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name: plot_opt_out | |
channels: | |
- simonboothroyd | |
- conda-forge | |
dependencies: | |
- black=22.3.0=pyhd8ed1ab_0 | |
- bokeh=2.4.2=py39h6e9494a_0 | |
- boost=1.74.0=py39ha1f3e3e_4 | |
- boost-cpp=1.74.0=hf3dc895_5 | |
- brotli=1.0.9=h0d85af4_6 |
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# A script to quickly run a torsion drive using QCEngine torsiondrive/geometric openff toolkit and rdkit uff | |
from openff.toolkit.topology import Molecule, Atom, Bond | |
from qcelemental.models.common_models import Model | |
from qcelemental.models import DriverEnum | |
from qcelemental.models.procedures import TDKeywords, TorsionDriveInput, QCInputSpecification, OptimizationSpecification, TorsionDriveResult | |
import qcengine as qcng | |
# Make our molecule | |
print("Building molecule") |
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""" | |
Analyses the optimize out file from a forcebalance run. | |
This is quite specific for the results of a water optimzation to multiple liquid property targets. | |
This will produce a csv file with all of the results per iteration for the properties and target parameters. | |
Graphs will also be produced for each iteration showing the csv data. | |
""" | |
import matplotlib.pyplot as plt | |
from typing import List, Dict, Tuple | |
import pandas as pd |
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#combine a protein and ligand to build an OpenMM system | |
# the molecules have been extracted from the PDB file and saved to sdf to work with openff, note they are still in the bound corrdinates. | |
from simtk import unit | |
from simtk.openmm import app | |
from openff.toolkit.topology import Molecule | |
import parmed | |
from openmmforcefields.generators import SystemGenerator | |
from simtk.openmm.app import modeller |
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{ | |
"c[nh2+]c[c@@h](c1ccc(c(c1)o)o)o-3": { | |
"index": "c[nh2+]c[c@@h](c1ccc(c(c1)o)o)o-3", | |
"attributes": { | |
"canonical_explicit_hydrogen_smiles": "[H]c1c(c(c(c(c1C([H])(C([H])([H])[N+]([H])([H])C([H])([H])[H])O[H])[H])O[H])O[H])[H]", | |
"canonical_isomeric_explicit_hydrogen_mapped_smiles": "[H:14][c:1]1[c:2]([c:5]([c:6]([c:3]([c:4]1[C@:9]([H:22])([C:8]([H:20])([H:21])[N+:10]([H:23])([H:24])[C:7]([H:17])([H:18])[H:19])[O:13][H:27])[H:16])[O:12][H:26])[O:11][H:25])[H:15]", | |
"canonical_isomeric_explicit_hydrogen_smiles": "[H]c1c(c(c(c(c1[C@]([H])(C([H])([H])[N+]([H])([H])C([H])([H])[H])O[H])[H])O[H])O[H])[H]", | |
"canonical_isomeric_smiles": "C[NH2+]C[C@@H](c1ccc(c(c1)O)O)O", | |
"canonical_smiles": "C[NH2+]CC(c1ccc(c(c1)O)O)O", | |
"inchi_key": "UCTWMZQNUQWSLP-VIFPVBQESA-O", |