updated documentation

README.md

@@ -27,6 +27,12 @@ lxml (v4.5.0)
 
 molmass (2020.6.10)
 
+keras (v2.4.3)
+
+tensorflow (v2.4.0)
+
+IsoSpecPy (v2.1.4)
+
 Memory usage can be very intensive when searching DIA data or MS/MS spectra acquired with wide isolation windows (>10 m/z). This may limit the number of parallel processes
 that can be run. If memory errors occur, reduce this value. 
 

src/DecoID/DecoID.py

@@ -794,6 +794,9 @@ class DecoID():
     :param resolution: int, Number of decimal places to consider for m/z values of MS/MS peaks
     :param label: str, optional label to add to the end of output files
     :param api_key: str, for use of mzCloud api, access key must be entered
+    :param mplus1PPM: float, ppm tolerance for finding subformulas in M+1 spectrum prediction. Set based on database
+    :param numConcurrentGroups: int, number of unique features to processes at once, if memory consumption is high, try reducing
+    :param scoringFunc: func, function to score metabolite ID matches. Defaults to the normalized dot product
     """
     def __init__(self,libFile,mzCloud_lib,numCores=1,resolution = 2,label="",api_key="none",mplus1PPM = 15,numConcurrentGroups=20,scoringFunc=dotProductSpectra):
         self.numConcurrentMzGroups = numConcurrentGroups