diff --git a/phasecalculator/runners/phasecalculatorrunner.py b/phasecalculator/runners/phasecalculatorrunner.py
index 037eb6367c61121f7d50f999b2630a42837a376a..fc6ff20dcdcccade2ca4d3f47a40920d78eb17d0 100755
--- a/phasecalculator/runners/phasecalculatorrunner.py
+++ b/phasecalculator/runners/phasecalculatorrunner.py
@@ -34,8 +34,23 @@ LOGGER.setLevel(logging.WARN)
def run_all_analysis(system_info, **kwargs):
-
- # TODO Logging output of analysis
+ """Generate required solvent and phase XML then run all relevant analysis.
+
+ Parameters
+ ----------
+ system_info : System
+ System information.
+ output_filename : str, optional
+ output file location for similarity matrix. The default is
+ "similaritymatrix.csv".
+ memory_req : str, optional
+ Memory settings for jar executable. The default is None.
+
+ Returns
+ -------
+ None.
+
+ """
phase_filename, solvent_list = create_phase_and_solvent_xml_files(system_info, **kwargs)
if system_info.calc_vle():
run_vle_analysis(system_info, phase_filename, **kwargs)
@@ -45,21 +60,26 @@ def run_all_analysis(system_info, **kwargs):
run_similarity_analysis(system_info, solvent_list, **kwargs)
def run_fgip_analysis(system_info, solvent_filename_dict_list, **kwargs):
- """
-
+ """Run FGIP analysis.
Parameters
----------
- system_info : TYPE
- DESCRIPTION.
- solvent_filename_dict_list : TYPE
- DESCRIPTION.
- **kwargs : TYPE
- DESCRIPTION.
+ system_info : System
+ System information.
+ solvent_filename_dict_list : dict
+ dictionary of solvent filenames with temperature information.
+ output_filename : str, optional
+ output file location for similarity matrix. The default is
+ "similaritymatrix.csv".
+ memory_req : str, optional
+ Memory settings for jar executable. The default is None.
Returns
-------
- None.
+ combined_results : list
+ combined results of FGIP generation.
+ combined_latex_blocks : str
+ combined latex blocks for figures.
"""
# TODO: for each solvent file/temp combo in dict
@@ -81,16 +101,19 @@ def run_fgip_analysis(system_info, solvent_filename_dict_list, **kwargs):
combined_latex_blocks += latex_blocks
return combined_results, combined_latex_blocks
def run_similarity_analysis(system_info, solvent_filename_dict, **kwargs):
- """
+ """Run similarity analysis.
Parameters
----------
- system_info : TYPE
- DESCRIPTION.
- solvent_filename_dict : TYPE
- DESCRIPTION.
- **kwargs : TYPE
- DESCRIPTION.
+ system_info : System
+ System information.
+ solvent_filename_dict : dict
+ dictionary of solvent filenames with temperature information.
+ output_filename : str, optional
+ output file location for similarity matrix. The default is
+ "similaritymatrix.csv".
+ memory_req : str, optional
+ Memory settings for jar executable. The default is None.
Returns
-------
@@ -115,25 +138,30 @@ def run_similarity_analysis(system_info, solvent_filename_dict, **kwargs):
output_type = system_info.output_information.similarity_output_type
out_res, poly_filename_list = simrun.extract_all_solvents_and_generate_polynomials(solvent_filename_dict_list,
output_dir)
- simrun.run_similarity_analysis(poly_filename_list, output_type, output_dir)
- #
+ simrun.run_similarity_analysis(poly_filename_list, output_type, output_dir, **kwargs)
+
def run_vle_analysis(system_info, phase_filename, **kwargs):
- """
+ """Run VLE phase calculation.
Parameters
----------
- system_info : TYPE
- DESCRIPTION.
- phase_filename : TYPE
- DESCRIPTION.
- **kwargs : TYPE
- DESCRIPTION.
+ system_info : System
+ System information.
+ phase_filename : str
+ Filename for phase XML.
+ memory_req : str, optional
+ Memory settings for jar executable. The default is None.
+
+ Raises
+ ------
+ FileNotFoundError
+ If jar file is not found.
Returns
-------
- TYPE
- DESCRIPTION.
+ CompletedProcess
+ result of system call.
"""
jar_path = system_info.runtime_information.phasetransfer_jar
@@ -158,32 +186,32 @@ def create_output_dir(system_info):
return output_path.as_posix()
def create_free_energy_output_filename(solvent_filename):
- """
+ """Create free energy filename for solvent file.
Parameters
----------
- solvent_filename : TYPE
- DESCRIPTION.
+ solvent_filename : str
+ Input solvent filename.
Returns
-------
- TYPE
- DESCRIPTION.
+ str
+ Output energy filename.
"""
return solvent_filename.replace(".xml","free.xml")
def create_binding_energy_output_filename(solvent_filename):
- """
+ """Create binding energy filename for solvent file.
Parameters
----------
- solvent_filename : TYPE
- DESCRIPTION.
+ solvent_filename : str
+ Input solvent filename.
Returns
-------
- TYPE
- DESCRIPTION.
+ str
+ Output energy filename.
"""
return solvent_filename.replace(".xml", "binding.xml")
@@ -192,35 +220,41 @@ def create_phase_output_filename(phase_filename):
Parameters
----------
- phase_filename : TYPE
- DESCRIPTION.
+ phase_filename : str
+ Input phase filename.
Returns
-------
- TYPE
- DESCRIPTION.
+ str
+ phase output filename.
"""
return phase_filename.replace(".xml", "calculated.xml")
def create_phase_and_solvent_xml_files(system_info, **kwargs):
- """
+ """Create solvent and phase files for given system.
Parameters
----------
- system_info : TYPE
- DESCRIPTION.
- filestem : TYPE, optional
- DESCRIPTION. The default is "system".
- **kwargs : TYPE
- DESCRIPTION.
+ system_info : System
+ System object.
+ filestem : str, optional
+ filename stem. The default is "system".
+ solvent_info_filename : str, optional
+ Filename for file containing solvent information. Defaults to file in
+ phasexmlcreator module.
+ name_inchikey_map : dict, optional
+ inchikey: name pairs. Defaults to names of solvents in pureinformation
+ module.
+
Returns
-------
- phase_file : TYPE
- DESCRIPTION.
- solvent_list : TYPE
- DESCRIPTION.
+ phase_file : str
+ Phase filename.
+ solvent_list : list of dict
+ List of dictionaries containing solvent filename and temperature information.
+
"""
return phasexmlrun.create_phase_and_solvent_files(system_info, **kwargs)
\ No newline at end of file
diff --git a/phasecalculator/runners/similarityanalysisrunner.py b/phasecalculator/runners/similarityanalysisrunner.py
index 97926d197eb0c5ce5568cb1ad21171c1a6b8fd64..a2573643739746c56a051057dcfa6b112fe4ccfc 100755
--- a/phasecalculator/runners/similarityanalysisrunner.py
+++ b/phasecalculator/runners/similarityanalysisrunner.py
@@ -32,18 +32,19 @@ LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
def run_similarity_analysis(poly_filename_list, output_type, output_dir, output_filename="similaritymatrix.csv"):
- """
+ """Run similarity analysis.
Parameters
----------
- poly_filename_list : TYPE
- DESCRIPTION.
- output_type : TYPE
- DESCRIPTION.
- output_dir : TYPE
- DESCRIPTION.
- output_filename : TYPE, optional
- DESCRIPTION. The default is "similaritymatrix.csv".
+ poly_filename_list : list of str
+ list of polynomial filenames.
+ output_type : str
+ Output type. Three options: "all", "mixturecomparison" or "purecomparison".
+ output_dir : str
+ output directory for results.
+ output_filename : str, optional
+ output file location for similarity matrix. The default is
+ "similaritymatrix.csv".
Returns
-------
@@ -59,21 +60,21 @@ def run_similarity_analysis(poly_filename_list, output_type, output_dir, output_
def extract_all_solvents_and_generate_polynomials(solv_energy_dict_list, directory_base):
- """
+ """Extract results for all solvents, and partition results based on temperature.
Parameters
----------
- solv_energy_dict_list : TYPE
- DESCRIPTION.
- directory_base : TYPE
- DESCRIPTION.
+ solv_energy_dict_list : list of dicts
+ Solvation energy files .
+ directory_base : str
+ Base output directory.
Returns
-------
- combined_out_res : TYPE
- DESCRIPTION.
- combined_filename_list : TYPE
- DESCRIPTION.
+ combined_out_res : list
+ List of polynomial generation results.
+ combined_filename_list : list of str
+ Polynomial filename list.
"""
combined_out_res = []
@@ -120,8 +121,8 @@ def extract_solvents_and_generate_polynomials(solvent_filename, energy_xml_filen
----------
solvent_filename : str
filename for solvent XML.
- energy_xml_filename : TYPE
- DESCRIPTION.
+ energy_xml_filename : str
+ energy XML filename.
directory : str
Directory to put files.