Interactions and Stability (InSty)

This module called InSty defines functions for calculating different types of interactions in protein structure, between proteins or between protein and ligand. The following interactions are available for protein interactions:

1. Hydrogen bonds
2. Salt Bridges
3. Repulsive Ionic Bonding
4. Pi stacking interactions
5. Pi-cation interactions
6. Hydrophobic interactions
7. Disulfide Bonds

class Interactions(title='Unknown')

Class for Interaction analysis of proteins.

buildInteractionMatrix(**kwargs)

Build matrix with protein interactions. Interactions are counted as follows:

1. Hydrogen bonds (HBs) +1
2. Salt Bridges (SBs) +1 (Salt bridges might be included in hydrogen bonds)
3. Repulsive Ionic Bonding (RIB) +1
4. Pi stacking interactions (PiStack) +1
5. Pi-cation interactions (PiCat) +1
6. Hydrophobic interactions (HPh) +1
7. Disulfide bonds (DiBs) +1

Some type of interactions could be removed from the analysis by replacing value 1 by 0. Example: >>> interactions = Interactions() >>> atoms = parsePDB(PDBfile).select(‘protein’) >>> interactions.calcProteinInteractions(atoms) >>> interactions.buildInteractionMatrix(RIB=0, HBs=0, HPh=0)

Parameters:

• HBs (int, float) – score per single hydrogen bond
• SBs (int, float) – score per single salt bridge
• RIB (int, float) – score per single repulsive ionic bonding
• PiStack (int, float) – score per pi-stacking interaction
• PiCat (int, float) – score per pi-cation interaction
• HPh (int, float) – score per hydrophobic interaction
• DiBs (int, float) – score per disulfide bond

calcProteinInteractions(atoms, **kwargs)

Compute all protein interactions (shown below) using default parameters.

1. Hydrogen bonds
2. Salt Bridges
3. RepulsiveIonicBonding
4. Pi stacking interactions
5. Pi-cation interactions
6. Hydrophobic interactions
7. Disulfide Bonds

Parameters:atoms (Atomic) – an Atomic object from which residues are selected

getAtoms()

Returns associated atoms.

getDisulfideBonds(**kwargs)

Returns the list of disulfide bonds.

Parameters:

• selection (str) – selection string
• selection2 (str) – selection string

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

getFrequentInteractors(contacts_min=3)

Provide a list of residues with the most frequent interactions based on the following interactions:

1. Hydrogen bonds (hb)
2. Salt Bridges (sb)
3. Repulsive Ionic Bonding (rb)
4. Pi stacking interactions (ps)
5. Pi-cation interactions (pc)
6. Hydrophobic interactions (hp)
7. Disulfide bonds (disb)

Parameters:contacts_min (int) – Minimal number of contacts which residue may form with other residues, by default 3.

getHydrogenBonds(**kwargs)

Returns the list of hydrogen bonds.

Parameters:

• selection (str) – selection string
• selection2 (str) – selection string

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

getHydrophobic(**kwargs)

Returns the list of hydrophobic interactions.

Parameters:

• selection (str) – selection string
• selection2 (str) – selection string

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

getInteractions(**kwargs)

Returns the list of all interactions.

Parameters:

• selection (str) – selection string
• selection2 (str) – selection string

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

getPiCation(**kwargs)

Returns the list of Pi-cation interactions.

Parameters:

• selection (str) – selection string
• selection2 (str) – selection string

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

getPiStacking(**kwargs)

Returns the list of Pi-stacking interactions.

Parameters:

• selection (str) – selection string
• selection2 (str) – selection string

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

getRepulsiveIonicBonding(**kwargs)

Returns the list of repulsive ionic bonding.

Parameters:

• selection (str) – selection string
• selection2 (str) – selection string

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

getSaltBridges(**kwargs)

Returns the list of salt bridges.

Parameters:

• selection (str) – selection string
• selection2 (str) – selection string

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

saveInteractionsPDB(**kwargs)

Save the number of potential interactions to PDB file in occupancy column.

Parameters:filename (str) – name of the PDB file which will be saved for visualization, it will contain the results in occupancy column.

setNewDisulfideBonds(interaction)

Replace default calculation of hydrophobic interactions by the one provided by user.

setNewHydrogenBonds(interaction)

Replace default calculation of hydrogen bonds by the one provided by user.

setNewHydrophobic(interaction)

Replace default calculation of hydrophobic interactions by the one provided by user.

setNewPiCation(interaction)

Replace default calculation of pi-cation interactions by the one provided by user.

setNewPiStacking(interaction)

Replace default calculation of pi-stacking interactions by the one provided by user.

setNewRepulsiveIonicBonding(interaction)

Replace default calculation of repulsive ionic bonding by the one provided by user.

setNewSaltBridges(interaction)

Replace default calculation of salt bridges by the one provided by user.

setTitle(title)

Set title of the model.

showCumulativeInteractionTypes(**kwargs)

Bar plot with the number of potential inetractions per residue. Particular type of interactions can be excluded by using keywords HBs=0, RIB=0, etc.

Parameters:

• HBs (int, float) – score per single hydrogen bond
• SBs (int, float) – score per single salt bridge
• RIB (int, float) – score per single repulsive ionic bonding
• PiStack (int, float) – score per pi-stacking interaction
• PiCat (int, float) – score per pi-cation interaction
• HPh (int, float) – score per hydrophobic interaction
• DiBs (int, float) – score per disulfide bond

showFrequentInteractors(cutoff=5, **kwargs)

Plots regions with the most frequent interactions.

Parameters:cutoff (int, float) – minimal score per residue which will be displayed. If cutoff value is to big, top 30% with the higest values will be returned. Default is 5.

Nonstandard resiudes can be updated in a following way: d = {‘CYX’: ‘X’, ‘CEA’: ‘Z’} >>> name.showFrequentInteractors(d)

showInteractors(**kwargs)

Display protein residues and their number of potential interactions with other residues from protein structure.

class InteractionsTrajectory(name='Unknown')

Class for Interaction analysis of DCD trajectory or multi-model PDB (Ensemble PDB).

calcProteinInteractionsTrajectory(atoms, trajectory=None, filename=None, **kwargs)

Compute all protein interactions (shown below) for DCD trajectory or multi-model PDB

using default parameters. (1) Hydrogen bonds (2) Salt Bridges (3) RepulsiveIonicBonding (4) Pi stacking interactions (5) Pi-cation interactions (6) Hydrophobic interactions (7) Disulfide Bonds

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• trajectory (class:.Trajectory) – trajectory file
• filename (pkl) – Name of pkl filename in which interactions will be storage
• selection (str) – selection string
• selection2 (str) – selection string
• start_frame (int) – index of first frame to read
• stop_frame (int) – index of last frame to read

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

getAtoms()

Returns associated atoms.

getDisulfideBonds(**kwargs)

Return the list of disulfide bonds computed from DCD trajectory.

Parameters:

• selection (str) – selection string
• selection2 (str) – selection string

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

getHydrogenBonds(**kwargs)

Return the list of hydrogen bonds computed from DCD trajectory.

Parameters:

• selection (str) – selection string
• selection2 (str) – selection string

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

getHydrophobic(**kwargs)

Return the list of hydrophobic interactions computed from DCD trajectory.

Parameters:

• selection (str) – selection string
• selection2 (str) – selection string

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

getInteractions(**kwargs)

Return the list of all interactions.

Parameters:

• selection (str) – selection string
• selection2 (str) – selection string

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

getInteractionsNumber()

Return the number of interactions in each frame.

getPiCation(**kwargs)

Return the list of Pi-cation interactions computed from DCD trajectory.

Parameters:

• selection (str) – selection string
• selection2 (str) – selection string

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

getPiStacking(**kwargs)

Return the list of Pi-stacking interactions computed from DCD trajectory.

Parameters:

• selection (str) – selection string
• selection2 (str) – selection string

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

getRepulsiveIonicBonding(**kwargs)

Return the list of repulsive ionic bonding computed from DCD trajectory.

Parameters:

• selection (str) – selection string
• selection2 (str) – selection string

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

getSaltBridges(**kwargs)

Return the list of salt bridges computed from DCD trajectory.

Parameters:

• selection (str) – selection string
• selection2 (str) – selection string

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

getTimeInteractions(filename=None, **kwargs)

Return a bar plots with the number of interactions per each frame.

Parameters:filename (str) – PNG file name

parseInteractions(filename)

Import interactions from analysis of trajectory which was saved via calcProteinInteractionsTrajectory().

Parameters:filename (pkl) – Name of pkl file in which interactions will be storage

setNewDisulfideBondsTrajectory(interaction)

Replace default calculation of disulfide bonds by the one provided by user.

setNewHydrogenBondsTrajectory(interaction)

Replace default calculation of hydrogen bonds by the one provided by user.

setNewHydrophobicTrajectory(interaction)

Replace default calculation of hydrophobic interactions by the one provided by user.

setNewPiCationTrajectory(interaction)

Replace default calculation of pi-cation interactions by the one provided by user.

setNewPiStackingTrajectory(interaction)

Replace default calculation of pi-stacking interactions by the one provided by user.

setNewRepulsiveIonicBondingTrajectory(interaction)

Replace default calculation of repulsive ionic bonding by the one provided by user.

setNewSaltBridgesTrajectory(interaction)

Replace default calculation of salt bridges by the one provided by user.

class LigandInteractionsTrajectory(name='Unknown')

Class for protein-ligand interaction analysis of DCD trajectory or multi-model PDB (Ensemble PDB). This class is using PLIP to provide the interactions. Install PLIP before using it.

## Instalation of PLIP using conda: >>> conda install -c conda-forge plip ## https://anaconda.org/conda-forge/plip # https://github.com/pharmai/plip/blob/master/DOCUMENTATION.md

## Instalation using PIP: >>> pip install plip

[SS15]

Salentin S., Schreiber S., Haupt V. J., Adasme M. F., Schroeder M.

PLIP: fully automated protein–ligand interaction profiler Nucl. Acids Res. 2015 43:W443-W447.

calcFrequentInteractors(**kwargs)

Returns a dictonary with residues involved in the interaction with ligand and their number of counts.

Parameters:selection (str) – selection string of ligand with chain ID e.g. “MESA” where MES is ligand resname and A is chain ID. Selection pointed as None will return all interactions together without ligands separation.

calcLigandInteractionsTrajectory(atoms, trajectory=None, **kwargs)

Compute protein-ligand interactions for DCD trajectory or multi-model PDB

using PLIP library.

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• trajectory (class:.Trajectory) – trajectory file
• filename (pkl) – Name of pkl filename in which interactions will be storage
• start_frame (int) – index of first frame to read
• stop_frame (int) – index of last frame to read
• output (bool) – parameter to print the interactions on the screen while analyzing the structure, use ‘info’.

getAtoms()

Returns associated atoms.

getInteractionTypes()

Show which interaction types were detected for ligands.

getLigandInteractions(**kwargs)

Return the list of protein-ligand interactions.

Parameters:

• filters (str) – selection string of ligand with chain ID or interaction type e.g. ‘SBs’ (HBs, SBs, HPh, PiStack, PiCat, HPh, watBridge)
• include_frames (bool) – used with filters, it will leave selected keyword in orginal lists, if False it will collect selected interactions in one list, Use True to assign new selection using setLigandInteractions. by default True

getLigandInteractionsNumber(**kwargs)

Return the number of interactions per each frame. Number of interactions can be a total number of interactions or it can be divided into interaction types.

Parameters:types (bool) – Interaction types can be included (True) or not (False). by default is True.

getLigandsNames()

Show which ligands are in a system.

parseLigandInteractions(filename)

Import interactions from analysis of trajectory which was saved via calcLigandInteractionsTrajectory().

Parameters:filename (pkl) – Name of pkl file in which interactions will be storage

saveInteractionsPDB(**kwargs)

Save the number of interactions with ligand to PDB file in occupancy column It will recognize the chains. If the system will contain one chain and many segments the PDB file will not be created in a correct way.

Parameters:

• filename (str) – name of the PDB file which will be saved for visualization, it will contain the results in occupancy column.
• ligand_sele (str) – ligand selection, by default is ‘all not (protein or water or ion)’.

setLigandInteractions(atoms, interaction)

Replace protein-ligand interactions for example byb using getLigandInteractions() with filters to select particular ligand.

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• interactions (list) – list of interactions

calcHydrogenBonds(atoms, **kwargs)

Compute hydrogen bonds for proteins and other molecules.

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• distDA (int, float) – non-zero value, maximal distance between donor and acceptor. default is 3.5 distA also works
• angleDHA (int, float) – non-zero value, maximal (180 - D-H-A angle) (donor, hydrogen, acceptor). default is 40. angle also works
• seq_cutoff_HB (int) – non-zero value, interactions will be found between atoms with index differences that are higher than seq_cutoff_HB. default is 25 atoms. seq_cutoff also works
• donors (list) – which atoms to count as donors default is [‘N’, ‘O’, ‘S’, ‘F’]
• acceptors (list) – which atoms to count as acceptors default is [‘N’, ‘O’, ‘S’, ‘F’]
• selection (str) – selection string
• selection2 (str) – selection string

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

Structure should contain hydrogens. If not they can be added using addMissingAtoms(pdb_name) function available in ProDy after Openbabel installation. conda install -c conda-forge openbabel

Note that the angle which it is considering is 180-defined angle D-H-A (in a good agreement with VMD) Results can be displayed in VMD by using showVMDinteraction()

calcChHydrogenBonds(atoms, **kwargs)

Finds hydrogen bonds between different chains. See more details in calcHydrogenBonds().

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• distA (int, float) – non-zero value, maximal distance between donor and acceptor. default is 3.5
• angle (int, float) – non-zero value, D-H-A angle (donor, hydrogen, acceptor). default is 40.
• seq_cutoff (int) – non-zero value, interactions will be found between atoms with index differences that are higher than seq_cutoff. default is 25 atoms.

Structure should contain hydrogens. If not they can be added using addMissingAtoms(pdb_name) function available in ProDy after Openbabel installation. conda install -c conda-forge openbabel

Note that the angle which it is considering is 180-defined angle D-H-A (in a good agreement with VMD) Results can be displayed in VMD.

calcSaltBridges(atoms, **kwargs)

Finds salt bridges in protein structure. Histidines are considered as charge residues.

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• distSB (int, float) – non-zero value, maximal distance between center of masses of N and O atoms of negatively and positevely charged residues. default is 5. distA also works
• selection (str) – selection string
• selection2 (str) – selection string

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

Results can be displayed in VMD.

calcRepulsiveIonicBonding(atoms, **kwargs)

Finds repulsive ionic bonding in protein structure i.e. between positive-positive or negative-negative residues. Histidine is not considered as a charged residue.

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• distRB (int, float) – non-zero value, maximal distance between center of masses between N-N or O-O atoms of residues. default is 4.5. distA works too
• selection (str) – selection string
• selection2 (str) – selection string

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

Results can be displayed in VMD.

calcPiStacking(atoms, **kwargs)

Finds π–π stacking interactions (between aromatic rings).

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• distPS (int, float) – non-zero value, maximal distance between center of masses of residues aromatic rings. default is 5. distA works too
• angle_min_PS (int, float) – minimal angle between aromatic rings. default is 0. angle_min works too
• angle_max_PS (int, float) – maximal angle between rings. default is 360. angle_max works too
• selection (str) – selection string
• selection2 (str) – selection string
• non_standard_PS (dict) – dictionary of non-standard residue in the protein structure that need to be included in calculations non_standard works too

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

Results can be displayed in VMD. By default three residues are included TRP, PHE, TYR and HIS. Additional selection can be added:

>>> non_standard = {"HSE": "noh and not backbone and not name CB", 
            "HSD": "noh and not backbone and not name CB"}
>>> calcPiStacking(atoms, non_standard)

Predictions for proteins only. To compute protein-ligand interactions use calcLigandInteractions() or define **kwargs.

calcPiCation(atoms, **kwargs)

Finds cation-Pi interaction i.e. between aromatic ring and positively charged residue (ARG and LYS).

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• distPC (int, float) – non-zero value, maximal distance between center of masses of aromatic ring and positively charge group. default is 5. distA works too
• selection (str) – selection string
• selection2 (str) – selection string
• non_standard_PC (dict) – dictionary of non-standard residue in the protein structure that need to be included in calculations non_standard also works

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

By default three residues are included TRP, PHE, TYR and HIS. Additional selection can be added:

>>> calcPiCation(atoms, 'HSE'='noh and not backbone and not name CB')
or
>>> non_standard = {"HSE": "noh and not backbone and not name CB", 
        "HSD": "noh and not backbone and not name CB"}
>>> calcPiCation(atoms, non_standard)

Results can be displayed in VMD. Predictions for proteins only. To compute protein-ligand interactions use calcLigandInteractions() or define **kwargs

calcHydrophobic(atoms, **kwargs)

Prediction of hydrophobic interactions between hydrophobic residues (ALA, ILE, LEU, MET, PHE, TRP, VAL, CG of ARG, and CG and CD of LYS).

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• distHPh (int, float) – non-zero value, maximal distance between atoms of hydrophobic residues. default is 4.5. distA works too
• non_standard_Hph (dict) – dictionary of non-standard residue in the protein structure that need to be included in calculations non_standard works too
• zerosHPh (bool) – zero values of hydrophobic overlaping areas included default is False

Last value in the output corresponds to the total hydrophobic overlaping area for two residues not only for the atoms that are included in the list. Atoms that which are listed are the closest between two residues and they will be inluded to draw the line in VMD.

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

Additional selection can be added as shown below (with selection that includes only hydrophobic part):

>>> calcHydrophobic(atoms, non_standard_Hph={'XLE'='noh and not backbone', 
                                        'XLI'='noh and not backbone'})

Predictions for proteins only. To compute protein-ligand interactions use calcLigandInteractions(). Results can be displayed in VMD by using showVMDinteraction()

Note that interactions between aromatic residues are omitted becasue they are provided by calcPiStacking().

calcDisulfideBonds(atoms, **kwargs)

Prediction of disulfide bonds.

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• distDB (int, float) – non-zero value, maximal distance between atoms of hydrophobic residues. default is 3. distA works too

calcMetalInteractions(atoms, distA=3.0, extraIons=['FE'], excluded_ions=['SOD', 'CLA'])

Interactions with metal ions (includes water, ligands and other ions).

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• distA (int, float) – non-zero value, maximal distance between ion and residue. default is 3.0
• extraIons (list) – ions to be included in the analysis.
• excluded_ions (list) – ions which should be excluded from the analysis.

calcHydrogenBondsTrajectory(atoms, trajectory=None, **kwargs)

Compute hydrogen bonds for DCD trajectory or multi-model PDB using default parameters.

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• trajectory (class:.Trajectory) – trajectory file
• distA (int, float) – non-zero value, maximal distance between donor and acceptor. default is 3.5
• angle (int, float) – non-zero value, maximal (180 - D-H-A angle) (donor, hydrogen, acceptor). default is 40.
• seq_cutoff (int) – non-zero value, interactions will be found between atoms with index differences that are higher than seq_cutoff. default is 20 atoms.
• selection (str) – selection string
• selection2 (str) – selection string
• start_frame (int) – index of first frame to read
• stop_frame (int) – index of last frame to read

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

calcSaltBridgesTrajectory(atoms, trajectory=None, **kwargs)

Compute salt bridges for DCD trajectory or multi-model PDB using default parameters.

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• trajectory (class:.Trajectory) – trajectory file
• distA (int, float) – non-zero value, maximal distance between center of masses of N and O atoms of negatively and positevely charged residues. default is 5.
• selection (str) – selection string
• selection2 (str) – selection string
• start_frame (int) – index of first frame to read
• stop_frame (int) – index of last frame to read

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

calcRepulsiveIonicBondingTrajectory(atoms, trajectory=None, **kwargs)

Compute repulsive ionic bonding for DCD trajectory or multi-model PDB using default parameters.

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• trajectory (class:.Trajectory) – trajectory file
• distA (int, float) – non-zero value, maximal distance between center of masses between N-N or O-O atoms of residues. default is 4.5.
• selection (str) – selection string
• selection2 (str) – selection string
• start_frame (int) – index of first frame to read
• stop_frame (int) – index of last frame to read

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

calcPiStackingTrajectory(atoms, trajectory=None, **kwargs)

Compute Pi-stacking interactions for DCD trajectory or multi-model PDB using default parameters.

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• trajectory (class:.Trajectory) – trajectory file
• distA (int, float) – non-zero value, maximal distance between center of masses of residues aromatic rings. default is 5.
• angle_min (int) – minimal angle between aromatic rings. default is 0.
• angle_max (int, float) – maximal angle between rings. default is 360.
• selection (str) – selection string
• selection2 (str) – selection string
• start_frame (int) – index of first frame to read
• stop_frame (int) – index of last frame to read

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

calcPiCationTrajectory(atoms, trajectory=None, **kwargs)

Compute Pi-cation interactions for DCD trajectory or multi-model PDB using default parameters.

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• trajectory (class:.Trajectory) – trajectory file
• distA (int, float) – non-zero value, maximal distance between center of masses of aromatic ring and positively charge group. default is 5.
• selection (str) – selection string
• selection2 (str) – selection string
• start_frame (int) – index of first frame to read
• stop_frame (int) – index of last frame to read

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

calcHydrophobicTrajectory(atoms, trajectory=None, **kwargs)

Compute hydrophobic interactions for DCD trajectory or multi-model PDB using default parameters.

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• trajectory (class:.Trajectory) – trajectory file
• distA (int, float) – non-zero value, maximal distance between atoms of hydrophobic residues. default is 4.5.
• selection (str) – selection string
• selection2 (str) – selection string
• start_frame (int) – index of first frame to read
• stop_frame (int) – index of last frame to read

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

calcDisulfideBondsTrajectory(atoms, trajectory=None, **kwargs)

Compute disulfide bonds for DCD trajectory or multi-model PDB using default parameters.

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• trajectory (class:.Trajectory) – trajectory file
• distA (int, float) – non-zero value, maximal distance between atoms of hydrophobic residues. default is 2.5.
• start_frame (int) – index of first frame to read
• stop_frame (int) – index of last frame to read

calcProteinInteractions(atoms, **kwargs)

Compute all protein interactions (shown below) using default parameters.

1. Hydrogen bonds
2. Salt Bridges
3. RepulsiveIonicBonding
4. Pi stacking interactions
5. Pi-cation interactions
6. Hydrophobic interactions
7. Disulfide Bonds

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• selection (str) – selection string
• selection2 (str) – selection string

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

calcStatisticsInteractions(data, **kwargs)

Return the statistics of interactions from PDB Ensemble or trajectory including: (1) the weight for each residue pair: corresponds to the number of counts divided by the number of frames (values >1 are obtained when residue pair creates multiple contacts); (2) average distance of interactions for each pair [in Ang] and (3) standard deviation [Ang.].

Parameters:

• data (list) – list with interactions from calcHydrogenBondsTrajectory() or other types
• weight_cutoff (int, float) – value above which results will be displayed 1 or more means that residue contact is present in all conformations/frames default value is 0.2 (in 20% of conformations contact appeared)

Example of usage: >>> atoms = parsePDB(‘PDBfile.pdb’) >>> dcd = Trajectory(‘DCDfile.dcd’) >>> dcd.link(atoms) >>> dcd.setCoords(atoms)

>>> data = calcPiCationTrajectory(atoms, dcd, distA=5)
or
>>> interactionsTrajectory = InteractionsTrajectory()
>>> data = interactionsTrajectory.getPiCation()

calcDistribution(interactions, residue1, residue2=None, **kwargs)

Distributions/histograms of pairs of amino acids. Histograms are normalized.

Parameters:

• interactions (list) – list of interactions
• residue1 (str) – residue name in 3-letter code and residue number
• residue2 (str) – residue name in 3-letter code and residue number
• metrics (str) – name of the data type ‘distance’ or ‘angle’ depends on the type of interaction

calcSASA(atoms, **kwargs)

Provide information about solvent accessible surface area (SASA) based on the sasa program. To use this function compiled hpb.so is needed.

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• selection (str) – selection string by default all the protein structure is used
• sasa_cutoff (float, int) – cutoff for SASA values default is 0.0
• resnames (bool) – residues name included default is False

calcVolume(atoms, **kwargs)

Provide information about volume for each residue/molecule/chain or other selection”. To use this function compiled hpb.so is needed.

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• selection (str) – selection string by default all the protein structure is used
• volume_cutoff – cutoff for volume default is 0.0 to include all the results
• split_residues (bool) – it will provide values for each residue default is False
• resnames (bool) – residues name included default is False True - will give residue names and values for each residue False - will give only the values for each residues

compareInteractions(data1, data2, **kwargs)

Comparison of two outputs from interactions. It will provide information about the disappearance and appearance of some interactions as well as the similarities in the interactions for the same system. Two conformations can be compared.

Parameters:

• data1 (list) – list with interactions from calcHydrogenBonds() or other types
• data2 (list) – list with interactions from calcHydrogenBonds() or other types
• filename – name of text file in which the comparison between two sets of interactions will be saved

type filename: str

Example of usage: >>> atoms1 = parsePDB(‘PDBfile1.pdb’).select(‘protein’) >>> atoms2 = parsePDB(‘PDBfile2.pdb’).select(‘protein’) >>> compareInteractions(calcHydrogenBonds(atoms1), calcHydrogenBonds(atoms2))

showInteractionsGraph(statistics, **kwargs)

Return residue-residue interactions as graph/network.

Parameters:

• statistics (list) – Results obtained from calcStatisticsInteractions analysis
• cutoff (int, float) – Minimal number of counts per residue in the trajectory by default 0.1.
• code (str) – representation of the residues, 3-letter or 1-letter by default 3-letter
• multiple_chains (bool) – display chain name for structure with many chains by default False
• edge_cmap (str) – color of the residue connection by default plt.cm.Blues (blue color)
• node_size (int) – size of the nodes which describes residues by default 300
• node_distance (int) – value which will scale residue-residue interactions by default 5
• font_size (int) – size of the font by default 14
• seed (int) – random number which affect the distribution of residues by default 42

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. Note that PLIP will not recognize ligand unless it will be HETATM in the PDB file.

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• sele (str) – a selection string for residues of interest default is ‘all not (water or protein or ion)’
• ignore_ligs (list) – List of ligands which will be excluded from the analysis.

To display results as a list of interactions use listLigandInteractions() and for visualization in VMD please use showLigandInteraction_VMD()

Requirements of usage: ## Instalation of Openbabel: >>> conda install -c conda-forge openbabel ## https://anaconda.org/conda-forge/openbabel

## Instalation of PLIP >>> conda install -c conda-forge plip ## https://anaconda.org/conda-forge/plip # https://github.com/pharmai/plip/blob/master/DOCUMENTATION.md

[SS15]

Salentin S., Schreiber S., Haupt V. J., Adasme M. F., Schroeder M.

PLIP: fully automated protein–ligand interaction profiler Nucl. Acids Res. 2015 43:W443-W447.

listLigandInteractions(PLIP_output, **kwargs)

Create a list of interactions from PLIP output created using calcLigandInteractions(). Results can be displayed in VMD.

Parameters:

• PLIP_output (PLIP object obtained from calcLigandInteractions()) – Results from PLIP for protein-ligand interactions.
• output (bool) – parameter to print the interactions on the screen while analyzing the structure (True | False) by default is False

Note that five types of interactions are considered: hydrogen bonds, salt bridges, pi-stacking, cation-pi, hydrophobic and water bridges.

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 (in TKConsole: play script_name.tcl). Different types of interactions can be saved separately (color can be selected) or all at once for all types of interactions (hydrogen bonds - blue, salt bridges - yellow, pi stacking - green, cation-pi - orangem, hydrophobic - silver, and disulfide bonds - black).

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• interactions (List of lists) – List of interactions for protein interactions.
• color (str) – color to draw interactions in VMD, not used only for single interaction type. default “red”
• filename (str) – name of TCL file where interactions will be saved.

Example (hydrogen bonds for protein only): >>> interactions = calcHydrogenBonds(atoms.protein, distA=3.2, angle=30) or all interactions at once: >>> interactions = calcProteinInteractions(atoms.protein)

showLigandInteraction_VMD(atoms, interactions, **kwargs)

Save information from PLIP for ligand-protein interactions in a TCL file which can be further used in VMD to display all intercations in a graphical interface (hydrogen bonds - blue, salt bridges - yellow, pi stacking - green, cation-pi - orange, hydrophobic - silver and water bridges - cyan).

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• interactions (list) – List of interactions lists for protein-ligand interactions.
• filename (str) – name of TCL file where interactions will be saved.

To obtain protein-ligand interactions: >>> calculations = calcLigandInteractions(atoms) >>> interactions = listLigandInteractions(calculations)

calcHydrogenBondsTrajectory(atoms, trajectory=None, **kwargs)

Compute hydrogen bonds for DCD trajectory or multi-model PDB using default parameters.

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• trajectory (class:.Trajectory) – trajectory file
• distA (int, float) – non-zero value, maximal distance between donor and acceptor. default is 3.5
• angle (int, float) – non-zero value, maximal (180 - D-H-A angle) (donor, hydrogen, acceptor). default is 40.
• seq_cutoff (int) – non-zero value, interactions will be found between atoms with index differences that are higher than seq_cutoff. default is 20 atoms.
• selection (str) – selection string
• selection2 (str) – selection string
• start_frame (int) – index of first frame to read
• stop_frame (int) – index of last frame to read

Selection: If we want to select interactions for the particular residue or group of residues:

selection=’chain A and resid 1 to 50’

If we want to study chain-chain interactions:

selection=’chain A’, selection2=’chain B’

calcHydrophobicOverlapingAreas(atoms, **kwargs)

Provide information about hydrophobic contacts between pairs of residues based on the regsurf program. To use this function compiled hpb.so is needed.

Parameters:

• atoms (Atomic) – an Atomic object from which residues are selected
• selection (str) – selection string of hydrophobic residues
• hpb_cutoff (float, int) – cutoff for hydrophobic overlaping area values default is 0.0
• cumulative_values ('pairs' or 'single_residues') – sum of results for pairs of residues or for single residues without distinguishing pairs, default is None

calcSminaBindingAffinity(atoms, trajectory=None, **kwargs)

Computing binding affinity of ligand toward protein structure using SMINA package [DRK13].

Parameters:

• atoms (Atomic, LigandInteractionsTrajectory) – an Atomic object from which residues are selected
• protein_selection (str) – selection string for the protein and other compoment of the system that should be included, e.g. “protein and chain A”, by default “protein”
• ligand_selection (str) – selection string for ligand, e.g. “resname ADP”, by default “all not protein”
• ligand_selection – scoring function (vina or vinardo) by default is “vina”
• atom_terms (bool) – write per-atom interaction term values. It will provide more information as dictionary for each frame/model, and details for atom terms will be saved in terms_*frame_number*.txt, by default is False

SMINA installation is required to compute ligand binding affinity: >> conda install -c conda-forge smina (for Anaconda)

For more information on SMINA see https://sourceforge.net/projects/smina/. If you benefited from SMINA, please consider citing [DRK13].

[DRK13]

(1, 2, 3) Koes D. R., Baumgartner M. P., Camacho C. J., Lessons Learned in

Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise, J. Chem. Inf. Model. 2013 53: 1893–1904.

calcSminaPerAtomInteractions(atoms, list_terms)

Computing the summary of per-atom interaction term values using SMINA package [DRK13]. It will return dictionary with per-atom interaction term values.

Parameters:

• atoms (Atomic, LigandInteractionsTrajectory) – an Atomic object from which residues are selected
• list_terms (list) – List of terms.txt files obtained from meth:.calcSminaBindingAffinity using atom_terms = True

Important: First text file in the list should be reference structure which correspond to the provided coordinates as atoms.

calcSminaTermValues(data)

Computing weights multiplied by term values, before weighting for each Term. As a results will are obtaining a dictionary.

Parameters:data (list) – List of results provided by Smina using meth:.calcSminaBindingAffinity with atom_terms = True

showSminaTermValues(data)

Display a histogram of weights multiplied by term values, before weighting for each Term. As a results will are obtaining a dictionary.

Parameters:data (list) – List of results provided by Smina using meth:.calcSminaBindingAffinity with atom_terms = True