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import coot_utils
import coot_gui_api
from gi.repository import Gtk
import coot
import gi
gi.require_version('Gtk', '4.0')
import coot_gui
def res_name_from_atom_spec(atom_spec):
imol = atom_spec[1]
res_name = coot.residue_name(imol,
atom_spec[2],
atom_spec[3],
atom_spec[4])
return res_name
def user_defined_add_single_bond_restraint():
m = "Click on 2 atoms to define the additional bond restraint"
coot.add_status_bar_text(m)
def make_restr(*args):
atom_spec_1 = args[0]
atom_spec_2 = args[1]
imol = atom_spec_1[1]
print("BL DEBUG:: imol: %s spec 1: %s and 2: %s" %
(imol, atom_spec_1, atom_spec_2))
coot.add_extra_bond_restraint(imol,
atom_spec_1[2],
atom_spec_1[3],
atom_spec_1[4],
atom_spec_1[5],
atom_spec_1[6],
atom_spec_2[2],
atom_spec_2[3],
atom_spec_2[4],
atom_spec_2[5],
atom_spec_2[6],
1.54, 0.02) # generic distance?!
coot.user_defined_click_py(2, make_restr)
def user_defined_add_arbitrary_length_bond_restraint(bond_length=2.0):
# maybe make a generic one....
def make_restr(text_list, continue_qm):
s = "Now click on 2 atoms to define the additional bond restraint"
coot.add_status_bar_text(s)
dist = text_list[0]
try:
bl = float(dist)
except:
bl = False
coot.add_status_bar_text(
"Must define a number for the bond length")
if bl:
# save distance for future use?!
def make_restr_dist(*args):
atom_spec_1 = args[0]
atom_spec_2 = args[1]
imol = atom_spec_1[1]
print("BL DEBUG:: imol: %s spec 1: %s and 2: %s" %
(imol, atom_spec_1, atom_spec_2))
coot.add_extra_bond_restraint(imol,
atom_spec_1[2],
atom_spec_1[3],
atom_spec_1[4],
atom_spec_1[5],
atom_spec_1[6],
atom_spec_2[2],
atom_spec_2[3],
atom_spec_2[4],
atom_spec_2[5],
atom_spec_2[6],
bl, 0.035)
coot.user_defined_click(2, make_restr_dist)
if continue_qm:
user_defined_add_arbitrary_length_bond_restraint(bl)
def stay_open(*args):
pass
# generic_single_entry("Add a User-defined extra distance restraint",
# "2.0",
# "OK...",
# lambda text: make_restr(text))
coot_gui.generic_multiple_entries_with_check_button(
[["Add a User-defined extra distance restraint",
str(bond_length)]],
["Stay open?", lambda active_state: stay_open(active_state)],
"OK...",
lambda text, stay_open_qm: make_restr(text, stay_open_qm))
# spec_1 and spec_2 are 7-element coot_utils.atom_specs
#
def add_base_restraint(imol, spec_1, spec_2, atom_name_1, atom_name_2, dist):
"""
spec_1 and spec_2 are 7-element coot_utils.atom_specs
"""
print("add_base_restraint", imol, spec_1,
spec_2, atom_name_1, atom_name_2, dist)
coot.add_extra_bond_restraint(imol,
spec_1[2],
spec_1[3],
spec_1[4],
atom_name_1,
spec_1[6],
spec_2[2],
spec_2[3],
spec_2[4],
atom_name_2,
spec_2[6],
dist, 0.035)
def a_u_restraints(spec_1, spec_2):
imol = spec_1[1]
print("BL DEBUG:: add_base_restraint a u", imol,
spec_1, spec_2, " N6 ", " O4 ", 3.12)
add_base_restraint(imol, spec_1, spec_2, " N6 ", " O4 ", 3.12)
add_base_restraint(imol, spec_1, spec_2, " N1 ", " N3 ", 3.05)
add_base_restraint(imol, spec_1, spec_2, " C2 ", " O2 ", 3.90)
add_base_restraint(imol, spec_1, spec_2, " N3 ", " O2 ", 5.12)
add_base_restraint(imol, spec_1, spec_2, " C6 ", " O4 ", 3.92)
add_base_restraint(imol, spec_1, spec_2, " C4 ", " C6 ", 8.38)
def g_c_restraints(spec_1, spec_2):
imol = spec_1[1]
print("BL DEBUG:: add_base_restraint gc", imol,
spec_1, spec_2, " O6 ", " N4 ", 3.08)
add_base_restraint(imol, spec_1, spec_2, " N6 ", " O4 ", 3.12)
add_base_restraint(imol, spec_1, spec_2, " N1 ", " N3 ", 3.04)
add_base_restraint(imol, spec_1, spec_2, " N2 ", " O2 ", 3.14)
add_base_restraint(imol, spec_1, spec_2, " C4 ", " N1 ", 7.73)
add_base_restraint(imol, spec_1, spec_2, " C5 ", " C5 ", 7.21)
def dna_a_t_restraints(spec_1, spec_2):
imol = spec_1[1]
add_base_restraint(imol, spec_1, spec_2, " C2 ", " O2 ", 3.49)
add_base_restraint(imol, spec_1, spec_2, " N1 ", " N3 ", 2.85)
add_base_restraint(imol, spec_1, spec_2, " N6 ", " O4 ", 3.23)
add_base_restraint(imol, spec_1, spec_2, " C6 ", " C8 ", 9.94)
add_base_restraint(imol, spec_1, spec_2, " N1 ", " O2 ", 3.52)
def dna_g_c_restraints(spec_1, spec_2):
imol = spec_1[1]
add_base_restraint(imol, spec_1, spec_2, " O6 ", " N4 ", 2.72)
add_base_restraint(imol, spec_1, spec_2, " N1 ", " N3 ", 2.81)
add_base_restraint(imol, spec_1, spec_2, " N2 ", " O2 ", 2.83)
add_base_restraint(imol, spec_1, spec_2, " N9 ", " N1 ", 8.83)
def user_defined_RNA_A_form():
def make_restr(*args):
spec_1 = args[0]
spec_2 = args[1]
print("BL DEBUG:: have specs", spec_1, spec_2)
res_name_1 = res_name_from_atom_spec(spec_1)
res_name_2 = res_name_from_atom_spec(spec_2)
print("BL DEBUG:: have resnames", res_name_1, res_name_2)
# just check the first letter, should be save
if (res_name_1[0] == "G" and
res_name_2[0] == "C"):
g_c_restraints(spec_1, spec_2)
if (res_name_1[0] == "C" and
res_name_2[0] == "G"):
g_c_restraints(spec_2, spec_1)
if (res_name_1[0] == "A" and
res_name_2[0] == "U"):
a_u_restraints(spec_1, spec_2)
if (res_name_1[0] == "U" and
res_name_2[0] == "A"):
a_u_restraints(spec_2, spec_1)
coot.user_defined_click_py(2, make_restr)
def user_defined_DNA_B_form():
def make_restr(*args):
spec_1 = args[0]
spec_2 = args[1]
res_name_1 = res_name_from_atom_spec(spec_1)
res_name_2 = res_name_from_atom_spec(spec_2)
if (res_name_1 == "DG" and
res_name_2 == "DC"):
dna_g_c_restraints(spec_1, spec_2)
if (res_name_1 == "DC" and
res_name_2 == "DG"):
dna_g_c_restraints(spec_2, spec_1)
if (res_name_1 == "DA" and
res_name_2 == "DT"):
dna_a_t_restraints(spec_1, spec_2)
if (res_name_1 == "DT" and
res_name_2 == "DA"):
dna_a_t_restraints(spec_2, spec_1)
coot.user_defined_click_py(2, make_restr)
def user_defined_add_helix_restraints():
def make_restr(*args):
spec_1 = args[0]
spec_2 = args[1]
chain_id_1 = spec_1[2]
chain_id_2 = spec_2[2]
res_no_1 = spec_1[3]
res_no_2 = spec_2[3]
imol = spec_1[1]
if (chain_id_1 == chain_id_2):
# if backwards, swap 'em
if res_no_2 < res_no_1:
tmp = res_no_1
res_no_1 = res_no_2
res_no_2 = tmp
for rn in range(res_no_1, res_no_2 - 2):
coot.add_extra_bond_restraint(imol,
chain_id_1, rn, "", " O ", "",
chain_id_1, rn + 3, "", " N ", "",
3.18, 0.035)
if (rn + 4 <= res_no_2):
coot.add_extra_bond_restraint(imol,
chain_id_1, rn, "", " O ", "",
chain_id_1, rn + 4, "", " N ", "",
2.91, 0.035)
coot.user_defined_click_py(2, make_restr)
def user_defined_delete_restraint():
def del_restr(*args):
spec_1 = args[0]
spec_2 = args[1]
imol = spec_1[1]
coot.delete_extra_restraint_py(imol, ["bond", spec_1[2:], spec_2[2:]])
coot.user_defined_click_py(2, del_restr)
# exte dist first chain A resi 19 ins . atom N second chain A resi 19 ins . atom OG value 2.70618 sigma 0.4
#
def extra_restraints2refmac_restraints_file(imol, file_name):
restraints = list_extra_restraints(imol)
if restraints:
fin = open(file_name, 'w')
for restraint in restraints:
if (restraint[0] == 'bond'):
chain_id_1 = restraint[1][1]
resno_1 = restraint[1][2]
inscode_1 = restraint[1][3]
atom_1 = restraint[1][4]
chain_id_2 = restraint[2][1]
resno_2 = restraint[2][2]
inscode_2 = restraint[2][3]
atom_2 = restraint[2][4]
value = restraint[3]
esd = restraint[4]
fin.write("EXTE DIST FIRST CHAIN %s RESI %i INS %s ATOM %s "
% (chain_id_1 if (chain_id_1 != "" and chain_id_1 != " ") else ".",
resno_1,
inscode_1 if (
inscode_1 != "" and inscode_1 != " ") else ".",
atom_1))
fin.write(" SECOND CHAIN %s RESI %i INS %s ATOM %s "
% (chain_id_2 if (chain_id_2 != "" and chain_id_2 != " ") else ".",
resno_2,
inscode_2 if (
inscode_2 != "" and inscode_2 != " ") else ".",
atom_2))
fin.write("VALUE %f SIGMA %f\n" % (value, esd))
fin.close()
def res_name2plane_atom_name_list(res_name):
if not (isinstance(res_name, str)):
return False
else:
if (res_name == "DG"):
return ["N1", "C6", "O6", "C2", "N2", "N3", "C5", "C4", "N9", "N7", "C8", "C1'"]
elif (res_name == "DA"):
return ["N1", "C6", "C2", "N6", "N3", "C5", "C4", "N9", "N7", "C8", "C1'"]
elif (res_name == "DT"):
return ["N3", "C2", "O2", "C4", "O4", "C5", "C7", "C6", "N1", "C1'"]
elif (res_name == "DC"):
return ["N3", "C2", "O2", "C4", "N4", "C5", "C6", "N1", "C1'"]
elif (res_name == "G"):
return ["N1", "C6", "O6", "C2", "N2", "N3", "C5", "C4", "N9", "N7", "C8", "C1'"]
elif (res_name == "A"):
return ["N1", "C6", "C2", "N6", "N3", "C5", "C4", "N9", "N7", "C8", "C1'"]
elif (res_name == "T"):
return ["N3", "C2", "O2", "C4", "O4", "C5", "C7", "C6", "N1", "C1'"]
elif (res_name == "U"):
return ["N3", "C2", "O2", "C4", "O4", "C5", "C6", "N1", "C1'"]
elif (res_name == "C"):
return ["N3", "C2", "O2", "C4", "N4", "C5", "C6", "N1", "C1'"]
else:
return []
# example?
# exte stac plan 1 firs resi 99 chai A atoms { CB CG CD1 CD2 CE1 CE2 CZ OH } plan 2 firs resi 61 chai B atoms { CB CG CD1 CD2 CE1 CE2 CZ } dist 3.4 sddi 0.2 sdan 6.0 type 1
#
def write_refmac_parallel_plane_restraint(file_name,
res_spec_0, res_spec_1,
atom_list_0, atom_list_1):
fout = open(file_name, 'w')
fout.write("EXTE STACK PLAN 1 FIRST RESIDUE ")
fout.write(str(coot_utils.residue_spec_to_res_no(res_spec_0)))
fout.write(" INS . ") # hack
fout.write(" CHAIN ")
fout.write(coot_utils.residue_spec_to_chain_id(res_spec_0))
fout.write(" ATOMS { ")
for atom_name in atom_list_0:
fout.write(" " + atom_name + " ")
fout.write(" } PLAN 2 FIRST RESIDUE ")
fout.write(str(coot_utils.residue_spec_to_res_no(res_spec_1)))
fout.write(" INS . ") # hack
fout.write(" CHAIN ")
fout.write(coot_utils.residue_spec_to_chain_id(res_spec_1))
fout.write(" ATOMS { ")
for atom_name in atom_list_1:
fout.write(" " + atom_name + " ")
fout.write(" } DIST 3.4 SDDI 0.2 SDAN 6.0 TYPE 1 \n")
fout.close()
# maybe some return value that it worked to write at some point
def add_parallel_planes_restraint(imol, rs_0, rs_1):
print("in add_parallel_planes_restraint: rs_0: %s rs_1 %s" % (rs_0, rs_1))
rn_0 = coot_utils.residue_spec_to_residue_name(imol, rs_0)
rn_1 = coot_utils.residue_spec_to_residue_name(imol, rs_1)
atom_ls_0 = res_name2plane_atom_name_list(rn_0)
atom_ls_1 = res_name2plane_atom_name_list(rn_1)
write_refmac_parallel_plane_restraint(
"tmp.rst", rs_0, rs_1, atom_ls_0, atom_ls_1)
coot.add_refmac_extra_restraints(imol, "tmp.rst")
def user_defined_add_planes_restraint():
coot.add_status_bar_text(
"Click on 2 atoms to define the additional parallel planes restraint")
def make_restr(*args):
atom_0 = args[0]
atom_1 = args[1]
rs_0 = coot_utils.atom_spec_to_residue_spec(atom_0)
rs_1 = coot_utils.atom_spec_to_residue_spec(atom_1)
imol = coot_utils.atom_spec_to_imol(atom_0)
rn_0 = coot.residue_name(imol,
res_spec_utils.residue_spec_to_chain_id(
coot_utils.atom_spec_to_residue_spec(atom_0)),
res_spec_utils.residue_spec_to_res_no(
coot_utils.atom_spec_to_residue_spec(atom_0)),
coot_utils.residue_spec_to_ins_code(coot_utils.atom_spec_to_residue_spec(atom_0)))
rn_1 = coot.residue_name(imol,
res_spec_utils.residue_spec_to_chain_id(
coot_utils.atom_spec_to_residue_spec(atom_1)),
res_spec_utils.residue_spec_to_res_no(
coot_utils.atom_spec_to_residue_spec(atom_1)),
coot_utils.residue_spec_to_ins_code(coot_utils.atom_spec_to_residue_spec(atom_1)))
print("BL DEBUG:: got resname 0", rn_0)
print("BL DEBUG:: got resname 1", rn_1)
atom_ls_0 = res_name2plane_atom_name_list(rn_0)
atom_ls_1 = res_name2plane_atom_name_list(rn_1)
write_refmac_parallel_plane_restraint("tmp.rst",
rs_0, rs_1,
atom_ls_0, atom_ls_1)
coot.add_refmac_extra_restraints(imol, "tmp.rst")
coot.user_defined_click_py(2, make_restr)
if True:
if coot_gui_api.main_menubar():
menu = coot_gui.coot_menubar_menu("Restraints")
coot_gui.add_simple_coot_menu_menuitem(
menu,
"Add Simple C-C Single Bond Restraint...",
lambda func: user_defined_add_single_bond_restraint())
coot_gui.add_simple_coot_menu_menuitem(
menu,
"Add Distance Restraint...",
lambda func: user_defined_add_arbitrary_length_bond_restraint())
coot_gui.add_simple_coot_menu_menuitem(
menu,
"Add Helix Restraints...",
lambda func: user_defined_add_helix_restraints())
coot_gui.add_simple_coot_menu_menuitem(
menu,
"RNA A form bond restraints...",
lambda func: user_defined_RNA_A_form())
coot_gui.add_simple_coot_menu_menuitem(
menu,
"DNA B form bond restraints...",
lambda func: user_defined_DNA_B_form())
def combobox_to_molecule_number(combobox):
imol = -1
tree_iter = combobox.get_active_iter()
if tree_iter is not None:
model = combobox.get_model()
it = model[tree_iter]
imol = it[0]
return imol
coot_gui.add_simple_coot_menu_menuitem(
menu,
"Read Refmac Extra Restraints...",
lambda func:
coot_gui.generic_chooser_and_file_selector("Apply restraints to molecule",
coot_utils.valid_model_molecule_qm,
"File:", "",
lambda imol, file_name:
coot.add_refmac_extra_restraints(imol, file_name)))
coot_gui.add_simple_coot_menu_menuitem(
menu,
"Delete Extra Restraints...",
lambda func:
coot_gui.molecule_chooser_gui("Delete Extra Restraints for Molecule:",
lambda imol:
coot.delete_all_extra_restraints(imol)))
def set_prosmart_sigma_limit_func(low, high):
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
aa_ins_code, aa_atom_name, aa_alt_conf]:
coot.set_extra_restraints_prosmart_sigma_limits(
aa_imol, low, high)
# coot_gui.add_simple_coot_menu_menuitem(
# menu,
# "ProSMART restraints interesting limit to 0.5...",
# lambda func: set_prosmart_sigma_limit_func(-0.5, 0.5)
# )
# coot_gui.add_simple_coot_menu_menuitem(
# menu,
# "ProSMART restraints interesting limit to 2.5...",
# lambda func: set_prosmart_sigma_limit_func(-2.5, 2.5)
# )
# def set_extra_restraints_display_func(state):
# with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
# aa_ins_code, aa_atom_name, aa_alt_conf]:
# coot.set_show_extra_restraints(aa_imol, state)
# coot_gui.add_simple_coot_menu_menuitem(
# menu,
# "Undisplay Extra Restraints",
# lambda func: set_extra_restraints_display_func(0))
# coot_gui.add_simple_coot_menu_menuitem(
# menu,
# "Display Extra Restraints",
# lambda func: set_extra_restraints_display_func(1))
# def set_prosmart_display_CA_func(state):
# with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
# aa_ins_code, aa_atom_name, aa_alt_conf]:
# coot.set_extra_restraints_representation_for_bonds_go_to_CA(
# aa_imol, state)
# ProSMART menu item - but who needs it?
# coot_gui.add_simple_coot_menu_menuitem(
# menu,
# "Extra Restraints to CA",
# lambda func: set_prosmart_display_CA_func(1))
coot_gui.add_simple_coot_menu_menuitem(
menu,
"Extra Restraints Standard Representation",
lambda func: set_prosmart_display_CA_func(0))
coot_gui.add_simple_coot_menu_menuitem(
menu,
"Delete an Extra Restraint...",
lambda func: user_defined_delete_restraint())
def delete_restraints_func():
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]:
coot.delete_extra_restraints_for_residue(
aa_imol, aa_chain_id, aa_res_no, aa_ins_code)
coot_gui.add_simple_coot_menu_menuitem(
menu,
"Delete Restraints for this residue",
lambda func: delete_restraints_func()
)
def del_deviant_restr_func(text):
try:
n = float(text)
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]:
coot.delete_extra_restraints_worse_than(aa_imol, n)
except:
print("BL WARNING:: no float given")
coot_gui.add_simple_coot_menu_menuitem(
menu,
"Delete Deviant Extra Restraints...",
lambda func: coot_gui.generic_single_entry("Delete Restraints worse than ",
"4.0", " Delete Outlying Restraints ",
lambda text: del_deviant_restr_func(text))
)
coot_gui.add_simple_coot_menu_menuitem(
menu,
"Save as REFMAC restraints...",
lambda func:
coot_gui.generic_chooser_and_file_selector("Save REFMAC restraints for molecule",
coot_utils.valid_model_molecule_qm,
" Restraints file name: ",
"refmac-restraints.txt",
lambda imol, file_name:
extra_restraints2refmac_restraints_file(imol, file_name)))
coot_gui.add_simple_coot_menu_menuitem(
menu,
"Add Parallel Planes Restraint...",
lambda func:
user_defined_add_planes_restraint()
)
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