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Merge pull request #6 from cclib/dev/bindings
Dev/bindings
2 parents 8737740 + 2d1b969 commit f5568c8

11 files changed

+7680
-1930
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‎CondaPkg.toml

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[pip.deps]
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cclib = ""

‎Project.toml

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version = "0.1.0"
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[deps]
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CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
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PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
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PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
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[compat]
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PyCall = "1"

‎src/Cclib.jl

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# Basically an exact application of
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# <https://github.com/JuliaPy/PyCall.jl#using-pycall-from-julia-modules>.
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#
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# The initialization strategy is similar to the one employed by SymPy.jl, see
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# <https://github.com/JuliaPy/SymPy.jl/blob/aea9fb5568022bbd68fe4b69d670ce2a22413a7c/src/SymPy.jl#L124>.
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__precompile__()
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module Cclib
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using PythonCall
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using CondaPkg
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using PyCall
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export bridge
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export io
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export method
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export parser
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export ccopen, ccwrite
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"""
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bridge
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Facilities for moving parsed data to other cheminformatic libraries.
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"""
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const bridge = PyCall.PyNULL()
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"""
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io
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Available writers for standard chemical representations.
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"""
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const io = PyCall.PyNULL()
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"""
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method
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Analyses and calculations based on data parsed by cclib.
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"""
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const method = PyCall.PyNULL()
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"""
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parser
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Parsers for all supported programs.
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"""
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const parser = PyCall.PyNULL()
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"""
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Guess the identity of a particular log file and return an instance of it.
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"""
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const ccopen = PyCall.PyNULL()
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"""
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Write the parsed data from an outputfile to a standard chemical representation.
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"""
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const ccwrite = PyCall.PyNULL()
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include("functions.jl")
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include("config.jl")
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const cclib = Ref{Py}()
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function __init__()
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cclib = PyCall.pyimport_conda("cclib", "cclib")
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# Version of the underlying cclib Python package.
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global __version__ = cclib.__version__
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copy!(bridge, PyCall.pyimport_conda("cclib.bridge", "cclib"))
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copy!(io, PyCall.pyimport_conda("cclib.io", "cclib"))
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copy!(method, PyCall.pyimport_conda("cclib.method", "cclib"))
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copy!(parser, PyCall.pyimport_conda("cclib.parser", "cclib"))
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copy!(ccopen, io.ccopen)
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copy!(ccwrite, io.ccwrite)
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cclib[] = pyimport("cclib")
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end
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end

‎src/config.jl

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export cclibtypes
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cclibtypes = Dict(
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"aonames" => Array{String},
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"aooverlaps" => Array{Float64, 2},
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"atombasis" => Array{Array{Int64}},
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"atomcharges" => Dict{String, Array{Float64}},
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"atomcoords" => Array{Float64, 3},
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"atommasses" => Array{Float64},
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"atomnos" => Array{Int64},
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"atomspins" => Dict{Array},
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"ccenergies" => Array{Float64, 2},
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"charge" => Int64,
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"coreelectrons" => Array{}, # specify subytpe?
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"dispersionenergies" => Array{Float64},
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"enthalpy" => Float64,
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"entropy" => Float64,
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"etenergies" => Array{Float64},
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# # subtypes for these?
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"etoscs" => Array{},
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"etdips" => Array{},
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"etveldips" => Array{},
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"etmagdips" => Array{},
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"etrotats" => Array{},
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"etsecs" => Array{Array},
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"etsyms" => Array{String},
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"freeenergy" => Float64,
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"fonames" => Array{String},
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"fooverlaps" => Array{}, # subtype ?
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"fragnames" => Array{String},
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"frags" => Array{Array},
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"gbasis" => Any, # PyQuante format
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"geotargets" => Array{},
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"geovalues" => Array{},
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"grads" => Array{},
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"hessian" => Array{},
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"homos" => Array{},
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"metadata" => Dict{Any, Any},
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"mocoeffs" => Array{Array{Float64}},
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"moenergies" => Array{Array{Float64}},
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"moments" => Array{Array},
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"mosyms" => Array{Array},
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"mpenergies" => Array{Array{Float64}},
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"mult" => Int64,
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"natom" => Int64,
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"nbasis" => Int64,
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"nmo" => Int64,
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"nmrtensors" => Any, # Find the right one for this one
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"nocoeffs" => Array{Array},
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"nooccnos" => Array{Array},
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"optdone" => Bool,
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"optstatus" => Array{},
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"polarizabilities" => Array{Array{Float64, 2}},
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"pressure" => Float64,
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"scancoords" => Array{},
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"scanenergies" => Array{},
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"scannames" => Array{String},
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"scanparm" => Array{Tuple},
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"scfenergies" => Array{Float64},
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"scftargets" => Array{Float64, 2},
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"scfvalues" => Array{Array{Float64, 2}},
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"temperature" => Float64,
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"time" => Array{},
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"transprop" => Dict{Any, Any},
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"vibanharms" => Array{},
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"vibdisps" => Array{},
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"vibfreqs" => Array{},
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"vibfconsts" => Array{},
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"vibirs" => Array{},
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"vibanharms" => Array{},
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"vibrmasses" => Array{},
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"vibsyms" => Array{String},
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"zpve" => Float64
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)

‎src/functions.jl

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export ccread
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function pyccread(file)
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data = cclib[].io.ccread(file)
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keys = pyconvert(Array, data.__dict__.keys())
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values = pyconvert(Array, data.__dict__.values())
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return Dict(zip(keys, values))
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end
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function ccread(pydict)
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datadict = pyccread(pydict)
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for (key, value) in datadict
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type = cclibtypes[key]
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datadict[key] = pyconvert(type, value)
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end
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return datadict
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end

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