用于psi4和rdkit的瘦包装库
Psikit的Python项目详细描述
psikit:psi4和rdkit的薄包装库
灵感来源于条目：Calculate HOMO and LUMO with Psi4
从conda安装rdkit和psi4
conda install -c psi4 psi4
conda install -c rdkit rdkit
conda install -c psi4 resp # optional
从github安装psikit
conda install -c psi4 psi4
conda install -c rdkit rdkit
conda install -c psi4 resp # optional
PSIKIT正在开发中。 最新版本的psikit可以从github安装。
pip install git+https://github.com/Mishima-syk/psikit
安装带有PIP的PSIKIT
PSIKIT正在开发中。 但当前版本的psikit可以从pypi或conda安装。
pip install psikit
conda install -c iwatobipen psikit
用法
单点计算
from psikit import Psikit
pk = Psikit()
pk.read_from_smiles("c1ccccc1")
print("SCF Energy: ", pk.energy())
print("HOMO: ", pk.HOMO)
print("LUMO: ", pk.LUMO)
x, y, z, total = pk.dipolemoment
print("SCF Total Dipole Moment: {}".format(total))
# SCF Energy: -230.712279648862
# HOMO: -0.32848562009092513
# LUMO: 0.1456515222506689
# SCF Total Dipole Moment: 3.292464934070545e-05
结构优化
pk = Psikit()
pk.read_from_smiles("c1ccccc1")
print("Optimized SCF Energy: ", pk.optimize())
# Optimizer: Optimization complete!
# Optimized SCF Energy: -230.71352354223438
计算resp charge
# REF http://ambermd.org/tutorials/advanced/tutorial1/files/resp_paper_jacs.pdf
pk = Psikit()
pk.read_from_smiles("CC(=O)O")
pk.optimize()
# Optimizer: Optimization complete!
# -227.82180859253418
pk.calc_resp_charges()
# array([-0.32506898, 0.83672649, -0.61924915, -0.66135715, 0.10450057,
# 0.10478188, 0.10780051, 0.45186584])
for atom in pk.mol.GetAtoms():
print(atom.GetSymbol(), "ESP:{}\tRESP:{}".format(atom.GetProp("EP"), atom.GetProp("RESP")))
# C ESP:-0.49662019588648315 RESP:-0.3250689814483399
# C ESP:0.91473263536048643 RESP:0.83672648554100837
# O ESP:-0.63823808477114718 RESP:-0.61924915363703359
# O ESP:-0.6763331997116846 RESP:-0.66135714989354499
# H ESP:0.14625849864628995 RESP:0.10450056830656008
# H ESP:0.14578513969681847 RESP:0.10478187811883517
# H ESP:0.1530843954112609 RESP:0.1078005104750676
# H ESP:0.45133081125445906 RESP:0.45186584253744722
### Compute Mulliken charges and Lowdin charges
pk = Psikit()
pk.read_from_smiles("CC(=O)O")
pk.optimize() # or pk.energy()
pk.calc_mulliken_charges()
# array([-0.42203029, 0.72794785, -0.55419051, -0.59333358, 0.16369722,
# 0.1636994 , 0.15462075, 0.35958916])
pk.calc_lowdin_charges()
#array([-0.30006577, 0.33900448, -0.35983788, -0.28463832, 0.12439944,
# 0.12810672, 0.11935266, 0.23367866])
Jupyter笔记本
许可证
在BSD license下发布的代码。
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