def view_trajectory(self):
"""
Output the trajectory as a DCD file and views it in VMD
"""
if self.args['grid_LJr'].endswith('.nc') and (not os.path.isfile(self.args['grid_LJr'][:-2]+'dx')):
import AlGDock.IO
IO_Grid = AlGDock.IO.Grid()
IO_Grid.read(self.args['grid_LJr'])
IO_Grid.write(self.args['grid_LJr'][:-2]+'dx')
scriptFN = 'script.vmd'
script = ''
script += 'set ligand [mol new '+self.args['ligand_prmtop']+']\n'
script += 'mol addfile '+self.args['output_dcd']+' type dcd waitfor all\n'
script += 'mol new {%s} type {dx} first 0 last -1 step 1 waitfor 1\n'%(self.args['grid_LJr'][:-2]+'dx')
script += 'mol modstyle 0 1 Isosurface 10.000000 0 2 0 1 1\n'
scriptF = open(scriptFN,'w')
scriptF.write(script)
scriptF.close()
import AlGDock
vmdFN = AlGDock.findPaths(['vmd'])['vmd']
vmd_args = [vmdFN] + ['-e', scriptFN]
import subprocess
p = subprocess.call(vmd_args)
def showMolecule(self, colorBy=None, label=False, dcdFN=None):
"""
Opens the molecule in VMD
:param colorBy: color atoms by 'Occupancy', or 'Beta'. None uses default colors.
"""
# Write PDB file
# To set Occupancy, change atom.occupancy
# To set Beta, change atom.temperature_factor
import os.path
pdbFN = os.path.join(MMTK.Database.molecule_types.directory,
'showMolecule.pdb')
outF = MMTK.PDB.PDBOutputFile(pdbFN)
outF.write(self.molecule)
outF.close()
# Write VMD script
script = 'set ligand [mol new ' + pdbFN + ']\n'
if colorBy is not None:
script += 'mol modcolor 0 $ligand ' + colorBy + '\n'
script += 'mol modstyle 0 0 CPK 1.000000 0.300000 10.000000 10.000000\n'
if label:
script += """
proc label_atoms { molid seltext } {
set sel [atomselect $molid $seltext]
set atomlist [$sel list]
foreach {atom} $atomlist {
set atomlabel [format "%d/%d" $molid $atom]
label add Atoms $atomlabel
}
$sel delete
}
label_atoms 0 all
"""
if dcdFN is not None:
script += 'animate delete all $ligand\n'
script += 'mol addfile ' + dcdFN + ' type dcd waitfor all\n'
scriptF = open('showMolecule.vmd', 'w')
scriptF.write(script)
scriptF.close()
# Find and run vmd
import AlGDock
vmdCommand = AlGDock.findPath(AlGDock.search_paths['vmd'])
import subprocess
subprocess.call([vmdCommand, '-e', 'showMolecule.vmd'])
# Remove files
os.remove(pdbFN)
os.remove('showMolecule.vmd')
def showMolecule(self, colorBy=None, label=False, dcdFN=None):
"""
Opens the molecule in VMD
:param colorBy: color atoms by 'Occupancy', or 'Beta'. None uses default colors.
"""
# Write PDB file
# To set Occupancy, change atom.occupancy
# To set Beta, change atom.temperature_factor
import os.path
pdbFN = os.path.join(MMTK.Database.molecule_types.directory,'showMolecule.pdb')
outF = MMTK.PDB.PDBOutputFile(pdbFN)
outF.write(self.molecule)
outF.close()
# Write VMD script
script = 'set ligand [mol new '+pdbFN+']\n'
if colorBy is not None:
script += 'mol modcolor 0 $ligand '+colorBy+'\n'
script += 'mol modstyle 0 0 CPK 1.000000 0.300000 10.000000 10.000000\n'
if label:
script += """
proc label_atoms { molid seltext } {
set sel [atomselect $molid $seltext]
set atomlist [$sel list]
foreach {atom} $atomlist {
set atomlabel [format "%d/%d" $molid $atom]
label add Atoms $atomlabel
}
$sel delete
}
label_atoms 0 all
"""
if dcdFN is not None:
script += 'mol addfile '+dcdFN+' type dcd waitfor all\n'
scriptF = open('showMolecule.vmd','w')
scriptF.write(script)
scriptF.close()
# Find and run vmd
import AlGDock
vmdCommand = AlGDock.findPath(AlGDock.search_paths['vmd'])
import subprocess
subprocess.call([vmdCommand, '-e', 'showMolecule.vmd'])
# Remove files
os.remove(pdbFN)
os.remove('showMolecule.vmd')
