def read_stx_conf(infile,title,atoms,x,v):
ifile=c_char_p(infile)
ttl=c_char_p(title)
m=matrix()
pbc=c_int(-1)
libgmx.read_stx_conf(ifile, ttl,byref(atoms),x,v,byref(pbc),m);
return pbc,m
def read_next_xtc(handle, natoms, xpointer): step = c_int() time = c_real() prec = c_real() bOK = c_int() box = matrix() ret=libgmx.read_next_xtc(handle,natoms,byref(step),byref(time),box,xpointer,byref(prec),byref(bOK)) # if ret!=1: # raise GMXctypesError,"read_next_xtc did not return 1" return step.value,time.value,box,prec.value,bOK.value,ret
def calc_fit_R(weights,atomsvec1,atomsvec2,natoms=None,dimensions=3,mtx=None):
if mNumPy:
if natoms==None:
if not len(weights)==len(atomsvec1)==len(atomsvec2):
raise TypeError("Array dimension don't match")
natoms=len(weights)
if mtx==None: mtx = N.empty((3,3),N_real)
else:
if mtx==None: mtx = matrix()
libgmx.calc_fit_R(dimensions,natoms,weights,atomsvec1,atomsvec2,mtx)
return mtx
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
def read_next_xtc(handle, natoms, xpointer):
step = c_int()
time = c_real()
prec = c_real()
bOK = c_int()
box = matrix()
ret = libgmx.read_next_xtc(handle, natoms, byref(step), byref(time), box,
xpointer, byref(prec), byref(bOK))
# if ret!=1:
# raise GMXctypesError,"read_next_xtc did not return 1"
return step.value, time.value, box, prec.value, bOK.value, ret
def read_first_xtc(handle): natoms = c_int() step = c_int() time = c_real() prec = c_real() bOK = c_int() box = matrix() xpointer = POINTER(rvec)() ret=libgmx.read_first_xtc(handle,byref(natoms),byref(step),byref(time),box,byref(xpointer),byref(prec),byref(bOK)) # if ret!=1: # raise GMXctypesError,"read_first_xtc did not return 1" return natoms.value,step.value,time.value,box,xpointer,prec.value,bOK.value,ret
def copy_mat(a = matrix):
b = matrix()
b[XX] = copy_rvec(a[XX])
b[YY] = copy_rvec(a[YY])
b[ZZ] = copy_rvec(a[ZZ])
return b
#static inline void copy_mat(matrix a,matrix b)
#{
# copy_rvec(a[XX],b[XX]);
# copy_rvec(a[YY],b[YY]);
# copy_rvec(a[ZZ],b[ZZ]);
#}
def read_first_xtc(handle):
natoms = c_int()
step = c_int()
time = c_real()
prec = c_real()
bOK = c_int()
box = matrix()
xpointer = POINTER(rvec)()
ret = libgmx.read_first_xtc(handle, byref(natoms), byref(step),
byref(time), box, byref(xpointer), byref(prec),
byref(bOK))
# if ret!=1:
# raise GMXctypesError,"read_first_xtc did not return 1"
return natoms.value, step.value, time.value, box, xpointer, prec.value, bOK.value, ret
def copy_mat(a=matrix):
b = matrix()
b[XX] = copy_rvec(a[XX])
b[YY] = copy_rvec(a[YY])
b[ZZ] = copy_rvec(a[ZZ])
return b
#static inline void copy_mat(matrix a,matrix b)
#{
# copy_rvec(a[XX],b[XX]);
# copy_rvec(a[YY],b[YY]);
# copy_rvec(a[ZZ],b[ZZ]);
#}
def calc_fit_R(weights,
atomsvec1,
atomsvec2,
natoms=None,
dimensions=3,
mtx=None):
if mNumPy:
if natoms == None:
if not len(weights) == len(atomsvec1) == len(atomsvec2):
raise TypeError("Array dimension don't match")
natoms = len(weights)
if mtx == None: mtx = N.empty((3, 3), N_real)
else:
if mtx == None: mtx = matrix()
libgmx.calc_fit_R(dimensions, natoms, weights, atomsvec1, atomsvec2, mtx)
return mtx
def calc_fit_R(natoms,weights,atomsvec1,atomsvec2,dimensions=3):
mtx = matrix()
libgmx.calc_fit_R(dimensions,natoms,weights,atomsvec1,atomsvec2,mtx)
return mtx
def calc_fit_R(natoms, weights, atomsvec1, atomsvec2, dimensions=3):
mtx = matrix()
libgmx.calc_fit_R(dimensions, natoms, weights, atomsvec1, atomsvec2, mtx)
return mtx