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Rotamer Library

With angles and bonds being rather rigid, the conformation of an amino acid sidechain can completely be described in terms of dihedral angles. Preferred combinations of such dihedral angles are a result of steric properties and can be gathered in rotamer libraries. Different libraries exist in the field and their main difference is, whether the provided sidechain conformations are dependent on their backbone or not. ProMod3 provides you with a BBDepRotamerLib organizing rotamers for the different aminoacids in equidistant phi/psi bins, as well as a simple RotamerLib. Both libraries are containers for RotamerLibEntry and are optimized for fast writing/loading from/to disk. Once initialized, the library is in a dynamic mode where rotamers can be added. No rotamers can be read at this stage. As soon as all required rotamers are added, the library can be made static. This is the mode you can get the rotamers out of it or dump it to disk.

The Non Backbone Dependent Rotamer Library

class promod3.sidechain.RotamerLib

Non backbone dependent rotamer library

static Load(filename)
static LoadPortable(filename)

Loads raw binary file generated with Save() (optimized for fast reading) / portable file generated with SavePortable() (slower but less machine-dependent).

Parameters:filename (str) – Path to the file from which to load.
Returns:A rotamer library
Return type:RotamerLib
Raises:RuntimeError if file cannot be opened or if file cannot be parsed (see here for details).
Save(filename)
SavePortable(filename)

Saves a raw / portable binary representation. Use portable files for distribution and convert locally to raw files. See here for details.

Parameters:filename (str) – Path to the file where it will be saved.
AddRotamer(id, rotamer)
Parameters:
Raises:

RuntimeError if the library is already static

QueryLib(id)

The query function follows following strategies in case of special id requests.

  • if id = HSD (d-protonated HIS) try to find HSD, fallback to HIS in case of failure
  • if id = HSE (e-protonated HIS) try to find HSE, fallback to HIS in case of failure
  • if id = CYH (“free” CYS) try to find CYH, fallback to CYS in case of failure
  • if id = CYD (“disulfid” CYS) try to find CYD, fallback to CYS in case of failure
  • if id = CPR (cis-PRO) try to find CPR, fallback to PRO in case of failure
  • if id = TPR (trans-PRO) try to find TPR, fallback to PRO in case of failure
Parameters:id (RotamerID) – Identity of rotamer of interest
Returns:list of RotamerLibEntry of nonzero probability sorted by their probability
Raises:RuntimeError if no entries for id can be found
MakeStatic()

Once all rotamers are added, the library can be made static to become readable and ready for io.

The Backbone Dependent Rotamer Library

class promod3.sidechain.BBDepRotamerLib(phi_bins, psi_bins)

Backbone dependent rotamer library

Parameters:
  • phi_bins (int) – number of bins for phi backbone dihedral
  • psi_bins (int) – number of bins for psi backbone dihedral
static Load(filename)
static LoadPortable(filename)

Loads raw binary file generated with Save() (optimized for fast reading) / portable file generated with SavePortable() (slower but less machine-dependent).

Parameters:filename (str) – Path to the file from which to load.
Returns:A rotamer library
Return type:BBDepRotamerLib
Raises:RuntimeError if file cannot be opened or if file cannot be parsed (see here for details).
Save(filename)
SavePortable(filename)

Saves a raw / portable binary representation. Use portable files for distribution and convert locally to raw files. See here for details.

Parameters:filename (str) – Path to the file where it will be saved.
Raises:RuntimeError if file cannot be opened.
AddRotamer(id, r1, r2, r3, r4, phi_bin, psi_bin, rotamer)
Parameters:
  • id (RotamerID) – Identity of rotamer to be added
  • r1 (int) – Configuration of chi1
  • r2 (int) – Configuration of chi2
  • r3 (int) – Configuration of chi3
  • r4 (int) – Configuration of chi4
  • phi_bin (int) – Phi backbone dihedral description
  • psi_bin (int) – Psi backbone dihedral description
  • rotamer (RotamerLibEntry) – the rotamer to be added
Raises:

RuntimeError if an invalid backbone angle bin is given or when the library is already static.

QueryLib(id, phi, psi)

The returned rotamers are either directly returned in the form as they are added to the library or can be interpolated. In the first option, phi and psi simply get transformed to the according bin using following formalism: bin = round((angle + pi)/bin_size). In case of interpolation, the chi angles of rotameric dihedral angles and the according standard deviations of the rotamers get bilinearly interpolated using the corresponding rotamers with same configuration from the neighbouring bins. No interplation is applied to non-rotameric dihedral angles (chi2 in ASP, ASN, HIS, PHE, TRP, TYR; chi3 in GLU, GLN). This behaviour can be controlled with SetInterpolate(). The query function follows following strategies in case of special id requests.

  • if id = HSD (d-protonated HIS) try to find HSD, fallback to HIS in case of failure
  • if id = HSE (e-protonated HIS) try to find HSE, fallback to HIS in case of failure
  • if id = CYH (“free” CYS) try to find CYH, fallback to CYS in case of failure
  • if id = CYD (“disulfid” CYS) try to find CYD, fallback to CYS in case of failure
  • if id = CPR (cis-PRO) try to find CPR, fallback to PRO in case of failure
  • if id = TPR (trans-PRO) try to find TPR, fallback to PRO in case of failure
Parameters:
  • id (RotamerID) – Identity of rotamer of interest
  • phi (float) – Phi backbone dihedral angle in range [-pi,pi[
  • psi (float) – Psi backbone dihedral angle in range [-pi,pi[
Returns:

list of RotamerLibEntry of nonzero probability for given phi/psi pair sorted by their probability

Raises:

RuntimeError if no entries for id can be found

MakeStatic()

Once all rotamers are added, the library can be made static to become readable and ready for io. Several things get checked during this process

  • For every phi/psi bin combination of a particular RotamerID, the same number of rotamers must have been added
  • All configuration combinations of the added rotamers in one phi/psi bin of a particular RotamerID must be unique
  • The configuration combinations of a particular RotamerID must be consistent across all phi/psi bins
Raises:RuntimeError if one of the points above is not fulfilled
SetInterpolate(interpolate)
Parameters:interpolate (bool) – Controls behaviour when QueryLib() gets called

The Library Entry Type

The entries for the rotamer libraries provide a basic container for rotamer dihedral angles and their corresponding standard deviations. They can be constructed by directly providing the values, but also by some static convenience functions. For analytical purposes they provide some comparison functionalities.

class promod3.sidechain.RotamerLibEntry
class promod3.sidechain.RotamerLibEntry(p, chi1, chi2, chi3, chi4, sig1, sig2, sig3, sig4)
Parameters:
  • p (float) – Probability of rotamer
  • chi1 (float) – Chi1 dihedral in range [-pi,pi[
  • chi2 (float) – Chi2 dihedral in range [-pi,pi[
  • chi3 (float) – Chi3 dihedral in range [-pi,pi[
  • chi4 (float) – Chi4 dihedral in range [-pi,pi[
  • sig1 (float) – Standard deviation for Chi1 dihedral
  • sig2 (float) – Standard deviation for Chi2 dihedral
  • sig3 (float) – Standard deviation for Chi3 dihedral
  • sig4 (float) – Standard deviation for Chi4 dihedral

Attributes:

probability

probability of rotamer

chi1

Chi1 dihedral in range [-pi,pi[, NaN if not defined

chi2

Chi2 dihedral in range [-pi,pi[, NaN if not defined

chi3

Chi3 dihedral in range [-pi,pi[, NaN if not defined

chi4

Chi4 dihedral in range [-pi,pi[, NaN if not defined

sig1

Standard deviation of Chi1 Dihedral, NaN if not defined

sig2

Standard deviation of Chi2 Dihedral, NaN if not defined

sig3

Standard deviation of Chi3 Dihedral, NaN if not defined

sig4

Standard deviation of Chi4 Dihedral, NaN if not defined

static FromResidue(res)

Creates a RotamerLibEntry from the given res. The function tries to automatically identify the RotamerID based on the residue name. The probability and standard deviations are set to 0.0, all not required chi angles with their corresponding standard deviations to NaN.

Parameters:res (ost.mol.ResidueHandle) – Source of dihedral angles
Returns:RotamerLibEntry
Raises:RuntimeError if residue name cannot be translated to RotamerID or when not all required atoms are present in res.
static FromResidue(res, id)

Creates a RotamerLibEntry from the given res. The probability gets set to zero and the standard deviations to 0. All not required chi angles with their corresponding standard deviations are NaN.

Parameters:
Returns:

RotamerLibEntry

Raises:

RuntimeError if not all required atoms are present in res.

IsSimilar(other, thresh)

Compares two RotamerLibEntries for their similarity in dihedral angles. The function goes from chi1 to chi4 and checks one after the other for similarity. The function doesn’t know the identity of the entries and can therefore not specifically treat symmetric rotamers (TYR,PHE,ASP,GLU) or rotamers with ambiguous naming in general.

Parameters:
  • other (RotamerLibEntry) – The Entry you want to compare with
  • thresh (float) – The max difference between two dihedrals to be considered similar
Returns:

bool Whether the two entries have the same amount of defined chi angles (not NaN) and whether they are within the specified threshold.

IsSimilar(other, thresh, id)

Compares two RotamerLibEntries for their similarity in dihedral angles. The function goes from chi1 to chi4 and checks one after the other for similarity. Sidechains with ambigous naming that are symmetric (TYR,PHE,ASP,GLU) get treated specifically. E.g. in case of aspartate, the chi2 is checked for its actual value, but also for its flipped state.

Parameters:
  • other (RotamerLibEntry) – The Entry you want to compare with
  • thresh (float) – The max difference between two dihedrals to be considered similar
  • id (RotamerID) – Identity of the entries to be compared
Returns:

bool Whether the two entries have the same amount of defined chi angles (not NaN) and whether they are within the specified threshold.

SimilarDihedral(other, dihedral_idx, thresh)

Compares a specific dihedral angle. The function doesn’t know the identity of the entries and can therefore not specifically treat symmetric rotamers (TYR,PHE,ASP,GLU) or rotamers with ambiguous naming in general.

Parameters:
  • other (RotamerLibEntry) – The Entry you want to compare with
  • dihedral_idx (int) – Index of the dihedral to be checked (0 for chi1, 3 for chi4)
  • thresh (float) – The max difference between two dihedrals to be considered similar
Returns:

bool Whether both dihedrals are defined (not NaN) and within the specified threshold

SimilarDihedral(other, dihedral_idx, thresh, id)

Compares a specific dihedral angle. Symmetric sidechains with ambigous naming (TYR,PHE,ASP,GLU) get treated specifically. E.g. in case of aspartate, the chi2 is checked for its actual value, but also for its flipped state.

Parameters:
  • other (RotamerLibEntry) – The Entry you want to compare with
  • dihedral_idx (int) – Index of the dihedral to be checked (0 for chi1, 3 for chi4)
  • thresh (float) – The max difference between two dihedrals to be considered similar
  • id (RotamerID) – Identity of the entries to be compared
Returns:

bool Whether both dihedrals are defined (not NaN) and within the specified threshold

Rotamer Configurations

In rotamers, one distinguishes between rotameric and non-rotameric sidechain dihedral angles. The rotameric ones are around SP3-SP3 hybridized bonds and typically have three distinct configurations (trans, gauche-, gauche+). The non-rotameric ones behave differently. ProMod3 offers some functionality to estimate those configurations.

class promod3.sidechain.DihedralConfiguration

Enumerates the possible sidechain dihedral configurations

  • TRANS - Trans configuration (120 < angle < -120)
  • GAUCHE_PLUS - Gauche+ configuration (0 < angle < 120)
  • GAUCHE_MINUS - Gauce- configuration (-120 < angle < 0)
  • NON_ROTAMERIC - Dihedral without SP3-SP3 bond
  • INVALID - Invalid configuration, e.g. chi3 of ALA (doesnt exist...)
promod3.sidechain.GetRotamericConfiguration(angle)

Evaluates the angle according to the ranges specified for DihedralConfiguration.

Parameters:angle (float) – Angle to be evaluated
Returns:TRANS, GAUCHE_PLUS or GAUCHE_MINUS. INVALID if angle is NaN.
promod3.sidechain.GetDihedralConfiguration(entry, id, dihedral_idx)

Estimates configuration of a sidechain dihedral angle in a specific RotamerLibEntry with the knowledge of its identity. This allows to also return NON_ROTAMERIC (e.g. chi2 for ASN).

Parameters:
  • entry (RotamerLibEntry) – Sidechain dihedral angle comes from here
  • id (RotamerID) – Identity of rotamer
  • dihedral_idx (int) – Specifies angle (0 => chi1, ..., 3 => chi4)
Returns:

Result of GetRotamericConfiguration() if specified angle is Rotameric, NON_ROTAMERIC if specified angle is valid and non rotameric, INVALID otherwise.

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