Source code for simbad.parsers.rotsearch_parser

"""Returns values for the top rotation peak from a rotsearch log file"""

__author__ = "Adam Simpkin"
__date__ = "08 May 2017"
__version__ = "0.1"

import simbad.parsers


[docs]class AmoreRotsearchParser(simbad.parsers._Parser):
    """Class to mine information from a rotsearch logfile"""

    def __init__(self, logfile):
        super(AmoreRotsearchParser, self).__init__(logfile)
        self.alpha = None
        self.beta = None
        self.gamma = None
        self.cc_f = None
        self.rf_f = None
        self.cc_i = None
        self.cc_p = None
        self.icp = None
        self.cc_f_z_score = None
        self.cc_p_z_score = None
        self.num_of_rot = None
        self.parse()

[docs]    def parse(self):
        with open(self.fname, "r") as f_in:
            for line in f_in:
                fields = line.strip().split()
                if len(fields) > 0 and fields[0] == "SOLUTIONRCD":
                    if float(fields[-3]) > 0:
                        try:
                            self.alpha = float(fields[2])
                            self.beta = float(fields[3])
                            self.gamma = float(fields[4])
                            self.cc_f = float(fields[8])
                            self.rf_f = float(fields[9])
                            self.cc_i = float(fields[10])
                            self.cc_p = float(fields[11])
                            self.icp = float(fields[12])
                            self.cc_f_z_score = float(fields[-3])
                            self.cc_p_z_score = float(fields[-2])
                            self.num_of_rot = float(fields[-1])

                        except ValueError:
                            self.alpha = float(fields[2])
                            self.beta = float(fields[3])
                            self.gamma = float(fields[4])
                            self.cc_f_z_score = float(fields[-3])
                            self.cc_p_z_score = float(fields[-2])
                            self.num_of_rot = float(fields[-1])
                        break

[docs]    def summary(self):
        pass

[docs]    def check_input(self):
        pass


[docs]class PhaserRotsearchParser(simbad.parsers._Parser):
    """Class to mine information from a phaser rotsearch logfile"""

    def __init__(self, logfile):
        super(PhaserRotsearchParser, self).__init__(logfile)
        self.rfact = None
        self.llg = 0
        self.rfz = 0
        self.parse()

[docs]    def parse(self):
        """Parse information from the logfile"""
        with open(self.fname, "r") as f_in:
            line = f_in.readline()
            while line:
                if "Minimum R-factor" in line:
                    fields = line.strip().split()
                    self.rfact = float(fields[-1])
                if "#SET" in line:
                    line = f_in.readline()
                    fields = line.strip().split()
                    self.llg = float(fields[1])
                    self.rfz = float(fields[2])
                line = f_in.readline()