def save_mol_as(root,mollist,gfx):
if mollist.curselection()==():
MB.showwarning('Info','Select a molecule in Mol List for saving it')
return
for molit in mollist.curselection():
for mol in gfx.mol:
if mollist.get(molit)==mol.un:
fn = FD.asksaveasfilename(parent=root,filetypes=[('PDB files','*.pdb')] ,title="Save molecule %s coordinates as..."%mol.un)
if len(fn ) > 0:
if not fn.endswith('.pdb'):
fn = fn +'.pdb'
mat = mol.acteur.GetMatrix() #recuperation de la mat de pv 4x4
R = array(sym.ExtractRotMat(mat)) #extraction de la matrice de rotation depuit la vtk 4x4
t = array([mat.GetElement(0,3),mat.GetElement(1,3),mat.GetElement(2,3)]) #extract tx,ty,tz
pdbin=open(mol.mod.fn,"r")
pdbout=open(fn,"w")
for ligne in pdbin:
if (ligne[0:6] == "ATOM " or ligne[0:6] == "HETATM"):
x = float(ligne[30:38])
y = float(ligne[38:46])
z = float(ligne[46:54])
r = array([x,y,z])
newr = dot(R,r) + t
ligne=ligne[:30]+"%8.3f%8.3f%8.3f"%tuple(newr)+ligne[54:]
pdbout.write(ligne)
#ferme les fichiers
pdbin.close()
pdbout.close()
return
def frame(self):
mol = self.gfx.mol[self.gfx.whichmol - 1]
mat = mol.acteur.GetMatrix()
(a, b, g) = sym.R2Eul(sym.ExtractRotMat(mat))
(x, y, z) = [
mat.GetElement(0, 3),
mat.GetElement(1, 3),
mat.GetElement(2, 3)
]
return '%.3f %.3f %.3f %.3f %.3f %.3f \n' % (a, b, g, x, y, z)
def build_fitin_file(self):
go = open('G0', 'w')
for mol in self.gfx.mol:
mat = mol.acteur.GetMatrix()
nbsymop = len(mol.lnbsm)
strsymlist = str(mol.lnbsm)[1:-1].replace(',', '')
(a, b, g) = sym.R2Eul(sym.ExtractRotMat(mat))
(x, y, z) = [
mat.GetElement(0, 3),
mat.GetElement(1, 3),
mat.GetElement(2, 3)
]
go.write(' #%2d %.3f %.3f %.3f %.3f %.3f %.3f %d %s\n' %
(mol.mod.id, a, b, g, x, y, z, nbsymop, strsymlist))
go.close()
def fitin_io(p, mol):
mat = mol.acteur.GetMatrix()
(a, b, g) = sym.R2Eul(sym.ExtractRotMat(mat))
(x, y,
z) = [mat.GetElement(0, 3),
mat.GetElement(1, 3),
mat.GetElement(2, 3)]
frame = '%.3f %.3f %.3f %.3f %.3f %.3f \n' % (a, b, g, x, y, z)
try:
p.stdin.write(frame)
l = p.stdout.read(77)
return float(l.split()[-1])
except:
MB.showwarning(
'Error',
'Problem in function ccprofile, process fitin must be dead ... RIP'
)
def build_nm_fitin_file(self):
no = open('N0', 'w')
for mol in self.gfx.mol:
mat = mol.acteur.GetMatrix()
nbsymop = len(mol.lnbsm)
strsymlist = str(mol.lnbsm)[1:-1].replace(',', '')
(a, b, g) = sym.R2Eul(sym.ExtractRotMat(mat))
(x, y, z) = [
mat.GetElement(0, 3),
mat.GetElement(1, 3),
mat.GetElement(2, 3)
]
if mol.id == self.currentmol.id:
cur = ' #%2d %.3f %.3f %.3f %.3f %.3f %.3f %d %s\n' % (
33, a, b, g, x, y, z, nbsymop, strsymlist)
else:
no.write(' #%2d %.3f %.3f %.3f %.3f %.3f %.3f %d %s\n' %
(mol.mod.id, a, b, g, x, y, z, nbsymop, strsymlist))
no.write(cur)
no.close()
def save_conf_as(self, gfx):
conf = self.currentmol.nmcl[self.gfx.itf.varconformerSitu.get() +
self.nbstep]
fn = FD.asksaveasfilename(
parent=self.gfx.itf.root,
filetypes=[('PDB files', '*.pdb')],
title="Save conformer %d coordinates as..." %
(self.gfx.itf.varconformerSitu.get() + self.nbstep))
if len(fn) > 0:
if not fn.endswith('.pdb'):
fn = fn + '.pdb'
mat = conf.GetMatrix() #recuperation de la mat de pv 4x4
R = array(sym.ExtractRotMat(
mat)) #extraction de la matrice de rotation depuit la vtk 4x4
t = array([
mat.GetElement(0, 3),
mat.GetElement(1, 3),
mat.GetElement(2, 3)
]) #extract tx,ty,tz
pdbin = open(
gfx.tmpdir + '/%s/' % self.currentmol.mod.un + 'out%s' %
(self.gfx.itf.varconformerSitu.get()), "r")
pdbout = open(fn, "w")
for ligne in pdbin:
if (ligne[0:6] == "ATOM " or ligne[0:6] == "HETATM"):
x = float(ligne[30:38])
y = float(ligne[38:46])
z = float(ligne[46:54])
r = array([x, y, z])
newr = dot(R, r) + t
ligne = ligne[:30] + "%8.3f%8.3f%8.3f" % tuple(
newr) + ligne[54:]
pdbout.write(ligne)
pdbin.close()
pdbout.close()
return
def cc_profile(gfx, mollist, anglemin, anglemax, step, axe):
if gfx.ifit != None:
MB.showwarning('Info', 'Stop Interactve Fitting')
return
for mol in gfx.mol:
if mollist.get(tk.ACTIVE) == mol.un:
chdir(gfx.workdir)
gfx.fit.build_fitin_file()
init_ifit_file(gfx, gfx.fit.fitreslow, gfx.fit.fitreshigh)
p = Popen(['e/fitin', 'G0'],
bufsize=0,
stdin=PIPE,
stdout=PIPE,
stderr=PIPE,
universal_newlines=True)
print 'Automatic Sampling Started'
profile = open('%s.%s.profile' % (axe, mol.un), 'w')
p.stdin.write('#%2d \n' % mol.id)
l = p.stdout.read(31)
print l
if axe == 'X':
v = (1, 0, 0)
elif axe == 'Y':
v = (0, 1, 0)
elif axe == 'Z':
v = (0, 0, 1)
else:
print 'strange axe ...'
return
mat = mol.acteur.GetMatrix()
mat3x3 = sym.ExtractRotMat(mat)
R = array(mat3x3)
ivect = dot(R, v)
(sa, sb, sg) = sym.R2Eul(mat3x3)
angle = anglemin
while angle < anglemax:
gfx.sym.render = 0
mol.acteur.SetOrientation(0, 0, 0)
RotaEuler(mol.acteur, sa, sb, sg)
gfx.sym.render = 1
mol.acteur.RotateWXYZ(angle, ivect[0], ivect[1], ivect[2])
cc = fitin_io(p, mol)
try:
print '%f %f' % (angle, cc)
except TypeError:
MB.showwarning(
'Error',
'cc_profile : Interactive Fitting encountered a problem; go to help'
)
return
profile.write('%f %f \n' % (angle, cc))
angle += step
profile.close()
gfx.sym.render = 0
mol.acteur.SetOrientation(0, 0, 0)
RotaEuler(mol.acteur, sa, sb, sg)
gfx.renwin.Render()
gfx.sym.render = 1
try:
p.stdin.write('\n')
except:
MB.showwarning(
'Error',
'cc_profile : Interactive Fitting terminated badly')
print 'Automatic Sampling Stopped'
system("gnuplot -persist <<ENDOF\n plot '%s' with line\nENDOF" %
'%s.%s.profile' % (axe, mol.un))
def printmolpv(gfx): for mol in gfx.mol: mat=mol.acteur.GetMatrix() (a,b,g) = sym.R2Eul(sym.ExtractRotMat(mat)) (x,y,z) = [mat.GetElement(0,3),mat.GetElement(1,3),mat.GetElement(2,3)] print' mol : %d : %.3f %.3f %.3f %.3f %.3f %.3f\n'%(mol.id,a,b,g,x,y,z)