ParmEd · swails · Sep 18, 2024 · Sep 13, 2024 · Sep 18, 2024
diff --git a/parmed/amber/_amberparm.py b/parmed/amber/_amberparm.py
@@ -2147,7 +2147,7 @@ def box(self, value):
                     box[4] = box[4].value_in_unit(u.degrees)
                 if u.is_quantity(box[5]):
                     box[5] = box[5].value_in_unit(u.degrees)
-            box = np.array(box, dtype=np.float64, copy=False, subok=True).reshape((-1, 6))
+            box = np.asanyarray(box, dtype=np.float64).reshape((-1, 6))
 
             # We are adding a box for the first time, so make sure we add some flags
             if self._box is None:
@@ -2373,7 +2373,7 @@ def positions(self):
     @property
     def velocities(self):
-        return np.array(self.vels, copy=False).reshape(self.natom, 3)
+        return np.asarray(self.vels).reshape(self.natom, 3)
 
     @property
     def box_vectors(self):

diff --git a/parmed/amber/asciicrd.py b/parmed/amber/asciicrd.py
@@ -317,7 +317,7 @@ def coordinates(self):
     def coordinates(self, stuff):
         if self._status == 'old':
             raise RuntimeError('Cannot set coordinates on an old restart')
-        stuff = np.array(stuff, copy=False).ravel()
+        stuff = np.asarray(stuff).ravel()
         if self.natom > 0 and len(stuff) != 3 * self.natom:
             raise ValueError(f'Got {len(stuff)} coordinates for {self.natom} atoms')
         if self._coords_written:
@@ -351,7 +351,7 @@ def velocities(self):
     def velocities(self, stuff):
         if self._status == 'old':
             raise RuntimeError('Cannot set velocities on an old restart')
-        stuff = np.array(stuff, copy=False).ravel()
+            stuff = np.asarray(stuff).ravel()
         if not self._coords_written:
             raise RuntimeError('Coordinates must be set before velocities')
         if self._cell_lengths_written or self._cell_angles_written:
@@ -413,7 +413,7 @@ def cell_lengths(self, stuff):
             raise RuntimeError('Can only write cell lengths once')
         if len(stuff) != 3:
             raise ValueError('Expected 3 numbers for cell lengths')
-        self._cell_lengths = np.array(stuff, copy=False)
+        self._cell_lengths = np.asarray(stuff)
         self._file.write('%12.7f%12.7f%12.7f' % (stuff[0], stuff[1], stuff[2]))
         self._cell_lengths_written = True
 
@@ -429,7 +429,7 @@ def cell_angles(self, stuff):
             raise RuntimeError('Can only write cell angles once')
         if len(stuff) != 3:
             raise ValueError('Expected 3 numbers for cell angles')
-        self._cell_angles = np.array(stuff, copy=False)
+        self._cell_angles = np.asarray(stuff)
         self._file.write('%12.7f%12.7f%12.7f\n' % (stuff[0],stuff[1],stuff[2]))
         self._cell_angles_written = True
 

diff --git a/parmed/amber/netcdffiles.py b/parmed/amber/netcdffiles.py
@@ -241,7 +241,7 @@ def coordinates(self):
 
     @coordinates.setter
     def coordinates(self, stuff):
-        stuff = np.array(stuff, copy=False).reshape((self.atom, 3))
+        stuff = np.asarray(stuff).reshape((self.atom, 3))
         self._ncfile.variables['coordinates'][:] = stuff
         self.flush()
 

diff --git a/parmed/formats/pdb.py b/parmed/formats/pdb.py
@@ -971,7 +971,7 @@ def write(struct, dest, renumber=True, coordinates=None, altlocs='all',
                 symm_line = "REMARK 290   SMTRY" + fmt % tuple(arr_list)
                 dest.write(symm_line)
         if coordinates is not None:
-            coords = np.array(coordinates, copy=False, subok=True)
+            coords = np.asanyarray(coordinates)
             try:
                 coords = coords.reshape((-1, len(struct.atoms), 3))
             except ValueError:
@@ -1646,7 +1646,7 @@ def write(struct, dest, renumber=True, coordinates=None,
         sym.append([struct.space_group])
         cont.append(sym)
         if coordinates is not None:
-            coords = np.array(coordinates, copy=False, subok=True)
+            coords = np.asanyarray(coordinates)
             try:
                 coords = coords.reshape((-1, len(struct.atoms), 3))
             except ValueError:

diff --git a/parmed/formats/pqr.py b/parmed/formats/pqr.py
@@ -257,7 +257,7 @@ def write(struct, dest, renumber=True, coordinates=None,
                     struct.box[0], struct.box[1], struct.box[2], struct.box[3],
                     struct.box[4], struct.box[5]))
         if coordinates is not None:
-            coords = np.array(coordinates, copy=False, subok=True)
+            coords = np.asanyarray(coordinates)
             try:
                 coords = coords.reshape((-1, len(struct.atoms), 3))
             except ValueError:

diff --git a/parmed/structure.py b/parmed/structure.py
@@ -1796,7 +1796,7 @@ def coordinates(self, value):
             if u.is_quantity(value):
                 value = value.value_in_unit(u.angstroms)
             value = list(value)
-            coords = np.array(value, dtype=np.float64, copy=False, subok=True)
+            coords = np.asanyarray(value, dtype=np.float64)
             coords = coords.reshape((-1, len(self.atoms), 3))
             if len(coords) > 0:
                 for a, xyz in zip(self.atoms, coords[0]):
@@ -1877,7 +1877,7 @@ def box(self, value):
                 box = value
             else:
                 box = _strip_box_units(list(value))
-            box = np.array(box, dtype=np.float64, copy=False, subok=True)
+            box = np.asanyarray(box, dtype=np.float64)
             if box.shape != (6,):
                 if len(box.shape) != 2 or box.shape[-1] != 6:
                     raise ValueError('Box information must be 6 floats')
@@ -1944,7 +1944,7 @@ def velocities(self, value):
                 except AttributeError:
                     pass
         else:
-            value = np.array(value, copy=False).reshape(
+            value = np.asarray(value).reshape(
                 (-1, len(self.atoms), 3))
             for atom, xyz in zip(self.atoms, value[0]):
                 atom.vx, atom.vy, atom.vz = xyz