GAMESS wrapper for Python
Project description
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
0.4.0 (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)
Ddded 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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