#ifndef SFF_H #define SFF_H #include #ifndef FALSE #define FALSE 0 #endif #ifndef TRUE #define TRUE 1 #endif #define UNDEF (-1) /* Fundamental sff types: */ typedef int INT_T; typedef size_t SIZE_T; #define NAB_DOUBLE_PRECISION 1 #define REAL_T double /* other nab types: */ typedef char STRING_T; typedef FILE FILE_T; // The NAME parameters control how the mask parser expects strings to look. // Originally, the parameter file assumes the atom, residue, symbol, etc. // names to be four characters. When stored as a string, the NULL character // is required, requiring a size of 5. It has been increased to 6 in cpptraj // to accomodate the slightly larger names that can be found in MOL2 files. // NAMESIZE: Default size for atom and residue names, 5 + NULL. // Amber atom/residue names are 4, but some mol2 atom types are larger. #define NAMESIZE 6 #define NAME_DEFAULT " " // Default type for atom names, res names, atom types etc typedef char NAME_T[NAMESIZE]; typedef struct parm { char ititl[81]; INT_T IfBox, Nmxrs, IfCap, Natom, Ntypes, Nbonh, Mbona, Ntheth, Mtheta, Nphih, Mphia, Nhparm, Nparm, Nnb, Nres, Nbona, Ntheta, Nphia, Numbnd, Numang, Nptra, Natyp, Nphb, Nat3, Ntype2d, Nttyp, Nspm, Iptres, Nspsol, Ipatm, Natcap, Numextra; NAME_T *AtomNames, *ResNames, *AtomType, *AtomTree; REAL_T *Charges, *Masses, *Rk, *Req, *Tk, *Teq, *Pk, *Pn, *Phase, *Solty, *Cn1, *Cn2, *HB12, *HB10, *Rborn, *Fs; REAL_T Box[4], Cutcap, Xcap, Ycap, Zcap, Fsmax; INT_T *Iac, *Iblo, *Cno, *Ipres, *ExclAt, *TreeJoin, *AtomRes, *BondHAt1, *BondHAt2, *BondHNum, *BondAt1, *BondAt2, *BondNum, *AngleHAt1, *AngleHAt2, *AngleHAt3, *AngleHNum, *AngleAt1, *AngleAt2, *AngleAt3, *AngleNum, *DihHAt1, *DihHAt2, *DihHAt3, *DihHAt4, *DihHNum, *DihAt1, *DihAt2, *DihAt3, *DihAt4, *DihNum, *Boundary, *AtomicNum; INT_T *N14pairs, *N14pairlist; REAL_T *Gvdw, *Scee, *Scnb, *N14sceelist, *N14scnblist; INT_T Nstrand, Ncomplex; /* HCP: number of strands/complexes */ INT_T *Ipstrand, *Ipcomplex; /* HCP: index into residue/strand list */ } PARMSTRUCT_T; typedef struct xmin_opt{ INT_T mol_struct_opt; INT_T maxiter; REAL_T grms_tol; INT_T method; INT_T numdiff; INT_T m_lbfgs; INT_T iter; REAL_T xmin_time; INT_T ls_method; INT_T ls_maxiter; REAL_T ls_maxatmov; REAL_T beta_armijo; REAL_T c_armijo; REAL_T mu_armijo; REAL_T ftol_wolfe; REAL_T gtol_wolfe; INT_T ls_iter; INT_T print_level; INT_T error_flag; } XMIN_OPT_T; typedef struct lmod_opt { INT_T niter; INT_T nmod; INT_T kmod; INT_T nrotran_dof; INT_T nconf; REAL_T minim_grms; REAL_T energy_window; REAL_T conf_separation_rms; INT_T eig_recalc; INT_T ndim_arnoldi; INT_T lmod_restart; INT_T n_best_struct; INT_T mc_option; REAL_T rtemp; REAL_T lmod_step_size_min; REAL_T lmod_step_size_max; INT_T nof_lmod_steps; REAL_T lmod_relax_grms; INT_T nlig; INT_T apply_rigdock; INT_T nof_poses_to_try; INT_T random_seed; INT_T print_level; REAL_T lmod_time; REAL_T aux_time; INT_T error_flag; } LMOD_OPT_T; /* the output for all non error emissions and some error ones too */ extern FILE *nabout; /* signatures for the public routines: */ #ifdef __cplusplus extern "C" { #endif INT_T conjgrad( REAL_T*, INT_T*, REAL_T*, REAL_T ( *func )( REAL_T*, REAL_T*, INT_T* ), REAL_T*, REAL_T*, INT_T* ); REAL_T gauss( REAL_T*, REAL_T* ); INT_T getxv( STRING_T*, INT_T, REAL_T, REAL_T*, REAL_T* ); INT_T getxyz( STRING_T**, INT_T*, REAL_T* ); REAL_T lmod(INT_T*natm, REAL_T *xyz, REAL_T *grad, REAL_T *energy, REAL_T *conflib, REAL_T *lmod_trajectory, INT_T *lig_start, INT_T *lig_end, INT_T *lig_cent, REAL_T *tr_min, REAL_T *tr_max, REAL_T *rot_min, REAL_T *rot_max, struct xmin_opt *xo, struct lmod_opt *lo ); INT_T lmod_opt_init( struct lmod_opt *lo, struct xmin_opt *xo ); INT_T md( INT_T, INT_T, REAL_T*, REAL_T*, REAL_T*, REAL_T ( *func )( REAL_T*, REAL_T*, INT_T* ) ); INT_T mdrat( INT_T, INT_T, REAL_T*, REAL_T*, REAL_T*, REAL_T*, REAL_T ( *mme )() ); INT_T mm_options( STRING_T* ); void mm_set_checkpoint( STRING_T** ); REAL_T mme( REAL_T*, REAL_T*, INT_T* ); REAL_T mme2( REAL_T*, REAL_T*, REAL_T*, REAL_T*, REAL_T*, INT_T*, INT_T*, INT_T*, INT_T *, INT_T *, INT_T *, INT_T *, INT_T*, INT_T* , char* ); REAL_T mme4( REAL_T*, REAL_T*, INT_T* ); REAL_T mme_rattle( REAL_T*, REAL_T*, INT_T* ); INT_T mme_init_sff( PARMSTRUCT_T*, INT_T*, INT_T*, REAL_T*, STRING_T* ); INT_T newton( REAL_T*, INT_T*, REAL_T*, REAL_T ( *func1 )( REAL_T*, REAL_T*, INT_T* ), REAL_T ( *func2 )( REAL_T*, REAL_T*, REAL_T*, REAL_T*, REAL_T*, INT_T*, INT_T*, INT_T*, INT_T*, INT_T*, INT_T*, INT_T*, INT_T*, INT_T*, char* ), REAL_T*, REAL_T*, INT_T* ); INT_T nmode( REAL_T*, INT_T, REAL_T ( *func)( REAL_T*, REAL_T*, REAL_T*, REAL_T*, REAL_T*, INT_T*, INT_T*, INT_T*, INT_T*, INT_T*, INT_T*, INT_T*, INT_T*, INT_T*, char* ), INT_T, INT_T, REAL_T, REAL_T, INT_T); INT_T putxv( STRING_T*, STRING_T*, INT_T, REAL_T, REAL_T*, REAL_T* ); INT_T putxyz( STRING_T**, INT_T*, REAL_T* ); REAL_T rand2( void ); INT_T sasad( REAL_T*, REAL_T*, REAL_T*, INT_T, REAL_T ); INT_T xmin_opt_init( struct xmin_opt* ); REAL_T xmin( REAL_T ( *func )( REAL_T*, REAL_T*, INT_T* ), INT_T*, REAL_T*, REAL_T*, REAL_T*, REAL_T*, struct xmin_opt* ); REAL_T xminC(INT_T*, INT_T*, INT_T*, REAL_T*, INT_T*, INT_T*, INT_T*, REAL_T*, REAL_T*, REAL_T*, REAL_T*, INT_T*, REAL_T*, INT_T*, INT_T*, INT_T*, INT_T*, REAL_T*, REAL_T*, REAL_T*, REAL_T*, REAL_T*, REAL_T*, INT_T*, INT_T*); INT_T mme_rism_max_memory(); /* prmtop routine public interfaces: */ INT_T free_prm( PARMSTRUCT_T* prm ); PARMSTRUCT_T* rdparm( STRING_T* name ); INT_T wrparm( PARMSTRUCT_T* prm, STRING_T* name ); /* chiral centers: */ typedef struct chiral_t { INT_T c_anum[ 4 ]; REAL_T c_dist; } CHIRAL_T; void chirvol( int, int, int, int, int, REAL_T *, REAL_T *, REAL_T * ); /* Distance geometry "bounds" matrix */ typedef struct bounds_t { PARMSTRUCT_T *b_prm; INT_T b_nres; INT_T b_natoms; INT_T *b_aoff; void **b_aindex; /* was ATOM_T; just an opaque pointer for now */ INT_T *b_nconnect; INT_T **b_connect; REAL_T **b_bmat; INT_T **b_boundList; REAL_T *b_lowerBoundPathLength; REAL_T *b_upperBoundPathLength; INT_T b_schiral; INT_T b_nchiral; CHIRAL_T *b_chiral; } BOUNDS_T; /* rism routine interfaces: */ /* 3D RISM section */ /* N.B.: must match the rismprm_t struct in amber_rism_interface.F90 */ typedef struct { REAL_T solvcut; REAL_T buffer; REAL_T grdspc[3]; REAL_T solvbox[3]; REAL_T mdiis_del; REAL_T mdiis_restart; REAL_T fcecut; REAL_T fcenormsw; REAL_T uccoeff[4]; REAL_T biasPotential; INT_T closureOrder; INT_T ng3[3]; INT_T rism; /* non-zero if RISM is turned on */ INT_T asympCorr; INT_T mdiis_nvec; INT_T mdiis_method; INT_T maxstep; INT_T npropagate; INT_T centering; INT_T zerofrc; INT_T apply_rism_force; INT_T polarDecomp; INT_T entropicDecomp; INT_T gfCorrection; INT_T pcplusCorrection; INT_T rismnrespa; INT_T fcestride; INT_T fcenbasis; INT_T fcenbase; INT_T fcecrd; INT_T fceweigh; INT_T fcetrans; INT_T fcesort; INT_T fceifreq; INT_T fcentfrcor; INT_T fcewrite; INT_T fceread; INT_T saveprogress; INT_T ntwrism; INT_T verbose; INT_T progress; INT_T write_thermo; INT_T selftest; /*This is an unused variable that aligns the type on eight byte boundaries*/ INT_T padding; } RismData; #ifdef RISMSFF void rism_force_( REAL_T*, REAL_T*, REAL_T*, INT_T*, INT_T* ); void rism_setparam_( RismData*, INT_T*, REAL_T*, INT_T*, INT_T*, STRING_T[10][8] , INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, STRING_T*, INT_T*, INT_T*, INT_T*, REAL_T*, REAL_T*, REAL_T*, REAL_T*, INT_T*, INT_T*); void rism_init_( INT_T*); void rism_list_param_(); void rism_writesolvdist_(INT_T*); void rism_solvdist_thermo_calc_(INT_T*,INT_T*); void rism_thermo_print_(INT_T*,REAL_T*); void rism_printtimer_(); void rism_max_memory_(); #endif /*RISMSFF*/ #ifdef __cplusplus } #endif /* from arpack: */ void arsecond_( double * ); #ifndef INC_AMBER_NETCDF_H #define INC_AMBER_NETCDF_H /*! \file AmberNetcdf.h * \author Daniel R. Roe * \date 2010-12-07 * \brief A C implementation of routines for reading and writing the Amber * Netcdf trajectory and restart formats. * * Based on Cpptraj implementation. * Original implementation of netcdf in Amber by Jon Mongan. */ // NOTE: It would be better to allocate memory for single-precision coords // upon loading netcdf traj, but since NAB does not really handle pointers // the memory must be allocated during every read/write. // NOTE: Any changes made to the structure below must also be made to // nab_netcdf.h, however due to nab not recognizing the double // type all double vars here must be float vars there. NAB float is // equivalent to double (see nab/defreal.h etc), but this is why there // have to be two separate definitions of this structure. /// Hold info for Amber Netcdf trajectory or restart struct AmberNetcdf { double temp0; // Temperature of current frame (if TempVID!=-1) double restartTime; // Simulation time if Amber restart int isNCrestart; // 0 if trajectory, 1 if restart int ncid; // Netcdf ID of the file when open int frameDID; // ID of frame dimension int ncframe; // Number of frames in the file int currentFrame; // Current frame number int atomDID; // ID of atom dimension int ncatom; // Number of atoms int ncatom3; // Number of coordinates (ncatom * 3) int coordVID; // ID of coordinates variable int velocityVID; // ID of velocities variable int cellAngleVID; // ID of box angle variable int cellLengthVID; // ID of box length variable int spatialDID; int labelDID; int cell_spatialDID; int cell_angularDID; int spatialVID; int timeVID; int cell_spatialVID; int cell_angularVID; int TempVID; }; // NOTE: To be NAB-useable, any functions added below must also be referenced in // nab/nabcode.h and nab/symbol.c int netcdfDebug(struct AmberNetcdf*); int netcdfLoad(struct AmberNetcdf*,char *); int netcdfClose(struct AmberNetcdf*); int netcdfWriteRestart(char *, int, double *, double *, double *, double, double); int netcdfCreate(struct AmberNetcdf*,char *, int, int); int netcdfGetVelocity(struct AmberNetcdf*, int, double *); int netcdfGetFrame(struct AmberNetcdf*, int, double*, double*); int netcdfGetNextFrame(struct AmberNetcdf*,double*,double*); int netcdfWriteFrame(struct AmberNetcdf*, int, double *, double *); int netcdfWriteNextFrame(struct AmberNetcdf*, double *, double *); int netcdfInfo(struct AmberNetcdf*); #endif /// ptrajmask: The enhanced atom selection mask parser from ptraj. /// Originally written by Viktor Hornak, Stony Brook University. /// Adapted as standalone code by Dan Roe, NIST. #ifdef __cplusplus extern "C" { #endif // The NAME parameters control how the mask parser expects strings to look. // Originally, the parameter file assumes the atom, residue, symbol, etc. // names to be four characters. When stored as a string, the NULL character // is required, requiring a size of 5. It has been increased to 6 in cpptraj // to accomodate the slightly larger names that can be found in MOL2 files. // NAMESIZE: Default size for atom and residue names, 5 + NULL. // Amber atom/residue names are 4, but some mol2 atom types are larger. #define NAMESIZE 6 #define NAME_DEFAULT " " // Default type for atom names, res names, atom types etc typedef char NAME[NAMESIZE]; // More defines #define MAXSELE 1000 #define ALL 0 #define NUMLIST 1 #define NAMELIST 2 #define TYPELIST 3 #define ELEMLIST 4 /* parseMaskString() * The main interface to the mask parser. Takes a mask expression and some * information from a parameter file (stored in a PARMSTRUCT_T struct), * atomic coords in X0Y0Z0X1Y1Z1... format, and a debug value controlling how * much debug information is printed (internally the global int prnlev). * It returns a integer mask array imask[i]=1|0, i=0,atoms-1 * which contains the resulting atom selection. */ int *parseMaskString(char*,PARMSTRUCT_T*,double*,int); #ifdef __cplusplus } #endif #endif