Source Code for Module Chem.FragmentCatalog

  1  # $Id: FragmentCatalog.py 2 2006-05-06 22:54:39Z glandrum $ 
  2  # 
  3  #  Copyright (C) 2003-2006 Rational Discovery LLC 
  4  # 
  5  #   @@ All Rights Reserved  @@ 
  6  # 
  7  import Chem 
  8  from Numeric import * 
  9  from rdfragcatalog import * 
 10  import sys 
 11  import sets 
 12   
 13 -def message(msg,dest=sys.stdout): 
 14    dest.write(msg) 
 15   
 16   
 17 -class BitGainsInfo(object): 
 18    id=-1 
 19    description='' 
 20    gain=0.0 
 21    nPerClass=None 
 22     
 23 -def ProcessGainsFile(fileName,nToDo=-1,delim=',',haveDescriptions=1): 
 24    inFile = open(fileName,'r') 
 25    nRead = 0 
 26    res = [] 
 27    for line in inFile.xreadlines(): 
 28      nRead += 1 
 29      splitL = [x.strip() for x in line.split(delim)] 
 30      if nRead != 1 and len(splitL): 
 31        bit = BitGainsInfo() 
 32        bit.id = int(splitL[0]) 
 33        col = 1 
 34        if haveDescriptions: 
 35          bit.description = splitL[col] 
 36          col += 1 
 37        bit.gain = float(splitL[col]) 
 38        col += 1 
 39        nPerClass = [] 
 40        for entry in splitL[col:]: 
 41          nPerClass.append(int(entry)) 
 42        bit.nPerClass = nPerClass   
 43        res.append(bit) 
 44        if len(res)==nToDo: 
 45          break 
 46    return res    
 47   
 48 -def BuildAdjacencyList(catalog,bits,limitInclusion=1,orderLevels=0): 
 49    adjs = {} 
 50    levels = {} 
 51    bitIds = [bit.id for bit in bits] 
 52    for bitId in bitIds: 
 53      entry = catalog.GetBitEntryId(bitId) 
 54      tmp = [] 
 55      order = catalog.GetEntryOrder(entry) 
 56      s = levels.get(order,sets.Set()) 
 57      s.add(bitId) 
 58      levels[order] = s 
 59      for down in catalog.GetEntryDownIds(entry): 
 60        id = catalog.GetEntryBitId(down) 
 61        if not limitInclusion or id in bitIds: 
 62          tmp.append(id) 
 63          order = catalog.GetEntryOrder(down) 
 64          s = levels.get(order,sets.Set()) 
 65          s.add(id) 
 66          levels[order] = s 
 67      adjs[bitId] = tmp 
 68    if orderLevels: 
 69      # we'll play a little game and sort the indices in each level by 
 70      #  the number of downlinks they have: 
 71      for order in levels.keys(): 
 72        ids = levels[order] 
 73        counts = [len(adjs[id]) for id in ids] 
 74        countOrder = argsort(counts) 
 75        l = [ids[x] for x in countOrder] 
 76        l.reverse() 
 77        levels[order] = l 
 78    return adjs,levels 
 79   
 80 -def GetMolsMatchingBit(mols,bit,fps): 
 81    res = [] 
 82    if isinstance(bit,BitGainsInfo): 
 83      bitId = bit.id 
 84    else: 
 85      bitId = bit 
 86    for i,mol in enumerate(mols): 
 87      fp = fps[i] 
 88      if fp[bitId]: 
 89        res.append(mol) 
 90    return res 
 91   
 92  xl = None 
 93 -def ShowMolsMatchingBit(mols,bit,fps,actName="",wrapper=None,col=1,row=1): 
 94    global xl 
 95    from Excel import Molecules 
 96    if wrapper is not None: 
 97      xl = wrapper 
 98    if xl is None: 
 99      xl = Molecules.ExcelWrapper() 
100      xl.Workbooks.Add() 
101      xl.ChemdrawNewWorksheet() 
102    mols = GetMolsMatchingBit(mols,bit,fps) 
103    i = row 
104    for mol in mols: 
105      xl[i,col] = Chem.MolToSmiles(mol) 
106      if actName and mol.HasProp(actName): 
107        xl[i,col+1] = mol.GetProp(actName) 
108      i+=1 
109    i = row 
110    for mol in mols: 
111      try: 
112        xl.ChemdrawConvertCellsToMols(i,col) 
113        xl.ChemdrawShowPictures(i,col) 
114      except: 
115        pass 
116      i+=1 
117    return mols 
118