def proportionByPositionNeighbors (stCount, pr_result):
l_out = []
l_typeatom = structure.classificationATOM("", out_list= 1)
# directory result
for substruct in stCount.keys() :
p_filout = pr_result + "proportion_" + substruct
l_out.append (p_filout)
filout = open(p_filout, "w")
filout.write ("\t".join(l_typeatom) + "\n")
for nb_neighbor in range(1,8) :
if not nb_neighbor in stCount[substruct].keys () :
continue
else :
filout.write(str(nb_neighbor))
print substruct, nb_neighbor
print stCount[substruct][nb_neighbor]
sum_neighbor = tool.sumDict(stCount[substruct][nb_neighbor])
for class_atom in l_typeatom :
filout.write("\t" + str(stCount[substruct][nb_neighbor][class_atom] / sum_neighbor))
filout.write("\n")
filout.close ()
return l_out
def resultNeighbor (countStruct, pr_result) :
"""
Three neighbors analysis -> write files
"""
# distance list
l_typeatom = structure.classificationATOM("", out_list= 1)
# directory result
for sub_struct in countStruct.keys() :
filout_neighbor = open (pr_result + "neighbor_" + sub_struct, "w")
filout_neighbor_count = open (pr_result + "neighbor_count_" + sub_struct, "w")
filout_distance = open (pr_result + "distance_" + sub_struct, "w")
filout_angle = open (pr_result + "angle_neighbors" + sub_struct, "w")
filout_neighbor.write ("\t".join(l_typeatom) + "\n")
filout_neighbor_count.write ("\t".join(l_typeatom) + "\n")
# barplot class of neighbors -> but not dynamic nb neighbor
for nb_neighbor in range(1,8) :
if nb_neighbor == "angle1_2" or nb_neighbor == "angle2_3" or nb_neighbor == "angle1_3" :
continue
filout_neighbor.write(str(nb_neighbor))
filout_neighbor_count.write(str(nb_neighbor))
filout_distance.write(str(nb_neighbor))
sum_neigbor = tool.sumDict(countStruct[sub_struct][nb_neighbor])
for class_atom in l_typeatom :
filout_neighbor.write("\t" + str(countStruct[sub_struct][nb_neighbor][class_atom] / sum_neigbor))
filout_neighbor_count.write("\t" + str(countStruct[sub_struct][nb_neighbor][class_atom]))
filout_neighbor.write("\n")
filout_neighbor_count.write("\n")
filout_distance.write("\t" + "\t".join(countStruct[sub_struct][nb_neighbor]["distance"]) + "\n")
filout_distance.write ("Classe\t" + "\t".join(countStruct[sub_struct][nb_neighbor]["classe"]) + "\n")
# angles between neighbors
nb_angle = len (countStruct[sub_struct]["angle1_2"])
i = 0
while i < nb_angle :
filout_angle.write (str (countStruct[sub_struct]["angle1_2"][i]) + "\t" +str (countStruct[sub_struct]["angle1_3"][i]) + "\t" +str (countStruct[sub_struct]["angle2_3"][i]) + "\n" )
i = i + 1
filout_distance.close ()
filout_neighbor.close ()
filout_neighbor_count.close ()
filout_angle.close ()
# write barplot file
barplotThreeAtomBarplot (countStruct, pr_result)
