def run_read_output_surf(self):
"""
Write the output file according to the template measurements
"""
tcl_name = output_folder + "/surface_output_" + str(
self.input_pdb_path).split("/")[-1][0:-4] + "_" + str(
self.current_chain) + ".tcl"
run_command = "play " + tcl_name
evaltcl(run_command)
def check_lammps(filename):
evaltcl("package require topotools 1.6")
evaltcl("topo readlammpsdata %s" % filename)
assert len(set(atomsel("same fragment as protein").resid)) == 284
assert len(set(atomsel("resname ACE NMA NME").resid)) == 4
assert len(atomsel("water")) == 32106
assert len(atomsel("same fragment as lipid")) == 12194
# Check for the corrrect number of alprenolols
assert len(atomsel("resname ALP")) == 420
assert len(set(atomsel("resname ALP").resid)) == 10
assert "OG301" in set(atomsel("resname ALP").name)
assert "O1" not in set(atomsel("resname ALP").name)
# Check coordinates are unique (not zero)
assert len(atomsel("resname ALP")) == 420
assert 0.0 not in atomsel("resname ALP").x
def test_evaltcl(file_rho):
from vmd import evaltcl, atomsel, molecule
molid = int(evaltcl("mol new"))
assert molecule.get_top() == molid
assert evaltcl("mol addfile %s type mae waitfor all" % file_rho)
assert "molecule%d" % molid in evaltcl("mol list")
with pytest.raises(ValueError):
evaltcl("atomsel all")
assert evaltcl("set all_atoms [atomselect %s \" all \" frame %s]" %
(molid, 0)) == "atomselect0"
assert set(evaltcl("$all_atoms get chain").split()) == \
set(atomsel("all").chain)
assert set(evaltcl("$all_atoms get name").split()) == \
set(atomsel("all").name)
with pytest.raises(ValueError):
evaltcl("$all_atoms get invalid")
def load_data(self, load_data, align=True):
"""Method for loading trajectory data
Parameters
----------
load_data : dict
dictionary of VMD read routine options. See
VMDMolecule.__init__() docs.
"""
if not isinstance(load_data, dict):
raise ValueError("load_data must be a dictionary with "
"key-value pairs corresponding to VMD "
"read command options.")
else:
mol.read(self.molid, **load_data)
if align:
self.self_align()
print("{} frames loaded.".format(mol.numframes(self.molid)))
evaltcl("display resetview")
def test_evaltcl(file_rho):
from vmd import evaltcl, atomsel, molecule
molid = int(evaltcl("mol new"))
assert molecule.get_top() == molid
assert evaltcl("mol addfile %s type mae waitfor all" % file_rho)
assert "molecule%d" % molid in evaltcl("mol list")
with pytest.raises(ValueError):
evaltcl("atomsel all")
assert evaltcl("set all_atoms [atomselect %s \" all \" frame %s]"
% (molid, 0)) == "atomselect0"
assert set(evaltcl("$all_atoms get chain").split()) == \
set(atomsel("all").chain)
assert set(evaltcl("$all_atoms get name").split()) == \
set(atomsel("all").name)
with pytest.raises(ValueError):
evaltcl("$all_atoms get invalid")
def _psf_to_gromacs(self):
# Save the .gro coordinate file with VMD
mid = molecule.load("psf", self.outprefix + ".psf", "pdb",
self.outprefix + ".pdb")
atomsel("all", mid).write("gro", self.outprefix + ".gro")
molecule.delete(mid)
# Write a temporary file for a topotools tcl script
f, temp = tempfile.mkstemp(prefix="topo",
suffix=".tcl",
dir=self.tmp_dir,
text=True)
with os.fdopen(f, 'w') as fh:
fh.write("package require topotools 1.6\n")
fh.write("mol load psf %s.psf pdb %s.pdb\n" %
(self.outprefix, self.outprefix))
fh.write("topo writegmxtop %s.top [list %s ]\n" %
(self.outprefix, " ".join(self.parameters)))
# Run the pbctools tcl script
output = evaltcl("play %s" % temp)
print(output)
def run_read_output_inter(self):
"""
Write the output file according to the template measurements
"""
output_name = "output/interface_output_A"
evaltcl('play output/get_interface.tcl.tpl')
#Load python packages
from vmd import evaltcl
import numpy as np
from molecule import load
from atomsel import atomsel
import molecule
import math
#Load nanotube package in VMD
evaltcl('package require nanotube')
#make a 5nm x 5nm grpahene sheet
NT=evaltcl('graphene -lx 5 -ly 5 -type zigzag -nlayers 1 -b 1 -a 0 -d 0 -i 0')
#Figure out the correct unit cell size and set it so we can get the correct PBC
all=atomsel()
CCdist=1.42
X=all.get('x')
Y=all.get('y')
pbc_x = np.max(X) - np.min(X) + CCdist
pbc_y = np.max(Y) - np.min(Y) + CCdist * np.sin(60./360.*math.pi*2)
pbc = [ pbc_x, pbc_y, 20 ]
#We need another VMD package to set the periodic boundary conditions / unit cell
evaltcl('package require pbctools')
#We need to use the VMD packag pbctools, which doesn't have a python interface,
#so we explicitly do this by hand with evaltcl
evaltcl('pbc set {%f %f %f}'%(pbc[0],pbc[1],pbc[2]))
evaltcl('package require topotools')
def call_tcl(self,file_path,proc):
#en construccion metodo para llamar funciones desde tcl
vmd.evaltcl(run)
return vmd.evaltcl("mycenter")
def write(self, psf_name):
"""
Writes the pdb/psf file.
Args:
psf_name (str): Prefix for the pdb/psf output files, extension
will be appended
Returns:
topologies (list of str): Topology files that were used in creating
the psf
"""
# Clean up all temp files from previous runs if present
# An earlier check will exit if it's not okay to overwrite here
self.psf_name = psf_name
try:
os.remove('%s.pdb'% self.psf_name)
os.remove('%s.psf'% self.psf_name)
except OSError:
pass
# Finds the psfgen package and sets the output file name
string = '''
set dir [file join $env(VMDDIR) plugins [vmdinfo arch] tcl psfgen1.6]
package ifneeded psfgen 1.6 [list load [file join $dir libpsfgen.so]]
package require psfgen
set output "%s"
resetpsf
''' % self.psf_name
self.file.write(string)
# Put our molecule on top
old_top = molecule.get_top()
molecule.set_top(self.molid)
# Print out topology files
self.file.write('\n')
print("Using the following topologies:")
for top in self.topologies:
print(" - %s" % top.split("/")[-1])
self.file.write(' topology %s\n' % top)
# Mark all atoms as unsaved with the user field
atomsel('all', molid=self.molid).set('user', 1.0)
check_atom_names(molid=self.molid)
# Now ions if present, changing the atom names
if len(atomsel('element Na Cl K', molid=self.molid)) > 0:
self._write_ion_blocks()
# Save water 10k molecules at a time
if len(atomsel('water', molid=self.molid)):
self._write_water_blocks()
# Now lipid
if len(atomsel(self.lipid_sel)):
self._write_lipid_blocks()
if not len(atomsel("resname %s" % _acids, molid=self.molid)):
print("\tDidn't find any protein.\n")
# Now handle the protein
# Save and reload the protein so residue looping is correct
prot_molid = self._renumber_protein_chains(molid=self.molid)
extpatches = set()
for frag in sorted(set(atomsel("resname %s" % _acids,
molid=prot_molid).get('fragment'))):
extpatches.update(self._write_protein_blocks(prot_molid, frag))
atomsel("same fragment as resname %s" % _acids,
molid=self.molid).set("user", 0.0)
# List all patches applied to the protein
print("Applying the following patches:\n")
print("\t%s" % "\t".join(extpatches))
self.file.write(''.join(extpatches))
self.file.write("\n")
# Regenerate angles and dihedrals after applying patches
# Angles must be regenerated FIRST!
# See http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2009-2010/4137.html
self.file.write("regenerate angles\nregenerate dihedrals\n")
# Check if there is anything else and let the user know about it
leftovers = atomsel('user 1.0', molid=self.molid)
for lig in set(leftovers.get('resname')):
residues = self._find_single_residue_names(resname=lig, molid=self.molid)
self._write_generic_block(residues)
# Write the output files and run
string = '''
writepsf x-plor cmap ${output}.psf
writepdb ${output}.pdb'''
self.file.write(string)
self.file.close()
evaltcl('play %s' % self.filename)
self._check_psf_output()
# Reset top molecule
molecule.set_top(old_top)
return self.topologies
def run_class_pdb(input_pdb_name):
"""
Generate the output file and generate the structures with hydrogens
"""
add_hydrogens(input_pdb_name)
evaltcl("play add_H.tcl.tpl")
def write(self, psf_name):
"""
Writes the pdb/psf file.
Args:
psf_name (str): Prefix for the pdb/psf output files, extension
will be appended
Returns:
topologies (list of str): Topology files that were used in creating
the psf
"""
# Clean up all temp files from previous runs if present
# An earlier check will exit if it's not okay to overwrite here
self.psf_name = psf_name
try:
os.remove('%s.pdb'% self.psf_name)
os.remove('%s.psf'% self.psf_name)
except OSError:
pass
# Finds the psfgen package and sets the output file name
string = '''
set dir [file join $env(VMDDIR) plugins [vmdinfo arch] tcl psfgen1.6]
package ifneeded psfgen 1.6 [list load [file join $dir libpsfgen.so]]
package require psfgen
set output "%s"
resetpsf
''' % self.psf_name
self.file.write(string)
# Put our molecule on top
old_top = molecule.get_top()
molecule.set_top(self.molid)
# Print out topology files
self.file.write('\n')
print("Using the following topologies:")
for top in self.topologies:
print(" - %s" % top.split("/")[-1])
self.file.write(' topology %s\n' % top)
# Mark all atoms as unsaved with the user field
atomsel('all', molid=self.molid).set('user', 1.0)
check_atom_names(molid=self.molid)
# Now ions if present, changing the atom names
if len(atomsel('ions', molid=self.molid)) > 0:
self._write_ion_blocks()
# Save water 10k molecules at a time
if len(atomsel('water', molid=self.molid)):
self._write_water_blocks()
# Now lipid
if len(atomsel(self.lipid_sel)):
self._write_lipid_blocks()
# Now handle the protein
# Save and reload the protein so residue looping is correct
if len(atomsel("resname %s" % _acids, molid=self.molid)):
extpatches = set()
for frag in sorted(set(atomsel("resname %s" % _acids,
molid=self.molid).get('fragment'))):
extpatches.update(self._write_protein_blocks(self.molid, frag))
atomsel("same fragment as resname %s" % _acids,
molid=self.molid).set("user", 0.0)
# List all patches applied to the protein
print("Applying the following patches:\n")
print("\t%s" % "\t".join(extpatches))
self.file.write(''.join(extpatches))
self.file.write("\n")
else:
print("\tDidn't find any protein. Continuing...\n")
# Regenerate angles and dihedrals after applying patches
# Angles must be regenerated FIRST!
# See http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2009-2010/4137.html
self.file.write("regenerate angles\nregenerate dihedrals\n")
# Check if there is anything else and let the user know about it
leftovers = atomsel('user 1.0', molid=self.molid)
for lig in set(leftovers.get('resname')):
residues = self._find_single_residue_names(resname=lig, molid=self.molid)
self._write_generic_block(residues)
# Write the output files and run
string = '''
writepsf x-plor cmap ${output}.psf
writepdb ${output}.pdb'''
self.file.write(string)
self.file.close()
evaltcl('play %s' % self.filename)
self._check_psf_output()
# Reset top molecule
molecule.set_top(old_top)
return self.topologies
