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import coot
import coot_utils
def new_molecule_with_nudged_residues(imol, residue_spec,
residue_delta, nudge_by):
imol_new = coot.copy_molecule(imol)
chain_id = res_spec_utils.residue_spec_to_chain_id(residue_spec)
resno_start = res_spec_utils.residue_spec_to_res_no(residue_spec) - residue_delta
resno_end = res_spec_utils.residue_spec_to_res_no(residue_spec) + residue_delta
if coot_utils.debug():
print("imol:", imol)
print("residue_spec:", residue_spec)
print("residue_delta:", residue_delta)
print("resno_start:", resno_start)
print("resno_end:", resno_end)
print("nudge_by:", nudge_by)
status = coot.nudge_residue_sequence(imol_new, chain_id, resno_start, resno_end,
nudge_by, 1)
if (status == 0):
# fail
s = "Failed to nudge around " + chain_id + " " + \
str(coot_utils.residue_spec_to_res_no(residue_spec))
coot.add_status_bar_text(s)
coot.close_molecule(imol_new)
return -1 # return a bad new molecule id
else:
return imol_new
def nudge_residues_gui(imol, residue_spec):
def delete_event(*args):
window.destroy()
return False
def change_nudge(*args):
v = adj.value
v_int = int(v) # rounding!?
rdt = entry.get_text()
try:
rd = int(rdt)
except:
print("BL WARNING:: could not convert %s to a number, set to 1 then." %rdt)
# or shall we bail!?
rd = 1
residue_delta = rd
imol_new = new_molecule_with_nudged_residues(imol, residue_spec,
residue_delta, v_int)
# return imol_ne # why, for who?
window = gtk.Window(gtk.WINDOW_TOPLEVEL)
vbox = gtk.VBox(False, 4)
hbox_0 = gtk.HBox(False, 4)
hbox_1 = gtk.HBox(False, 4)
hbox_2 = gtk.HBox(False, 4)
label_1 = gtk.Label(label=" Nudge by ")
label_2 = gtk.Label(label=" residues ")
label_n = gtk.Label(label=" Nudge ")
res_lab = " residues up and down from " + \
res_spec_utils.residue_spec_to_chain_id(residue_spec) + " " + \
str(coot_utils.residue_spec_to_res_no(residue_spec))
label_a = gtk.Label(label=res_lab)
m_lab = " Nudging residues from Molecule:\n " + \
str(imol) + ": " + \
coot_utils.strip_path(coot.molecule_name(imol))
label_m = gtk.Label(label=m_lab)
entry = gtk.Entry()
h_sep = gtk.HSeparator()
adj = gtk.Adjustment(0., -30., 59., 0.01, 1., 29.)
slider = gtk.HScale(adj)
buttons_hbox = gtk.HBox(False, 4)
cancel_button = gtk.Button(label=" Close ")
residue_delta = 5 # but isnt it a variable?!
window.set_title("Nudge Residues")
vbox.append(hbox_0)
vbox.append(hbox_1)
vbox.append(hbox_2)
vbox.append(h_sep)
vbox.append(buttons_hbox)
hbox_0.append(label_m)
hbox_1.append(label_n)
hbox_1.append(entry)
hbox_1.append(label_a)
hbox_2.append(label_1)
hbox_2.append(slider)
hbox_2.append(label_2)
buttons_hbox.pack_end(cancel_button, False, False, 4)
window.add(vbox)
window.set_size_request(350, 200)
entry.set_text("5")
entry.set_usize(30, -1)
slider.set_digits(0)
cancel_button.connect("clicked", delete_event)
adj.connect("value_changed", change_nudge)
window.show_all()
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