def find_hbonds(parsed, ifgatoms):
ifgsele = parsed.select('chain X and resnum 1 and name %s'%(' '.join(ifgatoms)))
# find any hbond donors
acc_hyd_don_list = []
ifgdon = ifgsele.select('element O N')
if ifgdon is not None:
for donor in ifgdon.iterAtoms():
hyds = pr.Contacts(parsed)(1.1, donor.getCoords()).select('element H D')
if hyds is not None:
for hyd in hyds.iterAtoms():
acceptors = pr.Contacts(parsed)(2.5, hyd.getCoords()).select('element O N \
and not (chain X and resnum 1)')
if acceptors is not None:
for acceptor in acceptors.iterAtoms():
acc_hyd_don_list.append([acceptor, hyd, donor])
# find any hbond acceptors
ifgacc = ifgsele.select('element O or (resname HIS and sidechain and element N)')
if ifgacc is not None:
for acceptor in ifgacc.iterAtoms():
hyds = pr.Contacts(parsed)(2.5, acceptor.getCoords()).select('element H D')
if hyds is not None:
for hyd in hyds.iterAtoms():
donors = pr.Contacts(parsed)(1.1, hyd.getCoords()).select('element O N \
and not (chain X and resnum 1)')
if donors is not None:
for donor in donors.iterAtoms():
acc_hyd_don_list.append([acceptor,hyd,donor])
hbond_list = check_hbond_angles(acc_hyd_don_list)
return hbond_list
def prody_contacts(**kwargs):
"""Identify contacts of a target structure with one or more ligands.
Contacting atoms (or extended subset of atoms, such as residues) are
outputted in PDB file format.
:arg target: target PDB identifier or filename
:arg ligand: ligand PDB identifier(s) or filename(s)
:arg select: atom selection string for target structure
:arg radius: contact radius (Å), default is ``4.0``
:arg extend: output same ``'residue'``, ``'chain'``, or ``'segment'`` along
with contacting atoms
:arg prefix: prefix for output file, default is *target* filename
:arg suffix: output filename suffix, default is *ligand* filename"""
import prody
LOGGER = prody.LOGGER
target = prody.parsePDB(kwargs['target'])
title = kwargs.get('prefix') or target.getTitle()
selstr = kwargs.get('select')
if selstr:
target = target.select(selstr)
contacts = prody.Contacts(target)
suffix = kwargs.get('suffix', '_contacts')
extend = kwargs.get('extend')
radius = float(kwargs.get('radius', 4.0))
ligands = kwargs.get('ligand')
if len(ligands) > 1:
outfn = lambda fn: title + suffix + '_' + fn + '.pdb'
else:
outfn = lambda fn: title + suffix + '.pdb'
for pdb in ligands:
ligand = prody.parsePDB(pdb)
sel = contacts(radius, ligand)
if sel:
LOGGER.info('{0} atoms from {1} contact {2}.'.format(
len(sel), pdb, str(target)))
if extend:
sel = target.select('same ' + extend + ' as sel', sel=sel)
LOGGER.info('Selection is extended to {0} atoms of the same '
'{1}(s).'.format(len(sel), extend))
pdbfn = outfn(ligand.getTitle())
LOGGER.info('Writing contacts into ' + pdbfn)
prody.writePDB(pdbfn, sel)
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 = []
translation = [float(x) for x in line.split('\t')[3:6]]
translation = getTranslation(translation)
score = float(line.split('\t')[-1])
decoylig.setCoords(decoylig.getCoords() - lig_init_cent)
# apply rotation
t = prody.Transformation(rotation, np.zeros(3))
t.apply(decoylig)
decoylig.setCoords(decoylig.getCoords() + translation + rec_init_cent)
mobile = rec + decoylig
decoy_contacts_rec = prody.Contacts(rec)
decoy_contacts_rec = decoy_contacts_rec.select(4, decoylig)
decoy_contacts_lig = prody.Contacts(decoylig)
decoy_contacts_lig = decoy_contacts_lig.select(4, rec)
#lig_contact_atoms = prody.matchChains( lig, decoy_contacts_lig, overlap=0.01, subset='all' )[0][0]
interface_resnums += (list(set(decoy_contacts_rec.getResnums())))
l_interface_resnums += (list(set(decoy_contacts_lig.getResnums())))
interface_residue_pairs.append([
set(decoy_contacts_rec.getResnums()),
set(decoy_contacts_lig.getResnums()), score
])
crec = set(decoy_contacts_rec.getResnums())
clig = set(decoy_contacts_lig.getResnums())
for r in crec:
rec_dict[r]['score'] += score
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:
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.parse_dssp(dssp_file, comb)
if comb.query_path:
self.possible_ifgs = self.find_possible_ifgs_rmsd(
comb, rmsd_threshold=comb.rmsd_threshold)
else:
self.possible_ifgs = self.find_possible_ifgs(comb)
else:
self.possible_ifgs = None
self.alphahull = self.set_alphahull()
self.segnames = sorted(np.unique(self.prody_pdb.getSegnames()))
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 = []