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#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* -------------------------------------------------------------------
#
#
#
import chempy.models
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 not isinstance(model, 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 resn not in tmpl:
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 at.name in aliases:
at.name = aliases[at.name]
dict[at.name] = b
if forcefield:
k = (resn,at.name)
if k in ffld:
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 not isinstance(model, 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 resn not in tmpl:
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 at.name in aliases:
at.name = aliases[at.name]
dict[at.name] = b
if forcefield:
k = (resn,at.name)
if k in ffld:
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 list(bonds.keys()):
if b[0] in dict and b[1] in dict:
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 not isinstance(model, 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 resn not in tmpl:
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 list(bonds.keys()):
if b[0] in dict and (b[1] not in dict):
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 (b[0] not in dict) and b[1] in dict:
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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