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Interface between Quantum Chemistry programs and RDKit

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chemhelp

Started out as common functionality I keep re-programming, now it is a collection of interfaces between RDKit and quantum chemistry

For example, want to optimize a molecule with PM3 in GAMESS?

from chemhelp import gamess
from chemhelp import cheminfo

methane = """ SDF CONTENT """

header = """ $basis gbasis=pm3 $end
 $contrl runtyp=optimize icharg={:} $end
 $statpt opttol=0.0005 nstep=300 projct=.F. $end """

molobj = cheminfo.sdfstr_to_molobj(methane)
stdout, stderr = gamess.calculate(molobj, header)
properties = gamess.read_properties_coordinates(stdout)
atoms = properties["atoms"]
coord = properties["coord"]
energy = properties["h"]

with consistent interfaces to MOPAC, GAMESS, Gaussian and MNDO

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