def __init__(self, filename, flags=TRX_READ_X):
self.status = c_int()
self.f = gmxframe()
self.ret = libgmx.read_first_frame(byref(self.status), filename, byref(self.f.fr), flags)
if not self.ret:
raise IOError("Failed to open %s. File not found or not a valid GROMACS trajectory." % (filename,))
self.natoms = self.f.natoms
if auto_mode == mNumPy:
if self.f.bX:
self.f.x = maprvec(self.f.fr.x, self.natoms)
if self.f.bV:
self.f.v = maprvec(self.f.fr.v, self.natoms)
if self.f.bF:
self.f.f = maprvec(self.f.fr.f, self.natoms)
def __init__(self, filename, flags=TRX_READ_X):
self.status = c_int()
self.f = gmxframe()
self.ret = libgmx.read_first_frame(byref(self.status), filename,
byref(self.f.fr), flags)
if not self.ret:
raise IOError(
"Failed to open %s. File not found or not a valid GROMACS trajectory."
% (filename, ))
self.natoms = self.f.natoms
if auto_mode == mNumPy:
if self.f.bX: self.f.x = maprvec(self.f.fr.x, self.natoms)
if self.f.bV: self.f.v = maprvec(self.f.fr.v, self.natoms)
if self.f.bF: self.f.f = maprvec(self.f.fr.f, self.natoms)
def __init__(self,filename):
toptitle=(c_char*256)()
top=t_topology()
xp=POINTER(rvec)()
vp=POINTER(rvec)()
cePBC=c_int(-1)
box=matrix()
bMass=c_int()
ret = libgmx.read_tps_conf(filename,byref(toptitle),byref(top),byref(cePBC),byref(xp),byref(vp),box,byref(bMass))
if ret!=1:
raise GMXctypesError("Error reading topology with read_tps_conf")
self.title,self.top,self.ePBC,self.x,self.v,self.box,self.bMass=toptitle.value,top,cePBC.value,xp,vp,box,bMass.value
self.natoms = self.top.atoms.nr
if auto_mode==mNumPy:
self.x = maprvec(self.x,self.natoms)
self.v = maprvec(self.v,self.natoms)
self.A = mapatom(self.top.atoms.atom,self.natoms)