def buildMassTable(model_name, psf_name, subset_selection):
model = loos.createSystem(model_name)
psf = loos.createSystem(psf_name)
# First, fix masses...
mass_table = {}
for atom in psf:
name = atom.name()
mass = atom.mass()
if name in mass_table:
if mass != mass_table[name]:
print('Error- multiple masses found for {} ({} vs {})'.format(
name, mass, mass_table[name]))
sys.exit(-10)
else:
mass_table[name] = mass
protein = loos.selectAtoms(model, subset_selection)
masses = []
for atom in protein:
name = atom.name()
if name not in mass_table:
print('Error- could not find {} in mass table'.format(name))
sys.exit(-11)
atom.mass(mass_table[name])
masses.append(mass_table[name])
return masses
def pick_structure(self):
# pick a structure file at random, and build up the filename
filename = os.path.join(self.path, random.choice(self.structures))
# read the file
lipid = loos.createSystem(filename)
# return the AtomicGroup
return lipid
def pick_structure(self):
# pick a structure file at random, and build up the filename
filename = os.path.join(self.path, random.choice(self.structures))
# read the file
lipid = loos.createSystem(filename)
# return the AtomicGroup
return lipid
def __init__(self, filename, template_box, target_box, segname):
self.filename = filename
self.box = target_box
self.template_box = template_box
self.segname = segname
self.template = loos.createSystem(filename)
for i in range(len(self.template)):
self.template[i].segid(segname)
self.buildBox()
def __init__(self, filename, template_box, target_box, segname):
self.filename = filename
self.box = target_box
self.template_box = template_box
self.segname = segname
self.template = loos.createSystem(filename)
for i in range(len(self.template)):
self.template[i].segid(segname)
self.buildBox()
def __init__(self, line):
(tag, model_file, psf_file, water_seg, scale_by_molecule) = line.split()
self.model_file = os.path.abspath(model_file)
self.psf_file = os.path.abspath(psf_file)
self.water_segname = water_seg.upper()
self.scale = int(scale_by_molecule)
self.model = loos.createSystem(self.model_file)
self.segments = self.model.splitByUniqueSegid()
self.has_water = False
for s in self.segments:
if s[0].segid() == self.water_segname:
self.has_water = True
break
def __init__(self, line):
(tag, model_file, psf_file, water_seg, scale_by_molecule) = line.split()
self.model_file = os.path.abspath(model_file)
self.psf_file = os.path.abspath(psf_file)
self.water_segname = water_seg.upper()
self.scale = int(scale_by_molecule)
self.model = loos.createSystem(self.model_file)
self.segments = self.model.splitByUniqueSegid()
self.has_water = False
for s in self.segments:
if s[0].segid() == self.water_segname:
self.has_water = True
break
def createWaterBox():
os.mkdir('water')
os.symlink('../water.inp', 'water.inp')
os.symlink('../water_small.pdb', 'water_small.pdb')
os.symlink('../water_small.psf', 'water_small.psf')
water_log = open('water.log', 'w')
water_err = open('water.err', 'w')
ok = subprocess.call(['/home/tromo/local/bin/namd2', '+p2', 'water.inp'], stdout = water_log, stderr = water_err)
if ok != 0:
print 'Water box processing failed with error code ', ok
sys.exit(-2)
subprocess.call(['fixdcd', 'water/water.dcd'])
# Get traj size...
water_model = loos.createSystem('water_small.psf')
water_traj = loos.pyloos.Trajectory('water/water.dcd', water_model)
last_water = water_traj[len(water_traj)-1]
savePDB('water_randomized.pdb', last_water)
sys.stderr.write("Will attempt to change permissions\n")
try:
os.chmod(config.directory,
stat.S_IREAD | stat.S_IWRITE | stat.S_IEXEC)
except OSError:
sys.stderr.write(" Unable to change permissions on directory\n")
os.exit(-1)
# We need a model containing just the protein and lipid, so we'll
# make a psfgen script, run it, use the psf to make the AtomicGroup,
temporary_psfname = os.path.join(config.directory, config.psfname)
psfgen_script = config.generate_psf(True, False, True, True,
temporary_psfname)
psfgen = PSFGen.PSFGen(psfgen_script, config.psfgen_binary)
psfgen.run()
system = loos.createSystem(temporary_psfname)
# If the "protein" is actually a bunch of independent molecules (e.g. a bunch of peptides),
# we'll want to scale them in x & y to match the expanded box.
if config.protein is not None and config.protein.scale:
protein_molecules = config.protein.model.splitByMolecule()
for m in protein_molecules:
centroid = m.centroid()
scaled = box_scaling * centroid
diff = scaled - centroid
diff.z(0.0) # we only want to translate in the xy plane
m.translate(diff)
molecules = system.splitByMolecule()
segments = []
for r2 in other.regions:
if r.is_neighbor(r2):
return True
return False
def print_indices(self):
for r in self.regions:
r.print_indices()
print
if __name__ == '__main__':
import sys
structure = loos.createSystem("trj_1.pdb")
#structure = loos.createSystem("example.pdb")
#structure = loos.createSystem("b2ar.pdb")
#box = loos.GCoord(55., 77, 100)
#box = loos.GCoord(55., 77, 100)
phos = loos.selectAtoms(structure, 'name == "P"')
upper = loos.AtomicGroup()
for p in phos:
if p.coords().z() > 0:
upper.append(p)
upper.periodicBox(structure.periodicBox())
print upper.isPeriodic()
"""
slice = loos.AtomicGroup()
for a in structure:
header = " ".join(sys.argv) print "# ", header system_file = sys.argv[1] traj_file = sys.argv[2] centering_selection_string = sys.argv[3] target_selection_string = sys.argv[4] zmin = float(sys.argv[5]) zmax = float(sys.argv[6]) znum_bins = int(sys.argv[7]) rmin = float(sys.argv[8]) rmax = float(sys.argv[9]) rnum_bins = int(sys.argv[10]) system = loos.createSystem(system_file) traj = loos.pyloos.Trajectory(traj_file, system) centering = loos.selectAtoms(system, centering_selection_string) target = loos.selectAtoms(system, target_selection_string) zbin_width = (zmax - zmin) / znum_bins rbin_width = (rmax - rmin) / rnum_bins rmin2 = rmin*rmin rmax2 = rmax*rmax hist = numpy.zeros( [rnum_bins, znum_bins]) for frame in traj:
sys.stderr.write("Will attempt to change permissions\n")
try:
os.chmod(config.directory,
stat.S_IREAD | stat.S_IWRITE | stat.S_IEXEC)
except OSError:
sys.stderr.write(" Unable to change permissions on directory\n")
os.exit(-1)
# We need a model containing just the protein and lipid, so we'll
# make a psfgen script, run it, use the psf to make the AtomicGroup,
temporary_psfname = os.path.join(config.directory, config.psfname)
psfgen_script = config.generate_psf(True, False, True, True, temporary_psfname)
psfgen = PSFGen.PSFGen(psfgen_script, config.psfgen_binary)
psfgen.run()
system = loos.createSystem(temporary_psfname)
segments = []
for segment in config.segments:
s = loos.selectAtoms(system, 'segname == "' + segment.segname + '"')
if (len(s) == 0):
sys.stderr.write("Selection failed assembling system: segment %s doesn't exist\n" % (segment.segname))
sys.stderr.write("Exiting...\n")
sys.exit(0)
segments.append(s)
# copy the protein coordinates into the system
if (config.protein is not None):
# create AtomicGroup containing all protein segments in case
This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
import loos
import sys
filename = sys.argv[1]
system = loos.createSystem(filename)
system.centerAtOrigin()
# loop over atoms and reverse the sign of the x coordinate
for i in range(system.size()):
# 2 different ways to assign to coordinates
# SWIG won't let us do: coords.x() = new_x
# so we can do this:
#system[i].coords().x(-system[i].coords().x())
# or this:
system[i].coords()[0] *= -1.0
system.centerAtOrigin()
# convert to PDB and print out
pdb = loos.PDB_fromAtomicGroup(system)
This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
import loos
import sys
filename = sys.argv[1]
system = loos.createSystem(filename)
system.centerAtOrigin()
# loop over atoms and reverse the sign of the x coordinate
for i in range(system.size()):
# 2 different ways to assign to coordinates
# SWIG won't let us do: coords.x() = new_x
# so we can do this:
#system[i].coords().x(-system[i].coords().x())
# or this:
system[i].coords()[0] *= -1.0
system.centerAtOrigin()
# convert to PDB and print out
pdb = loos.PDB_fromAtomicGroup(system)
def alignWithBackbone(target, fiducial):
tbb = loos.selectAtoms(target, 'backbone')
fbb = loos.selectAtoms(fiducial, 'backbone')
M = tbb.superposition(fbb)
X = loos.XForm()
X.load(M)
target.applyTransform(X)
if len(sys.argv) != 6:
print('Usage- extract.py PSF model traj fiducial frameno')
sys.exit(-1)
hdr = ' '.join(sys.argv)
source_model = loos.createSystem(sys.argv[1])
model = loos.createSystem(sys.argv[2])
traj = loos.pyloos.Trajectory(sys.argv[3], model)
fiducial = loos.createSystem(sys.argv[4])
frameno = int(sys.argv[5])
frame = traj[frameno]
alignWithBackbone(frame, fiducial)
matchMetadata(frame, source_model)
pdb = loos.PDB.fromAtomicGroup(frame)
pdb.remarks().add(hdr)
print(str(pdb))
sys.exit(0)
)
args = parser.parse_args()
cmd_string = sys.argv[0]
for i in range(1, len(sys.argv)):
arg = sys.argv[i].replace('\n', '\\n')
cmd_string += " '" + arg + "'"
print('# ', cmd_string)
if args.tsne:
print("# Warning: tSNE is experimental, and the resulting distances")
print("# aren't meaningful.")
if args.perplexity and not args.tsne:
print("# Warning: perplexity option is ignored without --tsne")
# Create the model & read in the trajectories
model = loos.createSystem(args.model)
allTrajs = loos.pyloos.VirtualTrajectory(skip=args.skip, stride=args.stride)
if args.align:
allTrajs = loos.pyloos.AlignedVirtualTrajectory(alignwith=args.align,
skip=args.skip,
stride=args.stride)
for trajname in args.traj:
allTrajs.append(
loos.pyloos.Trajectory(trajname,
model,
subset=args.selection,
skip=args.allskip,
stride=args.allstride))
# Set up lists to hold the coordinates...
sys.exit(0)
system_filename = sys.argv[1]
traj_filename = sys.argv[2]
skip = int(sys.argv[3])
zmin = float(sys.argv[4])
zmax = float(sys.argv[5])
padding = float(sys.argv[6])
selection_strings = sys.argv[
7:] # first selection gives the all atoms to use
# in area calculations, all others tell you
# how to group the areas
print("# ", " ".join(sys.argv))
system = loos.createSystem(system_filename)
traj = loos.createTrajectory(traj_filename, system)
traj.readFrame(skip)
traj.updateGroupCoords(system)
slicer = ZSliceSelector(zmin, zmax)
selections = []
selections.append(loos.selectAtoms(system, selection_strings[0]))
for s in selection_strings[1:]:
selections.append(loos.selectAtoms(selections[0], s))
frame = skip
string = ""
for i in range(len(selections)):
((side <= 0) and (prev_side <= 0)))
if not match:
return False
prev_side = side
# test the closing line segment
side = test_side(p, self.coords(self.vertices[-1]),
self.coords(self.vertices[0]))
match = (((side >= 0) and (prev_side >= 0)) or
((side <= 0) and (prev_side <= 0)))
return match
if __name__ == '__main__':
ag = loos.createSystem("rhod_only.pdb")
slicer = ZSliceSelector(-3.0, 3.0)
ag = loos.selectAtoms(ag, 'name == "CA"')
ag_slice = slicer(ag)
hull = ConvexHull(ag_slice)
hull.generate_hull()
hull.generate_vertices()
i = 0
for v in hull.vertices:
c = hull.coords(v)
print(i, v, c.x(), c.y(), c.z())
i += 1
if not match: return False
prev_side = side
# test the closing line segment
side = test_side(p, self.coords(self.vertices[-1]),
self.coords(self.vertices[0]))
match = ( ((side >= 0) and (prev_side >=0) ) or
((side <= 0) and (prev_side <=0) ) )
return match
if __name__ == '__main__':
from numpy import random
ag = loos.createSystem("rhod_only.pdb")
slicer = ZSliceSelector(-3.0,3.0)
ag = loos.selectAtoms(ag, 'name == "CA"')
ag_slice = slicer(ag)
hull = ConvexHull(ag_slice)
hull.generate_hull()
#print hull.hull.simplices
#print hull.hull.neighbors
hull.generate_vertices()
#print hull.vertices
#print hull.num_atoms()
i = 0
try:
os.chmod(config.directory,
stat.S_IREAD|stat.S_IWRITE|stat.S_IEXEC)
except OSError:
sys.stderr.write(" Unable to change permissions on directory\n")
os.exit(-1)
# We need a model containing just the protein and lipid, so we'll
# make a psfgen script, run it, use the psf to make the AtomicGroup,
temporary_psfname = os.path.join(config.directory, config.psfname)
psfgen_script = config.generate_psf(True, False, True, True, temporary_psfname)
psfgen = PSFGen.PSFGen(psfgen_script, config.psfgen_binary)
psfgen.run()
system = loos.createSystem(temporary_psfname)
segments = []
for segment in config.segments:
s = loos.selectAtoms(system, 'segname == "' + segment.segname + '"')
if (len(s) == 0):
sys.stderr.write("Selection failed assembling system: segment %s doesn't exist\n" %
(segment.segname)
)
sys.stderr.write("Exiting...\n")
sys.exit(0)
segments.append(s)
# copy the protein coordinates into the system
type=float)
args = parser.parse_args()
box = loos.GCoord(args.box_size, args.box_size, args.box_size)
half_box = 0.5 * args.box_size
half_z = half_box
if args.zbox:
box.z(args.zbox)
half_z = 0.5 * args.zbox
if args.z_exclude:
args.z_exclude = abs(args.z_exclude)
if args.protein:
protein = loos.createSystem(args.protein)
else:
protein = loos.AtomicGroup()
protein.periodicBox(box)
library = LipidLibrary.LipidLibrary(args.library_location)
if not args.no_center:
protein.centerAtOrigin()
accepts = 0
trials = 0
while accepts < args.num_ligands:
trials += 1
#!/usr/bin/env python
import sys
import loos
import numpy as np
left = loos.createSystem(sys.argv[2])
right = loos.createSystem(sys.argv[3])
left_bb = loos.selectAtoms(left, 'backbone && resid < 129')
right_bb = loos.selectAtoms(right, 'backbone && resid < 129')
nl = len(left_bb)
nr = len(right_bb)
if nl != nr:
print('***ERROR: systems have wrong size')
print("Left has size {}, but right has size {}".format(nl, nr))
print("Left:")
print(str(loos.PDB.fromAtomicGroup(left_bb)))
print("Right:")
print(str(loos.PDB.fromAtomicGroup(right_bb)))
sys.exit(-1)
D = np.zeros( (nl*3, 1) )
k = 0
for i in range(nl):
d = left_bb[i].coords() - right_bb[i].coords()
D[k, 0] = d[0]
help="Step size for striding through trajectories",
type=int,
default=1)
parser.add_argument('--no_h',
help="Exclude hydrogens from calculation",
action='store_true')
parser.add_argument('--pca',
help="Perform PCA on the per-residue profiles",
action='store_true')
parser.add_argument('--fullhelp',
help="Print detailed description of all options",
action=FullHelp)
args = parser.parse_args()
system = loos.createSystem(args.system_file)
protein = loos.selectAtoms(system, args.protein_selection)
probe = loos.selectAtoms(system, args.probe_selection)
if args.no_h:
protein = loos.selectAtoms(protein, '!hydrogen')
probe = loos.selectAtoms(probe, '!hydrogen')
residues = protein.splitByResidue()
probes = probe.splitByMolecule()
frame_index = 0
traj = loos.pyloos.Trajectory(args.traj[0],
system,
skip=args.skip,
stride=args.stride)
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
from math import *
import sys
import loos
import loos.pyloos
## Command line arguments
model_name = sys.argv[1]
traj_name = sys.argv[2]
selection = sys.argv[3]
# Define the system first
mol = loos.createSystem(model_name)
traj = loos.pyloos.Trajectory(traj_name, mol, subset=selection)
for frame in traj:
# Compute the principal axes for the subset of atoms given above
axes = frame.principalAxes()
# Print out time, and the dot-product between
# The Z-axis (i.e. membrane normal) and the first principal axes
# of the subset of atoms
print traj.index(), "\t", axes[0].z()
parser.add_argument('-x', '--traj', help='Filename of trajectory or trajectories', nargs='+')
parser.add_argument('-k', '--skip', help='Skip this amount from the start of the trajectory', type=int, default=0)
parser.add_argument('-i', '--stride', help='Step through the trajectory by this many frames', type=int, default=1)
parser.add_argument('-s', '--selection', help='Use this selection for computing the native hbonds', default='all')
parser.add_argument('-n', '--nativeHBs', help='a filename to write PDB with just the native HBs used', type=str, default='')
parser.add_argument('-b', '--bondlength', help='maximum length for HB.', type=float, default = 3.0)
parser.add_argument('-o', '--outfile', help='file to write timeseries to.', type=str, default='')
parser.add_argument('-a', '--angle', help='maximum valid D-H-A angle.', type=float, default = 30.0)
args = parser.parse_args()
# define the model, subset to selection at this point
if args.coords:
model = loos.selectAtoms(loos.loadStructureWithCoords(args.model, args.coords), args.selection)
else:
model = loos.selectAtoms(loos.createSystem(args.model), args.selection)
# add connectivity, anything within 1.65 A (loos default) is assumed covalently bound
if model.hasCoords():
if not model.hasBonds():
model.findBonds()
else: # if model doesn't have any coordinates, this analysis is nonsensical; exit with error.
print('Error: You must supply a model structure with coordinates.')
exit(-1)
# make hb detector object
model_hbs = loos.HBondDetector(args.bondlength, args.angle, model)
parser.add_argument("helix_ranges",
nargs="+",
help="list of colon-delimited residue number ranges specifying where the helices are")
parser.add_argument("-d", "--directory",
help="Directory to create output files",
default=".")
parser.add_argument("-t", "--threshold",
default=7,
type=int,
help="Number of atoms inside for the chain to be considered inside")
args = parser.parse_args()
system = loos.createSystem(args.system_file)
traj = loos.createTrajectory(args.traj_file, system)
protein = loos.selectAtoms(system, args.protein_string)
output_directory = args.directory
if not os.path.exists(output_directory):
try:
os.mkdir(output_directory)
except OSError as inst:
print 'Error creating output directory %s : ' % output_directory
print inst
sys.exit(1)
if not os.access(output_directory, os.W_OK):
print "Error: no permission to write to output directory ", output_directory
sys.exit(1)
% config.directory)
sys.stderr.write("Will attempt to change permissions\n")
try:
os.chmod(config.directory,
stat.S_IREAD|stat.S_IWRITE|stat.S_IEXEC)
except OSError:
sys.stderr.write(" Unable to change permissions on directory\n")
os.exit(-1)
# We need a model containing just the protein and lipid, so we'll
# make a psfgen script, run it, use the psf to make the AtomicGroup,
temporary_psfname = os.path.join(config.directory, config.psfname)
psfgen_script = config.generate_psf(True, False, True, True, temporary_psfname)
psfgen = PSFGen.PSFGen(psfgen_script, config.psfgen_binary)
psfgen.run()
system = loos.createSystem(temporary_psfname)
# If the "protein" is actually a bunch of independent molecules (e.g. a bunch of peptides),
# we'll want to scale them in x & y to match the expanded box.
if config.protein is not None and config.protein.scale:
protein_molecules = config.protein.model.splitByMolecule()
for m in protein_molecules:
centroid = m.centroid()
scaled = box_scaling*centroid
diff = scaled - centroid
diff.z(0.0) # we only want to translate in the xy plane
m.translate(diff)
molecules = system.splitByMolecule()
segments = []
"A": ["N1", "N3", "N7", "O2'", "O3'", "O4'", "O5'", "OP1", "OP2"],
"C": ["N3", "O2", "O2'", "O3'", "O4'", "O5'", "OP1", "OP2"],
"G": ["N3", "N7", "O6", "O2'", "O3'", "O4'", "O5'", "OP1", "OP2"],
"U": ["O2", "O4", "O2'", "O3'", "O4'", "O5'", "OP1", "OP2"]
}
N_acceptor = {s: len(rna_acceptors[s]) for s in rna_acceptors}
# Compare to square of distance and angle cutoffs because sqrt() is expensive
# Compare to sin of angle cutoff because planar groups can have normal
# vectors that are close to parallel or close to anti-parallel
dist_cutoff_sq = numpy.square(args.distance_cutoff)
stack_cutoff_sq = numpy.square(args.stack_cutoff)
angle_cutoff_sq = numpy.square(numpy.sin(args.angle_cutoff / rad2deg))
# Create system model
system = loos.createSystem(args.input_pdb)
# Get arginine residues
arg_atoms = loos.selectAtoms(system, args.protein)
all_arg_residues = arg_atoms.splitByResidue()
arg_residues = [res for res in all_arg_residues if is_valid_arg_residue(res)]
N_arg = len(arg_residues)
# If there are no arginines, then exit
if N_arg == 0:
quit()
# Get RNA residues
rna_atoms = loos.selectAtoms(system, args.rna)
all_rna_residues = rna_atoms.splitByResidue()
rna_residues = [res for res in all_rna_residues if is_valid_rna_residue(res)]
"""
simple_model_calc.py : simple skeleton of a program that reads in a
structure, makes a selection, then loops over the atoms.
Alan Grossfield
University of Rochester Medical Center
"""
import loos
import sys
header = " ".join(sys.argv)
print("#", header)
# parse the command line arguments -- in a more complex example,
# you'd use the argparse module
model_filename = sys.argv[1]
selection_string = sys.argv[2]
# Create the system
model = loos.createSystem(model_filename)
# Select a subset of the system
subset = loos.selectAtoms(model, selection_string)
# Iterate over atoms and calculate something#
for atom in subset:
# do something
continue
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
from math import *
import sys
import loos
import loos.pyloos
## Command line arguments
model_name = sys.argv[1]
traj_name = sys.argv[2]
selection = sys.argv[3]
# Define the system first
mol = loos.createSystem(model_name)
traj = loos.pyloos.Trajectory(traj_name, mol, subset=selection)
for frame in traj:
# Compute the principal axes for the subset of atoms given above
axes = frame.principalAxes()
# Print out time, and the dot-product between
# The Z-axis (i.e. membrane normal) and the first principal axes
# of the subset of atoms
print(traj.index(), "\t", axes[0].z())
import loos.pyloos
import argparse
import sys
parser = argparse.ArgumentParser()
parser.add_argument('model', help='Structure to use')
parser.add_argument('traj', help='Trajectory')
parser.add_argument('align', help='Selection to use for aligning')
parser.add_argument('--skip', help='Skip this amount from the start of the trajectory', type=int, default=0)
parser.add_argument('--stride', help='Step through the trajectory by this many frames', type=int, default=1)
parser.add_argument('--rmsd', help='Use this selection for computing the RMSD', default='all')
args = parser.parse_args()
# Create the model & read in the trajectory
model = loos.createSystem(args.model)
traj = loos.pyloos.Trajectory(args.traj, model, skip = args.skip, stride = args.stride)
patraj = loos.pyloos.AlignedVirtualTrajectory(traj, alignwith = args.align)
patraj.setSubset(args.rmsd)
average = loos.pyloos.averageStructure(traj)
avg_rmsd = 0
for structure in patraj:
rmsd = average.rmsd(structure)
avg_rmsd = avg_rmsd + rmsd
print "%d\t%f" % (patraj.index(), rmsd)
print "# Average rmsd = %f" % (avg_rmsd/len(patraj))
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
import loos
import sys
if len(sys.argv) == 1 or sys.argv[1] == '-h':
print 'Usage- renum-by-mol.py model [selection]'
sys.exit(0)
model = loos.createSystem(sys.argv[1])
if len(sys.argv) > 2:
model = loos.selectAtoms(model, sys.argv[2])
model.pruneBonds()
if model.hasBonds():
molecules = model.splitByMolecule()
else:
molecules = model.splitByUniqSegid()
for molecule in molecules:
residues = molecule.splitByResidue()
resid = 1
for residue in residues:
for atom in residue:
for r in self.regions:
for r2 in other.regions:
if r.is_neighbor(r2):
return True
return False
def print_indices(self):
for r in self.regions:
r.print_indices()
print
if __name__ == '__main__':
import sys
structure = loos.createSystem("trj_1.pdb")
#structure = loos.createSystem("example.pdb")
#structure = loos.createSystem("b2ar.pdb")
#box = loos.GCoord(55., 77, 100)
#box = loos.GCoord(55., 77, 100)
phos = loos.selectAtoms(structure, 'name == "P"')
upper = loos.AtomicGroup()
for p in phos:
if p.coords().z() > 0:
upper.append(p)
upper.periodicBox(structure.periodicBox())
print upper.isPeriodic()
"""
slice = loos.AtomicGroup()
#!/bin/env python
import loos
import sys
model = loos.createSystem(sys.argv[1])
for atom in model:
atom.bfactor(0.0)
subset = loos.selectAtoms(model, sys.argv[2])
for atom in subset:
atom.bfactor(1.0)
pdb = loos.PDB.fromAtomicGroup(model)
print str(pdb)