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import coot
import coot_utils
def add_pyranose_pseudo_ring_plane_restraints(comp_id):
import re
def filter_out(plane_name_sub_string, plane_restraints):
return [s for s in plane_restraints if not plane_name_sub_string in s[0]]
restraints = coot.monomer_restraints_py(comp_id)
if (not isinstance(restraints, dict)):
print("failed to get %s restraints" %comp_id)
else:
plane_restraints = restraints["_chem_comp_plane_atom"]
new_plane_restraints = [["pseudo-ring-1", [" C1 ", " C2 ", " C4 ", " C5 "], 0.01],
["pseudo-ring-2", [" C2 ", " C3 ", " C5 ", " O5 "], 0.01],
["pseudo-ring-3", [" C3 ", " C4 ", " O5 ", " C1 "], 0.01]] + \
filter_out("pseudo-ring-", plane_restraints) # should be list already
restraints["_chem_comp_plane_atom"] = new_plane_restraints
coot.set_monomer_restraints_py(comp_id, restraints)
def add_synthetic_pyranose_planes():
for comp_id in ["NAG", "BMA", "MAN", "GAL", "GLC", "FUC", "XYP", "BGC"]:
add_pyranose_pseudo_ring_plane_restraints(comp_id)
def use_unimodal_pyranose_ring_torsions():
for tlc in ["NAG", "BMA", "MAN", "GAL", "GLC", "FUC", "XYP", "BGC"]:
coot.use_unimodal_ring_torsion_restraints(tlc)
def multi_add_linked_residue(imol, res_spec, residues_to_add):
"---------------- multi-add-linked-residue", imol, res_spec
coot.set_go_to_atom_molecule(imol)
wm = coot.matrix_state()
coot.set_matrix(wm/4.)
current_refinement_rate = coot.dragged_refinement_steps_per_frame()
current_residue_spec = res_spec
for residue_to_add in residues_to_add:
coot_utils.set_go_to_atom_from_res_spec(current_residue_spec)
coot.set_dragged_refinement_steps_per_frame(300)
if (not isinstance(current_residue_spec, list)):
print("OOps not a proper res_spec %s with residue_to_add: %s" %(current_residue_spec, residue_to_add))
return False
else:
if not residue_to_add:
return "done" # odd return?! why?
else:
if (not isinstance(residue_to_add, list) and \
not len(residue_to_add) == 2):
print("Oops - not a residue_link string pair when adding new_res_pair")
else:
new_res = residue_to_add[0]
new_link = residue_to_add[1]
new_res_spec = coot.add_linked_residue(imol,
coot_utils.res_spec_to_chain_id(current_residue_spec),
coot_utils.res_spec_to_res_no(current_residue_spec),
coot_utils.res_spec_to_ins_code(current_residue_spec),
new_res, new_link, 2) # add and fit mode
# residues_near_residue takes a 3-part spec and makes 3-part specs
if new_res_spec:
ls = coot.residues_near_residue_py(imol, current_residue_spec, 1.9)
cho_restraints_from_models.add_cho_restraints_for_residue(imol, new_res_spec)
with AutoAccept():
coot.refine_residues_py(imol, [current_residue_spec] + ls)
# make the new res the one to add to (remove starting bool)
current_residue_spec = new_res_spec[1:]
# restore refinement mode and matrix weight
coot.set_dragged_refinement_steps_per_frame(current_refinement_rate)
coot.set_matrix(wm)
# return the new molecule number
#
def new_molecule_from_this_glyco_tree():
with coot_utils.UsingActiveAtom(True) as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code,
aa_atom_name, aa_alt_conf, aa_res_spec]:
tree_residues = glyco_tree_residues(aa_imol, aa_res_spec)
imol = new_molecule_by_residue_specs(aa_imol, tree_residues)
return imol
# also "precursor"
# high mannose was used for human
# high mannose is now used for human too
# call this "High Mannose" in the GUI
#
def oligomannose_tree():
ret = [["NAG-ASN", "NAG"],
["BETA1-4", "NAG"],
["BETA1-4", "BMA"],
[
["ALPHA1-6", "MAN"],
[
["ALPHA1-6", "MAN"],
["ALPHA1-3", "MAN"]
],
[
["ALPHA1-3", "MAN"],
["ALPHA1-2", "MAN"]
]
],
[
["ALPHA1-3", "MAN"],
["ALPHA1-2", "MAN"],
["ALPHA1-2", "MAN"],
["ALPHA1-3", "GLC"],
["ALPHA1-3", "GLC"],
["ALPHA1-2", "GLC"]
]
]
return ret
# Hybrid is for any system
#
# Plant Hybrid also allows an alpha1-3 FUC
#
# hybrid mammal
#
def hybrid_mammal_tree():
ret = [["NAG-ASN", "NAG"],
[
[["BETA1-4", "NAG"],
["BETA1-4", "BMA"],
[
[
["ALPHA1-6", "MAN"],
[
["ALPHA1-6", "MAN"],
["ALPHA1-3", "MAN"]
]
],
[
["ALPHA1-3", "MAN"],
["BETA1-2", "NAG"],
["BETA1-4", "GAL"],
[
["ALPHA2-3, SIA"],
["ALPHA2-6, SIA"]
]
],
["BETA1-4", "NAG"]
]
],
["ALPHA1-6", "FUC"]
]
]
return ret
# hybrid plant
#
def hybrid_plant_derived_tree():
ret = [["NAG-ASN", "NAG"],
[
[["BETA1-4", "NAG"],
["BETA1-4", "BMA"],
[
[
["ALPHA1-6", "MAN"],
[
["ALPHA1-6", "MAN"],
["ALPHA1-3", "MAN"]
]
],
[
["ALPHA1-3", "MAN"],
["BETA1-2", "NAG"],
["BETA1-4", "GAL"],
[
["ALPHA2-3, SIA"],
["ALPHA2-6, SIA"]
]
],
["XYP-BMA", "XYP"],
["BETA1-4", "NAG"]
]
],
["ALPHA1-6", "FUC"],
["ALPHA1-3", "FUC"]
]
]
return ret
# complex mammal
# biantennary mammal
def complex_mammal_tree():
ret = [["NAG-ASN", "NAG"],
[
[["BETA1-4", "NAG"],
["BETA1-4", "BMA"],
[
["ALPHA1-6", "MAN"],
["BETA1-2", "NAG"],
["BETA1-4", "GAL"],
[["ALPHA2-3", "SIA"],
["ALPHA2-6", "SIA"]
]
],
[
["ALPHA1-3", "MAN"],
["BETA1-2", "NAG"],
["BETA1-4", "GAL"],
[["ALPHA2-3", "SIA"],
["ALPHA2-6", "SIA"]
]
],
[
["BETA1-4", "NAG"]
]
],
["ALPHA1-6", "FUC"]
]
]
return ret
# complex plant
# plant biantennary
def complex_plant_tree():
ret = [["NAG-ASN", "NAG"],
[
[["BETA1-4", "NAG"],
["BETA1-4", "BMA"],
[
["ALPHA1-6", "MAN"],
[
[["BETA1-2", "NAG"],
["BETA1-4", "GAL"],
[["ALPHA2-3", "SIA"],
["ALPHA2-6", "SIA"]
]],
[["BETA1-6", "NAG"],
["BETA1-4", "GAL"]]
]
],
[
["ALPHA1-3", "MAN"],
[
[["BETA1-2", "NAG"],
["BETA1-4", "GAL"],
[["ALPHA2-3", "SIA"],
["ALPHA2-6", "SIA"]
]],
[["BETA1-4", "NAG"],
["BETA1-4", "GAL"]]
]
],
[
["BETA1-4", "NAG"]
],
[
["XYP-BMA", "XYP"]
]
],
["ALPHA1-3", "FUC"]
]
]
return ret
# old
def paucimannose_tree():
ret = [["NAG-ASN", "NAG"],
[ ["ALPHA1-3", "FUC"] ],
[ ["BETA1-4", "NAG"],
["BETA1-4", "BMA"],
[ ["XYP-BMA", "XYP"] ],
[ ["ALPHA1-3", "MAN"] ],
[ ["ALPHA1-6", "MAN"] ]
]
]
return ret
# now can be user defined
global add_linked_residue_tree_correlation_cut_off
add_linked_residue_tree_correlation_cut_off = 0.50
def add_linked_residue_add_cho_function(imol, parent, res_pair):
global add_linked_residue_tree_correlation_cut_off
def well_fitting_qm(res_spec):
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
aa_ins_code, aa_atom_name, aa_alt_conf]:
neighbs = coot.residues_near_residue_py(aa_imol, res_spec, 4)
c = coot.map_to_model_correlation(imol, [res_spec], neighbs, 0,
coot.imol_refinement_map())
print("######## new residue %s density correlation: %s" %(res_spec, c))
if (not coot_utils.isNumber(c)):
return False
else:
if c > add_linked_residue_tree_correlation_cut_off:
symm_clash = coot.clashes_with_symmetry(imol,
res_spec_utils.residue_spec_to_chain_id(res_spec),
res_spec_utils.residue_spec_to_res_no(res_spec),
coot_utils.residue_spec_to_ins_code(res_spec),
2.0)
if (symm_clash == 1):
return False
else:
return True
else:
return False
def centre_view_on_residue_centre(res_spec):
res_centre = residue_centre(imol,
res_spec_utils.residue_spec_to_chain_id(res_spec),
res_spec_utils.residue_spec_to_res_no(res_spec),
coot_utils.residue_spec_to_ins_code(res_spec))
if (isinstance(res_centre, list)):
coot.set_rotation_centre(*res_centre)
# main line
#
if (not isinstance(parent, list)):
print("WARNING:: OOps not a proper res_spec %s with residue_to_add: %s" %(parent, res_pair))
return False
else:
if not (len(res_pair) == 2):
print("Oops - not a residue-link string pair when adding res-pair", res_pair)
return False
else:
# OK! Go!
new_link = res_pair[0]
new_res_type = res_pair[1]
centre_view_on_residue_centre(parent)
tree_residues = glyco_tree_residues(imol, parent)
imol_save = new_molecule_by_residue_specs(imol,
tree_residues)
new_res_spec = coot.add_linked_residue(imol,
coot_utils.res_spec_to_chain_id(parent),
coot_utils.res_spec_to_res_no(parent),
coot_utils.res_spec_to_ins_code(parent),
new_res_type, new_link, 2)
# 2 = add and link mode
coot.set_mol_displayed(imol_save, 0)
coot.set_mol_active(imol_save, 0)
ls = coot.residues_near_residue_py(imol, parent, 1.9)
local_ls = [parent] + ls
cho_restraints_from_models.add_cho_restraints_for_residue(imol, new_res_spec)
coot.rotate_y_scene(100, 0.5)
with AutoAccept():
coot.refine_residues_py(imol, local_ls)
if (not isinstance(new_res_spec, list)):
# badness
return False
else:
# okay!?
preped_new_res_spec = new_res_spec[1:] # strip off leading result
if well_fitting_qm(preped_new_res_spec):
return preped_new_res_spec
else:
# ------------ bad fit -----------------
# delete residue and restore others
print("----------- That was not well fitting. Deleting:", preped_new_res_spec)
delete_extra_restraints_for_residue_spec(imol,
preped_new_res_spec)
coot_utils.delete_residue_by_spec(*preped_new_res_spec)
# restore glyco-tree residues from imol_save
coot.replace_fragment(imol, imol_save, "//")
return False
def add_linked_residue_tree(imol, parent, tree):
def func_test():
count = 10
pass # needed?
def process_tree(parent, tree, proc_func):
# helper function to test for a link, resname pair
#
def link_res_pair(pair):
# test if pair i.e. two elements
if len(pair) == 2:
# test if both are strings
res = [isinstance(x, str) for x in pair]
# could add tests for len pair[1] == 3 and "-" in pair[0]
return all(res)
return False
if not tree:
return []
if isinstance(tree[0], list) and not link_res_pair(tree[0]):
part_1 = process_tree(parent, tree[0], proc_func)
part_2 = process_tree(parent, tree[1:], proc_func)
return [part_1, part_2]
else:
new_res = proc_func(imol, parent, tree[0])
return [new_res, process_tree(new_res, tree[1:], proc_func)]
def is_just_an_ASN_qm(imol, glyco_tree):
print("glyco-tree:", glyco_tree)
if not isinstance(glyco_tree, list):
return False
else:
if not (len(glyco_tree) == 1):
return False
else:
with coot_utils.UsingActiveAtom(True) as [aa_imol, aa_chain_id, aa_res_no,
aa_ins_code, aa_atom_name, aa_alt_conf, aa_res_spec]:
res_spec = aa_res_spec
rn = coot.residue_name(imol,
res_spec_utils.residue_spec_to_chain_id(res_spec),
res_spec_utils.residue_spec_to_res_no(res_spec),
coot_utils.residue_spec_to_ins_code(res_spec))
if not isinstance(rn, str):
return False
else:
return rn == "ASN"
# main line of add_linked_residue_tree
#
add_synthetic_pyranose_planes()
use_unimodal_pyranose_ring_torsions()
coot.set_refine_with_torsion_restraints(1)
wm = coot.matrix_state()
coot.set_matrix(wm / 4.)
coot.set_residue_selection_flash_frames_number(1)
coot.set_go_to_atom_molecule(imol)
coot_utils.set_go_to_atom_from_res_spec(parent)
previous_m = coot.default_new_atoms_b_factor()
m = coot.median_temperature_factor(imol)
try:
new_m = m * 1.55
if new_m > 0:
coot.set_default_temperature_factor_for_new_atoms(new_m)
except:
print("BL INFO:: not changing default B for new carb atoms")
# prevent tree building if there is already a partial tree here
# (only proceed with the one ASN)
#
with coot_utils.UsingActiveAtom(True) as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code,
aa_atom_name, aa_alt_conf, aa_res_spec]:
start_tree = glyco_tree_residues(aa_imol, aa_res_spec)
# print "::::::::::::::::: start-tree:", start_tree
# why do we need both test here?
# 5n11 needs the is-just-an-ASN? test
# 5n09/5wzy needs the null test.
# Hmmm.
if not ((start_tree == []) or (is_just_an_ASN_qm(aa_imol, start_tree))):
coot.info_dialog("Must start on Single ASN")
print("start_tree:", start_tree)
else:
# OK, continue
start_pos_view = coot_utils.add_view_here("Glyco Tree Start Pos")
process_tree(parent, tree, add_linked_residue_add_cho_function)
coot.go_to_view_number(start_pos_view, 0)
with AutoAccept():
coot.refine_residues_py(aa_imol, glyco_tree_residues(aa_imol, aa_res_spec))
# add a test here that the tree here (centre of screen) matches a known tree.
#
# and that each is 4C1 (or 1C4 for FUC?) (XYP?)
#
# validate build - no more
# g = glyco_validate()
# BL says:: lets not auto delete since we may remove sugars in
# the middle of the tree (OK? doesnt take RSCC into account)
# 20180330-PE OK.
#
# g.auto_delete_residues()
# g.validation_dialog()
# reset
coot.set_default_temperature_factor_for_new_atoms(previous_m)
coot.set_matrix(wm)
def add_linked_residue_with_extra_restraints_to_active_residue(new_res_type,
link_type):
wm = coot.matrix_state()
coot.set_matrix(wm / 8.)
coot.set_refine_with_torsion_restraints(1)
coot.set_add_linked_residue_do_fit_and_refine(0)
with coot_utils.UsingActiveAtom(True) as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code,
aa_atom_name, aa_alt_conf, aa_res_spec]:
new_res_spec = coot.add_linked_residue(aa_imol, aa_chain_id, aa_res_no,
aa_ins_code, new_res_type, link_type, 2)
if isinstance(new_res_spec, list):
cho_restraints_from_models.add_cho_restraints_for_residue(aa_imol, new_res_spec)
# refine that
with AutoAccept():
residues = [aa_res_spec] + coot.residues_near_residue_py(aa_imol, aa_res_spec, 1.9)
coot.refine_residues_py(aa_imol, residues)
coot.set_matrix(wm)
def delete_all_cho():
delete_cho_ls = []
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code,
aa_atom_name, aa_alt_conf]:
if coot_utils.valid_model_molecule_qm(aa_imol):
with coot_utils.NoBackups(aa_imol):
for chain_id in coot_utils.chain_ids(aa_imol):
for res_serial in range(coot.chain_n_residues(chain_id, aa_imol)):
res_no = coot.seqnum_from_serial_number(aa_imol,
chain_id, res_serial)
rn = coot.residue_name(aa_imol, chain_id, res_no, "")
if (isinstance(rn, str)):
if rn in ["NAG", "MAN", "BMA", "FUC", "XYP",
"SIA", "GLC", "GAL"]:
residue_spec = [chain_id, res_no, ""]
delete_cho_ls.append(residue_spec)
# now we have delete_residues, we don't need to delete them one by one
# for cho_res_spec in delete_cho_ls:
# coot.delete_residue(aa_imol,
# res_spec_utils.residue_spec_to_chain_id(cho_res_spec),
# res_spec_utils.residue_spec_to_res_no(cho_res_spec), "")
coot.delete_residues_py(aa_imol, delete_cho_ls)
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