def load_chimerax(filename):
"""
Load a UCSF ChimeraX file written by SwissDock
Parameters
----------
filename : str
chimerax file (XML file with URL of target and ligands cluster)
"""
# UCSF Chimera Web Data Format
# www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.html
docked = get_docked()
print(f" PyViewDock: Loading \"{filename}\"")
# read ChimeraX file as XML
try:
chimerax_xml = ET.parse(filename).getroot()
target_url = chimerax_xml.find('web_files').find('file').get('loc')
commands = chimerax_xml.find('commands').find('py_cmd').text
cluster_url = re.findall('"(http[^"]+pdb)"', commands)[0]
target_filename = target_url.split('/')[-1]
cluster_filename = cluster_url.split('/')[-1]
if not all(
[target_url, cluster_url, target_filename, cluster_filename]):
raise ValueError
except FileNotFoundError:
print(" PyViewDock: Failed reading 'chimerax' file. File not found.")
except:
print(" PyViewDock: Failed reading 'chimerax' file. Invalid format.")
else:
# fetch files from server
try:
target_pdb = urlopen(target_url).read().decode('utf-8')
cluster_pdb = urlopen(cluster_url).readlines()
cluster_pdb = [i.decode('utf-8') for i in cluster_pdb]
cmd.read_pdbstr(target_pdb, 'target')
docked.load_dock4(cluster_pdb, 'cluster', 0)
except HTTPError:
print(
" PyViewDock: Failed reading 'chimerax' file. Bad server response. Too old?"
)
# find local files that match names in .chimerax directory
chimerax_directory = os.path.dirname(os.path.realpath(filename))
target_file = os.path.join(chimerax_directory, target_filename)
cluster_file = os.path.join(chimerax_directory, cluster_filename)
if os.path.isfile(target_file) and os.path.isfile(target_file):
print(
f" PyViewDock: Files found locally ({target_filename}, {cluster_filename}). Loading..."
)
importing.load(target_file)
load_dock4(cluster_file)
def load_ext(filename,
object='',
state=0,
format='',
finish=1,
discrete=-1,
quiet=1,
multiplex=None,
zoom=-1,
partial=0,
mimic=1,
object_props=None,
atom_props=None,
*,
_self=cmd):
"""
Wrapper to load function with extended funtionality
Formats
-------
.ff
fDynamo's force field file
.crd
fDynamo's coordinates file
.dynn
DYNAMON options/selection file
.*
default supported by PyMOL
"""
if not format:
format = os.path.basename(filename).rpartition('.')[-1]
# fDynamo's force field
if format.lower() == "ff":
load_ff(filename)
# DYNAMON dynn options/selection
elif format.lower() == "dynn":
load_dynn(filename)
# fDynamo's crd coordinates
elif format.lower() == "crd":
load_crd(filename, object)
# original load function
else:
importing.load(filename, object, state, format, finish, discrete,
quiet, multiplex, zoom, partial)
def load_ext(filename,
object='',
state=0,
format='',
finish=1,
discrete=-1,
quiet=1,
multiplex=None,
zoom=-1,
partial=0,
mimic=1,
object_props=None,
atom_props=None,
*,
_self=cmd):
"""
Wrapper to load function with extended funtionality
Formats
-------
.chimerax
XML file with URL of target and ligands cluster
.ene / .eneRST
energy table with reference numbers of structures from pyDock
"""
if not format:
file_dot_separated = os.path.basename(filename).rpartition('.')
name = "".join(file_dot_separated[:-2])
format = file_dot_separated[-1]
# Chimera X
if format.lower() == "chimerax":
load_chimerax(filename)
# pyDock
elif format.lower() in ("ene", "enerst"):
load_pydock(filename, name)
# original load function
else:
importing.load(filename, object, state, format, finish, discrete,
quiet, multiplex, zoom, partial)
def load_xyz(self, filename, object):
"""
Load a group of structures as an object from .xyz
with multiple states and docking information
Parameters
----------
filename : str
coordinates file (.xyz)
object : str
name to be include the new object
"""
self.__init__()
# read comments from xyz file
with open(filename, 'rt') as f:
xyz_file = f.readlines()
nline = 0
comments = []
while nline < len(xyz_file):
natoms = int(xyz_file[nline])
comments.append(xyz_file[nline + 1].strip())
nline += natoms + 2
# process comments
# TODO: broader processing and pattern recognition
if all(isinstance(i, float) for i in comments):
comments = [float(i) for i in comments]
# add entries to data class
for n, comm in enumerate(comments):
remarks = {'value': comm}
self.entries.append({
'internal': {
'object': object,
'state': n + 1
},
'remarks': remarks
})
# load structures into PyMOL
importing.load(filename, object=object, format='xyz', quiet=1)
def load_pydock(self, filename, object, max_n):
"""
Load a PyDock's group of structures as an object
with multiple states and read the docking information
Parameters
----------
filename : str
energy resume file (.ene / .eneRST)
object : str
basename to include the new objects (_rec / _lig)
max_n : int
maximum number of structures to load
"""
self.__init__()
rec_obj = object + "_rec"
lig_obj = object + "_lig"
basename = os.path.basename(filename).split('.')[0]
directory = os.path.dirname(os.path.realpath(filename))
# get list of matching pdb files
pdb_files = glob.glob(os.path.join(directory, "*.pdb"))
# find receptor and ligand files
try:
receptor_file = [i for i in pdb_files if "_rec.pdb" in i][0]
ligand_file = [i for i in pdb_files if "_lig.pdb" in i][0]
except:
print(
" PyViewDock: Failed loading pyDock file. Missing '_rec.pdb' or '_lig.pdb'."
)
return
# read energy file
with open(filename, "rt") as f:
energy_file = [
line.strip() for line in f.readlines()
if line.strip() and not line.startswith("----")
]
header = energy_file.pop(0).split()
for line in energy_file:
remarks = {
h: (int(v) if h in {'Conf', 'RANK'} else float(v))
for h, v in zip(header, line.split())
}
self.entries.append({
'remarks': deepcopy(remarks),
'internal': deepcopy(self.internal_empty)
})
# load receptor
importing.load(receptor_file, rec_obj)
# load ligands
loaded = []
not_found_warning = False
for n, entry in enumerate(self.entries):
if n + 1 > max_n: break
conf_num = entry['remarks']['Conf']
try:
conf_file = [i for i in pdb_files
if f"_{conf_num}.pdb" in i][0]
except IndexError:
not_found_warning = True
continue
else:
loaded.append(n)
entry['internal']['object'] = lig_obj
entry['internal']['state'] = len(loaded)
importing.load(conf_file, lig_obj, 0)
if not_found_warning:
print(
" PyViewDock: WARNING: Some ligands defined on the energy file could not been found and loaded."
)
# delete entries which pdb has not been found
for i in reversed(range(self.n_entries)):
if i not in loaded: del self.entries[i]
# remove atoms of receptor from ligand
cmd.remove(f"{lig_obj} in {rec_obj}")