leelasd

## mpirun -np 2 python helloworld.py 

"""
Parallel Hello World
"""

from mpi4py import MPI
import sys

size = MPI.COMM_WORLD.Get_size()

leelasd

#!/usr/bin/env python
# -*- coding: utf-8 -*-
# for chimera 1.4
from chimera import runCommand
import sys
rec_file = sys.argv[1]
basename = rec_file.split('/')[-1].split('.')[0]
#runCommand("open 0 receptor.pdb")
runCommand("open 0 %s"%rec_file)
runCommand("hbonds intramodel true distSlop 0.65 angleSlop 80 saveFile output/%s_hbonds.txt namingStyle serial"%basename)

leelasd

"""
Experimental wrapper to use Chimera's Python directly from console.

You can `import chimera` with no errors!

Usage
=====
1. Alias your /path/to/chimera/bin/python binary to something more user-friendly, like `chimerapy`.
2. Download these two files and put them together
3. Run `chimerapy -i chimera_cli.py`. (Tip: Realias `chimerapy` to this command).

leelasd

open prometryn.pdb 
preset apply pub 3
aromatic disk;
focus
center
color byatom  
repr bs  
copy file prometryn.png dpi 300 
stop

leelasd

## installing dependencies
## conda install boost
## conda install rdkit
## Download SAMPL1 database file from leelasd/SAMPL1 github repo
from __future__ import print_function
from rdkit import Chem
from rdkit.Chem import AllChem,Draw
import pandas as pd
df=pd.read_csv('SAMPL1_Dataset.csv')
mols = [Chem.MolFromSmiles(smi) for smi in df.SMILES]

leelasd

REMARK               Aniline            
REMARK    Created by BOSS 4.9 Feb 12 Linux 
ATOM      1  C00 UNK     1       0.000   1.400   0.000
ATOM      2  C01 UNK     1       0.000   0.695  -1.220
ATOM      3  C02 UNK     1      -0.000   0.694   1.219
ATOM      4  C03 UNK     1       0.006  -0.713  -1.220
ATOM      5  C04 UNK     1       0.006  -0.715   1.218
ATOM      6  C05 UNK     1       0.010  -1.420  -0.002
ATOM      7  N06 UNK     1      -0.001   2.739   0.001
ATOM      8  H07 UNK     1      -0.008   1.225  -2.162

leelasd

<ForceField>
<AtomTypes>
<Type name="opls_145" class="CA" element="C" mass="12.011000" />
<Type name="opls_146" class="HA" element="H" mass="1.008000" />
<Type name="opls_900" class="NT" element="N" mass="14.007000" />
<Type name="opls_916" class="CA" element="C" mass="12.011000" />
<Type name="opls_909" class="H" element="H" mass="1.008000" />
</AtomTypes>
<HarmonicBondForce>
<Bond class1="CA" class2="CA" length="0.140" k="392459.20"/>

leelasd

<ForceField>
 <AtomTypes>
  <Type name="tip3p-O" class="OW" element="O" mass="15.99943"/>
  <Type name="tip3p-H" class="HW" element="H" mass="1.007947"/>
 </AtomTypes>
 <Residues>
  <Residue name="HOH">
   <Atom name="O" type="tip3p-O"/>
   <Atom name="H1" type="tip3p-H"/>
   <Atom name="H2" type="tip3p-H"/>

leelasd

"""
dcdreporter.py: Outputs simulation trajectories in DCD format

This is part of the OpenMM molecular simulation toolkit originating from
Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org.

Portions copyright (c) 2012 Stanford University and the Authors.
Authors: Peter Eastman

leelasd

import numpy as np
from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
from sys import stdout

def getForceByClass(system, klass):
    for i in range(system.getNumForces()):
        f = system.getForce(i)
        if isinstance(f, klass):