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# bones_reader.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/>.
mapman_exe = os.path.join(os.getenv('HOME'), "bin/lx_mapman")
def generic_object_from_bones(bones_file):
import operator
from types import IntType
global atom_xyz_list, bone_list, conn_list
atom_xyz_list = []
bone_list = []
conn_list = []
#save_conn = False
def add_ordinate(s):
global atom_xyz_list
obj = list(map(float, s.split()))
atom_xyz_list.append(obj)
def add_bone(s):
global bone_list
obj = list(map(int, s.split()))
bone_list += obj
#def add_connection_pairs(s):
# conn_list += s.split()
def add_connection(s):
global conn_list
obj = list(map(int, s.split()))
conn_list += obj
def my_indexer(n):
# un-fortran indexing
if (n % 2 == 0):
# even
ret = n // 2
else:
ret = (n - 1) // 2
return ret - 1
# main body
if (os.path.isfile(bones_file)):
fin = open(bones_file, 'r')
lines = fin.readlines()
fin.close()
reading_atoms_flag = False
reading_atom_bone_flag = False
reading_connectivity_flag = False
reading_atom_colour_flag = False
reading_residue_name_flag = False
reading_residue_type_flag = False
reading_residue_pointers_flag = False
for line in lines:
# atom colour
if ("SKL_ATOM_COLOUR" in line):
print("found atom_colour.")
reading_connectivity_flag = False
#saved_conn = False
# connectivity
if (reading_connectivity_flag):
add_connection(line)
if ("SKL_CONNECTIVITY" in line):
print("found atom_connectivity.")
reading_connectivity_flag = True
reading_atom_bone_flag = False
# bones
if (reading_atom_bone_flag):
add_bone(line)
if ("SKL_ATOM_BONE" in line):
print("found atom_bone.")
reading_atoms_flag = False
reading_atom_bone_flag = True
# atoms
if (reading_atoms_flag):
add_ordinate(line)
if ("SKL_ATOM_XYZ" in line):
print("found atom_xyz")
reading_atoms_flag = True
print("length atom_xyz_list: %s length bone_list: %s length conn_list: %s" \
%(len(atom_xyz_list), len(bone_list), len(conn_list)))
lines_obj = coot.new_generic_object_number("Lines")
current_position = False
for connections in conn_list:
if (not current_position):
#print "(from %s) init move to : %s" %(connections,
# my_indexer(connections))
current_position = my_indexer(connections)
else:
xyz_index = my_indexer(connections)
if (connections % 2 == 0):
# even connections
# a move to:
#print "(from %s) move to: %s" %(connections, xyz_index)
current_position = xyz_index
else:
# a draw to:
#print "(from %s) line: %s %s" %(connections,
# current_position,
# xyz_index)
coot.to_generic_object_add_line(lines_obj, "green", 3,
atom_xyz_list[current_position][0],
atom_xyz_list[current_position][1],
atom_xyz_list[current_position][2],
atom_xyz_list[xyz_index][0],
atom_xyz_list[xyz_index][1],
atom_xyz_list[xyz_index][2])
current_position = my_indexer(connections)
coot.set_display_generic_object(lines_obj, 1)
else:
print("BL INFO:: no bones file %s found" %bones_file)
def bones_it(map_file_name):
bones_file = "my.bones"
data_lines = ["read m1 " + map_file_name + " ccp4",
"bo sk m1 0.5 0.15 1",
"bones connect",
bones_file,
"skl",
"5",
"quit"]
coot_utils.popen_command(mapman_exe, [], data_lines, "coot-mapman.log", True)
# now read in bones_file
generic_object_from_bones(bones_file)
# add a menu item:
menu = coot_gui.coot_menubar_menu("Mapman")
def bonesing_func(imol):
print("bonesing", imol)
coot.export_map(imol, "tmp.map")
bones_it("tmp.map")
# remove tmp map?
if (os.path.isfile("tmp.map")):
print("BL INFO:: removing temporary map file tmp.map")
os.remove("tmp.map")
add_simple_coot_menu_menuitem(menu, "Mapman Bones...",
lambda func: coot_gui.map_molecule_chooser_gui("Map to Bonesify:",
lambda imol: bonesing_func(imol)))
#generic_object_from_bones("my.bones")
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