def get_seq(selection):
selection += ' & n. ca & e. c'
m = cmd.get_model(selection)
seq3 = []
chains = []
resids = []
for i in m.atom:
seq3.append(i.resn)
chains.append(i.chain)
resids.append(i.resi)
seq1 = seq3_to_seq1(seq3)
return seq1,chains,resids
def get_seq(selection):
selection += ' & n. ca & e. c'
m = cmd.get_model(selection)
seq3 = []
chains = []
resids = []
for i in m.atom:
seq3.append(i.resn)
chains.append(i.chain)
resids.append(i.resi)
seq1 = seq3_to_seq1(seq3)
return seq1, chains, resids
def build_seq_phi_psi(seq_phi_psi_filename,line_style=0):
"""
usage: build_seq_phi_psi filename
will build the above sequence from information in a file stored as:
resname phi psi
resname phi psi
...
where resname is the 1-letter code for the amino acid
The created object will be named for the first amino acid in the sequence,
unless a pk1 selection exists, then it will build onto that atom.
Default is now to automatically show the structure as sticks, call it with
line_style=1 to revert to showing lines
"""
line_style = int(line_style)
# read file of residue name with associated phi,psi values to build
lines = open(seq_phi_psi_filename).readlines()
sequence = ''
phi_list = []
psi_list = []
sequence3 = []
counter = 0
for l in lines:
if len(l.split()) == 3:
counter += 1
seq,phi,psi = l.split()
if len(seq) == 3:
sequence3.append(seq)
elif len(seq) == 1:
sequence += seq
else:
print " Error: problem with sequence file -- not 3-letter or 1-letter code for residue name"
raise QuietException
else:
continue
phi_list.append(float(phi))
psi_list.append(float(psi))
print "Number of amino acid/phi/psi values read: ",counter
if counter == 0:
print " Error: problem with sequence file -- there should be three columns: amino-acid phi psi"
raise QuietException
if len(sequence3) > 0:
sequence = seq_convert.seq3_to_seq1(sequence3)
print "Building sequence: ",sequence
seq3=seq_convert.seq1_to_seq3(sequence)
#print seq3[0].lower()
if 'pk1' in cmd.get_names("selections"):
obj='pk1'
else:
obj=seq[0:3]
attach_amino_acid(obj,seq3[0].lower(),phi_list[0],psi_list[0])
print seq3[0].lower(),phi_list[0],psi_list[0]
for i in range(1,len(seq3)):
aa = seq3[i].lower()
attach_amino_acid('pk1',aa,phi_list[i],psi_list[i-1])
print seq3[i].lower(),phi_list[i],psi_list[i-1]
# hide lines and show sticks (comment out the next two lines, if you don't like this).
if line_style == 0:
print "hiding lines for: ",seq3[0]
print "showing sticks for: ",seq3[0]
cmd.hide('lines',seq3[0])
cmd.show('sticks',seq3[0])
def build_seq_phi_psi(seq_phi_psi_filename,line_style=0):
"""
usage: build_seq filename
will build the above sequence from information in a file stored as:
resname phi psi
resname phi psi
...
where resname is the 1-letter code for the amino acid
The created object will be named for the first amino acid in the sequence,
unless a pk1 selection exists, then it will build onto that atom.
Default is now to automatically show the structure as sticks, call it with
line_style=1 to revert to showing lines
"""
line_style = int(line_style)
# read file of residue name with associated phi,psi values to build
lines = file(seq_phi_psi_filename).readlines()
sequence = ''
phi_list = []
psi_list = []
sequence3 = []
for l in lines:
seq,phi,psi = l.split()
if len(seq) == 3:
sequence3.append(seq)
elif len(seq) == 1:
sequence += seq
else:
print " Error: problem with sequence file -- not 3-letter or 1-letter code for residue name"
raise QuietException
phi_list.append(float(phi))
psi_list.append(float(psi))
if len(sequence3) > 0:
sequence = seq_convert.seq3_to_seq1(sequence3)
print "Building sequence: ",sequence
seq3=seq_convert.seq1_to_seq3(sequence)
#print seq3[0].lower()
if 'pk1' in cmd.get_names("selections"):
obj='pk1'
else:
obj=seq[0:3]
attach_amino_acid(obj,seq3[0].lower(),phi_list[0],psi_list[0])
print seq3[0].lower(),phi_list[0],psi_list[0]
for i in xrange(1,len(seq3)):
aa = seq3[i].lower()
attach_amino_acid('pk1',aa,phi_list[i],psi_list[i-1])
print seq3[i].lower(),phi_list[i],psi_list[i-1]
# hide lines and show sticks (comment out the next two lines, if you don't like this).
if line_style == 0:
print "hiding lines for: ",seq3[0]
print "showing sticks for: ",seq3[0]
cmd.hide('lines',seq3[0])
cmd.show('sticks',seq3[0])