# Example for: selection.mutate()

# This will read a PDB file, change its sequence a little, build new
# coordinates for any of the additional atoms using only the internal
# geometry, and write the mutant PDB file.  It can be seen as primitive
# but rapid comparative modeling for substitution mutants. For more
# sophisticated modeling, see http://salilab.org/modeller/wiki/Mutate%20model
#
# For insertion and deletion mutants, follow the standard comparative
# modeling procedure.

from modeller import *

env = environ()
env.io.atom_files_directory = ['../atom_files']

# Read the topology library with non-hydrogen atoms only:
env.libs.topology.read(file='$(LIB)/top_heav.lib')
# To produce a mutant with all hydrogens, uncomment this line:
#env.libs.topology.read(file='$(LIB)/top_allh.lib')

# Read the CHARMM parameter library:
env.libs.parameters.read(file='$(LIB)/par.lib')

# Read the original PDB file and copy its sequence to the alignment array:
code = '1fas'
aln = alignment(env)
mdl = model(env, file=code)
aln.append_model(mdl, atom_files=code, align_codes=code)

# Select the residues to be mutated: in this case all ASP residues:
sel = selection(mdl).only_residue_types('ASP')

# The second example is commented out; it selects residues '1' and '10'.
#sel = selection(mdl.residues['1'], mdl.residues['10'])

# Mutate the selected residues into HIS residues (neutral HIS):
sel.mutate(residue_type='HIS')

# Add the mutated sequence to the alignment arrays (it is now the second
# sequence in the alignment):
aln.append_model(mdl, align_codes='1fas-1')

# Generate molecular topology for the mutant:
mdl.clear_topology()
mdl.generate_topology(aln['1fas-1'])

# Transfer all the coordinates you can from the template native structure
# to the mutant (this works even if the order of atoms in the native PDB
# file is not standard):
mdl.transfer_xyz(aln)

# Build the remaining unknown coordinates for the mutant:
mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES')

# Write the mutant to a file:
mdl.write(file='1fas-1.atm')