old_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  
  import numpy as np
  import molecules, os
  
  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 )
      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 )
      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 = True )
  
      return m
  
  
  if __name__ == '__main__':
      main()
  
new_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  
  import numpy as np
  import molecules, os
  
  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 )
      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 )
      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 )
  
      return m
  
  
  if __name__ == '__main__':
      main()
  
subject: fix AA bug in builder/tip3p