Metadata-Version: 1.1
Name: insilicolynxdqi
Version: 1.0.0
Summary: Medicinal Chemistry tool for calculating drug suitability parameters of compounds.
Home-page: http://www.insilicolynx.com/
Author: InSilicoLynx Limited
Author-email: contact@insilicolynx.com
License: BSD 3-clause
Description: ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
        README file for insilicolynxdqi
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        Change log
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        17th November 2017: First release written by Mark Wenlock.
        
        
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        Copyright
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        Copyright 2017 InSilicoLynx Limited
        All Rights Reserved.
        
        
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        Licence
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        The insilicolynxdqi software is covered by a BSD 3-clause license that is included in the LICENSE.txt file distributed with this software.
        
        
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        Description
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        Medicinal Chemistry tool for calculating drug suitability parameters of compounds.
        
        
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        Platform and version
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        The software named insilicolynxdqi has been tested for compatibility on the following systems:
        
        	Ubuntu 14.04 LTS system running Python 2.7.6
        	Ubuntu 14.04 LTS system running Python 3.4.3
        	Ubuntu 16.04 LTS system running Python 2.7.12
        	Ubuntu 16.04 LTS system running Python 3.5.2
        	Windows 7 system running Python 3.6.0
        
        The software named insilicolynxdqi should be compatible with Python 2.7(.z) and Python 3(.y.z) running on a Linux platform or a Win32 platform (where y and z are the version numbers of the 
        distribution).
        
        
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        To install on a local computer
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        (1) Save the compressed source distribution file on to a local computer.
        
        (2) Installation from the compressed source distribution file using pip:
        
        	Within a new terminal (Linux) or a new Command Prompt (Win32), change the working directory to the directory containing the compressed source distribution file and type:
        
        		>>> sudo pip install insilicolynxdqi-x.y.z.tar.gz (Linux)
        
        	or
        
        		>>> pip install insilicolynxdqi-x.y.z.zip (Win32)
        
        	where x, y and z are the version numbers of the distribution.	
        
        	Note, to uninstall:
        
        		>>> sudo pip uninstall insilicolynxdqi (Linux)
        
        	or
        
        		>>> pip uninstall insilicolynxdqi (Win32)
        
        
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        Using insilicolynxdqi within a Python script - generate in-vivo scenarios functionality
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        The following code is needed for accessing the generate in-vivo scenarios functionality of insilicolynxdqi:
        	
        	from insilicolynxdqi.run.generate_in_vivo_scenarios import GenerateInVivoScenarios
        	generateInVivoScenarios = GenerateInVivoScenarios()
        				
        	generateInVivoScenarios.run( args )
        	
        The possible arguments (i.e., args) for the generateInVivoScenarios.run() function include:
        
        	dataFile (df):
        
        		REQUIRED - full file name of the tab-delimited file containing the data set.  The following data column headers are required (note, the "species" text refers to dog, human or rat):
        
        			name
        			mol_wt
        			cl_in_vivo_plasma_(species)
        			cl_in_vivo_plasma_(species)_units
        			v_steady_state_(species)
        			v_steady_state_(species)_units
        
        		For calculation of free levels the additional data columns are also required:
        
        			ppb_(species)
        			ppb_(species)_units
        
        		For calculation based on oral dosing the additional data columns are also required:
        
        			charge_type
        			pka_a1 (dependent on charge_type)
        			pka_a2 (dependent on charge_type)
        			pka_b1 (dependent on charge_type)
        			pka_b2 (dependent on charge_type)
        			caco2_6p5_human
        			caco2_6p5_human_units
        			solubility_7p4
        			solubility_7p4_units
        		
        	speciesName (sn):
        
        		Species: d = dog, h = human, r = rat (default = h).
        
        	method (m):
        
        		Method: 1 (po 1c total), 2 (po 1c free), 3 (po 2c total), 4 (po 2c free), 5 (iv 2c total), 6 (iv 2c free) (default = 1).
        	
        	errorScenarios (es):
        
        		Number of error scenarios to consider (default = 0, can not equal 1).
        
        	errorParameters (ep):
        
        		Enter the parameter abbreviation for error consideration (in vivo clearance (cl), volume of distribution at steady state (v), Caco2 Papp A to B at pH 6.5 (caco2), aqueous 
        		solubility at pH 7.4 (solubility) and plasma protein binding (ppb)) e.g., cl v caco2 solubility ppb.  (Note, do not add speech marks.)
        
        	mappingsFile (mf):
        
        		Full file path of the file containing the column header mappings for the input data set.
        
        	rmsepFile (rf):
        
        		Full file path of the file containing the rmsep values for the associated QSAR models.
        
        	qsarDefaultRmsep (qdr):
        
        		Assumed RMSEP for a QSAR model without an entry in the rmsep file.  The value reflects the RMSEP between predicted and observed values both on a logarithmic base-10 scale for 
        		cl_in_vivo_plasma_(species), v_steady_state_(species), caco2_6p5_human, solubility_7p4 and predicted and observed values both on a logarithmic base-10 percent bound over percent 
        		free scale for ppb_(species) (default = 1.00).  (Note, the species text refers to dog, human or rat.)
        
        	qsarExperimentalStandardDeviation (qesd):
        
        		Assumed default experimental standard deviation associated to measured data.  For cl_in_vivo_plasma_(species), v_steady_state_(species), caco2_6p5_human and solubility_7p4 this 
        		value reflects a logarithmic base-10 scale, and for ppb_(species) this value reflects a logarithmic base-10 percent bound over percent free scale (default = 0.30).  (Note, the 
        		species text refers to dog, human or rat.)
        
        	defaultParameterStandardDeviation (dpsd):
        
        		Assumed default parameter standard deviation to be used in the absence of a valid compound standard deviation value and/or a valid compound similarity score.  For 
        		cl_in_vivo_plasma_(species), v_steady_state_(species), caco2_6p5_human and solubility_7p4 this value reflects a logarithmic base-10 scale, and for ppb_(species) this value reflects 
        		a logarithmic base-10 percent bound over percent free scale (default = 0.30).  (Note, the species text refers to dog, human or rat.)
        
        	nameSubstring (ns):
        
        		The substring appended to the name (followed by an integer) to indicate an error scenario row (default = _#).
        	
        	byPass (bp):
        		
        		Bypass the Python version and platform check: yes or no (default).
        
        Output of generateInVivoScenarios.run( args ):
        
        	dataFileNew:
        
        		The file path for the new data file generated by the library - permits joining with other functions within one Python script.	
        
        
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        Output - generate in-vivo scenarios functionality
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        A revised text file.
        
        
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        Using insilicolynxdqi within a Python script - perform in-vivo calculations functionality
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        The following code is needed for accessing the perform in-vivo calculations functionality of insilicolynxdqi:
        	
        	from insilicolynxdqi.run.perform_in_vivo_calculations import PerformInVivoCalculations
        	performInVivoCalculations = PerformInVivoCalculations()
        				
        	performInVivoCalculations.run( args )
        	
        The possible arguments (i.e., args) for the performInVivoCalculations.run() function include:
        
        	dataFile (df):
        
        		REQUIRED - full file name of the tab-delimited file containing the data set (i.e., the output data file from insilicolynxdqi_generate_scenarios).  The following data column 
        		headers are required (note, the "species" text refers to dog, human or rat):
        
        			name
        			mol_wt
        			cl_in_vivo_plasma_(species)
        			cl_in_vivo_plasma_(species)_qualifier
        			cl_in_vivo_plasma_(species)_units
        			v_steady_state_(species)
        			v_steady_state_(species)_qualifier
        			v_steady_state_(species)_units
        
        		For calculation of free levels the additional data columns are also required:
        
        			ppb_(species)
        			ppb_(species)_qualifier
        			ppb_(species)_units
        		
        		For calculation based on oral dosing the additional data columns are also required:
        
        			charge_type
        			pka_a1 (dependent on charge_type)
        			pka_a2 (dependent on charge_type)
        			pka_b1 (dependent on charge_type)
        			pka_b2 (dependent on charge_type)
        			caco2_6p5_human
        			caco2_6p5_human_qualifier			
        			caco2_6p5_human_units
        			solubility_7p4
        			solubility_7p4_qualifier
        			solubility_7p4_units
        
        	speciesName (sn):
        
        		Species: d = dog, h = human, r = rat (default = h).
        
        	method (m):
        
        		Method: 1 (po 1c total), 2 (po 1c free), 3 (po 2c total), 4 (po 2c free), 5 (iv 2c total), 6 (iv 2c free) (default = 1).
        
        	doseInterval (di):
        		
        		Dose interval (frequency), units: hours (default = 12.00).
        
        	simulationLength (sl):
        
        		Simulation length, units = hours (default = 168.00).
        
        	compartment (c):
        
        		Compartment to consider: c = central, p = peripheral, cp = central_peripheral or all (default = c).  (Note, not relevant for methods involving only one compartment.)		
        
        	name (n):
        
        		Name (of molecule) column header as it appears in the input data set (default = name).
        
        	upperVcentralToVssRatio (uvr):
        		Upper ratio for the volume of distribution in the central compartment to the volume of distribution at steady state (needs to be a number between 0.00 and less than 1.00) 
        		(default = 0.50).
        
        	vterminalToVssRatioLower (vrl):
        
        		Terminal volume of distribution to volume of distribution at steady state ratio lower limit (needs to be greater than or equal to 1.01) (default = 1.10).
        
        	vterminalToVssRatioUpper (vru):
        	
        		Terminal volume of distribution to volume of distribution at steady state ratio upper limit (needs to be less than or equal to 7.00) (default = 2.00).
        
        	defaultIvDose (did):
        
        		Default dose to use with iv scenarios only, units: mg kg-1 (default = 1.00).
        
        	absorptionDelay (ad):
        
        		Absorption delay to use with po scenarios only, units: hours (default = -1.00 (and hard coded values used: dog = 0.50; human = 1.00; rat = 0.25)).
        
        	intestinalTransitTime (itt):
        
        		Intestinal transit time to use with po scenarios only, units: hours (default = -1.00 (and hard coded values used: dog = 2.00; human = 4.00; rat = 1.50)).
        
        	saveRawDataFiles (srdf):
        		
        		Save raw data files: yes (default) or no.
        
        	byPass (bp):
        
        		Bypass the Python version and platform check: yes or no (default).
        
        Output of performInVivoCalculations.run( args ):
        
        	dataFileNew:
        
        		The file path for the new data file generated by the library - permits joining with the insilicolynxdqi Python library within one Python script.
        
        
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        Output - perform in-vivo calculations functionality
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        Multiple text files.
        
        
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        Using insilicolynxdqi within a Python script - analyse in-vivo calculations functionality
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        The following code is needed for accessing the analyse in-vivo calculations functionality of insilicolynxdqi:
        	
        	from insilicolynxdqi.run.analyse_in_vivo_calculations import AnalyseInVivoCalculations
        	analyseInVivoCalculations = AnalyseInVivoCalculations()
        				
        	analyseInVivoCalculations.run( args )
        	
        The possible arguments (i.e., args)  for the analyseInVivoCalculations.run() function include:
        
        	dataFile (df):
        	
        		REQUIRED - full file name of the tab-delimited file containing the data set (i.e., the output data file from insilicolynxdqi_perform_calculations) (enter file path prefix for 
        		multiple scenarios e.g., ../../folder/data_).
        
        	speciesName (sn):
        		
        		Species: d = dog, h = human, r = rat (default = h).
        
        	method (m):
        	
        		Method: 1 (po 1c total), 2 (po 1c free), 3 (po 2c total), 4 (po 2c free), 5 (iv 2c total), 6 (iv 2c free) (default = 0, user must specify a method if full file path provided).
        
        	nameSubstring (ns):
        
        		The substring appended to the name (followed by an integer) to indicate an error scenario row (default = _#).
        
        	compartment (c):
        
        		Compartment to consider: c = central, p = peripheral, cp = central_peripheral or all (default = c).  (Note, not relevant for methods involving only one compartment.)
        
        	removeOutliers (ro):
        		If the number of available records permits, the number of outliers to remove - to use with po scenarios only.
        
        	intervalLevelDistribution (ild):
        
        		If the number of available records permits, the (approximate) two-sided distribution interval level to calculate - accepted range : 70.00 percent to 100.00 percent 
        		(default = 80.00 percent).
        
        	confidenceMeanLevel (cml):
        
        		If the number of available records permits, the (approximate) two-sided confidence interval of the mean level to calculate - accepted range : 70.00 percent to 99.90 percent 
        		(default = 80.00 percent).  (Note, a minimum of four records is required to calculate the confidence intervals of the mean; and where the degrees of freedom is greater than 150 
        		the t-critical value is calculated for 150 degrees of freedom.)
        
        	smiles (s):
        	
        		If applicable, smiles column header as it appears in the input data set (default = smiles).
        
        	byPass (bp):
        
        		Bypass the Python version and platform check: yes or no (default).
        
        
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        Output - analyse in-vivo calculations functionality
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        Multiple text files.
        
        
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        Further information
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        Refer to INSTRUCTIONS_FOR_USE.txt file included in the distribution (../insilicolynxdqi/docs/).
        
        
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        Help
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        Email: contact@insilicolynx.com
        
        
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Keywords: insilicolynxdqi
Platform: Linux
Platform: Win32
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Chemistry
