class Event(object):
_attributes = ['estimated_pseudo_occupancy', 'estimated_bdc', 'global_correlation', 'local_correlation']
def __init__(self, id, cluster, info=None):
"""Class to hold information about an event in a dataset"""
# Process cluster object (points and values for Event)
assert isinstance(cluster, PointCluster), 'cluster must be of type PointCluster'
self.cluster = cluster
self.cluster.parent = self
# Give it a name
if id: self.id = id
else: self.id = cluster.id
# Allow a parent
self.parent = None
# Add Meta to the object
if info:
assert isinstance(info, Info)
for a in self._attributes: assert hasattr(info, a)
self.info = info
else:
self.info = Info(self._attributes)
def summary(self):
out = []
out.append('Event {!s} Summary'.format(self.id))
out.append(self.cluster.summary())
out.append(self.info.summary())
return '\n'.join(out)
def __init__(self, id, cluster, info=None):
"""Class to hold information about an event in a dataset"""
# Process cluster object (points and values for Event)
assert isinstance(cluster, PointCluster), 'cluster must be of type PointCluster'
self.cluster = cluster
self.cluster.parent = self
# Give it a name
if id: self.id = id
else: self.id = cluster.id
# Allow a parent
self.parent = None
# Add Meta to the object
if info:
assert isinstance(info, Info)
for a in self._attributes: assert hasattr(info, a)
self.info = info
else:
self.info = Info(self._attributes)
def __init__(self, events=None, id=None, info=None):
"""Class to hold information about an identified site (collection of events)"""
# List of Events
self.children = []
self.parent = None
self.id = id
# Add Meta to the object
if info:
assert isinstance(info, Info)
for a in self._attributes: assert hasattr(info, a)
self.info = info
else:
self.info = Info(self._attributes)
# Add Events
if events: self.add_events(events=events, update=True)
def __init__(self,
hierarchy_inputs=None,
hierarchies=None,
inputs=None,
labels=None):
# Object to stores all of the structure objects
self.structures = Info(['hierarchies', 'inputs', 'labels'])
# Unpack and store structure objects
if hierarchy_inputs:
self.structures.hierarchies = [
i.hierarchy for i in hierarchy_inputs
]
self.structures.inputs = [i.input for i in hierarchy_inputs]
else:
self.structures.hierarchies = hierarchies
self.structures.inputs = inputs
# Unpack and store labels
if not labels: labels = range(len(self.structures.hierarchies))
self.structures.labels = labels
#Initialise output tables
self.initialise_tables()
def initialise_tables(self):
"""Populate the index of the tables"""
# Object to contain all of the output data tables
self.tables = Info(['structures', 'residues', 'atoms'])
self._initialise_structure_table()
self._initialise_residue_table()
def sort_column_labels(mtz_object, return_labels=True):
"""Sort columns by type (F, I, etc). If return_labels=True, return labels, else return column data"""
col_labels = mtz_object.column_labels()
col_types = mtz_object.column_types()
lab_hash = {}
# H: Miller Indices, F: Amplitudes, I: Integers, P: Phases, Q: Standard Deviations, J: Intensities
mill = [col_labels[i] for i, t in enumerate(col_types) if t == 'H']
sfac = [col_labels[i] for i, t in enumerate(col_types) if t == 'F']
inty = [col_labels[i] for i, t in enumerate(col_types) if t == 'J']
sdev = [col_labels[i] for i, t in enumerate(col_types) if t == 'Q']
phas = [col_labels[i] for i, t in enumerate(col_types) if t == 'P']
ints = [col_labels[i] for i, t in enumerate(col_types) if t == 'I']
lab_hash['miller'] = mill
# Find the main F col
lab_hash['f'] = [s for s in sfac if (s in ['F','FP','FCTR','FOSC','FOBS'] \
or s.startswith('F_') or s.startswith('FP_') \
or s.upper().startswith('F-OBS') or s.upper().startswith('FOUT_'))]
# Use these if no others
if not lab_hash['f']:
lab_hash['f'] = [s for s in sfac if s.startswith('FP')]
# Find the main SIGF col
lab_hash['sigf'] = [s for s in sdev if (s in ['SIGF','SIGFP','SIGFOBS'] \
or s.startswith('SIGF_') or s.startswith('SIGFP_') \
or s.upper().startswith('SIGF-OBS') or s.upper().startswith('SIGFOUT_'))]
# Use these if no others
if not lab_hash['sigf']:
lab_hash['sigf'] = [s for s in sdev if s.startswith('SIGFP')]
# Find the I cols
lab_hash['i'] = [s for s in inty if s.startswith('I')]
# Find the SIGI cols
lab_hash['sigi'] = [s for s in sdev if s.startswith('SIGI')]
# Find the F_calc
lab_hash['calc_f'] = [
s for s in sfac if (s == 'FC' or s == 'FMODEL' or s.startswith('FC_')
or s.upper().startswith('F-MODEL'))
]
# Find the PHI_calcs
lab_hash['calc_p'] = [
p for p in phas
if (p == 'PHIC' or p == 'PHIFMODEL' or p.startswith('PHIC_')
or p.upper().startswith('PHIF-MODEL'))
]
# Find the main phase col
lab_hash['phi'] = lab_hash['p_calc']
# Find the RFree Flag
lab_hash['r_flags'] = [
r for r in ints if ('RFREE' in r.upper() or 'FREER' in r.upper()
or r == 'FREE' or r.upper().startswith('R-FREE'))
]
# 2FOFC cols
wt_f_map_opts = ['2FOFCWT', 'FWT']
wt_p_map_opts = ['PH2FOFCWT', 'PHWT', 'PHFWT']
# FOFC cols
wt_f_dif_opts = ['FOFCWT', 'DELFWT']
wt_p_dif_opts = ['PHFOFCWT', 'DELPHWT', 'PHDELWT']
# Record 2FOFC pair (composite map)
lab_hash['2fofc_f'] = [s for s in sfac if s in wt_f_map_opts]
lab_hash['2fofc_p'] = [p for p in phas if p in wt_p_map_opts]
# Record FOFC pair (different map)
lab_hash['fofc_f'] = [s for s in sfac if s in wt_f_dif_opts]
lab_hash['fofc_p'] = [p for p in phas if p in wt_p_dif_opts]
# XXX Will probably delete this later
for k in lab_hash:
for v in lab_hash[k]:
col_labels.remove(v)
lab_hash['unknown'] = col_labels
return Info(lab_hash)