def SuperimposeFirstNeighbors (st_atom, pr_result):
d_nb_neighbor = structure.nbNeighbor ()
for subs in st_atom.keys () :
if subs == "global" :
continue
l_at_ref = structure.substructureCoord(subs)
d_atom_superiposed = {}
pr_superimpose = pr_result + subs + "/"
pathManage.CreatePathDir(pr_superimpose)
nb_ind = d_nb_neighbor[subs] # number of considered neighbors
for at_central in st_atom[subs] :
PDB_ID = at_central["PDB"]
name_ligand = at_central["resName"]
# all atom ligand
l_at_lig = loadFile.ExtractInfoPDBID(PDB_ID)[name_ligand][0] # change not tested
l_at_subs = retrieveAtom.substructure (subs, at_central, l_at_lig)
v_atom_ref = mat(array(groupAtomCoord(l_at_ref[0:3])))
v_atom_central = mat(array(groupAtomCoord(l_at_subs[0:3])))
rotation, translocation = rigid_transform_3D(v_atom_central, v_atom_ref)
if rotation == None or translocation == None :
continue
v_atom_rotated = applyTranformation(rotation, translocation, v_atom_central)
l_atom_rotated = applyTranformation(rotation, translocation, l_atom_in=l_at_subs)
print rmse(v_atom_central, v_atom_ref), "RMSE 1"
print rmse(v_atom_ref, v_atom_rotated), "RMSE 2"
# print v_atom_rotated
# print "************compare**********"
# print l_at_subs
# print l_atom_rotated
l_neighbor = deepcopy(at_central["neighbors"])
if len (l_neighbor) < nb_ind :
continue
else :
l_combination = []
l_atom_neighbors = []
for i_neighbors in range (1, nb_ind + 1) :
atom_class, d_atom = statistic.searchMoreClose (l_neighbor)
l_combination.append (atom_class)
l_atom_neighbors.append (d_atom)
l_combination.sort ()
k = "_".join (l_combination)
if not k in d_atom_superiposed.keys () :
d_atom_superiposed[k] = []
l_atom_neighbor_rotated = applyTranformation(rotation, translocation, l_atom_in = l_atom_neighbors)
d_atom_superiposed[k] = d_atom_superiposed[k] + l_atom_rotated + l_atom_neighbor_rotated
for k in d_atom_superiposed.keys () :
# write gif
pr_init_gif = pr_superimpose + "gif/"
pathManage.CreatePathDir(pr_init_gif)
p_file_coord = writeFile.coordinates3D (d_atom_superiposed[k], pr_init_gif + k + ".coord", subs)
runScriptR.plot3D (p_file_coord, option = "global")
# write one PDB by atom close type
pr_init_PDB = pr_superimpose + "/PDB/"
pathManage.CreatePathDir(pr_init_PDB)
writeFile.coordinates3DPDB (d_atom_superiposed[k], subs, pr_init_PDB + k + ".pdb" )
def globalNeighbor (atom_interest_close, subs, p_dir_result, option_filter = 1) :
p_dir_result = pathManage.imposeNeighbors (p_dir_result)
# extract from ideal position
l_at_ref = structure.substructureCoord(subs)
l_superimpose_neighbor = []
l_superimpose_subs = []
l_RMSE = []
for at_central in atom_interest_close[subs] :
PDB_ID = at_central["PDB"]
serial_at_central = at_central["serial"]
name_ligand = at_central["resName"]
# all atom ligand
l_at_lig = loadFile.ExtractInfoPDBID(PDB_ID)[name_ligand][0] # change not tested
# for at_ligand in l_at_lig :
# print at_ligand
l_at_subs = retrieveAtom.substructure (subs, at_central, l_at_lig)
if subs == "GAI" :
v_atom_central = mat(array(groupAtomCoord(l_at_subs)))
v_atom_ref = mat(array(groupAtomCoord(l_at_ref)))
elif subs == "COO" :
v_atom_central = mat(array(groupAtomCoord(l_at_subs)))
v_atom_ref = mat(array(groupAtomCoord(l_at_ref[1:])))
else :
v_atom_central = mat(array(groupAtomCoord(l_at_subs)))
v_atom_ref = mat(array(groupAtomCoord(l_at_ref)))
rotation, translocation = rigid_transform_3D(v_atom_central, v_atom_ref)
if rotation == None or translocation == None :
continue
v_atom_rotated = applyTranformation(rotation, translocation, v_atom_central)
l_subs_rotated = applyTranformation(rotation, translocation, l_atom_in = l_at_subs)
RMSE_rot = rmse(v_atom_ref, v_atom_rotated)
print rmse(v_atom_central, v_atom_ref), "RMSE 1"
print rmse(v_atom_ref, v_atom_rotated), "RMSE 2"
l_RMSE.append (str(RMSE_rot))
# print v_atom_rotated
# print "************compare**********"
# print l_at_subs
# print l_subs_rotated
# print "/////////////////////////////"
l_atom_neighbors = deepcopy(at_central["neighbors"])
if option_filter == 1 :
# reduce the list of neighbor
criteria = structure.criteraAngle(subs)
d_min = criteria["distance"][0]
d_max = criteria["distance"][1]
n_neighbor = len (l_atom_neighbors)
i = 0
while i < n_neighbor :
if l_atom_neighbors[i]["distance"] < d_min or l_atom_neighbors[i]["distance"] > d_max :
del l_atom_neighbors[i]
n_neighbor = n_neighbor - 1
else :
i = i +1
try :
l_atom_neighbor_rotated = applyTranformation(rotation, translocation, l_atom_in=l_atom_neighbors)
l_superimpose_neighbor = l_superimpose_neighbor + l_atom_neighbor_rotated
l_superimpose_subs.append (l_subs_rotated)
except :
continue
# color with b factor
tool.colorAtomType (l_superimpose_neighbor)
# write gif
# pr_init_gif = p_dir_result + "/gif/" + subs + "/"
# pathManage.CreatePathDir(pr_init_gif)
# p_file_coord = writeFile.coordinates3D (l_superimpose_neighbor + l_superimpose_subs, pr_init_gif + subs + "_neigbor.coord", subs)
# runScriptR.plot3D (p_file_coord)
# write one PDB by atom close type
pr_init_PDB = p_dir_result + "/PDB/" + subs + "/"
pathManage.CreatePathDir(pr_init_PDB)
file_RMSE = open (pr_init_PDB + "RMSE", "w")
file_RMSE.write ("\n".join(l_RMSE) + "\n")
file_RMSE.close ()
writeFile.coordinates3DPDBbyNeighborType (l_superimpose_neighbor, l_superimpose_subs, subs, pr_init_PDB)
