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# what_check.py
# Copyright (C) 2008 Bernhard Lohkamp, The University of York
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# " 53" -> "53", " " -> ""
def strip_leading_spaces(str):
return str.lstrip()
# consider for coot_utils
def go_to_residue_by_spec(imol, spec):
def atom_spec_qm(spec):
return (len(spec) == 5)
# main line
coot_utils.set_go_to_atom_molecule(imol)
if (atom_spec_qm(spec)):
atom_name = spec[3]
else:
atom_name = " CA "
coot_utils.set_go_to_atom_chain_residue_atom_name(spec[0],
spec[1],
atom_name)
# consider for coot_utils
def residue_spec_to_string(spec):
print("DEBUG:: in residue_spec_to_string() with spec", spec)
if len(spec) == 4:
return (spec[1] + str(spec[2]) + spec[3])
else:
return (spec[0] + str(spec[1]) + spec[2])
# make this internal
#
# where line is something like " 53 HIS ( 53 ) A12"
# ignore xxxxI Cyy
# xxxx is 4char resno, I insertion code, C chain id, yy is model number
#
# return a residue spec, or False
#
def get_flip_residue(line):
l = len(line)
if (l < 19):
return False
else:
resno_string = line[11:15]
try:
resno = int(resno_string)
except:
return False
inscode_pre = line[15:16]
if (inscode_pre == " "):
inscode = ""
else:
inscode = inscode_pre
chain_id = line[18:19]
print("found", resno, inscode, chain_id)
return [chain_id, resno, inscode]
def convert_to_button_info(problemed_res_list):
#print "convert_to_button_info got", problemed_res_list
button_label = problemed_res_list[1]
problem_string = problemed_res_list[0]
action_func = problemed_res_list[2]
residue_spec_list = problemed_res_list[3]
o = map(lambda x: [problem_string, button_label, action_func, x],
residue_spec_list)
#print "convert_to_button_info returns", o
return o
# A problemed-res-list is improper pair where the car is a pair of
# string, one describing the problem, and the other being the "fix
# it" button label. The cdr is a list of residue specs.
#
# A problemed_flip_list_list is a list of those things.
#
def problem_residues2dialog(imol, problemed_res_list_list):
if (problemed_res_list_list):
def button_list():
ret = []
converted_list = map(convert_to_button_info, problemed_res_list_list)
for problemed_list in converted_list:
for flip_res_info in problemed_list:
flip_res_spec = flip_res_info[3]
button_label = flip_res_info[1]
action_func = flip_res_info[2]
problem_string = flip_res_info[0]
ret.append([[problem_string + " " + residue_spec_to_string(flip_res_spec),
"go_to_residue_by_spec(" + str(imol) + ", " + str(flip_res_spec) + ")"],
[button_label,
str(action_func) + "(" + str(imol) + ", " + str(flip_res_spec) + ")"]])
#print "BL DEBUG:: returning button_list", ret
return ret
coot_gui.dialog_box_of_pairs_of_buttons(imol,
"What-Check Report",
[270, 300],
# buttons is a list of: [[button_1_label, button_1_action,],
# [button_2_label, button_2_action]]
# The button_1_action function is a string.
# The button_2_action function is a string.
button_list(),
" Close ")
# action is either 'gui' (then we get a gui) or 'apply-actions', then the model
# modifications are automatically applied.
#
def parse_check_db(imol, file_name, action):
#
global my_flip, my_rsr, my_delete_atom, my_rotamer_search
def my_flip(imol_local, res_spec):
coot.do_180_degree_side_chain_flip(imol_local,
res_spec[0],
res_spec[1],
res_spec[2],
"")
def my_rsr(imol_local, res_spec):
coot_utils.with_auto_accept([refine_zone, imol_local, res_spec[0], res_spec[1],
res_spec[1], ""])
#
def my_delete_atom(imol, atom_spec):
ls = [imol] + atom_spec
print("calling delete_atom with args", ls)
coot.delete_atom(*ls)
#
def my_rotamer_search(imol, res_spec):
chain_id = res_spec[0]
resno = res_spec[1]
ins_code = res_spec[2]
altloc = ""
imol_map = coot.imol_refinement_map()
if (coot_utils.valid_map_molecule_qm(imol_map)):
print( "rotamer search with imol: %s chain: %s resno: %s inscode: %s" \
%(imol, chain_id, resno, ins_code))
coot.auto_fit_best_rotamer(resno, altloc, ins_code, chain_id, imol, imol_map, 1, 0.01)
else:
coot.add_status_bar_text("No refinement map available, no rotamer fit")
# return False or a residue spec:
def line2residue_spec(line):
if (len(line) >21):
resno_string = line[26:30]
try:
resno = int(resno_string)
except:
print("BL WARNING:: no int resno -> return")
return False
inscode_pre = line[40:41]
if (inscode_pre == "_"):
inscode = ""
else:
inscode = inscode_pre
chain_id_pre = line[19:20]
chain_id = " " if (chain_id_pre == "_") else chain_id_pre
return [chain_id, resno, inscode]
# return False or an atom_spec
# an atom_spec is [chain_id, resno, ins_code, atom_name, alt_conf]
#
def line2atom_spec(line):
if (len(line) > 53):
resno_string = line[26:30]
try:
resno = int(resno_string)
except:
return False
inscode_pre = line[40:41]
inscode = "" if (inscode_pre == "_") else inscode_pre
chain_id_pre = line[19:20]
chain_id = "" if (chain_id_pre == "_") else chain_id_pre
atom_name_pre = line[47:51]
atom_name = atom_name_pre
alt_conf = ""
print("found atom name %s resno %s (from %s) inscode %s (%s) chain_id %s" \
%(atom_name, resno, resno_string, inscode_pre, inscode, chain_id))
return [chain_id, resno, inscode, atom_name, alt_conf]
def apply_actions(imol, action_list):
for action in action_list:
func = action[0]
baddie_list = action[1]
print( "BL DEBUG:: action and baddie_list", action, baddie_list)
imol_list = map(lambda x: imol, baddie_list)
print( "BL DEBUG:: imol_list", imol_list)
print( "applying %s to %s" %(func, baddie_list))
print( "BL DEBUG:: len of lists", len(imol_list), len(baddie_list))
map(func, imol_list, baddie_list)
# main line
print( "parse_whatcheck_report: parsing output of what-if...")
found_flip_table = False
found_h2ohbo_table = False
found_BMPCHK_table = False
found_NAMCHK_table = False
found_PLNCHK_table = False
h2o_h_bond_less_list = []
plane_list = []
flip_list = []
namchk_list = []
bump_list = []
if (os.path.isfile(file_name)):
fin = open(file_name, 'r')
lines = fin.readlines()
fin.close()
for line in lines:
line = line.rstrip('\n') # remove trailing \n
if (line == "//"):
found_flip_table = False
found_h2ohbo_table = False
found_BMPCHK_table = False
found_NAMCHK_table = False
found_PLNCHK_table = False
if (found_flip_table):
if (len(line) > 12):
attr_type = line[0:11]
if (attr_type == " Name :"):
#print "found flip name", line
res = line2residue_spec(line)
if (res):
flip_list.append(res)
if (line == "CheckID : HNQCHK"):
found_flip_table = True
if (found_h2ohbo_table):
if (len(line) > 12):
attr_type = line[0:11]
if (attr_type == " Name :"):
#print "found h2obmo name", line
atom = line2atom_spec(line)
if (atom):
h2o_h_bond_less_list.append(atom)
if (line == "CheckID : H2OHBO"):
found_h2ohbo_table = True
if (found_BMPCHK_table):
if (len(line) > 12):
attr_type = line[0:11]
if (attr_type == " Name :"):
#print "found bump", line
res = line2residue_spec(line)
if (res):
bump_list.append(res)
if (line == "CheckID : BMPCHK"):
found_BMPCHK_table = True
if (found_NAMCHK_table):
if (len(line) > 12):
attr_type = line[0:11]
if (attr_type == " Name :"):
res = line2residue_spec(line)
if (res):
namchk_list.append(res)
if (line == "CheckID : NAMCHK"):
found_NAMCHK_table = True
if (found_PLNCHK_table):
if (len(line) > 12):
attr_type = line[0:11]
if (attr_type == " Name :"):
res = line2residue_spec(line)
if (res):
plane_list.append(res)
if (line == "CheckID : PLNCHK"):
found_PLNCHK_table = True
#print "Here flip_list is", flip_list
#print "Here h2o-h-bond-less-list is", h2o_h_bond_less_list
#print "Here bump_list is", bump_list
print( "Here plane_list is", plane_list)
if (action == 'gui'):
problem_residues2dialog(imol, [
["Needs flipping", "Flip it", "my_flip", flip_list],
["Water with no H-bonds", "Delete it", "my_delete_atom", h2o_h_bond_less_list],
["Has Bumps", "Rotamer Search", "my_rotamer_search", bump_list],
["Nomenclature error", "180 degree flip", "my_flip", namchk_list]])
elif (action == 'apply-actions'):
apply_actions(imol, [
# [my_flip, flip_list],
# [my_delete_atom, h2o_h_bond_less_list],
# [my_rotamer_search, bump_list],
[my_rsr, plane_list]
# [my_flip, namchk_list]
])
else:
print( "INFO:: wrong action input")
else:
print( "file not found", file_name)
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