Metadata-Version: 2.1
Name: knot_pull
Version: 0.1.6
Summary: Simplifier of 3D structures of molecules
Home-page: https://github.com/dzarmola/knot_pull
Author: Aleksandra Jarmolinska
Author-email: dzarmola@gmail.com
License: UNKNOWN
Description: # KnotPull - a simplifier for 3D structures
        
        KnotPull reduces a user provided 3D structure, to simplify it,
        while preserving the topology of the chain. It has been successfully
        used for knot detection in proteins and chromatine chains.
        
        It can return either a final, simplified structure, or a .pdb formatted
        trajectory of consecutive simplifications performed.
        
        ## Install
        `pip install knot_pull `
        
        (older versions) `pip install --index-url https://test.pypi.org/simple/ knot_pull`
        
        If installing with `pip --user` knot_pull_check and knot_pull_show
        will be installed in your user base
        (`python -c "import site; print(site.USER_BASE)"`), e.g.
        `$HOME/.local/bin/knot_pull_check`
        
        ## Running
        
        To run on a specific chain of a local pdb file:
        ```
        knot_pull_check -o -k -c A 3ris.pdb
        ```
        To run on a local xyz file (with format id<whitespace>x<whitespace>y<whitespace>z; chains separated by a line with "END"):
        ```
        knot_pull_check -o from_xyz.pdb -k 05.xyz
        ```
        To run on by structure id from RCSB PDB:
        ```
        knot_pull_check -k 4mcb
        ```
        
        To show coloured trajectory in PyMOL (if installed):
        ```
        knot_pull_shown my_output_file.pdb
        ```
        If PyMOL is nto available in system path it can be specified as the second argument
        
        ### Help:
        ```
        usage: knot_pull_check [-h] [-p] [-t] [-f {pdb,xyz,guess}] [-k] [-c CHAIN]
                               [-o [OUTPUT]] [-s [SAVE]]
                               [infile]
        
        Simplify the 3D structure while preserving the topology
        
        positional arguments:
          infile                Structure file which will be used
        
        optional arguments:
          -h, --help            show this help message and exit
          -p, --preserve_resnums
                                Keep original numbering
          -t, --trajectory      Write out all steps of the simplification [default is
                                1]
          -f {pdb,xyz,guess}, --format {pdb,xyz,guess}
                                Input file format: xyz or pdb [default is guess]
          -k, --detect_knot     Calculate the knot Dowker notation and assign the knot
                                type
          -c CHAIN, --chain CHAIN
                                Specify which chain you want to simplify.
          -o [OUTPUT], --output [OUTPUT]
                                Specify the output file. Format is guessed based on
                                extension [default pdb]. Default is stdout
          -s [SAVE], --save [SAVE]
                                Write out a savefile. If any argument is given here -
                                run from a savefile (knot detection only).
        
        ```
        
        ### Copyright (c) Aleksandra Jarmolińska
        
Keywords: protein chromatine topology knot dowker
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.2
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Requires-Python: >=2.7.*
Description-Content-Type: text/markdown
