"""
Created on 28 Feb 2013
@author: jmht
"""
import os
import sys
from ample.util import ample_util
[docs]def mrbump_cmd(name, mtz, mr_sequence, keyword_file):
"""Return the command to run mrbump"""
if sys.platform.startswith("win"):
mrbump = os.path.join(os.environ["CCP4"], "bin", "mrbump" + ample_util.SCRIPT_EXT)
else:
mrbump = os.path.join(os.environ["CCP4"], "bin", "mrbump")
cmd = [
mrbump,
"KEYIN",
"{0}".format(keyword_file),
"HKLIN",
"{0}".format(mtz),
"SEQIN",
"{0}".format(mr_sequence),
"HKLOUT",
"{0}.mtz".format(name),
"XYZOUT",
"{0}.pdb".format(name),
]
return " ".join(cmd)
[docs]def keyword_dict(ensemble_pdb, name, amoptd, extra_options={}):
"""Extract the mrbump keywords from the main ample dictionary and add/change any from
the extra_options dict"""
keywords = [
'arpwarp_cycles',
'buccaneer_cycles',
'debug',
'existing_mr_solution',
'F',
'FREE',
'mr_keys',
'mr_sg_all',
'mrbump_programs',
'native_pdb',
'nmasu',
'phaser_kill',
'phaser_rms',
'shelx_cycles',
'shelxe_exe',
'shelxe_rebuild_arpwarp',
'shelxe_rebuild_buccaneer',
'SIGF',
'refine_rebuild_arpwarp',
'refine_rebuild_buccaneer',
'use_shelxe',
]
# Pull out all mrbump options from the main ample dict
if sys.version_info.major == 3:
key_dict = dict((k, v) for k, v in amoptd.items() if k in keywords)
extra_options_d = extra_options.items()
else:
key_dict = dict((k, v) for k, v in amoptd.iteritems() if k in keywords)
extra_options_d = extra_options.iteritems()
# Change any/add options for this ensemble
for k, v in extra_options_d:
key_dict[k] = v
# Add ensemble_pdb and name
key_dict['name'] = name
key_dict['ensemble_pdb'] = ensemble_pdb
return key_dict
[docs]def mrbump_keyword_file(odict, fixed_iden=0.6):
"""
Create MRBUMP keywords
Args:
odict -- dictionary of options
jmht - check fixed_iden - 0.6 if not specified
"""
mrs = 'LABIN SIGF={0} F={1} FreeR_flag={2}\n'.format(odict['SIGF'], odict['F'], odict['FREE'])
mrs += 'JOBID {0}_mrbump\n'.format(odict['name'])
mrs += 'MRPROGRAM {0}\n'.format(" ".join(odict['mrbump_programs']))
mrs += 'LOCALFILE {0} CHAIN ALL RMS {1}'.format((odict['ensemble_pdb']), odict['phaser_rms'])
if 'ncopies' in odict and odict['ncopies'] > 0:
mrs += ' COPIES {0}'.format(odict['ncopies'])
mrs += '\n'
# Don't do any of the searches as we are providing a local file
mrs += 'SCOPSEARCH False\n'
mrs += 'PQSSEARCH False\n'
mrs += 'SSMSEARCH False\n'
mrs += 'DOFASTA False\n'
mrs += 'DOPHMMER False\n'
mrs += 'DOHHPRED False\n'
mrs += 'FAST False\n'
mrs += 'MDLD False\n'
mrs += 'MDLC False\n'
mrs += 'MDLM False\n'
mrs += 'MDLP False\n'
mrs += 'MDLS False\n'
mrs += 'MDLU True\n'
mrs += 'UPDATE False\n'
mrs += 'BUCC {0}\n'.format(odict['refine_rebuild_buccaneer'])
mrs += 'BCYCLES {0}\n'.format(odict['buccaneer_cycles'])
mrs += 'ARPWARP {0}\n'.format(odict['refine_rebuild_arpwarp'])
mrs += 'ACYCLES {0}\n'.format(odict['arpwarp_cycles'])
mrs += 'SHELXE {0}\n'.format(odict['use_shelxe'])
mrs += 'SHLXEXE {0}\n'.format(odict['shelxe_exe'])
mrs += 'SCYCLES {0}\n'.format(odict['shelx_cycles'])
mrs += 'FIXSG True\n'
mrs += 'PJOBS 1\n'
mrs += 'CHECK False\n'
mrs += 'LITE True\n'
mrs += 'PICKLE False\n'
mrs += 'TRYALL True\n'
mrs += 'USEACORN False\n'
mrs += 'USEENSEM False\n'
mrs += 'CLEAN False\n'
mrs += 'DEBUG {0}\n'.format(odict['debug'])
if odict['shelxe_rebuild_arpwarp'] or odict['shelxe_rebuild_buccaneer']:
# Rebuild SHELXE trace with both Buccaneer and ArpWarp
mrs += 'SXREBUILD True\n'
if odict['shelxe_rebuild_buccaneer']:
mrs += 'SXRBUCC True\n'
if odict['shelxe_rebuild_arpwarp']:
mrs += 'SXRARPW True\n'
if odict['nmasu'] > 0:
mrs += 'NMASU {0}\n'.format(odict['nmasu'])
if odict['existing_mr_solution']:
mrs += 'FIXED_XYZIN {0} IDEN {1}\n'.format(odict['existing_mr_solution'], fixed_iden)
if odict['native_pdb']:
mrs += 'PDBNATIVE {0}\n'.format(odict['native_pdb'])
if odict['phaser_kill'] > 0:
mrs += 'PKEY KILL TIME {0}\n'.format(odict['phaser_kill'])
if odict['mr_sg_all']:
mrs += 'PKEY SGALTERNATIVE SELECT ALL\n'
# Extra keywords
# This assumes everything in mr_keys is a list of [ KEYWORD, VALUE0, VALUE1, ...]
if odict['mr_keys']:
for l in odict['mr_keys']:
mrs += " ".join(l) + "\n"
mrs += 'END\n'
return mrs
