/* writePDBQ.cc */#ifndef WRITEPDBQSTATE/* writePDBQ.cc */#else /* WRITEPDBQSTATE *//* writePDBQState.cc */#endif /* WRITEPDBQSTATE */#ifndef WRITEPDBQSTATE#include <math.h>#endif /* not WRITEPDBQSTATE */#ifdef sgi    #include <stdio.h>    #include <string.h>    #include "structs.h"    #include "stateLibrary.h"    #include "writePDBQ.h"#ifdef WRITEPDBQSTATE    #include "stateLibrary.h"    #include "printEnergies.h"    #include "assert.h"#endif /* WRITEPDBQSTATE */#else    extern "C"    {        #include <stdio.h>        #include <string.h>        #include "structs.h"        #include "writePDBQ.h"#ifdef WRITEPDBQSTATE        #include "stateLibrary.h"        #include "printEnergies.h"        #include "assert.h"#endif /* WRITEPDBQSTATE */    }#endifextern int keepresnum;extern FILE *logFile;#ifndef WRITEPDBQSTATEvoid writePDBQ(  int irun,#else /* WRITEPDBQSTATE */void writePDBQState(  int   irun,#endif /* WRITEPDBQSTATE */                    char smFileName[MAX_CHARS],                    char dpfFN[MAX_CHARS],                    float sml_center[SPACE],#ifndef WRITEPDBQSTATE                    State state,#else /* WRITEPDBQSTATE */                    State *Ptr_state,#endif /* WRITEPDBQSTATE */                    int ntor,#ifndef WRITEPDBQSTATE                    float eintra,                    float einter,#else /* WRITEPDBQSTATE */                    float *Ptr_eintra,                    float *Ptr_einter,#endif /* WRITEPDBQSTATE */                    int natom,                    char atomstuff[MAX_ATOMS][MAX_CHARS],                    float crd[MAX_ATOMS][SPACE],                    float emap[MAX_ATOMS],                    float elec[MAX_ATOMS],                    float charge[MAX_ATOMS],#ifndef WRITEPDBQSTATE                    float torsFreeEnergy)#else /* WRITEPDBQSTATE */                    float torsFreeEnergy,                    float vt[MAX_TORS][SPACE],                    int   tlist[MAX_TORS][MAX_ATOMS],                    float crdpdb[MAX_ATOMS][SPACE],                    int   nonbondlist[MAX_NONBONDS][2],                    float e_internal[NEINT][ATOM_MAPS][ATOM_MAPS],                    int   type[MAX_ATOMS],                    int   Nnb,                    Boole B_calcIntElec,                    float q1q2[MAX_NONBONDS],                    float map[MAX_GRID_PTS][MAX_GRID_PTS][MAX_GRID_PTS][MAX_MAPS],                    float inv_spacing,                    float xlo,                    float ylo,                    float zlo,                    float xhi,                    float yhi,                    float zhi)#endif /* WRITEPDBQSTATE */{#ifndef WRITEPDBQSTATE    int i;    char rec14[14],rec9[9];#else /* WRITEPDBQSTATE */    int   i=0;    char  AtmNamResNamNum[14],AtmNamResNam[9];    Boole B_outside = FALSE;    for (i=0; i<14; i++) {        AtmNamResNamNum[i] = '\0';    }    for (i=0; i<9; i++) {        AtmNamResNam[i] = '\0';    }// new stuff {    printState( logFile, (*Ptr_state), 2 ); // the 2 is the level of detail: 2 is high, 0 is low    cnv_state_to_coords( (*Ptr_state),vt,tlist,ntor,crdpdb,crd,natom );    B_outside = FALSE;    for (i=0; (i<natom)&&(!B_outside); i++) {        B_outside = is_out_grid( crd[i][0], crd[i][1], crd[i][2]);    }    if (!B_outside) {        if (ntor > 0) {            *Ptr_eintra = eintcal( nonbondlist, e_internal, crd, type, Nnb, B_calcIntElec, q1q2);        } else {            *Ptr_eintra = 0.0;        }        *Ptr_einter = trilinterp( crd, charge, type, natom, map, inv_spacing, elec, emap, xlo, ylo, zlo);    } else {        *Ptr_eintra = *Ptr_einter = BIG;  // defined in constants.h    }// new stuff }#endif /* WRITEPDBQSTATE */#ifndef WRITEPDBQSTATE    pr( logFile, "\n" );#endif /* not WRITEPDBQSTATE */    pr( logFile, "DOCKED: MODEL     %4d\n", irun+1 );    pr( logFile, "DOCKED: USER    Run = %d\n", irun+1 );    pr( logFile, "DOCKED: USER    DPF = %s\n", dpfFN );#ifndef WRITEPDBQSTATE    printEnergies( einter, eintra, torsFreeEnergy, "DOCKED: USER    " );#else /* WRITEPDBQSTATE */    printEnergies( *Ptr_einter, *Ptr_eintra, torsFreeEnergy, "DOCKED: USER    " );#endif /* WRITEPDBQSTATE */    (void)fprintf( logFile, "DOCKED: USER    NEWDPF move %s\n", smFileName );    (void)fprintf( logFile, "DOCKED: USER    NEWDPF about %f %f %f\n", sml_center[X],sml_center[Y],sml_center[Z]);#ifndef WRITEPDBQSTATE    (void)fprintf( logFile, "DOCKED: USER    NEWDPF tran0 %f %f %f\n", state.T.x, state.T.y, state.T.z );    (void)fprintf( logFile, "DOCKED: USER    NEWDPF quat0 %f %f %f %f\n", state.Q.nx, state.Q.ny, state.Q.nz, Deg( state.Q.ang ) );#else /* WRITEPDBQSTATE */    (void)fprintf( logFile, "DOCKED: USER    NEWDPF tran0 %f %f %f\n", (*Ptr_state).T.x, (*Ptr_state).T.y, (*Ptr_state).T.z );    (void)fprintf( logFile, "DOCKED: USER    NEWDPF quat0 %f %f %f %f\n", (*Ptr_state).Q.nx, (*Ptr_state).Q.ny, (*Ptr_state).Q.nz, Deg( (*Ptr_state).Q.ang ) );#endif /* WRITEPDBQSTATE */    if (ntor > 0) {        (void)fprintf( logFile, "DOCKED: USER    NEWDPF ndihe %d\n", ntor );        (void)fprintf( logFile, "DOCKED: USER    NEWDPF dihe0 " );        for (i=0; i<ntor; i++) {#ifndef WRITEPDBQSTATE            (void)fprintf( logFile, "%.2f ", Deg(state.tor[i]) );#else /* WRITEPDBQSTATE */            (void)fprintf( logFile, "%.2f ", Deg((*Ptr_state).tor[i]) );#endif /* WRITEPDBQSTATE */        }/*i*/        (void)fprintf( logFile, "\n" );    }/*endif*/    (void)fprintf( logFile, "DOCKED: USER                              x       y       z       vdW   Elec        q\n" );    (void)fprintf( logFile, "DOCKED: USER                           _______ _______ _______ ________ _____    ______\n" );    if (keepresnum > 0) {        for (i = 0;  i < natom;  i++) {#ifndef WRITEPDBQSTATE            strncpy( rec14, &atomstuff[i][13], (size_t)13);            (void)fprintf( logFile, "DOCKED: ATOM  %5d  %.13s    %8.3f%8.3f%8.3f% +8.2f%+6.2f    %+6.3f\n", i+1, rec14,      crd[i][X], crd[i][Y], crd[i][Z], emap[i], elec[i], charge[i] );#else /* WRITEPDBQSTATE */            assert( i>=0 && i < natom);            strncpy( AtmNamResNamNum, &atomstuff[i][13], (size_t)13);            AtmNamResNamNum[13] = '\0'; // ensure string is NULL terminated!            (void)fprintf( logFile, "DOCKED: ATOM  %5d  %13s    %8.3f%8.3f%8.3f% +8.2f%+6.2f    %+6.3f\n", i+1, AtmNamResNamNum,      crd[i][X], crd[i][Y], crd[i][Z], emap[i], elec[i], charge[i] );#endif /* WRITEPDBQSTATE */        }/*i*/    } else {        for (i = 0;  i < natom;  i++) {#ifndef WRITEPDBQSTATE            strncpy( rec9, &atomstuff[i][13], (size_t)8);            (void)fprintf( logFile, "DOCKED: ATOM  %5d  %.8s%5d    %8.3f%8.3f%8.3f %+8.2f%+6.2f    %+6.3f\n", i+1, rec9,irun+1,crd[i][X], crd[i][Y], crd[i][Z], emap[i], elec[i], charge[i] );#else /* WRITEPDBQSTATE */            assert( i>=0 && i < natom);            strncpy( AtmNamResNam, &atomstuff[i][13], (size_t)8);            AtmNamResNam[8] = '\0'; // ensure string is NULL terminated!            (void)fprintf( logFile, "DOCKED: ATOM  %5d  %8s%5d    %8.3f%8.3f%8.3f %+8.2f%+6.2f    %+6.3f\n", i+1, AtmNamResNam,irun+1,crd[i][X], crd[i][Y], crd[i][Z], emap[i], elec[i], charge[i] );#endif /* WRITEPDBQSTATE */        }/*i*/    }/*endif*/    (void)fprintf( logFile, "DOCKED: TER\n" );#ifndef WRITEPDBQSTATE    (void)fprintf( logFile, "DOCKED: ENDMDL\n" );    pr( logFile, "DOCKED: ENDMDL\n");#endif /* WRITEPDBQSTATE */    (void)fprintf( logFile, UnderLine );    (void)fflush(  logFile );}#ifdef WRITEMOLASPDBQFUNC/***************************************************************/void writeMolAsPDBQ(Molecule *mol, FILE *output)/* write out the Molecule "mol" as a PDBQ formatted file to    the file pointed to by "output". */{    int i;    char rec14[14],rec9[9];    (void)fprintf( output, "\n" );    (void)fprintf( output, "DIAGNOSTIC: MODEL     %4d\n", 1 );    (void)fprintf( output, "DIAGNOSTIC: USER    NEWDPF tran0 %f %f %f\n", mol->S.T.x, mol->S.T.y, mol->S.T.z );    (void)fprintf( output, "DIAGNOSTIC: USER    NEWDPF quat0 %f %f %f %f\n", mol->S.Q.nx, mol->S.Q.ny, mol->S.Q.nz, ( (mol->S.Q.ang) * 57.29577951 ) );    if (mol->S.ntor > 0) {        (void)fprintf( output, "DIAGNOSTIC: USER    NEWDPF ndihe %d\n", mol->S.ntor );        (void)fprintf( output, "DIAGNOSTIC: USER    NEWDPF dihe0 " );        for (i=0; i<mol->S.ntor; i++) {            (void)fprintf( output, "%.2f ", ( (mol->S.tor[i]) * 57.29577951 ) );        }         (void)fprintf( output, "\n" );    }     (void)fprintf( output, "DIAGNOSTIC: USER                              x       y       z       vdW   Elec        q\n" );    (void)fprintf( output, "DIAGNOSTIC: USER                           _______ _______ _______ ________ _____    ______\n" );    if (keepresnum > 0) {        for (i = 0;  i < mol->natom;  i++) {            strncpy( rec14, &(mol->atomstr[i][13]), (size_t)13);            (void)fprintf( output, "DIAGNOSTIC: ATOM  %5d  %.13s    %8.3f%8.3f%8.3f% +8.2f%+6.2f    %+6.3f\n", i+1, rec14,      mol->crd[i][0], mol->crd[i][1], mol->crd[i][2], 0.0, 0.0, 0.0 );        }     } else {        for (i = 0;  i < mol->natom;  i++) {            strncpy( rec9, &(mol->atomstr[i][13]), (size_t)8);            (void)fprintf( output, "DIAGNOSTIC: ATOM  %5d  %.8s%5d    %8.3f%8.3f%8.3f %+8.2f%+6.2f    %+6.3f\n", i+1, rec9,1, mol->crd[i][0],  mol->crd[i][1],  mol->crd[i][2], 0.0, 0.0, 0.0 );        }     }     (void)fprintf( output, "DIAGNOSTIC: TER\n" );    (void)fprintf( output, "DIAGNOSTIC: ENDMDL\n" );    (void)fprintf( output, "_______________________________________________________________________________\n\n" );    (void)fflush(  output );}#endif /* WRITEMOLASPDBQFUNC *//* EOF */