def getPDB(self):
"""
Connect to pdb.org and download PDB files using PDBID
@type self: koala.PDBDownload.PDBDownload
"""
try:
pdb_org = "http://www.rcsb.org/pdb/files/"
pdbs = [] # pdbs id
i = 0
pdbsid = self.opts.inputIDs.split('#')
for pdbid in range(len(pdbsid)):
if len(pdbsid[pdbid]) > 0:
pdbidn = pdbsid[pdbid].strip()
pdbs.append(pdbidn)
i = i + 1
path_output, file_output = os.path.split(self.opts.output)
pdb_files = []
for i, pdbid in enumerate(pdbs):
url = "%s%s.pdb" % (pdb_org, pdbid)
open_url(url, path_output, "%s.pdb" % pdbid)
pdb_files.append(os.path.join(path_output, "%s.pdb" % pdbid))
send_multiple_outputs(
path_output,
pdb_files,
self.opts.galaxydir,
self.opts.outputID)
except Exception, e:
show_error_message(str(e))
def run_SplitPDB(self):
"""
Get the PDB input files and run the splitting
@type self: koala.SplitPDB.SplitPDB
"""
try:
self.path_runs.set_path_execute()
self.path_runs.set_execution_directory()
link_name = os.path.join(self.opts.outputdir, os.path.basename(self.opts.pdbName))
if not os.path.exists(link_name):
os.symlink(self.opts.inputPDB, link_name)
os.system("cp %s %s" % (link_name, self.path_runs.get_path_execution()))
pdbs = parse_pdb(
self.path_runs.get_path_execution(),
os.path.join(self.path_runs.get_path_execution(), self.opts.pdbName))
path_output, file_output = os.path.split(self.opts.output)
send_multiple_outputs(
self.path_runs.get_path_execution(),
pdbs, self.opts.galaxydir,
self.opts.outputID)
if self.opts.createCompressFile == "True":
if compress_files(pdbs, self.path_runs.get_path_execution(), self.opts.toolname):
path_output, file_output = os.path.split(self.opts.outputZip)
send_output_results(
path_output,
file_output,
os.path.join(
self.path_runs.get_path_execution(), '%s.zip' % self.opts.toolname))
except Exception, e:
show_error_message(str(e))
path_output, file_output = os.path.split(self.opts.output)
pdbs_accepted = list_directory(self.path_runs.get_path_execution(), "*.pdb")
if compress_files(pdbs_accepted, self.path_runs.get_path_execution(), "PDBsChecked"):
send_output_results(
path_output,
file_output,
os.path.join(self.path_runs.get_path_execution(), 'PDBsChecked.zip'))
if(os.path.exists(
os.path.join(self.path_runs.get_path_execution(), self.check_pdb_log))):
send_multiple_outputs(
path_output,
[os.path.join(self.path_runs.get_path_execution(), self.check_pdb_log)],
self.opts.galaxydir,
self.opts.outputID)
except Exception, e:
show_error_message(str(e))
if __name__ == '__main__':
op = optparse.OptionParser()
op.add_option('-i', '--inputPDBs', default=None)
op.add_option('-f', '--forceField', default='amber99sb-ildn')
op.add_option('-n', '--inputnames', default=None)
op.add_option('-o', '--output', default=None)
op.add_option('-d', '--outputdir', default=None)
op.add_option('-r', '--galaxyroot', default=None)
op.add_option('-s', '--compressedFile', default=None)