rdkit/Python/utils/chemutils.py

#
#  Copyright (C) 2000  greg Landrum
#
""" utility functions with "chemical know-how"

"""
import RDConfig
import string,re,os

if not RDConfig.usePgSQL:
  _atomDbName = os.path.join(RDConfig.RDDataDir,'atomdb.gdb')
else:
  _atomDbName = "::RDData"

def GetAtomicData(atomDict,descriptorsDesired,dBase=_atomDbName,
                  table='atomic_data',where='',
                  user='sysdba',password='masterkey',
                  includeElCounts=0):
  """ pulls atomic data from a database

    **Arguments**

      - atomDict: the dictionary to populate

      - descriptorsDesired: the descriptors to pull for each atom

      - dBase: the DB to use

      - table: the DB table to use

      - where: the SQL where clause

      - user: the user name to use with the DB

      - password: the password to use with the DB

      - includeElCounts: if nonzero, valence electron count fields are added to
         the _atomDict_

  """
  extraFields =['NVAL','NVAL_NO_FULL_F','NVAL_NO_FULL_D','NVAL_NO_FULL']
  from Dbase import DbModule
  cn = DbModule.connect(dBase,user,password)
  c = cn.cursor()
  descriptorsDesired = map(string.upper,descriptorsDesired)
  if 'NAME' not in descriptorsDesired:
    descriptorsDesired.append('NAME')
  if includeElCounts and 'CONFIG' not in descriptorsDesired:
    descriptorsDesired.append('CONFIG')
  for field in extraFields:
    if field in descriptorsDesired:
      descriptorsDesired.remove(field)
  toPull = string.join(descriptorsDesired,',')
  command = 'select %s from atomic_data %s'%(toPull,where)
  try:
    c.execute(command)
  except:
    print 'Problems executing command:',command
    return
  res = c.fetchall()
  for atom in res:
    tDict = {}
    for i in xrange(len(descriptorsDesired)):
      desc = descriptorsDesired[i]
      val = atom[i]
      tDict[desc] = val
    name=tDict['NAME']
    atomDict[name] = tDict
    if includeElCounts:
      config = atomDict[name]['CONFIG']
      atomDict[name]['NVAL'] = ConfigToNumElectrons(config)
      atomDict[name]['NVAL_NO_FULL_F'] = ConfigToNumElectrons(config,ignoreFullF=1)
      atomDict[name]['NVAL_NO_FULL_D'] = ConfigToNumElectrons(config,ignoreFullD=1)
      atomDict[name]['NVAL_NO_FULL'] = ConfigToNumElectrons(config,ignoreFullF=1,
                                                            ignoreFullD=1)      

def SplitComposition(compStr):
  """ Takes a simple chemical composition and turns into a list of element,# pairs.

      i.e. 'Fe3Al' -> [('Fe',3),('Al',1)]

      **Arguments**

       - compStr: the composition string to be processed

      **Returns**

       - the *composVect* corresponding to _compStr_

      **Note**

        -this isn't smart enough by half to deal with anything even
            remotely subtle, so be gentle.

  """
  target = r'([A-Z][a-z]?)([0-9\.]*)'

  theExpr = re.compile(target)
  
  matches = theExpr.findall(compStr)
  res = []
  for match in matches:
    if len(match[1])>0:
      res.append((match[0],float(match[1])))
    else:
      res.append((match[0],1))
      

  return res

def ConfigToNumElectrons(config,ignoreFullD=0,ignoreFullF=0):
  """ counts the number of electrons appearing in a configuration string

    **Arguments**

      - config: the configuration string (e.g. '2s^2 2p^4')

      - ignoreFullD: toggles not counting full d shells

      - ignoreFullF: toggles not counting full f shells

    **Returns**

      the number of valence electrons
      
  """
  arr = string.split(config,' ')

  nEl = 0
  for i in range(1,len(arr)):
    l = string.split(arr[i],'^')
    incr = int(l[1])
    if ignoreFullF and incr==14 and string.find(l[0],'f')!=-1 and len(arr) > 2:
      incr = 0
    if ignoreFullD and incr==10 and string.find(l[0],'d')!=-1 and len(arr) > 2:
      incr = 0
    nEl = nEl + incr
  return nEl

if __name__ == '__main__':
  
  print SplitComposition('Fe')
  print SplitComposition('Fe3Al')
  print SplitComposition('Fe99PdAl')
  print SplitComposition('TiNiSiSO12P')      
  temp = ['[Xe] 4f^12 6s^2','[Xe] 4f^14 5d^6 6s^2','[Xe] 4f^14 5d^10 6s^2',
          '[Xe] 4f^14 5d^10 6s^2 6p^1', '[Xe] 5d^10']
  print 'ignore all'
  for entry in temp:
    print entry, '\t\t\t\t', ConfigToNumElectrons(entry,ignoreFullD=1,ignoreFullF=1)
  print 'ignore d'
  for entry in temp:
    print entry, '\t\t\t\t', ConfigToNumElectrons(entry,ignoreFullD=1,ignoreFullF=0)
  print 'ignore f'
  for entry in temp:
    print entry, '\t\t\t\t', ConfigToNumElectrons(entry,ignoreFullD=0,ignoreFullF=1)
  print 'ignore None'
  for entry in temp:
    print entry, '\t\t\t\t', ConfigToNumElectrons(entry,ignoreFullD=0,ignoreFullF=0)