def fetch_emdb_map(id, directory, tmpDirectory):
""" get map from emd
:param id: 3D MAP ID in EMDB
:return: local 3Dmap filename
"""
import socket
# get computer name and select server
url_rest_api = "https://www.ebi.ac.uk/pdbe/api/emdb/entry/map/EMD-%d"
hname = socket.gethostname()
if hname.endswith('.edu') or hname.endswith('.gov'):
site = 'ftp.wwpdb.org'
url_pattern = 'ftp://%s/pub/emdb/structures/EMD-%s/map/%s'
elif hname.endswith('.cn'):
site = 'ftp.emdb-china.org'
url_pattern = 'ftp://%s/structures/EMD-%s/map/%s'
else:
site = 'ftp.ebi.ac.uk'
url_pattern = 'ftp://%s/pub/databases/emdb/structures/EMD-%s/map/%s'
map_name = 'emd_%s.map' % id
map_gz_name = map_name + '.gz'
map_url = url_pattern % (site, id, map_gz_name)
name = 'EMD-%d' % id
minimum_map_size = 8192 # bytes
url_rest_api = url_rest_api % id
try:
map_path, samplingAPI, originAPI = fetch_file(map_url, url_rest_api,
name, minimum_map_size,
directory, tmpDirectory,
map_name)
except Exception as e:
raise Exception("Cannot retrieve File from EMDB", e)
originAPI = array(originAPI) * samplingAPI # convert to Angstrom
#check consistency between file header and rest API
ccp4header = emconv.Ccp4Header(map_path, readHeader=True)
samplingHeader = ccp4header.computeSampling() # unit = A/px
originHeader = array(ccp4header.getOrigin()) # unit = A
if abs(samplingHeader - samplingAPI) >= 0.01:
print("###########################\n"
"WARNING: sampling rate stored in EMDB\n"
"database and 3D map header file do not match\n"
"API=%f, header=%f\n"
"###########################\n" % (samplingAPI, samplingHeader))
if norm(originHeader - originAPI) >= 0.1:
print("###########################\n"
"WARNING: origin stored in EMDB\n"
"database and 3D map header file do not match\n"
"API=%f, header=%f\n"
"###########################\n" % (originAPI, originHeader))
return map_path, samplingAPI, originAPI
def show(self, form, *params):
protocol = form.protocol
vol = protocol.inVolume.get()
fullPattern = vol.getFileName()
sampling = vol.getSamplingRate()
if ((str(fullPattern)).endswith('mrc')
or (str(fullPattern)).endswith('map')):
ccp4header = emconv.Ccp4Header(fullPattern, readHeader=True)
x, y, z = ccp4header.getOrigin(changeSign=True) # In Angstroms
else:
x, y, z = \
ImportOriginVolumeWizard._halfOriginCoordinates(vol, sampling)
form.setVar('x', round(x, 3))
form.setVar('y', round(y, 3))
form.setVar('z', round(z, 3))
form.setVar('samplingRate', round(sampling, 3))
def show(self, form, *params):
protocol = form.protocol
vol = protocol.inVolume.get()
fullPattern = vol.getLocation()
sampling = vol.getSamplingRate()
if ((str(fullPattern)).endswith('mrc')
or (str(fullPattern)).endswith('map')):
ccp4header = emconv.Ccp4Header(fullPattern, readHeader=True)
x, y, z = ccp4header.getOrigin(changeSign=True) # In Angstroms
else:
x, y, z = \
ImportOriginVolumeWizard._halfOriginCoordinates(vol, sampling)
def remove_tail_zeros(number):
return decimal.Decimal(number).normalize()
form.setVar('x', remove_tail_zeros(x))
form.setVar('y', remove_tail_zeros(y))
form.setVar('z', remove_tail_zeros(z))
form.setVar('samplingRate', remove_tail_zeros(sampling))
def show(self, form, *params):
protocol = form.protocol
filesPath = protocol.filesPath.get()
filesPattern = protocol.filesPattern.get()
if filesPattern:
fullPattern = os.path.join(filesPath, filesPattern)
else:
fullPattern = filesPath
sampling = protocol.samplingRate.get()
for fileName, fileId in protocol.iterFiles():
inputVol = emobj.Volume()
inputVol.setFileName(fileName)
if ((str(fullPattern)).endswith('mrc')
or (str(fullPattern)).endswith('map')):
ccp4header = emconv.Ccp4Header(fileName, readHeader=True)
x, y, z = ccp4header.getOrigin(changeSign=True) # In Angstroms
else:
x, y, z = self._halfOriginCoordinates(inputVol, sampling)
form.setVar('x', x)
form.setVar('y', y)
form.setVar('z', z)
def fetch_emdb_map(id, directory, tmpDirectory):
""" get map from emd
:param id: 3D MAP ID in EMDB
:return: local 3Dmap filename
"""
import socket
# get computer name and select server
url_rest_api = "https://www.ebi.ac.uk/pdbe/api/emdb/entry/map/EMD-%d"
hname = socket.gethostname()
if hname.endswith('.edu') or hname.endswith('.gov'):
site = 'ftp.wwpdb.org'
url_pattern = 'ftp://%s/pub/emdb/structures/EMD-%s/map/%s'
elif hname.endswith('.cn'):
site = 'ftp.emdb-china.org'
url_pattern = 'ftp://%s/structures/EMD-%s/map/%s'
else:
site = 'ftp.ebi.ac.uk'
url_pattern = 'ftp://%s/pub/databases/emdb/structures/EMD-%s/map/%s'
map_name = 'emd_%s.map' % id
map_gz_name = map_name + '.gz'
map_url = url_pattern % (site, id, map_gz_name)
name = 'EMD-%d' % id
minimum_map_size = 8192 # bytes
url_rest_api = url_rest_api % id
nTimes = 3
for i in range(nTimes): # if error repeat the fetch file up to nTimes
try:
# raise Exception("test") # uncomment to test this loop
map_path, samplingAPI, originAPI = fetch_file(
map_url, url_rest_api, name, minimum_map_size, directory,
tmpDirectory, map_name)
break
except Exception as e:
print("Retieving 3D map with id=", id,
"failed retrying (%d/%d)" % (i + 1, nTimes))
print("Error:", e)
# Loop statements may have an else clause; it is executed
# when the loop terminates through exhaustion of the iterable
else:
raise Exception("Cannot retrieve File from EMDB")
originAPI = array(originAPI) * samplingAPI # convert to Angstrom
# check consistency between file header and rest API
ccp4header = emconv.Ccp4Header(map_path, readHeader=True)
samplingHeader = ccp4header.computeSampling() # unit = A/px
originHeader = array(ccp4header.getOrigin()) # unit = A
if abs(samplingHeader - samplingAPI) >= 0.01:
print("###########################\n"
"WARNING: sampling rate stored in EMDB\n"
"database and 3D map header file do not match\n"
"API=%f, header=%f\n"
"###########################\n" % (samplingAPI, samplingHeader))
if norm(originHeader - originAPI) >= 0.1:
print("###########################\n"
"WARNING: origin stored in EMDB\n"
"database and 3D map header file do not match\n"
"API=%f, header=%f\n"
"###########################\n" % (originAPI, originHeader))
return map_path, samplingAPI, originAPI
