def test_rip(params):
util.goto_dir(params['sim_dir'])
print "> Pulse with RIP residue rotation"
util.goto_dir('rip')
simulate.pulse(
params['ff'], '../md_merge/md', 'md', 2000,
force.make_rip_fn(params['i_residue'], 300), 100)
def test_puff(params):
util.goto_dir(params['sim_dir'])
util.goto_dir('puff')
print "> Pulse with terminii push"
md = '../md_merge/md'
n = get_n_protein_residues_from_restart(md)
# make push function
pulse_fn = force.make_puff_fn(
[0, 1, 2], [n-3, n-2, n-1], 10.0, 0.1, 300)
simulate.pulse(params['ff'], md, 'md', 2000, pulse_fn, 100)
def test_puff(params):
util.goto_dir(params['sim_dir'])
util.goto_dir('puff')
print "> Pulse with terminii push"
md = '../md_merge/md'
n = get_n_protein_residues_from_restart(md)
# make push function
pulse_fn = force.make_puff_fn([0, 1, 2], [n - 3, n - 2, n - 1], 10.0, 0.1,
300)
simulate.pulse(params['ff'], md, 'md', 2000, pulse_fn, 100)
def test_traj_analysis(params):
util.goto_dir(params['sim_dir'])
util.goto_dir('md1')
trajectory.analyze_trajectory('md')
util.check_output('md.rmsd.per_frame')
util.check_output('md.rmsd.per_ps')
trajectory.analyze_trajectory('md', analyzer_classes=[VelocityAnalyzer])
util.check_output('md.velocity.per_frame')
util.check_output('md.velocity.per_ps')
def test_restraint(params):
print "> Equil with restraints on "
util.goto_dir(params['sim_dir'])
util.goto_dir('restraint')
in_md = '../md_merge/md'
restraint_pdb = os.path.abspath('md.restraint.pdb')
make_restraint_pdb(
in_md, [params['i_residue']], restraint_pdb, is_backbone_only=False)
simulate.langevin_thermometer(
params['ff'], in_md, 1000, 300, 'md', 10,
restraint_pdb=restraint_pdb)
def test_traj_analysis(params):
util.goto_dir(params['sim_dir'])
util.goto_dir('md1')
trajectory.analyze_trajectory('md')
util.check_output('md.rmsd.per_frame')
util.check_output('md.rmsd.per_ps')
trajectory.analyze_trajectory(
'md', analyzer_classes=[VelocityAnalyzer])
util.check_output('md.velocity.per_frame')
util.check_output('md.velocity.per_ps')
def test_user_defined_pulse(params):
util.goto_dir(params['sim_dir'])
util.goto_dir('user_pulse')
i, j = params['i_loop_start'], params['i_loop_end']
rotate_loop = RotateLoop(i, j, 0.7)
print "> make restraint_pdb"
restraint_pdb = os.path.abspath('md.restraint.pdb')
in_md = '../md_merge/md'
n = get_n_protein_residues_from_restart(in_md)
residue_indices = range(0, i) + range(j, n)
make_restraint_pdb(in_md, residue_indices, restraint_pdb)
pulse_fn = lambda soup: rotate_loop.apply(soup)
print "> Pulse with user-defined pulse_fn"
simulate.pulse(
params['ff'], '../md_merge/md', 'md', 5000, pulse_fn, 100,
restraint_pdb=restraint_pdb)
def test_restraint(params):
print "> Equil with restraints on "
util.goto_dir(params['sim_dir'])
util.goto_dir('restraint')
in_md = '../md_merge/md'
restraint_pdb = os.path.abspath('md.restraint.pdb')
make_restraint_pdb(in_md, [params['i_residue']],
restraint_pdb,
is_backbone_only=False)
simulate.langevin_thermometer(params['ff'],
in_md,
1000,
300,
'md',
10,
restraint_pdb=restraint_pdb)
def test_prepare_for_md(params):
util.goto_dir(sim_dir)
print os.getcwd()
pdb = params['pdb']
fetch.get_pdbs_with_http(pdb)
full_pdb = pdb + '.pdb'
clean_pdb = os.path.abspath(pdb) + '.clean.pdb'
pdbtext.clean_pdb(full_pdb, clean_pdb)
print "> Generating topologies"
simulate.pdb_to_top_and_crds(params['ff'], clean_pdb, 'sim')
print "> Minimizing structure"
util.goto_dir('min')
simulate.minimize(params['ff'], '../sim', 'min')
def test_prepare_for_md(params):
util.goto_dir(sim_dir)
print os.getcwd()
pdb = params['pdb']
fetch.get_pdbs_with_http(pdb)
full_pdb = pdb + '.pdb'
clean_pdb = os.path.abspath(pdb) + '.clean.pdb'
pdbtext.clean_pdb(full_pdb, clean_pdb)
print "> Generating topologies"
simulate.pdb_to_top_and_crds(params['ff'], clean_pdb, 'sim')
print "> Minimizing structure"
util.goto_dir('min')
simulate.minimize(params['ff'], '../sim', 'min')
def test_user_defined_pulse(params):
util.goto_dir(params['sim_dir'])
util.goto_dir('user_pulse')
i, j = params['i_loop_start'], params['i_loop_end']
rotate_loop = RotateLoop(i, j, 0.7)
print "> make restraint_pdb"
restraint_pdb = os.path.abspath('md.restraint.pdb')
in_md = '../md_merge/md'
n = get_n_protein_residues_from_restart(in_md)
residue_indices = range(0, i) + range(j, n)
make_restraint_pdb(in_md, residue_indices, restraint_pdb)
pulse_fn = lambda soup: rotate_loop.apply(soup)
print "> Pulse with user-defined pulse_fn"
simulate.pulse(params['ff'],
'../md_merge/md',
'md',
5000,
pulse_fn,
100,
restraint_pdb=restraint_pdb)
def test_basic_md_merge(params):
util.goto_dir(params['sim_dir'])
print "> Fixed-temp1"
util.goto_dir('md1')
simulate.langevin_thermometer(params['ff'], '../min/min', 1000, 300, 'md',
10)
print "> Fixed-temp2"
util.goto_dir('../md2')
simulate.langevin_thermometer(params['ff'], '../md1/md', 1000, 300, 'md',
10)
print "> Merge temp1-temp2"
util.goto_dir('../md_merge')
simulate.merge_trajectories(params['ff'], 'md', ['../md1/md', '../md2/md'])
def test_basic_md_merge(params):
util.goto_dir(params['sim_dir'])
print "> Fixed-temp1"
util.goto_dir('md1')
simulate.langevin_thermometer(
params['ff'], '../min/min', 1000, 300, 'md', 10)
print "> Fixed-temp2"
util.goto_dir('../md2')
simulate.langevin_thermometer(
params['ff'], '../md1/md', 1000, 300, 'md', 10)
print "> Merge temp1-temp2"
util.goto_dir('../md_merge')
simulate.merge_trajectories(
params['ff'], 'md', ['../md1/md', '../md2/md'])
import re
from pdbremix import v3
from pdbremix import pdbatoms
from pdbremix import simulate
from pdbremix import force
from pdbremix import util
from pdbremix import pdbtext
from pdbremix import trajectory
from pdbremix import fetch
from pdbremix import asa
from pdbremix import data
from pdbremix import rmsd
util.goto_dir('pdb')
# load the structures from the website
fetch.get_pdbs_with_http('1be9', '1rzx')
soup = pdbatoms.Soup('1be9.pdb')
soup2 = pdbatoms.Soup('1rzx.pdb')
# the structures loaded 1be9 and 1rzx are both PDZ
# domains. However, they don't quite map to each other
# This shows how you might select homologous residues
# and then extract the coordinates for RMSD calculation
def split_pairs(indices):
def test_rip(params):
util.goto_dir(params['sim_dir'])
print "> Pulse with RIP residue rotation"
util.goto_dir('rip')
simulate.pulse(params['ff'], '../md_merge/md', 'md', 2000,
force.make_rip_fn(params['i_residue'], 300), 100)
import os
import re
from pdbremix import v3
from pdbremix import pdbatoms
from pdbremix import simulate
from pdbremix import force
from pdbremix import util
from pdbremix import pdbtext
from pdbremix import trajectory
from pdbremix import fetch
from pdbremix import asa
from pdbremix import data
from pdbremix import rmsd
util.goto_dir('pdb')
# load the structures from the website
fetch.get_pdbs_with_http('1be9', '1rzx')
soup = pdbatoms.Soup('1be9.pdb')
soup2 = pdbatoms.Soup('1rzx.pdb')
# the structures loaded 1be9 and 1rzx are both PDZ
# domains. However, they don't quite map to each other
# This shows how you might select homologous residues
# and then extract the coordinates for RMSD calculation
def split_pairs(indices):
for i in range(0, len(indices), 2):
yield indices[i:i + 2]
for a in soup.atoms():
a.bfactor = 0.0
if a.res_type not in data.solvent_res_types:
a.bfactor = 1.0
soup.write_pdb(pdb)
sim_dir = "equilibrate"
pdb_code = '1cph'
ff = 'GROMACS4.5'
pdb_code = '2evq'
ff = 'AMBER11-GBSA'
ff = 'GROMACS4.5'
i_residue = 2
util.goto_dir(sim_dir)
# Get the PDB files from the website
fetch.get_pdbs_with_http(pdb_code)
# Format the PDB file to give one single conformation
clean_pdb = '2evq.clean.pdb'
pdbtext.clean_pdb(pdb_code+'.pdb', clean_pdb)
# Generate restart files from PDB
simulate.pdb_to_top_and_crds(ff, clean_pdb, 'sim')
# Make a protein positional restrain_protein.pdb file
make_protein_restraint_pdb('sim', 'restrain_protein.pdb')
# minimize system (mostly water) with protein positions fixed