Include Gromacs internal function for making Frames Whole

2019-10-24 12:45:13 +02:00
parent fa7e3347d9
commit b8b61380c8
2 changed files with 17 additions and 0 deletions
--- 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