class CHEWD(Frame):
def __init__(self, parent):
Frame.__init__(self, parent)
self.parent = parent
self.initUI()
self.selection = ""
self.pdb = ""
def initUI(self):
self.parent.title("CHemical Energy Wise Decomposition")
frame4 = Frame(self.parent)
frame4.grid(row=0, column=0, sticky="nsew")
self.wat = IntVar()
self.wat.set(1)
self.waterswap = Checkbutton(frame4,
text="Water Swap",
command=self.optionws,
variable=self.wat)
self.waterswap.grid(row=0, column=0)
self.lig = IntVar()
self.lig.set(0)
self.ligandswap = Checkbutton(frame4,
text="Ligand Swap",
command=self.optionls,
variable=self.lig)
self.ligandswap.grid(row=0, column=1)
self.mm = IntVar()
self.mm.set(0)
self.mmpbsa = Checkbutton(frame4,
text="MMPBSA",
command=self.optionmm,
variable=self.mm)
self.mmpbsa.grid(row=0, column=2)
frame1 = Frame(self.parent)
frame1.grid(row=1, column=0, sticky="nsew")
lbl1 = Label(frame1, text="Log file folder", width=12)
lbl1.grid(row=0, column=0)
self.entry1 = Entry(frame1)
self.entry1.grid(row=0, column=1, columnspan=4, sticky=W + E)
self.browserButton = Button(frame1,
text="Browser",
command=self.onOpen)
self.browserButton.grid(row=0, column=5, sticky="e")
lbl2 = Label(frame1, text="MMPBSA log file", width=12)
lbl2.grid(row=1, column=0)
self.entry2 = Entry(frame1, state=DISABLED)
self.entry2.grid(row=1, column=1, columnspan=4, sticky=W + E)
self.browserButtonMM = Button(frame1,
text="Browser",
command=self.onOpenMM,
state=DISABLED)
self.browserButtonMM.grid(row=1, column=5, sticky="e")
lbl3 = Label(frame1, text="MMPBSA PDB file", width=12)
lbl3.grid(row=2, column=0)
self.entry3 = Entry(frame1, state=DISABLED)
self.entry3.grid(row=2, column=1, columnspan=4, sticky=W + E)
self.browserButtonPDB = Button(frame1,
text="Browser",
command=self.onOpenPDB,
state=DISABLED)
self.browserButtonPDB.grid(row=2, column=5, sticky="e")
lbl4 = Label(frame1, text="Ligand Name", width=12)
lbl4.grid(row=3, column=0)
self.entry4 = Entry(frame1)
self.entry4.grid(row=3, column=1)
self.lblswap = Label(frame1,
text="Swap Ligand",
width=12,
state=DISABLED)
self.lblswap.grid(row=3, column=2)
self.swapentry = Entry(frame1, state=DISABLED)
self.swapentry.grid(row=3, column=3)
self.l1v = IntVar()
self.l1v.set(1)
self.lig1ck = Checkbutton(frame1,
text="Ligand 1",
command=self.changelig1,
state=DISABLED,
variable=self.l1v)
self.lig1ck.grid(row=4, column=0)
self.l2v = IntVar()
self.l2v.set(0)
self.lig2ck = Checkbutton(frame1,
text="Ligand 2",
command=self.changelig2,
state=DISABLED,
variable=self.l2v)
self.lig2ck.grid(row=4, column=2)
lbl5 = Label(frame1, text="Display Radius", width=12)
lbl5.grid(row=5, column=0)
self.entry5 = Entry(frame1)
self.entry5.grid(row=5, column=1)
self.entry5.insert(0, "5.0")
self.sv = IntVar()
self.sv.set(0)
self.surface = Checkbutton(frame1,
text="View Surface",
command=self.viewsurface,
variable=self.sv)
self.surface.grid(row=5, column=2)
self.vl = IntVar()
self.vl.set(1)
self.label = Checkbutton(frame1,
text="View Label",
command=self.viewlabel,
variable=self.vl)
self.label.grid(row=5, column=3)
lbl6 = Label(frame1, text="Min Value", width=12)
lbl6.grid(row=6, column=0)
self.entry6 = Entry(frame1)
self.entry6.grid(row=6, column=1)
self.entry6.insert(0, "-5")
lbl7 = Label(frame1, text="Max Value", width=12)
lbl7.grid(row=6, column=2)
self.entry7 = Entry(frame1)
self.entry7.grid(row=6, column=3)
self.entry7.insert(0, "+5")
lbl8 = Label(frame1, text="Starting log file", width=12)
lbl8.grid(row=7, column=0)
self.entry8 = Entry(frame1)
self.entry8.grid(row=7, column=1)
self.entry8.insert(0, "400")
lbl9 = Label(frame1, text="Ending log file", width=12)
lbl9.grid(row=7, column=2)
self.entry9 = Entry(frame1)
self.entry9.grid(row=7, column=3)
self.entry9.insert(0, "1000")
frame2 = Frame(self.parent)
frame2.grid(row=2, column=0, sticky="nsew")
self.vsb = Scrollbar(frame2, orient="vertical", command=self.OnVsb)
self.vsb.grid(row=1, column=3, sticky="ns")
self.lb1 = Listbox(frame2, yscrollcommand=self.vsb.set)
self.lb1.grid(row=1, column=0)
self.lb2 = Listbox(frame2, yscrollcommand=self.vsb.set)
self.lb2.grid(row=1, column=1)
self.lb3 = Listbox(frame2, yscrollcommand=self.vsb.set)
self.lb3.grid(row=1, column=2)
self.b1 = Button(frame2,
text="Residue Number",
state=DISABLED,
command=lambda: self.sortdata(0))
self.b1.grid(row=0, column=0, sticky=W + E)
self.b2 = Button(frame2,
text="Residue Name",
state=DISABLED,
command=lambda: self.sortdata(1))
self.b2.grid(row=0, column=1, sticky=W + E)
self.b3 = Button(frame2,
text="Energy Value",
state=DISABLED,
command=lambda: self.sortdata(2))
self.b3.grid(row=0, column=2, sticky=W + E)
OS = platform.system()
if (OS == "Linux"):
self.lb1.bind("<<ListboxSelect>>", self.OnSelect)
self.lb1.bind("<4>", self.OnMouseWheel)
self.lb1.bind("<5>", self.OnMouseWheel)
self.lb2.bind("<<ListboxSelect>>", self.OnSelect)
self.lb2.bind("<4>", self.OnMouseWheel)
self.lb2.bind("<5>", self.OnMouseWheel)
self.lb3.bind("<<ListboxSelect>>", self.OnSelect)
self.lb3.bind("<4>", self.OnMouseWheel)
self.lb3.bind("<5>", self.OnMouseWheel)
else:
self.lb1.bind("<<ListboxSelect>>", self.OnSelect)
self.lb1.bind("<MouseWheel>", self.OnMouseWheel)
self.lb2.bind("<<ListboxSelect>>", self.OnSelect)
self.lb2.bind("<MouseWheel>", self.OnMouseWheel)
self.lb3.bind("<<ListboxSelect>>", self.OnSelect)
self.lb3.bind("<MouseWheel>", self.OnMouseWheel)
frame3 = Frame(self.parent)
frame3.grid(row=3, column=0, sticky="nsew")
self.previous = Button(frame3,
text="Previous Frame",
state=DISABLED,
command=self.prevframe)
self.previous.grid(row=0, column=0, sticky=W + E)
self.scale = Scale(frame3,
command=self.onScale,
state=DISABLED,
orient=HORIZONTAL,
length=320,
showvalue=0)
self.scale.grid(row=0, column=1, sticky=W + E)
self.next = Button(frame3,
text="Next Frame",
state=DISABLED,
command=self.nextframe)
self.next.grid(row=0, column=2, sticky=W + E)
self.var = IntVar()
v = 000
self.var.set(v)
self.label = Label(frame3, text=0, textvariable=self.var)
self.label.grid(row=0, column=3)
self.ApplyButton = Button(frame3, text="Apply", command=self.Apply)
self.ApplyButton.grid(row=1, column=3, sticky="e")
ToolTip(lbl1, "Load the result directory of Sire Analysis")
ToolTip(self.browserButton,
"Load the result directory of Sire Analysis")
ToolTip(lbl4, "Enter the name of the Ligand in your coordinate file")
ToolTip(
lbl5,
"The radially distributed zone around ligand you want to be displayed"
)
ToolTip(
lbl6,
"Minimum scale value for the color distribution and it will be treated as blue"
)
ToolTip(
lbl7,
"Maximum scale value for the color distribution and it will be treated as red"
)
def wsvisualizer(self, index, lig, zone, min, max, label):
cmd.hide("all")
x = cmd.get_names("all")
cmd.show("cartoon", "bo. " + x[index])
cmd.show("sticks", x[index] + " and r. " + lig)
cmd.color("white", x[index] + " and pol.")
fp = open(tempfile.gettempdir() + "/temp.txt", "r")
#tt=0
stored.bfact = []
for line in fp:
stored.bfact.append(line)
#print(stored.bfact[tt]+"\t"+line+"\t"+str(tt))
#tt=tt+1
#print(tt)
fp.close()
cmd.alter(x[index], "b=stored.bfact.pop(0)")
cmd.spectrum("b", "blue_white_red", x[index], minimum=min, maximum=max)
cmd.ramp_new("ramp_obj",
x[index],
range=[min, 0, max],
color="[blue, white, red ]")
cmd.util.cbaw(x[index] + " and r. " + lig)
cmd.show(
"licorice", "( " + x[index] + " and (r. " + lig + " a. " + zone +
") ) and (not (" + x[index] +
" and (r. SWT or r. BWT or r. SWP))) ")
self.togglelabelws(label, index, lig, zone)
def lsvisualizer(self, index, lig, zone, min, max, hlig, label):
cmd.hide("all")
x = cmd.get_names("all")
cmd.show("cartoon", "bo. " + x[index])
cmd.show("sticks", x[index] + " and r. " + lig)
cmd.color("white", x[index] + " and pol.")
fp = open(tempfile.gettempdir() + "/temp.txt", "r")
stored.bfact = []
for line in fp:
stored.bfact.append(line)
fp.close()
cmd.alter(x[index], "b=stored.bfact.pop(0)")
cmd.spectrum("b", "blue_white_red", x[index], minimum=min, maximum=max)
cmd.ramp_new("ramp_obj",
x[index],
range=[min, 0, max],
color="[blue, white, red ]")
cmd.util.cbaw(x[index] + " and r. " + lig)
cmd.show(
"licorice", "( " + x[index] + " and (r. " + lig + " a. " + zone +
") ) and (not (" + x[index] +
" and (r. SWT or r. BWT or r. SWP))) ")
cmd.hide("licorice", x[index] + " and r. " + hlig)
self.togglelabells(label, index, lig, zone, hlig)
def wsupdateview(self, lig, zone, min, max, prev, index, label):
cmd.hide("all")
x = cmd.get_names("all")
cmd.label(
"( " + x[index] + " and (r. " + lig + " a. " + prev +
") ) and (not (" + x[index] +
" and (r. SWT or r. BWT or r. SWP))) " + " and name CA", "\" \"")
cmd.show("cartoon", "bo. " + x[index])
cmd.show("sticks", x[index] + " and r. " + lig)
cmd.color("white", x[index] + " and pol.")
fp = open(tempfile.gettempdir() + "/temp.txt", "r")
#tt=0
stored.bfact = []
for line in fp:
stored.bfact.append(line)
#print(stored.bfact[tt]+"\t"+line+"\t"+str(tt))
#tt=tt+1
#print(tt)
fp.close()
cmd.alter(x[index], "b=stored.bfact.pop(0)")
cmd.spectrum("b", "blue_white_red", x[index], minimum=min, maximum=max)
cmd.ramp_new("ramp_obj",
x[index],
range=[min, 0, max],
color="[blue, white, red ]")
cmd.util.cbaw(x[index] + " and r. " + lig)
cmd.show(
"licorice", "( " + x[index] + " and (r. " + lig + " a. " + zone +
") ) and (not (" + x[index] +
" and (r. SWT or r. BWT or r. SWP))) ")
self.togglelabelws(label, index, lig, zone)
def lsupdateview(self, lig, zone, min, max, prev, index, hlig, label):
cmd.hide("all")
x = cmd.get_names("all")
cmd.label(
"( " + x[index] + " and (r. " + lig + " a. " + prev +
") ) and (not (" + x[index] +
" and (r. SWT or r. BWT or r. SWP))) " + " and name CA", "\" \"")
cmd.show("cartoon", "bo. " + x[index])
cmd.show("sticks", x[index] + " and r. " + lig)
cmd.color("white", x[index] + " and pol.")
fp = open(tempfile.gettempdir() + "/temp.txt", "r")
stored.bfact = []
for line in fp:
stored.bfact.append(line)
fp.close()
cmd.alter(x[index], "b=stored.bfact.pop(0)")
cmd.spectrum("b", "blue_white_red", x[index], minimum=min, maximum=max)
cmd.ramp_new("ramp_obj",
x[index],
range=[min, 0, max],
color="[blue, white, red ]")
cmd.util.cbaw(x[index] + " and r. " + lig)
cmd.show(
"licorice", "( " + x[index] + " and (r. " + lig + " a. " + zone +
") ) and (not (" + x[index] +
" and (r. SWT or r. BWT or r. SWP))) ")
cmd.hide("licorice", x[index] + " and r. " + hlig)
self.togglelabells(label, index, lig, zone, hlig)
def wsloadallpdb(self, pdblist, path):
for x in pdblist:
cmd.load(path + "/" + x)
#print(path +"/"+ x)
cmd.hide("all")
def mmloadpdb(self, path):
cmd.load(path)
def togglesurface(self, sur):
x = cmd.get_names("all")
if (sur):
cmd.show("surf", x[int(self.scale.get())])
cmd.set("transparency", "0.7")
else:
cmd.hide("surf", x[int(self.scale.get())])
def wslistdisplay(self, prev, cur, index):
x = cmd.get_names("all")
cmd.hide("sticks", x[index] + " and i. " + prev)
cmd.label(x[index] + " and i. " + prev + " and name CA", "\" \"")
cmd.show("sticks", x[index] + " and i. " + cur)
cmd.label(x[index] + " and i. " + cur + " and name CA",
"\"%s %s\"%(resn,resi)")
def togglelabelws(self, label, index, lig, zone):
global prevz
x = cmd.get_names("all")
if (label):
cmd.label(
"( " + x[index] + " and (r. " + lig + " a. " + zone +
") ) and (not (" + x[index] +
" and (r. SWT or r. BWT or r. SWP))) " + " and name CA",
"\"%s %s\"%(resn,resi)")
prevz = self.entry5.get()
else:
cmd.label(
"( " + x[index] + " and (r. " + lig + " a. " + prevz +
") ) and (not (" + x[index] +
" and (r. SWT or r. BWT or r. SWP))) " + " and name CA",
"\" \"")
def togglelabells(self, label, index, lig, zone, hlig):
global prevz
x = cmd.get_names("all")
if (label):
cmd.label(
"( " + x[index] + " and (r. " + lig + " a. " + zone +
") ) and (not (" + x[index] +
" and (r. SWT or r. BWT or r. SWP))) " + " and name CA",
"\"%s %s\"%(resn,resi)")
cmd.label(x[index] + " and r. " + hlig + " and name CA", "\" \"")
prevz = self.entry5.get()
else:
cmd.label(
"( " + x[index] + " and (r. " + lig + " a. " + prevz +
") ) and (not (" + x[index] +
" and (r. SWT or r. BWT or r. SWP))) " + " and name CA",
"\" \"")
def viewlabel(self):
if (load > 0):
if (self.wat.get() == 1):
self.togglelabelws(self.vl.get(), int(self.scale.get()),
self.entry4.get(), self.entry5.get())
elif (self.lig.get() == 1):
if (self.l1v.get() == 1):
vl = self.entry4.get()
hl = self.swapentry.get()
if (self.l2v.get() == 1):
vl = self.swapentry.get()
hl = self.entry4.get()
self.togglelabells(self.vl.get(), int(self.scale.get()), vl,
self.entry5.get(), hl)
elif (self.mm.get() == 1):
self.togglelabelws(self.vl.get(), 0, self.entry4.get(),
self.entry5.get())
def viewsurface(self): ##
if (load > 0):
self.togglesurface(self.sv.get())
def optionws(self):
if (self.wat.get() == 1):
self.lig.set(0)
self.mm.set(0)
self.entry1.config(state="normal")
self.browserButton.config(state="normal")
self.swapentry.config(state=DISABLED)
self.lig1ck.config(state=DISABLED)
self.lig2ck.config(state=DISABLED)
self.lblswap.config(state=DISABLED)
self.entry2.config(state=DISABLED)
self.entry3.config(state=DISABLED)
self.browserButtonMM.config(state=DISABLED)
self.browserButtonPDB.config(state=DISABLED)
else:
self.wat.set(0)
self.lig.set(1)
self.mm.set(0)
self.swapentry.config(state="normal")
self.lig1ck.config(state="normal")
self.lig2ck.config(state="normal")
self.lblswap.config(state="normal")
self.entry1.config(state="normal")
self.browserButton.config(state="normal")
self.entry2.config(state=DISABLED)
self.entry3.config(state=DISABLED)
self.browserButtonMM.config(state=DISABLED)
self.browserButtonPDB.config(state=DISABLED)
def optionls(self):
if (self.lig.get() == 1):
self.wat.set(0)
self.mm.set(0)
self.swapentry.config(state="normal")
self.lig1ck.config(state="normal")
self.lig2ck.config(state="normal")
self.lblswap.config(state="normal")
self.entry1.config(state="normal")
self.browserButton.config(state="normal")
self.entry2.config(state=DISABLED)
self.entry3.config(state=DISABLED)
self.browserButtonMM.config(state=DISABLED)
self.browserButtonPDB.config(state=DISABLED)
else:
self.lig.set(0)
self.mm.set(0)
self.wat.set(1)
self.entry1.config(state="normal")
self.browserButton.config(state="normal")
self.swapentry.config(state=DISABLED)
self.lig1ck.config(state=DISABLED)
self.lig2ck.config(state=DISABLED)
self.lblswap.config(state=DISABLED)
self.entry2.config(state=DISABLED)
self.entry3.config(state=DISABLED)
self.browserButtonMM.config(state=DISABLED)
self.browserButtonPDB.config(state=DISABLED)
def optionmm(self):
if (self.mm.get() == 1):
self.lig.set(0)
self.wat.set(0)
self.swapentry.config(state=DISABLED)
self.lig1ck.config(state=DISABLED)
self.lig2ck.config(state=DISABLED)
self.lblswap.config(state=DISABLED)
self.entry8.config(state=DISABLED)
self.entry9.config(state=DISABLED)
self.entry1.config(state=DISABLED)
self.browserButton.config(state=DISABLED)
self.entry2.config(state="normal")
self.entry3.config(state="normal")
self.browserButtonMM.config(state="normal")
self.browserButtonPDB.config(state="normal")
else:
self.wat.set(1)
self.lig.set(0)
self.mm.set(0)
self.entry8.config(state="normal")
self.entry9.config(state="normal")
self.entry1.config(state="normal")
self.browserButton.config(state="normal")
self.entry2.config(state=DISABLED)
self.entry3.config(state=DISABLED)
self.browserButtonMM.config(state=DISABLED)
self.browserButtonPDB.config(state=DISABLED)
def changelig1(self): ##
if (self.l1v.get() == 1):
self.l2v.set(0)
else:
self.l2v.set(1)
if (load > 0):
if (self.l1v.get() == 1):
vl = self.entry4.get()
hl = self.swapentry.get()
if (self.l2v.get() == 1):
vl = self.swapentry.get()
hl = self.entry4.get()
self.lsupdateview(vl, self.entry5.get(), self.entry6.get(),
self.entry7.get(), prevz, int(self.scale.get()),
hl, self.vl.get())
def changelig2(self): ##
if (self.l2v.get() == 1):
self.l1v.set(0)
else:
self.l1v.set(1)
if (load > 0):
if (self.l1v.get() == 1):
vl = self.entry4.get()
hl = self.swapentry.get()
if (self.l2v.get() == 1):
vl = self.swapentry.get()
hl = self.entry4.get()
self.lsupdateview(vl, self.entry5.get(), self.entry6.get(),
self.entry7.get(), prevz, int(self.scale.get()),
hl, self.vl.get())
def loadmmpbsaresults(self):
fp = open(self.entry3.get(), "r")
e = 0
atomcount = 0
resnew = 0
rescount = 0
resnum = list()
residuename = list()
resv = list()
atomnum = list()
atomnums = list()
score = list()
r = ""
rn = ""
for line in fp:
if e == 2:
atomnum.append(atomnums)
break
t = line.split()
if line.find('TER') != -1:
e = e + 1
if line.find('ATOM') != -1:
if (resnew == 0):
r = t[4]
rn = t[3]
resnew = 1
resnum.append(r)
residuename.append(rn)
score.append(0)
elif (r != t[4]):
r = t[4]
rn = t[3]
atomnum.append(atomnums)
resnum.append(r)
residuename.append(rn)
score.append(0)
atomnums = list()
atomnums.append(atomcount)
atomcount = atomcount + 1
fp.close()
ll = len(score)
print(ll)
resv = list()
fp = open(self.entry2.get(), "r")
for line in fp:
t = line.split(',')
t2 = t[0].split()
if (len(t) == 20 and len(t2) == 2 and t2[0] != "LIG"):
for xx in range(ll):
if (int(resnum[xx]) == int(t2[1])):
#print(str(ll)+"\t"+str(len(t)))
score[xx] = float(t[17])
matchObj = re.match(r'Sidechain Energy Decomposition:', line,
re.M | re.I)
if matchObj:
break
fp.close()
x = len(score)
data = list()
for i in range(x):
data.append([resnum[i], score[i], residuename[i], atomnum[i]])
data.sort(key=lambda s: (int(s[0])))
scores = list()
for i in range(len(data)):
for j in range(len(data[i][3])):
scores.append("{0:.3f}".format(data[i][1]))
fp = open(tempfile.gettempdir() + "/temp.txt", "w")
xs = len(scores)
for i in range(xs):
fp.write(str(scores[i]) + "\n")
fp.close()
self.lb1.delete(0, END)
self.lb2.delete(0, END)
self.lb3.delete(0, END)
for i in range(x):
self.lb1.insert(END, data[i][0])
self.lb2.insert(END, data[i][2])
self.lb3.insert(END, round(data[i][1], 3))
self.b1.config(state="normal")
self.b2.config(state="normal")
self.b3.config(state="normal")
def changestate(self): ##
fp = open(self.entry1.get() + "/bound_mobile_000100_0.00500.pdb")
lend = 0
if (self.wat.get() == 1):
lend = 2
elif (self.lig.get() == 1):
lend = 4
e = 0
atomcount = 0
resnew = 0
rescount = 0
resnum = list()
residuename = list()
resv = list()
atomnum = list()
atomnums = list()
score = list()
r = ""
rn = ""
for line in fp:
if e == lend:
atomnum.append(atomnums)
break
t = line.split()
if line.find('TER') != -1:
e = e + 1
if line.find('ATOM') != -1:
if (resnew == 0):
r = t[4]
rn = t[3]
resnew = 1
resnum.append(r)
residuename.append(rn)
score.append(0)
elif (r != t[4]):
r = t[4]
rn = t[3]
atomnum.append(atomnums)
resnum.append(r)
residuename.append(rn)
score.append(0)
atomnums = list()
atomnums.append(atomcount)
atomcount = atomcount + 1
fp.close()
x = list()
tempx = list()
ll = len(score)
base = os.listdir(self.entry1.get())
for a in base:
if a.endswith(".log"):
tempx.append(a)
tempx.sort()
tlen = len(tempx)
ia = int(self.entry8.get())
while (ia <= int(self.entry9.get()) and ia < tlen):
x.append(tempx[ia])
ia += 1
c = 0
i = 0
for fn in x:
fp = open(self.entry1.get() + "/" + fn, "r")
if (c == 0):
for line in fp:
t = line.split()
if (len(t) == 8):
if (t[0] == "Residue("):
for xx in range(ll):
if (int(resnum[xx]) == int(t[3])):
score[xx] = float(t[5])
if (line == "PROTEIN BOX WATER FREE ENERGY COMPONENTS\n"):
c = c + 1
i = 0
break
else:
for line in fp:
t = line.split()
if (len(t) == 8):
if (t[0] == "Residue("):
for xx in range(ll):
if (int(t[3]) == int(resnum[xx])):
score[xx] = score[xx] + float(t[5])
i = i + 1
if (line == "PROTEIN BOX WATER FREE ENERGY COMPONENTS\n"):
c = c + 1
i = 0
break
fp.close()
x = len(score)
data = list()
for i in range(x):
data.append([resnum[i], score[i], residuename[i], atomnum[i]])
data.sort(key=lambda s: (int(s[0])))
for i in range(x):
data[i][1] = data[i][1] / c
scores = list()
for i in range(len(data)):
for j in range(len(data[i][3])):
scores.append("{0:.3f}".format(data[i][1]))
self.lb1.delete(0, END)
self.lb2.delete(0, END)
self.lb3.delete(0, END)
for i in range(x):
self.lb1.insert(END, data[i][0])
self.lb2.insert(END, data[i][2])
self.lb3.insert(END, round(data[i][1], 3))
fp = open(tempfile.gettempdir() + "/temp.txt", "w")
lx = len(scores)
for i in range(lx):
fp.write(str(scores[i]) + "\n")
fp.close()
self.b1.config(state="normal")
self.b2.config(state="normal")
self.b3.config(state="normal")
def prevframe(self):
global prevz, load
if (load > 0):
self.scale.set(self.scale.get() - 1)
def nextframe(self):
global prevz, load
if (load > 0):
self.scale.set(self.scale.get() + 1)
def onScale(self, val):
global prevz, load
if (load > 0):
v = self.lig1pdb[int(float(val))][14:19]
self.var.set(v)
if (self.scale.get() == 0):
self.previous.config(state=DISABLED)
if (self.scale.get() == len(self.lig1pdb) - 2):
self.next.config(state="normal")
if (self.scale.get() == 1):
self.previous.config(state="normal")
if (self.scale.get() == len(self.lig1pdb) - 1):
self.next.config(state=DISABLED)
if (self.wat.get() == 1):
self.wsupdateview(self.entry4.get(), self.entry5.get(),
self.entry6.get(), self.entry7.get(), prevz,
int(self.scale.get()), self.vl.get())
elif (self.lig.get() == 1):
if (self.l1v.get() == 1):
vl = self.entry4.get()
hl = self.swapentry.get()
if (self.l2v.get() == 1):
vl = self.swapentry.get()
hl = self.entry4.get()
self.lsupdateview(vl, self.entry5.get(), self.entry6.get(),
self.entry7.get(), prevz,
int(self.scale.get()), hl, self.vl.get())
def OnSelect(self, val):
global prev
sender = val.widget
idx = sender.curselection()
if (idx != ()):
dis = self.lb1.get(idx)
if (self.wat.get() == 1 or self.lig.get() == 1):
self.wslistdisplay(prev, dis, int(self.scale.get()))
elif (self.mm.get() == 1):
self.wslistdisplay(prev, dis, 0)
prev = dis
def sortdata(self, sc):
global dr1, dr2, dr3
tableData1 = self.lb1.get(0, END)
tableData2 = self.lb2.get(0, END)
tableData3 = self.lb3.get(0, END)
data = list()
nv = len(tableData1)
for x in range(nv):
data.append([tableData1[x], tableData2[x], tableData3[x]])
if (sc == 0):
lab = self.b1.cget('text')
if lab[0] == '[': self.b1.config(text=lab[4:])
lab = self.b2.cget('text')
if lab[0] == '[': self.b2.config(text=lab[4:])
lab = self.b3.cget('text')
if lab[0] == '[': self.b3.config(text=lab[4:])
lab = self.b1.cget('text')
if dr1 == 1: self.b1.config(text='[+] ' + lab)
else: self.b1.config(text='[-] ' + lab)
data.sort(key=lambda s: (int(s[sc])), reverse=dr1 == 1)
dr1 = dr1 * -1
if (sc == 1):
lab = self.b1.cget('text')
if lab[0] == '[': self.b1.config(text=lab[4:])
lab = self.b2.cget('text')
if lab[0] == '[': self.b2.config(text=lab[4:])
lab = self.b3.cget('text')
if lab[0] == '[': self.b3.config(text=lab[4:])
lab = self.b2.cget('text')
if dr2 == 1: self.b2.config(text='[+] ' + lab)
else: self.b2.config(text='[-] ' + lab)
data.sort(key=lambda s: (s[sc]), reverse=dr2 == 1)
dr2 = dr2 * -1
if (sc == 2):
lab = self.b1.cget('text')
if lab[0] == '[': self.b1.config(text=lab[4:])
lab = self.b2.cget('text')
if lab[0] == '[': self.b2.config(text=lab[4:])
lab = self.b3.cget('text')
if lab[0] == '[': self.b3.config(text=lab[4:])
lab = self.b3.cget('text')
if dr3 == 1: self.b3.config(text='[+] ' + lab)
else: self.b3.config(text='[-] ' + lab)
data.sort(key=lambda s: (float(s[sc])), reverse=dr3 == 1)
dr3 = dr3 * -1
nv = len(data)
self.lb1.delete(0, 'end')
self.lb2.delete(0, 'end')
self.lb3.delete(0, 'end')
for x in range(nv):
self.lb1.insert(END, data[x][0])
self.lb2.insert(END, data[x][1])
self.lb3.insert(END, data[x][2])
def onOpen(self):
global load
fold = tkFileDialog.askdirectory()
self.entry1.delete(0, 'end')
self.entry1.insert(0, fold)
load = 0
def onOpenMM(self):
global load
fold = tkFileDialog.askopenfilename()
self.entry2.delete(0, 'end')
self.entry2.insert(0, fold)
load = 0
def onOpenPDB(self):
global load
fold = tkFileDialog.askopenfilename()
self.entry3.delete(0, 'end')
self.entry3.insert(0, fold)
load = 0
def OnVsb(self, *args):
self.lb1.yview(*args)
self.lb2.yview(*args)
self.lb3.yview(*args)
def OnMouseWheel(self, event):
self.lb1.yview("scroll", event.delta, "units")
self.lb2.yview("scroll", event.delta, "units")
self.lb3.yview("scroll", event.delta, "units")
return "break"
def Apply(self):
global load, prevz
if (load == 0):
if (self.wat.get() == 1 or self.lig.get() == 1):
self.changestate()
self.base = os.listdir(self.entry1.get())
pdb1 = list()
for a in self.base:
matchObj = re.match(r'bound_mobile_\d{6}_0\.\d{5}\.pdb', a,
re.M | re.I)
if matchObj:
pdb1.append(a)
self.lig1pdb = list()
self.lig2pdb = list()
x = pdb1[1][22:27]
for a in pdb1:
matchObj = re.match(r'bound_mobile_\d{6}_0\.' + x + '.pdb',
a, re.M | re.I)
if matchObj:
self.lig1pdb.append(a)
else:
self.lig2pdb.append(a)
self.lig1pdb.sort()
self.lig2pdb.sort()
self.scale.configure(from_=0, to=len(self.lig1pdb) - 1)
self.scale.config(state="normal")
elif (self.mm.get() == 1):
self.loadmmpbsaresults()
self.mmloadpdb(self.entry3.get())
self.wsvisualizer(0, self.entry4.get(), self.entry5.get(),
self.entry6.get(), self.entry7.get(),
self.vl.get())
if (self.wat.get() == 1):
self.wsloadallpdb(self.lig1pdb, self.entry1.get())
self.next.config(state="normal")
v = self.lig1pdb[0][14:19]
self.var.set(v)
self.wsvisualizer(int(self.scale.get()), self.entry4.get(),
self.entry5.get(), self.entry6.get(),
self.entry7.get(), self.vl.get())
elif (self.lig.get() == 1):
if (self.l1v.get() == 1):
vl = self.entry4.get()
hl = self.swapentry.get()
if (self.l2v.get() == 1):
vl = self.swapentry.get()
hl = self.entry4.get()
self.wsloadallpdb(self.lig1pdb, self.entry1.get())
self.next.config(state="normal")
v = self.lig1pdb[0][14:19]
self.var.set(v)
self.lsvisualizer(int(self.scale.get()), vl, self.entry5.get(),
self.entry6.get(), self.entry7.get(), hl,
self.vl.get())
load = 1
else: #old code "else:"
if (self.wat.get() == 1):
self.wsupdateview(self.entry4.get(), self.entry5.get(),
self.entry6.get(), self.entry7.get(), prevz,
int(self.scale.get()), self.vl.get())
elif (self.lig.get() == 1):
if (self.l1v.get() == 1):
vl = self.entry4.get()
hl = self.swapentry.get()
if (self.l2v.get() == 1):
vl = self.swapentry.get()
hl = self.entry4.get()
self.lsupdateview(vl, self.entry5.get(), self.entry6.get(),
self.entry7.get(), prevz,
int(self.scale.get()), hl, self.vl.get())
elif (self.mm.get() == 1):
self.wsupdateview(self.entry4.get(), self.entry5.get(),
self.entry6.get(), self.entry7.get(), prevz,
0, self.vl.get())
prevz = self.entry5.get()
class CHEWDDialog(ModelessDialog):
name = "Energy Visualizer"
buttons = ("Apply", "Close")
help = ("Energy.html", CHEWD)
title = "CHemical Energy Wise Decomposition"
def fillInUI(self, parent):
#parent.resizable(0, 0)
frame4 = Frame(parent)
frame4.grid(row=0, column=0, sticky="nsew")
self.wat = IntVar()
self.wat.set(1)
self.waterswap = Checkbutton(frame4,
text="Water Swap",
command=self.optionws,
variable=self.wat)
self.waterswap.grid(row=0, column=0)
self.lig = IntVar()
self.lig.set(0)
self.ligandswap = Checkbutton(frame4,
text="Ligand Swap",
command=self.optionls,
variable=self.lig)
self.ligandswap.grid(row=0, column=1)
self.mm = IntVar()
self.mm.set(0)
self.mmpbsa = Checkbutton(frame4,
text="MMPBSA",
command=self.optionmm,
variable=self.mm)
self.mmpbsa.grid(row=0, column=2)
frame1 = Frame(parent)
frame1.grid(row=1, column=0, sticky="nsew")
lbl1 = Label(frame1, text="Log file folder", width=12)
lbl1.grid(row=0, column=0)
self.entry1 = Entry(frame1)
self.entry1.grid(row=0, column=1, columnspan=4, sticky=W + E)
self.browserButton = Button(frame1,
text="Browser",
command=self.onOpen)
self.browserButton.grid(row=0, column=5, sticky="e")
lbl2 = Label(frame1, text="MMPBSA log file", width=12)
lbl2.grid(row=1, column=0)
self.entry2 = Entry(frame1, state=DISABLED)
self.entry2.grid(row=1, column=1, columnspan=4, sticky=W + E)
self.browserButtonMM = Button(frame1,
text="Browser",
command=self.onOpenMM,
state=DISABLED)
self.browserButtonMM.grid(row=1, column=5, sticky="e")
lbl3 = Label(frame1, text="MMPBSA PDB file", width=12)
lbl3.grid(row=2, column=0)
self.entry3 = Entry(frame1, state=DISABLED)
self.entry3.grid(row=2, column=1, columnspan=4, sticky=W + E)
self.browserButtonPDB = Button(frame1,
text="Browser",
command=self.onOpenPDB,
state=DISABLED)
self.browserButtonPDB.grid(row=2, column=5, sticky="e")
lbl4 = Label(frame1, text="Ligand Name", width=12)
lbl4.grid(row=3, column=0)
self.entry4 = Entry(frame1)
self.entry4.grid(row=3, column=1)
self.lblswap = Label(frame1,
text="Swap Ligand",
width=12,
state=DISABLED)
self.lblswap.grid(row=3, column=2)
self.swapentry = Entry(frame1, state=DISABLED)
self.swapentry.grid(row=3, column=3)
self.l1v = IntVar()
self.l1v.set(1)
self.lig1ck = Checkbutton(frame1,
text="Ligand 1",
command=self.changelig1,
state=DISABLED,
variable=self.l1v)
self.lig1ck.grid(row=4, column=0)
self.l2v = IntVar()
self.l2v.set(0)
self.lig2ck = Checkbutton(frame1,
text="Ligand 2",
command=self.changelig2,
state=DISABLED,
variable=self.l2v)
self.lig2ck.grid(row=4, column=2)
lbl5 = Label(frame1, text="Display Radius", width=12)
lbl5.grid(row=5, column=0)
self.entry5 = Entry(frame1)
self.entry5.grid(row=5, column=1)
self.entry5.insert(0, "5.0")
self.sv = IntVar()
self.sv.set(0)
self.surface = Checkbutton(frame1,
text="View Surface",
command=self.viewsurface,
variable=self.sv)
self.surface.grid(row=5, column=2)
self.vl = IntVar()
self.vl.set(1)
self.label = Checkbutton(frame1,
text="View Label",
command=self.viewlabel,
variable=self.vl)
self.label.grid(row=5, column=3)
lbl6 = Label(frame1, text="Min Value", width=12)
lbl6.grid(row=6, column=0)
self.entry6 = Entry(frame1)
self.entry6.grid(row=6, column=1)
self.entry6.insert(0, "-5")
lbl7 = Label(frame1, text="Max Value", width=12)
lbl7.grid(row=6, column=2)
self.entry7 = Entry(frame1)
self.entry7.grid(row=6, column=3)
self.entry7.insert(0, "+5")
lbl8 = Label(frame1, text="Starting log file", width=12)
lbl8.grid(row=7, column=0)
self.entry8 = Entry(frame1)
self.entry8.grid(row=7, column=1)
self.entry8.insert(0, "400")
lbl9 = Label(frame1, text="Ending log file", width=12)
lbl9.grid(row=7, column=2)
self.entry9 = Entry(frame1)
self.entry9.grid(row=7, column=3)
self.entry9.insert(0, "1000")
frame2 = Frame(parent)
frame2.grid(row=2, column=0, sticky="nsew")
self.vsb = Scrollbar(frame2, orient="vertical", command=self.OnVsb)
self.vsb.grid(row=1, column=3, sticky="ns")
self.lb1 = Listbox(frame2, yscrollcommand=self.vsb.set)
self.lb1.grid(row=1, column=0)
self.lb2 = Listbox(frame2, yscrollcommand=self.vsb.set)
self.lb2.grid(row=1, column=1)
self.lb3 = Listbox(frame2, yscrollcommand=self.vsb.set)
self.lb3.grid(row=1, column=2)
self.b1 = Button(frame2,
text="Residue Number",
state=DISABLED,
command=lambda: self.sortdata(0))
self.b1.grid(row=0, column=0, sticky=W + E)
self.b2 = Button(frame2,
text="Residue Name",
state=DISABLED,
command=lambda: self.sortdata(1))
self.b2.grid(row=0, column=1, sticky=W + E)
self.b3 = Button(frame2,
text="Energy Value",
state=DISABLED,
command=lambda: self.sortdata(2))
self.b3.grid(row=0, column=2, sticky=W + E)
self.lb1.bind("<<ListboxSelect>>", self.OnSelect)
self.lb1.bind("<MouseWheel>", self.OnMouseWheel)
self.lb2.bind("<<ListboxSelect>>", self.OnSelect)
self.lb2.bind("<MouseWheel>", self.OnMouseWheel)
self.lb3.bind("<<ListboxSelect>>", self.OnSelect)
self.lb3.bind("<MouseWheel>", self.OnMouseWheel)
frame3 = Frame(parent)
frame3.grid(row=3, column=0, sticky="nsew")
self.previous = Button(frame3,
text="Previous Frame",
state=DISABLED,
command=self.prevframe)
self.previous.grid(row=0, column=0, sticky=W + E)
self.scale = Scale(frame3,
command=self.onScale,
state=DISABLED,
orient=HORIZONTAL,
length=320,
showvalue=0)
self.scale.grid(row=0, column=1, sticky=W + E)
self.next = Button(frame3,
text="Next Frame",
state=DISABLED,
command=self.nextframe)
self.next.grid(row=0, column=2, sticky=W + E)
self.var = IntVar()
v = 000
self.var.set(v)
self.label = Label(frame3, text=0, textvariable=self.var)
self.label.grid(row=0, column=3)
ToolTip(lbl1, "Load the result directory of Sire Analysis")
ToolTip(self.browserButton,
"Load the result directory of Sire Analysis")
ToolTip(lbl4, "Enter the name of the Ligand in your coordinate file")
ToolTip(
lbl5,
"The radially distributed zone around ligand you want to be displayed"
)
ToolTip(
lbl6,
"Minimum scale value for the color distribution and it will be treated as blue"
)
ToolTip(
lbl7,
"Maximum scale value for the color distribution and it will be treated as red"
)
def viewlabel(self):
if (load > 0):
if (self.wat.get() == 1):
CHEWD.togglelabelws(self.vl.get(), str(self.scale.get()),
self.entry4.get(), self.entry5.get())
elif (self.lig.get() == 1):
if (self.l1v.get() == 1):
vl = self.entry4.get()
hl = self.swapentry.get()
if (self.l2v.get() == 1):
vl = self.swapentry.get()
hl = self.entry4.get()
CHEWD.togglelabells(self.vl.get(), str(self.scale.get()), vl,
self.entry5.get(), hl)
elif (self.mm.get() == 1):
CHEWD.togglelabelws(self.vl.get(), "0", self.entry4.get(),
self.entry5.get())
def viewsurface(self):
if (load > 0):
CHEWD.togglesurface(self.sv.get())
def optionws(self):
if (self.wat.get() == 1):
self.lig.set(0)
self.mm.set(0)
self.entry1.config(state="normal")
self.browserButton.config(state="normal")
self.swapentry.config(state=DISABLED)
self.lig1ck.config(state=DISABLED)
self.lig2ck.config(state=DISABLED)
self.lblswap.config(state=DISABLED)
self.entry2.config(state=DISABLED)
self.entry3.config(state=DISABLED)
self.browserButtonMM.config(state=DISABLED)
self.browserButtonPDB.config(state=DISABLED)
else:
self.wat.set(0)
self.lig.set(1)
self.mm.set(0)
self.swapentry.config(state="normal")
self.lig1ck.config(state="normal")
self.lig2ck.config(state="normal")
self.lblswap.config(state="normal")
self.entry1.config(state="normal")
self.browserButton.config(state="normal")
self.entry2.config(state=DISABLED)
self.entry3.config(state=DISABLED)
self.browserButtonMM.config(state=DISABLED)
self.browserButtonPDB.config(state=DISABLED)
def optionls(self):
if (self.lig.get() == 1):
self.wat.set(0)
self.mm.set(0)
self.swapentry.config(state="normal")
self.lig1ck.config(state="normal")
self.lig2ck.config(state="normal")
self.lblswap.config(state="normal")
self.entry1.config(state="normal")
self.browserButton.config(state="normal")
self.entry2.config(state=DISABLED)
self.entry3.config(state=DISABLED)
self.browserButtonMM.config(state=DISABLED)
self.browserButtonPDB.config(state=DISABLED)
else:
self.lig.set(0)
self.mm.set(0)
self.wat.set(1)
self.entry1.config(state="normal")
self.browserButton.config(state="normal")
self.swapentry.config(state=DISABLED)
self.lig1ck.config(state=DISABLED)
self.lig2ck.config(state=DISABLED)
self.lblswap.config(state=DISABLED)
self.entry2.config(state=DISABLED)
self.entry3.config(state=DISABLED)
self.browserButtonMM.config(state=DISABLED)
self.browserButtonPDB.config(state=DISABLED)
def optionmm(self):
if (self.mm.get() == 1):
self.lig.set(0)
self.wat.set(0)
self.swapentry.config(state=DISABLED)
self.lig1ck.config(state=DISABLED)
self.lig2ck.config(state=DISABLED)
self.lblswap.config(state=DISABLED)
self.entry8.config(state=DISABLED)
self.entry9.config(state=DISABLED)
self.entry1.config(state=DISABLED)
self.browserButton.config(state=DISABLED)
self.entry2.config(state="normal")
self.entry3.config(state="normal")
self.browserButtonMM.config(state="normal")
self.browserButtonPDB.config(state="normal")
else:
self.wat.set(1)
self.lig.set(0)
self.mm.set(0)
self.entry8.config(state="normal")
self.entry9.config(state="normal")
self.entry1.config(state="normal")
self.browserButton.config(state="normal")
self.entry2.config(state=DISABLED)
self.entry3.config(state=DISABLED)
self.browserButtonMM.config(state=DISABLED)
self.browserButtonPDB.config(state=DISABLED)
def changelig1(self):
if (self.l1v.get() == 1):
self.l2v.set(0)
else:
self.l2v.set(1)
if (load > 0):
if (self.l1v.get() == 1):
vl = self.entry4.get()
hl = self.swapentry.get()
if (self.l2v.get() == 1):
vl = self.swapentry.get()
hl = self.entry4.get()
CHEWD.lsupdateview(vl, self.entry5.get(), self.entry6.get(),
self.entry7.get(), prevz, str(self.scale.get()),
hl, self.vl.get())
def changelig2(self):
if (self.l2v.get() == 1):
self.l1v.set(0)
else:
self.l1v.set(1)
if (load > 0):
if (self.l1v.get() == 1):
vl = self.entry4.get()
hl = self.swapentry.get()
if (self.l2v.get() == 1):
vl = self.swapentry.get()
hl = self.entry4.get()
CHEWD.lsupdateview(vl, self.entry5.get(), self.entry6.get(),
self.entry7.get(), prevz, str(self.scale.get()),
hl, self.vl.get())
def loadmmpbsaresults(self):
fp = open(self.entry2.get(), "r")
resv = list()
for line in fp:
t = line.split(',')
t2 = t[0].split()
if (len(t) == 20 and len(t2) == 2 and t2[0] != self.entry4.get()):
resv.append([int(t2[1]), float(t[17]), t2[0]])
matchObj = re.match(r'Sidechain Energy Decomposition:', line,
re.M | re.I)
if matchObj:
break
self.lb1.delete(0, END)
self.lb2.delete(0, END)
self.lb3.delete(0, END)
x = len(resv)
for i in range(x):
self.lb1.insert(END, resv[i][0])
self.lb2.insert(END, resv[i][2])
self.lb3.insert(END, resv[i][1])
fp = open(tempfile.gettempdir() + "/temp.txt", "w")
fc = open(tempfile.gettempdir() + "/clear.txt", "w")
fp.write("attribute: sireEnergy\n")
fp.write("recipient: residues\n")
fc.write("attribute: sireEnergy\n")
fc.write("recipient: residues\n")
for i in range(x):
fp.write("\t:" + str(resv[i][0]) + "\t" + str(resv[i][1]) + "\n")
fc.write("\t:" + str(resv[i][0]) + "\t0.0\n")
fp.close()
fc.close()
self.b1.config(state="normal")
self.b2.config(state="normal")
self.b3.config(state="normal")
def changestate(self):
x = list()
tempx = list()
if (self.wat.get() == 1):
base = os.listdir(self.entry1.get())
else:
base = os.listdir(self.entry1.get() + "/")
for a in base:
if a.endswith(".log"):
tempx.append(a)
tempx.sort()
tlen = len(tempx)
ia = int(self.entry8.get()) - 1
while (ia <= int(self.entry9.get()) and ia < tlen):
x.append(tempx[ia])
ia += 1
resv = list()
c = 0
i = 0
for fn in x:
if (self.wat.get() == 1):
fp = open(self.entry1.get() + "/" + fn, "r")
else:
fp = open(self.entry1.get() + "/" + fn, "r")
if (c == 0):
for line in fp:
t = line.split()
if (len(t) == 8):
if (t[0] == "Residue("):
resv.append([int(t[3]), float(t[5]), t[1]])
if (line == "PROTEIN BOX WATER FREE ENERGY COMPONENTS\n"):
c = c + 1
i = 0
break
else:
for line in fp:
t = line.split()
if (len(t) == 8):
if (t[0] == "Residue("):
resv[i][1] = resv[i][1] + float(t[5])
i = i + 1
if (line == "PROTEIN BOX WATER FREE ENERGY COMPONENTS\n"):
c = c + 1
i = 0
break
fp.close()
x = len(resv)
self.lb1.delete(0, END)
self.lb2.delete(0, END)
self.lb3.delete(0, END)
for i in range(x):
resv[i][1] = resv[i][1] / c
for i in range(x):
self.lb1.insert(END, resv[i][0])
self.lb2.insert(END, resv[i][2])
self.lb3.insert(END, round(resv[i][1], 3))
fp = open(tempfile.gettempdir() + "/temp.txt", "w")
fc = open(tempfile.gettempdir() + "/clear.txt", "w")
fp.write("attribute: sireEnergy\n")
fp.write("recipient: residues\n")
fc.write("attribute: sireEnergy\n")
fc.write("recipient: residues\n")
for i in range(x):
fp.write("\t:" + str(resv[i][0]) + "\t" + str(resv[i][1]) + "\n")
fc.write("\t:" + str(resv[i][0]) + "\t0.0\n")
fp.close()
fc.close()
self.b1.config(state="normal")
self.b2.config(state="normal")
self.b3.config(state="normal")
def prevframe(self):
global prevz, load
if (load > 0):
self.scale.set(self.scale.get() - 1)
def nextframe(self):
global prevz, load
if (load > 0):
self.scale.set(self.scale.get() + 1)
def onScale(self, val):
global prevz, load
if (load > 0):
v = self.lig1pdb[int(float(val))][14:19]
self.var.set(v)
if (self.scale.get() == 0):
self.previous.config(state=DISABLED)
if (self.scale.get() == len(self.lig1pdb) - 2):
self.next.config(state="normal")
if (self.scale.get() == 1):
self.previous.config(state="normal")
if (self.scale.get() == len(self.lig1pdb) - 1):
self.next.config(state=DISABLED)
if (self.wat.get() == 1):
CHEWD.wsupdateview(self.entry4.get(), self.entry5.get(),
self.entry6.get(), self.entry7.get(), prevz,
str(self.scale.get()), self.vl.get())
elif (self.lig.get() == 1):
if (self.l1v.get() == 1):
vl = self.entry4.get()
hl = self.swapentry.get()
if (self.l2v.get() == 1):
vl = self.swapentry.get()
hl = self.entry4.get()
CHEWD.lsupdateview(vl, self.entry5.get(), self.entry6.get(),
self.entry7.get(), prevz,
str(self.scale.get()), hl, self.vl.get())
def OnSelect(self, val):
global prev
sender = val.widget
idx = sender.curselection()
dis = self.lb1.get(idx)
if (self.wat.get() == 1):
CHEWD.wslistdisplay(self.entry4.get(), self.entry5.get(), prev,
dis, str(self.scale.get()), self.vl.get())
elif (self.lig.get() == 1):
if (self.l1v.get() == 1):
vl = self.entry4.get()
hl = self.swapentry.get()
if (self.l2v.get() == 1):
vl = self.swapentry.get()
hl = self.entry4.get()
CHEWD.lslistdisplay(vl, self.entry5.get(), prev, dis,
str(self.scale.get()), hl, self.vl.get())
elif (self.mm.get() == 1):
CHEWD.mmlistdisplay(self.entry4.get(), self.entry5.get(), prev,
dis, "0", self.vl.get())
prev = dis
def sortdata(self, sc):
global dr1, dr2, dr3
tableData1 = self.lb1.get(0, END)
tableData2 = self.lb2.get(0, END)
tableData3 = self.lb3.get(0, END)
data = list()
nv = len(tableData1)
for x in range(nv):
data.append([tableData1[x], tableData2[x], tableData3[x]])
if (sc == 0):
lab = self.b1.cget('text')
if lab[0] == '[': self.b1.config(text=lab[4:])
lab = self.b2.cget('text')
if lab[0] == '[': self.b2.config(text=lab[4:])
lab = self.b3.cget('text')
if lab[0] == '[': self.b3.config(text=lab[4:])
lab = self.b1.cget('text')
if dr1 == 1: self.b1.config(text='[+] ' + lab)
else: self.b1.config(text='[-] ' + lab)
data.sort(key=lambda s: (s[sc]), reverse=dr1 == 1)
dr1 = dr1 * -1
if (sc == 1):
lab = self.b1.cget('text')
if lab[0] == '[': self.b1.config(text=lab[4:])
lab = self.b2.cget('text')
if lab[0] == '[': self.b2.config(text=lab[4:])
lab = self.b3.cget('text')
if lab[0] == '[': self.b3.config(text=lab[4:])
lab = self.b2.cget('text')
if dr2 == 1: self.b2.config(text='[+] ' + lab)
else: self.b2.config(text='[-] ' + lab)
data.sort(key=lambda s: (s[sc]), reverse=dr2 == 1)
dr2 = dr2 * -1
if (sc == 2):
lab = self.b1.cget('text')
if lab[0] == '[': self.b1.config(text=lab[4:])
lab = self.b2.cget('text')
if lab[0] == '[': self.b2.config(text=lab[4:])
lab = self.b3.cget('text')
if lab[0] == '[': self.b3.config(text=lab[4:])
lab = self.b3.cget('text')
if dr3 == 1: self.b3.config(text='[+] ' + lab)
else: self.b3.config(text='[-] ' + lab)
data.sort(key=lambda s: (s[sc]), reverse=dr3 == 1)
dr3 = dr3 * -1
nv = len(data)
self.lb1.delete(0, 'end')
self.lb2.delete(0, 'end')
self.lb3.delete(0, 'end')
for x in range(nv):
self.lb1.insert(END, data[x][0])
self.lb2.insert(END, data[x][1])
self.lb3.insert(END, data[x][2])
def onOpen(self):
global load
fold = tkFileDialog.askdirectory()
self.entry1.delete(0, 'end')
self.entry1.insert(0, fold)
load = 0
def onOpenMM(self):
global load
fold = tkFileDialog.askopenfilename()
self.entry2.delete(0, 'end')
self.entry2.insert(0, fold)
load = 0
def onOpenPDB(self):
global load
fold = tkFileDialog.askopenfilename()
self.entry3.delete(0, 'end')
self.entry3.insert(0, fold)
load = 0
def OnVsb(self, *args):
self.lb1.yview(*args)
self.lb2.yview(*args)
self.lb3.yview(*args)
def OnMouseWheel(self, event):
self.lb1.yview("scroll", event.delta, "units")
self.lb2.yview("scroll", event.delta, "units")
self.lb3.yview("scroll", event.delta, "units")
return "break"
def Apply(self):
global load, prevz
if (load == 0):
if (self.wat.get() == 1 or self.lig.get() == 1):
self.changestate()
self.base = os.listdir(self.entry1.get())
pdb1 = list()
for a in self.base:
matchObj = re.match(r'bound_mobile_\d{6}_0\.\d{5}\.pdb', a,
re.M | re.I)
if matchObj:
pdb1.append(a)
self.lig1pdb = list()
self.lig2pdb = list()
#print x
x = pdb1[1][22:27]
for a in pdb1:
matchObj = re.match(r'bound_mobile_\d{6}_0\.' + x + '.pdb',
a, re.M | re.I)
if matchObj:
self.lig1pdb.append(a)
else:
self.lig2pdb.append(a)
self.lig1pdb.sort()
self.lig2pdb.sort()
self.scale.configure(from_=0, to=len(self.lig1pdb) - 1)
self.scale.config(state="normal")
elif (self.mm.get() == 1):
self.loadmmpbsaresults()
CHEWD.mmloadpdb(self.entry3.get())
CHEWD.mmvisualizer("0", tempfile.gettempdir(),
self.entry4.get(), self.entry5.get(),
self.entry6.get(), self.entry7.get(),
self.vl.get())
if (self.wat.get() == 1):
CHEWD.wsloadallpdb(self.lig1pdb, self.entry1.get())
self.next.config(state="normal")
v = self.lig1pdb[0][14:19]
self.var.set(v)
CHEWD.wsvisualizer(str(self.scale.get()),
tempfile.gettempdir(), self.entry4.get(),
self.entry5.get(), self.entry6.get(),
self.entry7.get(), self.vl.get())
elif (self.lig.get() == 1):
if (self.l1v.get() == 1):
vl = self.entry4.get()
hl = self.swapentry.get()
if (self.l2v.get() == 1):
vl = self.swapentry.get()
hl = self.entry4.get()
CHEWD.wsloadallpdb(self.lig1pdb, self.entry1.get())
self.next.config(state="normal")
v = self.lig1pdb[0][14:19]
self.var.set(v)
CHEWD.lsvisualizer(str(self.scale.get()),
tempfile.gettempdir(), vl,
self.entry5.get(), self.entry6.get(),
self.entry7.get(), hl, self.vl.get())
load = 1
else:
if (self.wat.get() == 1):
self.changestate()
CHEWD.clear(tempfile.gettempdir())
CHEWD.loadresults(tempfile.gettempdir())
CHEWD.wsupdateview(self.entry4.get(), self.entry5.get(),
self.entry6.get(), self.entry7.get(), prevz,
str(self.scale.get()), self.vl.get())
elif (self.lig.get() == 1):
self.changestate()
if (self.l1v.get() == 1):
vl = self.entry4.get()
hl = self.swapentry.get()
if (self.l2v.get() == 1):
vl = self.swapentry.get()
hl = self.entry4.get()
CHEWD.clear(tempfile.gettempdir())
CHEWD.loadresults(tempfile.gettempdir())
CHEWD.lsupdateview(vl, self.entry5.get(), self.entry6.get(),
self.entry7.get(), prevz,
str(self.scale.get()), hl, self.vl.get())
elif (self.mm.get() == 1):
CHEWD.mmupdateview(self.entry4.get(), self.entry5.get(),
self.entry6.get(), self.entry7.get(), prevz,
"0", self.vl.get())
prevz = self.entry5.get()
