Python calculate_all_to_all_mfpt示例

示例#1

文件： CalculateMFPTs.py 项目： lilipeng/msmbuilder

def run(T, state):
    if state != -1:
        logger.info("Calculating MFPTs to state %d" % state)
        m = tpt.calculate_mfpt([state], T)
        logger.info("Finished calculating MFPTs to state %d" % state)
    else:
        logger.info("Calculating MFPTs to all states")
        m = tpt.calculate_all_to_all_mfpt(T)
        logger.info("Finished calculating MFPTs to all states")

    return m

示例#2

文件： CalculateMFPTs.py 项目： autodataming/msmbuilder-legacy

def run(T, state):
    if state != -1:
        logger.info("Calculating MFPTs to state %d" % state)
        m = tpt.calculate_mfpt([state], T)
        logger.info("Finished calculating MFPTs to state %d" % state)
    else:
        logger.info("Calculating MFPTs to all states")
        m = tpt.calculate_all_to_all_mfpt(T)
        logger.info("Finished calculating MFPTs to all states")

    return m

示例#3

文件： test_tpt.py 项目： lilipeng/msmbuilder

 def test_mfpt(self):
     
     mfpt = tpt.calculate_mfpt(self.sinks, self.tprob, lag_time=self.lag_time)
     mfpt_ref = io.loadh( tpt_get("mfpt.h5"), 'Data')
     npt.assert_array_almost_equal(mfpt, mfpt_ref)
     
     ensemble_mfpt = tpt.calculate_ensemble_mfpt(self.sources, self.sinks, self.tprob, self.lag_time)
     ensemble_mfpt_ref = io.loadh( tpt_get("ensemble_mfpt.h5"), 'Data')
     npt.assert_array_almost_equal(ensemble_mfpt, ensemble_mfpt_ref)
     
     all_to_all_mfpt = tpt.calculate_all_to_all_mfpt(self.tprob)
     all_to_all_mfpt_ref = io.loadh( tpt_get("all_to_all_mfpt.h5"), 'Data')
     npt.assert_array_almost_equal(all_to_all_mfpt, all_to_all_mfpt_ref)

示例#4

 def test_mfpt(self):
     
     mfpt = tpt.calculate_mfpt(self.sinks, self.tprob, lag_time=self.lag_time)
     mfpt_ref = io.loadh(os.path.join(self.tpt_ref_dir, "mfpt.h5"), 'Data')
     npt.assert_array_almost_equal(mfpt, mfpt_ref)
     
     ensemble_mfpt = tpt.calculate_ensemble_mfpt(self.sources, self.sinks, self.tprob, self.lag_time)
     ensemble_mfpt_ref = io.loadh(os.path.join(self.tpt_ref_dir, "ensemble_mfpt.h5"), 'Data')
     npt.assert_array_almost_equal(ensemble_mfpt, ensemble_mfpt_ref)
     
     all_to_all_mfpt = tpt.calculate_all_to_all_mfpt(self.tprob)
     all_to_all_mfpt_ref = io.loadh(os.path.join(self.tpt_ref_dir, "all_to_all_mfpt.h5"), 'Data')
     npt.assert_array_almost_equal(all_to_all_mfpt, all_to_all_mfpt_ref)