ValueError: Invalid placeholder в строке

Question

Я попытался создать собственный шаблон для скрипта mutate_model.py (http://salilab.org/modeller/wiki/Mutate%20model) с использованием шаблона строки python, где я заменил значения для этих пяти переменных Model, resType, resPos, pdb, chain to replce and write новый файл со значениями, но я получаю сообщение об ошибке, как показано ниже:

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 

заранее спасибо

Answer 1

Это erroring, потому что у вас есть недопустимый идентификатор шаблона в строке

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

Из документов

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

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

Вы должны были бы использовать

$$(LIB) 

Кроме того, переменная случай не соответствует

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

Но вы проходите мимо resType1 и resPos1. Вы должны пройти в restype1 и respos1