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global cache_ligand_metrics
cache_ligand_metrics = False
# return 3 things
#
def mtz_file_name2refinement_column_labels(file_name):
columns = coot.get_mtz_columns(file_name)
read_success = columns.read_success
if (not read_success == 1):
# unhappy path
print("Failed to read columms from file %s for map molecule %s" \
%(file_name, imol_map()))
else:
# happy path
f_cols = columns.f_cols
sigf_cols = columns.sigf_cols
rfree_cols = columns.r_free_cols
l1 = f_cols.size()
l2 = sigf_cols.size()
l3 = rfree_cols.size()
if (not all([x > 0 for x in [l1, l2 ,l3]])):
# unhappy path
print("Failed to find columns of the necessary types from %s: %s %s %s!" \
%(file_name, l1, l2, l3))
return False, False, False
else:
# happy path
f_col_label = f_cols[0].column_label
sigf_col_label = sigf_cols[0].column_label
r_free_col_label = rfree_cols[0].column_label
return f_col_label, sigf_col_label, r_free_col_label
def ligand_validation_metrics_gui_list_wrapper_pre(
imol, chain_id, res_no, ins_code, refmac_input_mtz_file_name,
fp_col, sigfp_col, rfree_col, refmac_dir):
global cache_ligand_metrics
m = ligand_check.get_metrics_for_ligand(imol, chain_id, res_no, ins_code,
refmac_input_mtz_file_name,
fp_col, sigfp_col, rfree_col, refmac_dir)
if cache_ligand_metrics:
m = [0.935339450836182, 10.6290054321289,
[0, 10, 18, 70, 143],
[-0.0306930494488489, 0.386785203839611, 0.0146206432429434, 10865.0,
5373.01106146351, -27.3189968762454, 0.0173681300165985, 0.0280039555722363,
-8.86567375069092e-10, -0.0025144037621947, 0.117837198078632, 0.120915851909265],
[0.952432048573266, 13.3150000572205, 13.9800000190735, 0.176323987538941]]
if (not isinstance(m, list)):
# unhappy path
print("WARNING:: no ligand metrics found.")
else:
# happy path ;-)
diff_d = 0.05
d = m[0]
mwz = m[1] # Mogul Z
contact_info = m[2] # number of bad contacts
bc = contact_info[0]
low_is_good = 1
high_id_good = 0
# if mogul ran OK, then we can display the mogul markup
#
if (isinstance(mwz, list)):
mogul_out_file_name = mwz[1]
coot.mogul_markup(imol, chain_id, res_no, ins_code,
mogul_out_file_name)
mwz = mwz[0]
percentile_d = coot.get_ligand_percentile("density_correlation", d, high_id_good)
percentile_diff_d = coot.get_ligand_percentile("coot_diff_map_correlation", diff_d, low_is_good)
percentile_mwz = coot.get_ligand_percentile("mogul_z_worst", mwz, low_is_good)
percentile_bc = coot.get_ligand_percentile("bumps_1", bc, low_is_good)
if (percentile_d < 0):
# just an example, but means we do not have ligands-2016.db
txt = "BL INFO:: we dont have ligands-2016.db, so \n" + \
"percentiles are no available and graph meaningless!"
coot.info_dialog(txt)
input_to_sliders = [["Direct map density correl.", percentile_d, d],
[" Diff map density correl.", percentile_diff_d, diff_d],
[" Mogul Z-worst", percentile_mwz, mwz],
[" Bad contacts", percentile_bc, bc]]
ligand_validation_sliders.ligand_validation_metrics_gui_list_wrapper(input_to_sliders)
#if (use_gui_qm != 2):
# disable for now since I cannot run mogul and test it in real...
if (0):
menu = coot_gui.coot_menubar_menu("Ligand")
def ligand_metric_slider_func():
imol_map = coot.imol_refinement_map()
if (not coot_utils.valid_map_molecule_qm(imol_map)):
coot.add_status_bar_text("No valid refinement map molecule")
else:
l = refmac_parameters(imol_map)
if l:
refmac_input_mtz_file_name = l[0]
else:
refmac_input_coot.mtz_file_name = mtz_file_name(imol_map)
refmac_dir = coot_utils.get_directory("coot-refmac")
f_col_label, sigf_col_label, r_free_col_label = \
mtz_file_name2refinement_column_labels(refmac_input_mtz_file_name)
print(" f_col_label:", f_col_label)
print(" sigf-col-label:", sigf_col_label)
print("rfree-col-label:", r_free_col_label)
with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
aa_ins_code, aa_atom_name, aa_alt_conf]:
ligand_validation_sliders.ligand_validation_metrics_gui_list_wrapper_pre(
aa_imol, aa_chain_id, aa_res_no, aa_ins_code,
refmac_input_mtz_file_name,
f_col_label, sigf_col_label, r_free_col_label,
refmac_dir)
add_simple_coot_menu_menuitem(
menu, "Ligand Metric Sliders",
lambda func: ligand_metric_slider_func())
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