Commit 13213dd3 authored by Fabrice  ALLAIN's avatar Fabrice ALLAIN

*: update tutorial & fix NoneType issue for pdbqual when path are missing in the configuration file

parent f891072c
Configuration
Configuration
=============
The following tables list the available parameters with the corresponding
sections. In order to change default parameters, the tool can accept a
configuration file with the ``-c`` option in the :doc:`usage`. This
configuration file should follow the `INI <https://en.wikipedia.org/wiki/INI_file>`_ format.
configuration file should follow the
`INI <https://en.wikipedia.org/wiki/INI_file>`_ format. The default file can be
downloaded :download:`here <../src/aria/conbox/conf/config.ini>`.
.. note::
There is no need to give all the parameters in a configuration file. If a
field is not in the file, the CLI will take the value in the default file.
**Example:**
......@@ -14,15 +20,9 @@ configuration file should follow the `INI <https://en.wikipedia.org/wiki/INI_fil
; comment
parameter: value
main
----
.. note::
Leave these fields empty in order to use default files.
.. rst-class:: table-hover
+--------------------------+------+------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
......
BPT1_BOVIN structure prediction with EC map
===========================================
We show an example of *de novo* structure prediction from GREMLIN_ contacts
combined with secondary structure prediction. The files related to this example
can be found in the ``docs`` folder or :download:`here <../../examples.tar.gz>`.
.. note::
Even if data for this example are already in the ``docs/examples`` folder. You
have to change at least ``cns_executable`` and ``host_executable`` with the
path of your CNS_ executable (not supplied in this package) in the
configuration file . Otherwise, this example will not work.
Contact map analysis
--------------------
......
This diff is collapsed.
......@@ -20,7 +20,7 @@ interupperbounds_pdbstat:
intralowerbounds_pdbstat:
intratarget_pdbstat:
intraupperbounds_pdbstat:
ariaproject_template: 2.3.6
ariaproject_template: 2.3.7
procheck_executable:
prosa_executable:
whatif_executable:
......@@ -201,15 +201,15 @@ water_refinement_solvent: water
water_refinement_n_structures: 10
water_refinement_enabled: no
water_refinement_write_solvent_molecules: no
structure_analysis_enabled: yes
structures_analysis_enabled: yes
procheck_executable:
procheck_enabled: yes
procheck_enabled: no
prosa_executable:
prosa_enabled: yes
prosa_enabled: no
whatif_executable:
whatif_enabled: yes
whatif_enabled: no
clashlist_executable:
clashlist_enabled: no
clashlist_enabled: no
pickle_output: no
; --------------------------- Iteration parameters --------------------------- #
; /!\ Parameters below can be formatted as a list if we want different values
......
......@@ -24,21 +24,24 @@ class AriaEcPdbqual(CommandProtocol):
def run(self):
""":return:"""
LOG.info("Starting quality runs with %s file(s)", self.settings.pdbqual["infiles"])
LOG.info("Copying file(s) to output directory")
LOG.info("Copying file(s) to output directory %s", self.settings.pdbqual["output_directory"])
for infile in self.settings.pdbqual["infiles"]:
if os.path.abspath(infile) != os.path.abspath(self.settings.pdbqual["output_directory"]):
shutil.copy(infile, self.settings.pdbqual["output_directory"])
LOG.info(self.settings.pdbqual["output_directory"])
runChecks(
workingDirectory=self.settings.pdbqual["output_directory"],
trashDirectory=self.settings.pdbqual["trash_directory"],
procheckExe=self.settings.setup["procheck_executable"],
procheckExe=self.settings.setup["procheck_executable"]
if self.settings.setup["procheck_executable"] else '',
procheckOnOff=1 if self.settings.setup["procheck_enabled"] in ("yes", True, "True") else 0,
whatIfExe=self.settings.setup["whatif_executable"],
whatIfExe=self.settings.setup["whatif_executable"]
if self.settings.setup["whatif_executable"] else '',
whatifOnOff=1 if self.settings.setup["whatif_enabled"] in ("yes", True, "True") else 0,
clashlistExe=self.settings.setup["clashlist_executable"],
clashlistExe=self.settings.setup["clashlist_executable"]
if self.settings.setup["clashlist_executable"] else '',
clashlistOnOff=1 if self.settings.setup["clashlist_enabled"] in ("yes", True, "True") else 0,
prosaExe=self.settings.setup["prosa_executable"] if self.settings.main["prosa_executable"] else "",
prosaExe=self.settings.setup["prosa_executable"]
if self.settings.setup["prosa_executable"] else "",
prosaOnOff=1 if self.settings.setup["prosa_enabled"] in ("yes", True, "True") else 0,
cshExe=self.settings.pdbqual["csh_executable"],
howManyPdb=len(self.settings.pdbqual["infiles"]),
......@@ -56,4 +59,5 @@ class AriaEcPdbqual(CommandProtocol):
for infile in self.settings.pdbqual["infiles"]
if os.path.exists(os.path.join(
self.settings.pdbqual["output_directory"],
os.path.basename(infile)))]
os.path.basename(infile)))
]
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