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reorganization and improvements in protein-ligand interactions
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@karolamik13
karolamik13 committed Oct 15, 2023
1 parent 6715524 commit 2ec7c75
Showing 1 changed file with 57 additions and 55 deletions.
112 changes: 57 additions & 55 deletions prody/proteins/interactions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@
'calcPiCationTrajectory', 'calcHydrophobicTrajectory', 'calcDisulfideBondsTrajectory',
'calcProteinInteractions', 'calcStatisticsInteractions', 'calcDistribution',
'calcSASA', 'calcVolume','compareInteractions', 'showInteractionsGraph',
'calcLigandInteractions', 'listLigandInteractions',
'calcLigandInteractions', 'showLigandInteractions',
'showProteinInteractions_VMD', 'showLigandInteraction_VMD',
'calcHydrogenBondsTrajectory', 'calcHydrophobicOverlapingAreas',
'Interactions', 'InteractionsTrajectory']
Expand Down Expand Up @@ -2013,6 +2013,61 @@ def calcDistribution(interactions, residue1, residue2=None, **kwargs):
for i in additional_residues:
LOGGER.info(i)


def showLigandInteractions(PLIP_output):
"""Create a list of interactions from PLIP output created using calcLigandInteractions().
Results can be displayed in VMD.
:arg PLIP_output: Results from PLIP for protein-ligand interactions.
:type PLIP_output: PLIP object obtained from calcLigandInteractions()
Note that five types of interactions are considered: hydrogen bonds, salt bridges,
pi-stacking, cation-pi, hydrophobic and water bridges."""

Inter_list_all = []
for i in PLIP_output.all_itypes:
param_inter = [method for method in dir(i) if method.startswith('_') is False]

if str(type(i)).split('.')[-1].strip("'>") == 'hbond':
Inter_list = ['hbond',i.restype+str(i.resnr), i[0].type+'_'+str(i.d_orig_idx), i.reschain,
i.restype+str(i.resnr_l), i[2].type+'_'+str(i.a_orig_idx), i.reschain_l,
i.distance_ad, i.angle, i[0].coords, i[2].coords]

if str(type(i)).split('.')[-1].strip("'>") == 'saltbridge':
Inter_list = ['saltbridge',i.restype+str(i.resnr), '_'.join(map(str,i.negative.atoms_orig_idx)), i.reschain,
i.restype+str(i.resnr_l), '_'.join(map(str,i.positive.atoms_orig_idx)), i.reschain_l,
i.distance, None, i.negative.center, i.positive.center]

if str(type(i)).split('.')[-1].strip("'>") == 'pistack':
Inter_list = ['pistack',i.restype+str(i.resnr), '_'.join(map(str,i[0].atoms_orig_idx)), i.reschain,
i.restype+str(i.resnr_l), '_'.join(map(str,i[1].atoms_orig_idx)), i.reschain_l,
i.distance, i.angle, i[0].center, i[1].center]

if str(type(i)).split('.')[-1].strip("'>") == 'pication':
Inter_list = ['pication',i.restype+str(i.resnr), '_'.join(map(str,i[0].atoms_orig_idx)), i.reschain,
i.restype+str(i.resnr_l), '_'.join(map(str,i[1].atoms_orig_idx)), i.reschain_l,
i.distance, None, i[0].center, i[1].center]

if str(type(i)).split('.')[-1].strip("'>") == 'hydroph_interaction':
Inter_list = ['hydroph_interaction',i.restype+str(i.resnr), i[0].type+'_'+str(i[0].idx), i.reschain,
i.restype+str(i.resnr_l), i[2].type+'_'+str(i[2].idx), i.reschain_l,
i.distance, None, i[0].coords, i[2].coords]

if str(type(i)).split('.')[-1].strip("'>") == 'waterbridge':
water = i.water
Inter_list = ['waterbridge',i.restype+str(i.resnr), i[0].type+'_'+str(i[0].idx), i.reschain,
i.restype+str(i.resnr_l), i[3].type+'_'+str(i[3].idx), i.reschain_l,
[i.distance_aw, i.distance_dw], [i.d_angle, i.w_angle], i[0].coords, i[3].coords,
i.water.coords, i[7].residue.name+'_'+str(i[7].residue.idx)]

Inter_list_all.append(Inter_list)

for nr_k,k in enumerate(Inter_list_all):
LOGGER.info("%3i%22s%10s%26s%4s <---> %8s%12s%4s%6.1f" % (nr_k+1,k[0],k[1],k[2],k[3],k[4],k[5],k[6],k[7]))

return Inter_list_all


def calcLigandInteractions(atoms, **kwargs):
"""Provide ligand interactions with other elements of the system including protein,
water and ions. Results are computed by PLIP [SS15]_ which should be installed.
Expand Down Expand Up @@ -2098,6 +2153,7 @@ def calcLigandInteractions(atoms, **kwargs):
my_mol.analyze()
my_interactions = my_mol.interaction_sets[my_bsid] # Contains all interaction data
Ligands.append(my_interactions)
showLigandInteractions(my_interactions)
except:
LOGGER.info(my_bsid+" not analyzed")

Expand All @@ -2107,60 +2163,6 @@ def calcLigandInteractions(atoms, **kwargs):
raise ImportError("Install Openbabel and PLIP.")


def listLigandInteractions(PLIP_output):
"""Create a list of interactions from PLIP output created using calcLigandInteractions().
Results can be displayed in VMD.
:arg PLIP_output: Results from PLIP for protein-ligand interactions.
:type PLIP_output: PLIP object obtained from calcLigandInteractions()
Note that five types of interactions are considered: hydrogen bonds, salt bridges,
pi-stacking, cation-pi, hydrophobic and water bridges."""

Inter_list_all = []
for i in PLIP_output.all_itypes:
param_inter = [method for method in dir(i) if method.startswith('_') is False]

if str(type(i)).split('.')[-1].strip("'>") == 'hbond':
Inter_list = ['hbond',i.restype+str(i.resnr), i[0].type+'_'+str(i.d_orig_idx), i.reschain,
i.restype+str(i.resnr_l), i[2].type+'_'+str(i.a_orig_idx), i.reschain_l,
i.distance_ad, i.angle, i[0].coords, i[2].coords]

if str(type(i)).split('.')[-1].strip("'>") == 'saltbridge':
Inter_list = ['saltbridge',i.restype+str(i.resnr), '_'.join(map(str,i.negative.atoms_orig_idx)), i.reschain,
i.restype+str(i.resnr_l), '_'.join(map(str,i.positive.atoms_orig_idx)), i.reschain_l,
i.distance, None, i.negative.center, i.positive.center]

if str(type(i)).split('.')[-1].strip("'>") == 'pistack':
Inter_list = ['pistack',i.restype+str(i.resnr), '_'.join(map(str,i[0].atoms_orig_idx)), i.reschain,
i.restype+str(i.resnr_l), '_'.join(map(str,i[1].atoms_orig_idx)), i.reschain_l,
i.distance, i.angle, i[0].center, i[1].center]

if str(type(i)).split('.')[-1].strip("'>") == 'pication':
Inter_list = ['pication',i.restype+str(i.resnr), '_'.join(map(str,i[0].atoms_orig_idx)), i.reschain,
i.restype+str(i.resnr_l), '_'.join(map(str,i[1].atoms_orig_idx)), i.reschain_l,
i.distance, None, i[0].center, i[1].center]

if str(type(i)).split('.')[-1].strip("'>") == 'hydroph_interaction':
Inter_list = ['hydroph_interaction',i.restype+str(i.resnr), i[0].type+'_'+str(i[0].idx), i.reschain,
i.restype+str(i.resnr_l), i[2].type+'_'+str(i[2].idx), i.reschain_l,
i.distance, None, i[0].coords, i[2].coords]

if str(type(i)).split('.')[-1].strip("'>") == 'waterbridge':
water = i.water
Inter_list = ['waterbridge',i.restype+str(i.resnr), i[0].type+'_'+str(i[0].idx), i.reschain,
i.restype+str(i.resnr_l), i[3].type+'_'+str(i[3].idx), i.reschain_l,
[i.distance_aw, i.distance_dw], [i.d_angle, i.w_angle], i[0].coords, i[3].coords,
i.water.coords, i[7].residue.name+'_'+str(i[7].residue.idx)]

Inter_list_all.append(Inter_list)

for nr_k,k in enumerate(Inter_list_all):
LOGGER.info("%3i%22s%10s%26s%4s <---> %8s%12s%4s%6.1f" % (nr_k,k[0],k[1],k[2],k[3],k[4],k[5],k[6],k[7]))

return Inter_list_all


def showProteinInteractions_VMD(atoms, interactions, color='red',**kwargs):
"""Save information about protein interactions to a TCL file (filename)
which can be further use in VMD to display all intercations in a graphical interface
Expand Down

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