from __future__ import division
from olexFunctions import OlexFunctions
OV = OlexFunctions()
import numpy as np
import solvator_atom
import copy
import re
import olx
import olexex
import os
from shutil import copyfile
class Guest():
def __init__(self,
solvent_name,
occupancy,
p_path,
SFAC_by_symbol,
CART_TO_FRAC,
cluster_centroid=np.array([[0], [0], [0]])):
#def __init__(self, solvent_name, occupancy, p_path, SFAC_by_symbol, cluster_centroid = np.array([[0],[0],[0]])):
filename = os.path.join(p_path,
"solvents/") + str(solvent_name) + ".guest"
self.atoms = [
] # these atom coordinates are the original Cartesian coordinates and read from the .guest file and should remain unchanged.
self.transformed_atoms = [
] # these atom coordinates are fractional coordinates.
self.occupancy = occupancy
from olexFunctions import OlexFunctions
OV = OlexFunctions()
import os
import htmlTools
import olex
import olx
import olex_core
import re
instance_path = OV.DataDir()
p_path = os.path.dirname(os.path.abspath(__file__))
l = open(os.sep.join([p_path, 'def.txt'])).readlines()
d = {}
for line in l:
line = line.strip()
if not line or line.startswith("#"):
continue
d[line.split("=")[0].strip()] = line.split("=")[1].strip()
p_name = d['p_name']
p_htm = d['p_htm']
p_img = eval(d['p_img'])
p_scope = d['p_scope']
OV.SetVar('MScaling_plugin_path', p_path)
from PluginTools import PluginTools as PT
import gui.maps import olex import olex_core import olx from PIL import Image, ImageChops from olexFunctions import OlexFunctions import OlexVFS import helper_functions from ImageTools import ImageTools from fragmentdb_handler import FragmentTable from helper_functions import check_restraints_consistency, initialize_user_db, \ invert_atomlist_coordinates, frac_to_cart, atomic_distance from refine_model_tasks import Refmod OV = OlexFunctions() IT = ImageTools() # FragmentDB version number: FDB_VERSION = 13 r''' Ideas: - onreturn="html.Call(~name~.onchange)" - list of rings for FLAT restraints - http://interactivepython.org/courselib/static/pythonds/Graphs/Implementation.html - spy.styles.set_rim_colour(#hex) - what should we do with SADI C1 C2 - residues as default? - live invert during key press - better preview needed! - Why is "part 1 21" not in history node? save_file() possible?
from olexFunctions import OlexFunctions
OV = OlexFunctions()
import os
import sys
import htmlTools
import olex
import olx
import gui
import time
debug = bool(OV.GetParam("olex2.debug", False))
get_template = gui.tools.TemplateProvider.get_template
instance_path = OV.DataDir()
try:
from_outside = False
p_path = os.path.dirname(os.path.abspath(__file__))
except:
from_outside = True
p_path = os.path.dirname(os.path.abspath("__file__"))
l = open(os.sep.join([p_path, 'def.txt'])).readlines()
d = {}
for line in l:
line = line.strip()
if not line or line.startswith("#"):
@author: daniel
"""
import os
# import pprint
from FragmentDB.helper_functions import REL_RESTR_CARDS, SHX_CARDS, remove_partsymbol
try:
import olx # @UnresolvedImport
from olexFunctions import OlexFunctions
from ImageTools import ImageTools
except:
pass
try:
OV = OlexFunctions()
IT = ImageTools()
except:
pass
# import cProfile
# import pstats
# cp = cProfile.Profile()
# cp.enable(subcalls=True, builtins=True)
class Refmod(object):
"""
handles the refinement model of olex2
"""
def __init__(self):