From b8b61380c8f1b3a99001df88b6b5e595b06bba7b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Niels=20M=C3=BCller?= <post@nielsm.de>
Date: Thu, 24 Oct 2019 12:45:13 +0200
Subject: [PATCH] Include Gromacs internal function for making Frames Whole

---
 pygmx/topology.pxd | 8 ++++++++
 pygmx/tpxio.pyx    | 9 +++++++++
 2 files changed, 17 insertions(+)

diff --git a/pygmx/topology.pxd b/pygmx/topology.pxd
index a2eba49..fb369c2 100755
--- a/pygmx/topology.pxd
+++ b/pygmx/topology.pxd
@@ -146,3 +146,11 @@ cdef extern from "gromacs/topology/topology.h":
 # cdef extern from "gromacs/topology/topology.h":
         # generate a t_atoms struct for the system from gmx_mtop_t
         # t_atoms* mtop2atoms(gmx_mtop_t *mtop)
+cdef extern from "gromacs/topology/mtop_util.h":
+    t_atoms gmx_mtop_global_atoms(const gmx_mtop_t *mtop)
+
+cdef extern from "gromacs/pbcutil/rmpbc.h":
+    void rm_gropbc(const t_atoms *atoms, rvec x[], const matrix box);
+
+
+
diff --git a/pygmx/tpxio.pyx b/pygmx/tpxio.pyx
index facd13c..4d20442 100755
--- a/pygmx/tpxio.pyx
+++ b/pygmx/tpxio.pyx
@@ -251,3 +251,12 @@ cdef class TPXReader:
             &self.topology
         )
         self.topology_name = self.topology.name[0]
+
+
+@cython.binding(True)
+def make_xtcframe_whole(coords, box, <TPXReader>reader):
+    cdef t_atoms = gmx_mtop_global_atoms(reader.topology)
+    cdef np.ndarray[real, ndim=2] b = np.asarray(box, dtype=np.float32)
+    cdef np.ndarray[real, ndim=2] x = np.asarray(coords, dtype=np.float32)
+    rm_gropbc(const t_atoms *atoms, <rvec *>x.data, <matrix> b)
+    return x
\ No newline at end of file