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(pdbfile,prmtopfile,crdfile):
#READ PDB FILE
apdb=raf.pdb(pdbfile)
box=apdb.Get_Box()
coords=apdb.Get_Coords()
natoms=natoms= len(apdb.ATOMlines)
#JIGGLE COORDINATES
coords=jiggle(coords)
#INSTATIATE MDGX STRUCTS AND ARRAYS
U=ext.uform(prmtopfile, crdfile)
sites_cart=coords.flatten()
gradients=np.zeros(len(sites_cart))
target=np.zeros(10)
#GET INITIAL GRADIENTS AND ENERGIES
old_gradients,old_target=get_gradients_and_target(sites_cart, gradients, target, U)
#STEEPEST DESCENT ITERATIONS
i=0
while i<100:
sites_cart=steepest_descent(sites_cart, old_gradients)
new_gradients, new_target= get_gradients_and_target(sites_cart, gradients, target, U)
target_diff=old_target[0]-new_target[0]
delta_gradient_rms=old_target[9]-new_target[9]
print("%7.3f %7.3f %7.3f" %(new_target[0], target_diff, delta_gradient_rms))
if delta_gradient_rms<0.001 or target_diff<0.001:
break
old_gradients, old_target=new_gradients, new_target
i+=1
print("Minimization termination condition reached after %d steps." %i)
#CALCULATE RMSD
newcoords=np.reshape(sites_cart, (-1,3))
newcoords=raf.KabschAlign(coords, newcoords)
rmsd=raf.RMSD(coords,newcoords)
print("RMSD between original and minimized structure: %7.4f" %rmsd)
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
def get_amber_structs (prmtop, ambcrd):
return ext.uform(prmtop, ambcrd)