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add resolution argument and print not provided #2

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add resolution argument and print not provided #2

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19 changes: 14 additions & 5 deletions scripts/cryo-EM_preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -101,13 +101,15 @@ def write_data_to_mrc(filename, data, mrc):
parser.add_argument('--zone_PDB', type=str, help='reference PDB for map zoning')
parser.add_argument('--zone_sel', type=str, help='selection for map zoning')
parser.add_argument('--double', default=False, action='store_true')
parser.add_argument('--resolution', type=float, help='Resolution of the input map/PDB in Ångstroms (otherwise take from PDB header).'
)

args = parser.parse_args()

#### INPUT
# input MRC file
MRC_=vars(args)["map"]
# thresold
# threshold
THRES_=vars(args)["threshold"]
# half side of cubic box to calculate correlation in Angstrom
# typically 2 Ang
Expand Down Expand Up @@ -177,15 +179,22 @@ def write_data_to_mrc(filename, data, mrc):
# indices for slicing full matrix
imin = torch.max(torch.floor((xmin-x0)/dx).int(), torch.tensor([0,0,0]).to(torch.int).to(device_))
imax = torch.min(torch.ceil( (xmax-x0)/dx).int()+1, nbin)

# get resolution
parser = PDBParser()
structure = parser.get_structure("SYS", ZONE_PDB_)
res = structure.header["resolution"]
if hasattr(args, "resolution") and args.resolution is not None:
res = args.resolution
else:
parser = PDBParser()
structure = parser.get_structure("SYS", ZONE_PDB_)
res = structure.header["resolution"]
# printout
print("%37s %s" % ("Zoning based on PDB :", ZONE_PDB_))
print("%37s %s" % ("Zoning atoms selection :", ZONE_SEL_))
print("%37s %3.1lf" % ("Zoning cutoff [Ang] :", ZONE_CUT_))
print("%37s %3.2lf" % ("Resolution [Ang] :", res))
if res is not None:
print("%37s %3.2lf" % ("Resolution [Ang] :", res))
else:
print("Resolution [Ang]: not provided")
print("%37s %d" % ("Number of atoms :", len(pos_g)))
print("%37s %4.1lf" % ("Mass [kDa] :", mass))
# indexes of entries above threshold in minibox (tuple of 3 tensors)
Expand Down