def AreaCOO (pr_init):
"""calculation of volume around nitrogen of primary amine
in: filePDB with only primary amine, extreme value of l_angle, structure subs
out: file format filePDB with water
only one half of imidazole are inspected"""
subs = "COO"
pr_volume = pathManage.CreatePathDir(pr_init + "Volume/")
filout = open (pr_volume + "volume_" + subs + ".pdb", "w")
l_atom_sub = structure.substructureCoord(subs)
def_volume = structure.criteraAngle(subs)
writePDBfile.coordinateSection(filout, l_atom_sub, "HETATM")
angle_inf = def_volume["angle"][0]
angle_sup = def_volume["angle"][1]
d_inf = def_volume["distance"][0]
d_sup = def_volume["distance"][1]
for atom_sub in l_atom_sub :
if atom_sub["name"] == "O01" :
atomO1 = atom_sub
if atom_sub["name"] == "O02" :
atomO2 = atom_sub
if atom_sub["name"] == "C02" :
atomC2 = atom_sub
if atom_sub["name"] == "C01" :
atomC1 = atom_sub
atom_center = calcul.CenterPoint(atomO1, atomO2)
serial = 0
for x_test in [atom_center["x"] + x * 0.2 for x in range (-50,60)] :
for y_test in [atom_center["y"] + y * 0.2 for y in range (-50,60)] :
for z_test in [atom_center["z"] + z * 0.2 for z in range (-50,60)] :
atom_test = structure.genericAtom(x_test, y_test, z_test)
dist = calcul.distanceTwoatoms(atom_test, atom_center)
# case where the calculation of angle is impossible
try : angle = calcul.Angle3Atoms(atomC2, atom_center, atom_test)
except : continue
if dist <= d_sup and dist >= d_inf:
if angle >= angle_inf and angle <= angle_sup :
serial = serial + 1
atom_test["serial"] = serial
atom_test["resSeq"] = serial
writePDBfile.coordinateStructure(atom_test, "HETATM", filout)
filout.close()
WriteParameter (pr_volume + subs + ".param", subs, def_volume, serial)
def AeraTertiary (pr_init):
"""calculation of volume around nitrogen of primary amine
in: filePDB with only primary amine, extreme value of l_angle, structure subs
out: file format filePDB with water"""
subs = "III"
pr_volume = pathManage.CreatePathDir(pr_init + "Volume/")
filout = open (pr_volume + "volume_" + subs + ".pdb", "w")
l_atom_sub = structure.substructureCoord(subs)
def_volume = structure.criteraAngle(subs)
writePDBfile.coordinateSection(filout, l_atom_sub, "HETATM")
angle_inf = def_volume["angle"][0]
angle_sup = def_volume["angle"][1]
d_inf = def_volume["distance"][0]
d_sup = def_volume["distance"][1]
for atom_sub in l_atom_sub :
if atom_sub["element"] == "N" :
atomN = atom_sub
elif atom_sub["element"] == "C" :
if "atomC1" in locals() :
if "atomC2" in locals():
atomC3 = atom_sub
else :
atomC2 = atom_sub
else :
atomC1 = atom_sub
serial = 0
for x_test in [atomN["x"] + x * 0.2 for x in range (-50,60)] :
for y_test in [atomN["y"] + y * 0.2 for y in range (-50,60)] :
for z_test in [atomN["z"] + z * 0.2 for z in range (-50,60)] :
atom_test = structure.genericAtom(x_test, y_test, z_test)
distance = calcul.distanceTwoatoms(atom_test, atomN)
if distance < d_sup and distance > d_inf:
l_angles = calcul.angleTertiaryAmineCalculVol(atomN, atom_test, atomC1, atomC2, atomC3)
if l_angles[0] > angle_inf and l_angles[1] > angle_inf and l_angles[2] > angle_inf:
if l_angles[0] < angle_sup and l_angles[1] < angle_sup and l_angles[2] < angle_sup:
serial = serial + 1
atom_test["serial"] = serial
atom_test["resSeq"] = serial
writePDBfile.coordinateStructure(atom_test, "HETATM", filout)
filout.close()
WriteParameter (pr_volume + subs + ".param", subs, def_volume, serial)
def coordinates3DPDB (l_atom_in, l_atom_subs = [], subs = "", p_filout = "") :
if p_filout == "" :
return
filout = open (p_filout, "w")
l_atom_ref = structure.substructureCoord(subs)
writePDBfile.coordinateSection(filout, l_atom_ref , "HETATM")
writePDBfile.coordinateSection(filout, l_atom_subs , "HETATM")
writePDBfile.coordinateSection(filout, l_atom_in, "ATOM")
filout.close ()
def AreaGuanidium (pr_init):
"""calculation of volume around nitrogen of primary amine
in: filePDB with only primary amine, extreme value of l_angle, structure subs
out: file format filePDB with water"""
subs = "GAI"
pr_volume = pathManage.CreatePathDir(pr_init + "Volume/")
filout = open (pr_volume + "volume_" + subs + ".pdb", "w")
l_atom_sub = structure.substructureCoord(subs)
def_volume = structure.criteraAngle(subs)
writePDBfile.coordinateSection(filout, l_atom_sub, "HETATM")
#filout.close ()
#ddd
angle_inf = def_volume["angle"][0]
angle_sup = def_volume["angle"][1]
d_inf = def_volume["distance"][0]
d_sup = def_volume["distance"][1]
for atom_sub in l_atom_sub :
if atom_sub["name"] == "N01" :
atomN1 = atom_sub
if atom_sub["name"] == "C01" :
atomC1 = atom_sub
count = 0
for x_test in [atomC1["x"] + x * 0.3 for x in range (-100,100)] :
for y_test in [atomC1["y"] + y * 0.3 for y in range (-100,100)] :
for z_test in [atomC1["z"] + z * 0.3 for z in range (-100,100)] :
atom_test = structure.genericAtom(x_test, y_test, z_test)
distance = calcul.distanceTwoatoms(atom_test, atomC1)
l_angleC1 = calcul.anglePrimaryAmineCalculVol(atomC1, atomN1, atom_test)
# print distance, l_angleC1
if distance < d_sup and distance > d_inf:
if l_angleC1[0] > angle_inf and l_angleC1[0] < angle_sup :
count = count + 1
atom_test["count"] = count
atom_test["resSeq"] = count
writePDBfile.coordinateStructure(atom_test, "HETATM", filout)
filout.close()
WriteParameter (pr_volume + subs + ".param", subs, def_volume, count)
def coordinates3D (l_atom, p_filout, type_substruct) :
filout = open (p_filout, "w")
substruct = structure.substructureCoord(type_substruct)
for atom in substruct :
filout.write (str(atom["x"]) + "\t" + str(atom["y"]) + "\t" + str(atom["z"]) + "\t" + "REF" + "\n")
for atom in l_atom :
if not "occupancy" in atom.keys () :
filout.write (str(atom["x"]) + "\t" + str(atom["y"]) + "\t" + str(atom["z"]) + "\t" + structure.classificationATOM (atom) + "\n")
filout.close ()
return p_filout
def coordinates3DPDBbyNeighborType (l_atom_in, ll_atom_subs, subs, pr_init) :
d_file = {}
l_type_neighbors = structure.classificationATOM (out_list = 1)
l_atom_sub_ref = structure.substructureCoord(subs)
for type_neighbors in l_type_neighbors :
d_file[type_neighbors] = open (pr_init + subs + "_" + type_neighbors + ".pdb", "w")
writePDBfile.coordinateSection(d_file [type_neighbors], l_atom_sub_ref , "HETATM")
#writePDBfile.coordinateSection(d_file [type_neighbors], ll_atom_subs[0] , "HETATM")
#l_write = []
#for l_atom_subs in ll_atom_subs :
# writePDBfile.coordinateSection(d_file [type_neighbors], l_atom_subs , "HETATM")
# l_write = l_write + l_atom_subs
# writePDBfile.coordinateSection(d_file [type_neighbors], l_write , "HETATM")
for atom in l_atom_in :
type_neighbor = structure.classificationATOM (atom)
writePDBfile.coordinateSection(d_file [type_neighbor], [atom] , "ATOM", header = 0)
for type_neighbors in l_type_neighbors :
d_file[type_neighbors].close ()
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)