""" Provides a command-line utility for fetching PDB files and their associated reflection data. """ from __future__ import absolute_import, division, print_function # LIBTBX_SET_DISPATCHER_NAME phenix.fetch_pdb # LIBTBX_SET_DISPATCHER_NAME iotbx.fetch_pdb # XXX most of this code is unused when run from the command line, but the # PHENIX GUI includes a simple frontend that uses the phil interface. import libtbx.phil from libtbx.utils import Sorry, Usage from libtbx import easy_run import sys import os master_phil = libtbx.phil.parse(""" fetch_pdb .caption = PHENIX can automatically retrieve data from the PDB via the RCSB \ web server. If you intend to re-refine or re-build the structure we \ recommend creating a new project, but this is not required. Note that \ you may also use this tool to generate an MTZ file from the mmCIF \ structure factors (if available), but the options \ are more limited than what is available in the phenix.cif_as_mtz. .style = auto_align caption_img:icons/custom/pdb_import64.png \ caption_width:400 { pdb_ids = None .type = strings .short_caption = PDB ID(s) .input_size = 400 .style = bold action = *pdb_only all_data all_plus_mtz .type = choice .caption = Download_PDB_file(s) Download_all_data Download_all_data_and_convert_CIF_to_MTZ .style = bold site = *rcsb pdbe pdbj pdb-redo .type = choice .caption = RCSB PDBe PDBj PDB-REDO .short_caption = Mirror site .style = bold }""") # XXX for use in the PHENIX GUI only - run2 is used from the command line def run(args=(), params=None, out=sys.stdout): """ For use in PHENIX GUI only, fetches pdb filesand/or reflection data from the PDB. Parameters ---------- args : list of str, optional params : libtbx.phil.scope_extract, optional out : file, optional Returns ------- output_files : list of str errors : list of str """ assert (params is not None) output_files = [] errors = [] mirror = "--mirror=%s" % params.fetch_pdb.site for id in params.fetch_pdb.pdb_ids : args = [mirror, id] if (params.fetch_pdb.action in ["all_data","all_plus_mtz"]): args.insert(0, "--all") if (params.fetch_pdb.action == "all_plus_mtz"): args.insert(1, "--mtz") try : data_files = run2(args=args, log=out) print("\n".join(data_files), file=out) output_files.extend(data_files) except Exception as e: errors.append(str(e)) else : pdb_file = run2(args=[mirror,id], log=out) print(pdb_file, file=out) output_files.append(pdb_file) return output_files, errors def run2(args, log=sys.stdout): """ Fetches pdb files and/or reflection data from the PDB. Parameters ---------- args : list of str log : file, optional Returns ------- str or list of str List of file names that were downloaded. """ if len(args) < 1 : raise Usage("""\ phenix.fetch_pdb [-x|-f|--all] [--mtz] [-q] ID1 [ID2, ...] Command-line options: -x Get structure factors (mmCIF file) -c Get model file in mmCIF format -f Get sequence (FASTA file) --all Download all available data --mtz Download structure factors and PDB file, and generate MTZ -q suppress printed output """) from iotbx.pdb.fetch import get_pdb quiet = False convert_to_mtz = False data_type = "pdb" format = "pdb" mirror = "rcsb" ids = [] for arg in args : if (arg == "--all"): data_type = "all" elif (arg == "-x"): data_type = "xray" elif (arg == "-f"): data_type = "fasta" elif (arg == "-q"): quiet = True elif (arg == "--mtz"): convert_to_mtz = True data_type = "all" elif (arg == "-c"): format = "cif" elif (arg.startswith("--mirror=")): mirror = arg.split("=")[1] if (not mirror in ["rcsb", "pdbe", "pdbj", "pdb-redo"]): raise Sorry( "Unrecognized mirror site '%s' (choices: rcsb, pdbe, pdbj, pdb-redo)" % mirror) else : ids.append(arg) if (len(ids) == 0): raise Sorry("No PDB IDs specified.") if (data_type != "all"): #mirror = "rcsb" files = [] for id in ids : try: files.append(get_pdb(id, data_type, mirror, log, format=format)) except Sorry as e: if data_type == "pdb" and format == "pdb": # try with mmCIF print(" PDB format is not available, trying to get mmCIF", file=log) files.append(get_pdb(id, data_type, mirror, log, format="cif")) if (len(files) == 1): return files[0] return files else : files = [] for id in ids : for data_type_, data_format in [("pdb", "pdb"), ("fasta", "pdb"), ("xray", "pdb"), ("pdb", "cif")] : try: files.append(get_pdb(id, data_type_, mirror, log, format=data_format)) except Sorry as e: print (str(e)) if (convert_to_mtz): misc_args = ["--merge", "--map_to_asu", "--extend_flags", "--ignore_bad_sigmas"] easy_run.call("phenix.cif_as_mtz %s-sf.cif %s" % (id, " ".join(misc_args))) if os.path.isfile("%s-sf.mtz" % id): os.rename("%s-sf.mtz" % id, "%s.mtz" % id) print("Converted structure factors saved to %s.mtz" % id, file=log) # os.remove("%s-sf.cif" % id) files[-1] = os.path.abspath("%s.mtz" % id) if (not os.path.isfile("%s.mtz" % id)): raise Sorry("MTZ conversion failed - try running phenix.cif_as_mtz "+ "manually (and check %s-sf.cif for format errors)." % id) from iotbx.file_reader import any_file mtz_in = any_file("%s.mtz" % id) mtz_in.assert_file_type("hkl") for array in mtz_in.file_server.miller_arrays : if (array.anomalous_flag()): print(" %s is anomalous" % array.info().label_string(), file=log) return files def validate_params(params): """ Validates that the input parameters specify a PDB file to download. Parameters ---------- params : libtbx.phil.scope_extract Returns ------- bool Raises ------ Sorry Raised if a pdb file is not specified to be fetched within params. """ if (params.fetch_pdb.pdb_ids is None) or (len(params.fetch_pdb.pdb_ids)==0): raise Sorry("No PDB IDs specified!") return True if __name__ == "__main__" : run2(sys.argv[1:])