New upstream version 1.4.0~b+dfsg

Changelog

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### Next version

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# 1.4.0

* __Full Python 3 Compatibility__

* __Read PDB files from stdin with "-f -" and write to stdout with "-O" (capital "O")__

* Improves handling of fixed PDB files

* Option to turn off writing fixed PDB structures to a file ("--nofixfile")

### 1.3.5

* Preparation for Python 3: Imports

The command above will fetch the PDB entry 1vsn from the server, analyze all interactions and print out the results (verbose mode).

No output files are produced at this point.

The same can be done for local PDB files.

The same can be done for local PDB files (-f <file>) or for reading from stdin (-f -).

```bash

wget http://files.rcsb.org/download/1EVE.pdb

* Text report files (`-t`, human-readable)

* PyMOL session files (`-y`)

* Ray-traced images (`-p`)

* writing to stdout (`-O`), to be used in combination with XML or text report files

```bash

plip -i 1osn -pyx

This value corresponds approximately to the radius of benzene + 0.6 Å.

##### π-Cation Interactions

π-Cation interactions are reported for each pairing of a positive charge and an aromatic ring if the distance between the charge center and the aromatic ring center is less than PICATION_DIST_MAX.

π-Cation interactions are reported for each pairing of a positive charge and an aromatic ring if the distance between the charge center and the aromatic ring center is less than PICATION_DIST_MAX and the offset between the ring center and the charge is no larger than PISTACK_OFFSET_MAX.

In the case of a putative π-cation interaction with a tertiary amine of the ligand, an additional angle criterion is applied (see documentation in the source code).

##### Salt Bridges

Possible future features

========================

* Python 3 support

* support special characters in filenames (e.g. spanish accents), currently cause problems in XML report

* support for mmcif format

* support presets for hydrogenation

* detection of steric clashes

* detection of anion-pi interactions

* detection of electrostatic repulsion force_string

* detection of Keesom forces

* weak hydrogen bonding

* visualization: show hydrogen atoms in PyMOL for hydrogen bonds and adapt interaction vector accordingly

* use SMARTS for detection of chemical features (charged groups, etc.)

TXT = False

PICS = False

PYMOL = False

STDOUT = False

RAWSTRING = False # use raw strings for input / output

OUTPATH = './'

BASEPATH = './'

BREAKCOMPOSITE = False  # Break up composite ligands with covalent bonds

ALTLOC = False  # Consider alternate locations

PLUGIN_MODE = False  # Special mode for PLIP in Plugins (e.g. PyMOL)

NOFIX = False  # Turn off fixing of errors in PDB files

NOFIXFILE = False # Turn off writing to files for fixed PDB structures

PEPTIDES = []  # Definition which chains should be considered as peptide ligands

INTRA = None

KEEPMOD = False

from collections import defaultdict

# Own modules

from plip.modules.supplemental import *

import plip.modules.config

from .supplemental import *

from . import config

def filter_contacts(pairings):