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--- a/AmberTools/src/parmed/parmed/amber/_amberparm.py
+++ b/AmberTools/src/parmed/parmed/amber/_amberparm.py
@@ -2147,7 +2147,7 @@ class AmberParm(AmberFormat, Structure):
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 @@ class Rst7(object):
@property
def velocities(self):
""" Atomic velocities in units of angstroms/picoseconds """
- 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):
--- a/AmberTools/src/parmed/parmed/amber/asciicrd.py
+++ b/AmberTools/src/parmed/parmed/amber/asciicrd.py
@@ -317,7 +317,7 @@ class AmberAsciiRestart(_AmberAsciiCoordinateFile):
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 @@ class AmberAsciiRestart(_AmberAsciiCoordinateFile):
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 @@ class AmberAsciiRestart(_AmberAsciiCoordinateFile):
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 @@ class AmberAsciiRestart(_AmberAsciiCoordinateFile):
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
--- a/AmberTools/src/parmed/parmed/amber/netcdffiles.py
+++ b/AmberTools/src/parmed/parmed/amber/netcdffiles.py
@@ -241,7 +241,7 @@ class NetCDFRestart(metaclass=FileFormatType):
@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()
--- a/AmberTools/src/parmed/parmed/formats/pdb.py
+++ b/AmberTools/src/parmed/parmed/formats/pdb.py
@@ -971,7 +971,7 @@ class PDBFile(metaclass=FileFormatType):
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 @@ class CIFFile(metaclass=FileFormatType):
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:
--- a/AmberTools/src/parmed/parmed/formats/pqr.py
+++ b/AmberTools/src/parmed/parmed/formats/pqr.py
@@ -257,7 +257,7 @@ class PQRFile(metaclass=FileFormatType):
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:
--- a/AmberTools/src/parmed/parmed/structure.py
+++ b/AmberTools/src/parmed/parmed/structure.py
@@ -1796,7 +1796,7 @@ class Structure:
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 @@ class Structure:
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 @@ class Structure:
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
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