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# mutate.py
# Copyright 2005, 2006, 2009 by Bernhard Lohkamp
# Copyright 2004, 2005, 2006 by Paul Emsley, The University of York
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import coot
import coot_utils
# Mutate chain-id of molecule number imol given sequence.
#
# The number of residues in chain-id must match the length of sequence.
#
def mutate_chain(imol, chain_id, sequence):
if (len(sequence) != chain_n_iresidues(chain_id, imol)):
print("sequence mismatch: molecule", coot.chain_n_residues(
chain_id, imol), "new sequences:", len(sequence))
else:
coot.make_backup(imol) # do backup first
backup_mode = coot.backup_state(imol)
# turn off backup for imol
coot.turn_off_backup(imol)
baddies = 0
for ires in sequence.upper():
res = coot.mutate_single_residue_by_serial_number(
ires, chain_id, imol, sequence_list[ires])
if (res != 1):
baddies += 1
print("multi_mutate of %s residues had %s baddies" %
(len(sequence), baddies))
coot.set_have_unsaved_changes(imol)
if (backup_mode == 1):
coot.turn_on_backup(imol)
coot.update_go_to_atom_window_on_changed_mol(imol)
coot.graphics_draw()
# an internal function of mutate, This presumes a protein sequence
def multi_mutate(mutate_function, imol, start_res_no, chain_id, sequence):
if len(sequence) > 0:
baddies = 0
for ires in range(len(sequence)):
result = mutate_function(
start_res_no+ires, "", chain_id, imol, sequence[ires].upper())
if (result != 1):
# add a baddy if result was 0 (fail)
baddies += 1
print("multi_mutate of", len(sequence),
"residues had", baddies, "errors")
else:
print("BL WARNING:: no sequence or sequence of no length found!")
# The stop-res-no is inclusive, so usage e.g.
# mutate_resiude_range(0,"A",1,2,"AC")
#
# This presumes a protein sequence (not nucleic acid).
# not any more... sort of
#
def mutate_residue_range(imol, chain_id, start_res_no, stop_res_no, sequence):
if coot_utils.is_nucleotide_chain_qm(imol, chain_id):
mutate_nucleotide_range(
imol, chain_id, start_res_no, stop_res_no, sequence)
else:
coot.make_backup(imol)
n_residues = stop_res_no - start_res_no + 1
if (len(sequence) != n_residues):
print("sequence length mismatch:", len(sequence), n_residues)
else:
backup_mode = coot.backup_state(imol)
coot.turn_off_backup(imol)
multi_mutate(coot.mutate_single_residue_by_seqno, imol,
start_res_no, chain_id, sequence.upper())
coot.set_have_unsaved_changes(imol)
if backup_mode == 1:
coot.turn_on_backup(imol)
coot.update_go_to_atom_window_on_changed_mol(imol)
coot.graphics_draw()
# mutate and auto fit a residue range
#
# This presumes a protein sequence (not nucleic acid).
#
# The sequence is a string of one letter codes
#
# this has been replaced by an internal coot function now.
#
def mutate_and_autofit_residue_range(imol, chain_id, start_res_no, stop_res_no,
sequence):
# does nucleic acids now too
coot.mutate_residue_range(imol, chain_id, start_res_no, stop_res_no, sequence.upper())
mol_for_map = coot.imol_refinement_map()
if (mol_for_map >= 0):
backup_mode = coot.backup_state(imol)
coot.turn_off_backup(imol)
for ires in range(len(sequence)):
clash = 1
altloc = ""
inscode = ""
resno = ires + start_res_no
# print("debug:: auto-fit-best-rotamer ", resno, altloc, inscode, chain_id, imol, mol_for_map, clash, 0.5)
#score = coot.auto_fit_best_rotamer(resno, altloc, inscode, chain_id, imol, mol_for_map, clash, 0.5)
score = coot.auto_fit_best_rotamer(imol, chain_id, resno, inscode, altloc, mol_for_map, clash, 0.5)
print(" Best score: ", score)
# coot_utils.number_list(start_res_no,stop_res_no)
if (backup_mode == 1):
coot.turn_on_backup(imol)
else:
print("WARNING:: no map set for refinement. Can't fit")
# mutate and autofit whole chain
#
# This presumes a protein sequence (not nucleic acid).
# this has been replaced by an internal coot function now.
#
def mutate_and_auto_fit(residue_number, chain_id, mol, mol_for_map,
residue_type):
coot.mutate(mol, chain_id, residue_number, "", residue_type)
coot.auto_fit_best_rotamer(
residue_number, "", "", chain_id, mol, mol_for_map, 0, 0.5)
# a short-hand for mutate-and-auto-fit
def maf(*args):
mutate_and_auto_fit(*args)
# return a char (well string in python), return "A" for unknown residue_type
#
def three_letter_code2single_letter(residue_type):
dic_type_1lc = {"ALA": "A", "ARG": "R", "ASN": "N", "ASP": "D",
"CYS": "C", "GLN": "Q", "GLU": "E", "GLY": "G",
"HIS": "H", "ILE": "I", "LEU": "L", "LYS": "K",
"MET": "M", "PHE": "F", "PRO": "P", "SER": "S",
"THR": "T", "TRP": "W", "TYR": "Y", "VAL": "V"}
if (residue_type in dic_type_1lc):
res_type_1lc = dic_type_1lc[residue_type]
else:
# if not standard aa then set it to Ala
res_type_1lc = "A"
return res_type_1lc
# Mutate a residue range of nucleotides
# where sequence is a string (for example: "atgccgta")
#
def mutate_nucleotide_range(imol, chain_id, resno_start, resno_end, sequence):
from types import StringType
# return False on unknown letter. We don't need to be specific about
# RNA/DNA here because mutate-base uses canonical_base_name() to
# set the base name according to the residue type before it was
# mutated.
#
def nucleotide_letter2three_letter_code(letter):
# not entirely sure what should happening here,
# only upper case conversion!?
nt = ["A", "C", "G", "T", "U"]
up = letter.upper()
if up in nt:
return up
else:
return False
# main line
if (type(sequence) is not StringType):
s = "sequence must be a string"
coot.info_dialog(s)
print(s)
else:
residue_range_length = resno_end - resno_start + 1
seq_length = len(sequence)
if not (residue_range_length == seq_length):
s = "residue range must equal sequence length"
coot.info_dialog(s)
print(s)
else:
residue_types = list(map(nucleotide_letter2three_letter_code,
sequence.upper()))
for res_no, res_type in map(None,
list(range(resno_start, resno_end + 1)),
residue_types):
if res_type:
coot.mutate_base(imol, chain_id, res_no, "", res_type)
# a wrapper for mutate_single_residue_by_seqno (which uses slightly
# inconvenient single letter code)
#
# Here residue-type is the 3-letter code
# BL says:: not working, since mutate expects a 3 letter code. Maybe
# this function should work the other way round, i.e. take a 1 letter code
# and translate to 1 letter code for "new" mutate function.
#
def mutate_residue_redundant(residue_number, chain_id, imol,
residue_type, insertion_code):
ins_code = insertion_code
dic_type_1lc = {"ALA": "A", "ARG": "R", "ASN": "N", "ASP": "D",
"CYS": "C", "GLN": "Q", "GLU": "E", "GLY": "G",
"HIS": "H", "ILE": "I", "LEU": "L", "LYS": "K",
"MET": "M", "PHE": "F", "PRO": "P", "SER": "S",
"THR": "T", "TRP": "W", "TYR": "Y", "VAL": "V"}
if (residue_type in dic_type_1lc):
res_type_1lc = dic_type_1lc[residue_type]
else:
# if not standard aa then set it to Ala
res_type_1lc = "A"
coot.mutate(imol, chain_id, residue_number, "", res_type_1lc)
# Prompted by Tim Gruene's email to CCP4bb 20060201.
# Turn all residues (including GLY) of imol to ALA.
#
# type is an optional argument. if type is 'SER' then build polySer,
# if type is 'GLY', build polyGly.
#
# 1 or 2 args are:
#
# 1.) imol
#
# 2.) [optional] type, if type is "SER" then build polySer,
# if type is "GLY", build polyGly.
#
def poly_ala(imol, res_type=False):
if coot.is_valid_model_molecule(imol):
coot.make_backup(imol)
backup_mode = coot.backup_state(imol)
imol_map = coot.imol_refinement_map()
coot.turn_off_backup(imol)
dic_sg = {"SER": "S", "Ser": "S", "GLY": "G", "Gly": "G"}
if (res_type):
# residue name given!
if ((len(res_type) == 1) and (res_type in list(dic_sg.values()))):
single_letter_code = res_type
else:
if (res_type in dic_sg):
single_letter_code = dic_sg[res_type]
else:
print("BL WARNING:: unrecognised residue name %s given" % res_type)
return
else:
single_letter_code = "A"
for chain_id in coot_utils.chain_ids(imol):
n_residues = coot.chain_n_residues(chain_id, imol)
for serial_number in range(n_residues):
coot.mutate_single_residue_by_serial_number(serial_number,
chain_id,
imol,
single_letter_code)
if (backup_mode == 1):
coot.turn_on_backup(imol)
else:
print("BL WARNING:: no valid model molecule", imol)
# Delete (back to the CB stub) the side change in the range
# resno-start to resno-end
#
def delete_sidechain_range(imol, chain_id, resno_start, resno_end):
if coot_utils.valid_model_molecule_qm(imol):
coot.make_backup(imol)
backup_mode = coot.backup_state(imol)
coot.turn_off_backup(imol)
for resno in coot_utils.number_list(resno_start, resno_end):
coot.delete_residue_sidechain(imol, chain_id, resno, "", 0)
if (backup_mode == 1):
coot.turn_on_backup(imol)
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