示例#1
0
static int read_tng_structure(void *v, int *optflags,
                               molfile_atom_t *atoms)
{
    tngdata *tng = (tngdata *)v;
    char long_name[16], short_name[2];
    int64_t id;

    *optflags = MOLFILE_NOOPTIONS;
    for(int i = 0; i < tng->natoms; i++)
    {
        molfile_atom_t *atom = atoms+i;
        tng_atom_name_of_particle_nr_get(tng->tng_traj, i, long_name, 16);
        strcpy(atom->name, long_name);
        tng_atom_type_of_particle_nr_get(tng->tng_traj, i, long_name, 16);
        strcpy(atom->type, long_name);
        tng_residue_name_of_particle_nr_get(tng->tng_traj, i, long_name, 16);
        strcpy(atom->resname, long_name);
        tng_global_residue_id_of_particle_nr_get(tng->tng_traj, i, &id);
        atom->resid = (int)id;
//         fprintf(stderr, "resid: %d\n", (int)id);
        tng_chain_name_of_particle_nr_get(tng->tng_traj, i, short_name, 2);
        strcpy(atom->chain, short_name);
        atom->segid[0] = '\0';
    }
//     fprintf(stderr, "Structure opened\n");
    return MOLFILE_SUCCESS;
}
示例#2
0
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
}