schrodinger.protein.sequence module

Implementation of ProteinSequence, Sequence, and StructureSequence class.

StructureSequence allows iteration over all sequences in a given protein CT, and iteration over residues of each (in sequence order).

class schrodinger.protein.sequence.Sequence

Bases: object

class schrodinger.protein.sequence.SequenceProxy(seq)

Bases: schrodinger.models.json.JsonableClassMixin, schrodinger.protein.sequence.Sequence

A read-only wrapper for sequences. We use this to prevent users from directly modifying sequences which can corrupt undoability and residue anchoring.

MUTATION_METHODS = {'mutate', 'append', 'removeTerminalGaps', 'setStructure', 'addGapsByIndices', 'removeElements', 'removeAllGaps', 'addGapsBeforeIndices', 'insert', 'extend'}
toJsonImplementation()

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns:A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders
classmethod fromJsonImplementation(json_obj)

Abstract method that must be defined by all derived classes. Takes in a dictionary and constructs an instance of the derived class.

Parameters:json_dict (dict) – A dictionary loaded from a JSON string or file.
Returns:An instance of the derived class.

:rtype : cls

class schrodinger.protein.sequence.AbstractSequence(elements, name='', origin=None, entry_id='', entry_name='', pdb_id='', chain='', title='')

Bases: schrodinger.protein.sequence.Sequence, PyQt5.QtCore.QObject

Base class for biological sequences

Note: Protein-specific functionality should go in ProteinSequence.

Variables:
  • ORIGIN (enum.Enum) – Possible sequence origins
  • AnnotationClass (annotation.SequenceAnnotations) – Class to use for annotations
  • ElementClass (residue.SequenceElement) – Class to use for elements
  • alphabet (dict(str, residue.ElementType)) – A mapping of string representations of elements to element types
  • _gap_chars (tuple(str)) – A tuple of permissible gap characters in the element list; the first item will be used for serialization.
  • _unknown_res_type (residue.ElementType) – The type for an unknown residue
  • residuesChanged (QtCore.pyqtSignal) – A signal emitted when sequence residues are changed. Emitted with the indices of the first and last changed residues.
  • lengthAboutToChange (QtCore.pyqtSignal) – A signal emitted when the sequence length is about to change. Emitted with the old and new lengths.
  • lengthChanged (QtCore.pyqtSignal) – A signal emitted when the sequence length is changed. Emitted with the old and new lengths.
  • nameChanged (QtCore.pyqtSignal) – A signal emitted when the sequence name is changed.
  • visibilityChanged (QtCore.pyqtSignal) – A signal emitted when the visibility is changed.
  • structureChanged (QtCore.pyqtSignal) – A signal emitted when the structure changes.
  • annotationTitleChanged (QtCore.pyqtSignal) – A signal emitted when an annotation title is changed.
  • sequenceCopied (QtCore.pyqtSignal) – A signal emitted when this sequence is copied. Emitted with the sequence being copied and the newly created copy. This signal is used by the structure model to make sure that the newly created copy is kept in sync with the structure.
class ORIGIN

Bases: enum.Enum

An enumeration.

MAESTRO = 1
PYMOL = 2
AnnotationClass = None
ElementClass

alias of schrodinger.protein.residue.SequenceElement

alphabet = {}
residuesChanged
lengthAboutToChange
lengthChanged
nameChanged
visibilityChanged
structureChanged
annotationTitleChanged
sequenceCopied
gap_char
origin
Returns:A piece of metadata indicating where the sequence came from
Rtype origin:Sequence.ORIGIN or None
getSummary()

Returns a friendly, readable summary of the sequence

Return type:basestring
Returns:A summary of the sequence
classmethod makeSeqElement(element)
Parameters:element (str or cls.ElementClass) – A sequence element or string representation thereof
Returns:sequence element
Return type:cls.ElementClass
Raises:ValueError – If an element is not in cls.alphabet and cls._unknown_res_type is not defined
getSubsequence(start, end)

Return a sequence containing a subset of the elements in this one

Parameters:
  • start (int) – The index at which the subsequence should start
  • end (int) – The index at which the subsequence should end (exclusive)
Return type:

Sequence
Returns:

A sequence
name
fullname
Returns:a formatted name + optional chain name for the sequence
Return type:str
getAnnotation(index, annotation)

Returns the annotation at the specified index or None for a gap.

Raises:ValueError – if the annotation is not available
index(res, ignore_gaps=False)

Returns the index of the specified residue

Parameters:
  • res (schrodinger.structure._Residue) – The residue to find
  • ignore_gaps (bool) – Whether the index returned should ignore gaps in the sequence or not.
Raises:

A Value error if the residue is not present or if the res is None
Return type:

int
Returns:

The index of the residue
getGaps()
Return type:list(residue.Gap)
Returns:The gaps in the sequence.
addGapsByIndices(gap_idxs)

Add gaps to the sequence from a list of gap indices. Note that these indices are based on numbering after the insertion. To insert gaps using indices based on numbering before the insertion, see addGapsBeforeIndices.

Parameters:gap_idxs (list(int)) – A list of gap indices
addGapsBeforeIndices(indices)

Add one gap to the alignment before each of the specified residue positions. Note that these indices are based on numbering before the insertion. To insert gaps using indices based on numbering after the insertion, see addGapsByIndices.

Parameters:indices (list(int)) – A list of indices to insert gaps before.
getNumResidues()

Return the number of residues in the sequence, that is, the length of the sequence without gaps

Return type:int
Returns:The number of residues in the sequence
removeAllGaps()

Remove gaps from the sequence

insertElements(index, elements)

Insert a list of elements or sequence element into this sequence.

Parameters:
  • index (int) – The index at which to insert elements
  • elements (iterable(self.ElementClass) or iterable(str)) – A list of elements to insert
mutate(start, end, elements)

Mutate sequence elements starting at the given index to the provided elements.

Parameters:
  • start (int) – The index at which to start mutating
  • end (int) – The index of the last mutated element (exclusive)
  • elements (iterable(self.ElementClass) or iterable(str)) – The elements to which to mutate the sequence
removeElements(eles)

Remove elements from the sequence.

Parameters:eles (list(residue.AbstractSequenceElement)) – A list of elements to remove from the sequence.
Raises:ValueError – If any of the given elements are not in the sequence.
append(element)

Appends an element to the sequence

Parameters:element – The element to append to this sequence
Type:element: self.ElementClass or basestring
extend(elements)

Extends the sequence with elements from an iterable

Parameters:elements (iterable(self.ElementClass) or iterable(str)) – The iterable containing elements with which to extend this sequence
sanitize(start=0, end=None)

Remove gaps and unknown sequence elements from sequence

removeTerminalGaps()

Remove gaps from the end of the sequence

getTerminalGaps()

Return terminal gaps.

Returns:A list of terminal gaps (in ascending index order)
Return type:list(residue.Gap)
getGapCount()
Returns:the number of gaps in the sequence
Return type:int
getIdentity(reference, consider_gaps=True)

Return a float scoring the identity between the sequence and a reference sequence, assuming that they’re already aligned

Parameters:
Returns:

The sequence identity score (between 0.0 and 1.0)
Return type:

float
getSimilarity(reference, consider_gaps=True)

Return a float score of the similarity count between the sequence and a reference sequence, assuming that they’re already aligned.

Parameters:
Returns:

The sequence similarity score (between 0.0 and 1.0)
Return type:

float
getConservation(reference, consider_gaps=True)

Return a float scoring the homology conservation between the sequence and a reference sequence, assuming that they’re already aligned.

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

Parameters:
Returns:

The sequence conservation score (between 0.0 and 1.0)
Return type:

float
getSimilarityScore(reference)

Return the total score of similarity between the sequence and a reference sequence, assuming that they’re already aligned.

Since the similarity with a gap will always be 0.0, there is no need to consider gaps.

Parameters:reference (schrodinger.protein.sequence.Sequence) – A sequence to compare against
Returns:The total sequence similarity score
Return type:float
getNextResidueIndex(index)

Return the index of the next residue in the sequence (ignoring gaps) or None if it is the last residue.

Parameters:index (int) – The index of the residue
Returns:The index of the next residue in the sequence
Return type:int or None
getNextResidueIndices(index, num_indices=1)

Return a list of indices of the next n residues in the sequence (ignoring gaps) or an empty list if there is none. May return fewer than n indices if the end of the sequence is reached.

Parameters:
  • index (int) – The index of the residue to start with
  • num_indices (int) – The number of indices to return
Returns:

List of the indices of the next residues in the sequence
Return type:

list(int) or NoneType
getNextResidue(index)

Return the next residue in the sequence (ignoring gaps) or None if this is the last residue.

Parameters:index (int) – The index of the residue
Returns:The previous residue in the sequence
Return type:schrodinger.protein.residue.Residue
getPreviousResidueIndex(index)

Return the index of the previous residue in the sequence (ignoring gaps) or None if there is none.

Parameters:index (int) – The index of the residue
Returns:The index of the previous residue in the sequence
Return type:int or NoneType
getPreviousResidueIndices(index, num_indices=1)

Return a list of indices of the previous n residues in the sequence (ignoring gaps) or an empty list if there are none. May return fewer than n indices if the beginning of the sequence is reached.

Parameters:
  • index (int) – The index of the residue to start with
  • num_indices (int) – The number of indices to return
Returns:

The indices of the previous residues in the sequence
Return type:

list(int) or NoneType
getPreviousResidue(index)

Return the next residue in the sequence (ignoring gaps) or None if this is the first residue.

Parameters:index (int) – The index of the residue
Returns:The previous residue in the sequence
Return type:schrodinger.protein.residue.Residue
getGaplessLength()
Returns:Length of this sequence ignoring gaps
Return type:int
iterResidues()

Return an iterable of residues, ignoring gaps.

Returns:Iterable of residues
Return type:iter(Residue)
iterNeighbors()

Return an iterable of three element tuples consisting of (prev_res, curr_res, next_res), ignoring gaps.

None is used for neighbors of first and last residues in the sequence, and does not indicate gaps here.

Returns:Iterable of 3-tuples, each element of the each tuple being either a schrodinger.protein.residue.Residue or None
Return type:iter(tuple(Residue or NoneType, Residue, Residue or NoneType))
hasEntryID()

Return whether or not this sequence has an associated Entry ID in the Project Table.

Returns:Whether or not this sequence is associated with an entry ID.
Return type:bool
hasStructure()
Returns:Whether this sequence has an associated structure.
Return type:bool
getStructure()
Returns:The associated structure. Will return None if there is no associated structure.
Return type:schrodinger.structure.Structure or NoneType
setStructure(struc)

Set the associated structure. Can only be used on sequences with an associated structure.

Parameters:struc (schrodinger.structure.Structure) – The new structure for this sequence
Raises:RuntimeError – If there’s no structure associated with this sequence object.
onStructureChanged()
classmethod isValid(elements)
Parameters:elements (iterable(str) or str) – An iterable of string representations of elements making up the sequence
Returns:Tuple indicating whether valid and a set of invalid characters, if any
Return type:tuple(bool, set(str))
visibility
class schrodinger.protein.sequence.ProteinSequence(elements, name='', origin=None, entry_id='', entry_name='', pdb_id='', chain='', title='')

Bases: schrodinger.models.json.JsonableClassMixin, schrodinger.protein.sequence.AbstractSequence

AnnotationClass

alias of schrodinger.protein.annotation.ProteinSequenceAnnotations

ElementClass

alias of schrodinger.protein.residue.Residue

alphabet = {'2AS': ResidueType('D', '2AS', 'Aspartic acid'), '3AH': ResidueType('H', '3AH', 'Histidine'), '5HP': ResidueType('E', '5HP', 'Glutamic acid'), 'A': ResidueType('A', 'ALA', 'Alanine'), 'ACE': ResidueType('X', 'ACE', 'Capping Group'), 'ACL': ResidueType('R', 'ACL', 'Arginine'), 'AGM': ResidueType('R', 'AGM', 'Arginine'), 'AIB': ResidueType('A', 'AIB', 'Alanine'), 'ALA': ResidueType('A', 'ALA', 'Alanine'), 'ALM': ResidueType('A', 'ALM', 'Alanine'), 'ALO': ResidueType('T', 'ALO', 'Threonine'), 'ALY': ResidueType('K', 'ALY', 'Lysine'), 'ANF': ResidueType('X', 'ANF', 'Capping Group'), 'ARG': ResidueType('R', 'ARG', 'Arginine'), 'ARM': ResidueType('R', 'ARM', 'Arginine'), 'ARN': ResidueType('R', 'ARN', 'Arginine'), 'ASA': ResidueType('D', 'ASA', 'Aspartic acid'), 'ASB': ResidueType('D', 'ASB', 'Aspartic acid'), 'ASH': ResidueType('D', 'ASH', 'Aspartic acid'), 'ASK': ResidueType('D', 'ASK', 'Aspartic acid'), 'ASL': ResidueType('D', 'ASL', 'Aspartic acid'), 'ASN': ResidueType('N', 'ASN', 'Asparagine'), 'ASP': ResidueType('D', 'ASP', 'Aspartic acid'), 'ASQ': ResidueType('D', 'ASQ', 'Aspartic acid'), 'AYA': ResidueType('A', 'AYA', 'Alanine'), 'BCS': ResidueType('X', 'BCS', 'Cysteine'), 'BHD': ResidueType('D', 'BHD', 'Aspartic acid'), 'BMT': ResidueType('T', 'BMT', 'Threonine'), 'BNN': ResidueType('A', 'BNN', 'Alanine'), 'BUC': ResidueType('C', 'BUC', 'Cysteine'), 'BUG': ResidueType('L', 'BUG', 'Leucine'), 'C': ResidueType('C', 'CYS', 'Cysteine'), 'C5C': ResidueType('C', 'C5C', 'Cysteine'), 'C6C': ResidueType('C', 'C6C', 'Cysteine'), 'CCS': ResidueType('C', 'CCS', 'Cysteine'), 'CEA': ResidueType('C', 'CEA', 'Cysteine'), 'CGU': ResidueType('E', 'CGU', 'Glutamic acid'), 'CHG': ResidueType('A', 'CHG', 'Alanine'), 'CLE': ResidueType('L', 'CLE', 'Leucine'), 'CME': ResidueType('C', 'CME', 'Cysteine'), 'CSD': ResidueType('A', 'CSD', 'Alanine'), 'CSO': ResidueType('C', 'CSO', 'Cysteine'), 'CSP': ResidueType('C', 'CSP', 'Cysteine'), 'CSS': ResidueType('C', 'CSS', 'Cysteine'), 'CSW': ResidueType('C', 'CSW', 'Cysteine'), 'CSX': ResidueType('C', 'CSX', 'Cysteine'), 'CXM': ResidueType('M', 'CXM', 'Methionine'), 'CY1': ResidueType('C', 'CY1', 'Cysteine'), 'CY3': ResidueType('C', 'CY3', 'Cysteine'), 'CYG': ResidueType('C', 'CYG', 'Cysteine'), 'CYM': ResidueType('C', 'CYM', 'Cysteine'), 'CYP': ResidueType('C', 'CYP', 'Cysteine'), 'CYQ': ResidueType('C', 'CYQ', 'Cysteine'), 'CYS': ResidueType('C', 'CYS', 'Cysteine'), 'CYX': ResidueType('C', 'CYX', 'Cysteine'), 'D': ResidueType('D', 'ASP', 'Aspartic acid'), 'DAH': ResidueType('F', 'DAH', 'Phenylalanine'), 'DAL': ResidueType('X', 'DAL', 'Alanine'), 'DAR': ResidueType('X', 'DAR', 'Arginine'), 'DAS': ResidueType('X', 'DAS', 'Aspartic acid'), 'DCY': ResidueType('X', 'DCY', 'Cysteine'), 'DGL': ResidueType('X', 'DGL', 'Glutamic acid'), 'DGN': ResidueType('X', 'DGN', 'Glutamine'), 'DHA': ResidueType('A', 'DHA', 'Alanine'), 'DHI': ResidueType('X', 'DHI', 'Histidine'), 'DIL': ResidueType('X', 'DIL', 'Isoleucine'), 'DIV': ResidueType('V', 'DIV', 'Valine'), 'DLE': ResidueType('X', 'DLE', 'Leucine'), 'DLY': ResidueType('X', 'DLY', 'Lysine'), 'DNP': ResidueType('A', 'DNP', 'Alanine'), 'DPN': ResidueType('X', 'DPN', 'Phenylalanine'), 'DPR': ResidueType('X', 'DPR', 'Proline'), 'DSG': ResidueType('X', 'DSG', 'Asparagine'), 'DSN': ResidueType('X', 'DSN', 'Serine'), 'DSP': ResidueType('D', 'DSP', 'Aspartic acid'), 'DTH': ResidueType('X', 'DTH', 'Threonine'), 'DTR': ResidueType('X', 'DTR', 'Tryptophan'), 'DTY': ResidueType('X', 'DTY', 'Tyrosine'), 'DVA': ResidueType('X', 'DVA', 'Valine'), 'E': ResidueType('E', 'GLU', 'Glutamic acid'), 'EFC': ResidueType('C', 'EFC', 'Cysteine'), 'F': ResidueType('F', 'PHE', 'Phenylalanine'), 'FCO': ResidueType('X', 'FCO', 'Capping Group'), 'FLA': ResidueType('A', 'FLA', 'Alanine'), 'FME': ResidueType('M', 'FME', 'Methionine'), 'G': ResidueType('G', 'GLY', 'Glycine'), 'GGL': ResidueType('E', 'GGL', 'Glutamic acid'), 'GL3': ResidueType('G', 'GL3', 'Glycine'), 'GLH': ResidueType('E', 'GLH', 'Glutamic acid'), 'GLN': ResidueType('Q', 'GLN', 'Glutamine'), 'GLU': ResidueType('E', 'GLU', 'Glutamic acid'), 'GLY': ResidueType('G', 'GLY', 'Glycine'), 'GLZ': ResidueType('G', 'GLZ', 'Glycine'), 'GMA': ResidueType('E', 'GMA', 'Glutamic acid'), 'GSC': ResidueType('G', 'GSC', 'Glycine'), 'H': ResidueType('H', 'HIS', 'Histidine'), 'HAC': ResidueType('A', 'HAC', 'Alanine'), 'HAR': ResidueType('R', 'HAR', 'Arginine'), 'HIC': ResidueType('H', 'HIC', 'Histidine'), 'HID': ResidueType('H', 'HID', 'Histidine'), 'HIE': ResidueType('H', 'HIE', 'Histidine'), 'HIP': ResidueType('H', 'HIP', 'Histidine'), 'HIS': ResidueType('H', 'HIS', 'Histidine'), 'HMR': ResidueType('R', 'HMR', 'Arginine'), 'HPQ': ResidueType('F', 'HPQ', 'Phenylalanine'), 'HSD': ResidueType('H', 'HSD', 'Histidine'), 'HSE': ResidueType('H', 'HSE', 'Histidine'), 'HSP': ResidueType('H', 'HSP', 'Histidine'), 'HTR': ResidueType('W', 'HTR', 'Tryptophan'), 'HYP': ResidueType('X', 'HYP', 'Proline'), 'I': ResidueType('I', 'ILE', 'Isoleucine'), 'IIL': ResidueType('I', 'IIL', 'Isoleucine'), 'ILE': ResidueType('I', 'ILE', 'Isoleucine'), 'IND': ResidueType('X', 'IND', 'Capping Group'), 'IYR': ResidueType('Y', 'IYR', 'Tyrosine'), 'K': ResidueType('K', 'LYS', 'Lysine'), 'KCX': ResidueType('K', 'KCX', 'Lysine'), 'L': ResidueType('L', 'LEU', 'Leucine'), 'LEU': ResidueType('L', 'LEU', 'Leucine'), 'LLP': ResidueType('K', 'LLP', 'Lysine'), 'LLY': ResidueType('K', 'LLY', 'Lysine'), 'LTR': ResidueType('W', 'LTR', 'Tryptophan'), 'LYM': ResidueType('K', 'LYM', 'Lysine'), 'LYN': ResidueType('K', 'LYN', 'Lysine'), 'LYS': ResidueType('K', 'LYS', 'Lysine'), 'LYZ': ResidueType('K', 'LYZ', 'Lysine'), 'M': ResidueType('M', 'MET', 'Methionine'), 'MAA': ResidueType('A', 'MAA', 'Alanine'), 'MEN': ResidueType('N', 'MEN', 'Asparagine'), 'MET': ResidueType('M', 'MET', 'Methionine'), 'MHS': ResidueType('H', 'MHS', 'Histidine'), 'MIS': ResidueType('S', 'MIS', 'Serine'), 'MLE': ResidueType('L', 'MLE', 'Leucine'), 'MMO': ResidueType('R', 'MMO', 'Arginine'), 'MPA': ResidueType('X', 'MPA', 'Capping Group'), 'MPQ': ResidueType('G', 'MPQ', 'Glycine'), 'MSA': ResidueType('G', 'MSA', 'Glycine'), 'MSE': ResidueType('M', 'MSE', 'Methionine'), 'MVA': ResidueType('V', 'MVA', 'Valine'), 'N': ResidueType('N', 'ASN', 'Asparagine'), 'NCO': ResidueType('X', 'NCO', 'Capping Group'), 'NEM': ResidueType('H', 'NEM', 'Histidine'), 'NEP': ResidueType('H', 'NEP', 'Histidine'), 'NH2': ResidueType('X', 'NH2', 'Capping Group'), 'NLE': ResidueType('X', 'NLE', 'Leucine'), 'NLN': ResidueType('L', 'NLN', 'Leucine'), 'NLP': ResidueType('L', 'NLP', 'Leucine'), 'NMA': ResidueType('X', 'NMA', 'Capping Group'), 'NMC': ResidueType('G', 'NMC', 'Glycine'), 'OAS': ResidueType('S', 'OAS', 'Serine'), 'OCS': ResidueType('C', 'OCS', 'Cysteine'), 'OMT': ResidueType('M', 'OMT', 'Methionine'), 'P': ResidueType('P', 'PRO', 'Proline'), 'PAQ': ResidueType('Y', 'PAQ', 'Tyrosine'), 'PCA': ResidueType('E', 'PCA', 'Glutamic acid'), 'PEC': ResidueType('C', 'PEC', 'Cysteine'), 'PHE': ResidueType('F', 'PHE', 'Phenylalanine'), 'PHI': ResidueType('F', 'PHI', 'Phenylalanine'), 'PHL': ResidueType('F', 'PHL', 'Phenylalanine'), 'PR3': ResidueType('C', 'PR3', 'Cysteine'), 'PRO': ResidueType('P', 'PRO', 'Proline'), 'PRR': ResidueType('A', 'PRR', 'Alanine'), 'PTR': ResidueType('y', 'PTR', 'Tyrosine'), 'Q': ResidueType('Q', 'GLN', 'Glutamine'), 'R': ResidueType('R', 'ARG', 'Arginine'), 'S': ResidueType('S', 'SER', 'Serine'), 'SAC': ResidueType('S', 'SAC', 'Serine'), 'SAR': ResidueType('G', 'SAR', 'Glycine'), 'SCH': ResidueType('C', 'SCH', 'Cysteine'), 'SCS': ResidueType('C', 'SCS', 'Cysteine'), 'SCY': ResidueType('C', 'SCY', 'Cysteine'), 'SEL': ResidueType('S', 'SEL', 'Serine'), 'SEP': ResidueType('X', 'SEP', 'Serine'), 'SER': ResidueType('S', 'SER', 'Serine'), 'SET': ResidueType('S', 'SET', 'Serine'), 'SHC': ResidueType('C', 'SHC', 'Cysteine'), 'SHR': ResidueType('K', 'SHR', 'Lysine'), 'SMC': ResidueType('C', 'SMC', 'Cysteine'), 'SOC': ResidueType('C', 'SOC', 'Cysteine'), 'STY': ResidueType('Y', 'STY', 'Tyrosine'), 'SVA': ResidueType('S', 'SVA', 'Serine'), 'T': ResidueType('T', 'THR', 'Threonine'), 'THO': ResidueType('T', 'THO', 'Threonine'), 'THR': ResidueType('T', 'THR', 'Threonine'), 'TIH': ResidueType('A', 'TIH', 'Alanine'), 'TOSG': ResidueType('X', 'TOSG', 'Capping Group'), 'TPL': ResidueType('W', 'TPL', 'Tryptophan'), 'TPO': ResidueType('t', 'TPO', 'Threonine'), 'TPQ': ResidueType('A', 'TPQ', 'Alanine'), 'TRG': ResidueType('K', 'TRG', 'Lysine'), 'TRO': ResidueType('W', 'TRO', 'Tryptophan'), 'TRP': ResidueType('W', 'TRP', 'Tryptophan'), 'TYB': ResidueType('Y', 'TYB', 'Tyrosine'), 'TYM': ResidueType('Y', 'TYM', 'Tyrosine'), 'TYO': ResidueType('Y', 'TYO', 'Tyrosine'), 'TYQ': ResidueType('Y', 'TYQ', 'Tyrosine'), 'TYR': ResidueType('Y', 'TYR', 'Tyrosine'), 'TYS': ResidueType('Y', 'TYS', 'Tyrosine'), 'TYY': ResidueType('Y', 'TYY', 'Tyrosine'), 'UNK': ResidueType('X', 'UNK', 'Unknown'), 'V': ResidueType('V', 'VAL', 'Valine'), 'VAL': ResidueType('V', 'VAL', 'Valine'), 'W': ResidueType('W', 'TRP', 'Tryptophan'), 'Y': ResidueType('Y', 'TYR', 'Tyrosine')}
removeStructurelessResidues(start=0, end=None)

Remove any structureless residues

Parameters:
  • start (int) – The index at which to start filtering structureless residues.
  • end (int) – The index at which to end filtering
disulfide_bonds
Returns:A sorted tuple of the valid disulfide bonds.
Return type:tuple(residue.DisulfideBond)
toJsonImplementation()

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns:A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders
classmethod fromJsonImplementation(json_obj)

Abstract method that must be defined by all derived classes. Takes in a dictionary and constructs an instance of the derived class.

Parameters:json_dict (dict) – A dictionary loaded from a JSON string or file.
Returns:An instance of the derived class.

:rtype : cls

secondary_structures

A list of _SecondaryStructure namedtuples containing the type of secondary structure and where the secondary structures begin and end.

Returns:A list of namedtuples containing an SS_TYPE from schrodinger.structure and the residue indexes marking the limits of the secondary structure.
Return type:list(namedtuple(int, (int,int)))
encodeForPatternSearch(with_ss=False, with_flex=False, with_asa=False)

Convert to sequence dict expected by find_generalized_pattern.

Parameters:
  • with_ss (bool) – Whether to include secondary structure information.
  • with_flex (bool) – Whether to include flexibility information.
  • with_asa (bool) – Whether to include accessible surface area information.
Return type:

dict
Returns:

dictionary of sequence data
classmethod isValid(elements)
Parameters:elements (iterable(str) or str) – An iterable of string representations of elements making up the sequence
Returns:Tuple indicating whether valid and a set of invalid characters, if any
Return type:tuple(bool, set(str))
hydrophobicity_window_padding
isoelectric_point_window_padding
clearAllCaching()
class schrodinger.protein.sequence.NucleicAcidSequence(elements, **kwargs)

Bases: schrodinger.protein.sequence.ProteinSequence

AnnotationClass

alias of schrodinger.protein.annotation.NucleicAcidSequenceAnnotations

ElementClass

alias of schrodinger.protein.residue.Nucleotide

alphabet = {'1CC': NucleotideType('C', '1CC', 'Cytosine'), '1MA': NucleotideType('A', '1MA', 'Adenine'), '1MG': NucleotideType('G', '1MG', 'Guanine'), '2MG': NucleotideType('G', '2MG', 'Guanine'), '5FC': NucleotideType('C', '5FC', 'Cytosine'), '5HC': NucleotideType('C', '5HC', 'Cytosine'), '5MC': NucleotideType('C', '5MC', 'Cytosine'), '5MU': NucleotideType('U', '5MU', 'Uracil'), '6MA': NucleotideType('A', '6MA', 'Adenine'), '7MG': NucleotideType('G', '7MG', 'Guanine'), 'A': NucleotideType('A', 'A', 'Adenine'), 'ADP': NucleotideType('A', 'ADP', 'Adenine'), 'AMP': NucleotideType('A', 'AMP', 'Adenine'), 'ATP': NucleotideType('A', 'ATP', 'Adenine'), 'C': NucleotideType('C', 'C', 'Cytosine'), 'CDP': NucleotideType('C', 'CDP', 'Cytosine'), 'CMP': NucleotideType('C', 'CMP', 'Cytosine'), 'CTP': NucleotideType('C', 'CTP', 'Cytosine'), 'DA': NucleotideType('A', 'DA', 'Adenine'), 'DC': NucleotideType('C', 'DC', 'Cytosine'), 'DG': NucleotideType('G', 'DG', 'Guanine'), 'DI': ResidueType('DI', 'DI', 'Unknown'), 'DT': NucleotideType('T', 'DT', 'Thymine'), 'DU': NucleotideType('U', 'DU', 'Uracil'), 'G': NucleotideType('G', 'G', 'Guanine'), 'GDP': NucleotideType('G', 'GDP', 'Guanine'), 'GMP': NucleotideType('G', 'GMP', 'Guanine'), 'GTP': NucleotideType('G', 'GTP', 'Guanine'), 'H2U': NucleotideType('U', 'H2U', 'Uracil'), 'I': ResidueType('I', 'I', 'Unknown'), 'M2G': NucleotideType('G', 'M2G', 'Guanine'), 'OMC': NucleotideType('C', 'OMC', 'Cytosine'), 'OMG': NucleotideType('G', 'OMG', 'Guanine'), 'PSU': NucleotideType('Ψ', 'PSU', 'Uracil'), 'TDP': NucleotideType('T', 'TDP', 'Thymine'), 'TMP': NucleotideType('T', 'TMP', 'Thymine'), 'TTP': NucleotideType('T', 'TTP', 'Thymine'), 'U': NucleotideType('U', 'U', 'Uracil'), 'UDP': NucleotideType('U', 'UDP', 'Uracil'), 'UMP': NucleotideType('U', 'UMP', 'Uracil'), 'UTP': NucleotideType('U', 'UTP', 'Uracil'), 'YYG': ResidueType('X', 'YYG', 'Unknown')}
class schrodinger.protein.sequence.StructureSequence(st, atoms)

Bases: schrodinger.structure._AtomCollection

Class representing a sequence of protein residues.

residue

Returns residue iterator for all residues in the sequence

schrodinger.protein.sequence.get_structure_sequences(st)

Iterates over all sequences in the given structure.

schrodinger.protein.sequence.find_generalized_pattern(sequence_list, pattern, validate_pattern=False)

Finds a generalized sequence pattern within specified sequences. NOTE: The search is performed in the forward direction only.

Parameters:
  • sequence_list – list of sequence dictionaries to search.
  • pattern (str) –

    Pattern defined using extended PROSITE syntax.

    • standard IUPAC one-letter codes are used for all amino acids
    • each element in a pattern is separated using ‘-‘ symbol
    • symbol ‘x’ is used for position where any amino acid is accepted
    • ambiguities are listed using the acceptable amino acids between square brackets, e.g. [ACT] means Ala, Cys or Thr
    • amino acids not accepted for a given position are indicated by listing them between curly brackets, e.g. {GP} means ‘not Gly and not Pro’
    • repetition is indicated using parentheses, e.g. A(3) means Ala-Ala-Ala, x(2,4) means between 2 to 4 any residues
    • the following lowercase characters can be used as additional flags:
      • ’x’ means any amino acid
      • ’a’ means acidic residue: [DE]
      • ’b’ means basic residue: [KR]
      • ’o’ means hydrophobic residue: [ACFILPWVY]
      • ’p’ means aromatic residue: [WYF]
      • ’s‘ means solvent exposed residue
      • ’h’ means helical residue
      • ’e’ means extended residue
      • ’f’ means flexible residue
    • Each position can optionally by followed by @<res_num> expression that will match the position with a given residue number.
    • Entire pattern can be followed by :<index> expression that defines a ‘hotspot’ in the pattern. When the hotspot is defined, only a single residue corresponding to (pattern_match_start+index-1) will be returned as a match. The index is 1-based and can be used to place the hotspot outside of the pattern (can also be a negative number).

    Pattern examples:

    • N-{P}-[ST] : Asn-X-Ser or Thr (X != Pro)
    • N[sf]-{P}[sf]-[ST][sf] : as above, but all residues flexible OR solvent exposed
    • Nsf-{P}sf-[ST]sf : as above, but all residues flexible AND solvent exposed
    • Ns{f} : Asn solvent exposed AND not in flexible region
    • N[s{f}] : Asn solvent exposed OR not in flexible region
    • [ab]{K}{s}f : acidic OR basic, with exception of Lys, flexible AND not solvent exposed
    • Ahe : Ala helical AND extended - no match possible
    • A[he] : Ala helical OR extended
    • A{he} : Ala coiled chain conformation (not helical nor extended)
    • [ST] : Ser OR Thr
    • ST : Ser AND Thr - no match possible
  • validate_pattern (boolean) – If True, the function will validate the pattern without performing the search (the sequences parameter will be ignored) and return True if the pattern is valid, or False otherwise. The default is False.
Return type:

list of lists of integer tuples or False if the pattern is invalid
Returns:

False if the specified input pattern was incorrect. Otherwise, it returns a list of lists of matches for each input sequence. Each match is a (start, end) tuple where start and end are matching sequence positions.

Converts a StructureSequence object to dictionary required by find_generalized_pattern function. Because the conversion can be time consuming, it should be done once per sequence.

Optionally a list of atom SASAs for each atom in the CT can be specified. If it’s not specified, it will get calculated by calling analyze.calculate_sasa_by_atom().

Parameters:
  • seq (StructureSequence) – StructureSequence object
  • sasa_by_atom (list) – list of atom SASAs
Return type:

dict
Returns:

Dictionary of sequence information
schrodinger.protein.sequence.find_pattern(seq, pattern)

Find pattern matches in a specified StructureSequence object. Returns a list of matching positions.

Parameters:
  • seq (StructureSequence) – StructureSequence object
  • pattern (string) – Sequence pattern. The syntax is described in find_generalized_pattern.
Return type:

list of lists of integer tuples or None
Returns:

None if the specified input pattern was incorrect. Otherwise, it returns a list of lists of matches for each residue position in the input structure. Each match is a (start, end) tuple where start and end are matching sequence positions. If ‘hotspot’ is specified then start = end.
schrodinger.protein.sequence.get_pairwise_sequence_similarity(chain1, chain2, consider_gap=True, method='clustalw')

Given two single chain sequences, align them, and return sequence similarity among them.

Parameters:
  • chain1 (structure._Chain) – The first sequence chain.
  • chain2 (structure._Chain) – The second sequence chain.
  • consider_gap (bool) – Whether or not to consider gaps in the alignment, default to true.
  • method (string) – Which alignment method to use (‘muscle’ or ‘clustalw’)
Returns:

Sequence similarity of the alignment of the two.
Return type:

float, between 0.0 and 1.0
schrodinger.protein.sequence.create_alignment_from_chains(chains)

Return ProteinAlignment object comprised of two chains

Parameters:chains (iterable(structure._Chain)) – Chains to be aligned
schrodinger.protein.sequence.align_alignment(aln, second_aln=None, method='clustalw')

Perform alignment from an ProteinAlignment object

Parameters:
  • aln (ProteinAlignment) – Alignment data
  • method (string) – Which method/program to use
Returns:

Aligned sequences
Return type:

ProteinAlignment
schrodinger.protein.sequence.align_from_chains(chains, method='clustalw')

Perform alignment on a series of chains

Parameters:
  • chains (iterable(structure._Chain)) – Chains to be aligned
  • method (string) – Which method/program to use (choices ‘muscle’, ‘clustalw’)
Returns:

Aligned sequences
Return type:

ProteinAlignment
schrodinger.protein.sequence.get_aligned_residues(st1, st2)

This generator will yield 2 structure._Residue objects - one from each structure - for each position in aligned sequences.

Parameters:
  • st1 (structure.Structure) – First structure.
  • st2 (structure.Structure) – Second structure
Returns:

Generates tuples of 2 residues that align at each position.
Return type:

generator(structure._Residue or None, structure._Residue or None)
Raises:

ValueError – if structures don’t have equivalent chains.