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Resize lines to stay within 80 characters
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@DarioMarzella
DarioMarzella committed Aug 4, 2021
1 parent 26a17dd commit b2da493
Showing 1 changed file with 47 additions and 24 deletions.
71 changes: 47 additions & 24 deletions deeprank/features/Edesolv.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,8 @@
from Bio.PDB import PDBParser, SASA

except ImportError:
warnings.warn('Biopython module not found. Make sure you have Biopython 1.79 or later')
Error='Biopython module not found. Make sure you have Biopython 1.79 or later'
warnings.warn(Error)
raise


Expand Down Expand Up @@ -63,7 +64,8 @@ def compute_feature(self, chain1='A', chain2='B'):
pdb_db = pdb2sql(self.pdb)
self.db = interface(pdb_db)

#Create a temporary pdb-like string to calculate complex and free Edesolv
# Create a temporary pdb-like string
# to calculate complex and free Edesolv
temp_pdb = StringIO(('\n').join(pdb_db.sql2pdb()))
temp_pdb.seek(0)

Expand Down Expand Up @@ -116,15 +118,17 @@ def compute_feature(self, chain1='A', chain2='B'):

# Calculate complex sasa
try:
atom.cpx_sasa = struct[0][atom.chainID][atom.resid][atom.name].sasa
atom_spec = struct[0][atom.chainID][atom.resid][atom.name]
atom.cpx_sasa = atom_spec.sasa
except KeyError: #Handling alternative residues error
print('Alternative residue found at:', key)
brk_flag = True
pass

# Calculate unbound (translated) sasa
try:
atom.free_sasa = free_struct[0][atom.chainID][atom.resid][atom.name].sasa
atom_spec = free_struct[0][atom.chainID][atom.resid][atom.name]
atom.free_sasa = atom_spec.sasa
except KeyError: #Handling alternative residues error
print('Alternative residue found at:', key)
brk_flag = True
Expand All @@ -140,7 +144,8 @@ def compute_feature(self, chain1='A', chain2='B'):
# Assign solvation parameters
Assign_solv_param(atom, disulf_bond)

#Calculate atom complex edesolv, free edesolv and final edesolv (cpx - free)
# Calculate atom complex edesolv,
# free edesolv and final edesolv (cpx - free)
atom.esolcpx = atom.cpx_sasa * atom.solv
atom.esolfree = atom.free_sasa * atom.solv
atom.edesolv = atom.esolcpx - atom.esolfree
Expand All @@ -153,7 +158,8 @@ def compute_feature(self, chain1='A', chain2='B'):
k = tuple(chain + coords)

#Human readable
self.edesolv_data[(key[1], key[3], key[2], key[4])] = [atom.edesolv]
self.edesolv_data[(key[1], key[3],
key[2], key[4])] = [atom.edesolv]
#XYZ data
self.edesolv_data_xyz[k] = [atom.edesolv]

Expand Down Expand Up @@ -214,7 +220,9 @@ def Assign_solv_param(atom, disulf_bond=False):
Args:
atom (Atom): Edesolv.Atom object.
disulf_bond (bool, optional): Disulfide bond flag. If true, the atom is a sulfide involved in a disulfie bond. Defaults to False.
disulf_bond (bool, optional): Disulfide bond flag.
If true, the atom is a sulfide involved in a disulfie bond.
Defaults to False.
Returns:
None.
Expand All @@ -225,36 +233,44 @@ def Assign_solv_param(atom, disulf_bond=False):
alifac = 1.27
polfac = 2.30


if atom.position == "BB" or atom.position=="SC": #Check meaning and position of this line
# Check meaning and position of this line
if atom.position == "BB" or atom.position=="SC":
atom.solv = 0.0000

if (((atom.name.startswith('CG')) or (atom.name.startswith('CD')) or (atom.name.startswith('CE')) or (atom.name.startswith('CH')) or (atom.name.startswith('CZ')))
and (atom.resn=='PHE' or atom.resn=='TYR' or atom.resn=='HIS' or atom.resn=='TRP')):
if (((atom.name.startswith('CG')) or (atom.name.startswith('CD'))
or (atom.name.startswith('CE')) or (atom.name.startswith('CH'))
or (atom.name.startswith('CZ')))
and (atom.resn=='PHE' or atom.resn=='TYR'
or atom.resn=='HIS' or atom.resn=='TRP')):
atom.solv = 0.0176 * arofac
elif atom.name.startswith('C'):
atom.solv = 0.0151 * alifac
elif atom.name.startswith('NH') and atom.resn=='ARG':
atom.solv = -0.0273 * polfac
elif atom.name.startswith('NT') or (atom.name.startswith('NZ') and atom.resn=='LYS'):
elif (atom.name.startswith('NT')
or (atom.name.startswith('NZ') and atom.resn=='LYS')):
atom.solv = -0.0548 * polfac
elif atom.name.startswith('N'):
atom.solv = -0.0170 * polfac
elif (atom.name.startswith('OD') and atom.resn=='ASP') or (atom.name.startswith('OE') and atom.resn=='GLU'):
elif ((atom.name.startswith('OD') and atom.resn=='ASP')
or (atom.name.startswith('OE') and atom.resn=='GLU')):
atom.solv = -0.0299 * polfac
elif atom.name.startswith('OG') or atom.name=='OH':
atom.solv = -0.0185 * polfac
elif atom.name.startswith('O'):
atom.solv = -0.0136 * polfac
elif (atom.name.startswith('SD') and atom.resn=='MET') or (atom.name == 'SG' and disulf_bond == True): ## If S in CYS disulfide bond
## Check if S in CYS disulfide bond
elif ((atom.name.startswith('SD') and atom.resn=='MET')
or (atom.name == 'SG' and disulf_bond == True)):
atom.solv = 0.0022 * polfac
elif atom.name.startswith('S'):
atom.solv = 0.0112 * polfac
elif atom.name == 'SHA':
atom.solv = 0.0000

'''
# Corarse-Grained model from HADDOCK code for eventual future implementation
# Corarse-Grained model from HADDOCK code
# for eventual future implementation
if atom.position == "BB" and atom.resn=="ALA":
atom.solv = -0.0107
elif atom.position == "BB" and atom.resn=="GLY":
Expand Down Expand Up @@ -346,17 +362,19 @@ def Assign_solv_param(atom, disulf_bond=False):
'''

def get_disulfide_bonds(pdb_data):
'''Gets all the cysteine pairs that have the SG around 1.80 and 2.05 Angstron and the CB-SG-SG-CB angle around
+- 90°
'''Gets all the cysteine pairs that have the SG around 1.80 and 2.05
Angstrom and the CB-SG-SG-CB angle around +- 90°
Args:
pdb_data (pdb2sqlcore): pdb2sqlcore object
Returns:
disulfide_cys (list(tuple(str, int))): returns a list of chain IDs and resSeq numbers of cysteines bound in disulfide bonds
disulfide_cys (list(tuple(str, int))): returns a list of chain IDs and
resSeq numbers of cysteines bound in disulfide bonds
'''
cys_atoms = pdb_data.get('serial,chainID,resName,resSeq,name,x,y,z', resName='CYS')
cys_atoms = pdb_data.get('serial,chainID,resName,resSeq,name,x,y,z',
resName='CYS')
cys_dict = {}
for atom in cys_atoms:
try:
Expand All @@ -369,15 +387,19 @@ def get_disulfide_bonds(pdb_data):
for second_cys in cys_dict:
if second_cys != first_cys:
# calculate distance
dist = np.linalg.norm(cys_dict[first_cys]['SG']-cys_dict[second_cys]['SG'])
dist = np.linalg.norm(
cys_dict[first_cys]['SG']-cys_dict[second_cys]['SG'])
#if distance 1.80~2.05
if dist >= 1.80 and dist <= 2.10:
#calc dihedral
selection = [cys_dict[first_cys]['CB'], cys_dict[first_cys]['SG'],
cys_dict[second_cys]['CB'], cys_dict[second_cys]['SG']]
selection = [cys_dict[first_cys]['CB'],
cys_dict[first_cys]['SG'],
cys_dict[second_cys]['CB'],
cys_dict[second_cys]['SG']]
dihedral = get_dihedral(selection)
#if dihedral = ~+- 90
if (-91.0 <= dihedral <= -89.0) or (89.0 <= dihedral <= 91.0):
if ((-91.0 <= dihedral <= -89.0)
or (89.0 <= dihedral <= 91.0)):
disulfide_cys.extend([first_cys, second_cys])
#append to list to return

Expand All @@ -388,7 +410,8 @@ def get_dihedral(p):
"""Get dihedral angle from four points (atoms) 3D coordinates.
Args:
p (list): list of four points 3D coordinates. Each element must be a list of floats.
p (list): list of four points 3D coordinates.
Each element must be a list of floats.
Returns:
dihedral (float): Dihedral angle.
Expand Down

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