Trajectory Analysis

adjl_from_adjmat | From adjacency matrix to adjacency list |

adjl_from_progindex | Build the network from the already processed Progress Index... |

basin_optimization | Basin optimization of the SBR |

basins_recognition | Identifying basins in the SAPPHIRE plot |

contract_mst | Compute the contraction of the leaves in the minimum spanning... |

find_mahalanobis | Find the mahalanobis distance for a set of triplets |

gen_annotation | Compute the annotation of the progrex index |

generate_network | Create a network for each snapshots |

gen_progindex | Compute the progress index along with parent and... |

install_campari | Installing the original Fortran code |

keywords_from_keyfile | Transform a keyfile in a list of keywords |

msm | Building a Markov State Model |

mst_from_trj | Create the minimum spanning tree from time series |

multiplicate_trj | Multiplicate the trajectory variables |

plot_traces | Trace plotting (neural mainly) |

run_campari | Frontend for the original CAMPARI library |

sapphire_plot | Sapphire plot - plotting annotation and progrex index |

score_sapphire | Scoring the SAPPHIRE-plot basin division |

select_features | Multiple pre-processing methods for feature selection |

show_clustering_summary | Shows the clustering summary from log file |

write_pdb | Writing a pdb file from trajectory matrix in R |

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