From 1535f1e96970fedc2cd4d1f8b69ca13b8c1921fc Mon Sep 17 00:00:00 2001 From: David van der Spoel Date: Mon, 11 Jan 2010 14:46:30 +0100 Subject: [PATCH] Deleted old file --- src/mdlib/gmx_qhop_db.c | 276 ------------------------------------------------ 1 file changed, 276 deletions(-) delete mode 100644 src/mdlib/gmx_qhop_db.c diff --git a/src/mdlib/gmx_qhop_db.c b/src/mdlib/gmx_qhop_db.c deleted file mode 100644 index 7b585c964e..0000000000 --- a/src/mdlib/gmx_qhop_db.c +++ /dev/null @@ -1,276 +0,0 @@ -#include -#include -#include -#include "typedefs.h" -#include "smalloc.h" -#include "string2.h" -#include "futil.h" -#include "symtab.h" -#include "hackblock.h" -#include "resall.h" -#include "gmx_qhop_parm.h" -#include "gmx_qhop_xml.h" -#include "gmx_qhop_db.h" - -#if 0 -/* These routines link to invalid dependencies in kernel/resall.c! */ - -typedef struct { - int id,charge,natom; - int ndonor,*donor,nacceptor,*acceptor; -} qhop_resinfo_t; - -typedef struct { - int nrtp; - t_restp *rtp; - qhop_resinfo_t *resinfo; - int bts[4]; - int nrexcl; - bool bAllDih,bHH14,bRemoveDih; - t_atomtype atype; - t_symtab tab; - int ngqh; - gmx_qhop *gqh; - t_qhop_parameters *qhop_param; -} gmx_qhop_db_t; - -static void fill_resinfo(t_restp *rtp,qhop_resinfo_t *ri) -{ - int j,k,m; - bool bDonor; - double qtot; - - qtot = 0; - ri->natom = rtp->natom; - ri->ndonor = 0; - snew(ri->donor,ri->natom); - ri->nacceptor = 0; - snew(ri->acceptor,ri->natom); - for(j=0; (jnatom); j++) { - qtot += rtp->atom[j].q; - /* First check atoms usually involved in Hbonds */ - if ((rtp->atom[j].atomnumber == 7) || - (rtp->atom[j].atomnumber == 8) || - (rtp->atom[j].atomnumber == 9) || - (rtp->atom[j].atomnumber == 16)) { - ri->acceptor[ri->nacceptor++] = j; - /* Now check whether this atom has a proton, i.e. is a donor */ - bDonor = FALSE; - for(k=0; (krb[ebtsBONDS].nb); k++) { - if (strcasecmp(*(rtp->atomname[j]),rtp->rb[ebtsBONDS].b[k].a[0]) == 0) - for(m=0; (mnatom); m++) - if ((strcasecmp(*(rtp->atomname[m]),rtp->rb[ebtsBONDS].b[k].a[1]) == 0) && - (rtp->atom[m].atomnumber == 1) && - (rtp->atom[m].q > 0)) - bDonor = TRUE; - } - if (bDonor) - ri->donor[ri->ndonor++] = j; - } - } - ri->charge = qtot; -} - -static void lo_fill_qhp(gmx_qhop gqh,char *name,real *xx) -{ - double x; - int test; - - test = gmx_qhop_get_value(gqh,name,&x); - if (test == 1) - *xx = x; - else { - fprintf(stderr,"WARNING: Could not extract %s from qhop data for %s-%s\n", - name,gmx_qhop_get_donor(gqh),gmx_qhop_get_acceptor(gqh)); - *xx = 0; - } -} - -static void fill_qhp(t_qhop_parameters *qhp,gmx_qhop gqh) -{ - lo_fill_qhp(gqh,"alpha",&qhp->alpha); - lo_fill_qhp(gqh,"beta",&qhp->beta); - lo_fill_qhp(gqh,"gamma",&qhp->gamma); - lo_fill_qhp(gqh,"k_1",&qhp->k_1); - lo_fill_qhp(gqh,"k_2",&qhp->k_2); - lo_fill_qhp(gqh,"k_3",&qhp->k_3); - lo_fill_qhp(gqh,"m_1",&qhp->m_1); - lo_fill_qhp(gqh,"m_2",&qhp->m_2); - lo_fill_qhp(gqh,"m_3",&qhp->m_3); - lo_fill_qhp(gqh,"s_A",&qhp->s_A); - lo_fill_qhp(gqh,"t_A",&qhp->t_A); - lo_fill_qhp(gqh,"v_A",&qhp->v_A); - lo_fill_qhp(gqh,"s_B",&qhp->s_B); - lo_fill_qhp(gqh,"s_C",&qhp->s_C); - lo_fill_qhp(gqh,"t_C",&qhp->t_C); - lo_fill_qhp(gqh,"v_C",&qhp->v_C); - lo_fill_qhp(gqh,"f",&qhp->f); - lo_fill_qhp(gqh,"g",&qhp->g); - lo_fill_qhp(gqh,"h",&qhp->h); - lo_fill_qhp(gqh,"p_1",&qhp->p_1); - lo_fill_qhp(gqh,"q_1",&qhp->q_1); - lo_fill_qhp(gqh,"q_2",&qhp->q_2); - lo_fill_qhp(gqh,"q_3",&qhp->q_3); - lo_fill_qhp(gqh,"r_1",&qhp->r_1); - lo_fill_qhp(gqh,"r_2",&qhp->r_2); - lo_fill_qhp(gqh,"r_3",&qhp->r_3); -} - -static void dump_qhp(FILE *fp,t_qhop_parameters *qhp) -{ - fprintf(fp,"alpha = %g\n",qhp->alpha); - fprintf(fp,"beta = %g\n",qhp->beta); - fprintf(fp,"gamma = %g\n",qhp->gamma); - fprintf(fp,"k_1 = %g\n",qhp->k_1); - fprintf(fp,"k_2 = %g\n",qhp->k_2); - fprintf(fp,"k_3 = %g\n",qhp->k_3); - fprintf(fp,"m_1 = %g\n",qhp->m_1); - fprintf(fp,"m_2 = %g\n",qhp->m_2); - fprintf(fp,"m_3 = %g\n",qhp->m_3); - fprintf(fp,"s_A = %g\n",qhp->s_A); - fprintf(fp,"t_A = %g\n",qhp->t_A); - fprintf(fp,"v_A = %g\n",qhp->v_A); - fprintf(fp,"s_B = %g\n",qhp->s_B); - fprintf(fp,"s_C = %g\n",qhp->s_C); - fprintf(fp,"t_C = %g\n",qhp->t_C); - fprintf(fp,"v_C = %g\n",qhp->v_C); - fprintf(fp,"f = %g\n",qhp->f); - fprintf(fp,"g = %g\n",qhp->g); - fprintf(fp,"h = %g\n",qhp->h); - fprintf(fp,"p_1 = %g\n",qhp->p_1); - fprintf(fp,"q_1 = %g\n",qhp->q_1); - fprintf(fp,"q_2 = %g\n",qhp->q_2); - fprintf(fp,"q_3 = %g\n",qhp->q_3); - fprintf(fp,"r_1 = %g\n",qhp->r_1); - fprintf(fp,"r_2 = %g\n",qhp->r_2); - fprintf(fp,"r_3 = %g\n",qhp->r_3); -} - -gmx_qhop_db gmx_qhop_db_read(char *forcefield) -{ - gmx_qhop_db_t *qdb; - char buf[256]; - char *fn; - int i,j; - double qtot; - - snew(qdb,1); - open_symtab(&(qdb->tab)); - sprintf(buf,"%s-qhop",forcefield); - qdb->atype = read_atype(forcefield,&(qdb->tab)); - qdb->nrtp = read_resall(buf,qdb->bts,&(qdb->rtp),qdb->atype, - &(qdb->tab),&(qdb->bAllDih), - &(qdb->nrexcl),&(qdb->bHH14),&(qdb->bRemoveDih)); - snew(qdb->resinfo,qdb->nrtp); - for(i=0; (inrtp); i++) - fill_resinfo(&qdb->rtp[i],&qdb->resinfo[i]); - - sprintf(buf,"%s-qhop.dat",forcefield); - fn = (char *)libfn(buf); - /* Read the xml data file */ - qdb->gqh = gmx_qhops_read(fn,&qdb->ngqh); - sprintf(buf,"%s-qhop-debug.dat",forcefield); - gmx_qhops_write(buf,qdb->ngqh,qdb->gqh); - snew(qdb->qhop_param,qdb->ngqh); - for(i=0; (ingqh); i++) { - fill_qhp(&(qdb->qhop_param[i]),qdb->gqh[i]); - if (debug) { - fprintf(debug,"Donor: %s Acceptor: %s\n", - gmx_qhop_get_donor(qdb->gqh[i]), - gmx_qhop_get_acceptor(qdb->gqh[i])); - dump_qhp(debug,&(qdb->qhop_param[i])); - } - } - sfree(fn); - return (gmx_qhop_db) qdb; -} - -int gmx_qhop_db_write(char *fn,gmx_qhop_db qdb) -{ - gmx_qhop_db_t *db = (gmx_qhop_db_t *) qdb; - FILE *fp; - - fp=ffopen(fn,"w"); - print_resall(fp,db->bts,db->nrtp,db->rtp,db->atype,db->bAllDih, - db->nrexcl,db->bHH14,db->bRemoveDih); - ffclose(fp); - - return 1; -} - -int gmx_qhop_db_done(gmx_qhop_db qdb) -{ - fprintf(stderr,"gmx_qhop_db_done not implemented yet.\n"); - - return 1; -} - -int gmx_qhop_db_get_nstates(gmx_qhop_db qdb,char *resname) -{ - gmx_qhop_db_t *db = (gmx_qhop_db_t *) qdb; - int i,nstate=0; - - for(i=0; (inrtp); i++) { - if (strncmp(db->rtp[i].resname,resname,3) == 0) { - nstate++; - } - } - return nstate; -} - -int gmx_qhop_db_get_qstate(gmx_qhop_db qdb,char *resname,int istate) -{ - gmx_qhop_db_t *db = (gmx_qhop_db_t *) qdb; - int i,nstate=0; - - for(i=0; (inrtp); i++) { - if (strncmp(db->rtp[i].resname,resname,3) == 0) { - nstate++; - if (nstate == istate) - return db->resinfo[i].charge; - } - } - return nstate; -} - -char **gmx_qhop_db_get_donors(gmx_qhop_db qdb,char *resname,int state) -{ - return NULL; -} - -char **gmx_qhop_db_get_acceptors(gmx_qhop_db qdb,char *resname,int state) -{ - return NULL; -} - -int gmx_qhop_db_set_charges(gmx_qhop_db qdb,char *resname,int state, - int natoms,real q[]) -{ - return 0; -} - -int gmx_qhop_db_get_parameters(gmx_qhop_db qdb, - char *donor,char *acceptor, - t_qhop_parameters *qp) -{ - gmx_qhop_db_t *db = (gmx_qhop_db_t *) qdb; - char *aa,*dd; - int i; - - for(i=0; (ingqh); i++) { - aa = gmx_qhop_get_acceptor(db->gqh[i]); - dd = gmx_qhop_get_donor(db->gqh[i]); - if (strncmp(donor,dd,3) == 0) { - if (strncmp(acceptor,aa,3) == 0) { - memcpy(qp,&(db->qhop_param[i]),sizeof(*qp)); - - return 1; - } - } - } - return 0; -} - -#else -int gmx_qhop_db_dummy=0; -#endif -- 2.11.4.GIT