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#
# Copyright (C) 2000 greg Landrum
#
""" utility functions with "chemical know-how"
"""
import os
import re
from rdkit import RDConfig
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 rdkit.Dbase import DbModule
cn = DbModule.connect(dBase, user, password)
c = cn.cursor()
descriptorsDesired = [s.upper() for s in 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 = ','.join(descriptorsDesired)
command = 'select %s from atomic_data %s' % (toPull, where)
try:
c.execute(command)
except Exception:
print('Problems executing command:', command)
return
res = c.fetchall()
for atom in res:
tDict = {}
for i in range(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 = config.split(' ')
nEl = 0
for i in range(1, len(arr)):
l = arr[i].split('^')
incr = int(l[1])
if ignoreFullF and incr == 14 and l[0].find('f') != -1 and len(arr) > 2:
incr = 0
if ignoreFullD and incr == 10 and l[0].find('d') != -1 and len(arr) > 2:
incr = 0
nEl = nEl + incr
return nEl
if __name__ == '__main__': # pragma: nocover
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))
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