def rmsd(ind1, ind2, subjects, threshold, *args, **kwargs):
"""
Function to check if two individuals are two identical solution.
Parameters
----------
ind1, ind2 : dict
Dictionaries representing one individual.
threshold : float
Maximum RMSD value to consider two individuals as similar.
If rmsd > threshold, they are considered different.
subjects : list
List of molecules to measure.
Returns
-------
bool
Returns True if both individuals are equal.
"""
enable_chimera()
molecules_1 = [chimera.openModels.open(ind1[s])[0] for s in subjects]
molecules_2 = [chimera.openModels.open(ind2[s])[0] for s in subjects]
for m1, m2 in zip(molecules_1, molecules_2):
coords1 = m1.activeCoordSet.xyzArray()
coords2 = m2.activeCoordSet.xyzArray()
if coords1.shape[0] != coords2.shape[0]:
return False
rmsd_squared = _rmsd_squared(coords1, coords2)
if rmsd_squared > threshold * threshold:
return False
return True
##############
# dummyatoms: Cathionic Method algortihm for metal systems
#
#
# https://github.com/miniaoshi/dummyatoms
#
# Copyright 2017 Daniel Soler, Jaime Rodriguez
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
##############
import sys
import pytest
from pychimera import patch_environ, enable_chimera
if __name__ == '__main__':
patch_environ()
enable_chimera()
pytest.main(sys.argv[1:])
type=str,
help='Particle box size')
argparser.add_argument(
'--output_name',
default='./matrix_dictionary.txt',
type=str,
help=
'Name for output file containing a transformation matrix for each particle.'
)
args = argparser.parse_args()
#import pychimera.__main__
#update_dict = pychimera.__main__.run()
import pychimera
pychimera.patch_environ(nogui=True)
pychimera.enable_chimera()
import chimera
if (not args.particle_name_prefix) and (not args.particle_name_postfix):
sys.exit('You must provide a particle prefix or postfix')
sess = args.sessions_path
part_prefix = ''
if args.particle_name_prefix: part_prefix = args.particle_name_prefix
part_postfix = ''
if args.particle_name_postfix: part_postfix = args.particle_name_postfix
print('Will search for particles starting with %s and ending with %s' %
(part_prefix, part_postfix))
refname = args.reference_name
p_angpix = float(args.particle_angpix)
r_angpix = float(args.reference_angpix)
import pandas as pd
from io import StringIO
# If the script is invoked with a normal python interpreter,
# the environment must be patched. Not necessary if called
# with pychimera
# Ensure the shell environment variable $CHIMERADIR is set and
# points to the root directory of the Chimera installation.
# Should match the output of: $ chimera --root
if not sys.argv[0].endswith("pychimera"):
import pychimera
pychimera.patch_environ()
pychimera.enable_chimera()
import chimera
from chimera import openModels, Molecule
from chimera import runCommand as rc
from MatchMaker import (match, CP_BEST, GAP_OPEN,GAP_EXTEND, defaults, MATRIX, ITER_CUTOFF)
# HHSuite output parser/template
template = \
u"""
---|------|------------------------|----|-------|-------|------|-----|----|---------|--------------|
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
"""
def hhparse(hhresult_file):
def load_chimera(nogui=True):
pychimera.patch_environ(nogui=nogui)
pychimera.enable_chimera()
