def mask(mrc, top, conf, enrgmd_server, no_cut_box, keep_full):
"""mask mrc map to fitted atomic model.\n
Used to:\n
* make minimum box by keeping full data (for manual fit prep)\n
* create mask for atomic model
MRC is the name of the cryo EM volumetric data file [.mrc]\n
TOP is the name of the namd topology file [.top]\n
CONF is the name of the namd configuration file [.pdb, .coor]\n
"""
file_types = {
mrc: [".mrc"],
top: [".psf"],
conf: [".pdb", ".coor"],
}
for file, types in file_types.items():
_check_path(file, types)
model = AtomicModelFit(conf=conf,
top=top,
mrc=mrc,
generated_with_mrdna=enrgmd_server)
universe = model.get_universe()
mrc_masked = mrc.with_name(f"{mrc.stem}-masked.mrc")
write_mrc_from_atoms(
path=mrc,
atoms=universe.atoms,
path_out=mrc_masked,
context=40.0,
cut_box=no_cut_box,
keep_data=keep_full,
)
def pdb2cif(pdb, remove_h, is_snupi, flip_fields):
"""generate atomic model in mmCIF format from namd PDB
PDB is the name of the namd configuration file [.pdb]\n
"""
_check_path(pdb, [".pdb"])
structure = Structure(path=pdb,
remove_H=remove_h,
is_snupi=is_snupi,
flip_fields=flip_fields)
structure.parse_pdb()
# TODO-low: ask for additional info (name, author, etc)
output_name = pdb.with_suffix(".cif")
structure.write_cif(output_name)
def center_on_map(mrc, top, conf):
"""recenter atomic model center-of-mass on mrc cryo map center and write new .pdb.
MRC is the name of the cryo EM volumetric data file [.mrc]\n
TOP is the name of the namd topology file [.psf]\n
CONF is the name of the namd configuration, docked to the map [.pdb, .coor]\n
"""
file_types = {
mrc: [".mrc"],
top: [".psf"],
conf: [".pdb", ".coor"],
}
for file, types in file_types.items():
_check_path(file, types)
conf_docked = conf.with_name(f"{conf.stem}-docked.pdb")
copyfile(conf, conf_docked)
mrc_shift = get_mrc_center(mrc)
recenter_conf(top=top, conf=conf_docked, to_position=mrc_shift)
def mrdna(cadnano, mrc, sequence, gpu, prefix, multidomain, coarse_steps,
bond_cutoff, no_prep):
"""mrDNA simulation of CADNANO design file with custom settings.\n
followed by preperation of files for "dnaFit fit"\n
Note1: includes centering of model and masking of map\n
Note2: map and model are not rigid body docked "dnaFit vmd_info"
CADNANO is the name of the design file [.json]\n
SEQUENCE is the scaffold strand sequence file [.txt, .seq]\n
MRC is the name of the cryo EM volumetric data file [.mrc]\n
"""
file_types = {
cadnano: [".json"],
mrc: [".mrc"],
sequence: [".txt", ".seq"],
}
for file, types in file_types.items():
_check_path(file, types)
prefix = cadnano.stem if prefix is None else prefix
run_mrdna(
cad_file=cadnano,
seq_file=sequence,
prefix=prefix,
gpu=gpu,
multidomain=multidomain,
coarse_steps=coarse_steps,
bond_cutoff=bond_cutoff,
)
if not no_prep:
prep_cascaded_fitting(prefix,
cadnano,
sequence,
mrc,
multidomain=multidomain)
logger.info(
"Config file is moved to center of mass with mrc map but still \
has to be rotated before fitting. execute vmd_info for additional info"
)
def prep(cadnano, mrc, sequence, prefix, multidomain):
"""prepare mrDNA results for fitting "dnaFit fit".\n
Note1: includes centering of model and masking of map\n
Note2: map and model are not rigid body docked "dnaFit vmd_info"
CADNANO is the name of the design file [.json]\n
SEQUENCE is the scaffold strand sequence file [.txt, .seq]\n
MRC is the name of the cryo EM volumetric data file [.mrc]\n
"""
file_types = {
cadnano: [".json"],
mrc: [".mrc"],
sequence: [".txt", ".seq"],
}
for file, types in file_types.items():
_check_path(file, types)
prefix = cadnano.stem if prefix is None else prefix
prep_cascaded_fitting(prefix,
cadnano,
sequence,
mrc,
multidomain=multidomain)
def link(cadnano, sequence, top, conf, enrgmd_server):
"""links structural information of the CADNANO designfile to
fitted atomic model files TOP, CONF.\n
Note: linkage information ist stored in human readable csv format
CADNANO is the name of the design file [.json]\n
SEQUENCE is the scaffold strand sequence file [.txt, .seq]\n
TOP is the name of the namd topology file [.psf]\n
CONF is the name of the namd configuration file [.pdb, .coor]\n
"""
file_types = {
cadnano: [".json"],
sequence: [".txt", ".seq"],
top: [".psf"],
conf: [".pdb", ".coor"],
}
for file, types in file_types.items():
_check_path(file, types)
model = AtomicModelFit(conf=conf,
top=top,
mrc=None,
generated_with_mrdna=(not enrgmd_server))
model.write_linkage(json=cadnano, seq=sequence)
def fit(
cadnano,
sequence,
mrc,
top,
conf,
exb,
prefix,
timesteps,
resolution,
sr_fitting,
include_ss,
grid_pdb,
):
"""Cascaded mrDNA-driven MD flexible fitting (shrink wrap fitting) to MRC cryo data.\n
creates dnaFit folder. This folder will contain final results prefix-last.cif\n
Note1: run after mrDNA ("dnaFit mrdna") and manual rigid-body-docking ("dnaFit vmd_info")\n
Note2: SR-fitting (Short Range). Recommended for maps with resolution >> 10 Angstrom
CADNANO is the name of the design file [.json]\n
SEQUENCE is the scaffold strand sequence file [.txt, .seq]\n
MRC is the name of the cryo EM volumetric data file [.mrc]\n
TOP is the name of the namd topology file [.psf]\n
CONF is the name of the namd configuration file, docked to map (VMD) [.pdb, .coor]\n
EXB is the name of the enrgMD extrabond file (expect mrDNA > march 2021) [.exb]
"""
file_types = {
cadnano: [".json"],
sequence: [".seq", ".txt"],
mrc: [".mrc"],
top: [".psf"],
conf: [".pdb", ".coor"],
exb: [".exb"],
}
for file, types in file_types.items():
_check_path(file, types)
prefix = cadnano.stem if prefix is None else prefix
# TODO-low: gpu support
logger.info("GPU currently not supported for fitting. using CPU only.")
# create duplicates of input files in dnaFit folder
Path("dnaFit").mkdir(parents=True, exist_ok=True)
for file, types in file_types.items():
copyfile(file, f"./dnaFit/{prefix}{types[0]}")
home_directory = Path.cwd()
try:
os.chdir("dnaFit")
logger.debug("changing directory to: %s", Path.cwd())
# use duplicates instead of input
mrc = Path(f"./{prefix}.mrc").resolve()
cadnano = Path(f"./{prefix}.json").resolve()
sequence = Path(f"./{prefix}.seq").resolve()
top = Path(f"./{prefix}.psf").resolve()
conf = Path(f"./{prefix}.pdb").resolve()
exb = Path(f"./{prefix}.exb").resolve()
if not Path("./charmm36.nbfix").exists():
copytree(get_resource("charmm36.nbfix"), "./charmm36.nbfix")
cascade = Cascade(conf=conf,
top=top,
mrc=mrc,
exb=exb,
json=cadnano,
seq=sequence,
grid_pdb=grid_pdb)
model = cascade.run_cascaded_fitting(
base_time_steps=timesteps,
resolution=resolution,
is_sr=sr_fitting,
include_ss=include_ss,
)
model.write_linkage(cadnano, sequence)
model.write_output(dest=Path(home_directory),
write_mmcif=True,
mask_mrc=True)
finally:
os.chdir(home_directory)
logger.debug("changing directory to: %s", Path.cwd())