def build_seq(seq,ss=None,phi=None,psi=None):
"""
usage: build_seq seq [, ss=helix | phi=phi, psi=psi]
example: build_seq QGAADLESLGQYFEEMKTKLIQDMTE, ss=helix
will build the above sequence in a helical conformation
ss can be: helix or h or alpha (phi=-57, psi=-47)
antiparallel or beta (phi=-139, psi=-135)
parallel (phi=-119, psi=-113)
3/10 helix (phi=-40.7,psi=30)
polypro (phi=-78, psi=149) (polyproline helix type II)
Alternatively, you can specify the phi and psi angles directly:
build_seq QGAADLESLGQ, phi=-60, psi=-40
This will create an object named after the first residue: gln
unless a pk1 selection exists, then it will build onto that atom.
"""
if 'pk1' in cmd.get_names("selections"):
obj='pk1'
else:
obj=seq[0:3]
if phi == None or psi == None:
if ss == None:
phi = -139
psi = -135
else:
ss = ss.lower()
if ss[0:5] == 'helix' or ss[0] == 'h' or ss[0:5] == 'alpha':
phi = -57
psi = -47
elif ss[0:5] == 'antip' or ss[0:4] == 'beta':
phi = -139
psi = -135
elif ss[0:5] == 'paral':
phi = -119
psi = -113
elif ss[0:4] == '3/10':
phi = -40.7
psi = -30
elif ss[0:7] == 'polypro':
phi = -78
psi = 149
print "Building sequence: ",seq
seq3=seq_convert.seq1_to_seq3(seq)
attach_amino_acid(obj,seq3[0].lower(),phi,psi)
for aa in seq3[1:]:
aa = aa.lower()
attach_amino_acid('pk1',aa,phi,psi)
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])
