def usage(): usage = """%prog [options] <cyclic symmetry degree> <monomer PDB file> <density map> <resolution> <spacing> <density threshold> <origin X> <origin Y> <origin Z> A script that builds the parameters file for symmetric MultiFit. Notice: If you have negative numbers as input, add -- as the first parameter, so that the numbers are not treated as options.""" parser = OptionParser(usage) parser.add_option("-o", "--out", dest="out", default="multifit.output", metavar="FILE", help="the name of the MultiFit output file. The default " "filename is multifit.output") parser.add_option("-i", "--med", dest="med", metavar="FILE", default="", help="Print intermediate results to the named file.") parser.add_option( "-p", "--params", dest="params", default="multifit.param", help="the name of the MultiFit parameters file. The " "default filename is multifit.params") parser.add_option("-m", "--model", dest="model", default="asmb.model", help="the base filename of the solutions output by " "MultiFit (.X.pdb, where X is the solution number, " "is suffixed to create each output file name). " "The default filename is asmb.model") parser.add_option( "-n", "--numsols", dest="numsols", default=10, type="int", help="the number of solutions(fits) to report; " "default 10") (options, args) = parser.parse_args() if len(args) != 9: parser.error("incorrect number of arguments") return options, args
def parse_args(): usage = """%prog [options] <assembly input> <refined assembly input> <proteomics.input> <mapping.input> <combinations file> <combination index> Fit subunits locally around a combination solution with FFT.""" parser = OptionParser(usage) parser.add_option("-a", "--angle", dest="angle", type="float", default=5, help="angle delta (degrees) for FFT rotational " "search (default 5)") parser.add_option("-n", "--num", dest="num", type="int", default=100, help="Number of fits to report" "(default 100)") parser.add_option("-v", "--angle_voxel", dest="angle_voxel", type="int", default=10, help="Number of angles to keep per voxel" "(default 10)") parser.add_option("-t", "--max_trans", dest="max_trans", type="float", default=10., help="maximum translational search in A" "(default 10)") parser.add_option("-m", "--max_angle", dest="max_angle", type="float", default=30., help="maximum angular search in degrees" "(default 50)") options, args = parser.parse_args() if len(args) != 6: parser.error("incorrect number of arguments") return options, args
def usage(): usage = """%prog [options] <asmb> <asmb.proteomics> <asmb.mapping> <alignment.params> <combinations> <output: clustered combinations> Clustering of assembly solutions. This program uses the Python 'fastcluster' module, which can be obtained from http://math.stanford.edu/~muellner/fastcluster.html """ parser = OptionParser(usage) parser.add_option("-m", "--max", type="int", dest="max", default=999999999, help="maximum solutions to consider") parser.add_option("-r", "--rmsd", type="float", dest="rmsd", default=5, help="maximum rmsd within a cluster") options, args = parser.parse_args() if len(args) != 6: parser.error("incorrect number of arguments") return options, args
def parse_args(): usage = "usage %prog [options] <asmb.input> <proteomics.input> <mapping.input> <alignment params> <combinatins> <diameter> <output combinations>\n" usage+="A script for clustering an ensemble of solutions" parser = OptionParser(usage) parser.add_option("-m", "--max", type="int", dest="max", default=999999999, help="maximum number of combinations to consider") (options, args) = parser.parse_args() if len(args) != 7: parser.error("incorrect number of arguments") return [options,args]
def parse_args(): usage = """%prog [options] <assembly input> <output anchors prefix> Generate anchors for a density map.""" parser = OptionParser(usage) parser.add_option("-s", "--size", type="int", dest="size", default=-1, help="number of residues per bead") options, args = parser.parse_args() if len(args) != 2: parser.error("incorrect number of arguments") return options, args
def parse_args(): usage = """%prog [options] <parameter file> This program builds cyclic symmetric complexes in their density maps.""" parser = OptionParser(usage) parser.add_option("--chimera", dest="chimera", default="", metavar="FILE", help="the name of the Chimera output file, if desired") (options, args) = parser.parse_args() if len(args) != 1: parser.error("incorrect number of arguments") return args[0], options.chimera
def parse_args(): usage = """%prog [options] <asmb.input> <proteomics.input> <mapping.input> <combinations> <model prefix> Write output models. """ parser = OptionParser(usage) parser.add_option("-m", "--max", type="int", dest="max", default=None, help="maximum number of models to write") (options, args) = parser.parse_args() if len(args) != 5: parser.error("incorrect number of arguments") return options, args
def parse_args(): usage = """%prog [options] <asmb.input> <proteomics.input> <mapping.input> <combinations> <model prefix> Write output models. """ parser = OptionParser(usage) parser.add_option("-m", "--max", type="int", dest="max", default=None, help="maximum number of models to write") (options, args) = parser.parse_args() if len(args) != 5: parser.error("incorrect number of arguments") return options,args
def usage(): usage = """%prog [options] <asmb> <asmb.proteomics> <asmb.mapping> <alignment.params> <combinatins> <score combinations [output]> Score each of a set of combinations. """ parser = OptionParser(usage) parser.add_option("-m", "--max", dest="max",default=999999999, help="maximum number of fits considered") (options, args) = parser.parse_args() if len(args) != 6: parser.error("incorrect number of arguments") return [options,args]
def usage(): usage = """%prog [options] <asmb> <asmb.proteomics> <asmb.mapping> <alignment.params> <combinatins> <score combinations [output]> Score each of a set of combinations. """ parser = OptionParser(usage) parser.add_option("-m", "--max", dest="max", default=999999999, help="maximum number of fits considered") (options, args) = parser.parse_args() if len(args) != 6: parser.error("incorrect number of arguments") return [options, args]
def parse_args(): usage = "usage %prog [options] <asmb.input> <proteomics.input> <mapping.input> <alignment params> <combinatins> <diameter> <output combinations>\n" usage += "A script for clustering an ensemble of solutions" parser = OptionParser(usage) parser.add_option("-m", "--max", type="int", dest="max", default=999999999, help="maximum number of combinations to consider") (options, args) = parser.parse_args() if len(args) != 7: parser.error("incorrect number of arguments") return [options, args]
def parse_args(): usage = """%prog [options] <assembly name> <subunits file> <coarse level> <density map> <resolution> <spacing> <density threshold> <origin X> <origin Y> <origin Z> Build the parameters files for MultiFit. Notice: If you have negative numbers as input, add -- as the first parameter, so that the numbers are not treated as options.""" parser = OptionParser(usage) parser.add_option("-i", "--asmb_input", dest="asmb_input", default="asmb.input", help="the name of the MultiFit input file. The default " "filename is asmb.input") parser.add_option("-m", "--model", dest="model", default="asmb.model", help="the base filename of the solutions output by " "MultiFit (.X.pdb, where X is the solution number, " "is suffixed to create each output file name). " "The default filename is asmb.model") parser.add_option("-a", "--anchor_dir", dest="anchor_dir", default="./", help="the name of the directory to store anchor points. " "The default is ./") parser.add_option("-f", "--fit_dir", dest="fit_dir", default="./", help="the name of the directory to store fitting " "solutions. The default is ./") (options, args) = parser.parse_args() if len(args) < 10: parser.error("incorrect number of arguments") return options, args
def parse_args(): usage = """%prog [options] <assembly input> Fit subunits into a density map with FFT.""" parser = OptionParser(usage) parser.add_option("-c", "--cpu", dest="cpus", type="int", default=1, help="number of cpus to use (default 1)") parser.add_option("-a", "--angle", dest="angle", type="float", default=30, help="angle delta (degrees) for FFT rotational " "search (default 30)") parser.add_option("-n", "--num", dest="num", type="int", default=100, help="Number of fits to report" "(default 100)") parser.add_option("-v", "--angle_voxel", dest="angle_voxel", type="int", default=10, help="Number of angles to keep per voxel" "(default 10)") # parser.add_option("-n", "--num", dest="num", type="int", # default=100, # help="Number of fits to report" # "(default 100)") options, args = parser.parse_args() if len(args) != 1: parser.error("incorrect number of arguments") return options, args
def parse_args(): usage = """%prog [options] <asmb.input> <proteomics.input> <mapping.input> <combinations> Compare output models to a reference structure. The reference structure for each subunit is read from the rightmost column of the asmb.input file. """ parser = OptionParser(usage) parser.add_option("-m", "--max", type="int", dest="max", default=None, help="maximum number of models to compare") (options, args) = parser.parse_args() if len(args) != 4: parser.error("incorrect number of arguments") return options, args
def parse_args(): usage = """%prog [options] <asmb> <asmb.proteomics> <asmb.mapping> <alignment.params> <combinations[output]> <Fitting scores[output]> Align proteomics graph with the EM map. """ parser = OptionParser(usage) parser.add_option("-m", "--max", type="int", dest="max", default=999999999, help="maximum number of fits considered") options, args = parser.parse_args() if len(args) != 6: parser.error("incorrect number of arguments") return options, args
def parse_args(): usage = """%prog [options] <asmb.input> <scores> <output file> Write assembly transformation file in other formats. """ + "\n\n".join(x.__doc__ for x in formatters.values()) parser = OptionParser(usage) parser.add_option("-f", "--format", default='chimera', type="choice", choices=list(formatters.keys()), help="type of output to generate (" + ", ".join(formatters.keys()) + "; default: chimera)") options, args = parser.parse_args() if len(args) != 3: parser.error("incorrect number of arguments") return options, args
def parse_args(): usage = """%prog [options] <asmb.input> <proteomics> <mapping> <align param> Given a set of local fits (e.g. generated by fit_fft), the RMSD between each subunit and a reference orientation is calculated and added to each fitting file, in the final "RMSD to reference" column. (The original fitting file is not modified; a new fitting file is created with a '.RMSD' extension.) Note that the assembly input file must contain a reference PDB filename for each subunit (in the rightmost column). """ parser = OptionParser(usage) parser.add_option("-d", action="store_true", dest="use_dock", help="if set the docking transformation is used (and not the fitting transformation)") (options, args) = parser.parse_args() if len(args) != 4: parser.error("incorrect number of arguments") return [options, args]
def parse_args(): usage = """%prog [options] <asmb.input> <proteomics> <mapping> <align param> Given a set of local fits (e.g. generated by fit_fft), the RMSD between each subunit and a reference orientation is calculated and added to each fitting file, in the final "RMSD to reference" column. (The original fitting file is not modified; a new fitting file is created with a '.RMSD' extension.) Note that the assembly input file must contain a reference PDB filename for each subunit (in the rightmost column). """ parser = OptionParser(usage) parser.add_option("-d", action="store_true", dest="use_dock", help="if set the docking transformation is used (and not the fitting transformation)") (options, args) = parser.parse_args() if len(args) != 4: parser.error("incorrect number of arguments") return [options,args]
def parse_args(): usage = """%prog [options] <pdb file name> This program generates the Connolly surface for a given PDB file.""" parser = OptionParser(usage) parser.add_option("--density", dest="density", default=10.0, type="float", metavar="D", help="density of probe points, per cubic angstrom " "(default 10.0)") parser.add_option("--radius", dest="rp", default=1.8, type="float", metavar="R", help="probe radius in angstroms (default 1.8)") opts, args = parser.parse_args() if len(args) != 1: parser.error("incorrect number of arguments") return args[0], opts.density, opts.rp
def parse_args(): usage = """%prog [options] <asmb.input> <scores> <output file> Write assembly transformation file in other formats. """ + "\n\n".join([x.__doc__ for x in formatters.values()]) parser = OptionParser(usage) parser.add_option("-f", "--format", default='chimera', type="choice", choices=formatters.keys(), help="type of output to generate (" + ", ".join(formatters.keys()) + "; default: chimera)") options, args = parser.parse_args() if len(args) != 3: parser.error("incorrect number of arguments") return options, args
def parse_args(): usage = """%prog [options] <parameter file> <transformations file> <reference PDB> This program calculates the RMSD between modeled cyclic symmetric complexes and the reference structure. The RMSD and cross correlation of each complex is written into a file called rmsd.output. Notice: no structural alignment is performed!""" parser = OptionParser(usage) parser.add_option("--vec", dest="vec", default="", metavar="FILE", help="output the RMSDs as a vector into the named " "file, if specified") parser.add_option("--start", dest="start", default=0, type="int", help="first model in transformations file to compare " "with the reference (by default, model 0)") parser.add_option("--end", dest="end", default=-1, type="int", help="last model in transformations file to compare " "with the reference (by default, the final model)") (options, args) = parser.parse_args() if len(args) != 3: parser.error("incorrect number of arguments") return options, args
def parse_args(): usage = """%prog [options] <density.mrc> <number of clusters> <density threshold> <output.pdb> Segments all voxels in the given density map, above the given threshold, into the given number of clusters, and links between neighboring ones. The cluster centers are written out into a single output PDB file, each as a single CA atom. """ parser = OptionParser(usage) parser.add_option("--apix", type="float", default=None, help="map spacing, in angstroms/pix (default: read " "from MRC file)") parser.add_option("-x", "--x", type="float", default=None, help="X origin of the density map") parser.add_option("-y", "--y", type="float", default=None, help="Y origin of the density map") parser.add_option("-z", "--z", type="float", default=None, help="Z origin of the density map") parser.add_option("--cmm", type="str", default="", help="write results in CMM format") parser.add_option("--seg", type="str", default="", help="write out each cluster as an MRC file called " "<seg>_.mrc, and write load_segmentation.cmd file " "to easily load all segments into Chimera") parser.add_option("--txt", type="str", default="", help="write anchor points file in text format") options, args = parser.parse_args() if len(args) != 4: parser.error("incorrect number of arguments") return options, args