def __init__(self, dir=None, name="None"):
if dir != None:
self.pqrFile = FcfrpFile(dir,name+".pqr")
class FcfrpUtils():
def __init__(self, dir=None, name="None"):
if dir != None:
self.pqrFile = FcfrpFile(dir,name+".pqr")
def getRandomNumberFromPath(self, path):
# Give a path, this method returns Path Random number.
listPath = path.split("/")
tam = listPath.__len__()-1
i = 0
while i < tam:
n = listPath[tam-i]
if n != "":
return n
i = i + 1
# Calculate the geometric center of protin
def centroGeometricoProtein(self):
quantidade = 0
for line in self.pqrFile.getAsFile().readlines():
x = 0.0
y = 0.0
z = 0.0
coord = line.split()
if coord[0] == "ATOM":
quantidade = quantidade + 1
x = x + float(coord[5])
y = y + float(coord[6])
z = z + float(coord[7])
x = x/quantidade
y = y/quantidade
z = z/quantidade
centroGeometrico = (x, y, z)
self.pqrFile.close()
return centroGeometrico
# Calculate the ray of the protein
# It is the greater distance from atom to geometric center of protein
# cg -> centro geometrico
def raioProtein(self, cg):
maiorDistancia = 0.0
distance = 0.0
for line in self.pqrFile.getAsFile().readlines():
fields = line.split()
if fields[0] == "ATOM":
coord = (fields[5], fields[6], fields[7])
distance = self._getDistance(cg, coord)
if distance > maiorDistancia:
maiorDistancia = distance
distance = 0.0
return maiorDistancia
# Calculate the distance between two points in the tridimensional space
def _getDistance(self, p1, p2):
x1 = float(p1[0])
y1 = float(p1[1])
z1 = float(p1[2])
x2 = float(p2[0])
y2 = float(p2[1])
z2 = float(p2[2])
dx = float(x2 - x1)
dy = float(y2 - y1)
dz = float(z2 - z1)
d = sqrt(pow(dx, 2) + pow(dy, 2) + pow(dz, 2))
return d
def getVolumeRadiusProtein(self, dicProteinChainSeq, database):
#dicProteinChainSeq is a dictionary which has its key chain and its value chain residues
#Computes volume and radius of all chains of protein
volRet = 0.0
raioRet = 0.0
for chain, sequence in dicProteinChainSeq.iteritems():
vol, raio = self.getVolumeRadiusProteinChain(dicProteinChainSeq, database, chain)
volRet = volRet + vol
raioRet = raioRet + raio
return volRet, raioRet
def getVolumeRadiusProteinChain(self, dicProteinChainSeq, database, chainId):
#Computes volume and radius of chain of protein
vol = 0.0
raio = 0.0
sequence = dicProteinChainSeq[chainId]
for s in sequence:
#Computes the protein chain volume
vol = vol + database.getFullInformationAminoacid(database.getAminoIdFromDatabase(s))[8] #Radius amino acid
#Computes the protein chain radius
raio = raio + math.pow(((3*vol)/12.56),1.0/3)
return vol, raio
def getMassProteinChain(self, dicProteinChainSeq, database, chainId):
#Computes the mass of chain of protein
mass = 0.0
sequence = dicProteinChainSeq[chainId]
for s in sequence:
#Computes the protein chain mass
mass = mass + database.getFullInformationAminoacid(database.getAminoIdFromDatabase(s))[6] #Mass of protein
return mass
def getChainStr(self,listchain):
#Receives a list of chain (A;B;C) and returns a string such as 'A','B','C'
# This result will be used in select command
ChainsPBD = ""
for c in listchain:
c = "'" + c + "'"
if ChainsPBD.__len__() == 0:
ChainsPBD = ChainsPBD + str(c)
else:
ChainsPBD = ChainsPBD + "," + str(c)
return ChainsPBD
