def _protein_ligand_interactions(
pdb: str, as_string: bool) -> Tuple[dict, str, dict]:
"""Static method to calculate protein-ligand interactions for each ligand in
the pdb file.
Parameters
----------
pdb : str
File or string containing the protein-ligand complex.
as_string : bool
Variable to know if the pdb passed is a string or a file.
Returns
-------
all_interactions : dict
Dictionary which keys are ligand ids and values are all the interaction data
for that ligand.
pdb_string : str
The corrected pdb stucture as a string.
ligands : dict
Dictionary which keys are ligand Ids and values are pybel molecules
"""
mol_system = PDBComplex()
mol_system.load_pdb(pdb, as_string=as_string)
mol_system.analyze()
pdb_string = mol_system.corrected_pdb
# Dictionary with interactions for each small molecule in the protein
all_interactions = mol_system.interaction_sets
# Store ligands so we can extract their smiles later on.
ligands = dict()
for ligand in mol_system.ligands:
n_atoms = len(ligand.atomorder)
ligand_id = ":".join(
[ligand.hetid, ligand.chain,
str(ligand.position)])
# Filter ions and molecules with less than 5 atoms
if ligand.type != "SMALLMOLECULE" or n_atoms <= 5:
all_interactions.pop(ligand_id)
continue
# ligand.mol is an openbabel molecule
ligands[ligand_id] = ligand.mol
return all_interactions, pdb_string, ligands
def plipmd(topol=None, traj=None):
traj = list(traj.strip('[]').split(','))
u = md.Universe(topol, traj)
ligand_name = input(
'\n\n1) Type the ResName of your Ligand (must be 3 letter code -example: LIG -):\n>'
)
sol_name = input(
'\n2) Type the ResName of your Water (must be 3-4 letter code -example: WAT or SOL or TIP3P -):\n>'
)
for res in u.residues:
if res.resname == ligand_name:
res.resname = 'LIG'
if res.resname == sol_name:
res.resname = 'HOH'
if 'HI' in res.resname:
res.resname = 'HIS'
if 'CY' in res.resname:
res.resname = 'CYS'
for atom in u.atoms:
if atom.name == 'OH2':
atom.name = 'OW'
System = u.select_atoms('protein or (resname LIG or resname HOH)')
System = System.select_atoms(
'protein or resname LIG or (around 7 resname LIG)', updating=True)
for ts in u.trajectory[0:1]:
name = 'frame_tmp.pdb'
PDB = md.Writer(name, multiframe=False)
PDB.write(System)
plip_job = PDBComplex()
plip_job.load_pdb(name)
plip_job.analyze()
print('\nINFO:', plip_job, '\n')
ligand = input(
'3) Type the name of the ligand in trajectory to analyze (- example: LIG:S:152 -):\n>'
)
os.remove(name)
table = pd.DataFrame()
index = 0
print('\nINFO: Your trajectory lenght is:{} steps\n'.format(
range(len(u.trajectory))))
start = int(input('4) Type the starting STEP to analyze:\n>'))
finish = int(input('\n5) Type the ending STEP to analyze:\n>'))
bar = progressbar.ProgressBar(max_value=finish)
print(
'\n\n----- ----- ----- RUNNING THE ANALYSIS ----- ----- -----\n\n'
)
for i in range(start, finish):
name = 'frame_tmp.pdb'
PDB = md.Writer(name, multiframe=False)
for ts in u.trajectory[i:i + 1]:
PDB.write(System)
plip_job = PDBComplex()
plip_job.load_pdb(name)
plip_job.analyze()
interactions = plip_job.interaction_sets[ligand]
for interaction in interactions.all_itypes:
interaction_type = str(
type(interaction)).split('.')[-1].replace("'>", "")
table.loc[index, 'Frame'] = ts.frame
table.loc[index, 'Time'] = ts.time
table.loc[index, 'Type'] = interaction_type
table.loc[index, 'Residue'] = interaction.restype + str(
interaction.resnr)
table.loc[index, 'Ligand'] = interaction.restype_l + str(
interaction.resnr_l)
if interaction_type == 'hbond':
table.loc[index, 'Acceptor'] = interaction.atype
table.loc[index, 'AcceptorIdx'] = interaction.a.idx
table.loc[index, 'Donor'] = interaction.dtype
table.loc[index, 'DonorIdx'] = interaction.d.idx
table.loc[index, 'DistanceAD'] = interaction.distance_ad
table.loc[index, 'DistanceAH'] = interaction.distance_ah
table.loc[index, 'Angle'] = interaction.angle
table.loc[index, 'Force'] = interaction.type
table.loc[index, 'ProtIsDon'] = interaction.protisdon
elif interaction_type == 'pication':
table.loc[index, 'Charge'] = interaction.charge.type
table.loc[index, 'ChargedAtoms'] = ",".join(
[i.type for i in interaction.charge.atoms])
table.loc[index, 'Force'] = interaction.type
table.loc[index, 'RingType'] = interaction.ring.type
table.loc[index, 'RingAtoms'] = ",".join(
[i.type for i in interaction.ring.atoms])
table.loc[index, 'RingAtomsIdx'] = ",".join(
[str(i.idx) for i in interaction.ring.atoms])
elif interaction_type == 'saltbridge':
table.loc[index, 'NegAtoms'] = ",".join(
[i.type for i in interaction.negative.atoms])
table.loc[index, 'NegAtomsIdx'] = ",".join(
[str(i.idx) for i in interaction.negative.atoms])
table.loc[index, 'PosAtoms'] = ",".join(
[i.type for i in interaction.positive.atoms])
table.loc[index, 'PosAtomsIdx'] = ",".join(
[str(i.idx) for i in interaction.positive.atoms])
table.loc[index, 'Distance'] = interaction.distance
table.loc[index, 'ProtIsPos'] = interaction.protispos
elif interaction_type == 'hydroph_interaction':
table.loc[index, 'RecAtom'] = interaction.bsatom.type
table.loc[index, 'RecAtomIdx'] = interaction.bsatom.idx
table.loc[index, 'LigAtom'] = interaction.ligatom.type
table.loc[index, 'LigAtomIdx'] = interaction.ligatom.idx
table.loc[index, 'Distance'] = interaction.distance
elif interaction_type == 'pistack':
table.loc[index,
'RecRingType'] = interaction.proteinring.type
table.loc[index,
'LigRingType'] = interaction.ligandring.type
table.loc[index, 'RecRingAtoms'] = ",".join(
[i.type for i in interaction.proteinring.atoms])
table.loc[index, 'RecAtomsIdx'] = ",".join(
[str(i.idx) for i in interaction.proteinring.atoms])
table.loc[index, 'LigRingAtoms'] = ",".join(
[i.type for i in interaction.ligandring.atoms])
table.loc[index, 'LigRingAtomsIdx'] = ",".join(
[str(i.idx) for i in interaction.ligandring.atoms])
table.loc[index, 'Distance'] = interaction.distance
table.loc[index, 'Angle'] = interaction.angle
table.loc[index, 'Offset'] = interaction.offset
elif interaction_type == 'waterbridge':
table.loc[index, 'AccType'] = interaction.atype
table.loc[index, 'DonType'] = interaction.dtype
table.loc[index, 'WaterIdx'] = interaction.water_orig_idx
table.loc[index, 'DistanceAWat'] = interaction.distance_aw
table.loc[index, 'DistanceDWat'] = interaction.distance_dw
table.loc[index, 'AngleDon'] = interaction.d_angle
table.loc[index, 'AngleWat'] = interaction.w_angle
table.loc[index, 'ProtIsDon'] = interaction.protisdon
elif interaction_type == 'halogenbond':
table.loc[index, 'Acceptor'] = interaction.acctype
table.loc[index, 'Donor'] = interaction.acctype
table.loc[index, 'Distance'] = interaction.distance
table.loc[index, 'DonAngle'] = interaction.don_angle
table.loc[index, 'AccAngle'] = interaction.acc_angle
elif interaction_type == 'metal_complex':
table.loc[index, 'MetalType'] = interaction.metal.type
table.loc[index, 'Idx'] = interaction.metal.idx
table.loc[index, 'TargetType'] = interaction.target_type
table.loc[index, 'FunctGroup'] = interaction.target.fgroup
table.loc[index, 'Geometry'] = interaction.geometry
table.loc[index, 'Distance'] = interaction.distance
table.loc[index, 'Location'] = interaction.location
index = index + 1
bar.update(i + 1)
os.remove(name)
print(
'\n\n----- ----- ----- SAVING THE RESULTS, PLEASE WAIT ----- ----- -----\n\n'
)
table.set_index(['Frame', 'Time'], inplace=True)
table.sort_index(inplace=True)
table.to_excel('Interactions_Table.xlsx')
print(
'\n\n***** ***** ***** ALL DONE, DATA SAVED ON: Interactions_Table.xlsx ***** ***** *****\n\n'
)
def plipmd(topol=None, traj=None):
traj = list(traj.strip('[]').split(','))
u = md.Universe(topol, traj)
print('\nINFO: your system contains {} segments with labels {} \n'.format(
len(u.segments), list(u.segments.segids)))
if len(u.segments.segids) == 1:
print('''
WARNING: Only one segment was identified. Proceeding to manual segment definition\n\n
You must define the peptide residues using MDAnalysis format.
For instance: resid 1:20
This means peptide is from residue 1 to 20. Only peptide residues are required.
Peptide residues will be added to "P" chain.
Extra residues will be consider "RECEPTOR" (R). \n\n
''')
pep_residues = input(
'Type the peptide residues (example - resid 1:20 -):')
pep_segment = u.add_Segment(segid='P')
pep = u.select_atoms(pep_residues)
pep.residues.segments = pep_segment
rec_segment = u.add_Segment(segid='R')
rec = u.select_atoms('protein and (not segid P)')
rec.residues.segments = rec_segment
print('\nINFO: your system contains {} segments with labels {} \n'.
format(len(u.segments), list(u.segments.segids)))
peptide_segment = input('\n\n1) Type the segment of your peptide:\n>')
receptor_segment = input('\n\n1) Type the segment of your receptor:\n>')
sol_name = input(
'\n2) Type the ResName of your water model. Must be 3-4 letter code (example - WAT or SOL or TIP3 -):\n>'
)
for res in u.residues:
if res.resname == sol_name:
res.resname = 'HOH'
if 'HI' in res.resname or 'HSD' in res.resname:
res.resname = 'HIS'
if 'CY' in res.resname:
res.resname = 'CYS'
for atom in u.atoms:
if atom.name == 'OH2':
atom.name = 'OW'
System = u.select_atoms('protein or resname HOH', updating=True)
System = System.select_atoms('segid {} or (around 8 segid {})'.format(
peptide_segment, peptide_segment),
updating=True)
table = pd.DataFrame()
index = 0
print('\nINFO: Your trajectory lenght is:{} steps\n'.format(
range(len(u.trajectory))))
start = int(input('4) Type the starting STEP to analyze:\n>'))
finish = int(input('\n5) Type the ending STEP to analyze:\n>'))
bar = progressbar.ProgressBar(max_value=finish)
print(
'\n\n----- ----- ----- RUNNING THE ANALYSIS ----- ----- -----\n\n'
)
for i in range(start, finish):
try:
name = 'frame_tmp.pdb'
PDB = md.Writer(name, multiframe=False)
for ts in u.trajectory[i:i + 1]:
PDB.write(System)
#Prody for converting peptide ATOM to HETATM
pdb_file = parsePDB(name)
labels = [
True if i.getSegname() == peptide_segment else False
for i in pdb_file
]
pdb_file.setFlags('hetatm', labels)
writePDB(name, pdb_file)
plip_job = PDBComplex()
plip_job.load_pdb(name)
plip_job.analyze()
for key in plip_job.interaction_sets:
if key.split(':')[1] == peptide_segment:
for interaction in plip_job.interaction_sets.get(
key).all_itypes:
if interaction.reschain != peptide_segment:
table.loc[index, 'Frame'] = ts.frame
table.loc[index, 'Time'] = ts.time
interaction_type = str(
type(interaction)).split('.')[-1].replace(
"'>", "")
table.loc[index, 'Type'] = interaction_type
table.loc[
index,
'Protein'] = interaction.restype + str(
interaction.resnr
) + '_' + interaction.reschain
table.loc[
index,
'Peptide'] = interaction.restype_l + str(
interaction.resnr_l
) + '_' + interaction.reschain_l
if interaction_type == 'hbond':
table.loc[index,
'Acceptor'] = interaction.atype
table.loc[
index,
'AcceptorIdx'] = interaction.a.idx
table.loc[index,
'Donor'] = interaction.dtype
table.loc[index,
'DonorIdx'] = interaction.d.idx
table.loc[
index,
'DistanceAD'] = interaction.distance_ad
table.loc[
index,
'DistanceAH'] = interaction.distance_ah
table.loc[index,
'Angle'] = interaction.angle
table.loc[index,
'Force'] = interaction.type
table.loc[
index,
'ProtIsDon'] = interaction.protisdon
elif interaction_type == 'pication':
table.loc[
index,
'Charge'] = interaction.charge.type
table.loc[
index, 'ChargedAtoms'] = ",".join([
i.type
for i in interaction.charge.atoms
])
table.loc[index,
'Force'] = interaction.type
table.loc[
index,
'RingType'] = interaction.ring.type
table.loc[index, 'RingAtoms'] = ",".join([
i.type for i in interaction.ring.atoms
])
table.loc[
index, 'RingAtomsIdx'] = ",".join([
str(i.idx)
for i in interaction.ring.atoms
])
elif interaction_type == 'saltbridge':
table.loc[index, 'NegAtoms'] = ",".join([
i.type
for i in interaction.negative.atoms
])
table.loc[index, 'NegAtomsIdx'] = ",".join(
[
str(i.idx)
for i in interaction.negative.atoms
])
table.loc[index, 'PosAtoms'] = ",".join([
i.type
for i in interaction.positive.atoms
])
table.loc[index, 'PosAtomsIdx'] = ",".join(
[
str(i.idx)
for i in interaction.positive.atoms
])
table.loc[
index,
'Distance'] = interaction.distance
table.loc[
index,
'ProtIsPos'] = interaction.protispos
elif interaction_type == 'hydroph_interaction':
table.loc[
index,
'RecAtom'] = interaction.bsatom.type
table.loc[
index,
'RecAtomIdx'] = interaction.bsatom.idx
table.loc[
index,
'LigAtom'] = interaction.ligatom.type
table.loc[
index,
'LigAtomIdx'] = interaction.ligatom.idx
table.loc[
index,
'Distance'] = interaction.distance
elif interaction_type == 'pistack':
table.loc[
index,
'RecRingType'] = interaction.proteinring.type
table.loc[
index,
'LigRingType'] = interaction.ligandring.type
table.loc[index,
'RecRingAtoms'] = ",".join([
i.type for i in
interaction.proteinring.atoms
])
table.loc[index,
'RecAtomsIdx'] = ",".join([
str(i.idx) for i in
interaction.proteinring.atoms
])
table.loc[index,
'LigRingAtoms'] = ",".join([
i.type for i in
interaction.ligandring.atoms
])
table.loc[index,
'LigRingAtomsIdx'] = ",".join([
str(i.idx) for i in
interaction.ligandring.atoms
])
table.loc[
index,
'Distance'] = interaction.distance
table.loc[index,
'Angle'] = interaction.angle
table.loc[index,
'Offset'] = interaction.offset
elif interaction_type == 'waterbridge':
table.loc[index,
'AccType'] = interaction.atype
table.loc[index,
'DonType'] = interaction.dtype
table.loc[
index,
'WaterIdx'] = interaction.water_orig_idx
table.loc[
index,
'DistanceAWat'] = interaction.distance_aw
table.loc[
index,
'DistanceDWat'] = interaction.distance_dw
table.loc[index,
'AngleDon'] = interaction.d_angle
table.loc[index,
'AngleWat'] = interaction.w_angle
table.loc[
index,
'ProtIsDon'] = interaction.protisdon
elif interaction_type == 'halogenbond':
table.loc[index,
'Acceptor'] = interaction.acctype
table.loc[index,
'Donor'] = interaction.acctype
table.loc[
index,
'Distance'] = interaction.distance
table.loc[
index,
'DonAngle'] = interaction.don_angle
table.loc[
index,
'AccAngle'] = interaction.acc_angle
elif interaction_type == 'metal_complex':
table.loc[
index,
'MetalType'] = interaction.metal.type
table.loc[index,
'Idx'] = interaction.metal.idx
table.loc[
index,
'TargetType'] = interaction.target_type
table.loc[
index,
'FunctGroup'] = interaction.target.fgroup
table.loc[
index,
'Geometry'] = interaction.geometry
table.loc[
index,
'Distance'] = interaction.distance
table.loc[
index,
'Location'] = interaction.location
index = index + 1
bar.update(i + 1)
os.remove(name)
except Exception:
continue
print(
'\n\n----- ----- ----- SAVING THE RESULTS, PLEASE WAIT ----- ----- -----\n\n'
)
table.set_index(['Frame', 'Time'], inplace=True)
table.sort_index(inplace=True)
table.to_excel('Interactions_Table.xlsx')
print(
'\n\n***** ***** ***** ALL DONE, DATA SAVED ON: Interactions_Table.xlsx ***** ***** *****\n\n'
)
def plipmd(topol=None, traj=None):
traj = list(traj.strip('[]').split(','))
u = md.Universe(topol, traj)
bar = progressbar.ProgressBar(max_value=len(u.trajectory))
name = 'frame_tmp.pdb'
PDB = md.Writer(name, multiframe=False)
for ts in u.trajectory[0:1]:
PDB.write(u.atoms)
plip_job = PDBComplex()
plip_job.load_pdb(name)
plip_job.analyze()
print(plip_job)
ligand = input('Type the name of the ligand in trajectory to analyze:')
os.remove(name)
table = pd.DataFrame()
index = 0
for i in range(len(u.trajectory)):
name = 'frame_tmp.pdb'
PDB = md.Writer(name, multiframe=False)
for ts in u.trajectory[i:i + 1]:
PDB.write(u.atoms)
plip_job = PDBComplex()
plip_job.load_pdb(name)
plip_job.analyze()
interactions = plip_job.interaction_sets[ligand]
for interaction in interactions.all_itypes:
interaction_type = str(
type(interaction)).split('.')[-1].replace("'>", "")
table.loc[index, 'Frame'] = ts.frame
table.loc[index, 'Time'] = ts.time
table.loc[index, 'Type'] = interaction_type
table.loc[index, 'Residue'] = interaction.restype + str(
interaction.resnr)
table.loc[index, 'Ligand'] = interaction.restype_l + str(
interaction.resnr_l)
if interaction_type == 'hbond':
table.loc[index, 'Acceptor'] = interaction.atype
table.loc[index, 'AcceptorIdx'] = interaction.a.idx
table.loc[index, 'Donor'] = interaction.dtype
table.loc[index, 'DonorIdx'] = interaction.d.idx
table.loc[index, 'DistanceAD'] = interaction.distance_ad
table.loc[index, 'DistanceAH'] = interaction.distance_ah
table.loc[index, 'Angle'] = interaction.angle
table.loc[index, 'Force'] = interaction.type
table.loc[index, 'ProtIsDon'] = interaction.protisdon
elif interaction_type == 'pication':
table.loc[index, 'Charge'] = interaction.charge.type
table.loc[index, 'ChargedAtoms'] = ",".join(
[i.type for i in interaction.charge.atoms])
table.loc[index, 'Force'] = interaction.type
table.loc[index, 'RingType'] = interaction.ring.type
table.loc[index, 'RingAtoms'] = ",".join(
[i.type for i in interaction.ring.atoms])
table.loc[index, 'RingAtomsIdx'] = ",".join(
[str(i.idx) for i in interaction.ring.atoms])
elif interaction_type == 'saltbridge':
table.loc[index, 'NegAtoms'] = ",".join(
[i.type for i in interaction.negative.atoms])
table.loc[index, 'NegAtomsIdx'] = ",".join(
[str(i.idx) for i in interaction.negative.atoms])
table.loc[index, 'PosAtoms'] = ",".join(
[i.type for i in interaction.positive.atoms])
table.loc[index, 'PosAtomsIdx'] = ",".join(
[str(i.idx) for i in interaction.positive.atoms])
table.loc[index, 'Distance'] = interaction.distance
table.loc[index, 'ProtIsPos'] = interaction.protispos
elif interaction_type == 'hydroph_interaction':
table.loc[index, 'RecAtom'] = interaction.bsatom.type
table.loc[index, 'RecAtomIdx'] = interaction.bsatom.idx
table.loc[index, 'LigAtom'] = interaction.ligatom.type
table.loc[index, 'LigAtomIdx'] = interaction.ligatom.idx
table.loc[index, 'Distance'] = interaction.distance
elif interaction_type == 'pistack':
table.loc[index,
'RecRingType'] = interaction.proteinring.type
table.loc[index,
'LigRingType'] = interaction.ligandring.type
table.loc[index, 'RecRingAtoms'] = ",".join(
[i.type for i in interaction.proteinring.atoms])
table.loc[index, 'RecAtomsIdx'] = ",".join(
[str(i.idx) for i in interaction.proteinring.atoms])
table.loc[index, 'LigRingAtoms'] = ",".join(
[i.type for i in interaction.ligandring.atoms])
table.loc[index, 'LigRingAtomsIdx'] = ",".join(
[str(i.idx) for i in interaction.ligandring.atoms])
table.loc[index, 'Distance'] = interaction.distance
table.loc[index, 'Angle'] = interaction.angle
table.loc[index, 'Offset'] = interaction.offset
elif interaction_type == 'waterbridge':
table.loc[index, 'AccType'] = interaction.atype
table.loc[index, 'DonType'] = interaction.dtype
table.loc[index, 'WaterIdx'] = interaction.water_orig_idx
table.loc[index, 'DistanceAWat'] = interaction.distance_aw
table.loc[index, 'DistanceDWat'] = interaction.distance_dw
table.loc[index, 'AngleDon'] = interaction.d_angle
table.loc[index, 'AngleWat'] = interaction.w_angle
table.loc[index, 'ProtIsDon'] = interaction.protisdon
elif interaction_type == 'halogenbond':
table.loc[index, 'Acceptor'] = interaction.acctype
table.loc[index, 'Donor'] = interaction.acctype
table.loc[index, 'Distance'] = interaction.distance
table.loc[index, 'DonAngle'] = interaction.don_angle
table.loc[index, 'AccAngle'] = interaction.acc_angle
elif interaction_type == 'metal_complex':
table.loc[index, 'MetalType'] = interaction.metal.type
table.loc[index, 'Idx'] = interaction.metal.idx
table.loc[index, 'TargetType'] = interaction.target_type
table.loc[index, 'FunctGroup'] = interaction.target.fgroup
table.loc[index, 'Geometry'] = interaction.geometry
table.loc[index, 'Distance'] = interaction.distance
table.loc[index, 'Location'] = interaction.location
index = index + 1
bar.update(i)
os.remove(name)
table.set_index(['Frame', 'Time'], inplace=True)
table.sort_index(inplace=True)
table.to_excel('Interactions_Table.xlsx')
def plipmd(topol=None, traj=None):
if 'gro' in topol or '.tpr' in topol:
print('''\n\n
WARNING: For analysis using gromacs you SHOULD use .pdb topology
Recomended gromacs (gmx) command to generate a PDB topology file:\n
gmx trjconv -f xyz.gro -o xyz.pdb -s xyz.tpr
\n\n
''')
else:
pass
traj = list(traj.strip('[]').split(','))
u = md.Universe(topol, traj)
print('\nINFO: your system contains {} segments with labels {} \n'.format(
len(u.segments), list(u.segments.segids)))
if len(u.segments.segids) == 1:
print('''
WARNING: Only one segment was identified in system topology:{} \n\n
'''.format(list(u.segments.segids)))
else:
print(
'\nINFO: your system contains {} segments with labels: \n {} \n\n'.
format(len(u.segments), list(u.segments.segids)))
print('''
\nWARNING: Segments IDs are considered CHAIN names for analysis. Maybe you can consider to chance Segments ID\n\n
''')
user_confirmation = input(
'Do you want to define chain names to segments (yes/no):\n>')
if user_confirmation == 'yes':
chains_from_segments = input(
'Type the new name (chain) for every segment (SegId) in format: SegId1,A|SegID2,B|...|SegIdn,N:\n>'
)
names = chains_from_segments.replace(' ', '').split('|')
for name in names:
segid = name.split(',')[0]
newName = name.split(',')[1]
for segment in u.segments:
if segment.segid == segid:
segment.segid = newName
print(
'\nINFO: your system contains {} segments with labels: \n {} \n\n'
.format(len(u.segments), list(u.segments.segids)))
peptide_segment = input('\n\n1) Type the segment of your peptide:\n>')
receptor_segment = input('\n\n1) Type the segment of your receptor:\n>')
sol_name = input(
'\n2) Type the ResName of your water model. Must be 3-4 letter code (example - WAT or SOL or TIP3 -):\n>'
)
for res in u.residues:
if res.resname == sol_name:
res.resname = 'HOH'
if 'HI' in res.resname or 'HSD' in res.resname:
res.resname = 'HIS'
if 'CY' in res.resname:
res.resname = 'CYS'
for atom in u.atoms:
if atom.name == 'OH2':
atom.name = 'OW'
System = u.select_atoms('protein or resname HOH', updating=True)
System = System.select_atoms('segid {} or (around 8 segid {})'.format(
peptide_segment, peptide_segment),
updating=True)
table = pd.DataFrame()
index = 0
print('\nINFO: Your trajectory lenght is:{} steps\n'.format(
range(len(u.trajectory))))
start = int(input('4) Type the starting STEP to analyze:\n>'))
finish = int(input('\n5) Type the ending STEP to analyze:\n>'))
bar = progressbar.ProgressBar(max_value=finish)
print(
'\n\n----- ----- ----- RUNNING THE ANALYSIS ----- ----- -----\n\n'
)
for i in range(start, finish):
try:
name = 'frame_tmp.pdb'
PDB = md.Writer(name, multiframe=False)
for ts in u.trajectory[i:i + 1]:
PDB.write(System)
#Prody for converting peptide ATOM to HETATM
pdb_file = parsePDB(name)
labels = [
True if i.getSegname() == peptide_segment else False
for i in pdb_file
]
pdb_file.setFlags('hetatm', labels)
writePDB(name, pdb_file)
plip_job = PDBComplex()
plip_job.load_pdb(name)
plip_job.analyze()
for key in plip_job.interaction_sets:
if key.split(':')[1] == peptide_segment:
for interaction in plip_job.interaction_sets.get(
key).all_itypes:
if interaction.reschain != peptide_segment:
interaction_type = str(
type(interaction)).split('.')[-1].replace(
"'>", "")
table.loc[index, 'Frame'] = ts.frame
table.loc[index, 'Time'] = ts.time
table.loc[
index,
'Residue'] = interaction.restype + str(
interaction.resnr)
table.loc[index,
'Chain'] = interaction.reschain
table.loc[
index,
'Ligand'] = interaction.restype_l + str(
interaction.resnr_l)
if interaction_type == 'hbond':
table.loc[index, 'Type'] = 'H-bond'
table.loc[index,
'Acceptor'] = interaction.atype
table.loc[
index,
'AcceptorIdx'] = interaction.a.idx
table.loc[index,
'Donor'] = interaction.dtype
table.loc[index,
'DonorIdx'] = interaction.d.idx
table.loc[
index,
'DistanceAD'] = interaction.distance_ad
table.loc[
index,
'DistanceAH'] = interaction.distance_ah
table.loc[index,
'Angle'] = interaction.angle
table.loc[index,
'Force'] = interaction.type
table.loc[
index,
'ProtIsDon'] = interaction.protisdon
elif interaction_type == 'pication':
table.loc[index, 'Type'] = 'Pi-cation'
table.loc[
index,
'Charge'] = interaction.charge.type
table.loc[
index, 'ChargedAtoms'] = ",".join([
i.type
for i in interaction.charge.atoms
])
table.loc[index,
'Force'] = interaction.type
table.loc[
index,
'RingType'] = interaction.ring.type
table.loc[index, 'RingAtoms'] = ",".join([
i.type for i in interaction.ring.atoms
])
table.loc[
index, 'RingAtomsIdx'] = ",".join([
str(i.idx)
for i in interaction.ring.atoms
])
elif interaction_type == 'pistack':
table.loc[index, 'Type'] = 'Pi-stacking'
table.loc[
index,
'StackingType'] = interaction.type
table.loc[
index,
'RecRingType'] = interaction.proteinring.type
table.loc[
index,
'LigRingType'] = interaction.ligandring.type
table.loc[index,
'RecRingAtoms'] = ",".join([
i.type for i in
interaction.proteinring.atoms
])
table.loc[index,
'RecAtomsIdx'] = ",".join([
str(i.idx) for i in
interaction.proteinring.atoms
])
table.loc[index,
'LigRingAtoms'] = ",".join([
i.type for i in
interaction.ligandring.atoms
])
table.loc[index,
'LigRingAtomsIdx'] = ",".join([
str(i.idx) for i in
interaction.ligandring.atoms
])
table.loc[
index,
'Distance'] = interaction.distance
table.loc[index,
'Angle'] = interaction.angle
table.loc[index,
'Offset'] = interaction.offset
elif interaction_type == 'saltbridge':
table.loc[index, 'Type'] = 'Salt-bridge'
table.loc[index, 'NegAtoms'] = ",".join([
i.type
for i in interaction.negative.atoms
])
table.loc[index, 'NegAtomsIdx'] = ",".join(
[
str(i.idx)
for i in interaction.negative.atoms
])
table.loc[index, 'PosAtoms'] = ",".join([
i.type
for i in interaction.positive.atoms
])
table.loc[index, 'PosAtomsIdx'] = ",".join(
[
str(i.idx)
for i in interaction.positive.atoms
])
table.loc[
index,
'Distance'] = interaction.distance
table.loc[
index,
'ProtIsPos'] = interaction.protispos
elif interaction_type == 'hydroph_interaction':
table.loc[index, 'Type'] = 'Hydrophobic'
table.loc[
index,
'RecAtom'] = interaction.bsatom.type
table.loc[
index,
'RecAtomIdx'] = interaction.bsatom.idx
table.loc[
index,
'LigAtom'] = interaction.ligatom.type
table.loc[
index,
'LigAtomIdx'] = interaction.ligatom.idx
table.loc[
index,
'Distance'] = interaction.distance
elif interaction_type == 'waterbridge':
table.loc[index, 'Type'] = 'Water-bridge'
table.loc[index,
'AccType'] = interaction.atype
table.loc[index,
'DonType'] = interaction.dtype
table.loc[
index,
'WaterIdx'] = interaction.water_orig_idx
table.loc[
index,
'DistanceAWat'] = interaction.distance_aw
table.loc[
index,
'DistanceDWat'] = interaction.distance_dw
table.loc[index,
'AngleDon'] = interaction.d_angle
table.loc[index,
'AngleWat'] = interaction.w_angle
table.loc[
index,
'ProtIsDon'] = interaction.protisdon
elif interaction_type == 'halogenbond':
table.loc[index, 'Type'] = 'X-bond'
table.loc[index,
'Acceptor'] = interaction.acctype
table.loc[index,
'Donor'] = interaction.acctype
table.loc[
index,
'Distance'] = interaction.distance
table.loc[
index,
'DonAngle'] = interaction.don_angle
table.loc[
index,
'AccAngle'] = interaction.acc_angle
elif interaction_type == 'metal_complex':
table.loc[index, 'Type'] = 'Metal-complex'
table.loc[
index,
'MetalType'] = interaction.metal.type
table.loc[index,
'Idx'] = interaction.metal.idx
table.loc[
index,
'TargetType'] = interaction.target_type
table.loc[
index,
'FunctGroup'] = interaction.target.fgroup
table.loc[
index,
'Geometry'] = interaction.geometry
table.loc[
index,
'Distance'] = interaction.distance
table.loc[
index,
'Location'] = interaction.location
index = index + 1
bar.update(i + 1)
os.remove(name)
except Exception:
continue
print(
'\n\n----- ----- ----- SAVING THE RESULTS, PLEASE WAIT ----- ----- -----\n\n'
)
table.set_index(['Frame', 'Time'], inplace=True)
table.sort_index(inplace=True)
table.to_excel('Interactions_Table.xlsx')
print(
'\n\n***** ***** ***** ALL DONE, DATA SAVED ON: Interactions_Table.xlsx ***** ***** *****\n\n'
)
