rdkit.Chem.Pharm3D.EmbedLib

Package rdkit :: Package Chem :: Package Pharm3D :: Module EmbedLib |
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# Source Code for Module rdkit.Chem.Pharm3D.EmbedLib

       1  # $Id$
       2  #
       3  # Copyright (C) 2004-2008 Greg Landrum and Rational Discovery LLC
       4  #
       5  #   @@ All Rights Reserved @@
       6  #  This file is part of the RDKit.
       7  #  The contents are covered by the terms of the BSD license
       8  #  which is included in the file license.txt, found at the root
       9  #  of the RDKit source tree.
      10  #
      11  from __future__ import print_function
      12  from rdkit import RDConfig
      13
      14  import sys,time,math
      15  from rdkit.ML.Data import Stats
      16  import rdkit.DistanceGeometry as DG
      17  from rdkit import Chem
      18  import numpy
      19  from rdkit.Chem import rdDistGeom as MolDG
      20  from rdkit.Chem import ChemicalFeatures
      21  from rdkit.Chem import ChemicalForceFields
      22  import Pharmacophore,ExcludedVolume
      23  from rdkit import Geometry
      24  _times = {}
      25
      26  from rdkit import RDLogger as logging
      27  logger = logging.logger()
      28  defaultFeatLength=2.0
      29
      30 -def GetAtomHeavyNeighbors(atom):
      31    """ returns a list of the heavy-atom neighbors of the
      32    atom passed in:
      33
      34    >>> m = Chem.MolFromSmiles('CCO')
      35    >>> l = GetAtomHeavyNeighbors(m.GetAtomWithIdx(0))
      36    >>> len(l)
      37    1
      38    >>> isinstance(l[0],Chem.Atom)
      39    True
      40    >>> l[0].GetIdx()
      41    1
      42
      43    >>> l = GetAtomHeavyNeighbors(m.GetAtomWithIdx(1))
      44    >>> len(l)
      45    2
      46    >>> l[0].GetIdx()
      47    0
      48    >>> l[1].GetIdx()
      49    2
      50
      51    """
      52    res=[]
      53    for nbr in atom.GetNeighbors():
      54      if nbr.GetAtomicNum() != 1:
      55        res.append(nbr)
      56    return res
      57
      58 -def ReplaceGroup(match,bounds,slop=0.01,useDirs=False,dirLength=defaultFeatLength):
      59    """ Adds an entry at the end of the bounds matrix for a point at
      60     the center of a multi-point feature
      61
      62     returns a 2-tuple:
      63       new bounds mat
      64       index of point added
      65
      66     >>> boundsMat = numpy.array([[0.0,2.0,2.0],[1.0,0.0,2.0],[1.0,1.0,0.0]])
      67     >>> match = [0,1,2]
      68     >>> bm,idx = ReplaceGroup(match,boundsMat,slop=0.0)
      69
      70     the index is at the end:
      71     >>> idx == 3
      72     True
      73
      74     and the matrix is one bigger:
      75     >>> bm.shape == (4, 4)
      76     True
      77
      78     but the original bounds mat is not altered:
      79     >>> boundsMat.shape == (3, 3)
      80     True
      81
      82
      83     We make the assumption that the points of the
      84     feature form a regular polygon, are listed in order
      85     (i.e. pt 0 is a neighbor to pt 1 and pt N-1)
      86     and that the replacement point goes at the center:
      87     >>> print(', '.join(['%.3f'%x for x in bm[-1]]))
      88     0.577, 0.577, 0.577, 0.000
      89     >>> print(', '.join(['%.3f'%x for x in bm[:,-1]]))
      90     1.155, 1.155, 1.155, 0.000
      91
      92     The slop argument (default = 0.01) is fractional:
      93     >>> bm,idx = ReplaceGroup(match,boundsMat)
      94     >>> print(', '.join(['%.3f'%x for x in bm[-1]]))
      95     0.572, 0.572, 0.572, 0.000
      96     >>> print(', '.join(['%.3f'%x for x in bm[:,-1]]))
      97     1.166, 1.166, 1.166, 0.000
      98
      99
     100    """
     101    maxVal = -1000.0
     102    minVal = 1e8
     103    nPts = len(match)
     104    for i in range(nPts):
     105        idx0 = match[i]
     106        if i<nPts-1:
     107          idx1 = match[i+1]
     108        else:
     109          idx1 = match[0]
     110        if idx1<idx0:
     111          idx0,idx1 = idx1,idx0
     112        minVal = min(minVal,bounds[idx1,idx0])
     113        maxVal = max(maxVal,bounds[idx0,idx1])
     114    maxVal *= (1+slop)
     115    minVal *= (1-slop)
     116
     117    scaleFact = 1.0/(2.0*math.sin(math.pi/nPts))
     118    minVal *= scaleFact
     119    maxVal *= scaleFact
     120
     121    replaceIdx = bounds.shape[0]
     122    if not useDirs:
     123      bm = numpy.zeros((bounds.shape[0]+1,bounds.shape[1]+1),numpy.float)
     124    else:
     125      bm = numpy.zeros((bounds.shape[0]+2,bounds.shape[1]+2),numpy.float)
     126    bm[0:bounds.shape[0],0:bounds.shape[1]]=bounds
     127    bm[:replaceIdx,replaceIdx]=1000.
     128
     129    if useDirs:
     130      bm[:replaceIdx+1,replaceIdx+1]=1000.
     131      # set the feature - direction point bounds:
     132      bm[replaceIdx,replaceIdx+1]=dirLength+slop
     133      bm[replaceIdx+1,replaceIdx]=dirLength-slop
     134
     135    for idx1 in match:
     136      bm[idx1,replaceIdx]=maxVal
     137      bm[replaceIdx,idx1]=minVal
     138      if useDirs:
     139        # set the point - direction point bounds:
     140        bm[idx1,replaceIdx+1] = numpy.sqrt(bm[replaceIdx,replaceIdx+1]**2+maxVal**2)
     141        bm[replaceIdx+1,idx1] = numpy.sqrt(bm[replaceIdx+1,replaceIdx]**2+minVal**2)
     142    return bm,replaceIdx
     143
     144 -def EmbedMol(mol,bm,atomMatch=None,weight=2.0,randomSeed=-1,
     145               excludedVolumes=None):
     146    """  Generates an embedding for a molecule based on a bounds matrix and adds
     147    a conformer (id 0) to the molecule
     148
     149    if the optional argument atomMatch is provided, it will be used to provide
     150    supplemental weights for the embedding routine (used in the optimization
     151    phase to ensure that the resulting geometry really does satisfy the
     152    pharmacophore).
     153
     154    if the excludedVolumes is provided, it should be a sequence of
     155    ExcludedVolume objects
     156
     157    >>> m = Chem.MolFromSmiles('c1ccccc1C')
     158    >>> bounds = MolDG.GetMoleculeBoundsMatrix(m)
     159    >>> bounds.shape == (7, 7)
     160    True
     161    >>> m.GetNumConformers()
     162    0
     163    >>> EmbedMol(m,bounds,randomSeed=23)
     164    >>> m.GetNumConformers()
     165    1
     166
     167
     168    """
     169    nAts = mol.GetNumAtoms()
     170    weights=[]
     171    if(atomMatch):
     172      for i in range(len(atomMatch)):
     173        for j in range(i+1,len(atomMatch)):
     174          weights.append((i,j,weight))
     175    if(excludedVolumes):
     176      for vol in excludedVolumes:
     177        idx = vol.index
     178        # excluded volumes affect every other atom:
     179        for i in range(nAts):
     180          weights.append((i,idx,weight))
     181    coords = DG.EmbedBoundsMatrix(bm,weights=weights,numZeroFail=1,randomSeed=randomSeed)
     182    #for row in coords:
     183    #  print(', '.join(['%.2f'%x for x in row]))
     184
     185    conf = Chem.Conformer(nAts)
     186    conf.SetId(0)
     187    for i in range(nAts):
     188      conf.SetAtomPosition(i,list(coords[i]))
     189    if excludedVolumes:
     190      for vol in excludedVolumes:
     191        vol.pos = numpy.array(coords[vol.index])
     192
     193    #print('   % 7.4f   % 7.4f   % 7.4f Ar  0  0  0  0  0  0  0  0  0  0  0  0'%tuple(coords[-1]), file=sys.stderr)
     194    mol.AddConformer(conf)
     195
     196 -def AddExcludedVolumes(bm,excludedVolumes,smoothIt=True):
     197    """ Adds a set of excluded volumes to the bounds matrix
     198    and returns the new matrix
     199
     200    excludedVolumes is a list of ExcludedVolume objects
     201
     202
     203     >>> boundsMat = numpy.array([[0.0,2.0,2.0],[1.0,0.0,2.0],[1.0,1.0,0.0]])
     204     >>> ev1 = ExcludedVolume.ExcludedVolume(([(0,),0.5,1.0],),exclusionDist=1.5)
     205     >>> bm = AddExcludedVolumes(boundsMat,(ev1,))
     206
     207     the results matrix is one bigger:
     208     >>> bm.shape == (4, 4)
     209     True
     210
     211     and the original bounds mat is not altered:
     212     >>> boundsMat.shape == (3, 3)
     213     True
     214
     215     >>> print(', '.join(['%.3f'%x for x in bm[-1]]))
     216     0.500, 1.500, 1.500, 0.000
     217     >>> print(', '.join(['%.3f'%x for x in bm[:,-1]]))
     218     1.000, 3.000, 3.000, 0.000
     219
     220    """
     221    oDim = bm.shape[0]
     222    dim = oDim+len(excludedVolumes)
     223    res = numpy.zeros((dim,dim),numpy.float)
     224    res[:oDim,:oDim] = bm
     225    for i,vol in enumerate(excludedVolumes):
     226      bmIdx = oDim+i
     227      vol.index = bmIdx
     228
     229      # set values to all the atoms:
     230      res[bmIdx,:bmIdx] = vol.exclusionDist
     231      res[:bmIdx,bmIdx] = 1000.0
     232
     233      # set values to our defining features:
     234      for indices,minV,maxV in vol.featInfo:
     235        for index in indices:
     236          try:
     237            res[bmIdx,index] = minV
     238            res[index,bmIdx] = maxV
     239          except IndexError:
     240            logger.error('BAD INDEX: res[%d,%d], shape is %s'%(bmIdx,index,str(res.shape)))
     241            raise IndexError
     242
     243      # set values to other excluded volumes:
     244      for j in range(bmIdx+1,dim):
     245        res[bmIdx,j:dim] = 0
     246        res[j:dim,bmIdx] = 1000
     247
     248    if smoothIt: DG.DoTriangleSmoothing(res)
     249    return res
     250
     251 -def UpdatePharmacophoreBounds(bm,atomMatch,pcophore,useDirs=False,
     252                                dirLength=defaultFeatLength,
     253                                mol=None):
     254    """ loops over a distance bounds matrix and replaces the elements
     255    that are altered by a pharmacophore
     256
     257    **NOTE** this returns the resulting bounds matrix, but it may also
     258    alter the input matrix
     259
     260    atomMatch is a sequence of sequences containing atom indices
     261    for each of the pharmacophore's features.
     262
     263      >>> feats = [ChemicalFeatures.FreeChemicalFeature('HBondAcceptor', 'HAcceptor1', Geometry.Point3D(0.0, 0.0, 0.0)),
     264      ...                ChemicalFeatures.FreeChemicalFeature('HBondDonor', 'HDonor1', Geometry.Point3D(2.65, 0.0, 0.0)),
     265      ...   ]
     266      >>> pcophore=Pharmacophore.Pharmacophore(feats)
     267      >>> pcophore.setLowerBound(0,1, 1.0)
     268      >>> pcophore.setUpperBound(0,1, 2.0)
     269
     270      >>> boundsMat = numpy.array([[0.0,3.0,3.0],[2.0,0.0,3.0],[2.0,2.0,0.0]])
     271      >>> atomMatch = ((0,),(1,))
     272      >>> bm = UpdatePharmacophoreBounds(boundsMat,atomMatch,pcophore)
     273
     274
     275       In this case, there are no multi-atom features, so the result matrix
     276       is the same as the input:
     277       >>> bm is boundsMat
     278       True
     279
     280       this means, of course, that the input boundsMat is altered:
     281       >>> print(', '.join(['%.3f'%x for x in boundsMat[0]]))
     282       0.000, 2.000, 3.000
     283       >>> print(', '.join(['%.3f'%x for x in boundsMat[1]]))
     284       1.000, 0.000, 3.000
     285       >>> print(', '.join(['%.3f'%x for x in boundsMat[2]]))
     286       2.000, 2.000, 0.000
     287
     288    """
     289    replaceMap = {}
     290    for i,matchI in enumerate(atomMatch):
     291      if len(matchI)>1:
     292        bm,replaceIdx = ReplaceGroup(matchI,bm,useDirs=useDirs)
     293        replaceMap[i] = replaceIdx
     294
     295    for i,matchI in enumerate(atomMatch):
     296      mi = replaceMap.get(i,matchI[0])
     297      for j in range(i+1,len(atomMatch)):
     298        mj = replaceMap.get(j,atomMatch[j][0])
     299        if mi<mj:
     300          idx0,idx1 = mi,mj
     301        else:
     302          idx0,idx1 = mj,mi
     303        bm[idx0,idx1] = pcophore.getUpperBound(i,j)
     304        bm[idx1,idx0] = pcophore.getLowerBound(i,j)
     305
     306    return bm
     307
     308
     309
     310 -def EmbedPharmacophore(mol,atomMatch,pcophore,randomSeed=-1,count=10,smoothFirst=True,
     311                         silent=False,bounds=None,excludedVolumes=None,targetNumber=-1,
     312                         useDirs=False):
     313    """ Generates one or more embeddings for a molecule that satisfy a pharmacophore
     314
     315    atomMatch is a sequence of sequences containing atom indices
     316    for each of the pharmacophore's features.
     317
     318      - count: is the maximum number of attempts to make a generating an embedding
     319      - smoothFirst: toggles triangle smoothing of the molecular bounds matix
     320      - bounds: if provided, should be the molecular bounds matrix. If this isn't
     321         provided, the matrix will be generated.
     322      - targetNumber: if this number is positive, it provides a maximum number
     323         of embeddings to generate (i.e. we'll have count attempts to generate
     324         targetNumber embeddings).
     325
     326    returns: a 3 tuple:
     327      1) the molecular bounds matrix adjusted for the pharmacophore
     328      2) a list of embeddings (molecules with a single conformer)
     329      3) the number of failed attempts at embedding
     330
     331
     332      >>> m = Chem.MolFromSmiles('OCCN')
     333      >>> feats = [ChemicalFeatures.FreeChemicalFeature('HBondAcceptor', 'HAcceptor1', Geometry.Point3D(0.0, 0.0, 0.0)),
     334      ...                ChemicalFeatures.FreeChemicalFeature('HBondDonor', 'HDonor1', Geometry.Point3D(2.65, 0.0, 0.0)),
     335      ...   ]
     336      >>> pcophore=Pharmacophore.Pharmacophore(feats)
     337      >>> pcophore.setLowerBound(0,1, 2.5)
     338      >>> pcophore.setUpperBound(0,1, 3.5)
     339      >>> atomMatch = ((0,),(3,))
     340
     341      >>> bm,embeds,nFail = EmbedPharmacophore(m,atomMatch,pcophore,randomSeed=23,silent=1)
     342      >>> len(embeds)
     343      10
     344      >>> nFail
     345      0
     346
     347      Set up a case that can't succeed:
     348      >>> pcophore=Pharmacophore.Pharmacophore(feats)
     349      >>> pcophore.setLowerBound(0,1, 2.0)
     350      >>> pcophore.setUpperBound(0,1, 2.1)
     351      >>> atomMatch = ((0,),(3,))
     352
     353      >>> bm,embeds,nFail = EmbedPharmacophore(m,atomMatch,pcophore,randomSeed=23,silent=1)
     354      >>> len(embeds)
     355      0
     356      >>> nFail
     357      10
     358
     359    """
     360    global _times
     361    if not hasattr(mol,'_chiralCenters'):
     362      mol._chiralCenters = Chem.FindMolChiralCenters(mol)
     363
     364    if bounds is None:
     365      bounds = MolDG.GetMoleculeBoundsMatrix(mol)
     366    if smoothFirst: DG.DoTriangleSmoothing(bounds)
     367
     368    bm = bounds.copy()
     369    #print '------------'
     370    #print 'initial'
     371    #for row in bm:
     372    #  print ' ',' '.join(['% 4.2f'%x for x in row])
     373    #print '------------'
     374
     375    bm = UpdatePharmacophoreBounds(bm,atomMatch,pcophore,useDirs=useDirs,mol=mol)
     376
     377    if excludedVolumes:
     378      bm = AddExcludedVolumes(bm,excludedVolumes,smoothIt=False)
     379
     380    if not DG.DoTriangleSmoothing(bm):
     381      raise ValueError("could not smooth bounds matrix")
     382
     383    #print '------------'
     384    #print 'post replace and smooth'
     385    #for row in bm:
     386    #  print ' ',' '.join(['% 4.2f'%x for x in row])
     387    #print '------------'
     388
     389
     390    if targetNumber<=0:
     391      targetNumber=count
     392    nFailed = 0
     393    res = []
     394    for i in range(count):
     395      tmpM = bm[:,:]
     396      m2 = Chem.Mol(mol)
     397      t1 = time.time()
     398      try:
     399        if randomSeed<=0:
     400          seed = i*10+1
     401        else:
     402          seed = i*10+randomSeed
     403        EmbedMol(m2,tmpM,atomMatch,randomSeed=seed,
     404                 excludedVolumes=excludedVolumes)
     405      except ValueError:
     406        if not silent:
     407          logger.info('Embed failed')
     408        nFailed += 1
     409      else:
     410        t2 = time.time()
     411        _times['embed'] = _times.get('embed',0)+t2-t1
     412        keepIt=True
     413        for idx,stereo in mol._chiralCenters:
     414          if stereo in ('R','S'):
     415            vol = ComputeChiralVolume(m2,idx)
     416            if (stereo=='R' and vol>=0) or \
     417               (stereo=='S' and vol<=0):
     418              keepIt=False
     419              break
     420        if keepIt:
     421          res.append(m2)
     422        else:
     423          logger.debug('Removed embedding due to chiral constraints.')
     424        if len(res)==targetNumber: break
     425    return bm,res,nFailed
     426
     427 -def isNaN(v):
     428    """ provides an OS independent way of detecting NaNs
     429    This is intended to be used with values returned from the C++
     430    side of things.
     431
     432    We can't actually test this from Python (which traps
     433    zero division errors), but it would work something like
     434    this if we could:
     435    >>> isNaN(0)
     436    False
     437
     438    #>>> isNan(1/0)
     439    #True
     440
     441    """
     442    if v!=v and sys.platform=='win32':
     443      return True
     444    elif v==0 and v==1 and sys.platform!='win32':
     445      return True
     446    return False
     447
     448
     449 -def OptimizeMol(mol,bm,atomMatches=None,excludedVolumes=None,
     450                  forceConstant=1200.0,
     451                  maxPasses=5,verbose=False):
     452    """  carries out a UFF optimization for a molecule optionally subject
     453    to the constraints in a bounds matrix
     454
     455      - atomMatches, if provided, is a sequence of sequences
     456      - forceConstant is the force constant of the spring used to enforce
     457        the constraints
     458
     459     returns a 2-tuple:
     460       1) the energy of the initial conformation
     461       2) the energy post-embedding
     462     NOTE that these energies include the energies of the constraints
     463
     464
     465
     466      >>> m = Chem.MolFromSmiles('OCCN')
     467      >>> feats = [ChemicalFeatures.FreeChemicalFeature('HBondAcceptor', 'HAcceptor1', Geometry.Point3D(0.0, 0.0, 0.0)),
     468      ...                ChemicalFeatures.FreeChemicalFeature('HBondDonor', 'HDonor1', Geometry.Point3D(2.65, 0.0, 0.0)),
     469      ...   ]
     470      >>> pcophore=Pharmacophore.Pharmacophore(feats)
     471      >>> pcophore.setLowerBound(0,1, 2.5)
     472      >>> pcophore.setUpperBound(0,1, 2.8)
     473      >>> atomMatch = ((0,),(3,))
     474      >>> bm,embeds,nFail = EmbedPharmacophore(m,atomMatch,pcophore,randomSeed=23,silent=1)
     475      >>> len(embeds)
     476      10
     477      >>> testM = embeds[0]
     478
     479      Do the optimization:
     480      >>> e1,e2 = OptimizeMol(testM,bm,atomMatches=atomMatch)
     481
     482      Optimizing should have lowered the energy:
     483      >>> e2 < e1
     484      True
     485
     486      Check the constrained distance:
     487      >>> conf = testM.GetConformer(0)
     488      >>> p0 = conf.GetAtomPosition(0)
     489      >>> p3 = conf.GetAtomPosition(3)
     490      >>> d03 = p0.Distance(p3)
     491      >>> d03 >= pcophore.getLowerBound(0,1)-.01
     492      True
     493      >>> d03 <= pcophore.getUpperBound(0,1)+.01
     494      True
     495
     496      If we optimize without the distance constraints (provided via the atomMatches
     497      argument) we're not guaranteed to get the same results, particularly in a case
     498      like the current one where the pharmcophore brings the atoms uncomfortably
     499      close together:
     500      >>> testM = embeds[1]
     501      >>> e1,e2 = OptimizeMol(testM,bm)
     502      >>> e2 < e1
     503      True
     504      >>> conf = testM.GetConformer(0)
     505      >>> p0 = conf.GetAtomPosition(0)
     506      >>> p3 = conf.GetAtomPosition(3)
     507      >>> d03 = p0.Distance(p3)
     508      >>> d03 >= pcophore.getLowerBound(0,1)-.01
     509      True
     510      >>> d03 <= pcophore.getUpperBound(0,1)+.01
     511      False
     512
     513    """
     514    try:
     515      ff = ChemicalForceFields.UFFGetMoleculeForceField(mol)
     516    except Exception:
     517      logger.info('Problems building molecular forcefield',exc_info=True)
     518      return -1.0,-1.0
     519
     520    weights=[]
     521    if(atomMatches):
     522      for k in range(len(atomMatches)):
     523        for i in atomMatches[k]:
     524          for l in range(k+1,len(atomMatches)):
     525            for j in atomMatches[l]:
     526              weights.append((i,j))
     527    for i,j in weights:
     528      if j<i:
     529        i,j = j,i
     530      minV = bm[j,i]
     531      maxV = bm[i,j]
     532      ff.AddDistanceConstraint(i,j,minV,maxV,forceConstant)
     533    if excludedVolumes:
     534      nAts = mol.GetNumAtoms()
     535      conf = mol.GetConformer()
     536      idx = nAts
     537      for exVol in excludedVolumes:
     538        assert exVol.pos is not None
     539        logger.debug('ff.AddExtraPoint(%.4f,%.4f,%.4f)'%(exVol.pos[0],exVol.pos[1],
     540                                                         exVol.pos[2]))
     541        ff.AddExtraPoint(exVol.pos[0],exVol.pos[1],exVol.pos[2],True)
     542        indices = []
     543        for localIndices,foo,bar in exVol.featInfo:
     544          indices += list(localIndices)
     545        for i in range(nAts):
     546          v = numpy.array(conf.GetAtomPosition(i))-numpy.array(exVol.pos)
     547          d = numpy.sqrt(numpy.dot(v,v))
     548          if i not in indices:
     549            if d<5.0:
     550              logger.debug('ff.AddDistanceConstraint(%d,%d,%.3f,%d,%.0f)'%(i,idx,exVol.exclusionDist,1000,forceConstant))
     551              ff.AddDistanceConstraint(i,idx,exVol.exclusionDist,1000,
     552                                       forceConstant)
     553
     554          else:
     555            logger.debug('ff.AddDistanceConstraint(%d,%d,%.3f,%.3f,%.0f)'%(i,idx,bm[exVol.index,i],bm[i,exVol.index],forceConstant))
     556            ff.AddDistanceConstraint(i,idx,bm[exVol.index,i],bm[i,exVol.index],
     557                                     forceConstant)
     558        idx += 1
     559    ff.Initialize()
     560    e1 = ff.CalcEnergy()
     561    if isNaN(e1):
     562      raise ValueError('bogus energy')
     563
     564    if verbose:
     565      print(Chem.MolToMolBlock(mol))
     566      for i,vol in enumerate(excludedVolumes):
     567        pos = ff.GetExtraPointPos(i)
     568        print('   % 7.4f   % 7.4f   % 7.4f As  0  0  0  0  0  0  0  0  0  0  0  0'%tuple(pos), file=sys.stderr)
     569    needsMore=ff.Minimize()
     570    nPasses=0
     571    while needsMore and nPasses<maxPasses:
     572      needsMore=ff.Minimize()
     573      nPasses+=1
     574    e2 = ff.CalcEnergy()
     575    if isNaN(e2):
     576      raise ValueError('bogus energy')
     577
     578    if verbose:
     579      print('--------')
     580      print(Chem.MolToMolBlock(mol))
     581      for i,vol in enumerate(excludedVolumes):
     582        pos = ff.GetExtraPointPos(i)
     583        print('   % 7.4f   % 7.4f   % 7.4f Sb  0  0  0  0  0  0  0  0  0  0  0  0'%tuple(pos), file=sys.stderr)
     584    ff = None
     585    return e1,e2
     586
     587 -def EmbedOne(mol,name,match,pcophore,count=1,silent=0,**kwargs):
     588    """ generates statistics for a molecule's embeddings
     589
     590    Four energies are computed for each embedding:
     591        1) E1: the energy (with constraints) of the initial embedding
     592        2) E2: the energy (with constraints) of the optimized embedding
     593        3) E3: the energy (no constraints) the geometry for E2
     594        4) E4: the energy (no constraints) of the optimized free-molecule
     595           (starting from the E3 geometry)
     596
     597    Returns a 9-tuple:
     598        1) the mean value of E1
     599        2) the sample standard deviation of E1
     600        3) the mean value of E2
     601        4) the sample standard deviation of E2
     602        5) the mean value of E3
     603        6) the sample standard deviation of E3
     604        7) the mean value of E4
     605        8) the sample standard deviation of E4
     606        9) The number of embeddings that failed
     607
     608    """
     609    global _times
     610    atomMatch = [list(x.GetAtomIds()) for x in match]
     611    bm,ms,nFailed = EmbedPharmacophore(mol,atomMatch,pcophore,count=count,
     612                                       silent=silent,**kwargs)
     613    e1s = []
     614    e2s = []
     615    e3s = []
     616    e4s = []
     617    d12s = []
     618    d23s = []
     619    d34s = []
     620    for m in ms:
     621      t1 = time.time()
     622      try:
     623        e1,e2 = OptimizeMol(m,bm,atomMatch)
     624      except ValueError:
     625        pass
     626      else:
     627        t2 = time.time()
     628        _times['opt1'] = _times.get('opt1',0)+t2-t1
     629
     630        e1s.append(e1)
     631        e2s.append(e2)
     632
     633        d12s.append(e1-e2)
     634        t1 = time.time()
     635        try:
     636          e3,e4 = OptimizeMol(m,bm)
     637        except ValueError:
     638          pass
     639        else:
     640          t2 = time.time()
     641          _times['opt2'] = _times.get('opt2',0)+t2-t1
     642          e3s.append(e3)
     643          e4s.append(e4)
     644          d23s.append(e2-e3)
     645          d34s.append(e3-e4)
     646      count += 1
     647    try:
     648      e1,e1d = Stats.MeanAndDev(e1s)
     649    except Exception:
     650      e1 = -1.0
     651      e1d=-1.0
     652    try:
     653      e2,e2d = Stats.MeanAndDev(e2s)
     654    except Exception:
     655      e2 = -1.0
     656      e2d=-1.0
     657    try:
     658      e3,e3d = Stats.MeanAndDev(e3s)
     659    except Exception:
     660      e3 = -1.0
     661      e3d=-1.0
     662
     663    try:
     664      e4,e4d = Stats.MeanAndDev(e4s)
     665    except Exception:
     666      e4 = -1.0
     667      e4d=-1.0
     668    if not silent:
     669      print('%s(%d): %.2f(%.2f) -> %.2f(%.2f) : %.2f(%.2f) -> %.2f(%.2f)' %
     670            (name,nFailed,e1,e1d,e2,e2d,e3,e3d,e4,e4d))
     671    return e1,e1d,e2,e2d,e3,e3d,e4,e4d,nFailed
     672
     673 -def MatchPharmacophoreToMol(mol, featFactory, pcophore):
     674    """ generates a list of all possible mappings of a pharmacophore to a molecule
     675
     676    Returns a 2-tuple:
     677      1) a boolean indicating whether or not all features were found
     678      2) a list, numFeatures long, of sequences of features
     679
     680
     681      >>> import os.path
     682      >>> dataDir = os.path.join(RDConfig.RDCodeDir,'Chem/Pharm3D/test_data')
     683      >>> featFactory = ChemicalFeatures.BuildFeatureFactory(os.path.join(dataDir,'BaseFeatures.fdef'))
     684      >>> activeFeats = [ChemicalFeatures.FreeChemicalFeature('Acceptor', Geometry.Point3D(0.0, 0.0, 0.0)),
     685      ...  ChemicalFeatures.FreeChemicalFeature('Donor',Geometry.Point3D(0.0, 0.0, 0.0))]
     686      >>> pcophore= Pharmacophore.Pharmacophore(activeFeats)
     687      >>> m = Chem.MolFromSmiles('FCCN')
     688      >>> match,mList = MatchPharmacophoreToMol(m,featFactory,pcophore)
     689      >>> match
     690      True
     691
     692      Two feature types:
     693      >>> len(mList)
     694      2
     695
     696      The first feature type, Acceptor, has two matches:
     697      >>> len(mList[0])
     698      2
     699      >>> mList[0][0].GetAtomIds()
     700      (0,)
     701      >>> mList[0][1].GetAtomIds()
     702      (3,)
     703
     704      The first feature type, Donor, has a single match:
     705      >>> len(mList[1])
     706      1
     707      >>> mList[1][0].GetAtomIds()
     708      (3,)
     709
     710    """
     711    return MatchFeatsToMol(mol, featFactory, pcophore.getFeatures())
     712
     713 -def _getFeatDict(mol,featFactory,features):
     714    """ **INTERNAL USE ONLY**
     715
     716      >>> import os.path
     717      >>> dataDir = os.path.join(RDConfig.RDCodeDir,'Chem/Pharm3D/test_data')
     718      >>> featFactory = ChemicalFeatures.BuildFeatureFactory(os.path.join(dataDir,'BaseFeatures.fdef'))
     719      >>> activeFeats = [ChemicalFeatures.FreeChemicalFeature('Acceptor', Geometry.Point3D(0.0, 0.0, 0.0)),
     720      ...  ChemicalFeatures.FreeChemicalFeature('Donor',Geometry.Point3D(0.0, 0.0, 0.0))]
     721      >>> m = Chem.MolFromSmiles('FCCN')
     722      >>> d =_getFeatDict(m,featFactory,activeFeats)
     723      >>> sorted(list(d.keys()))
     724      ['Acceptor', 'Donor']
     725      >>> donors = d['Donor']
     726      >>> len(donors)
     727      1
     728      >>> donors[0].GetAtomIds()
     729      (3,)
     730      >>> acceptors = d['Acceptor']
     731      >>> len(acceptors)
     732      2
     733      >>> acceptors[0].GetAtomIds()
     734      (0,)
     735      >>> acceptors[1].GetAtomIds()
     736      (3,)
     737
     738    """
     739    molFeats = {}
     740    for feat in features:
     741      family = feat.GetFamily()
     742      if not family in molFeats:
     743        matches = featFactory.GetFeaturesForMol(mol,includeOnly=family)
     744        molFeats[family] = matches
     745    return molFeats
     746
     747 -def MatchFeatsToMol(mol, featFactory, features):
     748    """ generates a list of all possible mappings of each feature to a molecule
     749
     750    Returns a 2-tuple:
     751      1) a boolean indicating whether or not all features were found
     752      2) a list, numFeatures long, of sequences of features
     753
     754
     755      >>> import os.path
     756      >>> dataDir = os.path.join(RDConfig.RDCodeDir,'Chem/Pharm3D/test_data')
     757      >>> featFactory = ChemicalFeatures.BuildFeatureFactory(os.path.join(dataDir,'BaseFeatures.fdef'))
     758      >>> activeFeats = [ChemicalFeatures.FreeChemicalFeature('Acceptor', Geometry.Point3D(0.0, 0.0, 0.0)),
     759      ...  ChemicalFeatures.FreeChemicalFeature('Donor',Geometry.Point3D(0.0, 0.0, 0.0))]
     760      >>> m = Chem.MolFromSmiles('FCCN')
     761      >>> match,mList = MatchFeatsToMol(m,featFactory,activeFeats)
     762      >>> match
     763      True
     764
     765      Two feature types:
     766      >>> len(mList)
     767      2
     768
     769      The first feature type, Acceptor, has two matches:
     770      >>> len(mList[0])
     771      2
     772      >>> mList[0][0].GetAtomIds()
     773      (0,)
     774      >>> mList[0][1].GetAtomIds()
     775      (3,)
     776
     777      The first feature type, Donor, has a single match:
     778      >>> len(mList[1])
     779      1
     780      >>> mList[1][0].GetAtomIds()
     781      (3,)
     782
     783    """
     784    molFeats = _getFeatDict(mol,featFactory,features)
     785    res = []
     786    for feat in features:
     787      matches = molFeats.get(feat.GetFamily(),[])
     788      if len(matches) == 0 :
     789        return False, None
     790      res.append(matches)
     791    return True, res
     792
     793 -def CombiEnum(sequence):
     794    """ This generator takes a sequence of sequences as an argument and
     795    provides all combinations of the elements of the subsequences:
     796
     797    >>> gen = CombiEnum(((1,2),(10,20)))
     798    >>> next(gen)
     799    [1, 10]
     800    >>> next(gen)
     801    [1, 20]
     802
     803    >>> [x for x in CombiEnum(((1,2),(10,20)))]
     804    [[1, 10], [1, 20], [2, 10], [2, 20]]
     805
     806    >>> [x for x in CombiEnum(((1,2),(10,20),(100,200)))]
     807    [[1, 10, 100], [1, 10, 200], [1, 20, 100], [1, 20, 200], [2, 10, 100], [2, 10, 200], [2, 20, 100], [2, 20, 200]]
     808
     809    """
     810    if not len(sequence):
     811      yield []
     812    elif len(sequence)==1:
     813      for entry in sequence[0]:
     814        yield [entry]
     815    else:
     816      for entry in sequence[0]:
     817        for subVal in CombiEnum(sequence[1:]):
     818          yield [entry]+subVal
     819
     820 -def DownsampleBoundsMatrix(bm,indices,maxThresh=4.0):
     821    """ removes rows from a bounds matrix that are
     822    that are greater than a threshold value away from a set of
     823    other points
     824
     825    returns the modfied bounds matrix
     826
     827    The goal of this function is to remove rows from the bounds matrix
     828    that correspond to atoms that are likely to be quite far from
     829    the pharmacophore we're interested in. Because the bounds smoothing
     830    we eventually have to do is N^3, this can be a big win
     831
     832     >>> boundsMat = numpy.array([[0.0,3.0,4.0],[2.0,0.0,3.0],[2.0,2.0,0.0]])
     833     >>> bm = DownsampleBoundsMatrix(boundsMat,(0,),3.5)
     834     >>> bm.shape == (2, 2)
     835     True
     836
     837     we don't touch the input matrix:
     838     >>> boundsMat.shape == (3, 3)
     839     True
     840
     841     >>> print(', '.join(['%.3f'%x for x in bm[0]]))
     842     0.000, 3.000
     843     >>> print(', '.join(['%.3f'%x for x in bm[1]]))
     844     2.000, 0.000
     845
     846     if the threshold is high enough, we don't do anything:
     847     >>> boundsMat = numpy.array([[0.0,4.0,3.0],[2.0,0.0,3.0],[2.0,2.0,0.0]])
     848     >>> bm = DownsampleBoundsMatrix(boundsMat,(0,),5.0)
     849     >>> bm.shape == (3, 3)
     850     True
     851
     852     If there's a max value that's close enough to *any* of the indices
     853     we pass in, we'll keep it:
     854     >>> boundsMat = numpy.array([[0.0,4.0,3.0],[2.0,0.0,3.0],[2.0,2.0,0.0]])
     855     >>> bm = DownsampleBoundsMatrix(boundsMat,(0,1),3.5)
     856     >>> bm.shape == (3, 3)
     857     True
     858
     859    """
     860    nPts = bm.shape[0]
     861    k = numpy.zeros(nPts,numpy.int0)
     862    for idx in indices: k[idx]=1
     863    for i in indices:
     864      row = bm[i]
     865      for j in range(i+1,nPts):
     866        if not k[j] and row[j]<maxThresh:
     867          k[j]=1
     868    keep = numpy.nonzero(k)[0]
     869    bm2 = numpy.zeros((len(keep),len(keep)),numpy.float)
     870    for i,idx in enumerate(keep):
     871      row = bm[idx]
     872      bm2[i] = numpy.take(row,keep)
     873    return bm2
     874
     875 -def CoarseScreenPharmacophore(atomMatch,bounds,pcophore,verbose=False):
     876    """
     877
     878    >>> feats = [ChemicalFeatures.FreeChemicalFeature('HBondAcceptor', 'HAcceptor1', Geometry.Point3D(0.0, 0.0, 0.0)),
     879    ...                ChemicalFeatures.FreeChemicalFeature('HBondDonor', 'HDonor1', Geometry.Point3D(2.65, 0.0, 0.0)),
     880    ...                ChemicalFeatures.FreeChemicalFeature('Aromatic', 'Aromatic1', Geometry.Point3D(5.12, 0.908, 0.0)),
     881    ...                ]
     882    >>> pcophore=Pharmacophore.Pharmacophore(feats)
     883    >>> pcophore.setLowerBound(0,1, 1.1)
     884    >>> pcophore.setUpperBound(0,1, 1.9)
     885    >>> pcophore.setLowerBound(0,2, 2.1)
     886    >>> pcophore.setUpperBound(0,2, 2.9)
     887    >>> pcophore.setLowerBound(1,2, 2.1)
     888    >>> pcophore.setUpperBound(1,2, 3.9)
     889
     890    >>> bounds = numpy.array([[0,2,3],[1,0,4],[2,3,0]],numpy.float)
     891    >>> CoarseScreenPharmacophore(((0,),(1,)),bounds,pcophore)
     892    True
     893
     894    >>> CoarseScreenPharmacophore(((0,),(2,)),bounds,pcophore)
     895    False
     896
     897    >>> CoarseScreenPharmacophore(((1,),(2,)),bounds,pcophore)
     898    False
     899
     900    >>> CoarseScreenPharmacophore(((0,),(1,),(2,)),bounds,pcophore)
     901    True
     902
     903    >>> CoarseScreenPharmacophore(((1,),(0,),(2,)),bounds,pcophore)
     904    False
     905
     906    >>> CoarseScreenPharmacophore(((2,),(1,),(0,)),bounds,pcophore)
     907    False
     908
     909    # we ignore the point locations here and just use their definitions:
     910    >>> feats = [ChemicalFeatures.FreeChemicalFeature('HBondAcceptor', 'HAcceptor1', Geometry.Point3D(0.0, 0.0, 0.0)),
     911    ...                ChemicalFeatures.FreeChemicalFeature('HBondDonor', 'HDonor1', Geometry.Point3D(2.65, 0.0, 0.0)),
     912    ...                ChemicalFeatures.FreeChemicalFeature('Aromatic', 'Aromatic1', Geometry.Point3D(5.12, 0.908, 0.0)),
     913    ...                ChemicalFeatures.FreeChemicalFeature('HBondDonor', 'HDonor1', Geometry.Point3D(2.65, 0.0, 0.0)),
     914    ...                ]
     915    >>> pcophore=Pharmacophore.Pharmacophore(feats)
     916    >>> pcophore.setLowerBound(0,1, 2.1)
     917    >>> pcophore.setUpperBound(0,1, 2.9)
     918    >>> pcophore.setLowerBound(0,2, 2.1)
     919    >>> pcophore.setUpperBound(0,2, 2.9)
     920    >>> pcophore.setLowerBound(0,3, 2.1)
     921    >>> pcophore.setUpperBound(0,3, 2.9)
     922    >>> pcophore.setLowerBound(1,2, 1.1)
     923    >>> pcophore.setUpperBound(1,2, 1.9)
     924    >>> pcophore.setLowerBound(1,3, 1.1)
     925    >>> pcophore.setUpperBound(1,3, 1.9)
     926    >>> pcophore.setLowerBound(2,3, 1.1)
     927    >>> pcophore.setUpperBound(2,3, 1.9)
     928    >>> bounds = numpy.array([[0,3,3,3],[2,0,2,2],[2,1,0,2],[2,1,1,0]],numpy.float)
     929
     930    >>> CoarseScreenPharmacophore(((0,),(1,),(2,),(3,)),bounds,pcophore)
     931    True
     932
     933    >>> CoarseScreenPharmacophore(((0,),(1,),(3,),(2,)),bounds,pcophore)
     934    True
     935
     936    >>> CoarseScreenPharmacophore(((1,),(0,),(3,),(2,)),bounds,pcophore)
     937    False
     938
     939    """
     940    for k in range(len(atomMatch)):
     941      if len(atomMatch[k])==1:
     942        for l in range(k+1,len(atomMatch)):
     943          if len(atomMatch[l])==1:
     944            idx0 = atomMatch[k][0]
     945            idx1 = atomMatch[l][0]
     946            if idx1<idx0:
     947              idx0,idx1=idx1,idx0
     948            if bounds[idx1,idx0] >= pcophore.getUpperBound(k, l) or \
     949               bounds[idx0,idx1] <= pcophore.getLowerBound(k, l) :
     950              if verbose:
     951                print('\t  (%d,%d) [%d,%d] fail'%(idx1,idx0,k,l))
     952                print('\t    %f,%f - %f,%f' %
     953                      (bounds[idx1,idx0],pcophore.getUpperBound(k,l),
     954                       bounds[idx0,idx1],pcophore.getLowerBound(k,l)))
     955              #logger.debug('\t >%s'%str(atomMatch))
     956              #logger.debug()
     957              #logger.debug('\t    %f,%f - %f,%f'%(bounds[idx1,idx0],pcophore.getUpperBound(k,l),
     958              #                                    bounds[idx0,idx1],pcophore.getLowerBound(k,l)))
     959              return False
     960    return True
     961
     962 -def Check2DBounds(atomMatch,mol,pcophore):
     963    """ checks to see if a particular mapping of features onto
     964    a molecule satisfies a pharmacophore's 2D restrictions
     965
     966
     967      >>> activeFeats = [ChemicalFeatures.FreeChemicalFeature('Acceptor', Geometry.Point3D(0.0, 0.0, 0.0)),
     968      ...  ChemicalFeatures.FreeChemicalFeature('Donor',Geometry.Point3D(0.0, 0.0, 0.0))]
     969      >>> pcophore= Pharmacophore.Pharmacophore(activeFeats)
     970      >>> pcophore.setUpperBound2D(0,1,3)
     971      >>> m = Chem.MolFromSmiles('FCC(N)CN')
     972      >>> Check2DBounds(((0,),(3,)),m,pcophore)
     973      True
     974      >>> Check2DBounds(((0,),(5,)),m,pcophore)
     975      False
     976
     977    """
     978    dm = Chem.GetDistanceMatrix(mol,False,False,False)
     979    nFeats = len(atomMatch)
     980    for i in range(nFeats):
     981      for j in range(i+1,nFeats):
     982        lowerB = pcophore._boundsMat2D[j,i] #lowerB = pcophore.getLowerBound2D(i,j)
     983        upperB = pcophore._boundsMat2D[i,j] #upperB = pcophore.getUpperBound2D(i,j)
     984        dij=10000
     985        for atomI in atomMatch[i]:
     986          for atomJ in atomMatch[j]:
     987            try:
     988              dij = min(dij,dm[atomI,atomJ])
     989            except IndexError:
     990              print('bad indices:',atomI,atomJ)
     991              print('  shape:',dm.shape)
     992              print('  match:',atomMatch)
     993              print('    mol:')
     994              print(Chem.MolToMolBlock(mol))
     995              raise IndexError
     996        if dij<lowerB or dij>upperB:
     997          return False
     998    return True
     999
    1000 -def _checkMatch(match,mol,bounds,pcophore,use2DLimits):
    1001    """ **INTERNAL USE ONLY**
    1002
    1003    checks whether a particular atom match can be satisfied by
    1004    a molecule
    1005
    1006    """
    1007    atomMatch = ChemicalFeatures.GetAtomMatch(match)
    1008    if not atomMatch:
    1009      return None
    1010    elif use2DLimits:
    1011      if not Check2DBounds(atomMatch,mol,pcophore):
    1012        return None
    1013    if not CoarseScreenPharmacophore(atomMatch,bounds,pcophore):
    1014      return None
    1015    return atomMatch
    1016
    1017 -def ConstrainedEnum(matches,mol,pcophore,bounds,use2DLimits=False,
    1018                      index=0,soFar=[]):
    1019    """ Enumerates the list of atom mappings a molecule
    1020    has to a particular pharmacophore.
    1021    We do check distance bounds here.
    1022
    1023
    1024    """
    1025    nMatches = len(matches)
    1026    if index>=nMatches:
    1027      yield soFar,[]
    1028    elif index==nMatches-1:
    1029      for entry in matches[index]:
    1030        nextStep = soFar+[entry]
    1031        if index != 0:
    1032          atomMatch = _checkMatch(nextStep,mol,bounds,pcophore,use2DLimits)
    1033        else:
    1034          atomMatch = ChemicalFeatures.GetAtomMatch(nextStep)
    1035        if atomMatch:
    1036          yield soFar+[entry],atomMatch
    1037    else:
    1038      for entry in matches[index]:
    1039        nextStep = soFar+[entry]
    1040        if index != 0:
    1041          atomMatch = _checkMatch(nextStep,mol,bounds,pcophore,use2DLimits)
    1042          if not atomMatch:
    1043            continue
    1044        for val in ConstrainedEnum(matches,mol,pcophore,bounds,use2DLimits=use2DLimits,
    1045                                   index=index+1,soFar=nextStep):
    1046          if val:
    1047            yield val
    1048
    1049 -def MatchPharmacophore(matches,bounds,pcophore,useDownsampling=False,
    1050                         use2DLimits=False,mol=None,excludedVolumes=None,
    1051                         useDirs=False):
    1052    """
    1053
    1054    if use2DLimits is set, the molecule must also be provided and topological
    1055    distances will also be used to filter out matches
    1056
    1057    """
    1058    for match,atomMatch in ConstrainedEnum(matches,mol,pcophore,bounds,
    1059                                           use2DLimits=use2DLimits):
    1060      bm = bounds.copy()
    1061      bm = UpdatePharmacophoreBounds(bm,atomMatch,pcophore,useDirs=useDirs,mol=mol);
    1062
    1063      if excludedVolumes:
    1064        localEvs = []
    1065        for eV in excludedVolumes:
    1066          featInfo = []
    1067          for i,entry in enumerate(atomMatch):
    1068            info = list(eV.featInfo[i])
    1069            info[0] = entry
    1070            featInfo.append(info)
    1071          localEvs.append(ExcludedVolume.ExcludedVolume(featInfo,eV.index,
    1072                                                       eV.exclusionDist))
    1073        bm = AddExcludedVolumes(bm,localEvs,smoothIt=False)
    1074
    1075      sz = bm.shape[0]
    1076      if useDownsampling:
    1077        indices = []
    1078        for entry in atomMatch:
    1079          indices.extend(entry)
    1080        if excludedVolumes:
    1081          for vol in localEvs:
    1082            indices.append(vol.index)
    1083        bm = DownsampleBoundsMatrix(bm,indices)
    1084      if DG.DoTriangleSmoothing(bm):
    1085        return 0,bm,match,(sz,bm.shape[0])
    1086
    1087    return 1,None,None,None
    1088
    1089 -def GetAllPharmacophoreMatches(matches,bounds,pcophore,useDownsampling=0,
    1090                                 progressCallback=None,
    1091                                 use2DLimits=False,mol=None,
    1092                                 verbose=False):
    1093    res = []
    1094    nDone = 0
    1095    for match in CombiEnum(matches):
    1096      atomMatch = ChemicalFeatures.GetAtomMatch(match)
    1097      if atomMatch and use2DLimits and mol:
    1098        pass2D = Check2DBounds(atomMatch,mol,pcophore)
    1099        if verbose:
    1100          print('..',atomMatch)
    1101          print('  ..Pass2d:',pass2D)
    1102      else:
    1103        pass2D = True
    1104      if atomMatch and pass2D and \
    1105         CoarseScreenPharmacophore(atomMatch,bounds,pcophore,verbose=verbose):
    1106        if verbose:
    1107          print('  ..CoarseScreen: Pass')
    1108
    1109        bm = bounds.copy()
    1110        if verbose:
    1111          print('pre update:')
    1112          for row in bm:
    1113            print(' ',' '.join(['% 4.2f'%x for x in row]))
    1114        bm = UpdatePharmacophoreBounds(bm,atomMatch,pcophore);
    1115        sz = bm.shape[0]
    1116        if verbose:
    1117          print('pre downsample:')
    1118          for row in bm:
    1119            print(' ',' '.join(['% 4.2f'%x for x in row]))
    1120
    1121        if useDownsampling:
    1122          indices = []
    1123          for entry in atomMatch:
    1124            indices += list(entry)
    1125          bm = DownsampleBoundsMatrix(bm,indices)
    1126        if verbose:
    1127          print('post downsample:')
    1128          for row in bm:
    1129            print(' ',' '.join(['% 4.2f'%x for x in row]))
    1130
    1131        if DG.DoTriangleSmoothing(bm):
    1132          res.append(match)
    1133        elif verbose:
    1134          print('cannot smooth')
    1135        nDone+=1
    1136        if progressCallback:
    1137          progressCallback(nDone)
    1138    return res
    1139
    1140
    1141 -def ComputeChiralVolume(mol,centerIdx,confId=-1):
    1142    """ Computes the chiral volume of an atom
    1143
    1144    We're using the chiral volume formula from Figure 7 of
    1145    Blaney and Dixon, Rev. Comp. Chem. V, 299-335 (1994)
    1146
    1147      >>> import os.path
    1148      >>> dataDir = os.path.join(RDConfig.RDCodeDir,'Chem/Pharm3D/test_data')
    1149
    1150      R configuration atoms give negative volumes:
    1151      >>> mol = Chem.MolFromMolFile(os.path.join(dataDir,'mol-r.mol'))
    1152      >>> Chem.AssignStereochemistry(mol)
    1153      >>> mol.GetAtomWithIdx(1).GetProp('_CIPCode')
    1154      'R'
    1155      >>> ComputeChiralVolume(mol,1) < 0
    1156      True
    1157
    1158      S configuration atoms give positive volumes:
    1159      >>> mol = Chem.MolFromMolFile(os.path.join(dataDir,'mol-s.mol'))
    1160      >>> Chem.AssignStereochemistry(mol)
    1161      >>> mol.GetAtomWithIdx(1).GetProp('_CIPCode')
    1162      'S'
    1163      >>> ComputeChiralVolume(mol,1) > 0
    1164      True
    1165
    1166      Non-chiral (or non-specified) atoms give zero volume:
    1167      >>> ComputeChiralVolume(mol,0) == 0.0
    1168      True
    1169
    1170      We also work on 3-coordinate atoms (with implicit Hs):
    1171      >>> mol = Chem.MolFromMolFile(os.path.join(dataDir,'mol-r-3.mol'))
    1172      >>> Chem.AssignStereochemistry(mol)
    1173      >>> mol.GetAtomWithIdx(1).GetProp('_CIPCode')
    1174      'R'
    1175      >>> ComputeChiralVolume(mol,1)<0
    1176      True
    1177
    1178      >>> mol = Chem.MolFromMolFile(os.path.join(dataDir,'mol-s-3.mol'))
    1179      >>> Chem.AssignStereochemistry(mol)
    1180      >>> mol.GetAtomWithIdx(1).GetProp('_CIPCode')
    1181      'S'
    1182      >>> ComputeChiralVolume(mol,1)>0
    1183      True
    1184
    1185
    1186
    1187    """
    1188    conf = mol.GetConformer(confId)
    1189    Chem.AssignStereochemistry(mol)
    1190    center = mol.GetAtomWithIdx(centerIdx)
    1191    if not center.HasProp('_CIPCode'):
    1192      return 0.0
    1193
    1194    nbrs = center.GetNeighbors()
    1195    nbrRanks = []
    1196    for nbr in nbrs:
    1197      rank = int(nbr.GetProp('_CIPRank'))
    1198      pos = conf.GetAtomPosition(nbr.GetIdx())
    1199      nbrRanks.append((rank,pos))
    1200
    1201    # if we only have three neighbors (i.e. the determining H isn't present)
    1202    # then use the central atom as the fourth point:
    1203    if len(nbrRanks)==3:
    1204      nbrRanks.append((-1,conf.GetAtomPosition(centerIdx)))
    1205    nbrRanks.sort()
    1206
    1207    ps = [x[1] for x in nbrRanks]
    1208    v1 = ps[0]-ps[3]
    1209    v2 = ps[1]-ps[3]
    1210    v3 = ps[2]-ps[3]
    1211
    1212    res = v1.DotProduct(v2.CrossProduct(v3))
    1213    return res
    1214
    1215
    1216
    1217
    1218
    1219
    1220  #------------------------------------
    1221  #
    1222  #  doctest boilerplate
    1223  #
    1224 -def _test():
    1225    import doctest,sys
    1226    return doctest.testmod(sys.modules["__main__"])
    1227
    1228  if __name__ == '__main__':
    1229    import sys
    1230    failed,tried = _test()
    1231    sys.exit(failed)
    1232