ValueError: Invalid placeholder in string

Question

I tried to make my own template for mutate_model.py script (http://salilab.org/modeller/wiki/Mutate%20model) by using python string template where I substituted values for these five variables Model,resType,resPos,pdb,chain to replce and write a new file with values but I am getting a error like below:

MyAttempt:

import os
import re
import sys
import itertools
from modeller import *
from docopt import docopt
from string import Template
from modeller.automodel import *
from os.path import join, getsize    
from modeller.scripts import complete_pdb

Model="3o26"
resType="A"
resPos="275"
pdb="3o26.pdb"
chain="A"

dir=os.getcwd()
str = '''import sys
import os
from modeller import *
from modeller.optimizers import molecular_dynamics, conjugate_gradients
from modeller.automodel import autosched

def optimize(atmsel, sched):
    for step in sched:
        step.optimize(atmsel, max_iterations=200, min_atom_shift=0.001)
    refine(atmsel)
    cg = conjugate_gradients()
    cg.optimize(atmsel, max_iterations=200, min_atom_shift=0.001)

def refine(atmsel):
    md = molecular_dynamics(cap_atom_shift=0.39, md_time_step=4.0, md_return='FINAL')
    init_vel = True
    for (its, equil, temps) in ((200, 20, (150.0, 250.0, 400.0, 700.0, 1000.0)),
                            (200, 600,
                             (1000.0, 800.0, 600.0, 500.0, 400.0, 300.0))):
        for temp in temps:
            md.optimize(atmsel, init_velocities=init_vel, temperature=temp,
                     max_iterations=its, equilibrate=equil)
            init_vel = False

def make_restraints(mdl1, aln):
   rsr = mdl1.restraints
   rsr.clear()
   s = selection(mdl1)
   for typ in ('stereo', 'phi-psi_binormal'):
       rsr.make(s, restraint_type=typ, aln=aln, spline_on_site=True)
   for typ in ('omega', 'chi1', 'chi2', 'chi3', 'chi4'):
       rsr.make(s, restraint_type=typ+'_dihedral', spline_range=4.0,
            spline_dx=0.3, spline_min_points = 5, aln=aln,
            spline_on_site=True)

log.verbose()
env = environ(rand_seed=-49837)
env.io.hetatm = True
env.edat.dynamic_sphere=False
env.edat.dynamic_lennard=True
env.edat.contact_shell = 4.0
env.edat.update_dynamic = 0.39
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')
mdl1 = model(env, file=$pdb_filename)
ali = alignment(env)
ali.append_model(mdl1, atom_files=$pdb_filename, align_codes=$modelname)


s = selection(mdl1.chains[$chain].residues[$respos1]])#change
s.mutate(residue_type=$restyp1)#change

ali.append_model(mdl1, align_codes=$modelname)
mdl1.clear_topology()
mdl1.generate_topology(ali[-1])
mdl1.transfer_xyz(ali)
mdl1.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES')
mdl2 = model(env, file=$pdb_filename)
mdl1.res_num_from(mdl2,ali)

#WriteAndReadMutation
mdl1.write(file=$modelname+$restyp1+$respos1+$chain+'.tmp')#change
mdl1.read(file=$modelname+$restyp1+$respos1+$chain+'.tmp')#change

make_restraints(mdl1, ali)
mdl1.env.edat.nonbonded_sel_atoms=1
sched = autosched.loop.make_for_model(mdl1)

#MutationOptimization
s = selection(mdl1.atoms['CA:'+$respos1+':'+$chain].select_sphere(5))
mdl1.restraints.unpick_all()
mdl1.restraints.pick(s)
s.energy()
s.randomize_xyz(deviation=4.0)
mdl1.env.edat.nonbonded_sel_atoms=2
optimize(s,sched)
mdl1.env.edat.nonbonded_sel_atoms=1
optimize(s,sched)
s.energy()
mdl1.write(file="hi.txt")
os.remove($modelname+$restyp1+$respos1+$chain+'.tmp')'''

str = Template(str)
file = open(dir + '/' + 'mutate_models.py', 'w')
file.write(str.substitute(modelname=Model,resTyp1=resType,resPos1=resPos,pdb_filename=pdb,chain=chain))
file.close()


ERROR:
Traceback (most recent call last):
  File "ex.py", line 116, in <module>
    file.write(str.substitute(modelname=Model,resTyp1=resType,resPos1=resPos,pdb_filename=pdb,chain=chain))
  File "/usr/lib/python2.7/string.py", line 172, in substitute
    return self.pattern.sub(convert, self.template)
  File "/usr/lib/python2.7/string.py", line 169, in convert
    self._invalid(mo)
  File "/usr/lib/python2.7/string.py", line 146, in _invalid
(lineno, colno))
ValueError: Invalid placeholder in string: line 44, col 30

Expected output :

 Above mentioned five variables should be written by respective value and write a file

Thanks in advance

Smile

What have you done to debug? Your 'question' is asking us to debug for you. Please ask a specific and concise question with relevant code. – Beautician

Thanks for your reply . Actually I am new to string temple and I didnt get where does it gone wrong. I tried to figure out the order of variable and substituted value which was correct. so it would be really helpful if you tell me possible reason for the same. Thanking you in advance – Smile

Dude,I appreciate your advice but its really irritating . How do you know that I didnt try anything and put my query just like that. If you can help me you are welcome but dont say any stuffs just like that. thanks. – Smile

I'm assuming so because you didn't provide any details in the question. – Beautician

Ok,let me try this #26950801. it may work then I will let you know if I get any issue.thanks – Smile

Cant help but note that "restyp1" != "resTyp1". Python is case-sensitive, after all... Similar comment regarding "resPos1"... – Octillion

@Smile , just a advice , next time try to remove the comment code so it will be easier for the community to read through your code.Also please mention what have you tried to do to fix your code and as Andrew L said , ask a specific and concise question with relevant code. – Freida

Answer 1

It's erroring because you have an invalid template identifier in your string

env.libs.parameters.read(file='$(LIB)/par.lib')   # Notice the $(LIB)

From the docs

$$ is an escape; it is replaced with a single $.

Any other appearance of $ in the string will result in a ValueError being raised.

You would need to use

$$(LIB)

Also, your variable case doesn't match

mdl1.write(file=$modelname+$restyp1+$respos1+$chain+'.tmp')#change

But you're passing in resType1 and resPos1. You need to pass in restype1 and respos1

Lemures