1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
|
ligand_check_refmac_mtz = False
ligand_check_refmac_fobs_col = False
ligand_check_refmac_sigfobs_col = False
ligand_check_refmac_r_free_col = False
def ligand_check_refmac_columns(f_list, sigf_list, rfree_list):
# dummy function, not needed anywhere (as is)
# need the above as globals...
# happy path
# Using the first sigf (there should only be one typically)
# get the F label (Fx) from x/y/SIGFPx
#
pass
def jiggle_fit_active_residue():
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
aa_ins_code, aa_atom_name, aa_alt_conf]:
coot.fit_to_map_by_random_jiggle(aa_imol, aa_chain_id, aa_res_no,
aa_ins_code, 100, 1.0)
if (use_gui_qm != 2):
menu = coot_gui.coot_menubar_menu("Ligand")
coot_gui.add_simple_coot_menu_menuitem(
menu,
"Find Ligands...",
lambda func: coot.do_find_ligands_dialog())
coot_gui.add_simple_coot_menu_menuitem(
menu,
"Jiggle-Fit Ligand",
lambda func: jiggle_fit_active_residue())
coot_gui.add_simple_coot_menu_menuitem(
menu,
"Hydrogenate region",
lambda func: coot.hydrogenate_region(6))
coot_gui.add_simple_coot_menu_menuitem(
menu,
"SMILES -> 2D",
lambda func:
coot_gui.generic_single_entry("SMILES string",
"", " Send to 2D Viewer ",
lambda text: coot.smiles_to_ligand_builder(text)))
coot_gui.add_simple_coot_menu_menuitem(
menu,
"SMILES -> simple 3D",
lambda func:
coot_gui.generic_double_entry("Residue name", "SMILES string ", "LIG", "",
False, False,
"Import Molecule",
lambda text_1, text_2:
coot.import_rdkit_mol_from_smiles(text_1, text_2)))
coot_gui.add_simple_coot_menu_menuitem(
menu,
"Residue -> 2D",
lambda func:
coot_utils.using_active_atom(residue_to_ligand_builder,
"aa_imol", "aa_chain_id", "aa_res_no",
"aa_ins_code", 0.015))
if coot.enhanced_ligand_coot_p():
def flev_rdkit_func():
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
aa_ins_code, aa_atom_name, aa_alt_conf]:
prodrg_import.fle_view_with_rdkit(aa_imol, aa_chain_id, aa_res_no,
aa_ins_code, 4.2)
coot.set_flev_idle_ligand_interactions(1)
coot_gui.add_simple_coot_menu_menuitem(
menu,
"FLEV this residue",
lambda func: flev_rdkit_func()
)
coot_gui.add_simple_coot_menu_menuitem(
menu,
"Toggle FLEV Ligand Interactions",
lambda func: toggle_idle_ligand_interactions()
)
def go_solid_func(state):
set_display_generic_objects_as_solid(state)
graphics_draw()
add_simple_coot_menu_menuitem(
menu, "Solid Generic Objects",
lambda func: go_solid_func(1))
add_simple_coot_menu_menuitem(
menu, "Unsolid Generic Objects",
lambda func: go_solid_func(0))
def show_chem_func():
set_display_generic_objects_as_solid(1) # there may be consequences...
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
aa_ins_code, aa_atom_name, aa_alt_conf]:
coot.show_feats(aa_imol, aa_chain_id, aa_res_no, aa_ins_code)
coot_gui.add_simple_coot_menu_menuitem(
menu,
"Show Chemical Features",
lambda func: show_chem_func()
)
def rename_atoms_to_reference(menuitem):
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
aa_ins_code, aa_atom_name, aa_alt_conf]:
# user chooses cif_dict_file_name_out (provide default)
# reference_comp_id and new_comp_id
# args: entry_info_list, check_button_info, go_button_label, handle_go_function
coot_gui.generic_multiple_entries_with_check_button(
[[" Reference Residue Type: ", "ATP"],
[" New Residue Type: ", "RXC"],
["New Dictionary cif file name: ", "new-dictionary-RXC.cif"]],
False,
" OK ",
lambda ref_comp_id_txt_new_comp_id_txt_new_cif_file_name_txt: coot.match_this_residue_and_dictionary(aa_imol, aa_chain_id, aa_res_no, aa_ins_code, ref_comp_id_txt_new_comp_id_txt_new_cif_file_name_txt[2], ref_comp_id_txt_new_comp_id_txt_new_cif_file_name_txt[0], ref_comp_id_txt_new_comp_id_txt_new_cif_file_name_txt[1]))
coot_gui.add_simple_coot_menu_menuitem(
menu, "Rename Atom to Reference", rename_atoms_to_reference)
def go_solid_func(state):
set_display_generic_objects_as_solid(state)
coot.graphics_draw()
coot_gui.add_simple_coot_menu_menuitem(
menu, "Solid Generic Objects",
lambda func: go_solid_func(1))
coot_gui.add_simple_coot_menu_menuitem(
menu, "Unsolid Generic Objects",
lambda func: go_solid_func(0))
def tab_ligand_distortions_func():
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
aa_ins_code, aa_atom_name, aa_alt_conf]:
coot.print_residue_distortions(aa_imol, aa_chain_id, aa_res_no, aa_ins_code)
def display_ligand_distortions_func():
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
aa_ins_code, aa_atom_name, aa_alt_conf]:
set_display_generic_objects_as_solid(1)
coot.display_residue_distortions(aa_imol, aa_chain_id, aa_res_no, aa_ins_code)
coot_gui.add_simple_coot_menu_menuitem(
menu,
"Tabulate (on terminal) Ligand Distorsions",
lambda func: tab_ligand_distortions_func()
)
coot_gui.add_simple_coot_menu_menuitem(
menu,
"Display Ligand Distortions",
lambda func: display_ligand_distortions_func())
add_simple_coot_menu_menuitem(
menu,
"Quick Ligand Validate",
lambda func: gui_ligand_check_dialog_active_residue())
## # not interesting for the normal user!?
## def density_ligand_score_func():
## with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
## aa_ins_code, aa_atom_name, aa_alt_conf]:
## spec = [aa_chain_id, aa_res_no, aa_ins_code]
## r = coot.density_score_residue(aa_imol, spec, coot.imol_refinement_map())
## # BL says:: maybe a dialog for this?!
## print "density at ligand atoms:", r
## coot_gui.add_simple_coot_menu_menuitem(
## menu,
## "Density Score Ligand",
## lambda func: density_ligand_score_func()
## )
## def fetch_ligand_pdbe_func():
## with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
## aa_ins_code, aa_atom_name, aa_alt_conf]:
## comp_id = coot.residue_name(aa_imol, aa_chain_id, aa_res_no, aa_ins_code)
## print "here with residue name", comp_id
## s = coot_utils.get_SMILES_for_comp_id_from_pdbe(comp_id)
## if (isinstance(s, str)):
## pdbe_cif_file_name = os.path.join("coot-download", "PDBe-" + comp_id + ".cif")
## prodrg_import.import_from_3d_generator_from_mdl(pdbe_cif_file_name, comp_id)
## coot_gui.add_simple_coot_menu_menuitem(
## menu,
## "### [Fetch ligand description & generate restraints]",
## lambda func: fetch_ligand_pdbe_func()
## )
def probe_ligand_func():
global probe_command
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
aa_ins_code, aa_atom_name, aa_alt_conf]:
ss = "//" + aa_chain_id + "/" + str(aa_res_no)
imol_selection = coot.new_molecule_by_atom_selection(aa_imol, ss)
work_dir = coot_utils.get_directory("coot-molprobity")
tmp_selected_ligand_for_probe_pdb = os.path.join(work_dir,
"tmp-selected-ligand-for-probe.pdb")
tmp_protein_for_probe_pdb = os.path.join(work_dir,
"tmp-protein-for-probe.pdb")
generic_objects.probe_dots_file_name = os.path.join(work_dir, "probe.dots")
coot.set_mol_displayed(imol_selection, 0)
coot.set_mol_active(imol_selection, 0)
# BL comment: we assume H and view is correct.
#set_go_to_atom_molecule(imol)
#rc = residue_centre(imol, chain_id, res_no, ins_code)
#set_rotation_centre(*rc)
#hydrogenate_region(6)
coot.write_pdb_file(imol_selection, tmp_selected_ligand_for_probe_pdb)
coot.write_pdb_file(imol, tmp_protein_for_probe_pdb)
coot_utils.popen_command(probe_command, ["-u", "-once", str(aa_res_no), # -once or -both
"not " + str(aa_res_no),
"-density60",
tmp_selected_ligand_for_probe_pdb,
tmp_protein_for_probe_pdb],
[], generic_objects.probe_dots_file_name, False)
coot.handle_read_draw_probe_dots_unformatted(dots_file_name, aa_imol, 0)
coot.graphics_draw()
|
