Delete classify4me_prototypes.py from place

classify4me_prototypes.py

-#! /usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-Includes function that reads json files and classifies the stuctures 
-included on the basis of encyclopedia and the calculated in the preprocessor 
-space_group and normalized_wyckoff, and returns a dictionary with key - json
- file name and value - classification_name (with labels in the same format as 
-in the read_prototypes function).
-"""
-
-from __future__ import absolute_import
-
-__author__ = "Daria M. Tomecka"
-__copyright__ = "Copyright 2017, The NOMAD Project"
-__maintainer__ = "Daria M. Tomecka"
-__email__ = "tomeckadm@gmail.com;"
-__date__ = "18/05/17"
-
-import soap
-import sys
-import ase.io
-import json
-import numpy as np
-import pickle
-import h5py
-import time
-import datetime
-import os
-import logging
-
-from nomad_sim.wrappers import get_json_list
-from nomad_sim.wrappers import plot, logger
-from nomad_sim.utils_crystals import get_spacegroup
-from nomad_sim.utils_crystals import create_supercell
-from nomad_sim.wrappers import get_json_list
-from nomad_sim.nomad_structures import NOMADStructure
-from soap.tools import AseConfig
-
-
-#prototypes_file = os.path.normpath("/nomad-lab-base/analysis-tools/structural-similarity/python-modules/nomad_sim/structure_types.py")
-#Classification of json calculartion using encyclopedia preprocessor
-
-import sys
-#print(sys.path)
-sys.path.append('/home/beaker/py3k/lib/python3.5/')
-
-import Nomad
-import logging
-from Nomad.Preprocessing.System import structure, preprocessormaterial3d
-from Nomad import ProcessingEngine
-
-#LOGGER = logging.getLogger(__name__)
-#logging.basicConfig(level=logging.ERROR)
-
-json_list = beaker.json_list
-
-
-def classify_by_norm_wyckoff(json_list):
-    protos = {}
-    for json_file_name in json_list:
-        try:  
-            #try:
-            #    simulation_cell = json_file_name.get('lattice_vectors')
-            #    labels = json_file_name.get('atom_labels')
-            #    atom_pos = json_file_name.get('atom_positions')
-            #    if not simulation_cell or not labels or not atom_pos:
-            #        raise Exception("Parsed invalid geometry for space group %d, %s" % (spaceGroupNr, protoDict))
-
-                proc = ProcessingEngine(mode="debug")
-                results = proc.process(json_file_name)
-
-                preprocessor = list(results.values())
-                if len(preprocessor) == 1:
-                    preprocessor = preprocessor[0]
-                    spg_nr = preprocessor["space_group"]
-                    norm_wyckoff = preprocessor["normalized_wyckoff"]
-                    proto2 = preprocessor["structure_type"]
-                    protoDict = structure.get_structure_type(spg_nr, norm_wyckoff)
-                    #proto = '%d-%s' % (spg_nr, proto2)
-                    if protoDict is None:
-                        proto = "%d-_" % spg_nr
-                    else:
-                        #if protoDict.get("Notes","") not in ["", "_", "-", "–"]:
-                        #    proto = '%d-%s' % (spg_nr, protoDict)
-                        #else:
-                        #proto = '%d-%s' % (spg_nr, protoDict)
-                        proto = '%d-%s' % (spg_nr, protoDict.get("Prototype","-"))
-                    protos[json_file_name] = proto
-                else:
-                    logging.error("failed for %r",json_file_name)
-        except:
-            logging.exception("failure while computing for %r",json_file_name)
-            
-           
-    return protos
-
-#classify_by_norm_wyckoff(json_list)
-