def _executable(self):
""" Create executable and mark it executable """
from cadee.executables import exe
exe = exe.which('qdyn5')
if exe is None:
raise 'qdyn5 not found'
self.exe = exe
def get_exec_path(name):
#paths=[]
#for path in os.environ["PATH"].split(os.pathsep):
# path=path.strip('"')
# if not os.path.lexists(path):
# continue
# for ex in os.listdir(path):
# if name in ex:
# ex = os.path.join(path,ex)
# if not ex in paths:
# paths.append(ex)
#
#if not paths:
# print "No '%s' executable was found in your PATH. Please add the path to qfep to the config file manually." % name
#else:
# print "These '%s' executables were found in your PATH. Choose the correct one or write the path.\n" % name
# for i,path in enumerate(paths):
# print " [%d] %s" % (i, path)
# path=""
# while not path:
# try:
# inp=raw_input("? ")
# i=int(inp)
# path=paths[i]
# except ValueError:
# if inp:
# path=inp
# except IndexError:
# pass
# return path
#return ""
import cadee.executables.exe as exe
path = exe.which(name)
if path is None:
path = exe.which(name+'5')
if path is None:
print('Binary not found: ', name)
raise (Exception, 'Please install %s ', name)
print(path)
return path
def run_scwrl(out_pdb, out_log, in_pdb, in_seq):
"""Run SCWRL4. Use 'Scwrl4' - executable from $PATH"""
import cadee.executables.exe as exe
scwrl_exe = exe.which('Scwrl4')
if scwrl_exe is None:
raise Exception("FATAL: 'Scwrl4' - executable not found.")
scwrl_line = '{SCWRL} -i {SCWRL_PDB} -o {OUT} -s {SEQ} > {LOG}'
cmd = scwrl_line.format(SCWRL=scwrl_exe,
SCWRL_PDB=in_pdb,
OUT=out_pdb,
LOG=out_log,
SEQ=in_seq)
os.system(cmd)
if not os.path.isfile(out_pdb):
raise Exception("FATAL: 'Scwrl4' - executable did not create output!",
cmd)
def babel_pdb_for_scwrl(wtpdb,
proper_pdb='proper.pdb',
proper_fasta='proper.fasta',
temp_pdb='temp.pdb',
sprss_babel=True):
""" convert q-pdb to scwrl-compatible pdb """
if sprss_babel:
sprssbabel = '2>&1 | egrep -v "1 molecule converted|audit log messages"' # NOPEP8
else:
sprssbabel = ''
while os.path.exists(temp_pdb):
temp_pdb += '.pdb'
temp_pdb = '"' + temp_pdb + '"'
import config
import cadee.executables.exe as exe
# locate babel-exe
babel_exe = exe.which('babel')
if babel_exe is None:
raise Exception("FATAL: babel executable not found")
# prepare list of renamed residues
resren = ''
for rren in config.RESRENAME:
resren += 'sed -i "s/{0}/{1}/g" $f'.format(rren[0], rren[1]) + NLC
if not rren[1] in config.NATURAL_AA:
raise Exception('Can not replace ' + rren[0] + ' with' + rren[1] +
' which is not recognized by scwrl4!)') # NOPEP8
if len(config.NATURAL_AA) < 1:
raise Exception('Config is not OK. Check config.RESSCWRL4')
allnat = 'egrep "^(ATOM|HETATM).*('
for amino in config.NATURAL_AA:
allnat += amino + '|'
# kill the last |
if allnat[-1] == '|':
allnat = allnat[:-1]
else:
raise Exception('WTF')
allnat += ')" ' + proper_pdb + ' > $f '
cmd = """
f={TEMP_PDB}
{BABEL} -d ---errorlevel 0 {WT} $f {SPRSSBABEL}
# convert all protonated residues into standard residues
{RESREN}
# kill protons
sed -i '/H $/d' $f
# remove connect-records
sed -i '/CONECT/d' $f
mv $f {PROPER_PDB}
# kill everything that is not an natural amino acid
{ALLNAT}
{BABEL} ---errorlevel 1 $f {PROPER_PDB} {SPRSSBABEL}
/bin/rm $f
{BABEL} ---errorlevel 1 {PROPER_PDB} {PROPER_FASTA} {SPRSSBABEL}
exit 0
""".format(WT=wtpdb,
PROPER_PDB=proper_pdb,
PROPER_FASTA=proper_fasta,
TEMP_PDB=temp_pdb,
BABEL=babel_exe,
SPRSSBABEL=sprssbabel,
RESREN=resren,
ALLNAT=allnat)
logger.debug(cmd)
os.system(cmd)
print(' -OR-')
print(' Ensure the binaries are in $PATH.'.format(exe))
print()
print(' Q6 can be obtained free of charge from {0}.'.format(
'https://github.com/qusers/Q6'))
installation_failed()
if not (sys.version_info[0] == 2 and sys.version_info[1] == 7):
print('Need Python 2.7')
installation_failed()
# There are many versions of executables named Qdyn6.
# CADEE should stick to one version, so include with the cadee installation.
for qexe in QEXES:
if not exe.which(qexe, True):
print('Warning: Could not find {0} in {1}'.format(qexe, qexedir))
print(' Searching in $PATH...')
print()
if exe.which(qexe):
print(' Found {0} in {1}.'.format(qexe, exe.which(qexe)))
print()
print(' Will now copy {0} to {1}.'.format(qexe, qexedir))
# compatibility of python3 and python2
try:
input = raw_input
except NameError:
pass
ans = input(' Proceed (y/N)?').lower()
def get_executable(program):
"""Locate executable with name program"""
program = exe.which(program)
if program is None:
raise Exception("Executable not found")
return program