Metadata-Version: 2.0
Name: knot-pull
Version: 0.1.3
Summary: Simplifier of 3D structures
Home-page: https://github.com/dzarmola/knot_pull
Author: Aleksandra Jarmolinska
Author-email: dzarmola@gmail.com
License: UNKNOWN
Keywords: protein chromatine topology knot dowker
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python :: 2.7
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
Requires-Dist: numpy

# 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
(soon) `pip install knot_pull `

`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


