != hCount) {
throw FileParseException(
"mrvValence and hydrogenCount both specified for an atom, and they do not agree");
}
} else {
res->setNoImplicit(true);
res->setNumExplicitHs(hCount);
}
}
}
if (marvinAtom->radical != "") {
res->setNumRadicalElectrons(
marvinRadicalToRadicalElectrons.at(marvinAtom->radical));
}
if (marvinAtom->mrvMap != 0) {
res->setProp(common_properties::molAtomMapNumber, marvinAtom->mrvMap);
}
return res;
} catch (const std::exception &) {
delete res;
res = nullptr;
throw;
}
}
void molBondFromMarvinBond(const MarvinBond *marvinBond,
const MarvinMol *marvinMol, RWMol *mol,
bool &chiralityPossible) {
PRECONDITION(marvinBond, "bad marvin bond");
PRECONDITION(marvinMol, "bad marvin mol");
unsigned int bType = UINT_MAX;
Bond *bond = nullptr;
try {
int idx1 = marvinMol->getAtomIndex(marvinBond->atomRefs2[0]);
int idx2 = marvinMol->getAtomIndex(marvinBond->atomRefs2[1]);
Bond::BondType type = Bond::UNSPECIFIED;
;
// if there is a query type, that takes precidence over the bond type
std::string marvinBondType = marvinBond->getBondType();
if (marvinBondType == "SD") {
bType = 5;
type = Bond::UNSPECIFIED;
bond = new QueryBond;
bond->setQuery(makeSingleOrDoubleBondQuery());
} else if (marvinBondType == "SA") {
bType = 6;
type = Bond::UNSPECIFIED;
bond = new QueryBond;
bond->setQuery(makeSingleOrAromaticBondQuery());
} else if (marvinBondType == "DA") {
bType = 7;
type = Bond::UNSPECIFIED;
bond = new QueryBond;
bond->setQuery(makeDoubleOrAromaticBondQuery());
} else if (marvinBondType == "ANY") {
bType = 8;
type = Bond::UNSPECIFIED;
bond = new QueryBond;
bond->setQuery(makeBondNullQuery());
} else if (marvinBondType == "DATIVE") {
bond = new Bond();
type = Bond::DATIVE;
bType = 1;
} else if (marvinBondType == "HYDROGEN") {
bond = new Bond();
type = Bond::HYDROGEN;
bType = 1;
} else if (marvinBondType == "1") {
type = Bond::SINGLE;
bond = new Bond;
bType = 1;
} else if (marvinBondType == "2") {
type = Bond::DOUBLE;
bond = new Bond;
bType = 2;
} else if (marvinBondType == "3") {
type = Bond::TRIPLE;
bond = new Bond;
bType = 3;
} else if (marvinBondType == "A") {
bType = 4;
type = Bond::AROMATIC;
bond = new Bond;
}
bond->setBeginAtomIdx(idx1);
bond->setEndAtomIdx(idx2);
Bond::BondDir bondDir = Bond::NONE;
Bond::BondStereo bondStereo = Bond::STEREONONE;
unsigned int cfg = 0;
std::string temp =
boost::algorithm::to_lower_copy(marvinBond->bondStereo.value);
if (temp != "") {
if (temp == "w") {
bondDir = Bond::BEGINWEDGE;
} else if (temp == "h") {
bondDir = Bond::BEGINDASH;
} else {
std::ostringstream err;
err << "unrecognized bond stereo value"
<< marvinBond->bondStereo.value;
throw FileParseException(err.str());
}
} else if (marvinBond->bondStereo.convention != "") {
if (marvinBond->bondStereo.convention != "MDL") {
std::ostringstream err;
err << "unrecognized bond stereo conventrion"
<< marvinBond->bondStereo.convention;
throw FileParseException(err.str());
}
int mdlStereoVal = 0;
if (!getCleanNumber(marvinBond->bondStereo.conventionValue,
mdlStereoVal)) {
throw FileParseException(
"MDL Convention Value must be one of: 1, 3, 4, 6");
}
switch (mdlStereoVal) {
case 1:
bondDir = Bond::BEGINWEDGE;
break;
case 6:
bondDir = Bond::BEGINDASH;
break;
case 3: // "either" double bond
bondDir = Bond::EITHERDOUBLE;
break;
case 4: // "either" single bond
bondDir = Bond::UNKNOWN;
break;
default:
throw FileParseException(
"MDL Convention Value must be one of: 1, 3, 4, 6");
}
} else if (marvinBond->bondStereo.dictRef != "") {
if (marvinBond->bondStereo.dictRef == "cml:W") {
bondDir = Bond::BEGINWEDGE;
} else if (marvinBond->bondStereo.dictRef == "cml:H") {
bondDir = Bond::BEGINDASH;
} else {
throw FileParseException("dictRef must be one of: cml:W or cml:H");
}
} else {
// nothing to do, no stereo information
}
switch (bondDir) {
case Bond::BEGINWEDGE:
bType = 1; // overrides the type specification
type = Bond::SINGLE;
chiralityPossible = true;
cfg = 1;
break;
case Bond::BEGINDASH:
bType = 1; // overrides the type specification
type = Bond::SINGLE;
cfg = 3;
chiralityPossible = true;
break;
case Bond::EITHERDOUBLE:
bondStereo = Bond::STEREOANY;
bType = 2; // overrides the type specification
type = Bond::DOUBLE;
cfg = 2;
break;
case Bond::UNKNOWN:
bType = 1; // overrides the type specification
type = Bond::SINGLE;
cfg = 2;
break;
default:
// nothing to do
break;
}
bond->setBondType(type);
bond->setProp(common_properties::_MolFileBondType, bType);
bond->setBondDir(bondDir);
if (cfg != 0) {
bond->setProp(common_properties::_MolFileBondCfg, cfg);
}
if (bondStereo != Bond::STEREONONE) {
bond->setStereo(bondStereo);
}
// if we got an aromatic bond set the flag on the bond and the connected
// atoms)
if (bond->getBondType() == Bond::AROMATIC) {
bond->setIsAromatic(true);
}
mol->addBond(bond, true);
} catch (const std::exception &) {
delete bond;
throw;
}
}
std::unique_ptr<RWMol> parseMolecule(MarvinMol *marvinMol,
bool sanitize = false,
bool removeHs = false) {
PRECONDITION(marvinMol, "no molecule");
std::vector<MarvinStereoGroup *> stereoGroups;
std::unique_ptr<Conformer> confPtr;
Conformer *conf = nullptr;
std::unique_ptr<Conformer> conf3dPtr;
Conformer *conf3d = nullptr;
std::unique_ptr<RWMol> mol{new RWMol()};
try {
mol->setProp("_MolFileComments", "Generated by RDKit");
// set the atoms
if (marvinMol->hasAny2dCoords()) {
conf = new Conformer(marvinMol->atoms.size());
confPtr = std::unique_ptr<Conformer>(conf);
confPtr->set3D(false);
}
if (marvinMol->hasAny3dCoords()) {
conf3d = new Conformer(marvinMol->atoms.size());
conf3dPtr = std::unique_ptr<Conformer>(conf3d);
conf3d->set3D(true);
}
for (auto atomPtr : marvinMol->atoms) {
Atom *atom = molAtomFromMarvinAtom(atomPtr, marvinMol);
unsigned int aid = mol->addAtom(atom, false, true);
if (conf != nullptr) {
RDGeom::Point3D pos;
if (atomPtr->x2 != DBL_MAX && atomPtr->y2 != DBL_MAX) {
pos.x = atomPtr->x2;
pos.y = atomPtr->y2;
} else {
pos.x = 0.0;
pos.y = 0.0;
}
pos.z = 0.0;
conf->setAtomPos(aid, pos);
}
if (conf3d != nullptr) {
RDGeom::Point3D pos;
if (atomPtr->x3 != DBL_MAX && atomPtr->y3 != DBL_MAX &&
atomPtr->z3 != DBL_MAX) {
pos.x = atomPtr->x3;
pos.y = atomPtr->y3;
pos.z = atomPtr->z3;
} else {
pos.x = 0.0;
pos.y = 0.0;
pos.z = 0.0;
}
conf3d->setAtomPos(aid, pos);
}
// also collect the stereo groups here
if (atomPtr->mrvStereoGroup != "") {
RDKit::StereoGroupType groupType;
int groupNumber;
// get the group parts
std::string temp =
boost::algorithm::to_lower_copy(atomPtr->mrvStereoGroup);
if (temp == "abs") {
groupType = RDKit::StereoGroupType::STEREO_ABSOLUTE;
groupNumber = (-1);
} else if (boost::starts_with(temp, "and")) {
groupType = RDKit::StereoGroupType::STEREO_AND;
if (!getCleanNumber(temp.substr(3), groupNumber)) {
throw FileParseException(
"Group Number must be an integer in a stereo group AND# in a MRV file");
}
} else if (boost::starts_with(temp, "or")) {
groupType = RDKit::StereoGroupType::STEREO_OR;
if (!getCleanNumber(temp.substr(2), groupNumber)) {
throw FileParseException(
"Group Number must be an integer in a stereo group OR# in a MRV file");
}
} else {
throw FileParseException("Unrecognized group definition");
}
// see if the group already exists
MarvinStereoGroup *marvinStereoGroup;
auto groupIter =
find_if(stereoGroups.begin(), stereoGroups.end(),
[groupType, groupNumber](const MarvinStereoGroup *arg) {
return arg->groupNumber == groupNumber &&
arg->groupType == groupType;
});
if (groupIter != stereoGroups.end()) {
marvinStereoGroup = *groupIter;
} else {
marvinStereoGroup = new MarvinStereoGroup(groupType, groupNumber);
stereoGroups.push_back(marvinStereoGroup);
}
// add this atom to the group
marvinStereoGroup->atoms.push_back(
(unsigned int)marvinMol->getAtomIndex(atomPtr->id));
}
}
if (conf != nullptr) {
mol->addConformer(conf, true);
confPtr.release();
}
if (conf3d != nullptr) {
mol->addConformer(conf3d, true);
conf3dPtr.release();
}
// set the bonds
bool chiralityPossible = false;
for (auto bondPtr : marvinMol->bonds) {
molBondFromMarvinBond(bondPtr, marvinMol, mol.get(), chiralityPossible);
}
// add the stereo groups
std::vector<StereoGroup> groups;
for (auto groupPtr : stereoGroups) {
std::vector<Atom *> atoms;
std::vector<Bond *> bonds;
for (auto atomPtr : groupPtr->atoms) {
atoms.push_back(mol->getAtomWithIdx(atomPtr));
}
groups.emplace_back(groupPtr->groupType, std::move(atoms),
std::move(bonds), groupPtr->groupNumber);
}
if (!groups.empty()) {
mol->setStereoGroups(std::move(groups));
}
// // add the sgroup records
int sequenceId = 0;
// now the SuperatomSgroupsExpanded
for (auto &marvinSgroup : marvinMol->sgroups) {
auto sgroup = std::unique_ptr<SubstanceGroup>();
marvinSgroup->parseMoleculeSpecific(mol.get(), sgroup, sequenceId);
if (sgroup->getIsValid()) {
addSubstanceGroup(*mol, *sgroup.get());
}
// increment the sequenceId
sequenceId++;
}
mol->clearAllAtomBookmarks();
mol->clearAllBondBookmarks();
// calculate explicit valence on each atom:
for (auto atom : mol->atoms()) {
atom->calcExplicitValence(false);
atom->calcImplicitValence(false);
}
// update the chirality and stereo-chemistry
//
// NOTE: we detect the stereochemistry before sanitizing/removing
// hydrogens because the removal of H atoms may actually remove
// the wedged bond from the molecule. This wipes out the only
// sign that chirality ever existed and makes us sad... so first
// perceive chirality, then remove the Hs and sanitize.
//
if (chiralityPossible && conf != nullptr) {
DetectAtomStereoChemistry(*mol, conf);
} else if (conf3d != nullptr) {
mol->updatePropertyCache(false);
MolOps::assignChiralTypesFrom3D(*mol, conf3d->getId(), true);
}
if (conf) {
Atropisomers::detectAtropisomerChirality(*mol, conf);
} else if (conf3d) {
Atropisomers::detectAtropisomerChirality(*mol, conf3d);
} else {
Atropisomers::detectAtropisomerChirality(*mol, nullptr);
}
ClearSingleBondDirFlags(*mol);
if (sanitize) {
if (removeHs) {
// Bond stereo detection must happen before H removal, or
// else we might be removing stereogenic H atoms in double
// bonds (e.g. imines). But before we run stereo detection,
// we need to run mol cleanup so don't have trouble with
// e.g. nitro groups. Sadly, this a;; means we will find
// run both cleanup and ring finding twice (a fast find
// rings in bond stereo detection, and another in
// sanitization's SSSR symmetrization).
unsigned int failedOp = 0;
MolOps::sanitizeMol(*mol, failedOp, MolOps::SANITIZE_CLEANUP);
MolOps::detectBondStereochemistry(*mol);
MolOps::removeHs(*mol);
} else {
MolOps::sanitizeMol(*mol);
MolOps::detectBondStereochemistry(*mol);
}
MolOps::assignStereochemistry(*mol, true, true, true);
} else {
MolOps::detectBondStereochemistry(*mol);
}
if (mol->hasProp(common_properties::_NeedsQueryScan)) {
mol->clearProp(common_properties::_NeedsQueryScan);
QueryOps::completeMolQueries(mol.get());
}
// clean up
for (auto &stereoGroup : stereoGroups) {
delete stereoGroup;
}
return mol;
}
catch (const std::exception &) {
for (auto &stereoGroup : stereoGroups) {
delete stereoGroup;
}
throw;
}
}
MarvinMolBase *parseMarvinMolecule(
boost::property_tree::ptree molTree,
MarvinMolBase *parentMol = nullptr) // parent is for sub-mols
{
MarvinMolBase *res = nullptr;
try {
std::string role = "";
if (parentMol == nullptr) {
res = new MarvinMol(molTree);
} else // is is a sub-mol - used for sGroups
{
role = molTree.get<std::string>("<xmlattr>.role", "");
if (role == "") {
throw FileParseException(
"Expected a role for a sub-molecule in MRV file");
}
if (role == "SuperatomSgroup") {
// there are two types of superatomSgroups - regular and expanded.
// Expanded has a molecule attr of atomRefs
std::string atomRefs =
molTree.get<std::string>("<xmlattr>.atomRefs", "");
auto atomArray = molTree.get_child_optional("atomArray");
if (atomRefs == "" &&
atomArray) // no atomRefs means regular superatom
// - the atoms are in this superatom
{
res = new MarvinSuperatomSgroup(parentMol, molTree);
} else // if atomRefs and atomArray does not exist, this is an
// expanded superatom - the atoms are already in the parent
// mol
{
res = new MarvinSuperatomSgroupExpanded(parentMol, molTree);
}
} else if (role == "SruSgroup" || role == "CopolymerSgroup" ||
role == "ModificationSgroup") {
res = new MarvinSruCoModSgroup(parentMol, role, molTree);
} else if (role == "MultipleSgroup") {
res = new MarvinMultipleSgroup(parentMol, molTree);
} else if (role == "MulticenterSgroup") {
res = new MarvinMulticenterSgroup(parentMol, molTree);
} else if (role == "GenericSgroup") {
res = new MarvinGenericSgroup(parentMol, molTree);
} else if (role == "MonomerSgroup") {
res = new MarvinMonomerSgroup(parentMol, molTree);
} else if (role == "DataSgroup") {
res = new MarvinDataSgroup(parentMol, molTree);
} else {
throw FileParseException("Unexpected role " + role + " in MRV file");
}
}
for (auto &v : molTree) {
if (v.first == "molecule") {
auto *subMol = parseMarvinMolecule(v.second, res);
res->sgroups.push_back(std::unique_ptr<MarvinMolBase>(subMol));
}
}
return res;
} catch (const std::exception &) {
delete res;
throw;
}
};
MarvinReaction *parseMarvinReaction(
boost::property_tree::ptree rxnTree,
boost::property_tree::ptree documentTree,
bool parseArrowPlusesAndConditions =
false) // Arrows etc are not used in RDKIT) {
{
auto *res = new MarvinReaction();
try {
boost::property_tree::ptree childTree;
bool foundChild = false;
try {
childTree = rxnTree.get_child("reactantList");
foundChild = true;
} catch (const std::exception &) {
foundChild = false;
}
if (foundChild) {
for (auto &v : childTree) {
res->reactants.push_back(std::unique_ptr<MarvinMol>(
(MarvinMol *)parseMarvinMolecule(v.second)));
}
}
try {
childTree = rxnTree.get_child("agentList");
foundChild = true;
} catch (const std::exception &) {
foundChild = false;
}
if (foundChild) {
for (auto &v : childTree) {
res->agents.push_back(std::unique_ptr<MarvinMol>(
(MarvinMol *)parseMarvinMolecule(v.second)));
}
}
try {
childTree = rxnTree.get_child("productList");
foundChild = true;
} catch (const std::exception &) {
foundChild = false;
}
if (foundChild) {
for (auto &v : childTree) {
res->products.push_back(std::unique_ptr<MarvinMol>(
(MarvinMol *)parseMarvinMolecule(v.second)));
}
}
if (parseArrowPlusesAndConditions) {
// <arrow type="DEFAULT" x1="-11.816189911577812"
// y1="-10.001443743444021" x2="-8.401759471454618"
// y2="-10.001443743444021"/>
boost::property_tree::ptree arrow = rxnTree.get_child("arrow");
res->arrow.type = arrow.get<std::string>("<xmlattr>.type", "");
if (!getCleanNumber(arrow.get<std::string>("<xmlattr>.x1", ""),
res->arrow.x1) ||
!getCleanNumber(arrow.get<std::string>("<xmlattr>.y1", ""),
res->arrow.y1) ||
!getCleanNumber(arrow.get<std::string>("<xmlattr>.x2", ""),
res->arrow.x2) ||
!getCleanNumber(arrow.get<std::string>("<xmlattr>.y2", ""),
res->arrow.y1)) {
throw FileParseException(
"Arrow coordinates must all be large floating point numbers in MRV file");
}
for (auto &v : documentTree) {
if (v.first != "MReactionSign") {
continue;
}
auto *marvinPlus = new MarvinPlus();
res->pluses.push_back(std::unique_ptr<MarvinPlus>(marvinPlus));
marvinPlus->id = v.second.get<std::string>("<xmlattr>.id", "");
int pointCount = 0;
for (auto &v2 : v.second) {
if (v2.first == "MPoint") {
double x;
double y;
if (!getCleanNumber(v2.second.get<std::string>("<xmlattr>.x", ""),
x) ||
!getCleanNumber(v2.second.get<std::string>("<xmlattr>.y", ""),
y)) {
throw FileParseException(
"Plus sign coordinates must all be large floating point numbers in MRV file");
}
switch (pointCount) {
case 0: // first point - x1 and y1 are set
marvinPlus->x1 = x;
marvinPlus->y1 = y;
break;
case 1: // x2 is set, y1 is checked
marvinPlus->x2 = x;
if (marvinPlus->y1 != y) {
throw FileParseException(
"Plus sign coordinate Y in 2nd MPoint must be the same as that from the 1st MPoint in MRV file");
}
break;
case 2: // y2 is set, x2 is checked
marvinPlus->y2 = y;
if (marvinPlus->x2 != x) {
throw FileParseException(
"Plus sign coordinate X in 3rd MPoint must be the same as that from the 2nd MPoint in MRV file");
}
break;
case 3: // x2 and y2 are checked
if (marvinPlus->x1 != x) {
throw FileParseException(
"Plus sign coordinate X in 4th MPoint must be the same as that from the 1st MPoint in MRV file");
}
if (marvinPlus->y2 != y) {
throw FileParseException(
"Plus sign coordinate Y in 4th MPoint must be the same as that from the 3rd MPoint in MRV file");
}
break;
default:
throw FileParseException(
"Plus sign coordinate must have 4 MPoints in MRV file");
}
++pointCount;
}
}
}
for (auto &v : documentTree) {
if (v.first != "MTextBox") {
continue;
}
auto *marvinCondition = new MarvinCondition();
res->conditions.push_back(
std::unique_ptr<MarvinCondition>(marvinCondition));
marvinCondition->id = v.second.get<std::string>("<xmlattr>.id", "");
marvinCondition->halign =
v.second.get<std::string>("<xmlattr>.halign", "");
marvinCondition->valign =
v.second.get<std::string>("<xmlattr>.valign", "");
double fontScale;
std::string fontScaleStr =
v.second.get<std::string>("<xmlattr>.fontScale", "");
if (fontScaleStr != "") {
if (!getCleanNumber(fontScaleStr, fontScale)) {
throw FileParseException(
"Condition font scale must be a positive integer in MRV file");
}
} else {
fontScale = 0.0;
}
marvinCondition->fontScale = fontScale;
marvinCondition->text = v.second.get<std::string>("Field", "");
int pointCount = 0;
for (auto &v2 : v.second) {
if (v2.first == "MPoint") {
double x, y;
std::string xStr = v2.second.get<std::string>("<xmlattr>.x", "");
std::string yStr = v2.second.get<std::string>("<xmlattr>.y", "");
if (!getCleanNumber(xStr, x) || !getCleanNumber(yStr, y)) {
throw FileParseException(
"Condition coordinate must valid integers in MRV file");
}
switch (pointCount) {
case 0: // first point - x1 and y1 are set
marvinCondition->x = x;
marvinCondition->y = y;
break;
case 1:
case 2:
case 3: // x and Y are checked - must be the same as point 1
break;
default:
throw FileParseException(
"Condition defs must have 4 MPoints in MRV file");
}
++pointCount;
}
}
}
} // end of if (parseArrowPlusesAndConditions)
return res;
} catch (const std::exception &) {
delete res;
throw;
}
}
};
bool MrvDataStreamIsReaction(std::istream &inStream) {
PRECONDITION(inStream, "no stream");
Utils::LocaleSwitcher ls;
ptree tree;
// Parse the XML into the property tree.
read_xml(inStream, tree);
// see if the reaction header is present
try {
auto rxn = tree.get_child("cml.MDocument.MChemicalStruct.reaction");
} catch (const std::exception &) {
return false;
}
return true;
}
bool MrvDataStreamIsReaction(std::istream *inStream) {
PRECONDITION(inStream, "no stream");
return MrvDataStreamIsReaction(*inStream);
}
bool MrvBlockIsReaction(const std::string &molmrvText) {
std::istringstream inStream(molmrvText);
return MrvDataStreamIsReaction(inStream);
}
bool MrvFileIsReaction(const std::string &fName) {
std::ifstream inStream(fName.c_str());
if (!inStream || (inStream.bad())) {
std::ostringstream errout;
errout << "Bad input file " << fName;
throw BadFileException(errout.str());
}
if (!inStream.eof()) {
return MrvDataStreamIsReaction(inStream);
}
return false;
}
//------------------------------------------------
//
// Read a RWMol from a stream
//
//------------------------------------------------
std::unique_ptr<RWMol> MolFromMrvDataStream(std::istream &inStream,
const MrvParserParams &params) {
ptree tree;
// Parse the XML into the property tree.
read_xml(inStream, tree);
MarvinCMLReader reader;
return reader.parseMolecule(tree, params.sanitize, params.removeHs);
}
//------------------------------------------------
//
// Read a RWMol from a string
//
//------------------------------------------------
std::unique_ptr<RWMol> MolFromMrvBlock(const std::string &molmrvText,
const MrvParserParams &params) {
std::istringstream inStream(molmrvText);
return MolFromMrvDataStream(inStream, params);
}
//------------------------------------------------
//
// Read an RWMol from a file
//
//------------------------------------------------
std::unique_ptr<RWMol> MolFromMrvFile(const std::string &fName,
const MrvParserParams &params) {
std::ifstream inStream(fName.c_str());
if (!inStream || (inStream.bad())) {
std::ostringstream errout;
errout << "Bad input file " << fName;
throw BadFileException(errout.str());
}
if (inStream.eof()) {
return nullptr;
}
return MolFromMrvDataStream(inStream, params);
}
//------------------------------------------------
//
// Read a ChemicalReaction from a stream
//
//------------------------------------------------
std::unique_ptr<ChemicalReaction> ReactionFromMrvDataStream(
std::istream &inStream, const MrvParserParams &params) {
PRECONDITION(inStream, "no stream");
Utils::LocaleSwitcher ls;
ptree tree;
// Parse the XML into the property tree.
read_xml(inStream, tree);
MarvinCMLReader reader;
return reader.parseReaction(tree, tree.get_child("cml.MDocument"),
params.sanitize, params.removeHs);
}
//------------------------------------------------
//
// Read a ChemicalReaction from a string
//
//------------------------------------------------
std::unique_ptr<ChemicalReaction> ReactionFromMrvBlock(
const std::string &molmrvText, const MrvParserParams &params) {
std::istringstream inStream(molmrvText);
return ReactionFromMrvDataStream(inStream, params);
}
//------------------------------------------------
//
// Read a ChemicalReaction from a file
//
//------------------------------------------------
std::unique_ptr<ChemicalReaction> ReactionFromMrvFile(
const std::string &fName, const MrvParserParams &params) {
std::ifstream inStream(fName.c_str());
if (!inStream || (inStream.bad())) {
std::ostringstream errout;
errout << "Bad input file " << fName;
throw BadFileException(errout.str());
}
return ReactionFromMrvDataStream(inStream, params);
}
} // namespace MarvinParser
} // namespace v2
} // namespace RDKit
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