Coder Social home page Coder Social logo

confined-water-analysis's People

Contributors

flt17 avatar

Stargazers

 avatar  avatar

Watchers

 avatar

confined-water-analysis's Issues

support other trajectory files then dcd

Make use of full MDAnalysis trajectory capability and support other formats and filenames.

e.g. example form mlp-score using mdtraj:

def load_with_cell(filename_or_filenames, **kwargs):
    """Load a trajectory and inject cell dimensions from a topology PDB file if not present.
    All arguments and keyword arguments are passed on to `mdtraj.load`. The `top`
    keyword argument is used load a PDB file and get cell information from it.
    """

    # load the "topology frame" to get cell dimensions
    top = kwargs.get("top")
    if top is not None and isinstance(top, str):
        # load topology frame - just the first one from the file, in case there are more frames
        frame_top = mdt.load_frame(top, 0)
        unitcell_lengths = frame_top.unitcell_lengths
        unitcell_angles = frame_top.unitcell_angles
        if (unitcell_lengths is None) or (unitcell_angles is None):
            raise ValueError("Frame providing topology is missing cell information.")
    else:
        raise ValueError("Provide a PDB with cell dimensions.")

    # load the trajectory itself
    trj = mdt.load(filename_or_filenames, **kwargs)

    # inject the cell information
    len_trj = len(trj)
    trj.unitcell_lengths = unitcell_lengths.repeat(len_trj, axis=0)
    trj.unitcell_angles = unitcell_angles.repeat(len_trj, axis=0)

    return trj

replace findpeaks

findpeaks package is not available on conda

replace findpeaks package with different 2D peak finder

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.