From a7e02ba47cd17b58141351724a72fe95b17a55e8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Niels=20M=C3=BCller?= Date: Fri, 25 Oct 2019 14:06:41 +0200 Subject: [PATCH] Save Local Tpology with TPXReader for Gmx Whole Function --- pygmx/tpxio.pyx | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/pygmx/tpxio.pyx b/pygmx/tpxio.pyx index 821622e..82f2f09 100755 --- a/pygmx/tpxio.pyx +++ b/pygmx/tpxio.pyx @@ -120,6 +120,7 @@ cdef class TPXReader: t_tpxheader header t_inputrec input_record gmx_mtop_t topology + gmx_localtop_t *local_top real box[3][3] readonly int n_atoms, n_tcouple_groups, n_mol readonly char *topology_name @@ -253,14 +254,14 @@ cdef class TPXReader: &self.topology ) self.topology_name = self.topology.name[0] + self.local_top = gmx_mtop_generate_local_top(&self.topology, True) @cython.binding(True) def make_xtcframe_whole(coords, box, TPXReader reader): 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(&top.idef, -1, natoms) + cdef gmx_rmpbc_t gpbc = gmx_rmpbc_init(&reader.local_top.idef, -1, natoms) 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()