def __init__(self, model, pdb_file = None,
naccess_binary = 'naccess', tmp_directory = '/tmp'):
res_data, atm_data = run_naccess(model, pdb_file, naccess = naccess_binary,
temp_path = tmp_directory)
naccess_dict = process_rsa_data(res_data)
res_list = []
property_dict={}
property_keys=[]
property_list=[]
# Now create a dictionary that maps Residue objects to accessibility
for chain in model:
chain_id=chain.get_id()
for res in chain:
res_id=res.get_id()
if (chain_id, res_id) in naccess_dict:
item = naccess_dict[(chain_id, res_id)]
res_name = item['res_name']
assert (res_name == res.get_resname())
property_dict[(chain_id, res_id)] = item
property_keys.append((chain_id, res_id))
property_list.append((res, item))
res.xtra["EXP_NACCESS"]=item
else:
pass
AbstractResiduePropertyMap.__init__(self, property_dict, property_keys,
property_list)
def __init__(self,
model,
pdb_file=None,
naccess_binary='naccess',
tmp_directory='/tmp'):
res_data, atm_data = run_naccess(model,
pdb_file,
naccess=naccess_binary,
temp_path=tmp_directory)
naccess_dict = process_rsa_data(res_data)
res_list = []
property_dict = {}
property_keys = []
property_list = []
# Now create a dictionary that maps Residue objects to accessibility
for chain in model:
chain_id = chain.get_id()
for res in chain:
res_id = res.get_id()
if (chain_id, res_id) in naccess_dict:
item = naccess_dict[(chain_id, res_id)]
res_name = item['res_name']
assert (res_name == res.get_resname())
property_dict[(chain_id, res_id)] = item
property_keys.append((chain_id, res_id))
property_list.append((res, item))
res.xtra["EXP_NACCESS"] = item
else:
pass
AbstractResiduePropertyMap.__init__(self, property_dict, property_keys,
property_list)
def __init__(self, structure, dssp="dsspcmbi", id=None):
"""
@param model: the first model of the structure
@type model: L{Model}
@param pdb_file: a PDB file
@type pdb_file: string
@param dssp: the dssp executable (ie. the argument to os.system)
@type dssp: string
@param id: the structure id to use if parsed
@type id: string
"""
# create DSSP dictionary
structure, dssp_dict, dssp_keys = dssp_dict_from_structure(structure, dssp, id=id)
self.structure = structure
self.model = structure
while self.model.get_parent() != None:
self.model = self.model.get_parent()
self.model = self.model[0]
# assert isinstance(self.model, Model)
dssp_map = {}
dssp_list = []
# Now create a dictionary that maps Residue objects to
# secondary structure and accessibility, and a list of
# (residue, (secondary structure, accessibility)) tuples
for key in dssp_keys:
try:
chain_id, res_id = key
chain = self.model[chain_id]
res = chain[res_id]
except:
continue
aa, ss, acc = dssp_dict[key]
res.xtra[SS] = ss
res.xtra[ASA] = acc
# relative accessibility
resname = res.get_resname()
rel_acc = acc / MAX_ACC[resname]
if rel_acc > 1.0:
rel_acc = 1.0
res.xtra[RASA] = rel_acc
# Verify if AA in DSSP == AA in Structure
# Something went wrong if this is not true!
resname = to_one_letter_code[resname]
if resname == "C":
# DSSP renames C in C-bridges to a,b,c,d,...
# - we rename it back to 'C'
if _dssp_cys.match(aa):
aa = "C"
if not (resname == aa):
raise PDBException("Structure/DSSP mismatch at " + str(res))
dssp_map[key] = (res, ss, acc, rel_acc)
dssp_list.append((res, ss, acc, rel_acc))
AbstractResiduePropertyMap.__init__(self, dssp_map, dssp_keys, dssp_list)
def __init__(self, model, pdb_file, dssp="dssp"):
"""
@param model: the first model of the structure
@type model: L{Model}
@param pdb_file: a PDB file
@type pdb_file: string
@param dssp: the dssp executable (ie. the argument to os.system)
@type dssp: string
"""
# create DSSP dictionary
dssp_dict, dssp_keys=dssp_dict_from_pdb_file(pdb_file, dssp)
dssp_map={}
dssp_list=[]
# Now create a dictionary that maps Residue objects to
# secondary structure and accessibility, and a list of
# (residue, (secondary structure, accessibility)) tuples
for key in dssp_keys:
chain_id, res_id=key
chain=model[chain_id]
res=chain[res_id]
aa, ss, acc=dssp_dict[key]
res.xtra["SS_DSSP"]=ss
res.xtra["EXP_DSSP_ASA"]=acc
# relative accessibility
resname=res.get_resname()
rel_acc=acc/MAX_ACC[resname]
if rel_acc>1.0:
rel_acc=1.0
res.xtra["EXP_DSSP_RASA"]=rel_acc
# Verify if AA in DSSP == AA in Structure
# Something went wrong if this is not true!
resname=to_one_letter_code[resname]
if resname=="C":
# DSSP renames C in C-bridges to a,b,c,d,...
# - we rename it back to 'C'
if _dssp_cys.match(aa):
aa='C'
if not (resname==aa):
raise PDBException("Structure/DSSP mismatch at "+str(res))
dssp_map[key]=((res, ss, acc, rel_acc))
dssp_list.append((res, ss, acc, rel_acc))
AbstractResiduePropertyMap.__init__(self, dssp_map, dssp_keys, dssp_list)
def __init__(self, model, pdb_file, dssp="dssp"):
"""
::
@param model: the first model of the structure
@type model: L{Model} ::
@param pdb_file: a PDB file
@type pdb_file: string ::
@param dssp: the dssp executable (ie. the argument to os.system)
@type dssp: string
"""
# create DSSP dictionary
dssp_dict, dssp_keys = dssp_dict_from_pdb_file(pdb_file, dssp)
dssp_map = {}
dssp_list = []
def resid2code(res_id):
"""Serialize a residue's resseq and icode for easy comparison."""
return '%s%s' % (res_id[1], res_id[2])
# Now create a dictionary that maps Residue objects to
# secondary structure and accessibility, and a list of
# (residue, (secondary structure, accessibility)) tuples
for key in dssp_keys:
chain_id, res_id = key
chain = model[chain_id]
try:
res = chain[res_id]
except KeyError:
# In DSSP, HET field is not considered in residue identifier.
# Thus HETATM records may cause unnecessary exceptions.
# (See 3jui chain A res 593.)
# Try the lookup again with all HETATM other than water
res_seq_icode = resid2code(res_id)
for r in chain:
if r.id[0] not in (' ', 'W'):
# Compare resseq + icode
if resid2code(r.id) == res_seq_icode:
# Found a matching residue
res = r
break
else:
raise KeyError(res_id)
# For disordered residues of point mutations, BioPython uses the
# last one as default, But DSSP takes the first one (alternative
# location is blank, A or 1). See 1h9h chain E resi 22.
# Here we select the res in which all atoms have altloc blank, A or
# 1. If no such residues are found, simply use the first one appears
# (as DSSP does).
if res.is_disordered() == 2:
for rk in res.disordered_get_id_list():
# All atoms in the disordered residue should have the same
# altloc, so it suffices to check the altloc of the first
# atom.
altloc = res.child_dict[rk].get_list()[0].get_altloc()
if altloc in tuple('A1 '):
res.disordered_select(rk)
break
else:
# Simply select the first one
res.disordered_select(res.disordered_get_id_list()[0])
# Sometimes point mutations are put into HETATM and ATOM with altloc
# 'A' and 'B'.
# See 3piu chain A residue 273:
# <Residue LLP het=H_LLP resseq=273 icode= >
# <Residue LYS het= resseq=273 icode= >
# DSSP uses the HETATM LLP as it has altloc 'A'
# We check the altloc code here.
elif res.is_disordered() == 1:
# Check altloc of all atoms in the DisorderedResidue. If it
# contains blank, A or 1, then use it. Otherwise, look for HET
# residues of the same seq+icode. If not such HET residues are
# found, just accept the current one.
altlocs = set(a.get_altloc() for a in res.get_unpacked_list())
if altlocs.isdisjoint('A1 '):
# Try again with all HETATM other than water
res_seq_icode = resid2code(res_id)
for r in chain:
if r.id[0] not in (' ', 'W'):
if resid2code(r.id) == res_seq_icode and \
r.get_list()[0].get_altloc() in tuple('A1 '):
res = r
break
aa, ss, acc, phi, psi = dssp_dict[key]
res.xtra["SS_DSSP"] = ss
res.xtra["EXP_DSSP_ASA"] = acc
res.xtra["PHI_DSSP"] = phi
res.xtra["PSI_DSSP"] = psi
# Relative accessibility
resname = res.get_resname()
try:
rel_acc = acc / MAX_ACC[resname]
except KeyError:
# Invalid value for resname
rel_acc = 'NA'
else:
if rel_acc > 1.0:
rel_acc = 1.0
res.xtra["EXP_DSSP_RASA"] = rel_acc
# Verify if AA in DSSP == AA in Structure
# Something went wrong if this is not true!
# NB: DSSP uses X often
resname = SCOPData.protein_letters_3to1.get(resname, 'X')
if resname == "C":
# DSSP renames C in C-bridges to a,b,c,d,...
# - we rename it back to 'C'
if _dssp_cys.match(aa):
aa = 'C'
# Take care of HETATM again
if (resname != aa) and (res.id[0] == ' ' or aa != 'X'):
raise PDBException("Structure/DSSP mismatch at %s" % res)
dssp_map[key] = ((res, ss, acc, rel_acc, phi, psi))
dssp_list.append((res, ss, acc, rel_acc, phi, psi))
AbstractResiduePropertyMap.__init__(self, dssp_map, dssp_keys,
dssp_list)
def __init__(self, model, in_file, dssp="dssp", acc_array="Sander", file_type='PDB'):
"""Create a DSSP object.
Parameters
----------
model : Model
The first model of the structure
in_file : string
Either a PDB file or a DSSP file.
dssp : string
The dssp executable (ie. the argument to os.system)
acc_array : string
Accessible surface area (ASA) from either Miller et al. (1987),
Sander & Rost (1994), or Wilke: Tien et al. 2013, as string
Sander/Wilke/Miller. Defaults to Sander.
file_type: string
File type switch, either PDB or DSSP with PDB as default.
"""
self.residue_max_acc = residue_max_acc[acc_array]
# create DSSP dictionary
file_type = file_type.upper()
assert(file_type in ['PDB', 'DSSP'])
# If the input file is a PDB file run DSSP and parse output:
if file_type == 'PDB':
# Newer versions of DSSP program call the binary 'mkdssp', so
# calling 'dssp' will not work in some operating systems
# (Debian distribution of DSSP includes a symlink for 'dssp' argument)
try:
dssp_dict, dssp_keys = dssp_dict_from_pdb_file(in_file, dssp)
except OSError: # TODO: Use FileNotFoundError once drop Python 2
if dssp == 'dssp':
dssp = 'mkdssp'
elif dssp == 'mkdssp':
dssp = 'dssp'
else:
raise
dssp_dict, dssp_keys = dssp_dict_from_pdb_file(in_file, dssp)
# If the input file is a DSSP file just parse it directly:
elif file_type == 'DSSP':
dssp_dict, dssp_keys = make_dssp_dict(in_file)
dssp_map = {}
dssp_list = []
def resid2code(res_id):
"""Serialize a residue's resseq and icode for easy comparison."""
return '%s%s' % (res_id[1], res_id[2])
# Now create a dictionary that maps Residue objects to
# secondary structure and accessibility, and a list of
# (residue, (secondary structure, accessibility)) tuples
for key in dssp_keys:
chain_id, res_id = key
chain = model[chain_id]
try:
res = chain[res_id]
except KeyError:
# In DSSP, HET field is not considered in residue identifier.
# Thus HETATM records may cause unnecessary exceptions.
# (See 3jui chain A res 593.)
# Try the lookup again with all HETATM other than water
res_seq_icode = resid2code(res_id)
for r in chain:
if r.id[0] not in (' ', 'W'):
# Compare resseq + icode
if resid2code(r.id) == res_seq_icode:
# Found a matching residue
res = r
break
else:
raise KeyError(res_id)
# For disordered residues of point mutations, Biopython uses the
# last one as default, But DSSP takes the first one (alternative
# location is blank, A or 1). See 1h9h chain E resi 22.
# Here we select the res in which all atoms have altloc blank, A or
# 1. If no such residues are found, simply use the first one appears
# (as DSSP does).
if res.is_disordered() == 2:
for rk in res.disordered_get_id_list():
# All atoms in the disordered residue should have the same
# altloc, so it suffices to check the altloc of the first
# atom.
altloc = res.child_dict[rk].get_list()[0].get_altloc()
if altloc in tuple('A1 '):
res.disordered_select(rk)
break
else:
# Simply select the first one
res.disordered_select(res.disordered_get_id_list()[0])
# Sometimes point mutations are put into HETATM and ATOM with altloc
# 'A' and 'B'.
# See 3piu chain A residue 273:
# <Residue LLP het=H_LLP resseq=273 icode= >
# <Residue LYS het= resseq=273 icode= >
# DSSP uses the HETATM LLP as it has altloc 'A'
# We check the altloc code here.
elif res.is_disordered() == 1:
# Check altloc of all atoms in the DisorderedResidue. If it
# contains blank, A or 1, then use it. Otherwise, look for HET
# residues of the same seq+icode. If not such HET residues are
# found, just accept the current one.
altlocs = set(a.get_altloc() for a in res.get_unpacked_list())
if altlocs.isdisjoint('A1 '):
# Try again with all HETATM other than water
res_seq_icode = resid2code(res_id)
for r in chain:
if r.id[0] not in (' ', 'W'):
if resid2code(r.id) == res_seq_icode and \
r.get_list()[0].get_altloc() in tuple('A1 '):
res = r
break
(aa, ss, acc, phi, psi, dssp_index,
NH_O_1_relidx, NH_O_1_energy,
O_NH_1_relidx, O_NH_1_energy,
NH_O_2_relidx, NH_O_2_energy,
O_NH_2_relidx, O_NH_2_energy) = dssp_dict[key]
res.xtra["SS_DSSP"] = ss
res.xtra["EXP_DSSP_ASA"] = acc
res.xtra["PHI_DSSP"] = phi
res.xtra["PSI_DSSP"] = psi
res.xtra["DSSP_INDEX"] = dssp_index
res.xtra["NH_O_1_RELIDX_DSSP"] = NH_O_1_relidx
res.xtra["NH_O_1_ENERGY_DSSP"] = NH_O_1_energy
res.xtra["O_NH_1_RELIDX_DSSP"] = O_NH_1_relidx
res.xtra["O_NH_1_ENERGY_DSSP"] = O_NH_1_energy
res.xtra["NH_O_2_RELIDX_DSSP"] = NH_O_2_relidx
res.xtra["NH_O_2_ENERGY_DSSP"] = NH_O_2_energy
res.xtra["O_NH_2_RELIDX_DSSP"] = O_NH_2_relidx
res.xtra["O_NH_2_ENERGY_DSSP"] = O_NH_2_energy
# Relative accessibility
resname = res.get_resname()
try:
rel_acc = acc / self.residue_max_acc[resname]
except KeyError:
# Invalid value for resname
rel_acc = 'NA'
else:
if rel_acc > 1.0:
rel_acc = 1.0
res.xtra["EXP_DSSP_RASA"] = rel_acc
# Verify if AA in DSSP == AA in Structure
# Something went wrong if this is not true!
# NB: DSSP uses X often
try:
resname = three_to_one(resname)
except KeyError:
resname = 'X'
if resname == "C":
# DSSP renames C in C-bridges to a,b,c,d,...
# - we rename it back to 'C'
if _dssp_cys.match(aa):
aa = 'C'
# Take care of HETATM again
if (resname != aa) and (res.id[0] == ' ' or aa != 'X'):
raise PDBException("Structure/DSSP mismatch at %s" % res)
dssp_vals = (dssp_index, aa, ss, rel_acc, phi, psi,
NH_O_1_relidx, NH_O_1_energy,
O_NH_1_relidx, O_NH_1_energy,
NH_O_2_relidx, NH_O_2_energy,
O_NH_2_relidx, O_NH_2_energy)
dssp_map[key] = dssp_vals
dssp_list.append(dssp_vals)
AbstractResiduePropertyMap.__init__(self, dssp_map, dssp_keys,
dssp_list)
def __init__(self,
model,
in_file,
dssp="dssp",
acc_array="Sander",
file_type=""):
"""Create a DSSP object.
Parameters
----------
model : Model
The first model of the structure
in_file : string
Either a PDB file or a DSSP file.
dssp : string
The dssp executable (ie. the argument to subprocess)
acc_array : string
Accessible surface area (ASA) from either Miller et al. (1987),
Sander & Rost (1994), or Wilke: Tien et al. 2013, as string
Sander/Wilke/Miller. Defaults to Sander.
file_type: string
File type switch: either PDB, MMCIF or DSSP. Inferred from the
file extension by default.
"""
self.residue_max_acc = residue_max_acc[acc_array]
# create DSSP dictionary
if file_type == "":
file_type = os.path.splitext(in_file)[1][1:]
file_type = file_type.upper()
if file_type == "CIF":
file_type = "MMCIF"
assert file_type in [
"PDB",
"MMCIF",
"DSSP",
], "File type must be PDB, mmCIF or DSSP"
# If the input file is a PDB or mmCIF file run DSSP and parse output:
if file_type == "PDB" or file_type == "MMCIF":
# Newer versions of DSSP program call the binary 'mkdssp', so
# calling 'dssp' will not work in some operating systems
# (Debian distribution of DSSP includes a symlink for 'dssp' argument)
try:
dssp_dict, dssp_keys = dssp_dict_from_pdb_file(in_file, dssp)
except FileNotFoundError:
if dssp == "dssp":
dssp = "mkdssp"
elif dssp == "mkdssp":
dssp = "dssp"
else:
raise
dssp_dict, dssp_keys = dssp_dict_from_pdb_file(in_file, dssp)
# If the input file is a DSSP file just parse it directly:
elif file_type == "DSSP":
dssp_dict, dssp_keys = make_dssp_dict(in_file)
dssp_map = {}
dssp_list = []
def resid2code(res_id):
"""Serialize a residue's resseq and icode for easy comparison."""
return f"{res_id[1]}{res_id[2]}"
# DSSP outputs label_asym_id from the mmCIF file as the chain ID
# But MMCIFParser reads in the auth_asym_id
# Here we create a dictionary to map label_asym_id to auth_asym_id
# using the mmCIF file
if file_type == "MMCIF":
mmcif_dict = MMCIF2Dict(in_file)
mmcif_chain_dict = {}
for i, c in enumerate(mmcif_dict["_atom_site.label_asym_id"]):
if c not in mmcif_chain_dict:
mmcif_chain_dict[c] = mmcif_dict[
"_atom_site.auth_asym_id"][i]
dssp_mapped_keys = []
# Now create a dictionary that maps Residue objects to
# secondary structure and accessibility, and a list of
# (residue, (secondary structure, accessibility)) tuples
for key in dssp_keys:
chain_id, res_id = key
if file_type == "MMCIF":
chain_id = mmcif_chain_dict[chain_id]
dssp_mapped_keys.append((chain_id, res_id))
chain = model[chain_id]
try:
res = chain[res_id]
except KeyError:
# In DSSP, HET field is not considered in residue identifier.
# Thus HETATM records may cause unnecessary exceptions.
# (See 3jui chain A res 593.)
# Try the lookup again with all HETATM other than water
res_seq_icode = resid2code(res_id)
for r in chain:
if r.id[0] not in (" ", "W"):
# Compare resseq + icode
if resid2code(r.id) == res_seq_icode:
# Found a matching residue
res = r
break
else:
raise KeyError(res_id) from None
# For disordered residues of point mutations, Biopython uses the
# last one as default, But DSSP takes the first one (alternative
# location is blank, A or 1). See 1h9h chain E resi 22.
# Here we select the res in which all atoms have altloc blank, A or
# 1. If no such residues are found, simply use the first one appears
# (as DSSP does).
if res.is_disordered() == 2:
for rk in res.disordered_get_id_list():
# All atoms in the disordered residue should have the same
# altloc, so it suffices to check the altloc of the first
# atom.
altloc = res.child_dict[rk].get_list()[0].get_altloc()
if altloc in tuple("A1 "):
res.disordered_select(rk)
break
else:
# Simply select the first one
res.disordered_select(res.disordered_get_id_list()[0])
# Sometimes point mutations are put into HETATM and ATOM with altloc
# 'A' and 'B'.
# See 3piu chain A residue 273:
# <Residue LLP het=H_LLP resseq=273 icode= >
# <Residue LYS het= resseq=273 icode= >
# DSSP uses the HETATM LLP as it has altloc 'A'
# We check the altloc code here.
elif res.is_disordered() == 1:
# Check altloc of all atoms in the DisorderedResidue. If it
# contains blank, A or 1, then use it. Otherwise, look for HET
# residues of the same seq+icode. If not such HET residues are
# found, just accept the current one.
altlocs = {a.get_altloc() for a in res.get_unpacked_list()}
if altlocs.isdisjoint("A1 "):
# Try again with all HETATM other than water
res_seq_icode = resid2code(res_id)
for r in chain:
if r.id[0] not in (" ", "W"):
if resid2code(
r.id) == res_seq_icode and r.get_list(
)[0].get_altloc() in tuple("A1 "):
res = r
break
(
aa,
ss,
acc,
phi,
psi,
dssp_index,
NH_O_1_relidx,
NH_O_1_energy,
O_NH_1_relidx,
O_NH_1_energy,
NH_O_2_relidx,
NH_O_2_energy,
O_NH_2_relidx,
O_NH_2_energy,
) = dssp_dict[key]
res.xtra["SS_DSSP"] = ss
res.xtra["EXP_DSSP_ASA"] = acc
res.xtra["PHI_DSSP"] = phi
res.xtra["PSI_DSSP"] = psi
res.xtra["DSSP_INDEX"] = dssp_index
res.xtra["NH_O_1_RELIDX_DSSP"] = NH_O_1_relidx
res.xtra["NH_O_1_ENERGY_DSSP"] = NH_O_1_energy
res.xtra["O_NH_1_RELIDX_DSSP"] = O_NH_1_relidx
res.xtra["O_NH_1_ENERGY_DSSP"] = O_NH_1_energy
res.xtra["NH_O_2_RELIDX_DSSP"] = NH_O_2_relidx
res.xtra["NH_O_2_ENERGY_DSSP"] = NH_O_2_energy
res.xtra["O_NH_2_RELIDX_DSSP"] = O_NH_2_relidx
res.xtra["O_NH_2_ENERGY_DSSP"] = O_NH_2_energy
# Relative accessibility
resname = res.get_resname()
try:
rel_acc = acc / self.residue_max_acc[resname]
except KeyError:
# Invalid value for resname
rel_acc = "NA"
else:
if rel_acc > 1.0:
rel_acc = 1.0
res.xtra["EXP_DSSP_RASA"] = rel_acc
# Verify if AA in DSSP == AA in Structure
# Something went wrong if this is not true!
# NB: DSSP uses X often
try:
resname = three_to_one(resname)
except KeyError:
resname = "X"
if resname == "C":
# DSSP renames C in C-bridges to a,b,c,d,...
# - we rename it back to 'C'
if _dssp_cys.match(aa):
aa = "C"
# Take care of HETATM again
if (resname != aa) and (res.id[0] == " " or aa != "X"):
raise PDBException(f"Structure/DSSP mismatch at {res}")
dssp_vals = (
dssp_index,
aa,
ss,
rel_acc,
phi,
psi,
NH_O_1_relidx,
NH_O_1_energy,
O_NH_1_relidx,
O_NH_1_energy,
NH_O_2_relidx,
NH_O_2_energy,
O_NH_2_relidx,
O_NH_2_energy,
)
dssp_map[(chain_id, res_id)] = dssp_vals
dssp_list.append(dssp_vals)
if file_type == "MMCIF":
dssp_keys = dssp_mapped_keys
AbstractResiduePropertyMap.__init__(self, dssp_map, dssp_keys,
dssp_list)
def __init__(self, model, pdb_file, dssp="dssp"):
"""
::
@param model: the first model of the structure
@type model: L{Model} ::
@param pdb_file: a PDB file
@type pdb_file: string ::
@param dssp: the dssp executable (ie. the argument to os.system)
@type dssp: string
"""
# create DSSP dictionary
dssp_dict, dssp_keys = dssp_dict_from_pdb_file(pdb_file, dssp)
dssp_map = {}
dssp_list = []
def resid2code(res_id):
"""Serialize a residue's resseq and icode for easy comparison."""
return '%s%s' % (res_id[1], res_id[2])
# Now create a dictionary that maps Residue objects to
# secondary structure and accessibility, and a list of
# (residue, (secondary structure, accessibility)) tuples
for key in dssp_keys:
chain_id, res_id = key
chain = model[chain_id]
try:
res = chain[res_id]
except KeyError:
# In DSSP, HET field is not considered in residue identifier.
# Thus HETATM records may cause unnecessary exceptions.
# (See 3jui chain A res 593.)
# Try the lookup again with all HETATM other than water
res_seq_icode = resid2code(res_id)
for r in chain:
if r.id[0] not in (' ', 'W'):
# Compare resseq + icode
if resid2code(r.id) == res_seq_icode:
# Found a matching residue
res = r
break
else:
raise KeyError(res_id)
# For disordered residues of point mutations, BioPython uses the
# last one as default, But DSSP takes the first one (alternative
# location is blank, A or 1). See 1h9h chain E resi 22.
# Here we select the res in which all atoms have altloc blank, A or
# 1. If no such residues are found, simply use the first one appears
# (as DSSP does).
if res.is_disordered() == 2:
for rk in res.disordered_get_id_list():
# All atoms in the disordered residue should have the same
# altloc, so it suffices to check the altloc of the first
# atom.
altloc = res.child_dict[rk].get_list()[0].get_altloc()
if altloc in tuple('A1 '):
res.disordered_select(rk)
break
else:
# Simply select the first one
res.disordered_select(res.disordered_get_id_list()[0])
# Sometimes point mutations are put into HETATM and ATOM with altloc
# 'A' and 'B'.
# See 3piu chain A residue 273:
# <Residue LLP het=H_LLP resseq=273 icode= >
# <Residue LYS het= resseq=273 icode= >
# DSSP uses the HETATM LLP as it has altloc 'A'
# We check the altloc code here.
elif res.is_disordered() == 1:
# Check altloc of all atoms in the DisorderedResidue. If it
# contains blank, A or 1, then use it. Otherwise, look for HET
# residues of the same seq+icode. If not such HET residues are
# found, just accept the current one.
altlocs = set(a.get_altloc() for a in res.get_unpacked_list())
if altlocs.isdisjoint('A1 '):
# Try again with all HETATM other than water
res_seq_icode = resid2code(res_id)
for r in chain:
if r.id[0] not in (' ', 'W'):
if resid2code(r.id) == res_seq_icode and \
r.get_list()[0].get_altloc() in tuple('A1 '):
res = r
break
(aa, ss, acc, phi, psi, dssp_index, NH_O_1_relidx, NH_O_1_energy,
O_NH_1_relidx, O_NH_1_energy, NH_O_2_relidx, NH_O_2_energy,
O_NH_2_relidx, O_NH_2_energy) = dssp_dict[key]
res.xtra["SS_DSSP"] = ss
res.xtra["EXP_DSSP_ASA"] = acc
res.xtra["PHI_DSSP"] = phi
res.xtra["PSI_DSSP"] = psi
res.xtra["DSSP_INDEX"] = dssp_index
res.xtra["NH_O_1_RELIDX_DSSP"] = NH_O_1_relidx
res.xtra["NH_O_1_ENERGY_DSSP"] = NH_O_1_energy
res.xtra["O_NH_1_RELIDX_DSSP"] = O_NH_1_relidx
res.xtra["O_NH_1_ENERGY_DSSP"] = O_NH_1_energy
res.xtra["NH_O_2_RELIDX_DSSP"] = NH_O_2_relidx
res.xtra["NH_O_2_ENERGY_DSSP"] = NH_O_2_energy
res.xtra["O_NH_2_RELIDX_DSSP"] = O_NH_2_relidx
res.xtra["O_NH_2_ENERGY_DSSP"] = O_NH_2_energy
# Relative accessibility
resname = res.get_resname()
try:
rel_acc = acc / MAX_ACC[resname]
except KeyError:
# Invalid value for resname
rel_acc = 'NA'
else:
if rel_acc > 1.0:
rel_acc = 1.0
res.xtra["EXP_DSSP_RASA"] = rel_acc
# Verify if AA in DSSP == AA in Structure
# Something went wrong if this is not true!
# NB: DSSP uses X often
resname = SCOPData.protein_letters_3to1.get(resname, 'X')
if resname == "C":
# DSSP renames C in C-bridges to a,b,c,d,...
# - we rename it back to 'C'
if _dssp_cys.match(aa):
aa = 'C'
# Take care of HETATM again
if (resname != aa) and (res.id[0] == ' ' or aa != 'X'):
raise PDBException("Structure/DSSP mismatch at %s" % res)
dssp_vals = (dssp_index, aa, ss, rel_acc, phi, psi, NH_O_1_relidx,
NH_O_1_energy, O_NH_1_relidx, O_NH_1_energy,
NH_O_2_relidx, NH_O_2_energy, O_NH_2_relidx,
O_NH_2_energy)
dssp_map[key] = dssp_vals
dssp_list.append(dssp_vals)
AbstractResiduePropertyMap.__init__(self, dssp_map, dssp_keys,
dssp_list)
def __init__(self,
model,
in_file,
dssp="dssp",
acc_array="Sander",
file_type='PDB'):
"""Create a DSSP object.
Parameters
----------
model : Model
The first model of the structure
in_file : string
Either a PDB file or a DSSP file.
dssp : string
The dssp executable (ie. the argument to os.system)
acc_array : string
Accessible surface area (ASA) from either Miller et al. (1987),
Sander & Rost (1994), or Wilke: Tien et al. 2013, as string
Sander/Wilke/Miller. Defaults to Sander.
file_type: string
File type switch, either PDB or DSSP with PDB as default.
"""
self.residue_max_acc = residue_max_acc[acc_array]
# create DSSP dictionary
file_type = file_type.upper()
assert (file_type in ['PDB', 'DSSP'])
# If the input file is a PDB file run DSSP and parse output:
if file_type == 'PDB':
# Newer versions of DSSP program call the binary 'mkdssp', so
# calling 'dssp' will not work in some operating systems
# (Debian distribution of DSSP includes a symlink for 'dssp' argument)
try:
dssp_dict, dssp_keys = dssp_dict_from_pdb_file(in_file, dssp)
except FileNotFoundError:
if dssp == 'dssp':
dssp = 'mkdssp'
elif dssp == 'mkdssp':
dssp = 'dssp'
else:
raise
dssp_dict, dssp_keys = dssp_dict_from_pdb_file(in_file, dssp)
# If the input file is a DSSP file just parse it directly:
elif file_type == 'DSSP':
dssp_dict, dssp_keys = make_dssp_dict(in_file)
dssp_map = {}
dssp_list = []
def resid2code(res_id):
"""Serialize a residue's resseq and icode for easy comparison."""
return '%s%s' % (res_id[1], res_id[2])
# Now create a dictionary that maps Residue objects to
# secondary structure and accessibility, and a list of
# (residue, (secondary structure, accessibility)) tuples
for key in dssp_keys:
chain_id, res_id = key
chain = model[chain_id]
try:
res = chain[res_id]
except KeyError:
# In DSSP, HET field is not considered in residue identifier.
# Thus HETATM records may cause unnecessary exceptions.
# (See 3jui chain A res 593.)
# Try the lookup again with all HETATM other than water
res_seq_icode = resid2code(res_id)
for r in chain:
if r.id[0] not in (' ', 'W'):
# Compare resseq + icode
if resid2code(r.id) == res_seq_icode:
# Found a matching residue
res = r
break
else:
raise KeyError(res_id)
# For disordered residues of point mutations, BioPython uses the
# last one as default, But DSSP takes the first one (alternative
# location is blank, A or 1). See 1h9h chain E resi 22.
# Here we select the res in which all atoms have altloc blank, A or
# 1. If no such residues are found, simply use the first one appears
# (as DSSP does).
if res.is_disordered() == 2:
for rk in res.disordered_get_id_list():
# All atoms in the disordered residue should have the same
# altloc, so it suffices to check the altloc of the first
# atom.
altloc = res.child_dict[rk].get_list()[0].get_altloc()
if altloc in tuple('A1 '):
res.disordered_select(rk)
break
else:
# Simply select the first one
res.disordered_select(res.disordered_get_id_list()[0])
# Sometimes point mutations are put into HETATM and ATOM with altloc
# 'A' and 'B'.
# See 3piu chain A residue 273:
# <Residue LLP het=H_LLP resseq=273 icode= >
# <Residue LYS het= resseq=273 icode= >
# DSSP uses the HETATM LLP as it has altloc 'A'
# We check the altloc code here.
elif res.is_disordered() == 1:
# Check altloc of all atoms in the DisorderedResidue. If it
# contains blank, A or 1, then use it. Otherwise, look for HET
# residues of the same seq+icode. If not such HET residues are
# found, just accept the current one.
altlocs = set(a.get_altloc() for a in res.get_unpacked_list())
if altlocs.isdisjoint('A1 '):
# Try again with all HETATM other than water
res_seq_icode = resid2code(res_id)
for r in chain:
if r.id[0] not in (' ', 'W'):
if resid2code(r.id) == res_seq_icode and \
r.get_list()[0].get_altloc() in tuple('A1 '):
res = r
break
(aa, ss, acc, phi, psi, dssp_index, NH_O_1_relidx, NH_O_1_energy,
O_NH_1_relidx, O_NH_1_energy, NH_O_2_relidx, NH_O_2_energy,
O_NH_2_relidx, O_NH_2_energy) = dssp_dict[key]
res.xtra["SS_DSSP"] = ss
res.xtra["EXP_DSSP_ASA"] = acc
res.xtra["PHI_DSSP"] = phi
res.xtra["PSI_DSSP"] = psi
res.xtra["DSSP_INDEX"] = dssp_index
res.xtra["NH_O_1_RELIDX_DSSP"] = NH_O_1_relidx
res.xtra["NH_O_1_ENERGY_DSSP"] = NH_O_1_energy
res.xtra["O_NH_1_RELIDX_DSSP"] = O_NH_1_relidx
res.xtra["O_NH_1_ENERGY_DSSP"] = O_NH_1_energy
res.xtra["NH_O_2_RELIDX_DSSP"] = NH_O_2_relidx
res.xtra["NH_O_2_ENERGY_DSSP"] = NH_O_2_energy
res.xtra["O_NH_2_RELIDX_DSSP"] = O_NH_2_relidx
res.xtra["O_NH_2_ENERGY_DSSP"] = O_NH_2_energy
# Relative accessibility
resname = res.get_resname()
try:
rel_acc = acc / self.residue_max_acc[resname]
except KeyError:
# Invalid value for resname
rel_acc = 'NA'
else:
if rel_acc > 1.0:
rel_acc = 1.0
res.xtra["EXP_DSSP_RASA"] = rel_acc
# Verify if AA in DSSP == AA in Structure
# Something went wrong if this is not true!
# NB: DSSP uses X often
resname = SCOPData.protein_letters_3to1.get(resname, 'X')
if resname == "C":
# DSSP renames C in C-bridges to a,b,c,d,...
# - we rename it back to 'C'
if _dssp_cys.match(aa):
aa = 'C'
# Take care of HETATM again
if (resname != aa) and (res.id[0] == ' ' or aa != 'X'):
raise PDBException("Structure/DSSP mismatch at %s" % res)
dssp_vals = (dssp_index, aa, ss, rel_acc, phi, psi, NH_O_1_relidx,
NH_O_1_energy, O_NH_1_relidx, O_NH_1_energy,
NH_O_2_relidx, NH_O_2_energy, O_NH_2_relidx,
O_NH_2_energy)
dssp_map[key] = dssp_vals
dssp_list.append(dssp_vals)
AbstractResiduePropertyMap.__init__(self, dssp_map, dssp_keys,
dssp_list)