test-plip.ipynb

Kernel: Python 2 (Ubuntu Linux)

PLIP, locally installed

Python 2, Ubuntu Linux Kernel

Notes about setting up PLIP in a CoCalc project

1. create terminal file

2. mkdir plip and cd plip

3. open ~/.bashrc and then at the bottom: alias plip='~/pliptool/plip/plipcmd' and export PYTHONPATH=~/pliptool:${PYTHONPATH}

4. run "ctrl-d" and hit return in the terminal to restart your session with the new bashrc configuration

5. mkdir ~/plip/1vsn and then cd ~/plip/1vsn (instead of that tmp dir!)

6. but errors ???

import sys
import os

sys.path.insert(0, os.path.expanduser('~/pliptool'))

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

! ls -l ~/plip

total 198
-rw-r--r-- 1 user user 435456 Apr 17 13:10 1EVE.pdb
drwxr-xr-x 2 user user      2 Apr 17 12:51 1vsn
-rw-r--r-- 1 user user      0 Apr 17 12:57 plip-cocalc.md
-rw-r--r-- 1 user user  11629 Apr 17 13:10 test-plip.ipynb

from plip.modules.preparation import PDBComplex

my_mol = PDBComplex()
my_mol.load_pdb(os.path.expanduser('~/plip/1EVE.pdb')) # Load the PDB file into PLIP class
print my_mol # Shows name of structure and ligand binding sites
my_bsid = 'E20:A:2001' # Unique binding site identifier (HetID:Chain:Position)
my_mol.analyze()
my_interactions = my_mol.interaction_sets[my_bsid] # Contains all interaction data

# Now print numbers of all residues taking part in pi-stacking
print [pistack.resnr for pistack in s.pistacking] # Prints [84, 129]

TypeErrorTraceback (most recent call last)
<ipython-input-3-b5d766d7fab9> in <module>()
----> 1 from plip.modules.preparation import PDBComplex
      2 
      3 my_mol = PDBComplex()
      4 my_mol.load_pdb(os.path.expanduser('~/plip/1EVE.pdb')) # Load the PDB file into PLIP class
      5 print my_mol # Shows name of structure and ligand binding sites
/home/user/pliptool/plip/modules/preparation.py in <module>()
     11 
     12 # Own modules
---> 13 from .detection import *
     14 from .supplemental import *
     15 from . import config
/home/user/pliptool/plip/modules/detection.py in <module>()
     10 
     11 # Own modules
---> 12 from .supplemental import *
     13 from . import config
     14 
/home/user/pliptool/plip/modules/supplemental.py in <module>()
     25 # External libraries
     26 import pybel
---> 27 from pybel import *
     28 from openbabel import *
     29 import numpy as np
TypeError: Item in ``from list'' not a string

the cmd startup content

# Compatibility
from __future__ import print_function
from __future__ import absolute_import

# Own modules
from plip.modules.preparation import *
from plip.modules.plipremote import VisualizerData
from plip.modules.report import StructureReport,__version__
from plip.modules import config
from plip.modules.mp import parallel_fn
from plip.modules.webservices import check_pdb_status, fetch_pdb

# Python standard library
import sys
import argparse
from argparse import ArgumentParser
import time
import multiprocessing
import json

# External libraries
import lxml.etree as et

TypeErrorTraceback (most recent call last)
<ipython-input-3-6928ff32bc35> in <module>()
      4 
      5 # Own modules
----> 6 from plip.modules.preparation import *
      7 from plip.modules.plipremote import VisualizerData
      8 from plip.modules.report import StructureReport,__version__
/home/user/pliptool/plip/modules/preparation.py in <module>()
     11 
     12 # Own modules
---> 13 from .detection import *
     14 from .supplemental import *
     15 from . import config
/home/user/pliptool/plip/modules/detection.py in <module>()
     10 
     11 # Own modules
---> 12 from .supplemental import *
     13 from . import config
     14 
/home/user/pliptool/plip/modules/supplemental.py in <module>()
     25 # External libraries
     26 import pybel
---> 27 from pybel import *
     28 from openbabel import *
     29 import numpy as np
TypeError: Item in ``from list'' not a string

import pybel
import openbabel