schrodinger.protein.residue module

class schrodinger.protein.residue.BETA_STRAND_PROPENSITY

Bases: enum.Enum

AMBIVALENT = 3
NO_PROPENSITY = 1
STRAND_BREAKING = 2
STRAND_FORMING = 4
class schrodinger.protein.residue.DisulfideBond(res1, res2)

Bases: object

Representation of a disulfide bond.

isValid()

Check whether the disulfide bond is valid and if so, return its seqs.

Returns:False if the disulfide bond is invalid, the seqs otherwise.
Return type:bool or list(sequence.ProteinSequence, sequence.ProteinSequence)
is_inter_sequence

Check whether the bond is valid and inter-sequence.

Returns:Whether the bond is a valid, inter-sequence bond.
Return type:bool
Raises:ValueError – If the bond is not valid
is_intra_sequence

Check whether the bond is valid and intra-sequence.

Returns:Whether the bond is a valid, intra-sequence bond.
Return type:bool
Raises:ValueError – If the bond is not valid
res_pair
class schrodinger.protein.residue.ElementType(short_code, long_code, name)

Bases: object

makeVariant(long_code, short_code)

Create a variant of an element type with a new long and short code.

Parameters:
  • long_code (str) – A 2+ character string representing the element type
  • short_code (str) – A 1 character string representing the element type
Returns:

The variant element type
Return type:

ElementType
class schrodinger.protein.residue.HELIX_PROPENSITY

Bases: enum.Enum

AMBIVALENT = 4
HELIX_BREAKING = 5
LIKELY = 2
NO_PROPENSITY = 1
WEAK = 3
class schrodinger.protein.residue.HELIX_TERMINATION_TENDENCY

Bases: enum.Enum

AMBIVALENT = 3
HELIX_ENDING = 4
HELIX_STARTING = 2
NO_TENDENCY = 1
class schrodinger.protein.residue.Nucleotide(element_type, inscode=' ', resnum=None, seqres_only=False)

Bases: schrodinger.protein.residue.Residue

class schrodinger.protein.residue.NucleotideType(short_code, long_code, name, charge=None, hydrophobicity=None, hydrophilicity=None, helix_propensity=None, beta_strand_propensity=None, turn_propensity=None, helix_termination_tendency=None, exposure_tendency=None, steric_group=None, side_chain_chem=None, isoelectric_point=None)

Bases: schrodinger.protein.residue.ResidueType

class schrodinger.protein.residue.RESIDUE_CHARGE

Bases: enum.Enum

NEGATIVE = 2
NEUTRAL = 3
POSITIVE = 1
class schrodinger.protein.residue.Residue(element_type, inscode=' ', resnum=None, seqres_only=False)

Bases: schrodinger.protein.residue.SequenceElement

An amino acid residue.

beta_strand_propensity
Returns:Beta-strand propensity for the ResidueType of the residue
Return type:BETA_STRAND_PROPENSITY
charge
Returns:charge of the ResidueType of the residue
Return type:RESIDUE_CHARGE
exposure_tendency
Returns:Solvent exposure tendency for the ResidueType of the residue
Return type:SOLVENT_EXPOSURE_TENDENCY
getBinarySimilarity(ref_res, similarity_matrix={('B', 'N'): 3, ('W', 'L'): -2, ('G', 'G'): 6, ('X', 'S'): 0, ('X', 'D'): -1, ('K', 'G'): -2, ('S', 'E'): 0, ('X', 'M'): -1, ('Y', 'E'): -2, ('W', 'R'): -3, ('I', 'R'): -3, ('X', 'Z'): -1, ('H', 'E'): 0, ('V', 'M'): 1, ('N', 'R'): 0, ('I', 'D'): -3, ('F', 'D'): -3, ('W', 'C'): -2, ('N', 'A'): -2, ('W', 'Q'): -2, ('L', 'Q'): -2, ('S', 'N'): 1, ('Z', 'K'): 1, ('V', 'N'): -3, ('Q', 'N'): 0, ('M', 'K'): -1, ('V', 'H'): -3, ('G', 'E'): -2, ('S', 'L'): -2, ('P', 'R'): -2, ('D', 'A'): -2, ('S', 'C'): -1, ('E', 'D'): 2, ('Y', 'G'): -3, ('W', 'P'): -4, ('X', 'X'): -1, ('Z', 'L'): -3, ('Q', 'A'): -1, ('V', 'Y'): -1, ('W', 'A'): -3, ('G', 'D'): -1, ('X', 'P'): -2, ('K', 'D'): -1, ('T', 'N'): 0, ('Y', 'F'): 3, ('W', 'W'): 11, ('Z', 'M'): -1, ('L', 'D'): -4, ('M', 'R'): -1, ('Y', 'K'): -2, ('F', 'E'): -3, ('M', 'E'): -2, ('S', 'S'): 4, ('X', 'C'): -2, ('Y', 'L'): -1, ('H', 'R'): 0, ('P', 'P'): 7, ('K', 'C'): -3, ('S', 'A'): 1, ('P', 'I'): -3, ('Q', 'Q'): 5, ('L', 'I'): 2, ('P', 'F'): -4, ('B', 'A'): -2, ('Z', 'N'): 0, ('M', 'Q'): 0, ('V', 'I'): 3, ('Q', 'C'): -3, ('I', 'H'): -3, ('Z', 'D'): 1, ('Z', 'P'): -1, ('Y', 'W'): 2, ('T', 'G'): -2, ('B', 'P'): -2, ('P', 'A'): -1, ('C', 'D'): -3, ('Y', 'H'): 2, ('X', 'V'): -1, ('B', 'B'): 4, ('Z', 'F'): -3, ('M', 'L'): 2, ('F', 'G'): -3, ('S', 'M'): -1, ('M', 'G'): -3, ('Z', 'Q'): 3, ('S', 'Q'): 0, ('X', 'A'): 0, ('V', 'T'): 0, ('W', 'F'): 1, ('S', 'H'): -1, ('X', 'N'): -1, ('B', 'Q'): 0, ('K', 'A'): -1, ('I', 'Q'): -3, ('X', 'W'): -2, ('N', 'N'): 6, ('W', 'T'): -2, ('P', 'D'): -1, ('B', 'C'): -3, ('I', 'C'): -1, ('V', 'K'): -2, ('X', 'Y'): -1, ('K', 'R'): 2, ('Z', 'R'): 0, ('W', 'E'): -3, ('T', 'E'): -1, ('B', 'R'): -1, ('L', 'R'): -2, ('Q', 'R'): 1, ('X', 'F'): -1, ('T', 'S'): 1, ('B', 'D'): 4, ('Z', 'A'): -1, ('M', 'N'): -2, ('V', 'D'): -3, ('F', 'A'): -2, ('X', 'E'): -1, ('F', 'H'): -1, ('M', 'A'): -1, ('K', 'Q'): 1, ('Z', 'S'): 0, ('X', 'G'): -1, ('V', 'V'): 4, ('W', 'D'): -4, ('X', 'H'): -1, ('S', 'F'): -2, ('X', 'L'): -1, ('B', 'S'): 0, ('S', 'G'): 0, ('P', 'M'): -2, ('Y', 'M'): -1, ('H', 'D'): -1, ('B', 'E'): 1, ('Z', 'B'): 1, ('I', 'E'): -3, ('V', 'E'): -2, ('X', 'T'): 0, ('X', 'R'): -1, ('R', 'R'): 5, ('Z', 'T'): -1, ('Y', 'D'): -3, ('V', 'W'): -3, ('F', 'L'): 0, ('T', 'C'): -1, ('X', 'Q'): -1, ('B', 'T'): -1, ('K', 'N'): 0, ('T', 'H'): -2, ('Y', 'I'): -1, ('F', 'Q'): -3, ('T', 'I'): -1, ('T', 'Q'): -1, ('P', 'L'): -3, ('R', 'A'): -1, ('B', 'F'): -3, ('Z', 'C'): -3, ('M', 'H'): -2, ('V', 'F'): -1, ('F', 'C'): -2, ('L', 'L'): 4, ('M', 'C'): -1, ('C', 'R'): -3, ('D', 'D'): 6, ('E', 'R'): 0, ('V', 'P'): -2, ('S', 'D'): 0, ('E', 'E'): 5, ('W', 'G'): -2, ('P', 'C'): -3, ('F', 'R'): -3, ('B', 'G'): -1, ('C', 'C'): 9, ('I', 'G'): -4, ('V', 'G'): -3, ('W', 'K'): -3, ('G', 'N'): 0, ('I', 'N'): -3, ('Z', 'V'): -2, ('A', 'A'): 4, ('V', 'Q'): -2, ('F', 'K'): -3, ('T', 'A'): 0, ('B', 'V'): -3, ('K', 'L'): -2, ('L', 'N'): -3, ('Y', 'N'): -2, ('F', 'F'): 6, ('L', 'G'): -4, ('B', 'H'): 0, ('Z', 'E'): 4, ('Q', 'D'): 0, ('X', 'B'): -1, ('Z', 'W'): -3, ('S', 'K'): 0, ('X', 'K'): -1, ('V', 'R'): -3, ('K', 'E'): 1, ('I', 'A'): -1, ('P', 'H'): -2, ('B', 'W'): -4, ('K', 'K'): 5, ('H', 'C'): -3, ('E', 'N'): 0, ('Y', 'Q'): -1, ('H', 'H'): 8, ('B', 'I'): -3, ('C', 'A'): 0, ('I', 'I'): 4, ('V', 'A'): 0, ('W', 'I'): -3, ('T', 'F'): -2, ('V', 'S'): -2, ('T', 'T'): 5, ('F', 'M'): 0, ('L', 'E'): -3, ('M', 'M'): 5, ('Z', 'G'): -2, ('D', 'R'): -2, ('M', 'D'): -3, ('W', 'H'): -2, ('G', 'C'): -3, ('S', 'R'): -1, ('S', 'I'): -2, ('P', 'Q'): -1, ('Y', 'A'): -2, ('X', 'I'): -1, ('E', 'A'): -1, ('B', 'Y'): -3, ('K', 'I'): -3, ('H', 'A'): -2, ('P', 'G'): -2, ('F', 'N'): -3, ('H', 'N'): 1, ('B', 'K'): 0, ('V', 'C'): -1, ('T', 'L'): -1, ('P', 'K'): -1, ('W', 'S'): -3, ('T', 'D'): -1, ('T', 'M'): -1, ('P', 'N'): -2, ('K', 'H'): -1, ('T', 'R'): -1, ('Y', 'R'): -2, ('L', 'C'): -1, ('B', 'L'): -4, ('Z', 'Y'): -2, ('W', 'N'): -4, ('G', 'A'): 0, ('S', 'P'): -1, ('E', 'Q'): 2, ('C', 'N'): -3, ('H', 'Q'): 0, ('D', 'N'): 1, ('Y', 'C'): -2, ('L', 'H'): -3, ('E', 'C'): -4, ('Z', 'H'): 0, ('H', 'G'): -2, ('P', 'E'): -1, ('Y', 'S'): -2, ('G', 'R'): -2, ('B', 'M'): -3, ('Z', 'Z'): 4, ('W', 'M'): -1, ('Y', 'T'): -2, ('Y', 'P'): -3, ('Y', 'Y'): 7, ('T', 'K'): -1, ('Z', 'I'): -3, ('T', 'P'): -1, ('V', 'L'): 1, ('F', 'I'): 0, ('G', 'Q'): -2, ('L', 'A'): -1, ('M', 'I'): 1})

Returns if the residue and a reference residue are similar

Parameters:
Return type:

int
Returns:

1 if the similarity score is positive, otherwise 0.
getConservation(ref_res)

Return an int scoring the conservation between the sequence and a reference sequence, assuming that they’re already aligned

Return whether the residue and a reference residue have similar side-chain chemistry.

The similarity criterion is based on “side chain chemistry” descriptor matching.

Parameters:ref_res (schrodinger.protein.residue.Residue) – The reference residue
Return type:int
Returns:1 if the residue and reference residue are have similar side chain chemistry, 0 otherwise.
getIdentity(ref_res)

Return the identity between the residue and a reference residue

Parameters:ref_res (schrodinger.protein.residue.Residue) – The reference residue
Return type:int
Returns:1 if same as the reference residue, 0 otherwise.
getSimilarity(ref_res, similarity_matrix={('B', 'N'): 3, ('W', 'L'): -2, ('G', 'G'): 6, ('X', 'S'): 0, ('X', 'D'): -1, ('K', 'G'): -2, ('S', 'E'): 0, ('X', 'M'): -1, ('Y', 'E'): -2, ('W', 'R'): -3, ('I', 'R'): -3, ('X', 'Z'): -1, ('H', 'E'): 0, ('V', 'M'): 1, ('N', 'R'): 0, ('I', 'D'): -3, ('F', 'D'): -3, ('W', 'C'): -2, ('N', 'A'): -2, ('W', 'Q'): -2, ('L', 'Q'): -2, ('S', 'N'): 1, ('Z', 'K'): 1, ('V', 'N'): -3, ('Q', 'N'): 0, ('M', 'K'): -1, ('V', 'H'): -3, ('G', 'E'): -2, ('S', 'L'): -2, ('P', 'R'): -2, ('D', 'A'): -2, ('S', 'C'): -1, ('E', 'D'): 2, ('Y', 'G'): -3, ('W', 'P'): -4, ('X', 'X'): -1, ('Z', 'L'): -3, ('Q', 'A'): -1, ('V', 'Y'): -1, ('W', 'A'): -3, ('G', 'D'): -1, ('X', 'P'): -2, ('K', 'D'): -1, ('T', 'N'): 0, ('Y', 'F'): 3, ('W', 'W'): 11, ('Z', 'M'): -1, ('L', 'D'): -4, ('M', 'R'): -1, ('Y', 'K'): -2, ('F', 'E'): -3, ('M', 'E'): -2, ('S', 'S'): 4, ('X', 'C'): -2, ('Y', 'L'): -1, ('H', 'R'): 0, ('P', 'P'): 7, ('K', 'C'): -3, ('S', 'A'): 1, ('P', 'I'): -3, ('Q', 'Q'): 5, ('L', 'I'): 2, ('P', 'F'): -4, ('B', 'A'): -2, ('Z', 'N'): 0, ('M', 'Q'): 0, ('V', 'I'): 3, ('Q', 'C'): -3, ('I', 'H'): -3, ('Z', 'D'): 1, ('Z', 'P'): -1, ('Y', 'W'): 2, ('T', 'G'): -2, ('B', 'P'): -2, ('P', 'A'): -1, ('C', 'D'): -3, ('Y', 'H'): 2, ('X', 'V'): -1, ('B', 'B'): 4, ('Z', 'F'): -3, ('M', 'L'): 2, ('F', 'G'): -3, ('S', 'M'): -1, ('M', 'G'): -3, ('Z', 'Q'): 3, ('S', 'Q'): 0, ('X', 'A'): 0, ('V', 'T'): 0, ('W', 'F'): 1, ('S', 'H'): -1, ('X', 'N'): -1, ('B', 'Q'): 0, ('K', 'A'): -1, ('I', 'Q'): -3, ('X', 'W'): -2, ('N', 'N'): 6, ('W', 'T'): -2, ('P', 'D'): -1, ('B', 'C'): -3, ('I', 'C'): -1, ('V', 'K'): -2, ('X', 'Y'): -1, ('K', 'R'): 2, ('Z', 'R'): 0, ('W', 'E'): -3, ('T', 'E'): -1, ('B', 'R'): -1, ('L', 'R'): -2, ('Q', 'R'): 1, ('X', 'F'): -1, ('T', 'S'): 1, ('B', 'D'): 4, ('Z', 'A'): -1, ('M', 'N'): -2, ('V', 'D'): -3, ('F', 'A'): -2, ('X', 'E'): -1, ('F', 'H'): -1, ('M', 'A'): -1, ('K', 'Q'): 1, ('Z', 'S'): 0, ('X', 'G'): -1, ('V', 'V'): 4, ('W', 'D'): -4, ('X', 'H'): -1, ('S', 'F'): -2, ('X', 'L'): -1, ('B', 'S'): 0, ('S', 'G'): 0, ('P', 'M'): -2, ('Y', 'M'): -1, ('H', 'D'): -1, ('B', 'E'): 1, ('Z', 'B'): 1, ('I', 'E'): -3, ('V', 'E'): -2, ('X', 'T'): 0, ('X', 'R'): -1, ('R', 'R'): 5, ('Z', 'T'): -1, ('Y', 'D'): -3, ('V', 'W'): -3, ('F', 'L'): 0, ('T', 'C'): -1, ('X', 'Q'): -1, ('B', 'T'): -1, ('K', 'N'): 0, ('T', 'H'): -2, ('Y', 'I'): -1, ('F', 'Q'): -3, ('T', 'I'): -1, ('T', 'Q'): -1, ('P', 'L'): -3, ('R', 'A'): -1, ('B', 'F'): -3, ('Z', 'C'): -3, ('M', 'H'): -2, ('V', 'F'): -1, ('F', 'C'): -2, ('L', 'L'): 4, ('M', 'C'): -1, ('C', 'R'): -3, ('D', 'D'): 6, ('E', 'R'): 0, ('V', 'P'): -2, ('S', 'D'): 0, ('E', 'E'): 5, ('W', 'G'): -2, ('P', 'C'): -3, ('F', 'R'): -3, ('B', 'G'): -1, ('C', 'C'): 9, ('I', 'G'): -4, ('V', 'G'): -3, ('W', 'K'): -3, ('G', 'N'): 0, ('I', 'N'): -3, ('Z', 'V'): -2, ('A', 'A'): 4, ('V', 'Q'): -2, ('F', 'K'): -3, ('T', 'A'): 0, ('B', 'V'): -3, ('K', 'L'): -2, ('L', 'N'): -3, ('Y', 'N'): -2, ('F', 'F'): 6, ('L', 'G'): -4, ('B', 'H'): 0, ('Z', 'E'): 4, ('Q', 'D'): 0, ('X', 'B'): -1, ('Z', 'W'): -3, ('S', 'K'): 0, ('X', 'K'): -1, ('V', 'R'): -3, ('K', 'E'): 1, ('I', 'A'): -1, ('P', 'H'): -2, ('B', 'W'): -4, ('K', 'K'): 5, ('H', 'C'): -3, ('E', 'N'): 0, ('Y', 'Q'): -1, ('H', 'H'): 8, ('B', 'I'): -3, ('C', 'A'): 0, ('I', 'I'): 4, ('V', 'A'): 0, ('W', 'I'): -3, ('T', 'F'): -2, ('V', 'S'): -2, ('T', 'T'): 5, ('F', 'M'): 0, ('L', 'E'): -3, ('M', 'M'): 5, ('Z', 'G'): -2, ('D', 'R'): -2, ('M', 'D'): -3, ('W', 'H'): -2, ('G', 'C'): -3, ('S', 'R'): -1, ('S', 'I'): -2, ('P', 'Q'): -1, ('Y', 'A'): -2, ('X', 'I'): -1, ('E', 'A'): -1, ('B', 'Y'): -3, ('K', 'I'): -3, ('H', 'A'): -2, ('P', 'G'): -2, ('F', 'N'): -3, ('H', 'N'): 1, ('B', 'K'): 0, ('V', 'C'): -1, ('T', 'L'): -1, ('P', 'K'): -1, ('W', 'S'): -3, ('T', 'D'): -1, ('T', 'M'): -1, ('P', 'N'): -2, ('K', 'H'): -1, ('T', 'R'): -1, ('Y', 'R'): -2, ('L', 'C'): -1, ('B', 'L'): -4, ('Z', 'Y'): -2, ('W', 'N'): -4, ('G', 'A'): 0, ('S', 'P'): -1, ('E', 'Q'): 2, ('C', 'N'): -3, ('H', 'Q'): 0, ('D', 'N'): 1, ('Y', 'C'): -2, ('L', 'H'): -3, ('E', 'C'): -4, ('Z', 'H'): 0, ('H', 'G'): -2, ('P', 'E'): -1, ('Y', 'S'): -2, ('G', 'R'): -2, ('B', 'M'): -3, ('Z', 'Z'): 4, ('W', 'M'): -1, ('Y', 'T'): -2, ('Y', 'P'): -3, ('Y', 'Y'): 7, ('T', 'K'): -1, ('Z', 'I'): -3, ('T', 'P'): -1, ('V', 'L'): 1, ('F', 'I'): 0, ('G', 'Q'): -2, ('L', 'A'): -1, ('M', 'I'): 1})

Returns the similarity between the residue and a reference residue

Parameters:
Return type:

float
Returns:

similarity score based on the similarity matrix
helix_propensity
Returns:Helix propensity for the ResidueType of the residue
Return type:HELIX_PROPENSITY
helix_termination_tendency
Returns:Helix termination tendency for the ResidueType of the residue
Return type:HELIX_TERMINATION_TENDENCY
hydrophilicity
Returns:Hydrophilicity for the ResidueType on the Hopp-Woods scale, if available; otherwise None
Return type:float
hydrophobicity
Returns:Hydrophobicity for the ResidueType on the Kyte-Doolittle scale, if available; otherwise None.
Return type:float
isoelectric_point
Returns:A float representing the isoelectric point value for the ResidueType of the residue
long_code
rescode
short_code
side_chain_chem
Returns:Side chain chemistry for the ResidueType of the residue
Return type:SIDE_CHAIN_CHEM
ss_prediction_psipred

Returns a DSSP code matching the secondary structure prediction for the residue or None. Value is calculated from thePsiPred backend.

ss_prediction_sspro

Returns a DSSP code matching the secondary structure prediction for the residue or None. Value is calculated from the SSpro backend.

steric_group
Returns:Steric group for the ResidueType of the residue
Return type:STERIC_GROUP
turn_propensity
Returns:Turn propensity for the ResidueType of the residue
Return type:TURN_PROPENSITY
class schrodinger.protein.residue.ResidueType(short_code, long_code, name, charge=None, hydrophobicity=None, hydrophilicity=None, helix_propensity=None, beta_strand_propensity=None, turn_propensity=None, helix_termination_tendency=None, exposure_tendency=None, steric_group=None, side_chain_chem=None, isoelectric_point=None)

Bases: schrodinger.protein.residue.ElementType

class schrodinger.protein.residue.SIDE_CHAIN_CHEM

Bases: enum.Enum

ACIDIC_HYDROPHILIC = 2
BASIC_HYDROPHILIC = 3
IMINO_ACID = 8
NEUTRAL_HYDROPHILIC = 6
NEUTRAL_HYDROPHOBIC_ALIPHATIC = 4
NEUTRAL_HYDROPHOBIC_AROMATIC = 5
NO_SIDE_CHAIN_CHEM = 1
PRIMARY_THIOL = 7
class schrodinger.protein.residue.SOLVENT_EXPOSURE_TENDENCY

Bases: enum.Enum

AMBIVALENT = 3
BURIED = 4
NO_TENDENCY = 1
SURFACE = 2
class schrodinger.protein.residue.STERIC_GROUP

Bases: enum.Enum

AMBIVALENT = 3
AROMATIC = 5
NO_STERIC = 1
POLAR = 4
SMALL = 2
class schrodinger.protein.residue.SequenceElement(element_type)

Bases: object

class schrodinger.protein.residue.TURN_PROPENSITY

Bases: enum.Enum

AMBIVALENT = 3
NO_PROPENSITY = 1
TURN_BREAKING = 4
TURN_FORMING = 2
schrodinger.protein.residue.add_disulfide_bond(res1, res2)

Add a disulfide bond between two residues.

Parameters:
schrodinger.protein.residue.get_matrix_value(matrix, first, second)

Return a similarity matrix value for a specified pair of residues.

schrodinger.protein.residue.make_one_letter_map(res_list)
schrodinger.protein.residue.make_three_letter_map(res_list)
schrodinger.protein.residue.make_variants(variants)

Helper function to create modified amino acids and modified nucleotides

Parameters:
  • variants – A list of modified residues. The modified residue will have all the same properties as the standard one (hydophobicity, charge, etc.) but its long code (ie, its PDB residue name) will differ, and if a tuple of (string, string) is provided, both its long code and short code will differ.
  • variants – list of (ResidueType, list of string or (string,string))
Returns:

a list of residue variants
Return type:

list of ResidueType
schrodinger.protein.residue.merge_dicts(*dict_args)

Merge any number of dictionaries into a single dictionary.

Note that repeated keys will be silently overwritten with the last value.

schrodinger.protein.residue.remove_disulfide_bond(res1, res2)

Remove a disulfide bond between two residues.

Parameters: