def convertSomePDBtoDSSP(self, quantity):
#converts a given number of pdb to DSSP
for root, dirs, files in os.walk(self.pdbdir):
for filename in files:
quantity -= 1
if (quantity < 0):
break
print(quantity, ' )', filename, ' converted to dssp')
# here uses from prody import execDSSP
execDSSP(self.pdbdir + filename, outputdir=self.dsspdir)
break
def _launchDSSP(self, ag):
LOGGER.info('Running DSSP...')
LOGGER.timeit('_DSSP')
try:
pdb_file = writePDB('_temp.pdb', ag, secondary=False)
dssp_file = execDSSP(pdb_file, outputname='_temp')
ag = parseDSSP(dssp_file, ag)
except:
raise
finally:
os.remove('_temp.pdb')
os.remove('_temp.dssp')
LOGGER.report('DSSP finished in %.1fs.', '_DSSP')
return ag
def _launchDSSP(self, ag):
LOGGER.info('Running DSSP...')
LOGGER.timeit('_DSSP')
pdb_file = writePDB('_temp.pdb', ag, secondary=False)
try:
dssp_file = execDSSP(pdb_file, outputname='_temp')
except EnvironmentError:
raise EnvironmentError("dssp executable not found: please install "
"with 'sudo apt install dssp'")
ag = parseDSSP(dssp_file, ag)
os.remove('_temp.pdb')
os.remove('_temp.dssp')
LOGGER.report('DSSP finished in %.1fs.', '_DSSP')
return ag
def get_features(pdb_file: str,
dssp_dir: str,
only_dssp=True,
force_overwrite=True):
"""
Extract features from a pdb_file
Parameters
----------
pdb_file
dssp_dir
directory to store tmp dssp files
only_dssp
extract only dssp features (use if not interested in features)
force_overwrite
force rerun DSSP
Returns
-------
dict of features
"""
pdb_file = str(pdb_file)
name = Path(pdb_file).stem
protein = pd.parsePDB(pdb_file).select("protein")
pdb_file = str(Path(dssp_dir) / f"{name}.pdb")
pd.writePDB(pdb_file, protein)
protein = pd.parsePDB(pdb_file)
dssp_file = Path(dssp_dir) / f"{name}.dssp"
if force_overwrite or not dssp_file.exists():
dssp_file = pd.execDSSP(str(pdb_file),
outputname=name,
outputdir=str(dssp_dir))
protein = pd.parseDSSP(dssp=str(dssp_file), ag=protein, parseall=True)
data = get_dssp_features(protein)
if only_dssp:
return data
else:
data = {**data, **get_fluctuations(protein)}
data = {**data, **get_residue_depths(pdb_file)}
return data
def __init__(self, comb, pdb_acc_code, chain, **kwargs):
""" :comb: arg: instance of cls Comb with attributes pdbchain_dict, ifg_selection_info
:pdb_acc_code: type: str: 4 character pdb accession code
:param kwargs:
path_to_pdb
path_to_dssp
"""
#search for acc code in input_dir_pdb from comb object.
assert isinstance(pdb_acc_code,
str), 'PDB accession code needs to be a string'
pdb_file = [
file.name for file in os.scandir(comb.input_dir_pdb)
if pdb_acc_code in file.name
]
try:
if pdb_file:
pdb_file = pdb_file[0]
self.prody_pdb = pr.parsePDB(comb.input_dir_pdb + pdb_file,
altloc='A',
model=1)
elif 'path_to_pdb' in kwargs:
self.prody_pdb = pr.parsePDB(kwargs.get('path_to_pdb'),
altloc='A',
model=1)
else: # NEED TO UPDATE: note if going to fetch pdb, it should be sent through Reduce first...
try:
os.mkdir(comb.input_dir_pdb + 'raw')
os.mkdir(comb.input_dir_pdb + 'reduce')
except:
pass
pr.fetchPDB(pdb_acc_code,
compressed=False,
folder=comb.input_dir_pdb + 'raw')
os.system(comb.path_to_reduce + comb.reduce +
' -FLIP -Quiet -DB ' + comb.path_to_reduce +
'reduce_wwPDB_het_dict.txt ' + comb.input_dir_pdb +
'raw/' + pdb_acc_code.lower() + '.pdb > ' +
comb.input_dir_pdb + 'reduce/' +
pdb_acc_code.lower() + 'H.pdb')
self.prody_pdb = pr.parsePDB(comb.input_dir_pdb + 'reduce/' +
pdb_acc_code.lower() + 'H.pdb',
altloc='A',
model=1)
except NameError:
raise NameError(
'ParsePDB instance needs a pdb file path or a valid pdb accession code.'
)
self.pdb_acc_code = pdb_acc_code.lower()
self.pdb_chain = chain
if len(self.prody_pdb) == len(self.prody_pdb.select('icode _')) \
and self.prody_pdb.select('protein and chain ' + self.pdb_chain) is not None:
self.contacts = pr.Contacts(self.prody_pdb)
self.set_bonds()
if pdb_file:
self.fs_struct = freesasa.Structure(comb.input_dir_pdb +
pdb_file)
elif 'path_to_pdb' in kwargs:
self.fs_struct = freesasa.Structure(kwargs.get('path_to_pdb'))
else:
path = comb.input_dir_pdb + 'reduce/'
self.fs_struct = freesasa.Structure(path + next(
file.name for file in os.scandir(path)
if self.pdb_acc_code in file.name))
self.fs_result = freesasa.calc(self.fs_struct)
self.fs_result_cb_3A = self.freesasa_cb(probe_radius=3)
self.fs_result_cb_4A = self.freesasa_cb(probe_radius=4)
self.fs_result_cb_5A = self.freesasa_cb(probe_radius=5)
self.prody_pdb_bb_cb_atom_ind = self.prody_pdb.select(
'protein and (backbone or name CB) '
'and not element H D').getIndices()
dssp_file = [
file.name for file in os.scandir(comb.input_dir_dssp)
if pdb_acc_code in file.name
]
if dssp_file:
dssp_file = dssp_file[0]
self.dssp = pr.parseDSSP(comb.input_dir_dssp + dssp_file,
self.prody_pdb)
elif 'path_to_dssp' in kwargs:
self.dssp = pr.parseDSSP(kwargs.get('path_to_dssp'),
self.prody_pdb)
else:
if pdb_file:
pr.execDSSP(comb.input_dir_pdb + pdb_file,
outputdir=comb.input_dir_dssp)
elif 'path_to_pdb' in kwargs:
pr.execDSSP(kwargs.get('path_to_pdb'),
outputdir=comb.input_dir_dssp)
else:
path = comb.input_dir_pdb + 'reduce/' + next(
file.name
for file in os.scandir(comb.input_dir_pdb + 'reduce')
if pdb_acc_code in file.name)
pr.execDSSP(path, outputdir=comb.input_dir_dssp)
self.dssp = pr.parseDSSP(
comb.input_dir_dssp +
next(file.name for file in os.scandir(comb.input_dir_dssp)
if pdb_acc_code in file.name), self.prody_pdb)
self.possible_ifgs = self.find_possible_ifgs(comb)
else:
self.possible_ifgs = None
# valence and hydrogen bond data for vandermers and iFGs of ParsedPDB protein instance
# iFG specific:
self._ifg_pdb_info = []
self._ifg_atom_density = []
self._ifg_contact_water = []
self._ifg_contact_ligand = []
self._ifg_contact_metal = []
# vdM specific:
self._vdm_pdb_info = []
self._vdm_sasa_info = []
self._ifg_contact_vdm = []
self._ifg_hbond_vdm = []
self._ifg_hbond_water = []
self._ifg_hbond_ligand = []
self._ifg_ca_hbond_vdm = []
def convertiSinglePDBtoDSSP(self, file): # con estensione
if (os.path.isfile(self.pdbdir + file)):
execDSSP(self.pdbdir + file, outputdir=self.dsspdir)
else:
print("File " + self.pdbdir + file + " not found..\n")
def get_relative_solvent_accessibility(pdb_id,
residue_mapper,
chain,
full_pdb_solvent_accessibility=True,
aa_surface_area=AA_SA_VOL):
"""
Run DSSP on a PDB file and return the resulting AtomGroup
Parameters
----------
pdb_id
String containing PDB ID
residue_mapper
Dictionary of residue - unitprot mappings
chain
String containing the selected chain ID(s) from the residue mapper
full_pdb_solvent_accessibility
Boolean to use the full PDB for solvent accessibility calculations -- otherwise
only the chain residues will be selected. Default is True.
aa_surface_area
Dictionary with amino acid abbreviations as keys and surface area
calculations as values
Returns
-------
a numpy array containing relative solvent accessibility measurement for residues
"""
if full_pdb_solvent_accessibility:
dssp_chain = None
else:
dssp_chain = chain
with tempfile.TemporaryDirectory() as tdir:
pdb_file = os.path.join(tdir, '.'.join([pdb_id, 'pdb']))
dssp_file = os.path.join(tdir, '.'.join([pdb_id, 'dssp']))
# DSSP doesn't work with CIF-based atom groups, so must re-run here
pd.pathPDBFolder(tdir)
structure = pd.parsePDB(pdb_id, chain=dssp_chain)
# Must write PDB file for DSSP with only chain selections
# TODO how to silence output from the DSSP functions
pd.writePDB(pdb_file, structure)
pd.execDSSP(pdb_file, outputdir=tdir)
pd.parseDSSP(dssp_file, structure)
# Gather results
# There should not be missing residues
mapped_residue_list = list(residue_mapper.keys())
mapped_residue_list = ' '.join([str(x) for x in mapped_residue_list])
selection_string = f"resnum {mapped_residue_list}"
if dssp_chain is not None:
selection_string += f" AND chain {chain}"
iter_resi_list = sorted(
set(structure.select(selection_string).getResnums()))
rel_acc_list = list()
for resi in iter_resi_list:
dssp_resi = structure[(chain, resi)]
surface_accessibilty = dssp_resi.getData('dssp_acc')[0]
resn = dssp_resi.getResname()
rel_surface_accessibilty = surface_accessibilty / aa_surface_area[resn]
rel_acc_list.append(rel_surface_accessibilty)
return np.array(rel_acc_list)
def generateFeatures(modelFilename):
tempdir = tempfile.mkdtemp()
datadict = {}
modelPDB = prody.parsePDB(modelFilename)
if not modelPDB:
raise Exception('Model file %s cannot be parsed' % modelFilename)
#if model has no chainID, let's assign one. That makes STRIDE parser
#happy
if np.unique(modelPDB.getChids()) == ' ':
modelPDB.all.setChids('A')
modelFilename = os.path.join(tempdir,
os.path.basename(modelFilename))
modelFilename = prody.writePDB(modelFilename,
modelPDB,
autoext=False)
#run STRIDE
prody.parseSTRIDE(prody.execSTRIDE(modelFilename, outputdir=tempdir),
modelPDB)
datadict['STRIDEarea'] = pd.Series(modelPDB.ca.getData('stride_area'))
ss = pd.Series(modelPDB.ca.getSecstrs())
ss[ss == ''] = '-' #empty strings cause trouble in csv load/save
datadict['STRIDEss'] = ss
#run DSSP
prody.parseDSSP(prody.execDSSP(modelFilename, outputdir=tempdir), modelPDB)
datadict['DSSPacc'] = pd.Series(modelPDB.ca.getData('dssp_acc'))
ss = pd.Series(modelPDB.ca.getSecstrs())
ss[ss == ''] = '-'
datadict['DSSPss'] = ss
#run NetSurfP
netsurfp.parseNetSurfP(netsurfp.execNetSurfP(modelFilename,
outputdir=tempdir),
modelPDB)
datadict['NetSurfP_exp'] = \
pd.Series(modelPDB.ca.getData('netsurfp_exposure'))
datadict['NetSurfP_asa'] = \
pd.Series(modelPDB.ca.getData('netsurfp_asa'))
datadict['NetSurfP_rsa'] = \
pd.Series(modelPDB.ca.getData('netsurfp_rsa'))
datadict['NetSurfP_alpha'] = \
pd.Series(modelPDB.ca.getData('netsurfp_alphascore'))
datadict['NetSurfP_beta'] = \
pd.Series(modelPDB.ca.getData('netsurfp_betascore'))
datadict['NetSurfP_coil'] = \
pd.Series(modelPDB.ca.getData('netsurfp_coilscore'))
#run PSIPRED
psipred.parsePSIPRED(psipred.execPSIPRED(modelFilename,
outputdir=tempdir),
modelPDB)
datadict['PSIPRED_ss'] = \
pd.Series(modelPDB.ca.getData('psipred_ss'))
datadict['PSIPRED_coilscore'] = \
pd.Series(modelPDB.ca.getData('psipred_coilscore'))
datadict['PSIPRED_helixscore'] = \
pd.Series(modelPDB.ca.getData('psipred_helixscore'))
datadict['PSIPRED_strandscore'] = \
pd.Series(modelPDB.ca.getData('psipred_strandscore'))
dataframe = pd.DataFrame(datadict)
#remove temporary directory
shutil.rmtree(tempdir, ignore_errors=True)
return dataframe
def generateTrainingSet(inputdict, distance, output=None, combineOutput=True):
devnull = open(os.devnull, 'w')
subprocess.check_call('dssp --version', shell=True, stdout=devnull,
stderr=devnull)
subprocess.check_call('stride -h', shell=True, stdout=devnull,
stderr=devnull)
subprocess.check_call('netsurfp -h', shell=True, stdout=devnull,
stderr=devnull)
subprocess.check_call('runpsipred', shell=True, stdout=devnull,
stderr=devnull)
devnull.close()
finalData = pd.DataFrame() if combineOutput else []
for target, models in inputdict.items():
targetPDB = prody.parsePDB(target)
assert distance, "Distance is not valid"
tempdir = tempfile.mkdtemp()
# we don't want to run NetSurfP and PSIPRED over and over again for all
# model structures. we compute them for target structure and just reuse
# on model structures
netsurfp.parseNetSurfP(netsurfp.execNetSurfP(target, outputdir=tempdir),
targetPDB)
psipred.parsePSIPRED(psipred.execPSIPRED(target, outputdir=tempdir),
targetPDB)
for i, modelFilename in enumerate(models):
datadict = {}
modelPDB = prody.parsePDB(modelFilename)
if not modelPDB:
print('Model file %s cannot be parsed, skipping...' %
modelFilename)
continue
#if model has no chainID, let's assign one. That makes STRIDE parser
#happy
if np.unique(modelPDB.getChids()) == ' ':
modelPDB.all.setChids('A')
modelFilename = os.path.join(tempdir,
os.path.basename(modelFilename))
modelFilename = prody.writePDB(modelFilename,
modelPDB,
autoext=False)
#superimpose model onto target structure
match = prody.matchAlign(modelPDB, targetPDB, tarsel='calpha',
seqid=50, overlap=20)
mapmodel = match[1]
maptarget = match[2]
#and copy NetSurfP and PSIPRED data from target to model
copyDataFromTarget(targetPDB, modelPDB)
#run STRIDE
prody.parseSTRIDE(prody.execSTRIDE(modelFilename, outputdir=tempdir),
modelPDB)
datadict['STRIDEarea'] = \
pd.Series(modelPDB.ca.getData('stride_area')[mapmodel.getResindices()],
index=maptarget.getResindices())
ss = pd.Series(mapmodel.getSecstrs(), index=maptarget.getResindices())
ss[ss == ''] = '-' #empty strings cause trouble in csv load/save
datadict['STRIDEss'] = ss
#run DSSP
prody.parseDSSP(prody.execDSSP(modelFilename, outputdir=tempdir), modelPDB)
datadict['DSSPacc'] = \
pd.Series(modelPDB.ca.getData('dssp_acc')[mapmodel.getResindices()],
index=maptarget.getResindices())
ss = pd.Series(mapmodel.getSecstrs(), index=maptarget.getResindices())
ss[ss == ''] = '-' #empty strings cause trouble in csv load/save
datadict['DSSPss'] = ss
#save NetSurfP data
datadict['NetSurfP_exp'] = \
pd.Series(modelPDB.ca.getData('netsurfp_exposure')[mapmodel.getResindices()],
index=maptarget.getResindices())
datadict['NetSurfP_asa'] = \
pd.Series(modelPDB.ca.getData('netsurfp_asa')[mapmodel.getResindices()],
index=maptarget.getResindices())
datadict['NetSurfP_rsa'] = \
pd.Series(modelPDB.ca.getData('netsurfp_rsa')[mapmodel.getResindices()],
index=maptarget.getResindices())
datadict['NetSurfP_alpha'] = \
pd.Series(modelPDB.ca.getData('netsurfp_alphascore')[mapmodel.getResindices()],
index=maptarget.getResindices())
datadict['NetSurfP_beta'] = \
pd.Series(modelPDB.ca.getData('netsurfp_betascore')[mapmodel.getResindices()],
index=maptarget.getResindices())
datadict['NetSurfP_coil'] = \
pd.Series(modelPDB.ca.getData('netsurfp_coilscore')[mapmodel.getResindices()],
index=maptarget.getResindices())
#save PSIPRED data
datadict['PSIPRED_ss'] = \
pd.Series(modelPDB.ca.getData('psipred_ss')[mapmodel.getResindices()],
index=maptarget.getResindices())
datadict['PSIPRED_coilscore'] = \
pd.Series(modelPDB.ca.getData('psipred_coilscore')[mapmodel.getResindices()],
index=maptarget.getResindices())
datadict['PSIPRED_helixscore'] = \
pd.Series(modelPDB.ca.getData('psipred_helixscore')[mapmodel.getResindices()],
index=maptarget.getResindices())
datadict['PSIPRED_strandscore'] = \
pd.Series(modelPDB.ca.getData('psipred_strandscore')[mapmodel.getResindices()],
index=maptarget.getResindices())
#Compute class labels based on the distance argument
datadict['ClassLabel'] = pd.Series((np.abs(
prody.calcDistance(maptarget.copy(), mapmodel.copy())) < distance).astype(int),
index=maptarget.getResindices())
if combineOutput:
finalData = pd.concat([finalData, pd.DataFrame(datadict)])
else:
finalData.append(pd.DataFrame(datadict))
#remove temporary directory
shutil.rmtree(tempdir, ignore_errors=True)
if output:
if combineOutput:
finalData.to_csv(output, index=False, quoting=csv.QUOTE_NONNUMERIC)
#dataframe.to_csv(output)
else:
print('Warning! Output must be combined to be saved into a CSV '
'file')
return finalData
def make_dssp(pdbfile,outdir = "results"):
"""Make dssp for pdb file
Needs modify dssp bin name 'mkdssp' in prody dssp.py"""
return prody.execDSSP(pdbfile,outputdir=outdir)