def buildResList (self): # calls PDBReader to read the given pdb file and create a list (self.allResidues) of lists (x,y,z,atom name, residue name) of lists (all the values for that residue)
self.allResidues = []
try:
f = open(self.fName)
f.close()
except IOError:
print "Sorry, the file name \"" + str(self.fName) + "\" does not exist"
sys.exit()
self.a = PDBReader()
self.a.read_from_pdb(self.fName)
point_x = self.a.get_x()
point_y = self.a.get_y()
point_z = self.a.get_z()
point_atomName = self.a.get_atomName()
point_resName = self.a.get_resName()
point_resNum = self.a.get_resNum()
x =[]
y =[]
z =[]
atomName =[]
resName = []
amino = []
currentRes = point_resNum[0]
for i in range(0, len(point_x)):
if (point_resNum[i]==currentRes):
x.append(point_x[i])
y.append(point_y[i])
z.append(point_z[i])
temp = point_atomName[i]
temp2 = temp.strip()
atomName.append(temp2)
resName.append(point_resName[i])
else:
currentRes = point_resNum[i]
amino.append(x[:])
amino.append(y[:])
amino.append(z[:])
amino.append(atomName[:])
amino.append(resName[:])
self.allResidues.append(amino[:])
del amino[:]
del x[:]
del y[:]
del z[:]
del atomName[:]
del resName[:]
x.append(point_x[i])
y.append(point_y[i])
z.append(point_z[i])
temp = point_atomName[i]
temp2 = temp.strip()
atomName.append(temp2)
resName.append(point_resName[i])
if (i == (len(point_x)-1)):
amino.append(x[:])
amino.append(y[:])
amino.append(z[:])
amino.append(atomName[:])
amino.append(resName[:])
self.allResidues.append(amino[:])
break
def buildResList(
self
): # calls PDBReader to read the given pdb file and create a list (self.allResidues) of lists (x,y,z,atom name, residue name) of lists (all the values for that residue)
self.allResidues = []
try:
f = open(self.fName)
f.close()
except IOError:
print("Sorry, the file name \"" + str(self.fName) +
"\" does not exist")
sys.exit()
self.a = PDBReader()
self.a.read_from_pdb(self.fName)
point_x = self.a.get_x()
point_y = self.a.get_y()
point_z = self.a.get_z()
point_atomName = self.a.get_atomName()
point_resName = self.a.get_resName()
point_resNum = self.a.get_resNum()
x = []
y = []
z = []
atomName = []
resName = []
amino = []
currentRes = point_resNum[0]
for i in range(0, len(point_x)):
if (point_resNum[i] == currentRes):
x.append(point_x[i])
y.append(point_y[i])
z.append(point_z[i])
temp = point_atomName[i]
temp2 = temp.strip()
atomName.append(temp2)
resName.append(point_resName[i])
else:
currentRes = point_resNum[i]
amino.append(x[:])
amino.append(y[:])
amino.append(z[:])
amino.append(atomName[:])
amino.append(resName[:])
self.allResidues.append(amino[:])
del amino[:]
del x[:]
del y[:]
del z[:]
del atomName[:]
del resName[:]
x.append(point_x[i])
y.append(point_y[i])
z.append(point_z[i])
temp = point_atomName[i]
temp2 = temp.strip()
atomName.append(temp2)
resName.append(point_resName[i])
if (i == (len(point_x) - 1)):
amino.append(x[:])
amino.append(y[:])
amino.append(z[:])
amino.append(atomName[:])
amino.append(resName[:])
self.allResidues.append(amino[:])
break
class EMPDBModel(EM3DModel):
def __init__(self, gl_widget):
self.fName = ""
self.text = self.fName
self.dl = None
EM3DModel.__init__(self, gl_widget)
# basic shapes will be stored in these lists
self.gq = None # will be a glu quadric
self.cylinderdl = 0 # will be a cylinder with no caps
self.diskdl = 0 # this will be a flat disk
self.spheredl = 0 # this will be a low resolution sphere
self.highresspheredl = 0 # high resolution sphere
self.cappedcylinderdl = 0 # a capped cylinder
self.first_render_flag = True # this is used to catch the first call to the render function - so you can do an GL context sensitive initialization when you know there is a valid context
self.inspector = None # will be the inspector
self.radius = 100
self.perspective = False
self.colors = get_default_gl_colors()
self.vdtools = EMViewportDepthTools(self)
self.cam = Camera2(self)
self.cam.basicmapping = True #new by Ross
self.side_chain_renderer = {}
self.side_chain_renderer["ALA"] = AlaRenderer()
self.side_chain_renderer["ARG"] = ArgRenderer()
self.side_chain_renderer["ASP"] = AspRenderer()
self.side_chain_renderer["ASN"] = AsnRenderer()
self.side_chain_renderer["CYS"] = CysRenderer()
self.side_chain_renderer["GLY"] = GlyRenderer()
self.side_chain_renderer["GLN"] = GlnRenderer()
self.side_chain_renderer["GLU"] = GluRenderer()
self.side_chain_renderer["HIS"] = HisRenderer()
self.side_chain_renderer["ILE"] = IleRenderer()
self.side_chain_renderer["LEU"] = LeuRenderer()
self.side_chain_renderer["LYS"] = LysRenderer()
self.side_chain_renderer["MET"] = MetRenderer()
self.side_chain_renderer["PHE"] = PheRenderer()
self.side_chain_renderer["PRO"] = ProRenderer()
self.side_chain_renderer["SER"] = SerRenderer()
self.side_chain_renderer["THR"] = ThrRenderer()
self.side_chain_renderer["TRP"] = TrpRenderer()
self.side_chain_renderer["TYR"] = TyrRenderer()
self.side_chain_renderer["VAL"] = ValRenderer()
def buildResList (self): # calls PDBReader to read the given pdb file and create a list (self.allResidues) of lists (x,y,z,atom name, residue name) of lists (all the values for that residue)
self.allResidues = []
try:
f = open(self.fName)
f.close()
except IOError:
print "Sorry, the file name \"" + str(self.fName) + "\" does not exist"
sys.exit()
self.a = PDBReader()
self.a.read_from_pdb(self.fName)
point_x = self.a.get_x()
point_y = self.a.get_y()
point_z = self.a.get_z()
point_atomName = self.a.get_atomName()
point_resName = self.a.get_resName()
point_resNum = self.a.get_resNum()
x =[]
y =[]
z =[]
atomName =[]
resName = []
amino = []
currentRes = point_resNum[0]
for i in range(0, len(point_x)):
if (point_resNum[i]==currentRes):
x.append(point_x[i])
y.append(point_y[i])
z.append(point_z[i])
temp = point_atomName[i]
temp2 = temp.strip()
atomName.append(temp2)
resName.append(point_resName[i])
else:
currentRes = point_resNum[i]
amino.append(x[:])
amino.append(y[:])
amino.append(z[:])
amino.append(atomName[:])
amino.append(resName[:])
self.allResidues.append(amino[:])
del amino[:]
del x[:]
del y[:]
del z[:]
del atomName[:]
del resName[:]
x.append(point_x[i])
y.append(point_y[i])
z.append(point_z[i])
temp = point_atomName[i]
temp2 = temp.strip()
atomName.append(temp2)
resName.append(point_resName[i])
if (i == (len(point_x)-1)):
amino.append(x[:])
amino.append(y[:])
amino.append(z[:])
amino.append(atomName[:])
amino.append(resName[:])
self.allResidues.append(amino[:])
break
def createDefault(self):
return #display a default pdb here, currently not done
def current_text(self): return self.text
def cylinder_to_from(self,next,prev,scale=0.5):
dx = next[0] - prev[0]
dy = next[1] - prev[1]
dz = next[2] - prev[2]
from math import sqrt,acos,atan2,pi
try:
length = sqrt(dx**2 + dy**2 + dz**2)
except: return
if length == 0: return
alt = acos(dz/length)*180.0/pi
phi = atan2(dy,dx)*180.0/pi
glPushMatrix()
glTranslatef(prev[0],prev[1],prev[2] )
glRotatef(90+phi,0,0,1)
glRotatef(alt,1,0,0)
glScalef(scale,scale,length)
self.load_gl_color("silver")
glCallList(self.cylinderdl)
glPopMatrix()
def draw_objects(self):
self.init_basic_shapes() # only does something the first time you call it
if (self.text == ""):
#default drawing
self.createDefault()
return
#self.get_gl_widget().makeCurrent()
if (self.text != self.fName):
if (self.dl != None): glDeleteLists(self.dl, 1)
self.dl=None
self.fName = self.text
if (self.dl == None): #self.dl is the display list, every time a new file is added, this is changed back to None
self.dl=glGenLists(1)
glNewList(self.dl,GL_COMPILE)
self.buildResList()
for res in self.allResidues: #goes through self.allResidues and displays a sphere for every atom in the pdb
for i in range (0, len(res[0])):
glPushMatrix()
glTranslate(res[0][i], res[1][i], res[2][i])
glScale(1,1,1)
if (str(res[3][i])[0] == 'C'): self.load_gl_color("white")
elif (str(res[3][i])[0] == 'N'): self.load_gl_color("green")
elif (str(res[3][i])[0] == 'O'): self.load_gl_color("blue")
elif (str(res[3][i])[0] == 'S'): self.load_gl_color("red")
else: self.load_gl_color("silver")
glCallList(self.highresspheredl)
glPopMatrix()
# self.load_gl_color("silver")
for k in range (0, len(self.allResidues)):
res = self.allResidues[k]
key = res[4][0]
if self.side_chain_renderer.has_key(key): #goes through each residue and draws the newtwork of sticks connecting atoms
self.side_chain_renderer[key](res,self)
continue
if (k!=0): #connects residues together from the nitrogen of one residue to the O of the next residue
nt = [0,0,0]
pt = [0,0,0]
nt[0] = res[0][0]
nt[1] = res[1][0]
nt[2] = res[2][0]
pt[0] = self.allResidues[(k-1)][0][2]
pt[1] = self.allResidues[(k-1)][1][2]
pt[2] = self.allResidues[(k-1)][2][2]
self.cylinder_to_from(nt, pt, 0.2)
glEndList()
try: glCallList(self.dl)
except:
print "call list failed",self.dl
glDeleteLists(self.dl,1)
self.dl = None
def init_basic_shapes(self):
#self.get_gl_widget().makeCurrent()
if self.gq == None:
self.gq=gluNewQuadric() # a quadric for general use
gluQuadricDrawStyle(self.gq,GLU_FILL)
gluQuadricNormals(self.gq,GLU_SMOOTH)
gluQuadricOrientation(self.gq,GLU_OUTSIDE)
gluQuadricTexture(self.gq,GL_FALSE)
if ( self.cylinderdl == 0 ):
self.cylinderdl=glGenLists(1)
glNewList(self.cylinderdl,GL_COMPILE)
glPushMatrix()
gluCylinder(self.gq,1.0,1.0,1.0,12,2)
glPopMatrix()
glEndList()
if self.diskdl == 0:
self.diskdl=glGenLists(1)
glNewList(self.diskdl,GL_COMPILE)
gluDisk(self.gq,0,1,12,2)
glEndList()
if self.spheredl == 0:
self.spheredl=glGenLists(1)
glNewList(self.spheredl,GL_COMPILE)
gluSphere(self.gq,.5,4,2)
glEndList()
if self.highresspheredl == 0:
self.highresspheredl=glGenLists(1)
glNewList(self.highresspheredl,GL_COMPILE)
gluSphere(self.gq,.5,16,16)
glEndList()
if ( self.cappedcylinderdl == 0 ):
self.cappedcylinderdl=glGenLists(1)
glNewList(self.cappedcylinderdl,GL_COMPILE)
glCallList(self.cylinderdl)
glPushMatrix()
glTranslate(0,0,1)
glCallList(self.diskdl)
glPopMatrix()
glPushMatrix()
glRotate(180,0,1,0)
glCallList(self.diskdl)
glPopMatrix()
glEndList()
def get_inspector(self):
if self.inspector == None:
self.inspector = EMPDBInspector(self)
return self.inspector
def get_pdb_file(self):
return self.fName
def get_type(self):
return "EMPDBModel"
def load_gl_color(self,name):
color = self.colors[name]
glColor(color["ambient"])
glMaterial(GL_FRONT,GL_AMBIENT,color["ambient"])
glMaterial(GL_FRONT,GL_DIFFUSE,color["diffuse"])
glMaterial(GL_FRONT,GL_SPECULAR,color["specular"])
glMaterial(GL_FRONT,GL_EMISSION,color["emission"])
glMaterial(GL_FRONT,GL_SHININESS,color["shininess"])
def makeStick (self, res, index1, index2): #draws a cylinder between two atoms once the index for start and stop is given
n = [0,0,0]
p = [0,0,0]
p[0] = res[0][index1]
p[1] = res[1][index1]
p[2] = res[2][index1]
n[0] = res[0][index2]
n[1] = res[1][index2]
n[2] = res[2][index2]
self.cylinder_to_from(n, p, 0.2)
def render(self):
if self.first_render_flag:
if not self.perspective:self.get_gl_widget().load_orthographic()
else: self.get_gl_widget().load_perspective()
self.first_render_flag = False
#self.vdtools.set_update_P_inv()
glPushMatrix()
self.cam.position(True)
# the ones are dummy variables atm... they don't do anything
self.vdtools.update(1,1)
glPopMatrix()
glPushMatrix()
self.cam.position() #FIXME: figure out why translation doesn't work
self.draw_objects()
glPopMatrix()
def set_current_text(self,text): #changes self.text and updatesGL, when self.text changes, it redisplays using the new file
self.text = text
self.get_inspector().text.setText(self.text)
self.updateGL()
class EMPDBModel(EM3DModel):
def __init__(self, gl_widget):
self.fName = ""
self.text = self.fName
self.dl = None
EM3DModel.__init__(self, gl_widget)
# basic shapes will be stored in these lists
self.gq = None # will be a glu quadric
self.cylinderdl = 0 # will be a cylinder with no caps
self.diskdl = 0 # this will be a flat disk
self.spheredl = 0 # this will be a low resolution sphere
self.highresspheredl = 0 # high resolution sphere
self.cappedcylinderdl = 0 # a capped cylinder
self.first_render_flag = True # this is used to catch the first call to the render function - so you can do an GL context sensitive initialization when you know there is a valid context
self.inspector = None # will be the inspector
self.radius = 100
self.perspective = False
self.colors = get_default_gl_colors()
self.vdtools = EMViewportDepthTools(self)
self.cam = Camera2(self)
self.cam.basicmapping = True #new by Ross
self.side_chain_renderer = {}
self.side_chain_renderer["ALA"] = AlaRenderer()
self.side_chain_renderer["ARG"] = ArgRenderer()
self.side_chain_renderer["ASP"] = AspRenderer()
self.side_chain_renderer["ASN"] = AsnRenderer()
self.side_chain_renderer["CYS"] = CysRenderer()
self.side_chain_renderer["GLY"] = GlyRenderer()
self.side_chain_renderer["GLN"] = GlnRenderer()
self.side_chain_renderer["GLU"] = GluRenderer()
self.side_chain_renderer["HIS"] = HisRenderer()
self.side_chain_renderer["ILE"] = IleRenderer()
self.side_chain_renderer["LEU"] = LeuRenderer()
self.side_chain_renderer["LYS"] = LysRenderer()
self.side_chain_renderer["MET"] = MetRenderer()
self.side_chain_renderer["PHE"] = PheRenderer()
self.side_chain_renderer["PRO"] = ProRenderer()
self.side_chain_renderer["SER"] = SerRenderer()
self.side_chain_renderer["THR"] = ThrRenderer()
self.side_chain_renderer["TRP"] = TrpRenderer()
self.side_chain_renderer["TYR"] = TyrRenderer()
self.side_chain_renderer["VAL"] = ValRenderer()
def buildResList(
self
): # calls PDBReader to read the given pdb file and create a list (self.allResidues) of lists (x,y,z,atom name, residue name) of lists (all the values for that residue)
self.allResidues = []
try:
f = open(self.fName)
f.close()
except IOError:
print("Sorry, the file name \"" + str(self.fName) +
"\" does not exist")
sys.exit()
self.a = PDBReader()
self.a.read_from_pdb(self.fName)
point_x = self.a.get_x()
point_y = self.a.get_y()
point_z = self.a.get_z()
point_atomName = self.a.get_atomName()
point_resName = self.a.get_resName()
point_resNum = self.a.get_resNum()
x = []
y = []
z = []
atomName = []
resName = []
amino = []
currentRes = point_resNum[0]
for i in range(0, len(point_x)):
if (point_resNum[i] == currentRes):
x.append(point_x[i])
y.append(point_y[i])
z.append(point_z[i])
temp = point_atomName[i]
temp2 = temp.strip()
atomName.append(temp2)
resName.append(point_resName[i])
else:
currentRes = point_resNum[i]
amino.append(x[:])
amino.append(y[:])
amino.append(z[:])
amino.append(atomName[:])
amino.append(resName[:])
self.allResidues.append(amino[:])
del amino[:]
del x[:]
del y[:]
del z[:]
del atomName[:]
del resName[:]
x.append(point_x[i])
y.append(point_y[i])
z.append(point_z[i])
temp = point_atomName[i]
temp2 = temp.strip()
atomName.append(temp2)
resName.append(point_resName[i])
if (i == (len(point_x) - 1)):
amino.append(x[:])
amino.append(y[:])
amino.append(z[:])
amino.append(atomName[:])
amino.append(resName[:])
self.allResidues.append(amino[:])
break
def createDefault(self):
return #display a default pdb here, currently not done
def current_text(self):
return self.text
def cylinder_to_from(self, next, prev, scale=0.5):
dx = next[0] - prev[0]
dy = next[1] - prev[1]
dz = next[2] - prev[2]
from math import sqrt, acos, atan2, pi
try:
length = sqrt(dx**2 + dy**2 + dz**2)
except:
return
if length == 0: return
alt = acos(old_div(dz, length)) * 180.0 / pi
phi = atan2(dy, dx) * 180.0 / pi
glPushMatrix()
glTranslatef(prev[0], prev[1], prev[2])
glRotatef(90 + phi, 0, 0, 1)
glRotatef(alt, 1, 0, 0)
glScalef(scale, scale, length)
self.load_gl_color("silver")
glCallList(self.cylinderdl)
glPopMatrix()
def draw_objects(self):
self.init_basic_shapes(
) # only does something the first time you call it
if (self.text == ""):
#default drawing
self.createDefault()
return
#self.get_gl_widget().makeCurrent()
if (self.text != self.fName):
if (self.dl != None): glDeleteLists(self.dl, 1)
self.dl = None
self.fName = self.text
if (
self.dl == None
): #self.dl is the display list, every time a new file is added, this is changed back to None
self.dl = glGenLists(1)
glNewList(self.dl, GL_COMPILE)
self.buildResList()
for res in self.allResidues: #goes through self.allResidues and displays a sphere for every atom in the pdb
for i in range(0, len(res[0])):
glPushMatrix()
glTranslate(res[0][i], res[1][i], res[2][i])
glScale(1, 1, 1)
if (str(res[3][i])[0] == 'C'): self.load_gl_color("white")
elif (str(res[3][i])[0] == 'N'):
self.load_gl_color("green")
elif (str(res[3][i])[0] == 'O'):
self.load_gl_color("blue")
elif (str(res[3][i])[0] == 'S'):
self.load_gl_color("red")
else:
self.load_gl_color("silver")
glCallList(self.highresspheredl)
glPopMatrix()
# self.load_gl_color("silver")
for k in range(0, len(self.allResidues)):
res = self.allResidues[k]
key = res[4][0]
if key in self.side_chain_renderer: #goes through each residue and draws the network of sticks connecting atoms
self.side_chain_renderer[key](res, self)
continue
if (
k != 0
): #connects residues together from the nitrogen of one residue to the O of the next residue
nt = [0, 0, 0]
pt = [0, 0, 0]
nt[0] = res[0][0]
nt[1] = res[1][0]
nt[2] = res[2][0]
pt[0] = self.allResidues[(k - 1)][0][2]
pt[1] = self.allResidues[(k - 1)][1][2]
pt[2] = self.allResidues[(k - 1)][2][2]
self.cylinder_to_from(nt, pt, 0.2)
glEndList()
try:
glCallList(self.dl)
except:
print("call list failed", self.dl)
glDeleteLists(self.dl, 1)
self.dl = None
def init_basic_shapes(self):
#self.get_gl_widget().makeCurrent()
if self.gq == None:
self.gq = gluNewQuadric() # a quadric for general use
gluQuadricDrawStyle(self.gq, GLU_FILL)
gluQuadricNormals(self.gq, GLU_SMOOTH)
gluQuadricOrientation(self.gq, GLU_OUTSIDE)
gluQuadricTexture(self.gq, GL_FALSE)
if (self.cylinderdl == 0):
self.cylinderdl = glGenLists(1)
glNewList(self.cylinderdl, GL_COMPILE)
glPushMatrix()
gluCylinder(self.gq, 1.0, 1.0, 1.0, 12, 2)
glPopMatrix()
glEndList()
if self.diskdl == 0:
self.diskdl = glGenLists(1)
glNewList(self.diskdl, GL_COMPILE)
gluDisk(self.gq, 0, 1, 12, 2)
glEndList()
if self.spheredl == 0:
self.spheredl = glGenLists(1)
glNewList(self.spheredl, GL_COMPILE)
gluSphere(self.gq, .5, 4, 2)
glEndList()
if self.highresspheredl == 0:
self.highresspheredl = glGenLists(1)
glNewList(self.highresspheredl, GL_COMPILE)
gluSphere(self.gq, .5, 16, 16)
glEndList()
if (self.cappedcylinderdl == 0):
self.cappedcylinderdl = glGenLists(1)
glNewList(self.cappedcylinderdl, GL_COMPILE)
glCallList(self.cylinderdl)
glPushMatrix()
glTranslate(0, 0, 1)
glCallList(self.diskdl)
glPopMatrix()
glPushMatrix()
glRotate(180, 0, 1, 0)
glCallList(self.diskdl)
glPopMatrix()
glEndList()
def get_inspector(self):
if self.inspector == None:
self.inspector = EMPDBInspector(self)
return self.inspector
def get_pdb_file(self):
return self.fName
def get_type(self):
return "EMPDBModel"
def load_gl_color(self, name):
color = self.colors[name]
glColor(color["ambient"])
glMaterial(GL_FRONT, GL_AMBIENT, color["ambient"])
glMaterial(GL_FRONT, GL_DIFFUSE, color["diffuse"])
glMaterial(GL_FRONT, GL_SPECULAR, color["specular"])
glMaterial(GL_FRONT, GL_EMISSION, color["emission"])
glMaterial(GL_FRONT, GL_SHININESS, color["shininess"])
def makeStick(
self, res, index1, index2
): #draws a cylinder between two atoms once the index for start and stop is given
n = [0, 0, 0]
p = [0, 0, 0]
p[0] = res[0][index1]
p[1] = res[1][index1]
p[2] = res[2][index1]
n[0] = res[0][index2]
n[1] = res[1][index2]
n[2] = res[2][index2]
self.cylinder_to_from(n, p, 0.2)
def render(self):
if self.first_render_flag:
if not self.perspective: self.get_gl_widget().load_orthographic()
else: self.get_gl_widget().load_perspective()
self.first_render_flag = False
#self.vdtools.set_update_P_inv()
glPushMatrix()
self.cam.position(True)
# the ones are dummy variables atm... they don't do anything
self.vdtools.update(1, 1)
glPopMatrix()
glPushMatrix()
self.cam.position() #FIXME: figure out why translation doesn't work
self.draw_objects()
glPopMatrix()
def set_current_text(
self, text
): #changes self.text and updatesGL, when self.text changes, it redisplays using the new file
self.text = text
self.get_inspector().text.setText(self.text)
self.updateGL()