def guessbonds(coordinates, atomname, atomtype, resname, resid, chain, segname,
insertion, altloc):
# if it's a single frame, resize to be a 3d array
if coordinates.ndim == 2:
c = coordinates.shape
coordinates = coordinates.reshape((c[0], c[1], 1))
if coordinates.shape[2] > 1:
raise ValueError("Coordinates must be a single frame")
if (coordinates.strides[0] != 12 or coordinates.strides[1] != 4):
# It's a view -- need to make a copy to ensure contiguity of memory
coordinates = np.array(coordinates, dtype=np.float32)
if (coordinates.strides[0] != 12 or coordinates.strides[1] != 4):
raise ValueError("Coordinates is a view with unsupported strides")
if coordinates.dtype != np.float32:
raise ValueError("Coordinates is not float32")
# print(coordinates.shape)
natoms = coordinates.shape[0]
nframes = coordinates.shape[2]
# Sanity check the inputs
# print(natoms)
# print(len(atomname))
if len(atomname) != natoms:
raise NameError("'atomname' not natoms in length")
if len(atomtype) != natoms:
raise NameError("'atomtype' not natoms in length")
if len(resname) != natoms:
raise NameError("'resname' not natoms in length")
if len(resid) != natoms:
raise NameError("'resid' not natoms in length")
libdir = htmd.home(libDir=True)
parser = ct.cdll.LoadLibrary(os.path.join(libdir, "libvmdparser.so"))
c_natoms = ct.c_int(natoms)
c_atomname = pack_string_buffer(atomname)
c_atomtype = pack_string_buffer(atomtype)
c_resname = pack_string_buffer(resname)
c_chain = pack_string_buffer(chain)
c_segname = pack_string_buffer(segname)
c_insert = pack_string_buffer(insertion)
c_altLoc = pack_string_buffer(altloc)
c_resid = pack_int_buffer(resid)
c_nframes = ct.c_int(nframes)
c_coords = None
c_nbonds = (ct.c_int * 1)()
lenv = natoms * 10 # some dumb guess about the max # of bonds likely to be created -- natoms*5
c_bonds = (ct.c_int * lenv)()
z = 0
c_nbonds[0] = 0
c_coords = coordinates.ctypes.data_as(ct.POINTER(ct.c_float))
retval = fn = parser.guessbonds(c_natoms, c_nframes, c_atomtype,
c_atomname, c_resname, c_resid, c_chain,
c_segname, c_insert, c_altLoc, c_coords,
c_nbonds, c_bonds)
if (retval):
raise ValueError("Guessed bonding is bad")
#print(retval)
nbonds = c_nbonds[0]
bonds = np.empty((nbonds, 2), dtype=np.uint32)
for y in range(0, nbonds):
for x in range(0, 2):
bonds[y, x] = int(c_bonds[y * 2 + x])
retval = bonds
return retval.reshape(nbonds, 2)
def vmdselection(selection,
coordinates,
atomname,
atomtype,
resname,
resid,
chain=None,
segname=None,
insert=None,
altloc=None,
beta=None,
occupancy=None,
bonds=None):
import platform
libdir = htmd.home(libDir=True)
if coordinates.ndim == 2:
coordinates = np.atleast_3d(coordinates)
if coordinates.shape[1] != 3:
print(coordinates.shape)
raise NameError("Coordinates needs to be natoms x 3 x nframes")
if coordinates.dtype != np.float32:
raise ValueError("Coordinates is not float32")
if (coordinates.strides[0] != 12 or coordinates.strides[1] != 4):
# It's a view -- need to make a copy to ensure contiguity of memory
coordinates = np.array(coordinates, dtype=np.float32)
if (coordinates.strides[0] != 12 or coordinates.strides[1] != 4):
raise ValueError("Coordinates is a view with unsupported strides")
natoms = coordinates.shape[0]
nframes = coordinates.shape[2]
# Sanity check the inputs
# print(natoms)
# print (len(atomname))
if bonds is not None and bonds.shape[1] != 2:
raise NameError("'bonds' not nbonds x 2 in length")
if len(atomname) != natoms:
# print(natoms)
# print(len(atomname))
raise NameError("'atomname' not natoms in length")
if len(atomtype) != natoms:
raise NameError("'atomtype' not natoms in length")
if len(resname) != natoms:
raise NameError("'resname' not natoms in length")
if len(resid) != natoms:
raise NameError("'resid' not natoms in length")
if chain is not None and len(chain) != natoms:
raise NameError("'chain' not natoms in length")
if segname is not None and len(segname) != natoms:
raise NameError("'segname' not natoms in length")
if insert is not None and len(insert) != natoms:
raise NameError("'insert' not natoms in length")
if altloc is not None and len(altloc) != natoms:
raise NameError("'altloc' not natoms in length")
if beta is not None and len(beta) != natoms:
raise NameError("'beta' not natoms in length")
if occupancy is not None and len(occupancy) != natoms:
raise NameError("'occupancy' not natoms in length")
if platform.system() == "Windows":
ct.cdll.LoadLibrary(os.path.join(libdir, "libgcc_s_seh-1.dll"))
if (os.path.exists(os.path.join(libdir, "psprolib.dll"))):
ct.cdll.LoadLibrary(os.path.join(libdir, "psprolib.dll"))
parser = ct.cdll.LoadLibrary(os.path.join(libdir, "libvmdparser.so"))
c_selection = ct.create_string_buffer(selection.encode('ascii'),
len(selection) + 1)
c_natoms = ct.c_int(natoms)
c_nframes = ct.c_int(nframes)
c_atomname = pack_string_buffer(atomname)
c_atomtype = pack_string_buffer(atomtype)
c_resname = pack_string_buffer(resname)
c_resid = pack_int_buffer(resid)
c_chain = None
c_segname = None
c_insert = None
c_altloc = None
c_beta = None
c_occupancy = None
c_coords = None
c_nbonds = None
c_bonds = None
if chain is not None:
c_chain = pack_string_buffer(chain)
if segname is not None:
c_segname = pack_string_buffer(segname)
if insert is not None:
c_insert = pack_string_buffer(insert)
if altloc is not None:
c_altloc = pack_string_buffer(altloc)
if beta is not None:
c_beta = pack_double_buffer(beta)
if occupancy is not None:
c_occupancy = pack_double_buffer(occupancy)
c_bonds = None
nbonds = 0
if bonds is not None: # TODO: Replace the loops for bonds with ravel
nbonds = bonds.shape[0]
if nbonds > 0:
ll = nbonds * 2
c_bonds = (ct.c_int * ll)()
for z in range(0, nbonds):
for y in [0, 1]:
c_bonds[z * 2 + y] = bonds[z, y]
c_nbonds = ct.c_int(nbonds)
ll = natoms * nframes
c_output_buffer = (ct.c_int * ll)()
lenv = natoms * 3 * nframes
c_coords = coordinates.ctypes.data_as(ct.POINTER(ct.c_float))
retval = parser.atomselect(c_selection, c_natoms, c_beta, c_occupancy,
c_atomtype, c_atomname, c_resname, c_resid,
c_chain, c_segname, c_insert, c_altloc,
c_coords, c_nframes, c_nbonds, c_bonds,
c_output_buffer)
if retval != 0:
raise NameError('Could not parse selection "' + selection +
'". Is the selection a valid VMD atom selection?')
retval = np.empty((natoms, nframes), dtype=np.bool_)
for frame in range(nframes):
for atom in range(natoms):
retval[atom, frame] = c_output_buffer[frame * natoms + atom]
return np.squeeze(retval)
def vmdselection(selection, coordinates, atomname, atomtype, resname, resid, chain=None, segname=None, insert=None,
altloc=None, beta=None, occupancy=None, bonds=None):
if coordinates.ndim == 2:
coordinates = np.atleast_3d(coordinates)
if coordinates.shape[1] != 3:
print(coordinates.shape)
raise NameError("Coordinates needs to be natoms x 3 x nframes")
if coordinates.dtype != np.float32:
raise ValueError("Coordinates is not float32")
if(coordinates.strides[0] != 12 or coordinates.strides[1] != 4 ):
# It's a view -- need to make a copy to ensure contiguity of memory
coordinates = np.array( coordinates, dtype=np.float32 )
if(coordinates.strides[0] != 12 or coordinates.strides[1] != 4 ):
raise ValueError("Coordinates is a view with unsupported strides" )
natoms = coordinates.shape[0]
nframes = coordinates.shape[2]
# Sanity check the inputs
# print(natoms)
# print (len(atomname))
if bonds is not None and bonds.shape[1] != 2:
raise NameError("'bonds' not nbonds x 2 in length")
if len(atomname) != natoms:
# print(natoms)
# print(len(atomname))
raise NameError("'atomname' not natoms in length")
if len(atomtype) != natoms:
raise NameError("'atomtype' not natoms in length")
if len(resname) != natoms:
raise NameError("'resname' not natoms in length")
if len(resid) != natoms:
raise NameError("'resid' not natoms in length")
if chain is not None and len(chain) != natoms:
raise NameError("'chain' not natoms in length")
if segname is not None and len(segname) != natoms:
raise NameError("'segname' not natoms in length")
if insert is not None and len(insert) != natoms:
raise NameError("'insert' not natoms in length")
if altloc is not None and len(altloc) != natoms:
raise NameError("'altloc' not natoms in length")
if beta is not None and len(beta) != natoms:
raise NameError("'beta' not natoms in length")
if occupancy is not None and len(occupancy) != natoms:
raise NameError("'occupancy' not natoms in length")
c_selection = ct.create_string_buffer(selection.encode('ascii'), len(selection) + 1)
c_natoms = ct.c_int(natoms)
c_nframes = ct.c_int(nframes)
c_atomname = pack_string_buffer(atomname)
c_atomtype = pack_string_buffer(atomtype)
c_resname = pack_string_buffer(resname)
c_resid = pack_int_buffer(resid)
c_chain = None
c_segname = None
c_insert = None
c_altloc = None
c_beta = None
c_occupancy = None
c_coords = None
c_nbonds = None
c_bonds = None
if chain is not None:
c_chain = pack_string_buffer(chain)
if segname is not None:
c_segname = pack_string_buffer(segname)
if insert is not None:
c_insert = pack_string_buffer(insert)
if altloc is not None:
c_altloc = pack_string_buffer(altloc)
if beta is not None:
c_beta = pack_double_buffer(beta)
if occupancy is not None:
c_occupancy = pack_double_buffer(occupancy)
c_bonds = None
nbonds = 0
if bonds is not None: # TODO: Replace the loops for bonds with ravel
nbonds = bonds.shape[0]
if nbonds > 0:
ll = nbonds * 2
c_bonds = (ct.c_int * ll)()
for z in range(0, nbonds):
for y in [0, 1]:
c_bonds[z * 2 + y] = bonds[z, y]
c_nbonds = ct.c_int(nbonds)
ll = natoms * nframes
c_output_buffer = (ct.c_int * ll)()
lenv = natoms * 3 * nframes
c_coords = coordinates.ctypes.data_as(ct.POINTER(ct.c_float))
retval = parser.atomselect(
c_selection,
c_natoms,
c_beta,
c_occupancy,
c_atomtype,
c_atomname,
c_resname,
c_resid,
c_chain,
c_segname,
c_insert,
c_altloc,
c_coords,
c_nframes,
c_nbonds,
c_bonds,
c_output_buffer)
if retval != 0:
raise NameError('Could not parse selection "' + selection + '". Is the selection a valid VMD atom selection?')
retval = np.empty((natoms, nframes), dtype=np.bool_)
for frame in range(nframes):
for atom in range(natoms):
retval[atom, frame] = c_output_buffer[frame * natoms + atom]
return np.squeeze(retval)
def guessbonds(coordinates, atomname, atomtype, resname, resid, chain, segname, insertion, altloc):
# if it's a single frame, resize to be a 3d array
if coordinates.ndim == 2:
c = coordinates.shape
coordinates = coordinates.reshape((c[0], c[1], 1))
if coordinates.shape[2] > 1:
raise ValueError("Coordinates must be a single frame")
if(coordinates.strides[0] != 12 or coordinates.strides[1] != 4 ):
# It's a view -- need to make a copy to ensure contiguity of memory
coordinates = np.array( coordinates, dtype=np.float32 )
if(coordinates.strides[0] != 12 or coordinates.strides[1] != 4 ):
raise ValueError("Coordinates is a view with unsupported strides" )
if coordinates.dtype != np.float32:
raise ValueError("Coordinates is not float32")
# print(coordinates.shape)
natoms = coordinates.shape[0]
nframes = coordinates.shape[2]
# Sanity check the inputs
# print(natoms)
# print(len(atomname))
if len(atomname) != natoms:
raise NameError("'atomname' not natoms in length")
if len(atomtype) != natoms:
raise NameError("'atomtype' not natoms in length")
if len(resname) != natoms:
raise NameError("'resname' not natoms in length")
if len(resid) != natoms:
raise NameError("'resid' not natoms in length")
c_natoms = ct.c_int(natoms)
c_atomname = pack_string_buffer(atomname)
c_atomtype = pack_string_buffer(atomtype)
c_resname = pack_string_buffer(resname)
c_chain = pack_string_buffer(chain)
c_segname = pack_string_buffer(segname)
c_insert = pack_string_buffer(insertion)
c_altLoc = pack_string_buffer(altloc)
c_resid = pack_int_buffer(resid)
c_nframes = ct.c_int(nframes)
c_coords = None
c_nbonds = (ct.c_int * 1)()
lenv = natoms * 10 # some dumb guess about the max # of bonds likely to be created -- natoms*5
c_bonds = (ct.c_int * lenv)()
z = 0
c_nbonds[0] = 0
c_coords = coordinates.ctypes.data_as(ct.POINTER(ct.c_float))
retval = fn = parser.guessbonds(
c_natoms,
c_nframes,
c_atomtype,
c_atomname,
c_resname,
c_resid,
c_chain,
c_segname,
c_insert,
c_altLoc,
c_coords,
c_nbonds,
c_bonds
)
if(retval):
raise ValueError("Guessed bonding is bad")
#print(retval)
nbonds = c_nbonds[0]
bonds = np.empty((nbonds, 2), dtype=np.uint32)
for y in range(0, nbonds):
for x in range(0, 2):
bonds[y, x] = int(c_bonds[y * 2 + x])
retval = bonds
return retval.reshape(nbonds, 2)
def vmdselection(selection,
coordinates,
atomname,
atomtype,
resname,
resid,
chain=None,
segname=None,
insert=None,
altloc=None,
beta=None,
occupancy=None,
bonds=None):
maxseglen = np.max([len(x) for x in segname])
if maxseglen > 4:
logger.warning(
'More than 4 characters were used for segids. '
'Due to limitations in VMD atomselect segids will be ignored for the atomselection.'
)
segname = segname.copy()
segname[:] = ''
if coordinates.ndim == 2:
coordinates = np.atleast_3d(coordinates)
if coordinates.shape[1] != 3:
print(coordinates.shape)
raise NameError("Coordinates needs to be natoms x 3 x nframes")
if coordinates.dtype != np.float32:
raise ValueError("Coordinates is not float32")
if (coordinates.strides[0] != 12 or coordinates.strides[1] != 4):
# It's a view -- need to make a copy to ensure contiguity of memory
coordinates = np.array(coordinates, dtype=np.float32)
if (coordinates.strides[0] != 12 or coordinates.strides[1] != 4):
raise ValueError("Coordinates is a view with unsupported strides")
natoms = coordinates.shape[0]
nframes = coordinates.shape[2]
# Sanity check the inputs
# print(natoms)
# print (len(atomname))
if bonds is not None and bonds.shape[1] != 2:
raise NameError("'bonds' not nbonds x 2 in length")
if len(atomname) != natoms:
# print(natoms)
# print(len(atomname))
raise NameError("'atomname' not natoms in length")
if len(atomtype) != natoms:
raise NameError("'atomtype' not natoms in length")
if len(resname) != natoms:
raise NameError("'resname' not natoms in length")
if len(resid) != natoms:
raise NameError("'resid' not natoms in length")
if chain is not None and len(chain) != natoms:
raise NameError("'chain' not natoms in length")
if segname is not None and len(segname) != natoms:
raise NameError("'segname' not natoms in length")
if insert is not None and len(insert) != natoms:
raise NameError("'insert' not natoms in length")
if altloc is not None and len(altloc) != natoms:
raise NameError("'altloc' not natoms in length")
if beta is not None and len(beta) != natoms:
raise NameError("'beta' not natoms in length")
if occupancy is not None and len(occupancy) != natoms:
raise NameError("'occupancy' not natoms in length")
c_selection = ct.create_string_buffer(selection.encode('ascii'),
len(selection) + 1)
c_natoms = ct.c_int(natoms)
c_nframes = ct.c_int(nframes)
c_atomname = pack_string_buffer(atomname)
c_atomtype = pack_string_buffer(atomtype)
c_resname = pack_string_buffer(resname)
c_resid = pack_int_buffer(resid)
c_chain = None
c_segname = None
c_insert = None
c_altloc = None
c_beta = None
c_occupancy = None
c_coords = None
c_nbonds = None
c_bonds = None
if chain is not None:
c_chain = pack_string_buffer(chain)
if segname is not None:
c_segname = pack_string_buffer(segname)
if insert is not None:
c_insert = pack_string_buffer(insert)
if altloc is not None:
c_altloc = pack_string_buffer(altloc)
if beta is not None:
c_beta = pack_double_buffer(beta)
if occupancy is not None:
c_occupancy = pack_double_buffer(occupancy)
c_bonds = None
nbonds = 0
if bonds is not None: # TODO: Replace the loops for bonds with ravel
nbonds = bonds.shape[0]
if nbonds > 0:
ll = nbonds * 2
c_bonds = (ct.c_int * ll)()
for z in range(0, nbonds):
for y in [0, 1]:
c_bonds[z * 2 + y] = bonds[z, y]
c_nbonds = ct.c_int(nbonds)
ll = natoms * nframes
c_output_buffer = (ct.c_int * ll)()
lenv = natoms * 3 * nframes
c_coords = coordinates.ctypes.data_as(ct.POINTER(ct.c_float))
retval = parser.atomselect(c_selection, c_natoms, c_beta, c_occupancy,
c_atomtype, c_atomname, c_resname, c_resid,
c_chain, c_segname, c_insert, c_altloc,
c_coords, c_nframes, c_nbonds, c_bonds,
c_output_buffer)
if retval != 0:
raise NameError('Could not parse selection "' + selection +
'". Is the selection a valid VMD atom selection?')
retval = np.empty((natoms, nframes), dtype=np.bool_)
for frame in range(nframes):
for atom in range(natoms):
retval[atom, frame] = c_output_buffer[frame * natoms + atom]
return np.squeeze(retval)
def guessbonds(coordinates, element, name, resname, resid, chain, segname,
insertion, altloc):
# if it's a single frame, resize to be a 3d array
if coordinates.ndim == 2:
c = coordinates.shape
coordinates = coordinates.reshape((c[0], c[1], 1))
if coordinates.shape[2] > 1:
raise ValueError("Coordinates must be a single frame")
if coordinates.strides[0] != 12 or coordinates.strides[1] != 4:
# It's a view -- need to make a copy to ensure contiguity of memory
coordinates = np.array(coordinates, dtype=np.float32)
if coordinates.strides[0] != 12 or coordinates.strides[1] != 4:
raise ValueError("Coordinates is a view with unsupported strides")
if coordinates.dtype != np.float32:
raise ValueError("Coordinates is not float32")
natoms = coordinates.shape[0]
nframes = coordinates.shape[2]
if len(element) != natoms:
raise NameError("'element' not natoms in length")
if len(name) != natoms:
raise NameError("'name' not natoms in length")
if len(resname) != natoms:
raise NameError("'resname' not natoms in length")
if len(resid) != natoms:
raise NameError("'resid' not natoms in length")
c_natoms = ct.c_int(natoms)
c_element = pack_string_buffer(element)
c_name = pack_string_buffer(name)
c_resname = pack_string_buffer(resname)
c_chain = pack_string_buffer(chain)
c_segname = pack_string_buffer(segname)
c_insert = pack_string_buffer(insertion)
c_altLoc = pack_string_buffer(altloc)
c_resid = pack_int_buffer(resid)
c_nframes = ct.c_int(nframes)
c_nbonds = (ct.c_int * 1)()
maxbonds = natoms * 5 # some dumb guess about the max # of bonds likely to be created
tmp = maxbonds * 2
c_bonds = (ct.c_int * tmp)()
c_nbonds[0] = 0
c_coords = coordinates.ctypes.data_as(ct.POINTER(ct.c_float))
retval = parser.guessbonds(c_natoms, c_nframes, c_name, c_element,
c_resname, c_resid, c_chain, c_segname,
c_insert, c_altLoc, c_coords, c_nbonds,
ct.c_int(maxbonds), c_bonds)
if retval:
raise ValueError("Guessed bonding is bad")
nbonds = c_nbonds[0]
bonds = np.empty((nbonds, 2), dtype=np.uint32)
for y in range(0, nbonds):
for x in range(0, 2):
bonds[y, x] = int(c_bonds[y * 2 + x])
retval = bonds
return retval.reshape(nbonds, 2)
