def phi_psi(selection="(byres pk1)", quiet=1, _self=cmd):
'''
DESCRIPTION
"phi_psi" return the phi and psi angles for a protein atom
selection.
USAGE
'''
r = cmd.get_phipsi(selection)
if r!=None:
kees = r.keys()
kees.sort()
if not quiet:
_self.feedback('push')
_self.feedback('disable','executive','actions')
for a in kees:
_self.iterate("(%s`%d)"%a,"print ' %-9s "+
("( %6.1f, %6.1f )"%r[a])+
"'%(resn+'-'+resi+':')")
_self.feedback('pop')
elif _feedback(fb_module.cmd,fb_mask.errors,_self):
print "cmd-Error: can't compute phi_psi"
if _raising(r,_self): raise pymol.CmdException
return r
def phi_psi(selection="(byres pk1)", quiet=1, _self=cmd):
'''
DESCRIPTION
"phi_psi" return the phi and psi angles for a protein atom
selection.
USAGE
'''
r = cmd.get_phipsi(selection)
if r != None:
kees = r.keys()
kees.sort()
if not quiet:
_self.feedback('push')
_self.feedback('disable', 'executive', 'actions')
for a in kees:
_self.iterate(
"(%s`%d)" % a, "print ' %-9s " +
("( %6.1f, %6.1f )" % r[a]) + "'%(resn+'-'+resi+':')")
_self.feedback('pop')
elif _feedback(fb_module.cmd, fb_mask.errors, _self):
print "cmd-Error: can't compute phi_psi"
if _raising(r, _self): raise pymol.CmdException
return r
def ss(selection="(name ca and alt '',A)",state=1,_self=cmd):
pymol=_self._pymol
cmd=_self # NOT THREAD SAFE
print ' util.ss: WARNING: This is not a "correct" secondary structure'
print ' util.ss: assignment algorithm! Please use only as a last resort.'
cmd.feedback("push")
cmd.feedback("disable","executive","actions")
ss_pref = "_sss"
sss1 = ss_pref+"1"
cnt = cmd.select(sss1,"((byres ("+selection+")) and name ca and not het)")
print " util.ss: initiating secondary structure assignment on %d residues."%cnt
cas = cmd.index(sss1)
if not len(cas):
return
# set cartoon mode to auto over the selection
cmd.cartoon("auto",sss1)
print " util.ss: extracting sequence and relationships..."
# get CA list
res_list = []
pymol._ss = pymol.Scratch_Storage()
pymol._ss.res_list = res_list
cmd.iterate(sss1,'_ss.res_list.append((model,index))')
# generate atom-to-residue conversion dictionaries
ca_dict = {}
n_dict = {}
o_dict = {}
scr_dict = {} # scr = segment,chain,resi
pymol._ss.n_dict = n_dict
pymol._ss.o_dict = o_dict
pymol._ss.scr_dict = scr_dict
pymol._ss.ca_dict = ca_dict
cmd.iterate(sss1,
'_ss.scr_dict[(model,index)]=(segi,chain,resi)') # CA's
cmd.iterate("((byres "+sss1+") and n;n)"
,'_ss.scr_dict[(model,index)]=(segi,chain,resi)') # N's
cmd.iterate("((byres "+sss1+") and n;o)",
'_ss.scr_dict[(model,index)]=(segi,chain,resi)') # O's
cmd.iterate(sss1,
'_ss.ca_dict[(segi,chain,resi)] = (model,index)')
cmd.iterate("((byres "+sss1+") and n;n)",
'_ss.n_dict[(segi,chain,resi)] = (model,index)')
cmd.iterate("((byres "+sss1+") and n;o)",
'_ss.o_dict[(segi,chain,resi)] = (model,index)')
scr_dict[None]=None
o_dict[None]=None
n_dict[None]=None
ca_dict[None]=None
# create special version of cas with gaps
gap = [None,None,None,None]
# gap large enough to distinguish i+4 interations from gaps
last = None
for a in res_list:
if last!=None:
if(cmd.count_atoms(
"((neighbor(neighbor(neighbor (%s`%d)))) and (%s`%d))"%
(last[0],last[1],a[0],a[1]),quiet=1)==0):
gap.extend([None,None,None,None])
gap.append(a)
last = a
gap.extend([None,None,None,None])
print " util.ss: analyzing phi/psi angles (slow)..."
# generate reverse-lookup for gap indices
ss = {}
c = 0
gap_idx = {}
for a in gap:
gap_idx[a] = c
c = c + 1
# secondary structure database...
ss = {}
ss[None]=None
# make decisions based on phi/psi
for a in cas:
ss[a] = 'L' # default
phipsi = cmd.get_phipsi(sss1,state)
for a in phipsi.keys():
(phi,psi) = phipsi[a]
# print scr_dict[a],(phi,psi)
if (phi!=None) and (psi!=None):
if ((phi<-45) and (phi>-160) and
(psi<-170) or (psi>10)): # beta?
ss[a] = 's'
elif ((phi<-45) and (phi>-160) and
(psi>-80) and (psi<-25)): # helix?
ss[a] = 'H'
print " util.ss: finding hydrogen bonds..."
# find all pairwise hydrogen bonds and make note of them in dict
hb = cmd.find_pairs("((byres "+sss1+") and n;n)",
"((byres "+sss1+") and n;o)",mode=1,
cutoff=3.7,angle=55,
state1=state,state2=state)
hb_dict = {} # [((N-atom) (O-atom))] = 1
n_hb_dict = {} # [(N-atom)] = [(O-atom),...]
o_hb_dict = {} # [(O-atom)] = [(N-atom),...]
for a in hb:
# cmd.dist("(%s`%d)"%a[0],"(%s`%d)"%a[1])
hb_dict[a] = 1
n = a[0]
o = a[1]
if not n_hb_dict.has_key(n): n_hb_dict[n]=[]
if not o_hb_dict.has_key(o): o_hb_dict[o]=[]
n_hb_dict[n].append(o)
o_hb_dict[o].append(n)
# check to insure that all helical residues have at least an i +/- 4
# hydrogen bond
for c in xrange(4,len(gap)-4):
a = gap[c]
if ss[a]=='H':
aN = n_dict[scr_dict[a]]
aO = o_dict[scr_dict[a]]
am4O = o_dict[scr_dict[gap[c-4]]]
ap4N = n_dict[scr_dict[gap[c+4]]]
if not hb_dict.has_key((aN,am4O)):
if not hb_dict.has_key((ap4N,aO)):
ss[a]='L'
print " util.ss: verifying beta sheets..."
# check to insure that all beta residues have proper interactions
rep_dict = {}
repeat = 1
while repeat:
repeat = 0
c = 4
cc = len(gap)-4
while c<cc:
a1 = gap[c]
if (ss[a1] in ['s','S']) and not rep_dict.has_key(a1):
rep_dict[a1] = 1
valid = 0
scr_a1 = scr_dict[a1]
# look for antiparallel 2:2 H-bonds (NH-O=C + C=O-HN)
n_a1_atom = n_dict[scr_a1]
o_a1_atom = o_dict[scr_a1]
if (n_hb_dict.has_key(n_a1_atom) and
o_hb_dict.has_key(o_a1_atom)):
for n_hb_atom in n_hb_dict[n_a1_atom]:
for o_hb_atom in o_hb_dict[o_a1_atom]:
n_hb_scr = scr_dict[n_hb_atom]
o_hb_scr = scr_dict[o_hb_atom]
if o_hb_scr == n_hb_scr:
b1 = ca_dict[o_hb_scr]
if abs(c-gap_idx[b1])>2:
ss[b1] = 'S'
ss[a1] = 'S'
valid = 1
# look for antiparallel offset HB (i,i+2,j,j-2)
a3 = gap[c+2]
if (a3!=None):
scr_a3 = scr_dict[a3]
o_a1_atom = o_dict[scr_a1]
n_a3_atom = n_dict[scr_a3]
if (n_hb_dict.has_key(n_a3_atom) and
o_hb_dict.has_key(o_a1_atom)):
for n_hb_atom in n_hb_dict[n_a3_atom]:
for o_hb_atom in o_hb_dict[o_a1_atom]:
n_hb_scr = scr_dict[n_hb_atom]
o_hb_scr = scr_dict[o_hb_atom]
b1 = ca_dict[o_hb_scr]
if b1!=None:
b1_i = gap_idx[b1]
if abs(c-b1_i)>2: # no turns!
b3 = gap[b1_i-2]
if b3!=None:
b3_scr = scr_dict[b3]
if b3_scr == n_hb_scr:
a2 = gap[c+1]
b2 = gap[gap_idx[b1]-1]
ss[b1] = 'S'
ss[b3] = 'S'
ss[a1] = 'S'
ss[a3] = 'S'
if ss[a2]=='L': ss[a2] = 's'
if ss[b2]=='L': ss[b2] = 's'
valid = 1
# look for antiparallel offset HB (i,i-2,j,j+2)
a3 = gap[c-2]
if (a3!=None):
scr_a3 = scr_dict[a3]
n_a1_atom = n_dict[scr_a1]
o_a3_atom = o_dict[scr_a3]
if (n_hb_dict.has_key(n_a1_atom) and
o_hb_dict.has_key(o_a3_atom)):
for n_hb_atom in n_hb_dict[n_a1_atom]:
for o_hb_atom in o_hb_dict[o_a3_atom]:
n_hb_scr = scr_dict[n_hb_atom]
o_hb_scr = scr_dict[o_hb_atom]
b1 = ca_dict[o_hb_scr]
if b1!=None:
b1_i = gap_idx[b1]
if abs(c-b1_i)>2: # no turns!
b3 = gap[b1_i-2]
if b3!=None:
b3_scr = scr_dict[b3]
if b3_scr == n_hb_scr:
a2 = gap[c-1]
b2 = gap[gap_idx[b1]-1]
ss[b1] = 'S'
ss[b3] = 'S'
ss[a1] = 'S'
ss[a3] = 'S'
if ss[a2]=='L': ss[a2] = 's'
if ss[b2]=='L': ss[b2] = 's'
valid = 1
# look for parallel 1:3 HB (i,j-1,j+1)
n_a1_atom = n_dict[scr_a1]
o_a1_atom = o_dict[scr_a1]
if (n_hb_dict.has_key(n_a1_atom) and
o_hb_dict.has_key(o_a1_atom)):
for n_hb_atom in n_hb_dict[n_a1_atom]:
for o_hb_atom in o_hb_dict[o_a1_atom]:
n_hb_scr = scr_dict[n_hb_atom]
o_hb_scr = scr_dict[o_hb_atom]
b0 = ca_dict[n_hb_scr]
if b0!=None:
b2 = gap[gap_idx[b0]+2]
if b2!=None:
b2_scr = scr_dict[b2]
if b2_scr == o_hb_scr:
b1 = gap[gap_idx[b0]+1]
ss[a1] = 'S'
ss[b0] = 'S'
if ss[b1]=='L': ss[b1]='s'
ss[b2] = 'S'
valid = 1
repeat = 1
if not valid:
ss[a1] = 'L'
c = c + 1
# automatically fill 1 residue gaps in helices and well-defined sheets
c = 4
cc = len(gap)-6
while c<cc:
a1 = gap[c]
a3 = gap[c+2]
ss_a1 = ss[a1]
ss_a3 = ss[a3]
if (ss_a1==ss_a3) and (ss_a1 in ['S','H']):
a2 = gap[c+1]
ss[a2] = ss_a1
c = c + 1
# remove singleton sheet residues
c = 4
cc = len(gap)-4
while c<cc:
a0 = gap[c-1]
a1 = gap[c]
a2 = gap[c+1]
if ss[a1] in ['s','S']:
if ((not ss[a0] in ['s','S']) and
(not ss[a2] in ['s','S'])):
ss[a1] = 'L'
c = c + 1
# remove sheet residues which aren't next to another sheet
c = 4
cc = len(gap)-4
while c<cc:
a1 = gap[c]
if ss[a1]=='S':
a1 = gap[c]
scr_a1 = scr_dict[a1]
# look for hydrogen bonds to another sheet
n_a1_atom = n_dict[scr_a1]
o_a1_atom = o_dict[scr_a1]
certain = 0
if n_hb_dict.has_key(n_a1_atom):
for n_hb_atom in n_hb_dict[n_a1_atom]:
n_hb_ca_atom=ca_dict[scr_dict[n_hb_atom]]
if ss[n_hb_ca_atom]=='S':
certain = 1
break
if o_hb_dict.has_key(o_a1_atom):
for o_hb_atom in o_hb_dict[o_a1_atom]:
o_hb_ca_atom=ca_dict[scr_dict[o_hb_atom]]
if ss[o_hb_ca_atom]=='S':
certain = 1
break
if not certain:
ss[a1] = 's'
c = c + 1
# remove questionable sheet residues
c = 4
cc = len(gap)-4
while c<cc:
a0 = gap[c-1]
a1 = gap[c]
a2 = gap[c+1]
if ss[a1]=='s':
if (not ((ss[a0]=='S') and (ss[a2]=='S'))):
ss[a1] = 'L'
c = c + 1
# extend helices if hydrogen bonding requirements are met
rep_dict = {}
repeat = 1
while repeat:
repeat = 0
c = 4
cc = len(gap)-4
while c<cc:
a = gap[c]
if not rep_dict.has_key(a):
if ss[gap[c+1]]=='H':
rep_dict[a] = 1
if ss[a]!='H': # N-terminal end
aO = o_dict[scr_dict[a]]
ap4N = n_dict[scr_dict[gap[c+4]]]
ap3N = n_dict[scr_dict[gap[c+3]]]
if hb_dict.has_key((ap4N,aO)) or hb_dict.has_key((ap3N,aO)):
ss[a]='H'
repeat = 1
c = c - 5
if c<4: c=4
if ss[gap[c-1]]=='H':
a = gap[c]
if ss[a]!='H': # C-terminal end
rep_dict[a] = 1
aN = n_dict[scr_dict[a]]
am4O = o_dict[scr_dict[gap[c-4]]]
am3O = o_dict[scr_dict[gap[c-3]]]
if hb_dict.has_key((aN,am4O)) or hb_dict.has_key((aN,am3O)):
ss[a]='H'
repeat = 1
c = c - 5
if c<4: c=4
c = c + 1
# remove doubleton helices
c = 4
cc = len(gap)-5
while c<cc:
a0 = gap[c-1]
a1 = gap[c]
a2 = gap[c+1]
a3 = gap[c+2]
ss_a0 = ss[gap[c-1]]
ss_a1 = ss[gap[c]]
ss_a2 = ss[gap[c+1]]
ss_a3 = ss[gap[c+2]]
if ss_a1=='H':
if (ss_a2==ss_a1) and (ss_a0!=ss_a2) and (ss_a2!=ss_a3):
ss[a1] = 'L'
ss[a2] = 'L'
c = c + 1
# remove totally unreasonable helix and sheet residues
c = 4
cc = len(gap)-5
while c<cc:
a1 = gap[c]
ss_a1 = ss[gap[c]]
if ss_a1=='H':
if phipsi.has_key(a1):
(phi,psi) = phipsi[a1]
if (phi>0) and (phi<150):
ss[a1] = 'L'
elif((psi<-120) or (psi>140)):
ss[a1] = 'L'
elif ss_a1 in ['S','s']:
if phipsi.has_key(a1):
(phi,psi) = phipsi[a1]
if (phi>45) and (phi<160):
ss[a1] = 'L'
# if (psi<-30) and (psi>-150):
if (psi<-65) and (psi>-150):
ss[a1] = 'L'
c = c + 1
for x in range(1,3):
# remove singleton sheet residues
c = 4
cc = len(gap)-4
while c<cc:
a0 = gap[c-1]
a1 = gap[c]
a2 = gap[c+1]
if ss[a1] in ['s','S']:
if ((not ss[a0] in ['s','S']) and
(not ss[a2] in ['s','S'])):
ss[a1] = 'L'
c = c + 1
# remove sheet residues which aren't next to another sheet
c = 4
cc = len(gap)-4
while c<cc:
a1 = gap[c]
if ss[a1]=='S':
a1 = gap[c]
scr_a1 = scr_dict[a1]
# look for hydrogen bonds to another sheet
n_a1_atom = n_dict[scr_a1]
o_a1_atom = o_dict[scr_a1]
certain = 0
if n_hb_dict.has_key(n_a1_atom):
for n_hb_atom in n_hb_dict[n_a1_atom]:
n_hb_ca_atom=ca_dict[scr_dict[n_hb_atom]]
if ss[n_hb_ca_atom]=='S':
certain = 1
break
if o_hb_dict.has_key(o_a1_atom):
for o_hb_atom in o_hb_dict[o_a1_atom]:
o_hb_ca_atom=ca_dict[scr_dict[o_hb_atom]]
if ss[o_hb_ca_atom]=='S':
certain = 1
break
if not certain:
ss[a1] = 's'
c = c + 1
# remove questionable sheet residues
c = 4
cc = len(gap)-4
while c<cc:
a0 = gap[c-1]
a1 = gap[c]
a2 = gap[c+1]
if ss[a1]=='s':
if (not ((ss[a0]=='S') and (ss[a2]=='S'))):
ss[a1] = 'L'
c = c + 1
# lst = ss.keys()
# lst.sort()
# for a in lst: print scr_dict[a],ss[a]
# assign protein
for a in cas:
if ss[a]=='s':
ss[a]='S'
cmd.alter(sss1,"ss ='L'")
for a in cas:
if ss[a]!='L':
cmd.alter("(%s`%d)"%a,"ss='%s'"%ss[a])
cmd.feedback("pop")
del pymol._ss # IMPORTANT
cmd.delete(sss1)
cmd.rebuild(selection,'cartoon')
#
# print conn_hash.keys()
print " util.ss: assignment complete."