def convert_function(self, item):
id_pattern = '\/(?P<id>\w{4}_\d+)_'
#dockDestPath = os.path.join(self.dockingFolderPath)
receptor = item['receptor']
ligand_box = item['ligand_box']
ligand = item['ligand']
cry_id = re.search('\/(?P<id>\w{4}_\d+)_',
ligand_box).groupdict()['id']
cry_rec = cry_id.split('_')[0]
#print ligand
dec_id = re.search('\/(?P<id>[a-zA-Z0-9]+_decoys_\d+).pdb',
ligand).groupdict()['id']
destFileName = cry_id + '_' + dec_id + '.pdb'
dest_ligand = os.path.join(self.dockingFolderPath, cry_rec,
destFileName)
try_create_chain_parent_folder(dest_ligand)
cmd = "{} -r {} -l {} --autobox_ligand {} -o {} --num_modes=1000 --energy_range=1000 --cpu=1 ".format(
FLAGS.smina, receptor, ligand, ligand_box, dest_ligand)
print cmd
if not os.path.exists(dest_ligand):
os.system(cmd)
def convert(fast_file_path):
fast_name = os.path.basename(fast_file_path)
mix_name = fast_name.replace('ligand_fast', 'ligand_mix')
mix_name = mix_name.replace('.pdb', '.av4')
receptor = fast_name.split('_')[0]
crystalFolder = os.path.join(FLAGS.crystalPath, receptor)
similar_crystal = get_similar_crystal_file(crystalFolder, fast_file_path)
ligand_coords, ligand_atom_type, ligand_afinity = parseLigand(
fast_file_path)
print 'parsed {} , shape'.format(fast_name)
print ligand_coords.shape
filtered_coords, filtered_affinity = overlap_filter(
similar_crystal, ligand_coords, ligand_afinity)
mix_dest_path = os.path.join(FLAGS.mix_path, receptor, mix_name)
try_create_chain_parent_folder(mix_dest_path)
save_av4(mix_dest_path, filtered_affinity, ligand_atom_type,
filtered_coords)
def convert():
source = '/home/ubuntu/xiao/data/overlap/crystal_ligands'
dest = '/home/ubuntu/xiao/data/overlap/crystal'
for sourcePath in glob(os.path.join(source,'*','*.pdb')):
destPath = re.sub(source,dest,sourcePath)
cmd = 'obabel -ipdb {} -opdb {}'.format(sourcePath,destPath)
try_create_chain_parent_folder(destPath)
os.system(cmd)
def convert_function(self, item):
dockDestPath = os.path.join(self.dockingFolderPath)
receptor = item['receptor']
ligand_box = item['ligand_box']
ligand = item['ligand']
dest_ligand = ligand.replace(FLAGS.dockSourcePath, dockDestPath)
try_create_chain_parent_folder(dest_ligand)
cmd = "{} -r {} -l {} --autobox_ligand {} -o {} --num_modes=1000 --energy_range=1000 --cpu=1 ".format(
FLAGS.smina, receptor, ligand, ligand_box, dest_ligand)
if not os.path.exists(dest_ligand):
print cmd
os.system(cmd)
def convert(offset=None):
files = glob(os.path.join(sourcePath, '*.pdb'))
index = range(offset - 1, len(files),
FLAGS.orchestra_jobsize) if offset else range(0, len(files))
for i in index:
sourceFilePath = files[i]
destFilePath = sourceFilePath.replace(sourcePath, destPath)
destFilePath = destFilePath.replace('.pdb', '.mol2')
try_create_chain_parent_folder(destFilePath)
cmd = 'obabel -ipdb {} -omol2 -O {}'.format(sourceFilePath,
destFilePath)
os.popen(cmd)
print cmd
def select(index=None):
count = 0
ligand_list = glob(os.path.join(FLAGS.sourcePath, '*', '*.pdb'))
if index:
segment = len(ligand_list) / 1000
indexes = range((index - 1) * segment, index * segment)
else:
indexes = range(len(ligand_list))
for ind in indexes:
ligand = ligand_list[ind]
count += 1
print count
dest_ligand = ligand.replace(FLAGS.sourcePath, FLAGS.destPath)
dest_ligand = dest_ligand.replace('.', '_1.')
try_create_chain_parent_folder(dest_ligand)
cmd = 'obabel -ipdb {} -f 1 -l 1 -opdb -O {}'.format(
ligand, dest_ligand)
if not os.path.exists(dest_ligand):
os.system(cmd)
def convert(fast_path):
file_name = os.path.basename(fast_path)
dest_name = file_name.replace('.pdb', '.av4')
file_id = re.search('(^[a-zA-Z0-9]{4}_\d+)', file_name).group()
receptor = file_name.split('_')[0]
crystalFolder = os.path.join(FLAGS.crystalPath, receptor)
similar_crystal = get_similar_crystal_file(crystalFolder, fast_path)
lig_coords, lig_elements, lig_affinity = parsePDB()
filtered_coords, filtered_affinity = overlap_filter(
similar_crystal, lig_coords, lig_affinity)
av4_dest_path = os.path.join(FLAGS.super_dest_path, receptor, dest_name)
try_create_chain_parent_folder(av4_dest_path)
save_av4(av4_dest_path, filtered_affinity, lig_elements, filtered_coords)
def downloads(self,item):
download_address = self.get_address(item)
if os.path.exists(os.path.join(FLAGS.rowdata_folder,item+'.pdb')):
print item," exists"
return None
print 'download ',item
os.system('wget -P {} {}'.format(FLAGS.rowdata_folder,download_address))
pdbname = item.lower()
ligand_folder = os.path.join(FLAGS.splited_ligand_folder,pdbname)
try_create_chain_folder(ligand_folder)
try:
parsed = prody.parsePDB(os.path.join(FLAGS.rowdata_folder,item+'.pdb'))
except:
self.error_log('can not parse {}.\n'.format(item))
return None
hetero = parsed.select('(hetero and not water) or resname ATP or resname ADP or sesname AMP or resname GTP or resname GDP or resname GMP')
receptor = parsed.select('protein or nucleic')
if receptor is None:
self.error_log("{} doesn't have receptor.\n".format(item))
return None
if hetero is None:
self.error_log("{} doesn't have ligand.\n".format(item))
return None
ligand_flags = False
for each in prody.HierView(hetero).iterResidues():
if each.numAtoms() <= 10:
continue
else:
ligand_flags = True
ResId = each.getResindex()
ligand_path = os.path.join(FLAGS.splited_ligand_folder,pdbname,"{}_{}_ligand.pdb".format(pdbname,ResId))
try_create_chain_parent_folder(ligand_path)
prody.writePDB(ligand_path,each)
if ligand_flags:
receptor_path = os.path.join(FLAGS.splited_receptor_folder,pdbname+'.pdb')
prody.writePDB(receptor_path,receptor)
else:
self.error_log("{} doesn't convert, not ligand have more than 10 atoms.\n".format(item))
def entry_convert(self, item, coded):
'''
original pdb file contains multiple frames
use obabel for select one frame from it
:param item: row of dataframe
:param coded: bool
:return:
'''
source_file_path = item["SourcePath"]
if coded:
dest_file_path = item['code_destpath']
else:
dest_file_path = item['DestPath']
Id = item['FrameId']
cmd = 'obabel -ipdb {} -f {} -l {} -opdb -O {}'.format(source_file_path, Id, Id, dest_file_path)
try_create_chain_parent_folder(dest_file_path)
if not os.path.exists(dest_file_path):
os.popen(cmd)
def convert_function(self, item):
destPath = os.path.join(self.dockingFolderPath, 'fast',
'decked_ligands')
sourceFileName = item['Id'] + '_ligand_fast.pdb'
destFileName = item['Id'] + '_ligand_fast_.pdb'
sourceFilePath = os.path.join(FLAGS.sourcePath, item['PDBname'],
sourceFileName)
destFilePath = os.path.join(destPath, item['PDBname'], destFileName)
try_create_chain_parent_folder(destFilePath)
cmd = 'obabel -ipdb {} -opdb -O {} -m'.format(sourceFilePath,
destFilePath)
receptor_folder = os.path.join(self.dockingFolderPath, 'fast',
'receptors')
receptor_source = os.path.join(FLAGS.receptor_source, item['PDBname'],
item['PDBname'] + '.pdb')
receptor_dest = os.path.join(receptor_folder, item['PDBname'],
item['PDBname'] + '.pdb')
if not os.path.exists(receptor_dest):
try_create_chain_parent_folder(receptor_dest)
os.system('cp {} {}'.format(receptor_source, receptor_dest))
crystal_folder = os.path.join(self.dockingFolderPath, 'fast',
'crystal_ligands')
crystal_source = os.path.join(FLAGS.crystal_source, item['PDBname'],
item['Id'] + '_ligand.pdb')
crystal_dest = os.path.join(crystal_folder, item['PDBname'],
item['Id'] + '_ligand.pdb')
if not os.path.exists(crystal_dest):
try_create_chain_parent_folder(crystal_dest)
os.system('cp {} {}'.format(crystal_source, crystal_dest))
#print cmd
os.system(cmd)