Metadata-Version: 2.1
Name: pygamess
Version: 0.5.0
Summary: GAMESS wrapper for Python
Home-page: https://github.com/kzfm/pygamess
Author: Ohkawa Kazufumi
Author-email: kerolinq@gmail.com
License: MIT
Description: ==========
         pygamess
        ==========
        
        `pygamess` is a GAMESS wrapper for Python
        
        Requirements
        ------------
        * Python 3.7 or later (pygamess <0.5 only support Python2)
        * RDKit
        * GAMESS
        * ruamel.YAML
        
        Setup
        -----
        ::
        
            $ pip install pygamess
        
        set GAMESS_HOME environment in your .bashrc::
        
            $ export GAMESS_HOME=/usr/local/gamess
        
        Test
        -----
        ::
        
            $ pytest
        
        Basic Usage
        -----------
        
        single point calculation with RDKit
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        ::
        
            >>> from pygamess import Gamess
            >>> from rdkit import Chem
            >>> from rdkit.Chem import AllChem
            >>> m = Chem.MolFromSmiles("CC")
            >>> m = Chem.AddHs(m)
            >>> AllChem.EmbedMolecule(m)
            0
            >>> AllChem.UFFOptimizeMolecule(m,maxIters=200)
            0
            >>> g = Gamess()
            >>> nm = g.run(m)
            >>> nm.GetProp("total_energy")
            '-78.302511990200003'
        
        optimize calculation with RDKit
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        Change run_type::
        
            >>> from pygamess import Gamess
            >>> from rdkit import Chem
            >>> from rdkit.Chem import AllChem
            >>> m = Chem.MolFromSmiles("CC")
            >>> m = Chem.AddHs(m)
            >>> AllChem.EmbedMolecule(m)
            0
            >>> AllChem.UFFOptimizeMolecule(m,maxIters=200)
            0
            >>> g = Gamess()
            >>> g.run_type('optimize')
            >>> optimized_mol = g.run(mol)
            >>> optimized_mol.GetProp("total_energy")
            '-78.306179626599999'
        
        changing basis-sets
        ~~~~~~~~~~~~~~~~~~~
        
        Change basis set::
        
            >>> from pygamess import Gamess
            >>> from rdkit import Chem
            >>> from rdkit.Chem import AllChem
            >>> m = Chem.MolFromSmiles("CC")
            >>> m = Chem.AddHs(m)
            >>> AllChem.EmbedMolecule(m)
            0
            >>> AllChem.UFFOptimizeMolecule(m,maxIters=200)
            0
            >>> g = Gamess()
            >>> g.run_type = "optimize"
            >>> g.run(m).GetProp("total_energy")
            '-78.302511907400003'
            >>> g.basis_set("3-21G")
            {'gbasis': 'N21', 'ngauss': '3'}
            >>> g.run(m).GetProp("total_energy")
            '-78.790442552000002'
            >>> g.basis_set("6-31G")
            {'gbasis': 'N31', 'ngauss': '6'}
            >>> g.run(m).GetProp("total_energy")
            '-79.194024566899998'
            >>> g.basis_set("6-31G*")
            {'gbasis': 'N31', 'ndfunc': '1', 'ngauss': '6'}
            >>> g.run(m).GetProp("total_energy")
            '-79.225521673399996'
            >>> g.basis_set("6-31G**")
            {'gbasis': 'N31', 'ndfunc': '1', 'npfunc': '1', 'ngauss': '6'}
            >>> g.run(m).GetProp("total_energy")
            '-79.235082450899995'
            
        or edit property of Gamess instance::
        
            >>> g.basis = {'gbasis': 'sto', 'ngauss': '3'}
            >>> mol_sto3g = g.run(m)
            >>> mol_sto3g.GetProp("total_energy")
            '-78.302511907400003'
        
        print GAMESS INPUT
        ~~~~~~~~~~~~~~~~~~
        
        use input method::
        
            >>> g.input(mol)
        
        
        History
        -------
        
        0.5.0 (2020-09-13)
        ~~~~~~~~~~~~~~~~~~~~
        
        * Support Python3
        
        0.4.1.1 (2017-09-16)
        ~~~~~~~~~~~~~~~~~~~~
        
        * Update Readme
        
        0.4.1 (2017-09-16)
        ~~~~~~~~~~~~~~~~~~
        
        * Bug fixed (coordinates problem)
        
        0.4.0 (2017-09-13)
        ~~~~~~~~~~~~~~~~~~
        
        * Change the backend library from openbabel to RDKit
        
        0.3.0 (2012-03-31)
        ~~~~~~~~~~~~~~~~~~
        
        * Use internal rungms (default)
        * Added basis_set method(STO-3G,3-21G,6-31G,6-311G,6-31G*,6-31G**,AM1,PM3,MNDO)
        * Constructor can accept options
        * Bug fixed (spin multiplicity)
        
        0.2.2 (2012-03-30)
        ~~~~~~~~~~~~~~~~~~
        
        * Added charge settings
        * Method name changed (gamess_input -> input)
        
        0.2.1 (2012-03-23)
        ~~~~~~~~~~~~~~~~~~
        
        * Bug fixed (multiplicity setting for pybel) 
        * Bug fixed (print error when rungms exec failed)
        * Added document
        
        0.2.0 (2012-03-06)
        ~~~~~~~~~~~~~~~~~~
        
        * Run method can accept OBMol and Pybel-Molecule object
        
        0.1.2 (2011-09-23)
        ~~~~~~~~~~~~~~~~~~
        
        * Added CIS method (and optimization)
        
        0.1.1 (2011-08-06)
        ~~~~~~~~~~~~~~~~~~
        
        * Updated document
        * Semiempical method (AM1, PM3, MNDO)
        * Added statpt option
        * Changed default error print (10 lines)
        
        0.1 (2011-6-25)
        ~~~~~~~~~~~~~~~~~~
        * First release
        
Keywords: chemistry
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python
Requires: rdkit
Requires: ruamel.YAML
Description-Content-Type: text/x-rst
