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|
# shelx.py
# BL python adaption of shelx.scm by Paul Emsley
#
# Copyright (C) 2005, 2006, 2007 by Bernhard Lohkamp
# Copyright (C) 2007, 2008 by 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/>.
# Provide functions to handle shelx fcf file (which I believe to be old-style
# cif rather than mmCIF).
#
# So, in Coot, if it sees the extention of .fcf then it calls the
# fcf handler and the handler does the conversion, writes a new
# mmCIF file and then reads it.
#
import coot
from types import *
import numbers
def handle_shelx_fcf_file_old(filename):
import os
filename = os.path.normpath(filename)
# OK, so we have been passed a shelx fcf file.
# We need to run this through the awk filter.
# BL says: I guess in python it's easier to do it within python
output_mmCIF_file_name = filename + ".cif"
convert_shelx_fcf_to_cif(filename,output_mmCIF_file_name)
ret = coot.auto_read_cif_data_with_phases(output_mmCIF_file_name)
return ret
# read_cif_data_with_phases(output_mmCIF_file_name)
# coot.read_cif_data_with_phases_fo_fc(output_mmCIF_file_name)
def handle_shelx_fcf_file(filename):
return coot.read_small_molecule_data_cif(filename)
def convert_shelx_fcf_to_cif(fcf_filename,cif_filename):
import string, math
fin = False
fout = False
intable = 0
try:
fin = open(fcf_filename,'r')
except IOError:
print("BL ERROR:: Cannot read ", fcf_filename)
try:
fout = file(cif_filename,"w")
except IOError:
print("BL ERROR:: Cannot write ", cif_filename)
if (fin and fout):
lines = fin.readlines()
for line in lines:
if "_shelx_title" in line:
# dont write
pass
elif "_shelx_refln_list_code" in line:
# dont write
pass
elif "_shelx_F_calc_maximum" in line:
# dont write
pass
elif "_exptl_crystal_F_000" in line:
# dont write
pass
elif "_reflns_d_resolution_high" in line:
# dont write
pass
elif "_shelx_refln_list_code" in line:
# dont write
pass
elif "_shelx_F_calc_maximum" in line:
# dont write
pass
elif "_exptl_crystal_F_000" in line:
# dont write
pass
elif "_reflns_d_resolution_high" in line:
# dont write
pass
else:
if "_refln_F_squared_meas" in line:
line = line.replace("_refln_F_squared_meas"," _refln.F_meas")
if "_refln_F_squared_sigma" in line:
line = line.replace("_refln_F_squared_sigma"," _refln.F_meas_sigma")
# symm equivs:
if " _symmetry_equiv_pos_as_xyz" in line:
line = line.replace(" _symmetry_equiv_pos_as_xyz","_symmetry_equiv.pos_as_xyz")
if "_cell_length_a" in line:
line = line.replace("_cell_length_a","_cell.length_a ")
if "_refln_F_squared_meas" in line:
line = line.replace("_refln_F_squared_meas"," _refln.F_meas")
if "_refln_F_squared_sigma" in line:
line = line.replace("_refln_F_squared_sigma"," _refln.F_meas_sigma")
# symm equivs:
if "_symmetry_equiv_pos_as_xyz" in line:
line = line.replace("_symmetry_equiv_pos_as_xyz","_symmetry_equiv.pos_as_xyz")
if "_cell_length_a" in line:
line = line.replace("_cell_length_a","_cell.length_a ")
if "_cell_length_b" in line:
line = line.replace("_cell_length_b","_cell.length_b ")
if "_cell_length_c" in line:
line = line.replace("_cell_length_c","_cell.length_c ")
if "_cell_angle_alpha" in line:
line = line.replace("_cell_angle_alpha","_cell.angle_alpha ")
if "_cell_angle_beta" in line:
line = line.replace("_cell_angle_beta","_cell.angle_beta ")
if "_cell_angle_gamma" in line:
line = line.replace("_cell_angle_gamma","_cell.angle_gamma ")
if "_refln_index_h" in line:
line = line.replace("_refln_index_h"," _refln.index_h")
if "_cell_length_b" in line:
line = line.replace("_cell_length_b","_cell.length_b ")
if "_cell_length_c" in line:
line = line.replace("_cell_length_c","_cell.length_c ")
if "_cell_angle_alpha" in line:
line = line.replace("_cell_angle_alpha","_cell.angle_alpha ")
if "_cell_angle_beta" in line:
line = line.replace("_cell_angle_beta","_cell.angle_beta ")
if "_cell_angle_gamma" in line:
line = line.replace("_cell_angle_gamma","_cell.angle_gamma ")
if "_refln_index_h" in line:
line = line.replace("_refln_index_h"," _refln.index_h")
if "_refln_index_k" in line:
line = line.replace("_refln_index_k"," _refln.index_k")
if "_refln_index_l" in line:
line = line.replace("_refln_index_l"," _refln.index_l")
if "_refln_F_calc" in line:
line = line.replace("_refln_F_calc"," _refln.F_calc")
if "_refln_phase_calc" in line:
line = line.replace("_refln_phase_calc"," _refln.phase_calc")
intable = 1
if (intable == 1 and len(string.split(line))>5):
col = string.split(line)
col[3] = str(math.sqrt(float(col[3])))
if (float(col[3]) > 0.0):
col[4] = str(0.5 * (float(col[4]) + 0.0) / float(col[3]))
line = string.join(col) + "\n"
fout.write(line)
fin.close()
fout.close()
else:
print("BL ERROR:: IO error in conversion!")
global coot_shelxl_dir
coot_shelxl_dir = "coot-shelxl"
def remove_time_extensions(str):
# e.g. remove -2007-04-27_1326.24 from 03srv164-2007-04-27_1326.24
import re
pattern = "-20[0-9][0-9]-[01][0-9]-[0-3][0-9]_[0-2][0-9][0-5][-0-9].[0-5][-0-9]"
# we replace pattern with ''
result = re.sub(pattern,"",str)
return result
# BL says: shelxl_refine can have 3 arguments here:
#
# first: imol
#
# second: orig hkl file
#
# third: shelxh_flag , i.e. use shelxh instead of shelxl (in absenc of hkl
# inputfile this has to be written as: shelxh_flag=YOURSETTING
# True: use shelxh
# False: use shelxl (default)
#
def shelxl_refine(imol, hkl_file_in_maybe=False, shelxh_flag=False):
func = lambda ins_file_name: coot.write_shelx_ins_file(imol, ins_file_name)
shelxl_refine_inner(imol, hkl_file_in_maybe, func, shelxh_flag)
# shelxl refinement with input text
#
def shelxl_refine_primitive(imol, ins_text, hkl_file_in_maybe=False, shelxh_flag=False):
func = lambda ins_file_name: coot_utils.save_string_to_file(ins_text, ins_file_name, True)
shelxl_refine_inner(imol, hkl_file_in_maybe, func, shelxh_flag)
def shelxl_refine_inner(imol, hkl_file_in_maybe, func, shelxh_flag):
import os
import shutil
global coot_shelxl_dir
# First write out the imol-th molecule in shelx format.
# What should the filename be?
# Let's say that we read "abc.res"
# We want to create "abc-coot.ins". Ah, but what about the data file?
# Urg.
#
# This, as it stands, doesn't properly deal with incrementing the
# filenames.
if (shelxh_flag):
shelxl_exe = coot_utils.find_exe("shelxh", "PATH")
else:
shelxl_exe = coot_utils.find_exe("shelxl", "PATH")
if (not shelxl_exe):
print("WARNING:: can't find executable shelxl/h")
else:
orig_hkl_file = False
if (hkl_file_in_maybe and os.path.isfile(hkl_file_in_maybe)):
orig_hkl_file = hkl_file_in_maybe
dir = os.path.join(os.path.abspath("."), coot_shelxl_dir)
if (not os.path.isdir(dir)):
try:
os.mkdir(dir)
except:
pass
if (not os.path.isdir(dir)):
# We dont have shelxl dir and couldnt make it so exit!
print("Failed to make shelxl directory ", dir)
else:
# run shelx
stub = os.path.join(dir,(coot_utils.strip_path(coot_utils.strip_extension(coot.molecule_name(imol))) + "-" + coot_utils.unique_date_time_str()))
# BL says: shelxl only excepts filename <= 80 char, so check it before
if (len(stub) > 80):
print("BL WARNING:: filename %s too long! Has %s characters, only 80 are allowed!" %(stub, len(stub)))
else:
ins_filename = stub + ".ins"
res_filename = stub + ".res"
lst_filename = stub + ".lst"
fcf_filename = stub + ".fcf"
log_filename = stub + ".log"
hkl_filename = stub + ".hkl"
# BL says: non-unix OS python cant make a link. grr!
# So we have to make a copy of the passed hkl-file-in
# if we cannot create a link
# If we copied the file we maybe we should remove the
# copied file after use since it's large?!
#
# helper function to either link or copy file
# return True on sucess, False otherwise
def make_symlink(src_file, dst_file):
try:
print("make link from %s to %s" %(dst_file, src_file))
os.symlink(src_file, dst_file)
return True
except:
# failed to create link, try so copy
try:
print("copy %s to %s" %(src_file, dst_file))
shutil.copyfile(src_file, dst_file)
return True
except:
return False
# make a link to the passed hkl-file-in, if it was passed.
# (if not, we presume that this file (or the link) exists
# already. (Let's check that, and stop early if it doesn't
# exist)
if (orig_hkl_file):
symlink_target = False
if (len(orig_hkl_file) == 0):
# shouldnt happen!?
symlink_target = False
elif (hkl_filename[0:1] == "/" or hkl_filename[0:1] == "\\"):
# BL nore: maybe we shoudl use coot_utils.slash_start_qm here too?!
symlink_target = orig_hkl_file
else:
if (coot_utils.slash_start_qm(orig_hkl_file)):
symlink_target = orig_hkl_file
else:
symlink_target = "../" + orig_hkl_file
if symlink_target:
make_symlink(symlink_target, hkl_filename)
else:
# no input hklin or it wasnt an accessible file
#
# hklin was not given, let's generate a filename
# from the filename of the coordinates molecule
# imol, trial names are derived from the name of
# the coordinates molecule
trial_file_stub = coot_utils.strip_extension(coot.molecule_name(imol))
trial_hkl_file_name = trial_file_stub + ".hkl"
print("BL DEBUG:: looking for", trial_hkl_file_name)
if (os.path.isfile(trial_hkl_file_name)):
print("INFO:: hkl file %s found" %trial_hkl_file_name)
# BL says: I dont understand the following but I gues
# I have tp believe Paul (at least for now)
# if trial-hkl-file-name and hkl-filename
# are in the same directory (e.g
# shelx-coot), then (strange as it may
# seem) we *don't* put the directory name
# in the "file that exists" (the first
# argument - ie. the target). Bizarre but true.
hkl_filename_dir = os.path.abspath(hkl_filename)
trial_hkl_file_name_dir = os.path.abspath(trial_hkl_file_name)
print("BL DEBUG:: comparing path", hkl_filename_dir, trial_hkl_file_name_dir)
if (hkl_filename_dir == trial_hkl_file_name_dir):
# same dirs
# so lets strip off the dir of the target:
new_target = coot_utils.strip_path(trial_hkl_file_name)
make_symlink(new_target, hkl_filename)
else:
# different dirs, keep the dirs:
make_symlink(trial_hkl_file_name, hkl_filename)
else:
print("INFO:: hkl file %s does not exist!" %trial_hkl_file_name)
if (not os.path.isfile(hkl_filename)):
print("data (hkl) file %s not found - not running shelxl!" %hkl_filename)
else:
func(ins_filename)
# running shelxl creates stub.res
print("BL INFO:: Running shelxl as: ", shelxl_exe + " " + stub + " > " + log_filename)
shelx_status = coot_utils.popen_command(shelxl_exe, [stub], [], log_filename)
if (not shelx_status and
os.path.isfile(res_filename) and
os.path.isfile(fcf_filename)):
# it isn't a pdb file, but Coot knows what to do.
imol_res = coot.handle_read_draw_molecule_with_recentre(res_filename, 0)
handle_shelx_fcf_file(fcf_filename)
read_shelx_lst_file(lst_filename, imol_res)
else:
print("BL WARNING:: shelxl didnt run ok! No output files found!")
#handle_shelx_fcf_file("test.fcf")
#shelxl_refine(0,"./shelx_tut/lyso-tet.hkl")
# do-shelx-lst-file
#
# ie. create a interesting-things GUI for split (and other things?)
# in a shelx .lst file.
#
def read_shelx_lst_file(file_name, imol):
import os
import operator
# turn interesting-list into a GUI:
#
def gui_interesting_list(interesting_list):
if (interesting_list):
coot_gui.interesting_things_gui("Interesting Things from SHELX", interesting_list)
else:
print("INFO:: Nothing Interesting from LST file")
coot.add_status_bar_text("Nothing Interesting from LST file")
# chop off last char of string
def chop_end(s):
return s[:-1]
# return last char of string:
def last_char(s):
return s[-1]
# return a chain resno inscode atom-name altconf list
#
def make_atom_parts(atom_id):
list = []
ls = atom_id.rsplit("_",1)
if (len(ls)==2):
# chain resno inscode atom-name altconf
# The resno part can contain an alt conf specifier
# e.g.: 34 or 34a. So let's try to make it a number
# simply. If that fails, then strip off the last char
# and try again. If *that* is successful, return the
# resno and the last char is the altconf specifier.
# BL says:: we try to make it to integer, otherwise exception!?
resno = ls[1]
try:
resno = int(resno)
chain_id = chain_id_for_shelxl_residue_number(imol, resno)
if (not chain_id):
print("couldn't find chain id for resno ", resno)
return ["", resno, "", ls[0], ""]
else:
return [chain_id, resno, "", ls[0], ""]
except: # handle the alt conf
s = ls[1]
p = chop_end(s)
alt_conf = last_char(s)
try:
n = int(p)
except:
return ["", 1, "", "blank", ""] # failure
chain_id = chain_id_for_shelxl_residue_number(imol,n)
if (not chain_id):
print("couldn't find chain id for resno ", resno)
return ["", n, "", ls[0], alt_conf]
else:
return [chain_id, n, "", ls[0], alt_conf]
# So we have a line in a table something like these:
#
# " 2.7499 2.5580 0.1919 0.0400 DANG CN_2011 C_2011"
# " 1.5156 0.5000 FLAT O_1012 CA_1012 N_1013 CA_1013"
#
# It seems that there are either 4 leading numbers or 2 leading
# numbers. Let's parse up the line here and return (list
# observed target error sigma restraint) where observed and
# target are #f if there number is missing (e.g. a "FLAT"
# restraint).
#
# There are 2 regimes we understand, either
# number number number number restraint-descr atom-1-desc atom-2-desc
# or
# number number restraint-descr atom-stuff [.. atom-stuff]
#
# Actually here we will just make a string list of the
# atom-stuffs (after the restraint-descr) and parse that
# elsewhere (in do-gui) to find the atoms. The actual
# meaning of the atom-stuffs depends on the restraint-descr.
#
# return #f on something we don't understand
#
def parse_dr_line(line):
import string
bits = line.split()
if (len(bits) <=3):
return False # failed to understand
else:
try:
n0 = float(bits[0])
except:
n0 = False
try:
n1 = float(bits[1])
except:
n1 = False
try:
n2 = float(bits[2])
except:
n2 = False
try:
n3 = float(bits[3])
except:
n3 = False
if (not n0 and not n1):
return False # failed to understand
else:
if (n2 and n3):
# a 4 number line
if (len(bits)<=6):
return False # failed to understand
else:
lst = [n0, n1, n2, n3, bits[4], bits[5:]]
return lst
else:
# a 2 number line
if (len(bits)<=3): # shouldnt actually happen as we checked earlier!!! Paul!?
return False # failed to understand
else:
lst = [False, False, n0, n1, bits[2], bits[3:]]
return lst
#
def do_gui(disagreeable_restraints_list, interesting_list):
#print "BL DEBUG:: DR: ", disagreeable_restraints_list
dis_res_button_list = []
for dr_list in disagreeable_restraints_list:
restraint_type = dr_list[4]
drl_dict = {"BUMP": 0, "DANG": 0, "FLAT": 0,
"SIMU": 1, "ISOR": 1}
if (restraint_type in drl_dict):
drl_index = drl_dict[restraint_type]
else:
drl_index = 0
atom_parts = make_atom_parts(dr_list[5][drl_index])
stats_string = "not sure what?"
n2 = dr_list[2]
n3 = dr_list[3]
if (isinstance(n2, numbers.Number) and isinstance(n3, numbers.Number) and (n2 != 0)):
z = n3 / abs(n2)
stats_string = " " + str(n2) + " [Z=" + str(z) +"]"
else:
stats_string = ""
if (drl_index == 0):
rt = restraint_type + " "
else:
rt = restraint_type + " " + dr_list[5][0]
button_label = "Disagreeable Restraint " + rt + " " + atom_parts[0] + " " + \
str(atom_parts[1]) + " " + atom_parts[3] + stats_string
interesting_thing = [button_label, imol] + atom_parts
dis_res_button_list.append(interesting_thing)
gui_interesting_list(interesting_list + dis_res_button_list)
# main body
file_name = os.path.abspath(file_name)
if not coot_utils.valid_model_molecule_qm(imol):
print("WARNING:: Molecule number %i not valid" %imol)
else:
if not os.path.isfile(file_name):
print("WARNING:: shelx lst file: %s does not exist" %file_name)
else:
fin = False
interesting_list = []
try:
fin = open(file_name,'r')
except:
print("BL ERROR:: Cannot read ", file_name)
if (fin):
lines = fin.readlines()
split_list = []
disagreeable_restraints_list = []
dr_count = 0
for line in lines:
if ("may be split into" in line):
parts = line.split()
if len(parts)>6:
atom_id = parts[3]
# e.g; atom_id: CD1_1392
atom_parts = make_atom_parts(atom_id)
button_label = "Atom " + str(atom_parts[1]) + " " + atom_parts[3] + " may be split?"
split_list.append([button_label, imol] + atom_parts)
#split_list.append(atom_parts)
elif (" Observed Target Error Sigma Restraint" in line):
dr_count = 1
elif (dr_count == 1):
disagreeable_restraints_list = [] # reset the disagreeable-restraints-list
dr_count = 2
elif (dr_count == 2): # OK, in the disagreeable table
#print "BL DEBUG:: DR: ", line
dr_bits = parse_dr_line(line)
#print "BL DEBUG:: dr_bits: ", dr_bits,len(line)
if (type(dr_bits) is ListType):
disagreeable_restraints_list.append(dr_bits)
if (len(line) > 1):
dr_count = 2
else:
dr_count = 0
else:
pass
fin.close()
# print "BL DEBUG:: now run the gui with ", disagreeable_restraints_list, split_list
do_gui(disagreeable_restraints_list, split_list)
else:
print("BL ERROR:: unknown error opening file ", file_name)
#read_shelx_lst_file("test.lst",0)
# Read a shelx project (i.e. the .res file, the .lst file and the
# .fcf.cif file (if it exists (else read the .fcf file (if it
# exists)))
#
# If the file-name has an extension of .lst .res .ins .fcf .log .hkl
# then strip that off before adding new extensions.
#
def read_shelx_project(file_name):
import os
file_name = os.path.abspath(file_name)
extension = coot_utils.file_name_extension(file_name)
if (extension == "lst"):
file_stub = coot_utils.file_name_sans_extension(file_name)
elif (extension == "ins"):
file_stub = coot_utils.file_name_sans_extension(file_name)
elif (extension == "insh"):
file_stub = coot_utils.file_name_sans_extension(file_name)
elif (extension == "log"):
file_stub = coot_utils.file_name_sans_extension(file_name)
elif (extension == "hkl"):
file_stub = coot_utils.file_name_sans_extension(file_name)
elif (extension == "res"):
file_stub = coot_utils.file_name_sans_extension(file_name)
elif (extension == "fcf"):
file_stub = coot_utils.file_name_sans_extension(file_name)
else:
file_stub = file_name
res_file_name = file_stub + ".res"
lst_file_name = file_stub + ".lst"
fcf_file_name = file_stub + ".fcf"
fcf_cif_file_name = file_stub + ".fcf.cif"
print(" file_name: ", file_name)
print(" file_stub: ", file_stub)
print(" extension: ", extension)
if (os.path.isfile(res_file_name)):
print("Read res file ", res_file_name)
imol_res = coot.handle_read_draw_molecule_with_recentre(res_file_name, 0)
else:
print(" No res file ", res_file_name)
imol_res = -1
if (not coot_utils.valid_model_molecule_qm(imol_res)):
print("WARNING:: Bad molecule from res file read.")
else:
if (os.path.isfile(fcf_cif_file_name)):
if (not os.path.isfile(fcf_file_name)):
print(" Read fcf-cif file ", fcf_cif_file_name)
coot.auto_read_cif_data_with_phases(fcf_cif_file_name)
else:
# OK both xxx.fcf and xxx.fcf.cif exist, we
# only want to read the xxx.fcf.cif if it is
# more recent than xxx.fcf (if it is not, we
# want to handle-shelx-fcf-file.
from stat import ST_MTIME
fcf_date = os.stat(fcf_file_name)[ST_MTIME]
fcf_cif_date = os.stat(fcf_cif_file_name)[ST_MTIME]
# print " fcf_date %s fcf_cif_date %s" %(time.ctime(fcf_date), time.ctime(fcf_cif_date))
if (fcf_date < fcf_cif_date):
coot.auto_read_cif_data_with_phases(fcf_cif_file_name)
else:
handle_shelx_fcf_file(fcf_file_name)
# xxx.fcf.cif did not exist:
else:
if (os.path.isfile(fcf_file_name)):
print(" Read fcf file ", fcf_file_name)
handle_chelx_fcf_file(fcf_file_name)
else:
print("BL WARNING:: no fcf and or cif files found!")
if (os.path.isfile(lst_file_name)):
print(" ::Read lst file ", lst_file_name)
read_shelx_lst_file(lst_file_name, imol_res)
else:
print(" ::No lst file ", lst_file_name)
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