old_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  
  import numpy as np
  import molecules, os, polymer
  
  def pmma_monomer():
      """Return pmmma monomer building block as defined by SMILES
      format obtained in avogadro"""
      builddir = 'build'
      molfile = 'pmma_monomer.pdb'
      FILE = os.path.join( os.path.dirname( os.path.realpath( __file__) ) , os.path.join( builddir, molfile ))
      m = polymer.Monomer.from_pdb( FILE, in_AA = True, out_AA = True )
      return m
  
  
  def sulfuric_acid():
      """Return geo opt. 
      molecule with sulfur in origo, one oxygen in xz plane"""
      builddir = "build"
      molfile = "sulfur_opt.xyz"
      FILE = os.path.join( os.path.dirname( os.path.realpath( __file__) ) , os.path.join( builddir, molfile ))
      m = molecules.Molecule.from_xyz( FILE, in_AA = True, out_AA = False )
      return m
  
  
  def paranitro_aniline():
      """Return geo opt. 
      molecule with sulfur in origo, one oxygen in xz plane"""
      builddir = "build"
      molfile = "pna_opt.xyz"
      FILE = os.path.join( os.path.dirname( os.path.realpath( __file__) ) , os.path.join( builddir, molfile ))
      m = molecules.Molecule.from_xyz( FILE, in_AA= True, out_AA = False )
      return m
  
  def tip3p():
      """Return geo opt. 
      molecule with sulfur in origo, one oxygen in xz plane"""
      builddir = "build"
      molfile = "tip3p.xyz"
      FILE = os.path.join( os.path.dirname( os.path.realpath( __file__) ) , os.path.join( builddir, molfile ))
      m = molecules.Water.get_standard( AA = False )
      for ind, at in enumerate( m ):
          at.order = ind + 1
  
      return m
  
  
  if __name__ == '__main__':
      main()
  
new_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  
  import numpy as np
  import molecules, os, polymer
  
  def pmma_monomer():
      """Return pmmma monomer building block as defined by SMILES
      format obtained in avogadro"""
      builddir = 'build'
      molfile = 'pmma_monomer.pdb'
      FILE = os.path.join( os.path.dirname( os.path.realpath( __file__) ) , os.path.join( builddir, molfile ))
  
      m = polymer.Monomer.from_pdb( FILE, in_AA = True, out_AA = True )
      m._mono_name = "pmma"
      m._r = 1.46
      m._angle = 104.5
      m._dihedral = 180.0
      return m
  
  
  def sulfuric_acid():
      """Return geo opt. 
      molecule with sulfur in origo, one oxygen in xz plane"""
      builddir = "build"
      molfile = "sulfur_opt.xyz"
      FILE = os.path.join( os.path.dirname( os.path.realpath( __file__) ) , os.path.join( builddir, molfile ))
      m = molecules.Molecule.from_xyz( FILE, in_AA = True, out_AA = False )
      return m
  
  
  def paranitro_aniline():
      """Return geo opt. 
      molecule with sulfur in origo, one oxygen in xz plane"""
      builddir = "build"
      molfile = "pna_opt.xyz"
      FILE = os.path.join( os.path.dirname( os.path.realpath( __file__) ) , os.path.join( builddir, molfile ))
      m = molecules.Molecule.from_xyz( FILE, in_AA= True, out_AA = False )
      return m
  
  def tip3p():
      """Return geo opt. 
      molecule with sulfur in origo, one oxygen in xz plane"""
      builddir = "build"
      molfile = "tip3p.xyz"
      FILE = os.path.join( os.path.dirname( os.path.realpath( __file__) ) , os.path.join( builddir, molfile ))
      m = molecules.Water.get_standard( AA = False )
      for ind, at in enumerate( m ):
          at.order = ind + 1
  
      return m
  
  
  if __name__ == '__main__':
      main()
  
subject: change pmma parameters for bonding monomer