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hetatm.py

#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific. 
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------------------------------------------------------------------
#G* Please see the accompanying LICENSE file for further information. 
#H* -------------------------------------------------------------------
#I* Additional authors of this source file include:
#-* 
#-* 
#-*
#Z* -------------------------------------------------------------------

#
#
#

from chempy.neighbor import Neighbor
from chempy.models import Connected
from chempy import Bond
from chempy import place

MAX_BOND_LEN = 2.2
PEPT_CUTOFF = 1.7

#---------------------------------------------------------------------------------
def generate(model, topology= None, forcefield = None ):
   
   add_bonds(model,topology=topology,forcefield=forcefield)
   connected = model.convert_to_connected()
   add_hydrogens(connected,topology=topology,forcefield=forcefield)
   place.simple_unknowns(connected)
   return connected.convert_to_indexed()

#---------------------------------------------------------------------------------
def assign_types(model, topology = None, forcefield = None ):
   if str(model.__class__) != 'chempy.models.Indexed':
      raise ValueError('model is not an "Indexed" model object')
   nAtom = model.nAtom
   if nAtom:
      tmpl = topology.normal
      ffld = forcefield.normal
      res_list = model.get_residues()
      if len(res_list):
         for a in res_list:
            base = model.atom[a[0]]
            resn = base.resn
            if not tmpl.has_key(resn):
               raise RuntimeError("unknown residue type '"+resn+"'")
            else:
               # reassign atom names and build dictionary
               dict = {}
               aliases = tmpl[resn]['aliases']
               for b in range(a[0],a[1]):
                  at = model.atom[b]
                  if aliases.has_key(at.name):
                     at.name = aliases[at.name]
                  dict[at.name] = b
                  if forcefield:
                     k = (resn,at.name)
                     if ffld.has_key(k):
                        at.text_type = ffld[k]['type']
                        at.partial_charge = ffld[k]['charge']
                     else:
                        raise RuntimeError("no parameters for '"+str(k)+"'")

#---------------------------------------------------------------------------------
def add_bonds(model, topology = None, forcefield = None ):
   if str(model.__class__) != 'chempy.models.Indexed':
      raise ValueError('model is not an "Indexed" model object')
   nAtom = model.nAtom
   if nAtom:
      tmpl = topology.normal
      ffld = forcefield.normal
      res_list = model.get_residues()
      if len(res_list):
         for a in res_list:
            base = model.atom[a[0]]
            resn = base.resn
            if not tmpl.has_key(resn):
               raise RuntimeError("unknown residue type '"+resn+"'")
            else:
               # reassign atom names and build dictionary
               dict = {}
               aliases = tmpl[resn]['aliases']
               for b in range(a[0],a[1]):
                  at = model.atom[b]
                  if aliases.has_key(at.name):
                     at.name = aliases[at.name]
                  dict[at.name] = b
                  if forcefield:
                     k = (resn,at.name)
                     if ffld.has_key(k):
                        at.text_type = ffld[k]['type']
                        at.partial_charge = ffld[k]['charge']
                     else:
                        raise RuntimeError("no parameters for '"+str(k)+"'")
               # now add bonds for atoms which are present
               bonds = tmpl[resn]['bonds']
               mbond = model.bond
               for b in bonds.keys():
                  if dict.has_key(b[0]) and dict.has_key(b[1]):
                     bnd = Bond()
                     bnd.index = [ dict[b[0]], dict[b[1]] ]
                     bnd.order = bonds[b]['order']
                     mbond.append(bnd)
                     
#---------------------------------------------------------------------------------
def add_hydrogens(model,topology=None,forcefield=None):  
   if str(model.__class__) != 'chempy.models.Connected':
      raise ValueError('model is not a "Connected" model object')
   nAtom = model.nAtom
   if nAtom:
      if not model.index:
         model.update_index()
      ffld = forcefield.normal
      tmpl = topology.normal
      res_list = model.get_residues()
      if len(res_list):
         for a in res_list:
            base = model.atom[a[0]]
            resn = base.resn
            if not tmpl.has_key(resn):
               raise RuntimeError("unknown residue type '"+resn+"'")
            else:
               # build dictionary
               dict = {}
               for b in range(a[0],a[1]):
                  at = model.atom[b]
                  dict[at.name] = b
               # find missing bonds with hydrogens
               bonds = tmpl[resn]['bonds']
               mbond = model.bond
               for b in bonds.keys():
                  if dict.has_key(b[0]) and (not dict.has_key(b[1])):
                     at = model.atom[dict[b[0]]]
                     if at.symbol != 'H':
                        name = b[1]
                        symbol = tmpl[resn]['atoms'][name]['symbol']
                        if symbol == 'H':
                           newat = at.new_in_residue()
                           newat.name = name
                           newat.symbol = symbol
                           k = (resn,newat.name)
                           newat.text_type = ffld[k]['type']
                           newat.partial_charge = ffld[k]['charge']
                           idx1 = model.index[id(at)]
                           idx2 = model.add_atom(newat)
                           bnd = Bond()
                           bnd.index = [ idx1, idx2 ]
                           bnd.order = bonds[b]['order']
                           mbond[idx1].append(bnd)
                           mbond[idx2].append(bnd)
                  if (not dict.has_key(b[0])) and dict.has_key(b[1]):
                     at = model.atom[dict[b[1]]]
                     if at.symbol != 'H':
                        name = b[0]
                        symbol = tmpl[resn]['atoms'][name]['symbol']
                        if symbol == 'H':
                           newat = at.new_in_residue()
                           newat.name = name
                           newat.symbol = symbol
                           k = (resn,newat.name)
                           newat.text_type = ffld[k]['type']
                           newat.partial_charge = ffld[k]['charge']
                           idx1 = model.index[id(at)]
                           idx2 = model.add_atom(newat)
                           bnd = Bond()
                           bnd.index = [ idx1, idx2 ]
                           bnd.order = bonds[b]['order']
                           mbond[idx1].append(bnd)
                           mbond[idx2].append(bnd)


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