bougui505

ligand_atom_file                                             LIG
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               no
use_database_filter                                          no
orient_ligand                                                no
use_internal_energy                                          no
flexible_ligand                                              no
bump_filter                                                  no

bougui505

Open the url:

http://freedns.afraid.org/dynamic/

Login with your account

Select the link Direct URL beside <your_host>.ignorelist.com

Copy everything from the right of the ? in the address bar (alphanumeric string)

bougui505

def cartesian_to_spherical(xyz):
    ptsnew = np.zeros(xyz.shape)
    xy = xyz[:,0]**2 + xyz[:,1]**2
    ptsnew[:,0] = np.sqrt(xy + xyz[:,2]**2)
    ptsnew[:,1] = np.arctan2(np.sqrt(xy), xyz[:,2]) # for elevation angle defined from Z-axis down
    #ptsnew[:,4] = np.arctan2(xyz[:,2], np.sqrt(xy)) # for elevation angle defined from XY-plane up
    ptsnew[:,2] = np.arctan2(xyz[:,1], xyz[:,0])
    return ptsnew

def polar_projection(coords, center, rid=1, color=None, c=None, alpha=1, rows=1, columns=1, linewidth=1, s=25, threed=True, cmap=cm.jet):

bougui505

#!/usr/bin/env python
# -*- coding: UTF8 -*-
"""
author: Guillaume Bouvier
email: guillaume.bouvier@ens-cachan.org
creation date: 2014 04 29
license: GNU GPL
Please feel free to use and modify this, but keep the above information.
Thanks!
"""

bougui505

\pdfpageattr{/Group <</S /Transparency /I true /CS /DeviceRGB>>} %To manage transparency with latex beamer and acrobat reader

bougui505

import chimera
from DockPrep import prep
models = chimera.openModels.list(modelTypes=[chimera.Molecule])
prep(models)
from WriteMol2 import writeMol2
writeMol2(models, "dp.mol2")

bougui505

Host distant_hostname
    User your_username
    ProxyCommand ssh user@ssh_server exec nc distant_machine 22

bougui505

awk '$0 ~ /ATOM      1/ {i++} {print >> "pdbs/smap_"i".pdb"} {fflush("pdbs/smap_"i".pdb")}' smap.pdb

bougui505

#!/bin/bash
# -*- coding: UTF8 -*-
infile="$1"
outfile=/dev/shm/nfiles.txt
t_0=$(date +"%s")
for i in $(seq 1 10)
do
t=$(date +"%s")
delta_t=$(($t-$t_0))
nfiles=$(echo $infile | wc -w)

bougui505

#!/usr/bin/env python
# -*- coding: UTF8 -*-
"""
author: Guillaume Bouvier
email: guillaume.bouvier@ens-cachan.org
creation date: 2014 05 20
license: GNU GPL
Please feel free to use and modify this, but keep the above information.
Thanks!
"""