Clean up Code

pygmx/tpxio.pyx

@@ -34,7 +34,6 @@ cdef extern from "gromacs/fileio/tpxio.h":
                  int *natoms,
                  rvec *x,
                  rvec *v,
-                 # rvec *f,
                  gmx_mtop_t *mtop)
 
 
@@ -89,11 +88,12 @@ cdef index_groups_from_topology(gmx_mtop_t *topology):
 
 
 cdef open_tpx(const char* filename, t_inputrec *ir, matrix box, int *natoms, gmx_mtop_t *top):
-    #cdef stdio.FILE *old_stderr = stdio.stderr
-    #stdio.stderr = stdio.freopen('tmp', 'w', stdio.stderr)
+    
+    # unterdrücke GMX output durch internen stderr buffer...
     cdef char buffer[stdio.BUFSIZ]
     stdio.setbuf(stdio.stderr, buffer)
-    return_code = read_tpx(filename, ir, box, natoms, NULL, NULL, top)
+    cdef rvec *x, *v
+    return_code = read_tpx(filename, ir, box, natoms, x, v, top)
 
     for i in range(stdio.BUFSIZ):
         buffer[i] = 0
@@ -194,29 +194,39 @@ cdef class TPXReader:
                 types += mol_type * nmol
             return np.array(types)
 
-    @property
-    def nsteps(self):
-        return self.input_record.nsteps
+    property molecules:
+        "Get molecule indices from topology."
+        def __get__(self):
+            mols = [0] * self.n_atoms
+            molid = 0
+            for i in range(self.topology.mols.nr):
+                molid += 1
+                for j in range(self.topology.mols.index[i], self.topology.mols.index[i+1]):
+                    mols[j] = molid
+            return mols
+    # @property
+    # def nsteps(self):
+    #     return self.input_record.nsteps
 
-    @property
-    def nstxout(self):
-        return self.input_record.nstxout
+    # @property
+    # def nstxout(self):
+    #     return self.input_record.nstxout
 
-    @property
-    def nstvout(self):
-        return self.input_record.nstvout
+    # @property
+    # def nstvout(self):
+    #     return self.input_record.nstvout
 
-    @property
-    def nstfout(self):
-        return self.input_record.nstfout
+    # @property
+    # def nstfout(self):
+    #     return self.input_record.nstfout
 
-    @property
-    def nstxout_compressed(self):
-        return self.input_record.nstxout_compressed
+    # @property
+    # def nstxout_compressed(self):
+    #     return self.input_record.nstxout_compressed
 
-    @property
-    def nstenergy(self):
-        return self.input_record.nstenergy
+    # @property
+    # def nstenergy(self):
+    #     return self.input_record.nstenergy
 
 
     def read_ff(self):
@@ -235,7 +245,7 @@ cdef class TPXReader:
         # cdef np.ndarray[real, ndim=2] forces = np.empty((self.n_atoms, 3), dtype=np.float32)
         open_tpx(
             <char *>filename,
-            &self.input_record,
+            NULL,
             self.box,
             &self.n_atoms,
             &self.topology