def phipsi(selection="(pk1)",_self=cmd):
pymol=_self._pymol
cmd=_self # NOT THREAD SAFE
n_sele = "((byres (%s)) & name n)"%selection
c_sele = "((byres (%s)) & name c)"%selection
ca_sele = "((byres (%s)) & name ca)"%selection
cm_sele = "((neighbor (%s)) and not (byres (%s)))"%(n_sele,n_sele)
np_sele = "((neighbor (%s)) and not (byres (%s)))"%(c_sele,c_sele)
cmd.feedback("push")
cmd.feedback("disable","selector","everythin")
cm_cnt = cmd.select("_pp_cm",cm_sele)
n_cnt = cmd.select("_pp_n",n_sele)
c_cnt = cmd.select("_pp_c",c_sele)
ca_cnt = cmd.select("_pp_ca",ca_sele)
np_cnt = cmd.select("_pp_np",np_sele)
if(cm_cnt and n_cnt and ca_cnt and c_cnt):
phi = cmd.get_dihedral("_pp_c","_pp_ca","_pp_n","_pp_cm")
else:
phi = None
if(n_cnt and ca_cnt and c_cnt and np_cnt):
psi = cmd.get_dihedral("_pp_np","_pp_c","_pp_ca","_pp_n")
else:
psi = None
cmd.feedback("pop")
cmd.delete("_pp_cm")
cmd.delete("_pp_n")
cmd.delete("_pp_c")
cmd.delete("_pp_ca")
cmd.delete("_pp_np")
return (phi,psi)
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)