path: root/cad/plugins/NanoVision-1/src/Plugins/NanorexMMPImportExport/NanorexMMPImportExport.rl

// *********************** GENERATED BY RAGEL 6.0 *******************
// ** Do not edit directly. Edit NanorexMMPImportExport.rl instead **
// ******************************************************************

// Copyright 2008 Nanorex, Inc.  See LICENSE file for details.

#include "NanorexMMPImportExport.h"
#include <Nanorex/Interface/NXAtomData.h>
#include <Nanorex/Utility/NXUtility.h>
#include <QFileInfo>

#define VERBOSE

#if defined(VERBOSE)

#if 0
#define CDEBUG(s) DEBUG_MSG(inputFilename, lineNum, s)
inline void DEBUG_MSG(string const& filename, int line, string const& s)
{
	NXLOG_DEBUG(filename, NXUtility::itos(line)+": "+s);
/*    Nanorex::NXLogger* logger = Nanorex::NXLogger::Instance();
    if (logger != 0)
        logger->log(Nanorex::NXLogLevel_Info, filename, msg.str());*/
}
#endif

#define CERR(s) { cerr << inputFilename << ": " << NXUtility::itos(lineNum) \
<< ": " << s << endl; }
// #define CDEBUG(s) NXLOG_DEBUG(inputFilename, NXUtility::itos(lineNum)+": "+s)
#define CDEBUG(s) { cerr << inputFilename << ": " << NXUtility::itos(lineNum) \
<< ": " << s << endl; }
#define CLOG(s) NXLOG_INFO(inputFilename, NXUtility::itos(lineNum)+": "+s)

#else
#define CDEBUG(s)
#define CLOG(s)
#endif

#define CSEVERE(s) NXLOG_SEVERE(inputFilename, NXUtility::itos(lineNum)+": "+s)



%%{
# Ragel fsm
	
	machine mmp_parser;
	
	include group "group.rl";
	
	
	mmpformat_line =
		'mmpformat'  nonNEWLINEspace+
		digit{6} nonNEWLINEspace+
		'required' nonNEWLINEspace*
		(   ';' nonNEWLINEspace+
		    digit{6} nonNEWLINEspace+
		    'preferred'
		)?
		nonNEWLINEspace*
		EOL;
	
	kelvin_line =
		'kelvin'
		nonNEWLINEspace+
		whole_number % { kelvinTemp = intVal; }
	nonNEWLINEspace*
		EOL;
	
	end_line = 'end' nonNEWLINEspace+;
	
	
main := (nonNEWLINEspace* EOL)*
		mmpformat_line
		WHITESPACE*
		( kelvin_line
		  WHITESPACE*
		)?
		group_view_data_stmt_begin_line
		@ { fhold; fcall group_scanner; }
	WHITESPACE*
		group_mol_struct_stmt_begin_line
		@ { fhold; fcall group_scanner; }
	WHITESPACE*
		end1_line
		WHITESPACE*
		group_clipboard_stmt_begin_line
		@ { fhold; fcall group_scanner; }
	WHITESPACE*
		end_line
		any*
		;
	
# dynamic stack re-sizing
	prepush {
		cerr << "Ragel stack prepush: top = " << top << ", stackSize = " << stackSize << endl;
		if(top == stackSize) {
			stackSize += stackSize;
			stack.resize(stackSize, 0);
			cerr << "Resized stack to " << stackSize << endl;
		}
	}
	
}%%

%% # Ragel FSM data


// static data from Ragel

%% write data;


// static data from class NanorexMMPImportExport

char const NanorexMMPImportExport::_s_bondOrderString[NUM_BOND_TYPES] = {
	'1', '2', '3', 'a', 'g', 'c'
};

char const
NanorexMMPImportExport::_s_bondOrderNameString[NUM_BOND_TYPES][16] =
{
	"single", "double", "triple", "aromatic", "graphitic", "carbomeric"
};

char const NanorexMMPImportExport::_s_hybridizationName[8][8] = {
	"none", "sp", "sp2", "sp3", "X-hyb4", "X-hyb5", "X-hyb6", "X-hyb7"
};

/*static*/
void NanorexMMPImportExport::SetResult(NXCommandResult& commandResult,
                                       int errCode,
                                       string const& errMsg)
{
	commandResult.setResult(errCode);
	vector<QString> message;
	message.push_back(QObject::tr(errMsg.c_str()));
	commandResult.setParamVector(message);
}

// .............................................................................

/* static */
void NanorexMMPImportExport::ClearResult(NXCommandResult& commandResult)
{
	commandResult.setResult((int) NX_CMD_SUCCESS);
	vector<QString> message;
	commandResult.setParamVector(message);
}


/* CONSTRUCTOR */
NanorexMMPImportExport::NanorexMMPImportExport()
{
	reset();
}

/* DESTRUCTOR */
NanorexMMPImportExport::~NanorexMMPImportExport()
{
}


/* FUNCTION: reset */
void NanorexMMPImportExport::reset(void)
{
	inputFilename.clear();
	dataStoreInfo = (NXDataStoreInfo*) NULL;
	
	lineNum = 0;
	insideViewDataGroup = false;
	insideClipboardGroup = false;
	
	atomPtr = NULL;
	bondPtr = NULL;
	foundAtomList.clear();
	targetAtomList.clear();
	molPtr = NULL;
	molSetPtr = NULL;
	molSetPtrStack.clear();
	molStyle = "def";
	
	clipboardGroup = NULL;
	
	// defaultAtomStyle = "def";
	// defaultAtomStyleStack.clear();
	
	// ragel stack
	stackSize = 2;
	stack.clear();
	stack.resize(stackSize, 0);
	
    // initialize the ragel engine
	%% write init;
}


/* FUNCTION: importFromFile */
NXCommandResult*
NanorexMMPImportExport::
importFromFile(NXMoleculeSet *rootMoleculeSetPtr,
               NXDataStoreInfo *dsInfo,
               const std::string& theFilename,
               int /*frameSetId*/, int /*frameIndex*/)
{
	reset();
	bool success = true;
	
	ClearResult(commandResult);
	
	ifstream mmpfile(theFilename.c_str(), ios::in);
	if(!mmpfile) {
		populateCommandResult(&commandResult,
		                      (string("Couldn't open file: ") + theFilename)
		                      .c_str());
		success = false;
	}
	else {
		inputFilename = theFilename;
		dataStoreInfo = dsInfo;
		success = readMMP(mmpfile, rootMoleculeSetPtr);
	}
	
	// Set the meta information about the data store.
	if (success) {
		dataStoreInfo->setIsSingleStructure(true);
	}
	
	return &commandResult;
}


/* FUNCTION: readMMP */
bool NanorexMMPImportExport::readMMP(istream& instream,
                                     NXMoleculeSet *rootMoleculeSetPtr)
{
	p = RagelIstreamPtr(instream);
	pe = RagelIstreamPtr(instream, 0, ios::end);
	eof = pe;
	
	this->rootMoleculeSetPtr = rootMoleculeSetPtr;
	molSetPtr = NULL;
	// molSetPtrStack.push(molSetPtr);
	
    /// @todo handle first 'group' statement and molSetPtrStack initialization
	
    // Ragel parser implementation
	bool success = true;
	%% write exec;
	
    // End-of-parsing sanity checks
	if(molSetPtrStack.size() != 0) {
		NXLOG_WARNING("NanorexMMPImportExport",
		              "At least one group has no matching egroup statement");
	}
	return success;
}


/* FUNCTION newAtom */
void NanorexMMPImportExport::newAtom(int id, int atomicNum, int x, int y, int z,
                                     string const& style)
{
	if(molPtr == NULL) {
		CSEVERE("No parent molecule for atom");
		return;
	}
	
	// error if id was previously specified
	map<int,OBAtom*>::const_iterator atomExistsQuery =
		foundAtomList.find(id);
	if(atomExistsQuery != foundAtomList.end()) {
		NXLOG_SEVERE("NanorexMMPImportExport",
		             "Atom-id " + NXUtility::itos(id) + " is repeated");
		return;
	}
	
	
	atomPtr = molPtr->NewAtom();
	/// @note OpenBabel assigns atomicNum to a 'char' variable so modulo 256
	atomPtr->SetAtomicNum(atomicNum);
	/// @todo set implicit valence based on role (axis, strand etc)
	if(atomicNum >= 200)
		atomPtr->SetImplicitValence(4);
	NXAtomData *atomDataPtr = new NXAtomData(atomicNum);
	atomDataPtr->setIdx(id);
	atomDataPtr->setRenderStyleCode(style);
	assert(atomDataPtr->GetDataType() == NXAtomDataType);
	atomPtr->SetData(atomDataPtr); // atomic number
	assert(atomPtr->HasData(NXAtomDataType));
	// convert to Angstroms
	double const LENGTH_SCALE = 1.0e-3;
	atomPtr->SetVector(double(x) * LENGTH_SCALE,
	                   double(y) * LENGTH_SCALE,
	                   double(z) * LENGTH_SCALE);
	
	foundAtomList[id] = atomPtr;
	
	bondPtr = NULL;	
	
	CDEBUG("atom " + NXUtility::itos(atomId) + " (" + NXUtility::itos(atomicNum)
	       + ") (" + NXUtility::itos(x) + ',' + NXUtility::itos(y) + ',' +
	       NXUtility::itos(z) + ") " + atomStyle);
}


/* FUNCTION: newAtomInfo*/
void NanorexMMPImportExport::newAtomInfo(string const& key,
                                         string const& value)
{
	if(insideViewDataGroup)
		return;
	
	if(atomPtr != NULL) {
		if(key == "atomtype") { // hybridization info
			if(value == "sp") atomPtr->SetHyb(1);
			else if(value == "sp2") atomPtr->SetHyb(2);
			else if(value == "sp2_g") atomPtr->SetHyb(2);
			else if(value == "sp3") atomPtr->SetHyb(3);
			else if(value == "sp3d") atomPtr->SetHyb(3);
            // else ignore
		}
	}
	
	CDEBUG("info atom '" + key + "' = '" + value + "'");
}


/* FUNCTION: newBond */
void NanorexMMPImportExport::newBond(string const& bondType, int targetAtomId)
{
	if(insideViewDataGroup)
		return;
	
	assert(molPtr != NULL && atomPtr != NULL);
	
	map<int,OBAtom*>::iterator targetAtomExistsQuery =
		foundAtomList.find(targetAtomId);
	
	if(targetAtomExistsQuery == foundAtomList.end()) {
		CSEVERE("**ERROR** attempting to bond to non-existent atomID "
		        + NXUtility::itos(targetAtomId));
	}
	else {
		OBAtom *const targetAtomPtr = targetAtomExistsQuery->second;
		// guard against duplicates
		// also a hack to protect against Ragel's duplicate parsing
		// when encountering a blank line
		if(molPtr->GetBond(atomPtr, targetAtomPtr) == NULL) {
			// bond was not previously encountered, include
			int atomId = ((NXAtomData*)(atomPtr->GetData(NXAtomDataType)))->getIdx();
			CDEBUG("bonding atom #" + NXUtility::itos(atomId) +
			       " to atom #" + NXUtility::itos(targetAtomId));
			bondPtr = molPtr->NewBond();
			bondOrder = GetBondOrderFromType(bondType);
			bondPtr->SetBondOrder(bondOrder);
			atomPtr->AddBond(bondPtr);
			targetAtomPtr->AddBond(bondPtr);
			bondPtr->SetBegin(atomPtr);
			bondPtr->SetEnd(targetAtomPtr);
			CDEBUG("bond" + bondType + " " + NXUtility::itos(targetAtomId));
		}
		else {
			CSEVERE("bond to atom #" + NXUtility::itos(targetAtomId) +
			        " already exists");
		}
	}
	
}


/* FUNCTION: GetBondOrderFromType */
int NanorexMMPImportExport::GetBondOrderFromType(string const& type)
{
	if(type == "1")
		return 1;
	else if(type == "2")
		return 2;
	else if(type == "3")
		return 3;
	else if(type == "a")
		return 4;
	else if(type == "c")
		return 5;
	else if (type == "g")
		return 6;
	else {
		return -1;
	}
}


/* FUNCTION: newBondDirection */
void NanorexMMPImportExport::newBondDirection(int atomId1, int atomId2)
{
	/// @todo Implement post-FNANO08
	// no-op for FNANO08
}


/* FUNCTION: newMolecule */
void
NanorexMMPImportExport::newMolecule(string const& name, string const& style)
{
	if(insideViewDataGroup)
		return;
	
	atomPtr = NULL;
	bondPtr = NULL;
	molPtr = molSetPtr->newMolecule();
	molPtr->SetTitle(name.c_str());
	if(style == "")
		molStyle = "def";
	else
		molStyle = style;
	CDEBUG("mol (" + name + ") " + style);
}


/* FUNCTION: newViewDataGroup */
void NanorexMMPImportExport::newViewDataGroup(void)
{
	insideViewDataGroup = true;
	CDEBUG("[special] group (View Data)");
}


void
NanorexMMPImportExport::
newNamedView(std::string const& name,
             double const& qw, double const& qx, double const& qy,
             double const& qz, double const& scale,
             double const& povX, double const& povY,
             double const& povZ, double const& zoomFactor)
{
	// No need to convert to Angstroms - already NV1's internal units
	double const TO_ANG = 1.0 /*1.0e-10*/;
	if(insideViewDataGroup) {
		NXNamedView view(name,
		                 NXQuaternion<double>(qw, qx*TO_ANG,
		                                      qy*TO_ANG, qz*TO_ANG),
		                 scale*TO_ANG,
		                 NXVector3d(povX*TO_ANG, povY*TO_ANG, povZ*TO_ANG),
		                 zoomFactor);
		if(name == "HomeView")
			dataStoreInfo->setHomeView(view);
		else if(name == "LastView")
			dataStoreInfo->setLastView(view);
		else
			dataStoreInfo->addOtherView(view);
	}
	
	CDEBUG("csys (" + name + ") " +
	       '(' + NXUtility::dtos(qw) + ',' + NXUtility::dtos(qx) + ',' +
	       NXUtility::dtos(qz) + ',' + NXUtility::dtos(qz) + ") " +
	       '(' + NXUtility::dtos(scale) + ") " +
	       '(' + NXUtility::dtos(povX) + ',' + NXUtility::dtos(povY) + ',' +
	       NXUtility::dtos(povZ) + ") " +
	       '(' + NXUtility::dtos(zoomFactor) + ')');
}


/* FUNCTION: newMolStructGroup */
void NanorexMMPImportExport::newMolStructGroup(string const& name,
                                               string const& classification)
{
// 	if(insideClipboardGroup && molSetPtr == NULL) {
// 		// no active top-level group
// 		molSetPtr = new NXMoleculeSet;
// 		molSetPtr->setTitle(name);
// 		// dataStoreInfo->addClipboardStructure(molSetPtr);
// 	}
	
	// if in "View Data" group, ignore
	
	// if(molSetPtr != NULL) {
	/*else*/ if(!insideViewDataGroup) {
		// if in principal molecule-set group or active clipboard group
		
		if(molSetPtr == NULL) {
			// must be inside principal structure group
			assert(!insideClipboardGroup);
			molSetPtr = rootMoleculeSetPtr;
		}
// 		else if(!insideClipboardGroup && molSetPtr == NULL) {
// 			// entering principal structure group
// 			// all changes should go to supplied pointer
// 			molSetPtr = rootMoleculeSetPtr;
// 		}
		else {
			// If not at top-level inside principal structure group or
			// clipboard group, allocate new structure
			NXMoleculeSet *newMolSetPtr = new NXMoleculeSet;
			molSetPtr->addChild(newMolSetPtr);
			molSetPtrStack.push_back(molSetPtr);
			molSetPtr = newMolSetPtr;
		}
		molSetPtr->setTitle(name);
		molSetPtr->setGroupClassificationString(classification);
	}
	
	// ++molStructGroupLevel;
	
	CDEBUG("group (" + name + ") " + classification);
}


/* FUNCTION: newClipboardGroup */
void NanorexMMPImportExport::newClipboardGroup(void)
{
	assert(molSetPtr == NULL);
	assert(molSetPtrStack.size() == 0);
	
	if(!insideClipboardGroup && clipboardGroup == (NXMoleculeSet*) NULL) {
		clipboardGroup = new NXMoleculeSet;
		clipboardGroup->setTitle("Clipboard");
		molSetPtr = clipboardGroup;
		insideClipboardGroup = true;
		dataStoreInfo->setClipboardStructure(clipboardGroup);
		CDEBUG("[special] group (Clipboard)");
	}
	else {
		CSEVERE("Redefinition of 'Clipboard' group");
	}
}


/* FUNCTION: endGroup */
void NanorexMMPImportExport::endGroup(string const& name)
{
	// Must ensure that molSetPtr = NULL between top-level structure groups
	// Top-level structure groups are defined as the principal structure group
	// that occurs between the "View Data" and the "Clipboard" groups in the MMP
	// file, and those from various top-level 'group' statements in the
	// "Clipboard" group
	
	string groupName;
	if(insideViewDataGroup)
		groupName = "View Data";
	else if(insideClipboardGroup)
		groupName = (molSetPtr == NULL) ? "Clipboard" : molSetPtr->getTitle();
	else
		groupName = molSetPtr->getTitle();
	
	
	if(name != groupName) {
		NXLOG_WARNING("NanorexMMPImportExport",
		              "egroup (" + name + ") attempting to close "
		              "group (" + groupName + ')');
	}
	
	
	if(insideViewDataGroup) {
		insideViewDataGroup = false;
		molSetPtr = NULL;
	}
	else {
		// non top-level structure groups in clipboard or in the
		// principal structure group
		if(molSetPtrStack.size() == 0)  {
			molSetPtr = NULL;
			if(insideClipboardGroup)
				insideClipboardGroup = false;
		}
		else {
			molSetPtr = molSetPtrStack.back();
			molSetPtrStack.pop_back();
		}
	}
	
	CDEBUG("egroup (" + groupName + ')');
}


/* FUNCTION: newOpenGroupInfo */
void NanorexMMPImportExport::newOpenGroupInfo(std::string const& key,
                                              std::string const& value)
{
	/// @todo
	CDEBUG("info opengroup " + key + " = " + value);
}


/* FUNCTION: newChunkInfo */
void
NanorexMMPImportExport::newChunkInfo(std::string const& key,
                                     std::string const& value)
{
	CDEBUG("info chunk " + key + " = " + value);
	
	if(insideViewDataGroup)
		return;
	
	/// @todo
}


/* FUNCTION: end1 */
void NanorexMMPImportExport::end1(void)
{
	/// @todo
	CDEBUG("end1");
}


/* FUNCTION: exportToFile */
NXCommandResult*
NanorexMMPImportExport::
exportToFile(NXMoleculeSet *molSetPtr,
             NXDataStoreInfo */*dataStoreInfo*/,
             const std::string& theFilename,
             int /*frameSetId*/, int /*frameIndex*/)
{
	NXCommandResult *result = new NXCommandResult();
	result->setResult(NX_CMD_SUCCESS);
	
	ofstream mmpfile(theFilename.c_str(), ios::out);
	if(!mmpfile) {
		populateCommandResult(result,
		                      (string("Couldn't open file: ") + theFilename)
		                      .c_str());
	}
	else {
		PrintMoleculeSet(mmpfile, molSetPtr);
		mmpfile.close();
	}
	return result;
}


/* FUNCTION: GetAtomID */
/* static */
int NanorexMMPImportExport::GetAtomID(OBAtom *atomPtr)
{
	NXAtomData *atomIDData = 
		dynamic_cast<NXAtomData*>(atomPtr->GetData(NXAtomDataType));
	int atomID = atomIDData->getIdx();
	return atomID;
}


/* FUNCTION: GetAtomRenderStyleCode */
/* static */
string const&
NanorexMMPImportExport::GetAtomRenderStyleCode(OBAtom *const atomPtr)
{
	NXAtomData *atomDataPtr =
		dynamic_cast<NXAtomData*>(atomPtr->GetData(NXAtomDataType));
	string const& atomStyle = atomDataPtr->getRenderStyleCode();
	return atomStyle;
}


/* FUNCTION: PrintMolecule */
/* static */
void NanorexMMPImportExport::PrintMolecule(ostream& o,
OBMol *const molPtr)
{
	set<int> prevAtomIdx;
	set<int> prevBondIdx; /// @todo - replace with simple bond count
	
	o << "mol (" << molPtr->GetTitle() << ')' << endl;
	
	OBAtomIterator atomIter;
	OBAtom *atomPtr = NULL;
    // For each atom ...
	for(atomPtr = molPtr->BeginAtom(atomIter);
	    atomPtr != NULL;
	    atomPtr = molPtr->NextAtom(atomIter))
	{
        // ... write the 'atom' line ...
		int atomID = GetAtomID(atomPtr);
		o << "atom " << atomID << " (" << atomPtr->GetAtomicNum() << ") " << '('
			<< atomPtr->x() << ',' << atomPtr->y() << ',' << atomPtr->z()
			<< ") " << GetAtomRenderStyleCode(atomPtr) << endl;
		
		if(atomPtr->GetHyb() != 0) {
			o << "info atom atomtype = "
				<< _s_hybridizationName[atomPtr->GetHyb()];
		}
		
        // ... write the 'bond' lines for this atom ...
        // ... first sort bonds by type ...
		OBBondIterator bondIter;
		OBBond *bondPtr = NULL;
		vector<int> bondCategories[6];
		for(bondPtr = atomPtr->BeginBond(bondIter);
		    bondPtr != NULL;
		    bondPtr = atomPtr->NextBond(bondIter))
		{
            // write bond statement only if target atom was previously written
			OBAtom *nbrAtomPtr = bondPtr->GetNbrAtom(atomPtr);
			int nbrAtomID = GetAtomID(nbrAtomPtr);
			if(prevAtomIdx.find(nbrAtomID) != prevAtomIdx.end()) {
				int bondOrder = bondPtr->GetBondOrder();
				bondCategories[bondOrder-1].push_back(nbrAtomID);
                // record bond for sanity check at end
				prevBondIdx.insert(bondPtr->GetIdx());
			}
		}
		
        // ... write the bonds, one line per type ...
		for(int i=0; i<6; ++i) {
			int J = bondCategories[i].size();
			if(J > 0) {
				o << "bond" << _s_bondOrderString[i];
				for(int j=0; j<J; ++j)
					o << ' ' << bondCategories[i][j];
				o  << endl;
			}
		}
		
        // record atom as 'previously written'
		prevAtomIdx.insert(atomID);
	}
	
    // debug diagnostics
	ostringstream debugMsg;
	debugMsg << "# atoms check ";
	if(molPtr->NumAtoms() == prevAtomIdx.size())
		debugMsg << "PASS ("  << molPtr->NumAtoms() << ')' << endl;
	else
		debugMsg << "FAIL: "
		<< molPtr->NumAtoms() << " != " << prevAtomIdx.size()<< endl;
	
	debugMsg << "# bonds check ";
	if(molPtr->NumBonds() == prevBondIdx.size())
		debugMsg << "PASS (" << molPtr->NumBonds() << ')' << endl;
	else
		debugMsg << "FAIL: "
		<< molPtr->NumBonds() << " != " << prevBondIdx.size()<< endl;
	
	debugMsg.flush();
	NXLOG_DEBUG("NanorexMMPImportExport::PrintMoleculeSet",
	            debugMsg.str().c_str());
}


/* FUNCTION: PrintMoleculeSet */
/* static */
void NanorexMMPImportExport::PrintMoleculeSet(ostream& o,
                                              NXMoleculeSet *const molSetPtr)
{
	// Iterate over all child molecules
	OBMolIterator molIter;
	for(molIter = molSetPtr->moleculesBegin();
	    molIter != molSetPtr->moleculesEnd();
	    ++molIter)
	{
		PrintMolecule(o, *molIter);
	}
	
    // Iterate over all child molecule sets
	NXMoleculeSetIterator molSetIter;
	for(molSetIter = molSetPtr->childrenBegin();
	    molSetIter != molSetPtr->childrenEnd();
	    ++molSetIter)
	{
		PrintMoleculeSet(o, *molSetIter);
	}
}


/* FUNCTION: populateCommandResult */
void
NanorexMMPImportExport::populateCommandResult (NXCommandResult* result,
                                               const string& message)
{
	result->setResult(NX_PLUGIN_REPORTS_ERROR);
	vector<QString> resultVector;
	resultVector.push_back("OpenBabelImportExport");
	resultVector.push_back(message.c_str());
	result->setParamVector(resultVector);
}

Q_EXPORT_PLUGIN2 (NanorexMMPImportExport, NanorexMMPImportExport)