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import matplotlib.pyplot as plt

data = read_xvg("name_of_file.xvg")
plt.plot(data[:,0], data[:,1])
plt.show()

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import mbuild
import foyer
import mosdef_cassandra as mc
import unyt as u
from mosdef_cassandra.utils.get_files import (
    get_example_ff_path,
    get_example_mol2_path,
)

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import numpy as np
import pytest
import hypothesis

import mbuild as mb
from mbuild.formats.xyz import write_xyz
from mbuild.utils.io import get_fn
from mbuild.tests.base_test import BaseTest
from mbuild.exceptions import MBuildError
from mbuild.lib.moieties import H2O

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import foyer
import mbuild as mb
import unyt as u
import gmso
from gmso.lib.potential_templates import PotentialTemplateLibrary
from gmso.external import from_parmed
from gmso.formats.top import write_top
from gmso.formats.gro import write_gro

def gmso_top():

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cation = mb.load('cation.mol2')

for idx, particle in enumerate(cation.particles()):
    if idx == 0:
        particle.name = 'C_E'
        
# Atom type system
# `structure` is a parmed structure
# Have to change the name or parmed will error when trying to save the structure
for atom in structure.atoms:

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import mbuild as mb
import foyer
import antefoyer


alkane = mb.load('CCCC', smiles=True)

packing_box = mb.Box([5, 5, 5])

# Initialize gaff force field 

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@pytest.mark.parametrize('orientations,constraints',
               [((True, False, False),["constrain_rotation x"]),
                ((False, True, False),["constrain_rotation y"]),
                ((False, False, True),["constrain_rotation z"]),
                ((True, True, False),["constrain_rotation x",
                    "constrain_rotation y"]),
                ((False, True, True),["constrain_rotation y",
                    "constrain_rotation z"]),
                ((True, False, True),["constrain_rotation x",
                    "constrain_rotation z"])])

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project = signac.get_project()
for job in project.find_jobs():  
    fig, ax = plt.subplots()
    if os.path.isfile(os.path.join(job.workspace(), 'all-reducs.pkl')):
     with open(os.path.join(job.workspace(), 'all-reducs.pkl'), 'rb') as f:
         reduc = pickle.load(f)
     c = deepcopy(reduc)
     cluster_sizes = []
     for proc in c:
         for matrix in proc:

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import signac
import os

project = signac.get_project()

for job in project.find_jobs():
  sq = os.path.join(job.workspace(), 'sq.txt')

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import mdtraj as md
import numpy as np
import matplotlib.pyplot as plt
from scattering.scattering import structure_factor

# Load trajectory with MDTraj
trj = md.load('sample.trr', top='sample.gro')
il = trj.topology.select('resid 0')
trj_il = trj.atom_slice(il)