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md

Classes:

  • MD –

    Class a wrapper around TIES_MD API that exposes a simplified interface.

MD 

MD(sim_dir, sim_name='complex', fast=False)

Class a wrapper around TIES_MD API that exposes a simplified interface.

:param sim_dir: str, points to where the simulation is running i.e where the TIES.cfg file is. :param sim_name: str, the prefix to the input param and topo file i.e complex for complex.pdb/prmtop. :param fast: boolean, if True the setting is TIES.cfg will be overwritten with minimal TIES protocol.

Methods:

  • run –

    Wrapper for TIES_MD.TIES.run()

  • analysis –

    Wrapper for TIES_MD.ties_analysis()

Source code in ties/md.py 
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def __init__(self, sim_dir, sim_name='complex', fast=False):
    cwd = os.getcwd()
    self.sim_dir = os.path.join(cwd, sim_dir)
    self.analysis_dir = os.path.join(self.sim_dir, '..', '..', '..')
    #This is the main TIES MD object we call it options as the user interacts with this object to change options
    self.options = TIES(cwd=self.sim_dir, exp_name=sim_name)

    if fast:
        #modify md to cut as many corners as possible i.e. reps, windows, sim length
        self.options.total_reps = 3
        self.options.global_lambdas = [0.00, 0.05, 0.1, 0.3, 0.5, 0.7, 0.9, 0.95, 1.00]
        self.options.sampling_per_window = 2*unit.nanoseconds()

    self.options.setup()

run 

run()

Wrapper for TIES_MD.TIES.run()

:return: None

Source code in ties/md.py 
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def run(self):
    '''
    Wrapper for TIES_MD.TIES.run()

    :return: None
    '''
    self.options.run()

analysis 

analysis(legs, analysis_cfg='./analysis.cfg')

Wrapper for TIES_MD.ties_analysis()

:param legs: list of strings, these are the thermodynamic legs of the simulation i.e. ['lig', 'com']. :param analysis_cfg: str, for what the analysis config file is called.

:return: None

Source code in ties/md.py 
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def analysis(self, legs, analysis_cfg='./analysis.cfg'):
    '''
    Wrapper for TIES_MD.ties_analysis()

    :param legs: list of strings, these are the thermodynamic legs of the simulation i.e. ['lig', 'com'].
    :param analysis_cfg: str, for what the analysis config file is called.

    :return: None
    '''
    os.chdir(self.analysis_dir)
    if not os.path.exists('exp.dat'):
        ties_analysis.make_exp(verbose=False)

    #read the experimental data
    with open('exp.dat') as f:
        data = f.read()
    exp_js = json.loads(data)

    ana_cfg = ties_analysis.Config(analysis_cfg)
    ana_cfg.simulation_legs = legs
    ana_cfg.exp_data = exp_js
    ana = ties_analysis.Analysis(ana_cfg)
    ana.run()