def _openHTML(self, e=None):
reportHtml = self.protocol.createHtmlReport()
reportPath = reportHtml.reportPath
if pwutils.exists(reportPath):
text._open_cmd(reportPath)
else:
self.showInfo('Your html file is not ready yet. Please try again in a minute.')
def visualize(self, obj, **args):
data = self.protocol._getPath('emxData/data.mrc')
DataView(data).show()
# open EMX file in web browser
fn = self.protocol._getPath('emxData/data.emx')
text._open_cmd(fn, self.getTkRoot())
def _showHtmlReport(self, paramName=None):
reportPath = self.protocol._getFileName('reportHtml',
run=self.protocol._getRun())
if pwutils.exists(reportPath):
text._open_cmd(reportPath, self.getTkRoot())
else:
self.showInfo(
'Your html report is not ready yet. Please try again in a minute.'
)
def _openHTML(self, e=None):
reportHtml = self.protocol.createHtmlReport()
reportPath = reportHtml.reportPath
if pwutils.exists(reportPath):
text._open_cmd(reportPath)
else:
self.showInfo(
'Your html file is not ready yet. Please try again in a minute.'
)
def _openConfigFile(self, configFile, userOnly=False):
""" Open an Scipion configuration file, if the user have one defined,
also open that one with the defined text editor.
"""
if not userOnly:
_open_cmd(pw.getConfigPath(configFile))
userHostConf = os.path.join(pwutils.getHomePath(), '.config',
'scipion', configFile)
if os.path.exists(userHostConf):
_open_cmd(userHostConf)
def _openConfigFile(self, configFile, userOnly=False):
""" Open an Scipion configuration file, if the user have one defined,
also open that one with the defined text editor.
"""
if not userOnly:
_open_cmd(pw.getConfigPath(configFile))
userHostConf = os.path.join(pwutils.getHomePath(),
'.config', 'scipion', configFile)
if os.path.exists(userHostConf):
_open_cmd(userHostConf)
def _openConfigFile(configFile):
""" Open an Scipion configuration file, if the user have one defined,
also open that one with the defined text editor.
"""
_open_cmd(configFile)
def _chainPair(self, e=None):
if self.doInvert.get():
commandDisplayInteractions = """
SELECT count(*), protId_2, modelId_2, chainId_2,
aaName_2 || aaNumber_2, protId_1, modelId_1,
chainId_1, aaName_1 || aaNumber_1
FROM view_ND_2
WHERE modelId_1='{}' AND protId_1='{}' AND chainId_1='{}'
AND modelId_2='{}' AND protId_2='{}' AND chainId_2='{}'
GROUP BY protId_1, modelId_1, chainId_1,
aaNumber_1, aaName_1, protId_2,
modelId_2, chainId_2, aaNumber_2,
aaName_2
ORDER BY protId_2, modelId_2, chainId_2,
protId_1, modelId_1, chainId_1,
aaNumber_2, aaName_2, aaNumber_1, aaName_1;
"""
else:
commandDisplayInteractions = """
SELECT count(*), protId_1, modelId_1, chainId_1,
aaName_1 || aaNumber_1, protId_2, modelId_2,
chainId_2, aaName_2 || aaNumber_2
FROM view_ND_2
WHERE modelId_1='{}' AND protId_1='{}' AND chainId_1='{}'
AND modelId_2='{}' AND protId_2='{}' AND chainId_2='{}'
GROUP BY protId_1, modelId_1, chainId_1,
aaNumber_1, aaName_1, protId_2,
modelId_2, chainId_2, aaNumber_2,
aaName_2
ORDER BY protId_1, modelId_1, chainId_1,
protId_2, modelId_2, chainId_2,
aaNumber_1, aaName_1, aaNumber_2, aaName_2;
"""
f = open(self.getInteractionFileName(), 'w')
if len(self.all_pair_chains) == self.chainPair.get():
f.write("No contacts found by applying symmetry: Is the symmetry "
"center equal to the origin of coordinates?")
else:
row = self.all_pair_chains[self.chainPair.get()]
command = commandDisplayInteractions.format(
row[1], row[2], row[3], row[4], row[5], row[6])
# print command
rows_count = self.c.execute(command)
all_rows = self.c.fetchall()
f.write("RESULTS for: {}\n".format(', '.join(str(s) for s in row)))
f.write(
"# atoms, prot_1, model_1, chain_1, AA_1, prot_2, model_2, chain2, AA_2\n"
)
first = None
last = None
first2 = None
last2 = None
aaDistance = self.aaDistance.get()
for row in all_rows:
AA_1 = row[4]
AA_1Int = int(AA_1[3:])
AA_2 = row[8]
AA_2Int = int(AA_2[3:])
if first is None:
first = AA_1
last = first
lastInt = AA_1Int
first2 = AA_2
firstInt2 = AA_2Int
last2 = first2
lastInt2 = AA_2Int
else:
if (AA_1Int - lastInt) > aaDistance:
f.write(">>>> {first}".format(first=first))
if last != first:
f.write("_{last}".format(last=last))
f.write(" ---- {first}".format(first=first2))
if last2 != first2:
f.write("_{last}".format(last=last2))
if (lastInt2 - firstInt2) > 20:
f.write("????\n\n")
else:
f.write("?\n\n")
first = AA_1
last = first
lastInt = AA_1Int
first2 = AA_2
firstInt2 = AA_2Int
last2 = AA_2
lastInt2 = AA_2Int
else:
last = AA_1
lastInt = int(AA_1[3:])
tmpLastInt2 = int(AA_2[3:])
if lastInt2 < tmpLastInt2:
last2 = AA_2
lastInt2 = tmpLastInt2
if firstInt2 > tmpLastInt2:
first2 = AA_2
firstInt2 = tmpLastInt2
f.write(', '.join(str(s) for s in row) + "\n")
# print first, last, first2, last2, firstInt2, lastInt2
f.write(">>>> {first}".format(first=first))
if last != first:
f.write("_{last}".format(last=last))
f.write(" ---- {first}".format(first=first2))
if last2 != first2:
f.write("_{last}".format(last=last2))
if (lastInt2 - firstInt2) > 20:
f.write("????\n\n")
else:
f.write("?\n\n")
f.close()
_open_cmd(self.getInteractionFileName(), self.getTkRoot())
def _visualizeChainPairFile(self, e=None):
"""Show file with the chains that interact."""
_open_cmd(self.getPairChainsFileName(), self.getTkRoot())
def onGeneral(self):
# Config -> General
_open_cmd(pw.getConfigPath('scipion.conf'))
def _visualizeLogFile(self, e=None):
"""Show refmac log file."""
refineLogFileName = self.protocol._getExtraPath(
self.protocol.refineLogFileName)
_open_cmd(refineLogFileName, self.getTkRoot())
def main(args=None):
parser = optparse.OptionParser(description=__doc__)
add = parser.add_option # shortcut
add('--overwrite',
action='store_true',
help="Rewrite the configuration files using the original templates.")
add(UPDATE_PARAM,
action='store_true',
help=(
"Updates you local config files with the values in the template, "
"only for those missing values."))
add('--notify',
action='store_true',
help="Allow Scipion to notify usage data (skips user question) "
"TO BE DEPRECATED, use unattended param instead")
add('--unattended',
action='store_true',
help="Scipion will skipping questions")
add('-p', help='Prints the config variables associated to plugin P')
add(COMPARE_PARAM,
action='store_true',
help="Check that the configurations seems reasonably well set up.")
add('--show',
action='store_true',
help="Show the config files used in the default editor")
options, args = parser.parse_args(args)
if args: # no args which aren't options
sys.exit(parser.format_help())
unattended = options.notify or options.unattended
if options.p:
import pyworkflow.utils as pwutils
pluginName = options.p
plugin = (pwutils.Config.getDomain().importFromPlugin(
pluginName, 'Plugin'))
if plugin is not None:
plugin._defineVariables()
print("Variables defined by plugin '%s':\n" % pluginName)
for k, v in plugin._vars.items():
print("%s = %s" % (k, v))
print("\nThese variables can be added/edited in '%s'" %
os.environ[SCIPION_CONFIG])
else:
print(
"No plugin found with name '%s'. Module name is expected,\n"
"i.e. 'scipion3 config -p xmipp3' shows the config variables "
"defined in 'scipion-em-xmipp' plugin." % pluginName)
sys.exit(0)
elif options.show:
from pyworkflow.gui.text import _open_cmd
scipionConf = os.environ[SCIPION_CONFIG]
homeConf = os.environ[SCIPION_LOCAL_CONFIG]
_open_cmd(scipionConf)
if homeConf != scipionConf and os.path.exists(homeConf):
_open_cmd(os.environ[SCIPION_LOCAL_CONFIG])
sys.exit(0)
try:
# where templates are
templates_dir = getTemplatesPath()
scipionConfigFile = os.environ[SCIPION_CONFIG]
# Global installation configuration files.
for fpath, tmplt in [
(scipionConfigFile, SCIPION_CONF),
(getConfigPathFromConfigFile(scipionConfigFile,
PROTOCOLS), PROTOCOLS),
(getConfigPathFromConfigFile(scipionConfigFile, HOSTS), HOSTS)
]:
if not exists(fpath) or options.overwrite:
print(fpath, tmplt)
createConf(fpath,
join(templates_dir, getTemplateName(tmplt)),
unattended=unattended)
else:
checkConf(fpath,
join(templates_dir, getTemplateName(tmplt)),
update=options.update,
unattended=unattended)
# Check paths for the config
checkPaths(os.environ[SCIPION_CONFIG])
except Exception as e:
# This way of catching exceptions works with Python 2 & 3
print('Config error: %s\n' % e)
import traceback
traceback.print_exc()
sys.exit(1)
def onGeneral(self):
# Config -> General
_open_cmd(pw.getConfigPath('scipion.conf'))
def visualize(self, obj, **kwargs):
_open_cmd(obj._getPath("report.pdf"))
def _generateHTML(self, e=None):
reportHtml = self.protocol.createHtmlReport()
reportPath = reportHtml.generate(self.protocol.isFinished())
text._open_cmd(reportPath)
