def cercar_centre_proteina(self):
sx = 0
sy = 0
sz = 0
atms = 0
for linia in self.linies:
if linia[0:4] == "ATOM":
atom = Entitat.flinia_atoms(linia)
x = atom[Atributs.campsAtoms("xcoor")]
y = atom[Atributs.campsAtoms("ycoor")]
z = atom[Atributs.campsAtoms("zcoor")]
sx += x
sy += y
sz += z
atms += 1
dx = 0 - round(sx / atms, 4)
dy = 0 - round(sy / atms, 4)
dz = 0 - round(sz / atms, 4)
return (dx, dy, dz)
def crear_entitat(self):
self.models.append(1)
widModel = 1
idModel = 1
wnmodels = 1
widChain = ""
wwidChain = ""
widnumSeqres = 0
idTAtom = True
widTResidu = True
idCA = False
wnAtoms = 0
primer = True
xCA = 0.0
yCA = 0.0
zCA = 0.0
totalAtoms = 0
wclau = ""
# posicions dels camps necessaris en el registre d'atoms del pdb
ntipus = Atributs.campsAtoms("tipus")
nnumser = Atributs.campsAtoms("numser")
nsigatom = Atributs.campsAtoms("sigatom")
nnomResidu = Atributs.campsAtoms("nomResidu")
nidChain = Atributs.campsAtoms("idChain")
nidnumSeqres = Atributs.campsAtoms("numSeqres")
nxcoor = Atributs.campsAtoms("xcoor")
nycoor = Atributs.campsAtoms("ycoor")
nzcoor = Atributs.campsAtoms("zcoor")
nelemQuim = Atributs.campsAtoms("elemQuim")
# Càlcul del centre de la proteian i diferencia respecte a les coordenades (0,0.0)
self.dx, self.dy, self.dz = Entitat.cercar_centre_proteina(self)
primer = True
''' Models '''
sx = 0
sy = 0
sz = 0
num = 0
idCA = False
for lin in self.linies:
tipus = lin[0:6]
if tipus == "MODEL ":
idModel = Atributs.get_models(lin)
if idModel > 1:
self.models.append(idModel)
nmodels += 1
''' Ordre dels camps en el registre de atom'''
if tipus == "ATOM " or tipus == "HETATM":
linia = Entitat.flinia_atoms(lin)
nomResidu = linia[nnomResidu]
if nomResidu != "HOH":
clau = ""
tipus = linia[ntipus]
sigatom = linia[nsigatom]
idChain = linia[nidChain]
idAtom = linia[nnumser]
idnumSeqres = linia[nidnumSeqres]
xcoor = round(linia[nxcoor] + self.dx,
4) # Coordenada transformada,
ycoor = round(linia[nycoor] + self.dy,
4) # Coordenada transformada
zcoor = round(linia[nzcoor] + self.dz,
4) # Coordenada transformada
sx = sx + xcoor
sy = sy + ycoor
sz = sz + zcoor
num += 1
elemQuim = linia[nelemQuim]
''' Clau de comparacio'''
clau = str(idModel) + idChain + str(idnumSeqres).rjust(
4, "0")
''' Proteina o Estranys '''
if tipus == "ATOM":
idTAtom = True
else:
idTAtom = False
idTResidu = idTAtom
''' Molecules '''
if idChain != wwidChain:
wwidChain = idChain
if idChain in self.molecules:
pass
else:
self.molecules.append(idChain)
''' carbono alfa'''
if sigatom == "CA":
idCA = True
xCA = xcoor
yCA = ycoor
zCA = zcoor
if primer:
widModel = idModel
widChain = idChain
widAtom = idAtom
widnumSeqres = idnumSeqres
wnomResidu = nomResidu
widTResidu = idTResidu
wclau = clau
primer = False
self.atoms.append([
idModel, idChain, idnumSeqres, idAtom, sigatom,
nomResidu, xcoor, ycoor, zcoor, elemQuim, idCA,
idTAtom
])
wnAtoms = 1
totalAtoms = 1
elif clau != wclau:
self.atoms.append([
idModel, idChain, idnumSeqres, idAtom, sigatom,
nomResidu, xcoor, ycoor, zcoor, elemQuim, idCA,
idTAtom
])
if idCA == False:
xCA = round(sx / num, 4)
yCA = round(sy / num, 4)
zCA = round(sz / num, 4)
self.residus.append([
widModel, widChain, widnumSeqres, wnomResidu, xCA,
yCA, zCA, wnAtoms, widTResidu
])
sx = 0
sy = 0
sz = 0
num = 0
xCA = 0.0
yCA = 0.0
zCA = 0.0
idCA = False
wnAtoms = 1
totalAtoms += 1
widModel = idModel
widChain = idChain
widnumSeqres = idnumSeqres
wnomResidu = nomResidu
widTResidu = idTResidu
wclau = clau
elif clau == wclau:
self.atoms.append([
idModel, idChain, idnumSeqres, idAtom, sigatom,
nomResidu, xcoor, ycoor, zcoor, elemQuim, idCA,
idTAtom
])
wnAtoms += 1
totalAtoms += 1
else:
continue
# ultim registre
if idCA == False:
if num > 0:
xCA = round(sx / num, 4)
yCA = round(sy / num, 4)
zCA = round(sz / num, 4)
xCA = sx + self.dx
yCA = sy + self.dy
zCA = sz + self.dz
self.residus.append([
widModel, widChain, widnumSeqres, wnomResidu, xCA, yCA, zCA,
wnAtoms, widTResidu
])
caps = [linia for linia in self.linies if linia[0:6] == "TITLE "]
text = ""
for cap in caps:
nom = str(cap[10:80].strip(' \t\n\r'))
text = text + nom
self.capcalera = text
return self.capcalera, self.models, self.molecules, self.residus, self.atoms, self.nomtaula