def __init__(self, motif_type=''):
MotifAtlasBaseClass.__init__(self)
self.success = False
self.motifs_root = self.config['locations']['releases_dir']
self.motif_type = motif_type.upper()
self.done = []
self.folders = []
def __init__(self):
MotifAtlasBaseClass.__init__(self)
self.loopSearchDir = self.config['locations']['loops_search_dir']
self.precomputedData = self.config['locations']['loops_mat_files']
self.loop_regex = '(IL|HL)_\w{4}_\d{3}'
self.pdb_regex = '^[0-9A-Za-z]{4}$'
self.update = True # determines whether to update existing values in the db
def __init__(self):
"""
"""
MotifAtlasBaseClass.__init__(self)
self.cache_dir = self.config['locations']['cache']
if not os.path.exists(self.cache_dir):
os.mkdir(self.cache_dir)
self.baseurl = 'http://rna.bgsu.edu/rna3dhub'
def __init__(self):
MotifAtlasBaseClass.__init__(self)
self.success = False
self.num_jobs = 4
self.pdb_ids = []
self.loop_ids = []
self.best_loops = [] # loops to be clustered
self.fr3d_root = self.config['locations']['fr3d_root']
self.retries_left = 3
self.script_prefix = 'aAa_script_'
self.mlab_input_filename = os.path.join(self.fr3d_root, 'loops.txt')
def __init__(self):
MotifAtlasBaseClass.__init__(self)
self.commit_every = 100
self.file_types = ['.pdb', '.pdb1']
root = self.config['locations']['fr3d_root']
self.pdb_files_folder = os.path.join(root, 'FR3D', 'PDBFiles')
self.known = ['A', 'C', 'G', 'U']
query = session.query(PdbModifiedCorrespondecies.modified_unit)
for entry in query.all():
self.known.append(entry.modified_unit)
def __init__(self):
"""
"""
MotifAtlasBaseClass.__init__(self)
self.temp_file = 'temp.csv'
self.nrlists_root = self.config['locations']['nrlists_dir']
self.resolutions = ['1,5A','2A','2,5A','3A','3,5A','4A','20A','All_Resolution']
self.resolution_labels = ['1.5','2.0','2.5','3.0','3.5','4.0','20.0','all']
self.done = []
self.list_done()
self.lists = sorted(os.listdir(self.nrlists_root))
self.success = False # status of the current update
def __init__(self):
"""
locations is where pdbs will be placed
pdbs is an array the files to download
"""
MotifAtlasBaseClass.__init__(self)
self.baseurl = 'http://www.rcsb.org/pdb/files/'
self.ba_url = 'http://www.pdb.org/pdb/rest/getEntityInfo?structureId='
self.filetypes = ['.pdb', '.pdb1', '.cif']
self.locations = []
self.pdbs = []
self.config['email']['subject'] = 'Pdb File Sync'
def __init__(self, ensembles=None, release_mode="", release_description="", upload_mode=""):
MotifAtlasBaseClass.__init__(self)
self.c = ensembles # collections, NRCollectionMerger
self.motifs = []
self.loops = []
self.history = []
self.final_ids = dict()
self.intersection = []
self.release_diff = []
self.added_groups = []
self.removed_groups = []
self.updated_groups = []
self.old_updated_groups = []
self.same_groups = []
self.added_pdbs = []
self.removed_pdbs = []
self.upload_mode = upload_mode
self.release_mode = release_mode
self.release_description = release_description
def __init__(self):
MotifAtlasBaseClass.__init__(self)
self.success = False
def __init__(self):
MotifAtlasBaseClass.__init__(self)
def __init__(self):
MotifAtlasBaseClass.__init__(self)
self.pdb_file_types = ['.pdb', '.pdb1']
self.pdb_files_folder = os.path.join(self.config['locations']['fr3d_root'],
'FR3D',
'PDBFiles')
def __init__(self):
"""
"""
MotifAtlasBaseClass.__init__(self)
self.output = ''
def __init__(self):
MotifAtlasBaseClass.__init__(self)
self.loop_types = ['IL','HL','J3']
