static int write_tng_structure(void *v, int optflags, const molfile_atom_t *atoms)
{
/* VMD atoms do not contain molecule information, which
* complicates TNG writing a bit. */
tng_molecule_t tng_mol;
tng_chain_t tng_chain;
tng_residue_t tng_residue;
tng_atom_t tng_atom;
tngdata *tng = (tngdata *)v;
/* A dummy molecule must be added. All atoms will be added to it. */
tng_molecule_add(tng->tng_traj, "MOL", &tng_mol);
for(int i = 0; i < tng->natoms; i++)
{
if(tng_molecule_chain_find(tng->tng_traj, tng_mol, atoms[i].chain, -1, &tng_chain) !=
TNG_SUCCESS)
{
tng_molecule_chain_add(tng->tng_traj, tng_mol, atoms[i].chain, &tng_chain);
}
if (tng_chain_residue_find(tng->tng_traj, tng_chain, atoms[i].resname,
atoms[i].resid, &tng_residue) != TNG_SUCCESS)
{
tng_chain_residue_w_id_add(tng->tng_traj, tng_chain, atoms[i].resname,
atoms[i].resid, &tng_residue);
}
tng_residue_atom_add(tng->tng_traj, tng_residue, atoms[i].name, atoms[i].type, &tng_atom);
}
return MOLFILE_SUCCESS;
}
static void addTngMoleculeFromTopology(tng_trajectory_t tng,
const char *moleculeName,
const t_atoms *atoms,
gmx_int64_t numMolecules,
tng_molecule_t *tngMol)
{
if (tng_molecule_add(tng, moleculeName, tngMol) != TNG_SUCCESS)
{
gmx_file("Cannot add molecule to TNG molecular system.");
}
/* FIXME: The TNG atoms should contain mass and atomB info (for free
* energy calculations), i.e. in when it's available in TNG (2.0). */
for (int atomIt = 0; atomIt < atoms->nr; atomIt++)
{
const t_atom *at = &atoms->atom[atomIt];
/* FIXME: Currently the TNG API can only add atoms belonging to a
* residue and chain. Wait for TNG 2.0*/
if (atoms->nres > 0)
{
const t_resinfo *resInfo = &atoms->resinfo[at->resind];
char chainName[2] = {resInfo->chainid, 0};
tng_chain_t tngChain = NULL;
tng_residue_t tngRes = NULL;
tng_atom_t tngAtom = NULL;
if (tng_molecule_chain_find (tng, *tngMol, chainName,
(gmx_int64_t)-1, &tngChain) !=
TNG_SUCCESS)
{
tng_molecule_chain_add (tng, *tngMol, chainName,
&tngChain);
}
/* FIXME: When TNG supports both residue index and residue
* number the latter should be used. Wait for TNG 2.0*/
if (tng_chain_residue_find(tng, tngChain, *resInfo->name,
at->resind + 1, &tngRes)
!= TNG_SUCCESS)
{
tng_chain_residue_add(tng, tngChain, *resInfo->name, &tngRes);
}
tng_residue_atom_add(tng, tngRes, *(atoms->atomname[atomIt]), *(atoms->atomtype[atomIt]), &tngAtom);
}
}
tng_molecule_cnt_set(tng, *tngMol, numMolecules);
}
/* Create a TNG molecule representing the selection groups
* to write */
static void add_selection_groups(tng_trajectory_t tng,
const gmx_mtop_t *mtop)
{
const gmx_moltype_t *molType;
const t_atoms *atoms;
const t_atom *at;
const t_resinfo *resInfo;
const t_ilist *ilist;
int nAtoms = 0, i = 0, j, molIt, atomIt, nameIndex;
int atom_offset = 0;
tng_molecule_t mol, iterMol;
tng_chain_t chain;
tng_residue_t res;
tng_atom_t atom;
tng_bond_t tngBond;
gmx_int64_t nMols;
char *groupName;
/* The name of the TNG molecule containing the selection group is the
* same as the name of the selection group. */
nameIndex = *mtop->groups.grps[egcCompressedX].nm_ind;
groupName = *mtop->groups.grpname[nameIndex];
tng_molecule_alloc(tng, &mol);
tng_molecule_name_set(tng, mol, groupName);
tng_molecule_chain_add(tng, mol, "", &chain);
for (molIt = 0; molIt < mtop->nmoltype; molIt++)
{
molType = &mtop->moltype[mtop->molblock[molIt].type];
atoms = &molType->atoms;
for (j = 0; j < mtop->molblock[molIt].nmol; j++)
{
bool bAtomsAdded = FALSE;
for (atomIt = 0; atomIt < atoms->nr; atomIt++, i++)
{
char *res_name;
int res_id;
if (ggrpnr(&mtop->groups, egcCompressedX, i) != 0)
{
continue;
}
at = &atoms->atom[atomIt];
if (atoms->nres > 0)
{
resInfo = &atoms->resinfo[at->resind];
/* FIXME: When TNG supports both residue index and residue
* number the latter should be used. */
res_name = *resInfo->name;
res_id = at->resind + 1;
}
else
{
res_name = (char *)"";
res_id = 0;
}
if (tng_chain_residue_find(tng, chain, res_name, res_id, &res)
!= TNG_SUCCESS)
{
/* Since there is ONE chain for selection groups do not keep the
* original residue IDs - otherwise there might be conflicts. */
tng_chain_residue_add(tng, chain, res_name, &res);
}
tng_residue_atom_w_id_add(tng, res, *(atoms->atomname[atomIt]),
*(atoms->atomtype[atomIt]),
atom_offset + atomIt, &atom);
nAtoms++;
bAtomsAdded = TRUE;
}
/* Add bonds. */
if (bAtomsAdded)
{
for (int k = 0; k < F_NRE; k++)
{
if (IS_CHEMBOND(k))
{
ilist = &molType->ilist[k];
if (ilist)
{
int l = 1;
while (l < ilist->nr)
{
int atom1, atom2;
atom1 = ilist->iatoms[l] + atom_offset;
atom2 = ilist->iatoms[l+1] + atom_offset;
if (ggrpnr(&mtop->groups, egcCompressedX, atom1) == 0 &&
ggrpnr(&mtop->groups, egcCompressedX, atom2) == 0)
{
tng_molecule_bond_add(tng, mol, ilist->iatoms[l],
ilist->iatoms[l+1], &tngBond);
}
l += 3;
}
}
}
}
/* Settle is described using three atoms */
ilist = &molType->ilist[F_SETTLE];
if (ilist)
{
int l = 1;
while (l < ilist->nr)
{
int atom1, atom2, atom3;
atom1 = ilist->iatoms[l] + atom_offset;
atom2 = ilist->iatoms[l+1] + atom_offset;
atom3 = ilist->iatoms[l+2] + atom_offset;
if (ggrpnr(&mtop->groups, egcCompressedX, atom1) == 0)
{
if (ggrpnr(&mtop->groups, egcCompressedX, atom2) == 0)
{
tng_molecule_bond_add(tng, mol, atom1,
atom2, &tngBond);
}
if (ggrpnr(&mtop->groups, egcCompressedX, atom3) == 0)
{
tng_molecule_bond_add(tng, mol, atom1,
atom3, &tngBond);
}
}
l += 4;
}
}
}
atom_offset += atoms->nr;
}
}
if (nAtoms != i)
{
tng_molecule_existing_add(tng, &mol);
tng_molecule_cnt_set(tng, mol, 1);
tng_num_molecule_types_get(tng, &nMols);
for (gmx_int64_t k = 0; k < nMols; k++)
{
tng_molecule_of_index_get(tng, k, &iterMol);
if (iterMol == mol)
{
continue;
}
tng_molecule_cnt_set(tng, iterMol, 0);
}
}
else
{
tng_molecule_free(tng, &mol);
}
}
void gmx_tng_setup_atom_subgroup(tng_trajectory_t tng,
const int nind,
const int *ind,
const char *name)
{
#if GMX_USE_TNG
gmx_int64_t nAtoms, cnt, nMols;
tng_molecule_t mol, iterMol;
tng_chain_t chain;
tng_residue_t res;
tng_atom_t atom;
tng_function_status stat;
tng_num_particles_get(tng, &nAtoms);
if (nAtoms == nind)
{
return;
}
stat = tng_molecule_find(tng, name, -1, &mol);
if (stat == TNG_SUCCESS)
{
tng_molecule_num_atoms_get(tng, mol, &nAtoms);
tng_molecule_cnt_get(tng, mol, &cnt);
if (nAtoms == nind)
{
stat = TNG_SUCCESS;
}
else
{
stat = TNG_FAILURE;
}
}
if (stat == TNG_FAILURE)
{
/* The indexed atoms are added to one separate molecule. */
tng_molecule_alloc(tng, &mol);
tng_molecule_name_set(tng, mol, name);
tng_molecule_chain_add(tng, mol, "", &chain);
for (int i = 0; i < nind; i++)
{
char temp_name[256], temp_type[256];
/* Try to retrieve the residue name of the atom */
stat = tng_residue_name_of_particle_nr_get(tng, ind[i], temp_name, 256);
if (stat != TNG_SUCCESS)
{
temp_name[0] = '\0';
}
/* Check if the molecule of the selection already contains this residue */
if (tng_chain_residue_find(tng, chain, temp_name, -1, &res)
!= TNG_SUCCESS)
{
tng_chain_residue_add(tng, chain, temp_name, &res);
}
/* Try to find the original name and type of the atom */
stat = tng_atom_name_of_particle_nr_get(tng, ind[i], temp_name, 256);
if (stat != TNG_SUCCESS)
{
temp_name[0] = '\0';
}
stat = tng_atom_type_of_particle_nr_get(tng, ind[i], temp_type, 256);
if (stat != TNG_SUCCESS)
{
temp_type[0] = '\0';
}
tng_residue_atom_w_id_add(tng, res, temp_name, temp_type, ind[i], &atom);
}
tng_molecule_existing_add(tng, &mol);
}
/* Set the count of the molecule containing the selected atoms to 1 and all
* other molecules to 0 */
tng_molecule_cnt_set(tng, mol, 1);
tng_num_molecule_types_get(tng, &nMols);
for (gmx_int64_t k = 0; k < nMols; k++)
{
tng_molecule_of_index_get(tng, k, &iterMol);
if (iterMol == mol)
{
continue;
}
tng_molecule_cnt_set(tng, iterMol, 0);
}
#else
GMX_UNUSED_VALUE(tng);
GMX_UNUSED_VALUE(nind);
GMX_UNUSED_VALUE(ind);
GMX_UNUSED_VALUE(name);
#endif
}
