def energies_sites(self, compute_gradients=False):
#Convert flex arrays to C arrays
sites_cart_c=ext.ExtractVec(self.sites_cart.as_double())
gradients_c=ext.ExtractVec(flex.double(self.sites_cart.size() * 3, 0))
energy_components_c=ext.ExtractVec(self.energy_components)
# Call c++ interface to call mdgx to calculate new gradients and target
ext.callMdgx(sites_cart_c, gradients_c, energy_components_c, self.mdgx_structs)
if (compute_gradients) :
gradients = self.gradients_factory(gradients_c) * -1
else :
gradients = self.gradients_factory(
flex.double(self.sites_cart.size() * 3,0))
result = energies(
compute_gradients=compute_gradients,
gradients=gradients,
gradients_size=None,
gradients_factory=None,
normalization=False)
result.number_of_restraints = self.number_of_restraints
result.residual_sum = float(energy_components_c[0])
result.energy_components = list(energy_components_c)
result.finalize_target_and_gradients()
#result.show()
return result
def get_gradients_and_target(sites_cart,gradients,target, U): sites_cart_c=ext.VectorOfDouble() sites_cart_c.extend(i for i in sites_cart) gradients_c=ext.VectorOfDouble() gradients_c.extend(i for i in gradients) target_c=ext.VectorOfDouble() target_c.extend(i for i in target) ext.callMdgx(sites_cart_c, gradients_c, target_c, U) gradients=np.array(gradients_c) target=np.array(target_c) return gradients, target
def run(pdbfile,prmtopfile,crdfile):
# coords=raf.pdb(pdbfile).Get_Coords()
#~ coords=jiggle(coords)
U=ext.uform(prmtopfile, crdfile)
gradients=flex.double(150)
print gradients
gradients_flex=ext.ExtractVec(gradients)
n=list(coords.flatten())
sites_cart_c=ext.ExtractVec2(n)
nowendithere
gradients_c=ext.ExtractVec(gradients)
target_c=ext.ExtractVec(target)
ext.callMdgx(sites_cart_c, gradients_c, target_c, U)
gradients=flex.vec3_double(gradients_c)*-1
target= flex.double(target_c)
def run(pdb,prmtop, crd): #===================================================================# # # # BEFORE C++ # # # #===================================================================# #file i/o pdb_file = os.path.abspath(pdb) pdb_inp = iotbx.pdb.input(file_name=pdb_file) pdb_atoms = pdb_inp.atoms_with_labels() symm = pdb_inp.crystal_symmetry() xray_structure = pdb_inp.xray_structure_simple(enable_scattering_type_unknown=True) # initiate flex arrays for coordinates, gradients, energy sites_cart=xray_structure.sites_cart() gradients=flex.double(len(sites_cart)*3) target=flex.double([6.7,1.0,2.0,3.0,4.0,5.0,0.0,0.0,0.0,0.0]) print "Number of atom sites: %d " %sites_cart.size() print "\nGradients and target BEFORE C call:" print list(gradients[1:10]) print target[0] #===================================================================# # # # CALL C++ # # # #===================================================================# U=ext.uform(prmtop, crd) #Convert flex arrays to C arrays sites_cart_c=ext.ExtractVec(sites_cart.as_double()) gradients_c=ext.ExtractVec(gradients) target_c=ext.ExtractVec(target) # Call c++ interface to call mdgx to calculate new gradients and target ext.callMdgx(sites_cart_c, gradients_c, target_c, U) # Convert back into python types (eg. into flex arrays for phenix to use) gradients=flex.vec3_double(gradients_c)*-1 target= flex.double(target_c) #===================================================================# # # # AFTER C++ # # # #===================================================================# print "\nGradients and target AFTER C call:" print list(gradients[0:10]) print target[0] print target[9] print "\n" print "Amber_total_energy: %7.6f" %(target[0]) print " bonds (n= ): %7.6f" %(target[1]) print " angles (n= ): %7.6f" %(target[2]) print " dihedrals (n= ): %7.6f" %(target[3]) print " electrostatics: %7.6f" %(target[4]) print " vanderWaals: %7.6f" %(target[5]) print "\n\n" return 0