chromaquant 0.4.0__py3-none-any.whl → 0.5.0__py3-none-any.whl

chromaquant/Manual/label-type.py

@@ -1,179 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-
-COPYRIGHT STATEMENT:
-
-ChromaQuant – A quantification software for complex gas chromatographic data
-
-Copyright (c) 2024, by Julia Hancock
-              Affiliation: Dr. Julie Elaine Rorrer
-	      URL: https://www.rorrerlab.com/
-
-License: BSD 3-Clause License
-
----
-
-SCRIPT FOR LABELING A LIST OF COMPOUNDS ACCORDING TO PREDEFINED
-COMPOUND TYPE RULES
-
-Julia Hancock
-7-9-2024
-
-"""
-
-""" PACKAGES """
-import pandas as pd
-
-
-""" CONTAIN DICTIONARIES """
-#This dictionary contain lists of substrings to be checked against compound name strings to
-#assign a compound type
-
-#Six compound types exist: linear alkanes (L), branched alkanes (B), aromatics (A), cycloalkanes (C),
-#alkenes/alkynes (E), and other (O)
-
-#Each compound type abbreviation will have an entry in the dictionary corresponding to a list of
-#substrings to be checked against a compound name string
-
-contains = {'L':['methane','ethane','propane','butane','pentane','hexane','heptane','octane','nonane',\
-                 'decane','undecane','hendecane','dodecane','tridecane','tetradecane','pentadecane','hexadecane','heptadecane','octadecane','nonadecane',\
-                 'icosane','eicosane','heneicosane','henicosane','docosane','tricosane','tetracosane','pentacosane','hexacosane','cerane','heptacosane','octacosane','nonacosane',\
-                 'triacontane','hentriacontane','untriacontane','dotriacontane','dicetyl','tritriacontane','tetratriacontane','pentatriacontane','hexatriacontane','heptatriacontane','octatriacontane','nonatriacontane',\
-                 'tetracontane','hentetracontane','dotetracontane','tritetracontane','tetratetracontane','pentatetracontane','hexatetracontane','heptatetracontane','octatetracontane','nonatetracontane','pentacontane'],\
-            
-            'B':['iso','methyl','ethyl','propyl','butyl','pentyl','hexyl','heptyl','octyl','nonyl',\
-                 'decyl','undecyl','dodecyl','tridecyl','tetradecyl','pentadecyl','hexadecyl','heptadecyl','octadecyl','nonadecyl',\
-                 'icosyl','eicosyl','heneicosyl','henicosyl','docosyl','tricosyl','tetracosyl','pentacosyl','hexacosyl','heptacosyl','octacosyl','nonacosyl',\
-                 'triacontyl','hentriacontyl','untriacontyl','dotriacontyl','tritriacontyl','tetratriacontyl','pentatriacontyl','hexatriacontyl','heptatriacontyl','octatriacontyl','nonatriacontyl',\
-                 'tetracontyl','hentetracontyl','dotetracontyl','tritetracontyl','tetratetracontyl','pentatetracontyl','hexatetracontyl','heptatetracontyl','octatetracontyl','nonatetracontyl','pentacontyl'],
-            
-            'A':['benzyl','benzo','phenyl','benzene','toluene','xylene','mesitylene','durene','naphthalene','fluorene','anthracene','phenanthrene','phenalene',\
-                 'tetracene','chrysene','triphenylene','pyrene','pentacene','perylene','corannulene','coronene','ovalene','indan','indene','tetralin'],\
-            
-            'C':['cyclo','menthane'],\
-            
-            'E':['ene','yne'],\
-            
-            'O':[]}
-
-#List of contains keys in order of priority
-keyLoop = ['A','C','E','B','L']
-
-#List of elements to be excluded and automatically labelled as 'O'
-elementExclude = ['He','Li','Be','B','N','O','F','Ne','Na','Mg','Al','Si','P',\
-                  'S','Cl','Ar','K','Ca','Sc','Ti','V','Cr','Mn','Fe','Co',\
-                  'Ni','Cu','Zn']
-
-""" FUNCTIONS """
-
-#Function that returns a compound type abbreviation corresponding to a compound
-def assignType(compoundName,contains,keyLoop):
-    
-    #Define default compound type abbreviation as 'O'
-    CTA = 'O'
-    
-    #Function that accepts a list of substrings to check against a string and returns a boolean
-    def stringSearch(string,subList):
-        #Define export boolean default value
-        checkTF = False
-        #For every substring in subList...
-        for i in range(len(subList)):
-            
-            #If the substring can be found in the string...
-            if subList[i] in string:
-                #Assign boolean to True and break
-                checkTF = True
-                break
-            #Otherwise, pass
-            else:
-                pass
-        
-        return checkTF
-    
-    #Ordered list of keys to be looped through
-    keyLoop = ['A','C','E','B','L']
-    
-    #Loop through every key (compound type abbreviation) in contains
-    for i in keyLoop:
-        
-        #If at least one substring in the key's list is found in compoundName...
-        if stringSearch(compoundName,contains[i]):
-            #Assign the compound type abbreviation to the current key and break the loop
-            CTA = i
-            break
-        #Otherwise, pass
-        else:
-            pass
-    
-    return CTA
-
-#Function that checks if formula string contains any of a list of elements
-def checkElements(compoundFormula,elementList):
-    #Assign default export boolean to False
-    checkTF = False
-    
-    #For every substring in elementList...
-    for i in range(len(elementList)):
-        #If the substring can be found in the compound formula...
-        if elementList[i] in compoundFormula:
-            #Set boolean to True and break
-            checkTF = True
-            break
-        #Otherwise, pass
-        else:
-            pass
-    
-    return checkTF
-            
-
-""" CODE """
-
-#Define file path
-path = "/Users/connards/Desktop/University/Rorrer Lab/Scripts/AutoQuant/data/example/raw data/example_GS2_FIDpMS.csv"
-
-#Read csv at file path, assign to DataFrame importDF
-importDF = pd.read_csv(path)
-
-#For every entry in the csv, assign a compound type abbreviation
-for i, row in importDF.iterrows():
-    
-    #Retrieve compound name and formula from row entry
-    compoundName = row['Compound Name']
-    compoundFormula = row['Formula']
-    
-    #If the compound formula is a string...
-    if isinstance(compoundFormula,str):
-        
-        #If the formula contains excluded elements...
-        if checkElements(compoundFormula,elementExclude):
-            
-            #Assign 'O' to the row's compound type abbreviation entry
-            importDF.at[i,'Compound Type Abbreviation'] = 'O'
-        
-        #Otherwise...
-        else:
-            
-            #If the compound name is a string...
-            if isinstance(compoundName,str):
-            
-                #Change compound name to lowercase
-                compoundName = compoundName.lower()
-                #Get a corresponding compound type abbreviation
-                CTA = assignType(compoundName, contains, keyLoop)
-                #Assign this CTA to the row's compound type abbreviation entry
-                importDF.at[i,'Compound Type Abbreviation'] = CTA
-            
-            #Otherwise, pass
-            else:
-                pass
-    
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