chromaquant 0.3.1__py3-none-any.whl

chromaquant/Manual/label-type.py

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+#!/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
+    
+
+
+
+
+
+
+
+    
+