#!/usr/bin/env python # (C) 2022 Cadence Design Systems, Inc. (Cadence) # All rights reserved. # TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is # provided to current licensees or subscribers of Cadence products or # SaaS offerings (each a "Customer"). # Customer is hereby permitted to use, copy, and modify the Sample Code, # subject to these terms. Cadence claims no rights to Customer's # modifications. Modification of Sample Code is at Customer's sole and # exclusive risk. Sample Code may require Customer to have a then # current license or subscription to the applicable Cadence offering. # THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, # EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT # NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A # PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall Cadence be # liable for any damages or liability in connection with the Sample Code # or its use. ############################################################################# # Utility to load a previously generated MMP index # and dump a listing of the transformations derived from matched pairs found # --------------------------------------------------------------------------- # MatchedPairTransformList.py index_file # # index_file: filename of MMP index ############################################################################# from openeye import oechem from openeye import oemedchem import sys # simple statistics import math def average(x): return (sum(x) * 1.0 / len(x)) def variance(x): return list(map(lambda y: (y - average(x)) ** 2, x)) def stddev(x): return math.sqrt(average(variance(x))) def cmp(x, y): """ Replacement for built-in function cmp that was removed in Python 3 Compare the two objects x and y and return an integer according to the outcome. The return value is negative if x < y, zero if x == y and strictly positive if x > y. """ return (x > y) - (x < y) class MMPXform: def __init__(self, xform, avg, std, num): self.xform = xform self.avg = avg self.std = std self.num = num def __cmp__(self, other): return cmp(self.avg, other.avg) def MMPTransformList(itf): # check MMP index mmpimport = itf.GetString("-mmpindex") if not oemedchem.OEIsMatchedPairAnalyzerFileType(mmpimport): oechem.OEThrow.Fatal('Not a valid matched pair index input file, {}'.format(mmpimport)) # load MMP index mmp = oemedchem.OEMatchedPairAnalyzer() if not oemedchem.OEReadMatchedPairAnalyzer(mmpimport, mmp): oechem.OEThrow.Fatal("Unable to load index {}".format(mmpimport)) if not mmp.NumMols(): oechem.OEThrow.Fatal('No records in loaded MMP index file: {}'.format(mmpimport)) if not mmp.NumMatchedPairs(): oechem.OEThrow.Fatal('No matched pairs found in MMP index file, ' + 'use -fragGe,-fragLe options to extend indexing range') # request a specific context for the transform activity, here 0-bonds chemctxt = oemedchem.OEMatchedPairContext_Bond0 askcontext = itf.GetString("-context")[:1] if askcontext == '0': chemctxt = oemedchem.OEMatchedPairContext_Bond0 elif askcontext == '1': chemctxt = oemedchem.OEMatchedPairContext_Bond1 elif askcontext == '2': chemctxt = oemedchem.OEMatchedPairContext_Bond2 elif askcontext == '3': chemctxt = oemedchem.OEMatchedPairContext_Bond3 elif askcontext == 'a' or askcontext == 'A': chemctxt = oemedchem.OEMatchedPairContext_AllBonds else: oechem.OEThrow.Fatal("Invalid context specified: " + askcontext + ", only 0|1|2|3|A allowed") bPrintTransforms = itf.GetBool("-printlist") # if a data field was specified, retrieve the SD data field name field = None if itf.HasString("-datafield"): field = itf.GetString("-datafield") if not bPrintTransforms and field is None: oechem.OEThrow.Info('Specify one of -datafield or -printlist, otherwise nothing to do!') return extractOptions = oemedchem.OEMatchedPairTransformExtractOptions() # specify amount of chemical context at the site of the substituent change extractOptions.SetContext(chemctxt) # controls how transforms are extracted (direction and allowed properties) extractOptions.SetOptions(oemedchem.OEMatchedPairTransformExtractMode_Sorted | oemedchem.OEMatchedPairTransformExtractMode_NoSMARTS) # walk the transforms from the indexed matched pairs xforms = [] xfmidx = 0 for mmpxform in oemedchem.OEMatchedPairGetTransforms(mmp, extractOptions): xfmidx += 1 if bPrintTransforms: print("{0:2} {1}".format(xfmidx, mmpxform.GetTransform())) # compute delta property mmpidx = 0 prop = [] for mmppair in mmpxform.GetMatchedPairs(): mmpidx += 1 mmpinfo = "\t{0:2}: ({1:2},{2:2})".format(mmpidx, mmppair.FromIndex(), mmppair.ToIndex()) for tag in mmppair.GetDataTags(): mmpinfo = mmpinfo + " {0}=({1},{2})".format(tag, mmppair.GetFromSDData(tag), mmppair.GetToSDData(tag)) if tag == field: fromData = None toData = None try: fromData = float(mmppair.GetFromSDData(tag)) except ValueError: fromData = None try: toData = float(mmppair.GetToSDData(tag)) except ValueError: toData = None if fromData is not None and toData is not None: prop.append(toData - fromData) if bPrintTransforms: print(mmpinfo) # skip if property not found if len(prop): xforms.append(MMPXform(mmpxform, average(prop), stddev(prop), len(prop))) if not field: return 0 if field and not len(xforms): oechem.OEThrow.Error("No matched pairs found with {} data".format(field)) print("") print("*** Transforms sorted by delta ({})".format(field)) xforms.sort(key=lambda c: -abs(float(c.avg))) idx = 0 for xfm in xforms: idx += 1 if (extractOptions.GetOptions() & oemedchem.OEMatchedPairTransformExtractMode_NoSMARTS) != 0: # not 'invertable' if SMARTS qualifiers were applied if xfm.avg < 0.: xfm.avg = -1. * xfm.avg xfm.xform.Invert() print("{0:2} {2}=(avg={3:.2f},stdev={4:.2f},num={5}) {1}".format(idx, xfm.xform.GetTransform(), field, xfm.avg, xfm.std, xfm.num)) ############################################################ InterfaceData = """ # matchedpairtransformlist interface file !BRIEF -mmpindex index.mmpidx [ -datafield sdDataField ] !CATEGORY MatchedPairTransformList !CATEGORY I/O !PARAMETER -mmpindex 1 !TYPE string !REQUIRED true !BRIEF Input filename of serialized matched pair index to load !END !END !CATEGORY options !PARAMETER -context 1 !ALIAS -c !TYPE string !DEFAULT 0 !BRIEF chemistry context to use for the transformation [0|1|2|3|A] !END !PARAMETER -printlist 2 !ALIAS -p !TYPE bool !DEFAULT 1 !BRIEF print all transforms and matched pairs !END !PARAMETER -datafield 3 !ALIAS -d !TYPE string !BRIEF sort transforms based on delta change in this property !END !END !END """ def main(argv=[__name__]): itf = oechem.OEInterface(InterfaceData) if not oechem.OEParseCommandLine(itf, argv): oechem.OEThrow.Fatal("Unable to interpret command line!") MMPTransformList(itf) if __name__ == "__main__": sys.exit(main(sys.argv))