270 lines
9.9 KiB
Python
270 lines
9.9 KiB
Python
#!/usr/bin/python
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# author J.Beale
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"""
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# aim
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to make an mtz from an hkl file output from partialator or process_hkl
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runs f2mtz and then truncate for create an mtz with other intensities and structure factors
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# usage to make mtz from manually entered lengths and angles
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python make_mtz.py -i <path to .hkl file from partialator>
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-o name of .mtz file
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-p project name in mtz
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-x xtal name in mtz
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-d dataset name in mtz
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-g spacegroup
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-c list of cell lengths and angles to use - 59.3,59.3,153.1,90.0,90.0,90.0
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-r number of residues
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-A resolution range - e.g. 40.0,2.0
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# usage to make mtz from the mean angles and lengths in stream file
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python make_mtz.py -i <path to .hkl file from partialator>
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-o name of .mtz file
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-p project name in mtz
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-x xtal name in mtz
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-d dataset name in mtz
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-g spacegroup
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-r number of residues
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-A resolution range - e.g. 40.0,2.0
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-s <path to stream file>
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-u True
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# usage to get list of mean lengths and angles from stream files
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python make_mtz.py -s <path to stream file>
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# output
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- .mtz file - just intensities
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- f2mtz.log file
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- _F.mtz file - intensities and structure factors
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- cuts data to desired resolution
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- truncate.log file
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"""
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# modules
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import subprocess
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import pandas as pd
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import numpy as np
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import argparse
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import os
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import regex as re
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def get_mean_cell( stream_file ):
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# open stream file
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stream = open( stream_file, "r" ).read()
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# get uc values from stream file
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# example - Cell parameters 7.71784 7.78870 3.75250 nm, 90.19135 90.77553 90.19243 deg
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# scrub clen and return - else nan
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try:
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pattern = r"Cell\sparameters\s(\d+\.\d+)\s(\d+\.\d+)\s(\d+\.\d+)\snm,\s(\d+\.\d+)\s(\d+\.\d+)\s(\d+\.\d+)\sdeg"
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cell_lst = re.findall( pattern, stream )
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except AttributeError:
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return np.nan
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# make cellss into df and convert to float
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cols = [ "a", "b", "c", "alpha", "beta", "gamma" ]
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cell_df = pd.DataFrame( cell_lst, columns=cols )
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cell_df = cell_df.astype(float)
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# calculate mean cells values
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mean_a = round( cell_df.a.mean()*10, 3 )
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mean_b = round( cell_df.b.mean()*10, 3 )
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mean_c = round( cell_df.c.mean()*10, 3 )
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mean_alpha = round( cell_df.alpha.mean(), 3 )
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mean_beta = round( cell_df.beta.mean(), 3 )
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mean_gamma = round( cell_df.gamma.mean(), 3 )
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mean_cell = [ mean_a, mean_b, mean_c, mean_alpha, mean_beta, mean_gamma ]
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return mean_cell, len(cell_lst)
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def make_mtz( hklout_file, mtzout_file, project, crystal, dataset, cell, spacegroup, residues, res_range ):
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# make_mtz file name
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mtz_run_file = "make_mtz.sh"
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# make F file name
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Fout_file = os.path.splitext( mtzout_file )[0] + "_F.mtz"
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# write file
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mtz_sh = open( mtz_run_file, "w" )
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mtz_sh.write( "#!/bin/sh\n\n" )
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mtz_sh.write( "module purge\n" )
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mtz_sh.write( "module load ccp4/8.0\n\n" )
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mtz_sh.write( "f2mtz HKLIN {0} HKLOUT {1} << EOF_hkl > f2mtz.log\n".format( hklout_file, mtzout_file ) )
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mtz_sh.write( "TITLE Reflections from CrystFEL\n" )
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mtz_sh.write( "NAME PROJECT {0} CRYSTAL {1} DATASET {2}\n".format( project, crystal, dataset ) )
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mtz_sh.write( "CELL {0} {1} {2} {3} {4} {5}\n".format( cell[0], cell[1], cell[2], cell[3], cell[4], cell[5] ) )
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mtz_sh.write( "SYMM {0}\n".format( spacegroup ) )
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mtz_sh.write( "SKIP 3\n" )
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mtz_sh.write( "LABOUT H K L I_stream SIGI_stream\n" )
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mtz_sh.write( "CTYPE H H H J Q\n" )
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mtz_sh.write( "FORMAT '(3(F4.0,1X),F10.2,10X,F10.2)'\n" )
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mtz_sh.write( "SKIP 3\n" )
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mtz_sh.write( "EOF_hkl\n\n\n" )
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mtz_sh.write( "echo 'done'\n" )
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mtz_sh.write( "echo 'I and SIGI from CrystFEL stream saved as I_stream and SIGI_stream'\n" )
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mtz_sh.write( "echo 'I filename = {0}'\n\n\n".format( mtzout_file ) )
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mtz_sh.write( "echo 'running truncate'\n" )
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mtz_sh.write( "echo 'setting resolution range to {0}-{1}'\n".format( res_range[0], res_range[1] ) )
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mtz_sh.write( "echo 'assuming that there are {0} residues in assymetric unit'\n\n\n".format( residues ) )
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mtz_sh.write( "truncate HKLIN {0} HKLOUT {1} << EOF_F > truncate.log\n".format( mtzout_file, Fout_file ) )
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mtz_sh.write( "truncate YES\n" )
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mtz_sh.write( "anomalous NO\n" )
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mtz_sh.write( "nresidue {0}\n".format( residues ) )
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mtz_sh.write( "resolution {0} {1}\n".format( res_range[0], res_range[1] ) )
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mtz_sh.write( "plot OFF\n" )
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mtz_sh.write( "labin IMEAN=I_stream SIGIMEAN=SIGI_stream\n" )
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mtz_sh.write( "labout F=F_stream SIGF=SIGF_stream\n" )
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mtz_sh.write( "end\n" )
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mtz_sh.write( "EOF_F\n\n\n" )
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mtz_sh.write( "echo 'done'\n" )
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mtz_sh.write( "echo 'I_stream and SIGI_stream from f2mtz converted to F_stream and F_stream'\n" )
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mtz_sh.write( "echo 'F filename = {0} (contains both Is and Fs)'".format( Fout_file ) )
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mtz_sh.close()
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# make file executable
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subprocess.call( [ "chmod", "+x", "{0}".format( mtz_run_file ) ] )
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# run
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subprocess.call( [ "./{0}".format( mtz_run_file ) ] )
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def cut_hkl_file( hklin_file, hklout_file ):
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# setup
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hklout = open( hklout_file, 'w')
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collect_lines = True
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# Open the input file for reading
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with open( hklin_file, 'r') as f:
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for line in f:
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if line.strip() == 'End of reflections':
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collect_lines = False # Stop collecting lines
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if collect_lines:
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hklout.write( line )
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hklout.close()
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def main( hklin_file, hklout_file, mtzout, project, crystal, dataset, cell, spacegroup, residues, res_range ):
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# remove final lines from crystfel hkl out
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print( "removing final lines from crystfel hklin" )
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cut_hkl_file( hklin_file, hklout_file )
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print( "done" )
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# running make mtz
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print( "making mtz" )
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print( "using cell constants\n{0} {1} {2} A {3} {4} {5} deg".format( cell[0], cell[1], cell[2], cell[3], cell[4], cell[5] ) )
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print( "Titles in mtz will be:\nPROJECT {0} CRYSTAL {1} DATASET {2}".format( project, crystal, dataset ) )
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make_mtz( hklout_file, mtzout, project, crystal, dataset, cell, spacegroup, residues, res_range )
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print( "done" )
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# remove *cut.hkl out
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cwd = os.getcwd()
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files = os.listdir( cwd )
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for file in files:
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if file.endswith( "cut.hkl" ):
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os.remove( file )
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def list_of_floats(arg):
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return list(map(float, arg.split(',')))
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if __name__ == "__main__":
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parser = argparse.ArgumentParser()
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parser.add_argument(
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"-i",
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"--hklin",
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help=".hkl output from partialator or process_hkl",
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type=os.path.abspath
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)
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parser.add_argument(
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"-o",
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"--mtzout",
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help="name of mtz out file. The default will by the hklin with .mtz appended",
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type=str
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)
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parser.add_argument(
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"-p",
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"--project",
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help="name of PROJECT flag in mtz file. The default is - SERIAL-XTAL",
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type=str,
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default="SERIAL-XTAL"
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)
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parser.add_argument(
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"-x",
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"--crystal",
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help="name of CRYSTAL flag in mtz file. The default is - XTALS",
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type=str,
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default="XTALS"
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)
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parser.add_argument(
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"-d",
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"--dataset",
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help="name of DATASET flag in mtz file. The default is - DARK",
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type=str,
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default="DARK"
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)
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parser.add_argument(
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"-g",
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"--spacegroup",
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help="spacegroup for making mtz, e.g P41212",
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type=str
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)
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parser.add_argument(
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"-c",
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"--cell",
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help="list of complete cell length and angles, e.g. 59.3,59.3,153.1,90.0,90.0,90.0. They all should be floats",
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type=list_of_floats
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)
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parser.add_argument(
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"-r",
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"--residues",
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help="number of residues for truncate, e.g., hewl = 129",
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type=int
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)
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parser.add_argument(
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"-A",
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"--resolution_range",
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help="list of 2 floats - low res then high res cut off, e.g., 50.0,1.3",
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type=list_of_floats
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)
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parser.add_argument(
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"-s",
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"--stream_file",
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help="this will simply output the mean unit cell for the subsequent make_mtz run",
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type=os.path.abspath,
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)
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parser.add_argument(
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"-u",
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"--use_stream",
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help="set -u True if you want to use the average lengths and angles from the stream file. Lengths and angles will be automatically averaged when appropriate",
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type=bool,
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default=False
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)
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args = parser.parse_args()
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# logic on which task to perform
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if args.stream_file:
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print( "reading stream file" )
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cell, xtals = get_mean_cell( args.stream_file )
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print( "found {0} xtals".format( xtals ) )
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print( "mean lengths = {0}, {1}, {2} A".format( cell[0], cell[1], cell[2] ) )
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print( "mean angles = {0}, {1}, {2} deg".format( cell[3], cell[4], cell[5] ) )
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print( "# for input to make_mtz = {0},{1},{2},{3},{4},{5}".format( cell[0], cell[1], cell[2], cell[3], cell[4], cell[5] ) )
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if args.use_stream:
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hklout_file = os.path.splitext( args.hklin )[0] + "_cut.hkl"
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if args.mtzout:
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mtzout = args.mtzout
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else:
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mtzout = os.path.splitext( args.hklin )[0] + ".mtz"
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main( args.hklin, hklout_file, mtzout, args.project, args.crystal, args.dataset, cell, args.spacegroup, args.residues, args.resolution_range )
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if args.stream_file == None and args.use_stream == False:
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hklout_file = os.path.splitext( args.hklin )[0] + "_cut.hkl"
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if args.mtzout:
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mtzout = args.mtzout
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else:
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mtzout = os.path.splitext( args.hklin )[0] + ".mtz"
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main( args.hklin, hklout_file, mtzout, args.project, args.crystal, args.dataset, args.cell, args.spacegroup, args.residues, args.resolution_range )
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