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);
}
