Leela S. Dodda leelasd

## center.sh
#!/usr/bin/env bash

TRAJIN=traj.xtc
TRAJOUT=trajfin.xtc

# delete the trajectory so gromacs wont display silly backup messages
if [ -e $TRAJOUT ]
then
  rm -f $TRAJOUT
fi

## center.sh
#!/usr/bin/env bash

TRAJIN=traj.xtc
TRAJOUT=trajfin.xtc

# delete the trajectory so gromacs wont display silly backup messages
if [ -e $TRAJOUT ]
then
  rm -f $TRAJOUT
fi

## run_md-npt.sh
#PBS -l nodes=2:ppn=12
#PBS -N JobName

cd ${PBS_O_WORKDIR}
NPROCS=`wc -l <$PBS_NODEFILE`
MPIRUN="mpirun -machinefile $PBS_NODEFILE -n $NPROC"

export GMX_MAXBACKUP=1000  # max number of gro backup

GMDIR=/home/kmtu/local/gromacs-4.6.6/bin

## atom_pair_distances.py
import itertools
import mdtraj, mdtraj.geometry
import pandas as pd

traj = mdtraj.load("./traj.xtc", top="native.pdb")

top, bonds = traj.top.to_dataframe()

atoms = np.array(["H", "HA", "N", "CA", "C", "CB"])

## split_complex_v2.py
#!/usr/bin/env python

import sys
from prody import *
from rdkit import Chem
from rdkit.Chem import AllChem
from io import StringIO
import pypdb

## dupe.py
#!/usr/bin/env python

import sys
import os
from rdkit import Chem


def molecule_supplier_from_name(input_file_name):
    ext = os.path.splitext(input_file_name)[-1]
    if ext == ".smi":

## compare_rocs_plec.ipynb

      
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                leelasd
                / compare_rocs_plec.ipynb
            
            
              Created
              July 3, 2020 19:03
                — forked from PatWalters/compare_rocs_plec.ipynb
            
          
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## run_md.py
#!/usr/bin/env python
# coding: utf-8

##########################################################################
# this script was generated by openmm-builder. to customize it further,
# you can save the file to disk and edit it with your favorite editor.
##########################################################################

# REQUIRES:
# * OpenMM (core dynamics)

## bio_align.py
#!/usr/bin/env python

"""Sequence-based structural alignment of two proteins."""

import argparse
import pathlib

from Bio.PDB import FastMMCIFParser, MMCIFIO, PDBParser, PDBIO, Superimposer
from Bio.PDB.Polypeptide import is_aa

## hydrophobic_moment.py
#!/usr/bin/env python

"""
Calculates a set of properties from a protein sequence:
    - hydrophobicity (according to a particular scale)
    - mean hydrophobic dipole moment assuming it is an alpha-helix.
    - total charge (at pH 7.4)
    - amino acid composition
    - discimination factor according to Rob Keller (IJMS, 2011)
	#!/usr/bin/env bash

	TRAJIN=traj.xtc
	TRAJOUT=trajfin.xtc

	# delete the trajectory so gromacs wont display silly backup messages
	if [ -e $TRAJOUT ]
	then
	rm -f $TRAJOUT
	fi
	#PBS -l nodes=2:ppn=12
	#PBS -N JobName

	cd ${PBS_O_WORKDIR}
	NPROCS=`wc -l <$PBS_NODEFILE`
	MPIRUN="mpirun -machinefile $PBS_NODEFILE -n $NPROC"

	export GMX_MAXBACKUP=1000 # max number of gro backup

	GMDIR=/home/kmtu/local/gromacs-4.6.6/bin
	import itertools
	import mdtraj, mdtraj.geometry
	import pandas as pd

	traj = mdtraj.load("./traj.xtc", top="native.pdb")

	top, bonds = traj.top.to_dataframe()

	atoms = np.array(["H", "HA", "N", "CA", "C", "CB"])
	#!/usr/bin/env python

	import sys
	from prody import *
	from rdkit import Chem
	from rdkit.Chem import AllChem
	from io import StringIO
	import pypdb
	#!/usr/bin/env python

	import sys
	import os
	from rdkit import Chem


	def molecule_supplier_from_name(input_file_name):
	ext = os.path.splitext(input_file_name)[-1]
	if ext == ".smi":
	#!/usr/bin/env python
	# coding: utf-8

	##########################################################################
	# this script was generated by openmm-builder. to customize it further,
	# you can save the file to disk and edit it with your favorite editor.
	##########################################################################

	# REQUIRES:
	# * OpenMM (core dynamics)
	#!/usr/bin/env python

	"""Sequence-based structural alignment of two proteins."""

	import argparse
	import pathlib

	from Bio.PDB import FastMMCIFParser, MMCIFIO, PDBParser, PDBIO, Superimposer
	from Bio.PDB.Polypeptide import is_aa
	#!/usr/bin/env python

	"""
	Calculates a set of properties from a protein sequence:
	- hydrophobicity (according to a particular scale)
	- mean hydrophobic dipole moment assuming it is an alpha-helix.
	- total charge (at pH 7.4)
	- amino acid composition
	- discimination factor according to Rob Keller (IJMS, 2011)