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 AreaPrimary (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 = "I" 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" : atomC = 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_angle = calcul.anglePrimaryAmineCalculVol(atomN, atomC, atom_test) if l_angle[0] > angle_inf : if l_angle[0] < 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)