def maxmins(atoms):
xmax = -999999999
xmin = 999999999
ymax = -999999999
ymin = 999999999
zmax = -99999999
zmin = 999999999
xs = 0
ys = 0
zs = 0
num = 0
nx = Atributs.atomt("xcoor")
ny = Atributs.atomt("ycoor")
nz = Atributs.atomt("zcoor")
for i in range(len(atoms) - 1):
linia = atoms[i]
x = linia[nx]
y = linia[ny]
z = linia[nz]
if x > xmax: xmax = x
if x <= xmin: xmin = x
if y > ymax: ymax = y
if y <= ymin: ymin = y
if z > zmax: zmax = z
if z <= zmin: zmin = z
num += 1
xs = xs + x
ys = ys + y
zs = zs + z
llista = [xmin, ymin, zmin], [xmax, ymax, zmax], [(round(xs / num, 4)),
round(ys / num, 4),
round(zs / num, 4)]
return (llista)
def __init__(self, fitxer):
self.fitxer = fitxer
E = Entitat(self.fitxer)
self.linies = E.get_linies()
dadestotals = E.crear_entitat()
self.capcalera = dadestotals[0]
self.molecules = dadestotals[2]
self.residus = dadestotals[3]
self.atoms = dadestotals[4]
self.nom_taula = dadestotals[5]
self.nomResidu = Atributs.residut("nomResidu")
self.nomElement = Atributs.atomt("elemQuim")
self.idTResidu = Atributs.residut("idTResidu")
self.idTAtom = Atributs.atomt("idTAtom")
def plot_atoms(self):
xs = []
ys = []
zs = []
cs = []
watoms = []
if self.tipus == 1:
watoms = [
atom for atom in self.atoms
if atom[Atributs.atomt("idTAtom")] == True
]
if self.tipus == 2:
watoms = [
residu for residu in self.residus
if residu[Atributs.residut("idTResidu")] == True
]
self.tipus2 = 1
for linia in watoms:
if self.tipus == 1:
x = linia[Atributs.atomt("xcoor")]
y = linia[Atributs.atomt("ycoor")]
z = linia[Atributs.atomt("zcoor")]
if self.tipus == 2:
x = linia[Atributs.residut("xcoor")]
y = linia[Atributs.residut("ycoor")]
z = linia[Atributs.residut("zcoor")]
# Get color
chain = linia[Atributs.atomt("idChain")]
colors = Colors(chain, 1)
col = colors.color_molecula()
xs.append(x)
ys.append(y)
zs.append(z)
cs.append(col)
fig = plt.figure(figsize=(10, 5))
ax = fig.add_subplot(111, projection='3d')
ax.set_facecolor([0.98, 0.92, 0.84]) # blanc antic
ax.text2D(-0.10,
0.95,
self.capcalera,
horizontalalignment='left',
verticalalignment='top',
family='Serif',
size=9,
transform=ax.transAxes)
ax.scatter(xs, ys, zs, c=cs, marker='o', alpha=0.35)
ax.set_xlabel('Eix X')
ax.set_ylabel('Eix Y')
ax.set_zlabel('Eix Z')
plt.show()
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 get_residus(self):
a = Atributs(self, )
self.lresidus = []
self.lresidusn = []
self.lresiduts = []
self.lresidutsn = []
self.lreshets = []
self.lreshetsn = []
self.sig = []
self.nom_amino = []
# self.nom, self.lletra, self.sig, self.tipologia = a.llista_aminoacids()
self.mestre_aminoacids = a.mestre_aminoacids
n = len(self.mestre_aminoacids)
for i in range(len(self.mestre_aminoacids)):
self.sig.append(self.mestre_aminoacids[i][0])
self.nom_amino.append(self.mestre_aminoacids[i][2])
for residu in self.residus:
res = residu[self.nomResidu]
prot = residu[self.idTResidu]
if prot:
if res in self.sig:
if res in self.lresidus:
idx = self.lresidus.index(res)
self.lresidusn[idx] = int(self.lresidusn[idx]) + 1
else:
self.lresidus.append(res)
self.lresidusn.append(1)
else:
if res in self.lresiduts:
idx = self.lresiduts.index(res)
self.lresidutsn[idx] = int(self.lresidutsn[idx]) + 1
else:
self.lresiduts.append(res)
self.lresidutsn.append(1)
else:
if res in self.lreshets:
idx = self.lreshets.index(res)
self.lreshetsn[idx] = int(self.lreshetsn[idx]) + 1
else:
self.lreshets.append(res)
self.lreshetsn.append(1)
return self.lresidus, self.lresidusn, self.lresiduts, self.lresidutsn, self.lreshets, self.lreshetsn
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
def plot_linies(self):
# Coordenades
tx = 0.0
ty = 0.0
tz = 0.0
txp = 0.0
typ = 0.0
tzp = 0.0
self.tipus2 = 2
fig = plt.figure(figsize=(11, 5))
ax = fig.add_subplot(111, projection='3d')
ax.set_facecolor([0.98, 0.92, 0.84]) # blanc antic
ax.text2D(-0.10,
0.95,
self.capcalera,
horizontalalignment='left',
verticalalignment='top',
family='Serif',
size=9,
transform=ax.transAxes)
# ax.text2D(0.05, 0.95, self.capcalera, transform=ax.transAxes)
# Posicions en el refistre de residus
chain = Atributs.residut("idChain")
s = Atributs.residut("idResidu")
amin = Atributs.residut("nomResidu")
x = Atributs.residut("xcoor")
y = Atributs.residut("ycoor")
z = Atributs.residut("zcoor")
prot = Atributs.residut("idTResidu")
# Vectors plot
punt_inici_x = []
punt_inici_y = []
punt_inici_z = []
punt_final_x = []
punt_final_y = []
punt_final_z = []
colamin = []
# Nomes aminoacids de la proteina residu[prot] == True
cadena = [residu for residu in self.residus if residu[prot] == True]
residus_net = cadena
n = len(residus_net) - 1
for i in range(n):
linia = residus_net[i]
chain1 = linia[chain]
amino = linia[amin]
tx = linia[x]
ty = linia[y]
tz = linia[z]
res1 = [chain1 + str(linia[s])]
if i < n:
liniapost = residus_net[i + 1]
chain2 = liniapost[chain]
txp = liniapost[x]
typ = liniapost[y]
tzp = liniapost[z]
res2 = [chain2 + str(liniapost[s])]
else:
pass
# Get color
if self.tipus == 1:
colors = Colors(chain1, 1)
cl = colors.color_molecula()
elif self.tipus == 2:
aminos = ('ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'PHE', 'GLN',
'GLU', 'GLY', 'HIS', 'ILE', 'LEU', 'LYS', 'PRO',
'MET', 'SER', 'THR', 'TYR', 'TRP', 'VAL')
if amino in aminos:
ccolors = Colors(amino, 2)
cl = ccolors.color_tipus()
else:
cl = ('k')
else:
cl = ('c')
punt_inici_x.append(tx)
punt_inici_y.append(ty)
punt_inici_z.append(tz)
colamin.append(cl)
if i < n and chain1 == chain2:
punt_final_x.append(txp)
punt_final_y.append(typ)
punt_final_z.append(tzp)
else:
punt_final_x.append(tx)
punt_final_y.append(ty)
punt_final_z.append(tz)
for i in range(n):
xs = [punt_inici_x[i], punt_final_x[i]]
ys = [punt_inici_y[i], punt_final_y[i]]
zs = [punt_inici_z[i], punt_final_z[i]]
col = colamin[i]
ax.plot(xs, ys, zs, linewidth=2, color=col)
# linea = []
# linea = [x for x in punt_inici_x if x == 0]
# ax.set_xlabel('Eix X')
# ax.set_ylabel('Eix Y')
# ax.set_zlabel('Eix Z')
plt.show()
def plot2d_3d(self):
fig = plt.figure(figsize=(11, 5))
ax = fig.add_subplot(111, projection='3d')
ax.text2D(-0.10,
-0.10,
self.capcalera,
horizontalalignment='left',
verticalalignment='top',
family='Serif',
size=8,
transform=ax.transAxes)
self.tipus2 = 1
ax_xy = fig.add_subplot(331)
ax_xy.set_title('X/Y')
ax_xz = fig.add_subplot(333)
ax_xz.set_title('X/Z')
ax_zy = fig.add_subplot(334)
ax_zy.set_title('Z/Y')
ax.set_facecolor([0.98, 0.92, 0.84]) # blanc antic
zx, zy, zz = [], [], []
idchains = Atributs.residut("idChain")
idresidus = Atributs.residut("idResidu")
idresatom = Atributs.atomt("idResidu")
aprot = Atributs.atomt("idTAtom")
idx = Atributs.atomt("xcoor")
idy = Atributs.atomt("ycoor")
idz = Atributs.atomt("zcoor")
vella_mol = ""
for chain_id in self.molecules:
if chain_id != vella_mol:
atr = Colors(chain_id)
nom = atr.color_molecula()
vella_mol = chain_id
xs = []
ys = []
zs = []
wresidus = [
res for res in self.residus if res[idchains] == chain_id
]
for residu in wresidus:
watoms = []
watoms = [
atom for atom in self.atoms
if atom[idresatom] == residu[idresidus]
and atom[idchains] == chain_id and atom[aprot] == True
]
for atom in watoms:
x = atom[idx]
y = atom[idy]
z = atom[idz]
xs.append(x)
ys.append(y)
zs.append(z)
atr = Colors(chain_id, 1)
nom = atr.color_molecula()
ax.scatter(xs, ys, zs, marker='*', color=nom, alpha=0.35)
ax_xy.scatter(xs, ys, marker='.', color=nom, alpha=0.15)
ax_xz.scatter(xs, zs, marker='.', color=nom, alpha=0.15)
ax_zy.scatter(zs, ys, marker='.', color=nom, alpha=0.15)
# ax.text2D(0.05, 0.95, self.capcalera, transform=ax.transAxes)
# ax.text(9, 0, 0,self.capcalera , color='red')
plt.show()
##!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys
import os
from codi.atributs.atributs import Atributs
so =sys.platform
if so == 'win32' or so=="win64":
os.system('cls')
else:
os.system('clear')
a = Atributs()
nom, lletra, sig, volum, tipus1, tipus2, escala = a.llista_aminoacids()
frase = "Aminoàcid".ljust(15, " ") + " SIG "+"Lletra " + "Tipologia" +" " +"Masa relativa(*) "
print(frase)
print "--------------- ----- ---- --------- ------------"
for i in range(len(sig)):
frase= nom[i].ljust(15, " ") +" "+ sig[i].ljust(3, " ")+" "+lletra[i] +" " + str(tipus2[i])+ " "+ str(escala[i])
print(frase)
print(" ")
print (" * massa relativa a la massa de la Glicina = 1 ")
print(" ")
tipologia = ( 'Tipologia Descripció',
'----------------------',
' 1 Hidrofòbics',
' 2 Hidrofílics',
' 3 Àcids',
' 4 Bàsics' )