/*!
* \param[out] g Index group structure.
* \param[in] top Topology structure.
* \param[in] fnm File name for the index file.
* Memory is automatically allocated.
*
* One or both of \p top or \p fnm can be NULL.
* If \p top is NULL, an index file is required and the groups are read
* from the file (uses Gromacs routine init_index()).
* If \p fnm is NULL, default groups are constructed based on the
* topology (uses Gromacs routine analyse()).
* If both are null, the index group structure is initialized empty.
*/
void
gmx_ana_indexgrps_init(gmx_ana_indexgrps_t **g, t_topology *top,
const char *fnm)
{
t_blocka *block = NULL;
char **names = NULL;
if (fnm)
{
block = init_index(fnm, &names);
}
else if (top)
{
block = new_blocka();
analyse(&top->atoms, block, &names, FALSE, FALSE);
}
else
{
*g = new gmx_ana_indexgrps_t(0);
return;
}
try
{
*g = new gmx_ana_indexgrps_t(block->nr);
for (int i = 0; i < block->nr; ++i)
{
gmx_ana_index_t *grp = &(*g)->g[i];
grp->isize = block->index[i+1] - block->index[i];
snew(grp->index, grp->isize);
for (int j = 0; j < grp->isize; ++j)
{
grp->index[j] = block->a[block->index[i]+j];
}
grp->nalloc_index = grp->isize;
(*g)->names.push_back(names[i]);
}
}
catch (...)
{
for (int i = 0; i < block->nr; ++i)
{
sfree(names[i]);
}
sfree(names);
done_blocka(block);
sfree(block);
throw;
}
for (int i = 0; i < block->nr; ++i)
{
sfree(names[i]);
}
sfree(names);
done_blocka(block);
sfree(block);
}
void chk_ndx(const char *fn)
{
t_blocka *grps;
char **grpname;
int i, j;
grps = init_index(fn, &grpname);
if (debug)
{
pr_blocka(debug, 0, fn, grps, FALSE);
}
else
{
printf("Contents of index file %s\n", fn);
printf("--------------------------------------------------\n");
printf("Nr. Group #Entries First Last\n");
for (i = 0; (i < grps->nr); i++)
{
printf("%4d %-20s%8d%8d%8d\n", i, grpname[i],
grps->index[i+1]-grps->index[i],
grps->a[grps->index[i]]+1,
grps->a[grps->index[i+1]-1]+1);
}
}
for (i = 0; (i < grps->nr); i++)
{
sfree(grpname[i]);
}
sfree(grpname);
done_blocka(grps);
}
static real constr_r_max_moltype(FILE *fplog,
gmx_moltype_t *molt,t_iparams *iparams,
t_inputrec *ir)
{
int natoms,nflexcon,*path,at,count;
t_blocka at2con;
real r0,r1,r2maxA,r2maxB,rmax,lam0,lam1;
if (molt->ilist[F_CONSTR].nr == 0 &&
molt->ilist[F_CONSTRNC].nr == 0) {
return 0;
}
natoms = molt->atoms.nr;
at2con = make_at2con(0,natoms,molt->ilist,iparams,
EI_DYNAMICS(ir->eI),&nflexcon);
snew(path,1+ir->nProjOrder);
for(at=0; at<1+ir->nProjOrder; at++)
path[at] = -1;
r2maxA = 0;
for(at=0; at<natoms; at++) {
r0 = 0;
r1 = 0;
count = 0;
constr_recur(&at2con,molt->ilist,iparams,
FALSE,at,0,1+ir->nProjOrder,path,r0,r1,&r2maxA,&count);
}
if (ir->efep == efepNO) {
rmax = sqrt(r2maxA);
} else {
r2maxB = 0;
for(at=0; at<natoms; at++) {
r0 = 0;
r1 = 0;
count = 0;
constr_recur(&at2con,molt->ilist,iparams,
TRUE,at,0,1+ir->nProjOrder,path,r0,r1,&r2maxB,&count);
}
lam0 = ir->init_lambda;
if (EI_DYNAMICS(ir->eI))
lam0 += ir->init_step*ir->delta_lambda;
rmax = (1 - lam0)*sqrt(r2maxA) + lam0*sqrt(r2maxB);
if (EI_DYNAMICS(ir->eI)) {
lam1 = ir->init_lambda + (ir->init_step + ir->nsteps)*ir->delta_lambda;
rmax = max(rmax,(1 - lam1)*sqrt(r2maxA) + lam1*sqrt(r2maxB));
}
}
done_blocka(&at2con);
sfree(path);
return rmax;
}
void done_moltype(gmx_moltype_t *molt)
{
done_atom(&molt->atoms);
done_block(&molt->cgs);
done_blocka(&molt->excls);
for (int f = 0; f < F_NRE; f++)
{
sfree(molt->ilist[f].iatoms);
molt->ilist[f].nalloc = 0;
}
}
void done_top(t_topology *top)
{
int i;
done_atom (&(top->atoms));
/* For GB */
done_atomtypes(&(top->atomtypes));
done_symtab(&(top->symtab));
done_block(&(top->cgs));
done_block(&(top->mols));
done_blocka(&(top->excls));
}
/*!
* \param[out] g Index group structure.
* \param[in] top Topology structure.
* \param[in] fnm File name for the index file.
* Memory is automatically allocated.
*
* One or both of \p top or \p fnm can be NULL.
* If \p top is NULL, an index file is required and the groups are read
* from the file (uses Gromacs routine init_index()).
* If \p fnm is NULL, default groups are constructed based on the
* topology (uses Gromacs routine analyse()).
* If both are null, the index group structure is initialized empty.
*/
void
gmx_ana_indexgrps_init(gmx_ana_indexgrps_t **g, t_topology *top,
const char *fnm)
{
t_blocka *block = NULL;
char **names = NULL;
int i, j;
if (fnm)
{
block = init_index(fnm, &names);
}
else if (top)
{
block = new_blocka();
analyse(&top->atoms, block, &names, FALSE, FALSE);
}
else
{
snew(*g, 1);
(*g)->nr = 0;
(*g)->g = NULL;
return;
}
gmx_ana_indexgrps_alloc(g, block->nr);
for (i = 0; i < block->nr; ++i)
{
gmx_ana_index_t *grp = &(*g)->g[i];
grp->isize = block->index[i+1] - block->index[i];
snew(grp->index, grp->isize);
for (j = 0; j < grp->isize; ++j)
{
grp->index[j] = block->a[block->index[i]+j];
}
grp->name = names[i];
grp->nalloc_index = grp->isize;
}
done_blocka(block);
sfree(block);
sfree(names);
}
void done_top(t_topology *top)
{
sfree(top->idef.functype);
sfree(top->idef.iparams);
for (int f = 0; f < F_NRE; ++f)
{
sfree(top->idef.il[f].iatoms);
top->idef.il[f].iatoms = NULL;
top->idef.il[f].nalloc = 0;
}
done_atom(&(top->atoms));
/* For GB */
done_atomtypes(&(top->atomtypes));
done_symtab(&(top->symtab));
done_block(&(top->cgs));
done_block(&(top->mols));
done_blocka(&(top->excls));
}
static void make_shake_sblock_serial(struct gmx_constr *constr,
t_idef *idef, t_mdatoms *md)
{
int i, j, m, ncons;
int bstart, bnr;
t_blocka sblocks;
t_sortblock *sb;
t_iatom *iatom;
atom_id *inv_sblock;
/* Since we are processing the local topology,
* the F_CONSTRNC ilist has been concatenated to the F_CONSTR ilist.
*/
ncons = idef->il[F_CONSTR].nr/3;
init_blocka(&sblocks);
gen_sblocks(NULL, 0, md->homenr, idef, &sblocks, FALSE);
/*
bstart=(idef->nodeid > 0) ? blocks->multinr[idef->nodeid-1] : 0;
nblocks=blocks->multinr[idef->nodeid] - bstart;
*/
bstart = 0;
constr->nblocks = sblocks.nr;
if (debug)
{
fprintf(debug, "ncons: %d, bstart: %d, nblocks: %d\n",
ncons, bstart, constr->nblocks);
}
/* Calculate block number for each atom */
inv_sblock = make_invblocka(&sblocks, md->nr);
done_blocka(&sblocks);
/* Store the block number in temp array and
* sort the constraints in order of the sblock number
* and the atom numbers, really sorting a segment of the array!
*/
#ifdef DEBUGIDEF
pr_idef(fplog, 0, "Before Sort", idef);
#endif
iatom = idef->il[F_CONSTR].iatoms;
snew(sb, ncons);
for (i = 0; (i < ncons); i++, iatom += 3)
{
for (m = 0; (m < 3); m++)
{
sb[i].iatom[m] = iatom[m];
}
sb[i].blocknr = inv_sblock[iatom[1]];
}
/* Now sort the blocks */
if (debug)
{
pr_sortblock(debug, "Before sorting", ncons, sb);
fprintf(debug, "Going to sort constraints\n");
}
qsort(sb, ncons, (size_t)sizeof(*sb), pcomp);
if (debug)
{
pr_sortblock(debug, "After sorting", ncons, sb);
}
iatom = idef->il[F_CONSTR].iatoms;
for (i = 0; (i < ncons); i++, iatom += 3)
{
for (m = 0; (m < 3); m++)
{
iatom[m] = sb[i].iatom[m];
}
}
#ifdef DEBUGIDEF
pr_idef(fplog, 0, "After Sort", idef);
#endif
j = 0;
snew(constr->sblock, constr->nblocks+1);
bnr = -2;
for (i = 0; (i < ncons); i++)
{
if (sb[i].blocknr != bnr)
{
bnr = sb[i].blocknr;
constr->sblock[j++] = 3*i;
}
}
/* Last block... */
constr->sblock[j++] = 3*ncons;
if (j != (constr->nblocks+1))
{
fprintf(stderr, "bstart: %d\n", bstart);
fprintf(stderr, "j: %d, nblocks: %d, ncons: %d\n",
j, constr->nblocks, ncons);
for (i = 0; (i < ncons); i++)
{
fprintf(stderr, "i: %5d sb[i].blocknr: %5u\n", i, sb[i].blocknr);
}
for (j = 0; (j <= constr->nblocks); j++)
{
fprintf(stderr, "sblock[%3d]=%5d\n", j, (int)constr->sblock[j]);
}
gmx_fatal(FARGS, "DEATH HORROR: "
"sblocks does not match idef->il[F_CONSTR]");
}
sfree(sb);
sfree(inv_sblock);
}
void set_lincs(t_idef *idef,t_mdatoms *md,
gmx_bool bDynamics,t_commrec *cr,
struct gmx_lincsdata *li)
{
int start,natoms,nflexcon;
t_blocka at2con;
t_iatom *iatom;
int i,k,ncc_alloc,ni,con,nconnect,concon;
int type,a1,a2;
real lenA=0,lenB;
gmx_bool bLocal;
li->nc = 0;
li->ncc = 0;
/* This is the local topology, so there are only F_CONSTR constraints */
if (idef->il[F_CONSTR].nr == 0)
{
/* There are no constraints,
* we do not need to fill any data structures.
*/
return;
}
if (debug)
{
fprintf(debug,"Building the LINCS connectivity\n");
}
if (DOMAINDECOMP(cr))
{
if (cr->dd->constraints)
{
dd_get_constraint_range(cr->dd,&start,&natoms);
}
else
{
natoms = cr->dd->nat_home;
}
start = 0;
}
else if(PARTDECOMP(cr))
{
pd_get_constraint_range(cr->pd,&start,&natoms);
}
else
{
start = md->start;
natoms = md->homenr;
}
at2con = make_at2con(start,natoms,idef->il,idef->iparams,bDynamics,
&nflexcon);
if (idef->il[F_CONSTR].nr/3 > li->nc_alloc || li->nc_alloc == 0)
{
li->nc_alloc = over_alloc_dd(idef->il[F_CONSTR].nr/3);
srenew(li->bllen0,li->nc_alloc);
srenew(li->ddist,li->nc_alloc);
srenew(li->bla,2*li->nc_alloc);
srenew(li->blc,li->nc_alloc);
srenew(li->blc1,li->nc_alloc);
srenew(li->blnr,li->nc_alloc+1);
srenew(li->bllen,li->nc_alloc);
srenew(li->tmpv,li->nc_alloc);
srenew(li->tmp1,li->nc_alloc);
srenew(li->tmp2,li->nc_alloc);
srenew(li->tmp3,li->nc_alloc);
srenew(li->lambda,li->nc_alloc);
if (li->ncg_triangle > 0)
{
/* This is allocating too much, but it is difficult to improve */
srenew(li->triangle,li->nc_alloc);
srenew(li->tri_bits,li->nc_alloc);
}
}
iatom = idef->il[F_CONSTR].iatoms;
ncc_alloc = li->ncc_alloc;
li->blnr[0] = 0;
ni = idef->il[F_CONSTR].nr/3;
con = 0;
nconnect = 0;
li->blnr[con] = nconnect;
for(i=0; i<ni; i++)
{
bLocal = TRUE;
type = iatom[3*i];
a1 = iatom[3*i+1];
a2 = iatom[3*i+2];
lenA = idef->iparams[type].constr.dA;
lenB = idef->iparams[type].constr.dB;
/* Skip the flexible constraints when not doing dynamics */
if (bDynamics || lenA!=0 || lenB!=0)
{
li->bllen0[con] = lenA;
li->ddist[con] = lenB - lenA;
/* Set the length to the topology A length */
li->bllen[con] = li->bllen0[con];
li->bla[2*con] = a1;
li->bla[2*con+1] = a2;
/* Construct the constraint connection matrix blbnb */
for(k=at2con.index[a1-start]; k<at2con.index[a1-start+1]; k++)
{
concon = at2con.a[k];
if (concon != i)
{
if (nconnect >= ncc_alloc)
{
ncc_alloc = over_alloc_small(nconnect+1);
srenew(li->blbnb,ncc_alloc);
}
li->blbnb[nconnect++] = concon;
}
}
for(k=at2con.index[a2-start]; k<at2con.index[a2-start+1]; k++)
{
concon = at2con.a[k];
if (concon != i)
{
if (nconnect+1 > ncc_alloc)
{
ncc_alloc = over_alloc_small(nconnect+1);
srenew(li->blbnb,ncc_alloc);
}
li->blbnb[nconnect++] = concon;
}
}
li->blnr[con+1] = nconnect;
if (cr->dd == NULL)
{
/* Order the blbnb matrix to optimize memory access */
qsort(&(li->blbnb[li->blnr[con]]),li->blnr[con+1]-li->blnr[con],
sizeof(li->blbnb[0]),int_comp);
}
/* Increase the constraint count */
con++;
}
}
done_blocka(&at2con);
/* This is the real number of constraints,
* without dynamics the flexible constraints are not present.
*/
li->nc = con;
li->ncc = li->blnr[con];
if (cr->dd == NULL)
{
/* Since the matrix is static, we can free some memory */
ncc_alloc = li->ncc;
srenew(li->blbnb,ncc_alloc);
}
if (ncc_alloc > li->ncc_alloc)
{
li->ncc_alloc = ncc_alloc;
srenew(li->blmf,li->ncc_alloc);
srenew(li->blmf1,li->ncc_alloc);
srenew(li->tmpncc,li->ncc_alloc);
}
if (debug)
{
fprintf(debug,"Number of constraints is %d, couplings %d\n",
li->nc,li->ncc);
}
set_lincs_matrix(li,md->invmass,md->lambda);
}
void set_histp(t_atoms *pdba, rvec *x, real angle, real dist)
{
static const char *prot_acc[] = {
"O", "OD1", "OD2", "OE1", "OE2", "OG", "OG1", "OH", "OW"
};
#define NPA asize(prot_acc)
static const char *prot_don[] = {
"N", "NH1", "NH2", "NE", "ND1", "ND2", "NE2", "NZ", "OG", "OG1", "OH", "NE1", "OW"
};
#define NPD asize(prot_don)
gmx_bool *donor, *acceptor;
gmx_bool *hbond;
gmx_bool bHDd, bHEd;
rvec xh1, xh2;
int natom;
int i, j, nd, na, hisind, type = -1;
int nd1, ne2, cg, cd2, ce1;
t_blocka *hb;
char *atomnm;
natom = pdba->nr;
i = 0;
while (i < natom &&
gmx_strcasecmp(*pdba->resinfo[pdba->atom[i].resind].name, "HIS") != 0)
{
i++;
}
if (natom == i)
{
return;
}
/* A histidine residue exists that requires automated assignment, so
* doing the analysis of donors and acceptors is worthwhile. */
fprintf(stderr,
"Analysing hydrogen-bonding network for automated assignment of histidine\n"
" protonation.");
snew(donor, natom);
snew(acceptor, natom);
snew(hbond, natom);
snew(hb, 1);
nd = na = 0;
for (j = 0; (j < natom); j++)
{
if (in_strings(*pdba->atomname[j], NPA, prot_acc) != -1)
{
acceptor[j] = TRUE;
na++;
}
if (in_strings(*pdba->atomname[j], NPD, prot_don) != -1)
{
donor[j] = TRUE;
nd++;
}
}
fprintf(stderr, " %d donors and %d acceptors were found.\n", nd, na);
chk_allhb(pdba, x, hb, donor, acceptor, dist);
if (debug)
{
pr_hbonds(debug, hb, pdba);
}
fprintf(stderr, "There are %d hydrogen bonds\n", hb->nra);
/* Now do the HIS stuff */
hisind = -1;
while (i < natom)
{
if (gmx_strcasecmp(*pdba->resinfo[pdba->atom[i].resind].name, "HIS") != 0)
{
i++;
}
else
{
if (pdba->atom[i].resind != hisind)
{
hisind = pdba->atom[i].resind;
/* Find the atoms in the ring */
nd1 = ne2 = cg = cd2 = ce1 = -1;
while (i < natom && pdba->atom[i].resind == hisind)
{
atomnm = *pdba->atomname[i];
if (strcmp(atomnm, "CD2") == 0)
{
cd2 = i;
}
else if (strcmp(atomnm, "CG") == 0)
{
cg = i;
}
else if (strcmp(atomnm, "CE1") == 0)
{
ce1 = i;
}
else if (strcmp(atomnm, "ND1") == 0)
{
nd1 = i;
}
else if (strcmp(atomnm, "NE2") == 0)
{
ne2 = i;
}
i++;
}
if (!((cg == -1 ) || (cd2 == -1) || (ce1 == -1) ||
(nd1 == -1) || (ne2 == -1)))
{
calc_ringh(x[nd1], x[cg], x[ce1], xh1);
calc_ringh(x[ne2], x[ce1], x[cd2], xh2);
bHDd = chk_hbonds(nd1, pdba, x, acceptor, hbond, xh1, angle, dist);
chk_hbonds(nd1, pdba, x, donor, hbond, xh1, angle, dist);
bHEd = chk_hbonds(ne2, pdba, x, acceptor, hbond, xh2, angle, dist);
chk_hbonds(ne2, pdba, x, donor, hbond, xh2, angle, dist);
if (bHDd)
{
if (bHEd)
{
type = ehisH;
}
else
{
type = ehisA;
}
}
else
{
type = ehisB;
}
fprintf(stderr, "Will use %s for residue %d\n",
hh[type], pdba->resinfo[hisind].nr);
}
else
{
gmx_fatal(FARGS, "Incomplete ring in HIS%d",
pdba->resinfo[hisind].nr);
}
snew(pdba->resinfo[hisind].rtp, 1);
*pdba->resinfo[hisind].rtp = gmx_strdup(hh[type]);
}
}
}
done_blocka(hb);
sfree(hb);
sfree(donor);
sfree(acceptor);
sfree(hbond);
}