GAMESS wrapper for Python
Project description
==========
pygamess
==========
`pygamess` is a GAMESS wrapper for Python
Requirements
------------
* Python 2.6 or later (not support 3.x)
* RDKit
* GAMESS
Features
--------
* nothing
Setup
-----
::
$ pip install pygamess
set GAMESS_HOME environment in your .bashrc::
$ export GAMESS_HOME=/usr/local/gamess
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'
change 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
-------
0.4.1.1 (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
pygamess
==========
`pygamess` is a GAMESS wrapper for Python
Requirements
------------
* Python 2.6 or later (not support 3.x)
* RDKit
* GAMESS
Features
--------
* nothing
Setup
-----
::
$ pip install pygamess
set GAMESS_HOME environment in your .bashrc::
$ export GAMESS_HOME=/usr/local/gamess
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'
change 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
-------
0.4.1.1 (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
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