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// Copyright 2008 Nanorex, Inc. See LICENSE file for details.
#ifndef NANOREXMMPIMPORTEXPORT_H
#define NANOREXMMPIMPORTEXPORT_H
#include <openbabel/mol.h>
#include "Nanorex/Utility/NXLogger.h"
#include "Nanorex/Utility/NXCommandResult.h"
#include "Nanorex/Interface/NXNanoVisionResultCodes.h"
#include "Nanorex/Interface/NXDataImportExportPlugin.h"
#include <Nanorex/Interface/NXAtomData.h>
#include <Nanorex/Interface/NXMoleculeSet.h>
#include <Nanorex/Interface/NXNamedView.h>
#include "RagelIstreamPtr.h"
#include <fstream>
#include <vector>
#include <sstream>
#include <set>
#include <map>
#include <cmath>
// #include <stack>
using namespace std;
using namespace Nanorex;
/* CLASS: NanorexMMPImportExport */
class NanorexMMPImportExport : public QObject, public NXDataImportExportPlugin
{
Q_OBJECT;
Q_INTERFACES(Nanorex::NXDataImportExportPlugin);
public:
NanorexMMPImportExport();
~NanorexMMPImportExport();
// NXDataImportExportPlugin implementation
NXCommandResult* importFromFile(NXMoleculeSet* moleculeSet,
NXDataStoreInfo* dataStoreInfo,
const std::string& theFilename,
int frameSetId, int frameIndex);
NXCommandResult* exportToFile(NXMoleculeSet* moleculeSet,
NXDataStoreInfo* dataStoreInfo,
const std::string& theFilename,
int frameSetId, int frameIndex);
string const& getRequiredVersion(void) const { return requiredVersion; }
string const getPreferredVersion(void) const { return preferredVersion; }
double const& getTemperature(void) const { return kelvinTemp; }
private:
string inputFilename;
NXDataStoreInfo *dataStoreInfo;
// extracted data that can be queried later
string requiredVersion;
string preferredVersion;
double kelvinTemp;
// state variables
int lineNum;
// scratch variables to write parsed values to
OBMol *molPtr; ///< current molecule
OBAtom *atomPtr; ///< current atom
OBBond *bondPtr; ///< current bond
NXMoleculeSet *molSetPtr;
///< current molecule-set. This is initialized by the input in
///< importFromFile() which points to the molecule-structure of interest
///< to the user. When inside the Clipboard group, this is NULL at the top
///< level in between groups. Each top-level node will have to be allocated
///< and assigned to this.
bool insideViewDataGroup;
NXMoleculeSet *clipboardGroup;
bool insideClipboardGroup;
int atomicNum, atomId, bondOrder;
string atomStyle;
map<int,OBAtom*> foundAtomList;
vector<OBAtom*> targetAtomList;
string stringVal, stringVal2;
int intVal, intVal2;
double doubleVal;
// named-view temporaries
std::string csysViewName;
double csysQw, csysQx, csysQy, csysQz;
double csysScale, csysZoomFactor;
double csysPovX, csysPovY, csysPovZ;
// molecule-set 'stack' to help with recursive 'group' specification
NXMoleculeSet *rootMoleculeSetPtr;
std::vector<NXMoleculeSet*> molSetPtrStack;
std::string molStyle;
// int molStructGroupLevel; ///< level in recursive specification
// std::vector<std::string> defaultAtomStyleStack; // track with recursion into groups
// Ragel + parser state variables
int cs, top, act;
int x, y, z;
int stackSize;
std::vector<int> stack;
// Ragel pointers to input stream
RagelIstreamPtr p, pe, eof, ts, te;
RagelIstreamPtr charStringWithSpaceStart, charStringWithSpaceStop;
RagelIstreamPtr lineStart;
NXCommandResult commandResult;
// helper functions
void reset(void);
bool readMMP(istream& instream, NXMoleculeSet *rootMoleculeSetPtr);
// void createNewMolecule(void);
// void createNewMoleculeSet(void);
// void closeMoleculeSet(void);
// void applyAtomType(string const& keyStr, string const& valueStr);
// "slots" called for matched patterns
void newAtom(int id, int atomicNum, int x, int y, int z,
string const& style);
void newBond(string const& type, int targetAtomId);
void newBondDirection(int atomId1, int atomId2);
void newMolecule(string const& name, string const& style);
void newViewDataGroup();
void 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);
void newMolStructGroup(std::string const& name,
std::string const& classification);
void endMolStructGroup(std::string const& name);
void newClipboardGroup();
void endGroup(std::string const& groupName);
void newAtomInfo(std::string const& key, std::string const& value);
void newOpenGroupInfo(std::string const& key, std::string const& value);
void newChunkInfo(std::string const& key, std::string const& value);
void end1();
// Static data and function members
static int const NUM_BOND_TYPES = 6;
static char const _s_bondOrderString[NUM_BOND_TYPES];
static char const _s_bondOrderNameString[NUM_BOND_TYPES][16];
static char const _s_hybridizationName[8][8];
static void PrintMoleculeSet(ostream& o,
NXMoleculeSet *const molSetPtr);
static void PrintMolecule(ostream& o, OBMol *const molPtr);
static int GetBondOrderFromType(string const& type);
static int GetAtomID(OBAtom *atomPtr);
// static char const *const GetAtomRenderStyleName(OBAtom *const atomPtr);
static string const& GetAtomRenderStyleCode(OBAtom *const atomPtr);
static void populateCommandResult(NXCommandResult* result,
const string& message);
static void SetResult(NXCommandResult& cmdResult,
int errCode, std::string const& errMsg);
static void ClearResult(NXCommandResult& cmdResult);
friend class NanorexMMPImportExportTest;
};
#endif // NANOREXMMPIMPORTEXPORT_H
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