CVS diff Molecule.h

Difference for src/Molecule.h from version 1.1119 to 1.1120

version 1.1119

version 1.1120

Line 85

#define EXCHCK_FULL 1

#define EXCHCK_MOD 2

class ResidueLookupElem

{

public:

char mySegid[11];

ResidueLookupElem *next; // stored as a linked list

int firstResid; // valid resid is >= firstResid

int lastResid; // valid resid is <= lastResid

ResizeArray<int> atomIndex; // 0-based index for first atom in residue

ResidueLookupElem(void) { next = 0; firstResid = -1; lastResid = -1; }

~ResidueLookupElem(void) { delete next; }

int lookup(const char *segid, int resid, int *begin, int *end) const;

ResidueLookupElem* append(const char *segid, int resid, int aid);

};

// Ported by JLai -- JE

typedef struct go_val

{

Line 107

Line 122

} GoPair;

// End of port - JL

#define QMLSSMODEDIST 1

#define QMLSSMODECOM 2

#define QMFormatORCA 1

#define QMFormatMOPAC 2

#define QMFormatUSR 3

#define QMCHRGNONE 0

#define QMCHRGMULLIKEN 1

#define QMCHRGCHELPG 2

#define QMSCHEMECS 1

#define QMSCHEMERCD 2

#define QMSCHEMEZ1 3

#define QMSCHEMEZ2 4

#define QMSCHEMEZ3 5

//only used for compressing the molecule information

typedef struct seg_resid

{

Line 634

Line 666

// GO ENERGY CALCULATION CODE

// End of port - JL

private:

/////////////////////////

// Begin QM

/////////////////////////

int qmDroppedBonds, qmDroppedAngles, qmDroppedDihedrals;

int qmDroppedImpropers, qmDroppedCrossterms;

Bool qmReplaceAll; // Indicates if all forces should be replaced.

int qmNumQMAtoms; // Number of QM atoms, from all groups.

// Array of abbreviated element names for all atoms.

char **qmElementArray;

// Array of elements for dummy atoms.

char **qmDummyElement;

// Number of QM atoms in each QM group

int *qmGrpSizes;

// QM group for each atom of the system. 0 means MM atom.

Real *qmAtomGroup;

// Number of different QM regions

int qmNumGrps ;

// QM Atom charges.

Real *qmAtmChrg ;

// global indices of all QM atoms.

int *qmAtmIndx ;

// Number of QM-MM bonds.

int qmNumBonds ;

// IDs of each group, that is, the value in the qmColumn, per group.

Real *qmGrpID ;

// The total charge of each QM group.

Real *qmGrpChrg;

// The multiplicity of QM groups

Real *qmGrpMult;

// Number of QM-MM bonds in each group.

int *qmGrpNumBonds ;

// Sequential list of bonds between a MM atom and a QM atom.

// (with the bonded atoms ins this order: MM first, QM second).

int **qmMMBond ;

// List of bond indexes for each QM group.

int **qmGrpBonds ;

// List of atom indexes for MM atoms in QM-MM bonds, per group.

// This is used to check if a point charge is actually an MM atom

// that need to be ignored, and will be substituted by a dummy atom (for example).

int **qmMMBondedIndx ;

// List of indices for MM atoms which will receive fractions of charges from

// the MM atom of a QM-MM bond. This is used in the Charge Shift scheme.

int **qmMMChargeTarget;

// Number of target MM atoms per QM-MM bond. Targets will receive the partial

// charge of the MM atom in a QM-MM bond. (in Charge shift scheme)

int *qmMMNumTargs;

// List of distances from thr QM atom where the dummy atom will be placed.

BigReal *qmDummyBondVal;

// Indicate if point charges will be used in QM calculations.

Bool qmNoPC;

/////////////////////////

// These variables are used in case mechanichal embedding is requested (NoPC = TRUE)

// AND there are QM-MM bonds in the system.

// Indicates the number of items in the arrays for Mechanical embedding with QM-MM bonds.

int qmMeNumBonds;

// Indicates the indices of MM atoms which participate in QM-MM bonds.

int *qmMeMMindx;

// Indicates the QM group to which the QM-MM bonds belongs.

Real *qmMeQMGrp;

/////////////////////////

// Indicates frequency of selection of point charges.

int qmPCFreq;

// Custom PC array;

int *qmCustomPCIdxs;

// Number of Indexes associated with each QM Group.

int *qmCustPCSizes;

// Total number of custom PC charges.

int qmTotCustPCs;

// Number of solvent molecules that will be selected and updated by NAMD, per group.

int *qmLSSSize;

// Number of atoms per solvent molecule. We need all molecules to have the same size.

int qmLSSResidueSize;

// IDs of all atoms belonging to QM solvent molecules, from all groups.

int *qmLSSIdxs;

// MAss of each atom in LSS solvent molecules.

Mass *qmLSSMass;

// Atom IDs of QM atoms which will be used to select solvent molecules by distance.

int *qmLSSRefIDs;

// Mass of each QM atom used as reference for solvent selection.

Mass *qmLSSRefMass ;

// Number of atom IDs/Mass per group.

int *qmLSSRefSize;

int qmLSSFreq;

int qmLSSTotalNumAtms;

// This will map each classical solvent atom with a global index of solvent residues,

// so we don't depend on segment names and repeated residue indices.

std::map<int,int> qmClassicSolv ;

/////////////////////////

// end QM

/////////////////////////

public:

// QM

void set_qm_replaceAll(Bool newReplaceAll) { qmReplaceAll = newReplaceAll; } ;

const Real * get_qmAtomGroup() const {return qmAtomGroup; } ;

Real get_qmAtomGroup(int indx) const {return qmAtomGroup[indx]; } ;

Real *get_qmAtmChrg() {return qmAtmChrg; } ;

const int *get_qmAtmIndx() {return qmAtmIndx; } ;

int get_numQMAtoms() {return qmNumQMAtoms; } ;

const char *const * get_qmElements() {return qmElementArray;} ;

int get_qmNumGrps() const {return qmNumGrps; } ;

const int * get_qmGrpSizes() {return qmGrpSizes; } ;

Real * get_qmGrpID() { return qmGrpID; } ;

Real *get_qmGrpChrg() {return qmGrpChrg; } ;

Real *get_qmGrpMult() {return qmGrpMult; } ;

int get_qmNumBonds() { return qmNumBonds; } ;

const BigReal * get_qmDummyBondVal() { return qmDummyBondVal; } ;

const int * get_qmGrpNumBonds() { return qmGrpNumBonds; } ;

const int *const * get_qmMMBond() { return qmMMBond; } ;

const int *const * get_qmGrpBonds() { return qmGrpBonds; } ;

const int *const * get_qmMMBondedIndx() { return qmMMBondedIndx; } ;

const char *const * get_qmDummyElement() { return qmDummyElement; } ;

const int *const * get_qmMMChargeTarget() { return qmMMChargeTarget; } ;

const int * get_qmMMNumTargs() { return qmMMNumTargs; } ;

int* get_qmLSSSize() { return qmLSSSize;} ;

int* get_qmLSSIdxs() { return qmLSSIdxs;} ;

Mass *get_qmLSSMass() { return qmLSSMass; } ;

int get_qmLSSFreq() { return qmLSSFreq; } ;

int get_qmLSSResSize() { return qmLSSResidueSize; } ;

int *get_qmLSSRefIDs() { return qmLSSRefIDs ; } ;

int *get_qmLSSRefSize() { return qmLSSRefSize ; } ;

Mass *get_qmLSSRefMass() {return qmLSSRefMass; } ;

std::map<int,int> &get_qmMMSolv() { return qmClassicSolv;} ;

Bool get_qmReplaceAll() {return qmReplaceAll; } ;

Bool get_noPC() { return qmNoPC; } ;

int get_qmMeNumBonds() { return qmMeNumBonds; } ;

int *get_qmMeMMindx() { return qmMeMMindx; } ;

Real *get_qmMeQMGrp() { return qmMeQMGrp; } ;

int get_qmPCFreq() { return qmPCFreq; } ;

int get_qmTotCustPCs() { return qmTotCustPCs; } ;

int *get_qmCustPCSizes() { return qmCustPCSizes; } ;

int *get_qmCustomPCIdxs() { return qmCustomPCIdxs; } ;

void prepare_qm(const char *pdbFileName, Parameters *params, ConfigList *cfgList) ;

void delete_qm_bonded() ;

// end QM

Molecule(SimParameters *, Parameters *param);

Molecule(SimParameters *, Parameters *param, char *filename, ConfigList *cfgList=NULL);

Molecule(SimParameters *simParams, Parameters *param, molfile_plugin_t *pIOHdl, void *pIOFileHdl, int natoms);

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Removed in v.1.1119
changed lines
	Added in v.1.1120

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