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 load_traj(TOP, TRAJ, beg_frame, end_frame, stride):
"""
Loads in topology and trajectory into VMD
Parameters
----------
TOP: MD Topology
TRAJ: MD Trajectory
beg_frame: int
end_frame: int
stride: int
Returns
-------
trajid: int
simulation molid object
"""
top_file_type = get_file_type(TOP)
traj_file_type = get_file_type(TRAJ)
trajid = molecule.load(top_file_type, TOP)
if TRAJ is not None:
molecule.read(trajid,
traj_file_type,
TRAJ,
beg=beg_frame,
end=end_frame,
skip=stride,
waitfor=-1)
else:
molecule.read(trajid,
top_file_type,
TOP,
beg=beg_frame,
end=end_frame,
skip=stride,
waitfor=-1)
return trajid
def load_traj(top_path, traj_path):
top_file_type = getFileType(top_path)
trajid = molecule.load(top_file_type, top_path)
if (traj_path != None):
traj_file_type = getFileType(traj_path)
molecule.read(trajid,
traj_file_type,
traj_path,
beg=start,
end=stop,
skip=stride,
waitfor=-1)
def getWaterLocations(f, TOP, TRAJ, printNumFrames):
print("Start getWaterLocations()")
molid = molecule.load(getFileType(TOP), TOP)
molecule.read(molid, getFileType(TRAJ), TRAJ, beg=1, end=-1, skip=1, waitfor=-1)
n_frames = molecule.numframes(molid)
if(printNumFrames): f.write("numFrames:" + str(n_frames) + "\n")
grid = create_grid(n_frames)
print_file_header(f)
waters = atomsel.atomsel('water', molid= molid)
# waters = atomsel.atomsel('resname IP3', molid= molid)
coords = getAllCoords(molid, n_frames)
return grid, waters, coords, n_frames
def load_traj(top_path, traj_path):
"""
Load trajectory and topology into VMD display
"""
top_file_type = getFileType(top_path)
trajid = molecule.load(top_file_type, top_path)
if (traj_path != None):
traj_file_type = getFileType(traj_path)
molecule.read(trajid,
traj_file_type,
traj_path,
beg=start,
end=stop,
skip=stride,
waitfor=-1)
def load_traj(struct_file_name, traj_file_names):
struct_file_name = struct_file_name.replace("_strip_waters", "")
top_file_type = getFileType(struct_file_name)
print("topo name", struct_file_name)
trajid = molecule.load(top_file_type, struct_file_name)
for traj_index, traj_file_name in enumerate(traj_file_names):
if (traj_index > 0): break
traj_file_name = traj_file_name.replace("_strip_waters", "")
print("traj name", traj_file_name)
traj_file_type = getFileType(traj_file_name)
molecule.read(trajid,
traj_file_type,
traj_file_name,
beg=start,
end=stop,
skip=stride,
waitfor=-1)
print("Finished Loading Trajectory")
molrep.delrep(0, 0)
if (display_mode == "-d"):
molrep.addrep(0,
style='NewRibbons',
color='ColorID 8',
selection="protein")
# molrep.addrep(0, style = 'HBonds 3.0 110', selection = 'protein and not carbon', color = 'Type')
molrep.addrep(
0,
style='HBonds 3.8 70',
selection="(water within 3.5 of protein) or protein and not carbon",
color="Type")
molrep.set_autoupdate(0, 1, 1)
elif (display_mode == "-s"):
molrep.addrep(0,
style="VDW",
selection="name CA",
material="Transparent")
else:
print("Input Format Incorrect")
exit(1)
animate.goto(0)
def load_top(TOPOLOGY, DISPLAY_MODE):
top_file_type = getFileType(TOPOLOGY)
trajid = molecule.load(top_file_type, TOPOLOGY)
molrep.delrep(0, 0)
# molrep.addrep(0, selection= "water within 4 of protein")
if (DISPLAY_MODE == "-d"):
molrep.addrep(0,
style="NewRibbons",
color="ColorID 8",
material="Transparent",
selection="protein")
elif (DISPLAY_MODE == "-s"):
molrep.addrep(0,
style="NewRibbons",
color="ColorID 8",
material="Transparent",
selection="protein")
molrep.addrep(0,
style="CPK",
color="ColorID 8",
material="Transparent",
selection="name CA")
t0=time()
coord_ent.selectIds(sel)
t1=time()
atomsel.atomsel(sel)
t2=time()
print "MSYS: %s ms" % ((t1-t0)*1000)
print "VMD: %s ms" % ((t2-t1)*1000)
return rc
if len(sys.argv)<2:
DMSROOT='tests/files'
path='%s/2f4k.dms' % DMSROOT
else:
path=sys.argv[1]
coord_vmd=molecule.load(path.split('.')[-1], path)
coord_ent = msys.Load(path)
coord_ent.select('none')
compare_atomsel(coord_ent,"protein or water and element O")
compare_atomsel(coord_ent,"protein and water or element O")
compare_atomsel(coord_ent,"protein or (water and element O)")
compare_atomsel(coord_ent,"(protein and water) or element O")
compare_atomsel(coord_ent,"ctnumber 1")
compare_atomsel(coord_ent,"ctnumber 2")
compare_atomsel(coord_ent,"ctnumber 3")
compare_atomsel(coord_ent,"ctnumber 4")
compare_atomsel(coord_ent,"all")
compare_atomsel(coord_ent,"none")
compare_atomsel(coord_ent,"index 10 20 30",perf=True)
strout+= (' ' + str(a))
strout+='}'
return strout
#Add a bunch of toy sphere molecules
z0=3.33
#two spheres in x direction
for x in np.linspace(5,45,5):
#two sphere in y direction
for y in np.linspace(5,45,5):
for z0 in [3.]:
#load the O atom from O.pdb
O=load('pdb','O.pdb')
#Move the O atom into the right place
all=atomsel()
all.moveby([x,y,z0])
#Set resid to 0 (for now, doesn't matter, just needs to be something
# so that the simulation program isn't unhappy
all=atomsel()
all.set('resid',0)
#So far we have 26 molecfules (1 graphene, 25 O). We need to combine them into one thing
#so that we can treat them together. We use topotools to do this
combined=evaltcl('::TopoTools::mergemols %s'%list2tcl(molecule.listall()))
def maeToPdb(input_mae_path, output_pdb_file_path):
molid = molecule.load('mae', input_mae_path)
molecule.write(molid, 'pdb', output_pdb_file_path)
print("Finished Conversion for: " + str(input_mae_path))
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,
style=licor_style,
material="AOChalky",
color="ColorID 7")
if molecule.exists(1) != 1:
#molecule.load("lammpsdata", cbz_gaff2_lmpdat, "dcd", cbz_gaff2_dcd)
molecule.load("lammpsdata", cbz_gaff2_lmpdat)
molrep.modrep(1,
0,
sel=sel_no_h,
style=licor_style,
material="AOChalky",
def loadTopology(top_file_path): global trajid input_top_file_type = getFileType(top_file_path) trajid = molecule.load(input_top_file_type, top_file_path) return trajid
def load_traj(TOP_PATH):
top_file_type = getFileType(TOP_PATH)
trajid = molecule.load(top_file_type, TOP_PATH)
self.trj_changes.plotDistance(('(A)ASP-1:CA', '(A)SER-20:CA'), lam=self.lam)
def test_matrixPlotChange(self):
changes = self.trj_changes.changes(self.lam)
v = changes.values()[0]
self.trj_changes.matrixPlotChange(v, lam=self.lam)
##############################
# Visualizing changes in VMD #
##############################
class TestVMDDisplay(unittest.TestCase):
def setUp(self):
from analyze_changed_distances import WorkdirChanges
wkdir_changes = WorkdirChanges('all_pairs')
common_changes = wkdir_changes.commonResidueChangesByNumChangeTimes(100)
self.changes = wkdir_changes.trajectoryChanges('serial').changesByNumChangeTimes(100, residue_pairs=common_changes)
assert len(self.changes)
def test_VMDDisplay(self):
from analyze_changed_distances import VMDDisplay
VMDDisplay(self.changes, window=5, molid=0)
if __name__ == '__main__':
os.chdir(os.getenv('EXAMPLESDIR', 'examples'))
molid = molecule.load('mae', 'TrpCage.mae')
VMDevaltcl('mol addfile {TrpCage.dcd} type {dcd} first 0 last -1 step 1 waitfor all 0')
cv.set_times(molid, np.loadtxt('TrpCage.times.txt'))
unittest.main(verbosity=2)
self.trj_changes.matrixPlotChange(v, lam=self.lam)
##############################
# Visualizing changes in VMD #
##############################
class TestVMDDisplay(unittest.TestCase):
def setUp(self):
from analyze_changed_distances import WorkdirChanges
wkdir_changes = WorkdirChanges('all_pairs')
common_changes = wkdir_changes.commonResidueChangesByNumChangeTimes(
100)
self.changes = wkdir_changes.trajectoryChanges(
'serial').changesByNumChangeTimes(100,
residue_pairs=common_changes)
assert len(self.changes)
def test_VMDDisplay(self):
from analyze_changed_distances import VMDDisplay
VMDDisplay(self.changes, window=5, molid=0)
if __name__ == '__main__':
os.chdir(os.getenv('EXAMPLESDIR', 'examples'))
molid = molecule.load('mae', 'TrpCage.mae')
VMDevaltcl(
'mol addfile {TrpCage.dcd} type {dcd} first 0 last -1 step 1 waitfor all 0'
)
cv.set_times(molid, np.loadtxt('TrpCage.times.txt'))
unittest.main(verbosity=2)
tic = time.clock()
if (len(sys.argv) < 4):
print "Usage: python wrapAlignAmber.py <topology file> <trajectory file> <out wrapped trajectory file>"
sys.exit()
#### Read in input topology, trajectory files, outTraj file
top_file = sys.argv[1]
traj_file = sys.argv[2]
out_traj_file = sys.argv[3]
if ("-crys" in sys.argv):
include_crys = True
else:
include_crys = False
#### load topology and trajectories
traj_molid = molecule.load('pdb', top_file)
molecule.read(traj_molid, 'netcdf', traj_file, beg=0, end=-1, waitfor=-1)
#### align all frames
refsel = atomsel("protein", molid=traj_molid, frame=0)
for i in range(molecule.numframes(traj_molid)):
molecule.set_frame(traj_molid, i)
b = atomsel("protein", molid=traj_molid, frame=i)
T = b.fit(refsel)
atomsel("all", molid=traj_molid, frame=i).move(T)
#### Read out file
if (include_crys == True):
molecule.write(traj_molid, 'dcd', out_traj_file, beg=0, end=-1)
else:
molecule.write(traj_molid, 'dcd', out_traj_file, beg=1, end=-1)
sys.exit()
#### Read in input topology, trajectory files, outTraj file
(top_file, traj_dir, traj_file_type,
out_traj_file) = (sys.argv[1], sys.argv[2], sys.argv[3], sys.argv[4])
createDirectory(out_traj_file)
output_directory = os.path.dirname(out_traj_file)
#### Copy topology file to output directory
# print("cp " + top_file + " " + output_directory)
os.system("cp " + top_file + " " + output_directory)
print("Subsampling Trajectory: " + traj_dir)
#### load topology and trajectories
traj_molid = molecule.load(getFileType(top_file), top_file)
if (traj_file_type == "nc"):
traj_fragments_list = glob.glob(traj_dir + "/Prod_*/Prod_*.nc")
elif (traj_file_type == "dcdconvert"):
traj_fragments_list = glob.glob(traj_dir + "/Prod_*/Prod_*.dcd")
elif (traj_file_type == "dcd"):
traj_fragments_list = glob.glob(traj_dir + "/*.dcd")
traj_fragments_list.sort(key=natural_keys)
for index, traj_fragment_file in enumerate(traj_fragments_list):
print("Fragment Index " + str(index) + " : " + traj_fragment_file)
molecule.read(traj_molid,
getFileType(traj_fragment_file),
traj_fragment_file,
beg=0,
end=-1,
