1 #ifndef GROMACSTOPFILE_H
2 #define GROMACSTOPFILE_H
7 #define LONGNAMESIZE 20
95 GenericAtom(
const char *theType,
int theTypeNum,
int theResNum,
96 const char *theResType,
97 const char *theAtomName,
Real theCharge,
Real theMass);
146 void addAtom(
const char *theType,
int theTypeNum,
int theResNum,
147 const char *theResType,
148 const char *theAtomName,
Real theCharge,
Real theMass);
151 void addBond(
int atomi,
int atomj,
int type);
152 void addAngle(
int atomi,
int atomj,
int atomk,
int type);
153 void addDihedral(
int atomi,
int atomj,
int atomk,
int atoml,
int type);
221 void getType(
int num,
char *type)
const;
253 void addType(
const char *typea,
const char *typeb,
Real b0,
264 int getParams(
const char *typea,
const char *typeb,
int funct,
297 void addType(
const char *typea,
const char *typeb,
298 const char *typec,
Real th0,
299 Real kth,
int funct);
310 int getParams(
const char *typea,
const char *typeb,
311 const char *typec,
int funct,
360 void addType(
const char *typea,
const char *typeb,
361 const Real *c,
int mult,
int funct);
367 void getParams(
int num,
Real *c,
int *mult,
int *funct)
const;
379 int getParams(
const char *typea,
const char *typeb,
380 const char *typec,
const char *typed,
int funct,
381 Real *c,
int *mult)
const;
399 int getIndex(
const char *typea,
const char *typeb)
const;
404 void add14Type(
const char *typea,
const char *typeb,
410 int getParams(
const char *typea,
const char *typeb,
468 Real *gaussRepulsive);
483 Real fudgeLJ, fudgeQQ;
531 void getAtom(
int num,
int *residue_number,
char *residue_name,
532 char *atom_name,
char *atom_type,
int *atom_typenum,
558 void getBond(
int num,
int *atomi,
int *atomj,
int *bondtype)
const;
571 void getAngle(
int num,
int *atomi,
int *atomj,
int *atomk,
572 int *angletype)
const;
584 void getDihedral(
int num,
int *atomi,
int *atomj,
int *atomk,
585 int *atoml,
int *type)
const;
607 Real *gaussRepulsive);
619 #endif // GROMACSTOPFILE_H
void getBond(int num, int *atomi, int *atomj, int *bondtype) const
GenericMol(const char *theName)
int addPairGaussType2(int typea, int typeb, Real gA, Real gMu1, Real gSigma1)
GenericBond(int i, int j, int theType)
int getParams(const char *typea, const char *typeb, Real *c6, Real *c12, Real *c6pair, Real *c12pair) const
void getPairLJArrays2(int *indexA, int *indexB, Real *pairC6, Real *pairC12)
static bool GroGaussCompare(GroGaussPair, GroGaussPair)
int getNumDihedrals() const
int getNumDihedrals() const
const GenericBond * getBond(int n) const
const char * getAtomName() const
void add14Type(const char *typea, const char *typeb, Real c6pair, Real c12pair)
void getVDWParams(int typea, int typeb, Real *c6, Real *c12, Real *c6pair, Real *c7) const
void getType(int num, char *type) const
void addType(const char *type, Real m, Real q, Real c6, Real c12)
int getParams(const char *type, Real *m, Real *q, Real *c6, Real *c12) const
const char * getType() const
int getNumExclusions() const
const GenericAngle * getAngle(int n) const
void addType(const char *typea, const char *typeb, const char *typec, Real th0, Real kth, int funct)
void getBondParams(int num, Real *b0, Real *kB, int *funct) const
int getIndex(Real b0, Real kB, int funct)
void getDihedral(int num, int *atomi, int *atomj, int *atomk, int *atoml, int *type) const
char * getSystemName() const
int getIndex(Real th0, Real kth, int funct)
void addType(const char *typea, const char *typeb, const Real *c, int mult, int funct)
int getNumGaussPair() const
const char * getResType() const
void getParams(int num, Real *b0, Real *kB, int *funct) const
void getParams(int num, Real *c, int *mult, int *funct) const
GromacsTopFile(char *filename)
void getExclusions(int *, int *) const
int addPairLJType2(int typea, int typeb, Real c6, Real c12)
void getParams(int num, Real *th0, Real *kth, int *funct) const
void addAngle(int atomi, int atomj, int atomk, int type)
const GenericAtom * getAtom(int n) const
int getNumDihedralParams() const
const GenericMol * getMol() const
void addType(const char *typea, const char *typeb, Real c6, Real c12)
void addType(const char *typea, const char *typeb, Real b0, Real kB, int funct)
int getNumAtomParams() const
void getPairLJArrays2(int *indexA, int *indexB, Real *pairC6, Real *pairC12)
const GenericDihedral * getDihedral(int n) const
int getIndex(const Real *c, int mult, int funct)
void getAngle(int num, int *atomi, int *atomj, int *atomk, int *angletype) const
void getDihedralParams(int num, Real *c, int *mult, int *funct) const
static bool GroLJCompare(GroLJPair, GroLJPair)
GenericAngle(int i, int j, int k, int theType)
int getNumAngleParams() const
void getAtomParams(int num, char *type) const
k< npairi;++k){TABENERGY(const int numtypes=simParams->tableNumTypes;const float table_spacing=simParams->tableSpacing;const int npertype=(int)(namdnearbyint(simParams->tableMaxDist/simParams->tableSpacing)+1);) int table_i=(r2iilist[2 *k] >> 14)+r2_delta_expc;const int j=pairlisti[k];#define p_j BigReal diffa=r2list[k]-r2_table[table_i];#define table_four_i TABENERGY(register const int tabtype=-1-(lj_pars->A< 0?lj_pars->A:0);) BigReal kqq=kq_i *p_j-> charge
int getNumBondParams() const
void getPairGaussArrays2(int *indexA, int *indexB, Real *gaussA, Real *gaussMu1, Real *gaussSigma1, Real *gaussMu2, Real *gaussSigma2, Real *gaussRepulsive)
int getNumDihedrals() const
void getPairGaussArrays2(int *indexA, int *indexB, Real *gaussA, Real *gaussMu1, Real *gaussSigma1, Real *gaussMu2, Real *gaussSigma2, Real *gaussRepulsive)
const char * getName() const
void addBond(int atomi, int atomj, int type)
void addDihedral(int atomi, int atomj, int atomk, int atoml, int type)
GenericAtom(const char *theType, int theTypeNum, int theResNum, const char *theResType, const char *theAtomName, Real theCharge, Real theMass)
GenericDihedral(int i, int j, int k, int l, int theType)
void addAtom(const char *theType, int theTypeNum, int theResNum, const char *theResType, const char *theAtomName, Real theCharge, Real theMass)
void getAtom(int num, int *residue_number, char *residue_name, char *atom_name, char *atom_type, int *atom_typenum, Real *charge, Real *mass) const
void getAngleParams(int num, Real *th0, Real *kth, int *funct) const
MolInst(const GenericMol *theMol, int theNum)