def vmd_load_molecule(coordsfile,
filetype="lammpsdata",
dcd=None,
selection="all",
scale=1.0,
molid=0,
vmd_material="Basic1Pantone",
style="CPK 1.000000 0.300000 12.000000 12.000000"):
"""
"""
if not molecule.exists(molid):
# load molecule in vmd
if dcd is not None:
molecule.load(filetype, coordsfile, "dcd", dcd)
else:
molecule.load(filetype, coordsfile)
molrep.modrep(molid,
0,
style=style,
material=vmd_material,
color="Name",
sel=selection)
#trans.scale(scale)
VMD.evaltcl("scale to {}".format(scale))
def vmd_prepare_scene():
"""Change the lighting and background so it is the same for each image when rendering."""
VMD.evaltcl("light 1 off")
VMD.evaltcl("display shadows off")
color_display = color.get_colormap("Display")
color_display["Background"] = "white"
color.set_colormap("Display", color_display)
display.set(depthcue=0)
display.update()
display.update_ui()
def vmd_render_scene(image_out,
image_size=[2000, 2000],
renderer="TachyonLOptiXInternal",
frame_idx=0):
"""
Render the image using renderer with resolution image_size.
"""
disp_default_size = display.get("size")
# higher resolution
display.set(size=image_size)
display.update()
display.update_ui()
VMD.evaltcl("light 0 off")
render.render(renderer, "{}.ppm".format(image_out))
VMD.evaltcl("light 0 on")
image = Image.open("{}.ppm".format(image_out))
image.save("{}.png".format(image_out), format="PNG")
#display.set(size=disp_default_size)
display.update()
display.update_ui()
os.remove("{}.ppm".format(image_out))
def main():
options, args = PARSER.parse_args()
if len(args) != 2:
sys.stderr.write("This script requires exactly 2 arguments.")
quit(1)
forward, backward = args
output = os.path.abspath(options.output)
forward = os.path.abspath(forward)
backward = os.path.abspath(backward)
if not os.path.isdir(output):
os.mkdir(output)
os.chdir(output)
forward = fix_fepout(forward, output)
backward = fix_fepout(backward, output)
VMD.evaltcl('package require parsefep')
VMD.evaltcl('parsefep -forward %s -backward %s -bar' % (forward, backward))
quit()
MDFF_POTENTIAL = 'mdff-potential.dx'
MDFF_WEIGHTS = 'mdff-weights.pdb'
MDFF_CONSTRAINT_HBONDS = 'mdff-hbonds.dat'
MDFF_CONSTRAINT_CISPEPTIDE = 'mdff-cispeptide.dat'
MDFF_CONSTRAINT_CHIRALITY = 'mdff-chirality.dat'
model = Molecule.create()
model.load(PSF)
model.load(PDB)
template = Molecule.create()
template.load(MDFF_TEMPLATE_PSF)
template.load(MDFF_TEMPLATE_PDB)
# Load mdff
VMD.evaltcl('package require mdff')
# Generate simulated MDFF map
VMD.evaltcl('mdff sim [atomselect {molid} protein] -res 5 -o {outfile}'.format(
molid=template.molid, outfile=MDFF_MAP))
# Convert map to potential
VMD.evaltcl('mdff griddx -i {infile} -o {outfile}'.format(
infile=MDFF_MAP, outfile=MDFF_POTENTIAL))
# Generate scaling factors
VMD.evaltcl('mdff gridpdb -psf {psf} -pdb {pdb} -o {outfile}'.format(
psf=PSF, pdb=PDB, outfile=MDFF_WEIGHTS))
# Generate additional constraints to prevent overfitting
# Prepare secondary structure restraints
VMD.evaltcl('package require ssrestraints')
VMD.evaltcl('ssrestraints -psf {psf} -pdb {pdb} -o {outfile} -hbonds'.format(
from pyvmd.atoms import Selection
from pyvmd.molecules import Molecule, FORMAT_PDB, FORMAT_PSF
TEMPLATE_PDB = '../structures/3j5p.pdb'
TMP_DIR = tempfile.mkdtemp(prefix='vmd_')
TOPOLOGY = '/usr/lib/vmd/plugins/noarch/tcl/readcharmmtop1.1/top_all27_prot_lipid_na.inp'
# Load template
template = Molecule.create()
template.load(TEMPLATE_PDB)
# Center the template
center = measure.center(Selection('all', template))
Selection('all', template).atomsel.moveby((-center[0], -center[1], -center[2]))
# Rotate the template, so model takes less space
VMD.evaltcl('[atomselect %d all] move [transaxis z -35]' % template.molid)
# Save individual chains
for chain in 'ABCD':
print "Saving monomer %s" % chain
Selection('chain {} and resid 393 to 502'.format(chain), template).atomsel.write(FORMAT_PDB, '{}/{}1.pdb'.format(TMP_DIR, chain))
Selection('chain {} and resid 508 to 719'.format(chain), template).atomsel.write(FORMAT_PDB, '{}/{}2.pdb'.format(TMP_DIR, chain))
# Load psfgen and topology
VMD.evaltcl("package require psfgen")
VMD.evaltcl("topology %s" % TOPOLOGY)
# Aliasing
VMD.evaltcl("pdbalias residue HIS HSE")
VMD.evaltcl("pdbalias atom ILE CD1 CD")
# Alias terminal oxygen for nitrogen from CT3 patch
VMD.evaltcl("pdbalias atom ALA OXT NT")
def main():
# Read name of input and output files from command line
if len(sys.argv)!= 6:
print("Wrong number of arguments.")
print("Usage: " + sys.argv[0] + " <input file of simulation parameters>" + " <input file of particle details>" + " <output vmd file>" + " <orbital outputfile>" + "<energy output file>")
quit()
else:
parameter_file = sys.argv[1]
particle_file = sys.argv[2]
outfile_name = sys.argv[3]
orb_file = sys.argv[4]
energy_file = sys.argv[5]
# create bodies
# the input file has all positions in metres and velocities in ms^-1
system = Particle3D.create_particle(particle_file)
# centre of mass correction for the bodies
com_correction(system)
# begginings of position and distance lists for calculating orbitals and apsis
positions = []
distances = []
for s in system:
positions.append((s.label,[]))
distances.append((s.label,[]))
add_to_pos_lists(system,distances,positions)
# read in simulation parameters from parameter file
parameters = open(parameter_file, "r")
lines = parameters.readlines()
parameters.close()
params = []
for l in lines:
l = l.strip()
param, value = l.split(":")
params.append((param,value))
dt = list(map(lambda x: int(x[1]),(filter(lambda x: "dt" == x[0], params))))[0] # timestep in seconds
n = list(map(lambda x: int(x[1]),(filter(lambda x: "n" == x[0], params))))[0] # for every n timesteps we will write to vmd, calculate energies etc (no unit)
num_steps = list(map(lambda x: int(x[1]),(filter(lambda x: "num_steps" == x[0], params))))[0] # number of timesteps (no unit)
# open vmd file to write to and initialise that it is on its first point
vmd_file = open(outfile_name , "w")
point = 1
# initialise time
time = 0
# get initial forces
forces = calc.Find_all_forces(system)
# get inital energies
energies = calc.Calculate_total_energy(system)
tot_energy = energies[0]
kin_energy = energies[1]
pot_energy = energies[2]
# append energies and time to corresponding lists
time_list = [time]
tot_energy_list = [tot_energy]
kin_energy_list = [kin_energy]
pot_energy_list = [pot_energy]
# start the time integration loop
for i in range(num_steps):
# update particle position
calc.Update_position(system,forces, dt)
# update forces
new_forces = calc.Find_all_forces(system)
# update particle velocities by averaging current and new forces
average_forces = []
for i in range(0,len(forces)):
average_force = (forces[i] + new_forces[i])/2
average_forces.append(average_force)
calc.Update_velocity(system,average_forces, dt)
# re define force
forces = new_forces
# increse time
time += dt
# every n timesteps
if time % n == 0:
VMD.Write_vmd(system,point,vmd_file) # write to vmd file
point += 1 # update point
# get energies
energies = calc.Calculate_total_energy(system)
tot_energy = energies[0]
kin_energy = energies[1]
pot_energy = energies[2]
#update energy and time lists
tot_energy_list.append(tot_energy)
kin_energy_list.append(kin_energy)
pot_energy_list.append(pot_energy)
time_list.append(time)
# append to position and distance lists
add_to_pos_lists(system,distances,positions)
# close vmd file
vmd_file.close()
# open orbital output file and write to it the apsides and orbital periods
orb_file = open(orb_file , "w")
for p in positions:
if p[0] == 'Moon': # ensure moon orbits Earth
orbitting = 0
for i in positions:
if i[0] == 'Earth':
orbitting = i
# check at least one orbit has occured and if not suggests larger number steps
test = orbit(p[1],orbitting[1],time_list)
if isinstance(test, str):
orb_file.write("For " + str(p[0]) + " try a larger number of steps to allow completion of at least one orbit. \n")
# otherwise prints relevant inormation to orbital file
else:
orb_file.write("The orbit of the " + str(p[0]) + " is: ")
orb_file.write(str(orbit(p[1],orbitting[1],time_list)) + " days, \n")
orb_file.write("and the apo- and periapses are (respectively): ")
orb_file.write(str(Apsides(distances[positions.index(p)][1]))+ " metres. \n")
elif p[0] == 'Sun': # ignores sun
pass
else: # makes all other calculations on assumption of orbitting sun
for i in positions:
if i[0] == 'Sun':
orbitting = i
# check at least one orbit has occured and if not suggest larger number steps
test = orbit(p[1],orbitting[1],time_list)
if isinstance(test, str):
orb_file.write("For " + str(p[0]) + " try a larger number of steps to allow completion of at least one orbit. \n")
# otherwise prints relevant inormation to orbital file
else:
orb_file.write("The orbit of " + str(p[0]) + " is: ")
orb_file.write(str(orbit(p[1],orbitting[1],time_list)) + " days, \n")
orb_file.write("and the apo- and periapses are (respectively): ")
orb_file.write(str(Apsides(distances[positions.index(p)][1]))+ " metres. \n")
# close orbital output file
orb_file.close()
energy_file = open(energy_file , "w")
energy_file.write("The total energies, kinetic energies, potential energies (in Joules) are as follows: \n")
for i in range(len(tot_energy_list)):
energy_file.write(str(tot_energy_list[i]) + "," + str(kin_energy_list[i]) + "," + str(pot_energy_list[i]) + "\n")
# close energy file
energy_file.close()
# plotting total energy, kinetic energy and potential energy of the system against time
pyplot.title('Energy Fluctuation Solar System Total Energy vs Time')
pyplot.xlabel('Time,s')
pyplot.ylabel('Total Energy, J')
pyplot.plot(time_list, tot_energy_list)
pyplot.show()
pyplot.title('Energy Fluctuation Solar System Kinetic Energy vs Time')
pyplot.xlabel('Time,s')
pyplot.ylabel('Kinetic Energy, J')
pyplot.plot(time_list, kin_energy_list)
pyplot.show()
pyplot.title('Energy Fluctuation Solar System Potential Energy vs Time')
pyplot.xlabel('Time,s')
pyplot.ylabel('Potential Energy, J')
pyplot.plot(time_list, pot_energy_list)
pyplot.show()
home = os.environ["HOME"]
# structure files
cbz_gOpt = "{}/Research/FORCE_FIELDS/AMBER/Molecules/CBZ_gaff2/1.resp_charges/2-geomOpt/CBZ_gau_Opt_log.xyz".format(
home)
#cbz_gaff2_lmpdat = "{}/Research/FORCE_FIELDS/AMBER/Molecules/CBZ_gaff2/4.2.test_MDs/Iteration_3-2/Iteration-3-2_best.lmpdat".format(home)
#cbz_gaff2_dcd = "{}/Research/FORCE_FIELDS/AMBER/Molecules/CBZ_gaff2/4.2.test_MDs/Iteration_3-2/Iteration-3-2_best_in_vacuo.dcd".format(home)
#cbz_gaff_lmpdat = "{}/Research/FORCE_FIELDS/AMBER/Molecules/CBZ_gaff2/4.2.test_MDs/Standard_gaff/CBZ.lmpdat".format(home)
#cbz_gaff_dcd = "{}/Research/FORCE_FIELDS/AMBER/Molecules/CBZ_gaff2/4.2.test_MDs/Standard_gaff/Standard_gaff_in_vacuo.dcd".format(home)
cbz_gaff2_lmpdat = "{}/Research/PAPERS/2017_12/CBZ_FF-evaluation/results/average_structures/cbz_gaff2_average.lmpdat".format(
home)
cbz_gaff_lmpdat = "{}/Research/PAPERS/2017_12/CBZ_FF-evaluation/results/average_structures/cbz_gaff_average.lmpdat".format(
home)
# change the scene
VMD.evaltcl("display shadows off")
color_display = color.get_colormap("Display")
color_display["Background"] = "white"
color.set_colormap("Display", color_display)
display.set(depthcue=0)
# load mol and change its representation
# geometry optimized cbz
licor_style = "Licorice 0.1 50 50"
sel_no_h = "not element H"
if molecule.exists(0) != 1:
molecule.load("xyz", cbz_gOpt)
molrep.modrep(0,
0,
sel=sel_no_h,
# quenching
QUENCH_DCD = QUENCH_DCD_RAW.format(MAINDIR, CURCYCLE)
molecule.read(CURCYCLE, "dcd", QUENCH_DCD, beg=0, end=-1, waitfor=-1)
# annealing - heating up
EQUIL_ANNEAL_DCD = EQUIL_ANNEAL_DCD_RAW.format(MAINDIR, CURCYCLE)
molecule.read(CURCYCLE,
"dcd",
EQUIL_ANNEAL_DCD,
beg=0,
end=-1,
waitfor=-1)
# annealing - productive
ANNEAL_DIR = "{}/anneal_{}".format(MAINDIR, CURCYCLE)
PROD_ANNEAL_DCDS = get_files(
"{0}/anneal_{1}/".format(ANNEAL_DIR, CURCYCLE),
PROD_ANNEAL_DCD_RAW.format(CURCYCLE))
for CUR_DCD in PROD_ANNEAL_DCDS:
print(CUR_DCD)
molecule.read(CURCYCLE, "dcd", CUR_DCD, beg=0, end=-1, waitfor=-1)
pdb.set_trace()
# requenching
REQUENCH_DCD = REQUENCH_DCD_RAW.format(MAINDIR, CURCYCLE)
molecule.read(CURCYCLE, "dcd", REQUENCH_DCD, beg=0, end=-1, waitfor=-1)
VMD.evaltcl("mol off {}".format(CURCYCLE))
# Warning: this is Python 2.5
from Tkinter import *
# A minimal plugin class that just creates an empty window
class MyPlugin:
def __init__(self):
self.root = Tk()
self.root.title("My Plugin Window")
# Function to start the plugin. Must return the window handle.
def startMyPlugin():
return MyPlugin().root
if __name__ == "__main__":
import VMD
# Register the plugin so that it's not actually created until the
# first request to open the window.
VMD.registerExtensionMenu("myplugin", startMyPlugin)
# Create the plugin now and add it to the Extensions menu.
# VMD.addExtensionMenu("myplugin", MyPlugin().root)
return self.rotation.x(), self.rotation.y(), self.rotation.z(), self.rotation.w()
def assign(item, frame):
item['Rotation']['x'] = frame.get_vec()[0]
item['Rotation']['y'] = frame.get_vec()[1]
item['Rotation']['z'] = frame.get_vec()[2]
item['Rotation']['w'] = frame.get_vec()[3]
item['BoneName_byte'] = frame.name
def addOneMore(r):
buff = r.bone_record[0]
buff = copy.deepcopy(buff)
r.bone_record.append(buff)
return buff
r = VMD.VMDReader('sample_reference.vmd')
r.bone_record = r.bone_record[:1]
joints = [[8,9],[9,10], [8,14],[14,15],[15,16], [8,11],[11,12],[12,13], [8,7],[7,0], [4,5],[5,6],[0,4], [0,1],[1,2],[2,3]]
time = 0
for i in range(586):
time += 1
pts = np.float32(sio.loadmat('./pred3d/%08d.mat'%i)['pts'])
print(pts.shape)
buf = []
for i in range(17):
buf.append(QVector3D(pts[i][0], -pts[i][1], pts[i][2]))
pts = buf
# lowerbody
# generate VMD scripts
import sys
sys.path.append('../../src/vmd/')
from getSettings import getSettings
from VMD import *
if __name__ == '__main__':
# ---- input settings ---- #
celltype, chrom_lst = getSettings(sys.argv[1:])
Vmd = VMD()
for chrId in chrom_lst:
# ---- generate individual pdb/psf files ---- #
Vmd.genPdb(celltype, chrId)
Vmd.genPsf(celltype, chrId)
# ---- generate individual VMD scripts ---- #
Vmd.genVMDScript(celltype, chrId)
print