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 manageTMalign(path_protein):
list_atoms = parsePDB.loadCoordSectionPDB(path_protein)
dico_residues = parsePDB.arrangeResidues(list_atoms)
list_res = dico_residues.keys()
list_res.sort()
filout = open(path_protein, "w")
for resID in list_res:
for atom in dico_residues[resID]:
writePDBfile.coordinateStructure(atom, "ATOM", filout)
filout.close()
return path_protein
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 manageTMalign (path_protein ) :
list_atoms = parsePDB.loadCoordSectionPDB(path_protein)
dico_residues = parsePDB.arrangeResidues(list_atoms)
list_res = dico_residues.keys()
list_res.sort ()
filout = open (path_protein, "w")
for resID in list_res :
for atom in dico_residues[resID] :
writePDBfile.coordinateStructure(atom, "ATOM", filout)
filout.close ()
return path_protein
def separeByChain (path_PDB_file):
"""
separe PDB file by chain
"""
file_PDB_parsed = parsePDB.loadCoordSectionPDB(path_PDB_file, section="")
l_file = []
file_open_write = {}
for atom_PDB in file_PDB_parsed :
chain = atom_PDB["chainID"]
if not chain in file_open_write.keys () :
file_open_write [chain] = open(path_PDB_file[0:-4] + "_" + chain + ".pdb", "w")
l_file.append (path_PDB_file[0:-4] + "_" + chain + ".pdb")
writePDBfile.coordinateStructure(atom_PDB, file_open_write [chain] )
else :
writePDBfile.coordinateStructure(atom_PDB, file_open_write [chain] )
# close files
for chain in file_open_write.keys () :
file_open_write[chain].close ()
return l_file
def separeByChain(path_PDB_file):
"""
separe PDB file by chain
"""
file_PDB_parsed = parsePDB.loadCoordSectionPDB(path_PDB_file, section="")
l_file = []
file_open_write = {}
for atom_PDB in file_PDB_parsed:
chain = atom_PDB["chainID"]
if not chain in file_open_write.keys():
file_open_write[chain] = open(
path_PDB_file[0:-4] + "_" + chain + ".pdb", "w")
l_file.append(path_PDB_file[0:-4] + "_" + chain + ".pdb")
writePDBfile.coordinateStructure(atom_PDB, file_open_write[chain])
else:
writePDBfile.coordinateStructure(atom_PDB, file_open_write[chain])
# close files
for chain in file_open_write.keys():
file_open_write[chain].close()
return l_file
