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Support conversion to CMLR #2694

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Support conversion to CMLR #2694

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52 changes: 52 additions & 0 deletions src/formats/xml/cmlreactformat.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -11,13 +11,15 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
***********************************************************************/

#include <memory>
#include "openbabel/babelconfig.h"
#include <openbabel/mol.h>
#include <openbabel/atom.h>
#include <openbabel/bond.h>
#include <openbabel/obiter.h>
#include <openbabel/elements.h>
#include "openbabel/reaction.h"
#include "openbabel/reactionfacade.h"
#include "openbabel/xml.h"
#include "openbabel/kinetics.h"
#include "openbabel/text.h"
Expand All @@ -27,6 +29,36 @@ using namespace std;
namespace OpenBabel
{

unique_ptr<OBReaction> convertToReaction(OBMol *mol) {
OBReactionFacade rf(mol);

// Check if the molecule is in a valid state to represent a reaction
if (rf.IsValid()) {
OBMol compMol;
auto reaction = unique_ptr<OBReaction>(new OBReaction());
// Iterate over reaction roles and components
for (unsigned role = OBReactionRole::REACTANT; role <= OBReactionRole::PRODUCT; ++role) {
unsigned numComponents = rf.NumComponents(static_cast<OBReactionRole>(role));
for (unsigned i = 0; i < numComponents; ++i) {
if (rf.GetComponent(&compMol, static_cast<OBReactionRole>(role), i)) {
auto sharedCompMol = make_shared<OBMol>(compMol);
if (role == OBReactionRole::REACTANT) {
reaction->AddReactant(sharedCompMol);
} else if (role == OBReactionRole::PRODUCT) {
reaction->AddProduct(sharedCompMol);
} else {
reaction->AddAgent(sharedCompMol);
}
}
}
}
return reaction;
} else {
obErrorLog.ThrowError(__FUNCTION__, "Cannot convert to OBReaction", obError);
}
return unique_ptr<OBReaction>();
}

class CMLReactFormat : XMLBaseFormat
{
public:
Expand Down Expand Up @@ -317,6 +349,16 @@ bool CMLReactFormat::WriteChemObject(OBConversion* pConv)
//WriteChemObject() always deletes the object retrieved by GetChemObject
OBBase* pOb=pConv->GetChemObject();
OBReaction* pReact = dynamic_cast<OBReaction*>(pOb);

unique_ptr<OBReaction> upReact;
if (!pReact) {
OBMol* mol = dynamic_cast<OBMol*>(pOb);
if (mol && mol->IsReaction()) {
upReact = convertToReaction(mol);
pReact = upReact.get();
}
}

if (pReact == nullptr)
{
//If sent a molecule, add it to the list.
Expand Down Expand Up @@ -413,6 +455,16 @@ bool CMLReactFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)

//Cast output object to the class type need, i.e. OBReaction
OBReaction* pReact = dynamic_cast<OBReaction*>(pOb);

unique_ptr<OBReaction> upReact;
if (!pReact) {
OBMol* mol = dynamic_cast<OBMol*>(pOb);
if (mol && mol->IsReaction()) {
upReact = convertToReaction(mol);
pReact = upReact.get();
}
}

if (pReact == nullptr)
return false;

Expand Down