def draw_ENM(structure_filepath, script_filepath, structure_name="CAonly", output_dir='.', view=None):
""" Draws elastic network model of a structure and saves image.
"""
cmd.delete('all')
cmd.load(structure_filepath, "CAonly")
cmd.run(script_filepath)
# Set name
if structure_name == "CAonly":
pass
else:
cmd.set_name("CAonly", structure_name)
# Set view
if view == None:
cmd.orient()
else:
cmd.set_view(view)
cmd.viewport(width=1200, height=1200)
cmd.zoom(complete=1)
png_filepath = os.path.join(output_dir, structure_name) + ".png"
pse_filepath = os.path.join(output_dir, structure_name) + ".pse"
cmd.save(pse_filepath)
cmd.set('ray_opaque_background', 0)
cmd.png(png_filepath, width=1200, height=1200, ray=1)
return (pse_filepath, png_filepath)
def tview(pdbid: str):
species = str(int(log.get_struct(pdbid)['taxid'].values[0]))
l22chain = log.get_struct(pdbid).uL22.values[0]
l4chain = log.get_struct(pdbid).uL4.values[0]
l22_res = int(log.get_struct(pdbid).constrictionResidueL22_id.values[0])
l4_res = int(log.get_struct(pdbid).constrictionResidueL4_id.values[0])
# cmd.delete('all')
pdbid = pdbid.upper()
TUNNELS = os.getenv("TUNNELS")
SCOOP_RADIUS = os.getenv("SCOOP_RADIUS")
TUNNEL_SCRIPT = os.path.join(TUNNELS, species, pdbid, 'pymol',
'complex.py')
inputstructpath = os.path.join(
TUNNELS, species, pdbid, '{}_{}Ascoop.pdb'.format(pdbid, SCOOP_RADIUS))
csvpaths = os.path.join(
TUNNELS,
species,
pdbid,
'csv',
)
cmd.load(inputstructpath)
cmd.color('gray', 'all')
if not os.path.exists(TUNNEL_SCRIPT):
print("TUNNEL SCRIPT NOT FOUND.")
return
cmd.run(TUNNEL_SCRIPT)
cmd.hide('everything', 'Tunnels')
cmd.show('mesh', 'Tunnels')
# tunnels = os.listdir(csvpaths)
# tunnumbers = map(lambda x: re.findall(r'\d+',x)[0], tunnels)
# [cmd.delete(f'Tunnel{tunN}') if tunN not in choices else None for tunN in tunnumbers]
# paint_tunnel(pdbid)
sele_ptc(9606)
# cmd.select('PTC', 'resi 2055 or resi 2056 or resi 2451 or resi 2452 or resi 2507 or resi 2506')
# cmd.create('PTC',"PTC")
# cmd.color('blue', 'PTC')
cmd.select(
'ConstrictionSite', 'c. {} and resi {} or c. {} and resi {}'.format(
l22chain, l22_res, l4chain, l4_res))
cmd.create('ConstrictionSite', "ConstrictionSite")
cmd.show('everything', 'ConstrictionSite')
cmd.color('magenta', 'ConstrictionSite')
cmd.reset()
def show_chain_in_PDB(entry):
PDB = entry[:4]
chain = entry[-1:]
cmd.reinitialize('everything')
cmd.set("bg_rgb", "white")
cmd.run("%s/B_strands_%s.py" % (PyMOL_script_dir, PDB))
cmd.show("cartoon", "all")
def remred():
pdb_list = glob.glob("*.pdb")
for pdb in pdb_list:
cmd.load(pdb)
cmd.run("/usr/local/bin/all_against_all.py")
cmd.do(
"align_all_to_all(selection='all',cutoff=0,cycles=0,full_matrix=1,method='align')"
)
def show_chain_in_PDB(entry):
PDB = entry[:4]
chain = entry[-1:]
cmd.reinitialize('everything')
cmd.do('@~/.pymolrc')
cmd.set("bg_rgb", "white")
cmd.run("%s/strands_%s.py" % (PyMOL_script_dir, PDB))
cmd.show("cartoon", "all")
cmd.set("cartoon_transparency", .85, PDB)
cmd.set("cartoon_transparency", 0.05, "%s_barrel" % PDB)
def images(B):
#cmd.do("cd {}".format(B))
pdb_list = glob.glob("*.pdb")
for pdb in pdb_list:
cmd.load(pdb)
cmd.run("/usr/local/bin/all_against_all.py")
cmd.select("all_ps", "name PS1+PS2+PS3")
cmd.do(
"align_all_to_all(selection='all_ps',cutoff=0,cycles=0,full_matrix=1,method='align')"
)
cmd.remove("het")
cmd.remove("all_ps")
cmd.show("sticks", "all")
cmd.hide("sticks", "all_ps")
cmd.hide("sphere", "all_ps")
cmd.set("sphere_scale", 0.30, "all_ps")
cmd.orient("all")
cmd.multisave("{}.pdb".format(B))
cmd.set("ray_opaque_background", 0)
cmd.ray(2400)
cmd.set("antialias", 1)
cmd.png("{}.png".format(B), 1200, 1200, 300)
cmd.quit()
# Update cached modules
for module, (url, hash_remote) in modules.items():
module_path = Path(cachedir / module)
try:
assert module_path.exists()
# Change this to test for changes (/w file hashes)
with open(module_path, 'rb') as file_to_hash:
b_file = file_to_hash.read()
# Apparently git uses this weird way of hashing files which includes
# "blob {length of file}\0" (\0 being NULL)
b_blob = b'blob ' + bytearray(str(len(b_file)), 'utf-8') + b'\0'
hash_local = sha(b_blob + b_file).hexdigest()
print(f"Reading {module} hash")
print(f"Remote hash {hash_remote}")
print(f"Local hash {hash_local}")
assert hash_local == hash_remote
print(f"{module} is up to date")
except AssertionError:
print(f"Caching {module}")
with open(module_path, 'wb') as fout:
reponse = requests.get(url)
fout.write(reponse.content)
# Cache first, load later..
for module in modules.keys():
# Finally load the module and inform the user
module_path = Path(cachedir / module)
cmd.run(str(module_path.absolute()))
print(f"Loaded {module}")
def main():
"""
parses arguments user input and initializes stir based on user input
provides help for usage
"""
parser = HelpfulParser(
prog='stir',
formatter_class=argparse.RawDescriptionHelpFormatter,
add_help=False,
description=
'A python wrapper for pymol and several helpful tools and scripts\n'
'mainly focused on martini coarse-grained trajectories.\n\n'
'The accepted file formats are:\n'
'- structure: gro, pdb\n'
'- scene: pse\n'
'- topology: top, itp, tpr\n'
'- trajectory: xtc',
epilog='Examples:\n'
'\tstir system.gro topol.top md.xtc\n'
'\tstir system.gro --keep-water -r supercell 3,3,1\n'
'\tstir system.gro topol.tpr --pymol -qi myscript.pml',
)
files_group = parser.add_argument_group('file arguments')
files_group.add_argument(
dest='files',
action=FilesAction,
nargs='+',
help=
'a structure or scene file is required. Topology files allow for topology '
'reconstruction. Trajectory files are also accepted. Order does not matter'
)
opt_group = parser.add_argument_group('optional stir arguments')
opt_group.add_argument(
'--keep-water',
dest='keepwater',
action='store_true',
help='do not delete waters from the system. Decreases performance')
opt_group.add_argument('-g',
'--gmx',
dest='gmx',
type=str,
default=None,
help='path to the gromacs executable')
opt_group.add_argument(
'-r',
'--run-tool',
dest='runtool',
metavar='token',
type=str,
default=[],
nargs='*',
action='append',
help='a command to be run after loading. (e.g.: supercell 3,3,1). '
'Can be specified multiple times')
gar_group = parser.add_argument_group('optional garnish arguments')
gar_group.add_argument(
'--no-fix',
dest='nofix',
action='store_false', # store false!
help='disable the atom-id-based fix for the elastic network in garnish '
'(use if your system has messy, non-sequential numbering.')
gar_group.add_argument(
'--no-prot',
dest='noprot',
action='store_false', # store false!
help=
'do not guess protein backbone beads (use if normal guessing makes mistakes'
)
gar_group.add_argument(
'--no-garnish',
dest='nogarnish',
action='store_true',
help='do not run garnish on the system (use with atomistic systems)')
traj_group = parser.add_argument_group('optional trajectory arguments')
traj_group.add_argument(
'-s',
'--skip',
dest='skip',
metavar='n',
type=int,
default=1,
help=
'load trajectory frames skipping this interval. Useful to reduce memory load'
)
traj_group.add_argument(
'-b',
'--begin',
dest='begin',
metavar='frame',
type=int,
default=1,
help=
'first frame to load from trajectory. Only acts on first trajectory file'
)
traj_group.add_argument(
'-e',
'--end',
dest='end',
metavar='frame',
type=int,
default=-1,
help=
'last frame to load from trajectory. Only acts on last trajectory file'
)
traj_group.add_argument('-m',
'--max',
dest='max',
metavar='n',
type=int,
default=0,
help='maximum number of frames to load')
more_group = parser.add_argument_group('pymol arguments')
more_group.add_argument(
'-p',
'--pymol',
dest='pymol',
default=[],
nargs=argparse.REMAINDER,
help='all following arguments will be passed directly to pymol. '
'Accepts options and .pml scripts')
help_group = parser.add_argument_group('info')
help_group.add_argument('-h',
'--help',
action='help',
help='show this help message and exit')
help_group.add_argument('-V',
'--version',
action='version',
version=f'%(prog)s {__version__}')
args = parser.parse_args()
struct = args.files['struct']
scene = args.files['scene']
topol = args.files['topol']
traj = args.files['traj']
# make sure we only have 1 structure OR scene file and at most one topol
if not bool(struct) ^ bool(scene): # not xor
parser.error('you must provide either a structure or scene file')
elif len(struct) > 1 or len(scene) > 1 or len(topol) > 1:
parser.error(
'only one system can be opened at once... for now!') # TODO?
# sanitize trajectory args
if args.skip < 1:
args.skip = 1
if args.begin < 1:
args.begin = 1
if args.end < 1 and args.end != -1:
args.end = 1
if args.max < 0:
args.max = 0
pymol_args = []
scripts = []
for arg in args.pymol:
p = clean_path(arg)
if p.suffix in ('.pml', '.py'):
if not p.is_file():
raise FileNotFoundError(f'{p} does not exist')
scripts.append(str(p))
else:
pymol_args.append(str(p))
# initialize pymol
__main__.pymol_argv = ['pymol'] + pymol_args
pymol.finish_launching()
# run pymolrc and load all the stir tools
config.pymolrc()
view.load()
supercell.load()
render.load()
edit.load()
# load garnish
garnish.extend_garnish()
cmd.sync()
# open the structure
if scene:
cmd.load(scene[0])
elif struct:
cmd.load(struct[0])
cmd.sync()
# get the loaded object's name, so we can load the traj into it as new states
sys_obj = cmd.get_object_list()[0]
# load trajectories, leaving out waters if not asked for
if traj:
skip = args.skip
max_states = args.max
selection = 'all'
if not args.keepwater:
selection = 'not resname W+WN'
config.trajectory()
for i, t in enumerate(traj):
cmd.sync()
start = 1
if i == 0:
start = args.begin
stop = -1
if i == len(traj) - 1:
stop = args.end
if args.max != 0:
max_states = args.max - cmd.count_states()
if max_states < 1:
break
cmd.load_traj(t,
sys_obj,
interval=skip,
start=start,
stop=stop,
max=max_states,
selection=selection)
cmd.sync()
# also, delete waters from first frame
if not args.keepwater:
cmd.remove('resname W+WN')
cmd.sync()
if not args.nogarnish:
# sanitize topol
if not topol:
topol = [None]
garnish.garnish(file=topol[0],
gmx=args.gmx,
fix_elastics=args.nofix,
guess_prot=args.noprot,
show=False)
cmd.sync()
# load garnish data into pymol
view.nicesele()
cmd.sync()
view.set_vdw()
cmd.sync()
view.set_chains()
cmd.sync()
# run nice with the default settings, or with balls if no topol was given
view.nice()
cmd.sync()
# finally run user-requested tools
for tool in args.runtool:
command = ' '.join(tool)
cmd.do(command)
cmd.sync()
# and user-provided scripts
for scr in scripts:
cmd.run(scr)
cmd.sync()
# add command for simple help function
cmd.extend('stir', stir_help)
# print some help after everything is loaded
stir_help()
cmd.sync()
def run(what):
return cmd.run(what)
from pymol import cmd
cmd.reinitialize()
cmd.run('/Users/joy/src/elfin/src/PyMolUtils/LineUtils.py')
cmd.load('/Users/joy/src/elfin/src/Python/Greedy.py')
print '\n\n\n\n\n\n\n'
print 'Loaded'
# For quick testing
# main(['/Users/joy/src/elfin/bm/l10/6vjex8d.json'])
# main(['/Users/joy/src/elfin/bm/l10/kmb0yfh.json'])
# main(['/Users/joy/src/elfin/bm/fun/M.csv'])
main(['/Users/joy/src/elfin/bm/fun/S.csv', 's=2.50'])
def reload():
"""Reload PyMOL4RNA.py"""
cmd.run(RNA_TOOLS_PATH + "/rna_tools/tools/PyMOL4RNA/PyMOL4RNA.py")
def reload():
"""Reload PyMOL4RNA.py"""
cmd.run(RNA_PDB_TOOLS + "/rna_tools/utils/PyMOL4RNA/PyMOL4RNA.py")
def main():
from argparse import ArgumentParser
from sys import argv
parser = ArgumentParser(
description="Open and display a WORDOM PSN and cross correlation " +
"analysis as an correlated interaction Allosteric " +
"Communication Graph (ciACG) in PyMOL.")
parser.add_argument(
"-c",
nargs='*',
default=[0.0],
metavar="float",
help="Cutoff to use for showing connections in graph, provide" +
" white space separated list for a series of cutoffs."
", default=0.0")
parser.add_argument("-pdb",
nargs=1,
metavar="PDBfile",
help="PDB file to draw")
parser.add_argument("-plot",
action="store_true",
default=False,
help="Plot ciACG value distribution")
parser.add_argument("-acg",
nargs=1,
metavar="ACGfile",
help="ACG file to read (.frm)")
parser.add_argument("-rmp",
nargs=1,
metavar="RMPfile",
help="ResidueMap file to read (.rmp)")
parser.add_argument(
"-pml",
nargs='*',
metavar="PMLfile",
default=None,
help="PyMOL scripts to run with cmd.run(), before coloring of bonds.")
parser.add_argument("-cnt",
nargs=1,
metavar="COUNTfile",
default=[None],
help="Counts output file to write (.frm)")
parser.add_argument("-frq",
nargs=1,
metavar="FREQfile",
default=[None],
help="Normed frequency output file to write (.frm)")
parser.add_argument(
"-prc",
nargs=1,
metavar="PROCESSfile",
default=[None],
help=
"Processed frames and endpoints output file to write (.pyo), a tuple of Counter()s - (frames, endpoints)."
)
parser.add_argument("-frames",
nargs='*',
metavar="FRAMEfile",
help="WORDOM .frame files to process")
arguments = parser.parse_args(argv[1:])
# Finish pymol launch
pymol.finish_launching(['pymol'])
# Set variables here
pdb = arguments.pdb[0]
cutoffs = [float(c) for c in arguments.c]
acg = arguments.acg[0]
rmp = arguments.rmp[0]
pml = arguments.pml
cnt = arguments.cnt[0]
frq = arguments.frq[0]
prc = arguments.prc[0]
frames = arguments.frames
with open(acg, 'rb') as infile:
cigraph_table = pickle.load(infile)
with open(rmp, 'rb') as infile:
residuemap = pickle.load(infile)
counts, files_processed, frames_processed, pathways_processed = process_framefiles(
frames, residuemap)
print("{} pathways found in {} frames from {} files".format(
len(pathways_processed), len(frames_processed), len(files_processed)))
# Save counts
dump_pyobject(counts, cnt, suffix="frm")
# Save processing Counter()s
dump_pyobject((frames_processed, pathways_processed), prc, suffix="pyo")
# Normalize
frequencies = normalize_pathway_counts_wrt_no_frames_and_endpoints(
counts, frames_processed, pathways_processed)
# Save frequencies
dump_pyobject(frequencies, frq, suffix="frm")
# Align tables
frequencies_aligned, cigraph_table_aligned = align_dataframes(
frequencies, cigraph_table, fill_value=0.0)
pathways = matrix_from_pandas_dataframe(frequencies_aligned)
# Draw the loaded ciACG
cigraph = matrix_from_pandas_dataframe(cigraph_table_aligned)
levels = draw_ciacg(cigraph, residuemap, pdb, cutoffs)
# Run scripts prior to coloring of bonds
if pml is not None:
for script in pml:
cmd.run(script)
# Highlight the pathways
rgb_matrix, colored, colors = highlight_pathways(pathways, residuemap)