def alignsg(sele):
allsg = cmd.get_model("(("+sele+") and (name VSG))").atom
allsf = cmd.get_model("(("+sele+") and (name S5,S6,S7,S8))").atom
while allsg:
closest = [9e9,None,None]
for sga in allsg:
for sfa in allsf:
sg = Vec(sga.coord)
sf = Vec(sfa.coord)
if (sg-sf).length() < closest[0]:
closest = [(sg-sf).length(),sga,sfa]
sga,sfa = closest[1:]
allsg.remove(sga)
allsf.remove(sfa)
if closest[0] > 10.0: break
cmd.do("alter_state 1, (("+sele+") and (resi %s and name %s))"%(sga.resi,sga.name)+",x=%f"%sfa.coord[0])
cmd.do("alter_state 1, (("+sele+") and (resi %s and name %s))"%(sga.resi,sga.name)+",y=%f"%sfa.coord[1])
cmd.do("alter_state 1, (("+sele+") and (resi %s and name %s))"%(sga.resi,sga.name)+",z=%f"%sfa.coord[2])
def alignsg(sele):
allsg = cmd.get_model("((" + sele + ") and (name VSG))").atom
allsf = cmd.get_model("((" + sele + ") and (name S5,S6,S7,S8))").atom
while allsg:
closest = [9e9, None, None]
for sga in allsg:
for sfa in allsf:
sg = Vec(sga.coord)
sf = Vec(sfa.coord)
if (sg - sf).length() < closest[0]:
closest = [(sg - sf).length(), sga, sfa]
sga, sfa = closest[1:]
allsg.remove(sga)
allsf.remove(sfa)
if closest[0] > 10.0: break
cmd.do("alter_state 1, ((" + sele + ") and (resi %s and name %s))" %
(sga.resi, sga.name) + ",x=%f" % sfa.coord[0])
cmd.do("alter_state 1, ((" + sele + ") and (resi %s and name %s))" %
(sga.resi, sga.name) + ",y=%f" % sfa.coord[1])
cmd.do("alter_state 1, ((" + sele + ") and (resi %s and name %s))" %
(sga.resi, sga.name) + ",z=%f" % sfa.coord[2])
def set_rotamer(sel, chi1, chi2=0,chi3=0,chi4=0):
at = cmd.get_model("byres ("+sel+")").atom[0]
list = [chi1,chi2,chi3,chi4]
for i in range(len(CHIS[at.resn])):
print "Setting Chi"+str(i+1)+" to "+str(list[i])
editing.set_dihedral(sel + ' and name '+CHIS[at.resn][i][0],
sel + ' and name '+CHIS[at.resn][i][1],
sel + ' and name '+CHIS[at.resn][i][2],
sel + ' and name '+CHIS[at.resn][i][3], str(list[i]))
# Remove some objects that got created
cmd.delete("pk1")
cmd.delete("pk2")
cmd.delete("pkmol")
def createAtomAlongBond(modelName, distance, resiA, atomNameA, resiB, atomNameB, atomNameC):
model = cmd.get_model(modelName)
p1 = getAtomCoords(model, str(resiA), atomNameA)
p2 = getAtomCoords(model, str(resiB), atomNameB)
if p1 is None:
print "atom not found!", modelName, resiA, atomNameA
elif p2 is None:
print "atom not found!", modelName, resiB, atomNameB
else:
p3 = calculateNewPoint(p1, p2, distance)
# the details of the new atom
atomDetails = {}
atomDetails['residueName'] = "HOH"
atomDetails['residueNumber'] = "1"
atomDetails['symbol'] = "O"
atomDetails['name'] = atomNameC
atomDetails['coords'] = p3
# make an atom with index n+1 and chain "X"
newAtom = makeAtom(model.nAtom + 1, atomDetails, "X")
model.add_atom(newAtom)
model.update_index()
cmd.load_model(model, "newpeptide")
def createRotamerPDBs(sel,ncutoff=10,pcutoff=0,prefix="ROTAMER"):
# Get atoms from selection
atoms = cmd.get_model("byres ("+sel+")")
# Set up some variables..
residues = ['dummy'] # Keep track of residues already done
# Loop through atoms in selection
for at in atoms.atom:
if at.resn in ('GLY','ALA') or "%s:%s:%s" % (at.chain,at.resn,at.resi) in residues:
continue
# Add to residue list (keep track of which ones we've done)
residues.append("%s:%s:%s" % (at.chain,at.resn,at.resi))
# Check for a null chain id (some PDBs contain this)
unit_select = ""
if not at.chain == "":
unit_select = "chain "+str(at.chain)+" and "
# Define selections for residue
residue_def = unit_select+'resi '+str(at.resi)
# Get bin (phi,psi) definitions for this residue
bin = doRotamers(residue_def, type='bins')
# Store crystal angle
crystal_angles = [0.0,0.0,0.0,0.0]
for angle in range(3):
try:
crystal_angles[angle] = bin[3][angle]
except IndexError:
break
# Retreive list of rotamers for this phi,psi bin + residue type
match_rotamers = rotdat["%s:%s:%s" % (bin[0],str(bin[1]),str(bin[2]))]
count = 0
for item in range(len(match_rotamers)):
# Store probablity
prob = match_rotamers[item][0]
# Check cutoffs
if float(prob) <= float(pcutoff):
continue
if float(count) >= float(ncutoff):
break
# Increment count
count += 1
# Output to screen ...
print "Residue %s%s, rotamer %i, prob %s" % (str(at.resn),str(at.resi),int(item),str(prob))
# Set to new rotamer
set_rotamer(residue_def,match_rotamers[item][1],match_rotamers[item][2],match_rotamers[item][3],match_rotamers[item][4])
# Store in PDB file
cmd.save("%s_%s%s_%i_%s.pdb" % (prefix,str(at.resn),str(at.resi),int(item),str(prob)))
# Reset crystal angle
set_rotamer(residue_def,crystal_angles[0],crystal_angles[1],crystal_angles[2],crystal_angles[3])
def doRotamers(sel,angles=[], type="color"):
# Read in Rotamer library if not already done
if len(rotdat) == 0:
readRotLib()
# Set up some variables..
residues = ['dummy'] # Keep track of residues already done
probs = [] # probability of each residue conformation
phi = 0 # phi,psi angles of current residue
psi = 0
# Get atoms from selection
atoms = cmd.get_model("byres ("+sel+")")
# Loop through atoms in selection
for at in atoms.atom:
try:
# Don't process Glycines or Alanines
if not (at.resn == 'GLY' or at.resn == 'ALA'):
if at.chain+":"+at.resn+":"+at.resi not in residues:
residues.append(at.chain+":"+at.resn+":"+at.resi)
# Check for a null chain id (some PDBs contain this)
unit_select = ""
if at.chain != "":
unit_select = "chain "+str(at.chain)+" and "
# Define selections for residue i-1, i and i+1
residue_def = unit_select+'resi '+str(at.resi)
residue_def_prev = unit_select+'resi '+str(int(at.resi)-1)
residue_def_next = unit_select+'resi '+str(int(at.resi)+1)
# Compute phi/psi angle
phi = cmd.get_dihedral(residue_def_prev+' and name C',residue_def+' and name N',residue_def+' and name CA',residue_def+' and name C')
psi = cmd.get_dihedral(residue_def+' and name N',residue_def+' and name CA',residue_def+' and name C',residue_def_next+' and name N')
if type == "set":
print "Changing "+at.resn+str(at.resi)+" from "+str(phi)+","+str(psi)+" to "+str(angles[0])+","+str(angles[1])
cmd.set_dihedral(residue_def_prev+' and name C',residue_def+' and name N',residue_def+' and name CA',residue_def+' and name C',angles[0])
cmd.set_dihedral(residue_def+' and name N',residue_def+' and name CA',residue_def+' and name C',residue_def_next+' and name N', angles[1])
continue
# Find correct 10x10 degree bin
phi_digit = abs(int(phi)) - abs(int(phi/10)*10)
psi_digit = abs(int(psi)) - abs(int(psi/10)*10)
# Remember sign of phi,psi angles
phi_sign = 1
if phi < 0: phi_sign = -1
psi_sign = 1
if psi < 0: psi_sign = -1
# Compute phi,psi bins
phi_bin = int(math.floor(abs(phi/10))*10*phi_sign)
if phi_digit >= 5: phi_bin = int(math.ceil(abs(phi/10))*10*phi_sign)
psi_bin = int(math.floor(abs(psi/10))*10*psi_sign)
if psi_digit >= 5: psi_bin = int(math.ceil(abs(psi/10))*10*psi_sign)
print "Given "+at.resn+":"+at.resi+" PHI,PSI ("+str(phi)+","+str(psi)+") : bin ("+str(phi_bin)+","+str(psi_bin)+")"
# Get current chi angle measurements
chi = []
for i in range(len(CHIS[at.resn])):
chi.append(cmd.get_dihedral(residue_def + ' and name '+CHIS[at.resn][i][0],
residue_def + ' and name '+CHIS[at.resn][i][1],
residue_def + ' and name '+CHIS[at.resn][i][2],
residue_def + ' and name '+CHIS[at.resn][i][3]))
print "CHIs: "+str(chi)
if type == 'bins':
return [at.resn, phi_bin,psi_bin]
# Compute probabilities for given chi angles
prob = 0
prob_box = 22
for item in range(len(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)])):
print "Rotamer from db: "+str(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item])
if chi[0]:
if chi[0] >= float(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][1]) - (prob_box/2) and \
chi[0] <= float(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][1]) + (prob_box/2):
if len(chi) == 1:
prob = rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][0]
break
if chi[1] >= float(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][2]) - (prob_box/2) and \
float(chi[1] <= rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][2]) + (prob_box/2):
if len(chi) == 2:
prob = rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][0]
break
if chi[2] >= float(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][3]) - (prob_box/2) and \
float(chi[2] <= rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][3]) + (prob_box/2):
if len(chi) == 3:
prob = rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][0]
break
if chi[3] >= float(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][4]) - (prob_box/2) and \
float(chi[3] <= rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][4]) + (prob_box/2):
prob = rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][0]
break
print "PROB OF ROTAMER: "+str(prob)
print "---------------------------"
probs.append([residue_def, prob])
except:
# probs.append([residue_def, -1])
print "Exception found"
continue
# Color according to rotamer probability
rot_color(probs)
'cmd.get_names()' ,
'cmd.delete("all")' ,
'cmd.get_names()' ,
'cmd.get_model("nonexistent")' ,
'cmd.space("cmyk")',
'cmd.space("unknown")',
'cmd.space("rgb")',
'cmd.space()',
])
cmd.delete("all")
cmd.load("dat/pept.pdb")
mdl = cmd.get_model("pept")
print mdl.__class__
print len(mdl.atom)
mdl = cmd.get_model("none")
print mdl.__class__
print len(mdl.atom)
map( x, [
'cmd.get_model("nonexistent")',
'cmd.create("test","none",quiet=0)',
'cmd.create("test2","nonexistent")',
'cmd.create("test3","?allowed",quiet=0)',
'cmd.fragment("arg")',
'cmd.fragment("nonexistent")',
])
