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Save Local Tpology with TPXReader for Gmx Whole Function

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Niels Müller
2019-10-25 14:06:41 +02:00
parent 92addd3148
commit a7e02ba47c
1 changed files with 3 additions and 2 deletions
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5
pygmx/tpxio.pyx
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@ -120,6 +120,7 @@ cdef class TPXReader:
t_tpxheader header t_tpxheader header
t_inputrec input_record t_inputrec input_record
gmx_mtop_t topology gmx_mtop_t topology
gmx_localtop_t *local_top
real box[3][3] real box[3][3]
readonly int n_atoms, n_tcouple_groups, n_mol readonly int n_atoms, n_tcouple_groups, n_mol
readonly char *topology_name readonly char *topology_name
@ -253,14 +254,14 @@ cdef class TPXReader:
&self.topology &self.topology
) )
self.topology_name = self.topology.name[0] self.topology_name = self.topology.name[0]
self.local_top = gmx_mtop_generate_local_top(&self.topology, True)
@cython.binding(True) @cython.binding(True)
def make_xtcframe_whole(coords, box, TPXReader reader): def make_xtcframe_whole(coords, box, TPXReader reader):
cdef int natoms = reader.topology.natoms cdef int natoms = reader.topology.natoms
cdef gmx_localtop_t *top = gmx_mtop_generate_local_top(&reader.topology, True) cdef gmx_rmpbc_t gpbc = gmx_rmpbc_init(&reader.local_top.idef, -1, natoms)
cdef gmx_rmpbc_t gpbc = gmx_rmpbc_init(&top.idef, -1, natoms)
cdef np.ndarray[real, ndim=2] b = np.asarray(box, dtype=np.float32) cdef np.ndarray[real, ndim=2] b = np.asarray(box, dtype=np.float32)
cdef np.ndarray[real, ndim=2] x = np.array(coords, dtype=np.float32).copy() cdef np.ndarray[real, ndim=2] x = np.array(coords, dtype=np.float32).copy()