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# Copyright 2006 Joel Bard
# Copyright 2006 by Bernhard Lohkamp
# Copyright 2006 by Paul Emsley, 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, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor,
# Boston, MA 02110-1301, USA
# Read in cns coeff-data (given filenames) and a pdb molecule filename to make
# maps.
#
def cns2coot(twofofc_coeffs, fofc_coeffs, model_pdb):
import os, string
# remove any trailing spaces of string
# BL says: maybe somthing for coot-utils?
# ..and has already a buikld-in function in python
def trim_trailing_spaces(s):
f = string.rstrip(s)
return f
# return [] on bad, else return a 6 memberes list.
def get_cell_from_pdb(pdb_file):
s = []
fin = False
try:
fin = open(pdb_file,'r')
except IOError:
print("BL WARNING:: Cannot read ", pdb_file)
if (fin):
lines = fin.readlines()
for line in lines:
if "CRYST1" in line:
s = string.split(line)
s = s[1:7]
fin.close()
break
else:
print("BL WARNING:: IOError in ", pdb_file)
return s
# return "" on bad, else return a string that is the space group.
#
# have to go through all sorts of hoops because sometimes we might
# get P 21 and sometimes we might get P 1 21 1 for example
# sftools needs P21, can't handle P1211
# that being said - there must be a better way
# set SYMM1=`awk 'BEGIN { FIELDWIDTHS="55 11 4" } /CRYST1/ {gsub(" ","",$2); coot_utils.printf "%s\n", $2}' $3`
#
def get_symm_from_pdb_file(pdb_file):
s = ""
fin = False
try:
fin = open(pdb_file,'r')
except IOError:
print("BL WARNING:: Cannot read ", pdb_file)
if (fin):
lines = fin.readlines()
for line in lines:
if "CRYST1" in line:
s = string.split(line)
s = s[7:]
s = string.join(s,"")
fin.close()
break
else:
print("BL WARNING:: IOError in ", pdb_file)
return s
def get_symm_from_pdb_file_2(pdb_file):
s = ""
fin = False
try:
fin = open(pdb_file,'r')
except IOError:
print("BL WARNING:: Cannot read ", pdb_file)
if (fin):
lines = fin.readlines()
for line in lines:
if "CRYST1" in line:
s = string.split(line)
s = s[7:]
s = string.join(s)
fin.close()
break
else:
print("BL WARNING:: IOError in ", pdb_file)
return s
# Return a symmetry string
# on problem, return False. Use that to exit (elsewhere).
#
def get_symm_from_symop_lib(symm2):
try:
e = os.environ['CCP4']
except:
print("CCP4 not set up.")
return False
if (e):
s = False
e = os.path.join(e,"lib","data","symop.lib")
fin = False
try:
fin=open(e,'r')
except:
print("Problems opening ", e)
if (fin):
lines = fin.readlines()
for line in lines:
if symm2 in line:
t = string.split(line)
s = t[3]
break
fin.close()
return s
else:
print("Problems with CCP4 set up")
# main body
map1_prefix = coot_utils.strip_extension(twofofc_coeffs)
map2_prefix = coot_utils.strip_extension(fofc_coeffs)
map1_tmp = map1_prefix + "_tmp.pdb"
map2_tmp = map2_prefix + "_tmp.pdb"
cell = get_cell_from_pdb(model_pdb)
print("map1_prefix: ", map1_prefix)
print("map2_prefix: ", map2_prefix)
print("cell: ", cell)
symm1 = get_symm_from_pdb_file(model_pdb)
pdbset_log = "cns2coot-pdbset-tmp.log"
print("symm1: ", symm1)
coot_utils.popen_command("pdbset",["XYZIN",model_pdb,"XYZOUT",map1_tmp],["CELL " + string.join(cell), "SPACEGROUP " + symm1],pdbset_log,0)
symm2 = get_symm_from_pdb_file_2(map1_tmp)
print("symm2: ", symm2)
symm = get_symm_from_symop_lib(symm2)
if not(symm):
print("Failed to find symm in symop.lib!")
else:
print("INFO:: SYMM is ", symm)
map1_mtz = map1_prefix + ".mtz"
map2_mtz = map2_prefix + ".mtz"
map_coot_mtz = map1_prefix + "-coot.mtz"
cad_log = "cns2coot-cad-tmp.log"
sftools_1_log = "cns2coot-sftools-1-tmp.log"
sftools_2_log = "cns2coot-sftools-2-tmp.log"
if os.path.isfile(map1_mtz):
os.remove(map1_mtz)
if os.path.isfile(map2_mtz):
os.remove(map2_mtz)
coot_utils.popen_command("sftools", [] ,["read " + twofofc_coeffs, "cns", string.join(cell), symm, "END", "W", "P", "R", "SET LABELS", "FOM", "PHIC", "SCALE", "FWT", "PHWT", "WRITE " + map1_mtz] , sftools_1_log, 0)
coot_utils.popen_command("sftools", [] ,["read " + fofc_coeffs, "cns", string.join(cell), symm, "END", "W", "P", "R", "SET LABELS", "FOM", "PHIC", "SCALE", "DELFWT", "PHDELWT", "WRITE " + map2_mtz] , sftools_2_log, 0)
coot_utils.popen_command("cad", ["HKLIN1", map1_mtz, "HKLIN2", map2_mtz, "HKLOUT", map_coot_mtz],["LABIN FILE_NUMBER 1 E1=FOM E2=PHIC E3=FWT E4=PHWT", "LABIN FILE_NUMBER 2 E1=DELFWT E2=PHDELWT", "END"], cad_log, 0)
if os.path.isfile(map1_mtz):
os.remove(map1_mtz)
if os.path.isfile(map2_mtz):
os.remove(map2_mtz)
# now load them in Coot
#
coot.read_pdb(model_pdb)
coot.make_and_draw_map_with_reso_with_refmac_params(map_coot_mtz, "FWT", "PHWT", "", 0, 0, 0, "Fobs:None-specified", "SigF:None-specified", "RFree:None-specified", 0, 0, 0, -1.00, -1.00)
coot.make_and_draw_map_with_reso_with_refmac_params(map_coot_mtz, "DELFWT", "DELPHWT", "", 0, 1, 0, "Fobs:None-specified", "SigF:None-specified", "RFree:None-specified", 0, 0, 0, -1.00, -1.00)
#cns_coot("2fo-fc_Fum480.coeff","fo-fc_Fum480.coeff","bindividual_Fum480.pdb")
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