schrodinger.protein.annotation module

Implementation of Multiple Sequence Viewer Annotation class.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.protein.annotation.LIGAND_CONTACTS

alias of schrodinger.protein.annotation.LIGAND_CONTACT

class schrodinger.protein.annotation.AntibodyCDRLabel

Bases: enum.Enum

An enumeration.

H1 = 5
H2 = 6
H3 = 7
L1 = 2
L2 = 3
L3 = 4
NotCDR = 1
class schrodinger.protein.annotation.AntibodyCDRScheme(*args, **kwargs)

Bases: schrodinger.models.json.JsonableEnum

An enumeration.

AHo = 5
Chothia = 1
EnhancedChothia = 4
IMGT = 3
Kabat = 2
class schrodinger.protein.annotation.AntibodyCDR(label, start, end)

Bases: tuple

end

Alias for field number 2

label

Alias for field number 0

start

Alias for field number 1

class schrodinger.protein.annotation.Consensus

Bases: enum.Enum

An enumeration.

not_conserved = ' '
fully_conserved = '*'
strongly_conserved = ':'
weakly_conserved = '.'
class schrodinger.protein.annotation.SequenceAnnotations(seq)

Bases: PyQt5.QtCore.QObject

Knows how to annotate a sequence

Annotations can be set at the level of the sequence as a whole, or be per sequence element annotations. If an attribute is accessed on the SequenceAnnotations object, the attribute is first looked for on the object and if not found is assumed to be a per sequence element annotation. If the elements in the sequence lack the attribute, an AttributeError will be raised.

Variables:titleChanged (QtCore.pyqtSignal) – A signal emitted after an annotation’s title (row header) changes.
titleChanged
sequence
class schrodinger.protein.annotation.ProteinSequenceAnnotations(seq)

Bases: schrodinger.protein.annotation.SequenceAnnotations

Knows how to annotate a ProteinSequence

Variables:
  • CLOSE_LIG_DIST (int) – The distance (in angstroms) from a ligand to consider a residue as a “close contact”
  • FAR_LIG_DIST (int) – The distance (in angstroms) from a ligand to consider a residue as a “far contact”
FAR_LIG_DIST = 6
CLOSE_LIG_DIST = 3
class ANNOTATION_TYPES

Bases: object

antibody_cdr = 18
b_factor = 13
beta_strand_propensity = 5
disulfide_bonds = 3
exposure_tendency = 8
helix_propensity = 4
helix_termination_tendency = 7
hydrophobicity = 11
isoelectric_point = 12
ligand_contacts = 17
rescode = 2
resnum = 1
sasa = 19
secondary_structure = 16
side_chain_chem = 10
steric_group = 9
turn_propensity = 6
window_hydrophobicity = 14
window_isoelectric_point = 15
RES_PROPENSITY_ANNOTATIONS = {<ANNOTATION_TYPES.side_chain_chem: 10>, <ANNOTATION_TYPES.exposure_tendency: 8>, <ANNOTATION_TYPES.turn_propensity: 6>, <ANNOTATION_TYPES.helix_termination_tendency: 7>, <ANNOTATION_TYPES.helix_propensity: 4>, <ANNOTATION_TYPES.beta_strand_propensity: 5>, <ANNOTATION_TYPES.steric_group: 9>}
window_hydrophobicity

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

invalidateWindowHydrophobicity()

Invalidate the cached window hydrophobicity data. Note that this method is also called from the sequence when the window size changes.

window_isoelectric_point

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

invalidateWindowIsoelectricPoint()

Invalidate the cached window isoelectric point data. Note that this method is also called from the sequence when the window size changes.

sasa

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

getAntibodyCDR(col, scheme)

Returns the antibody CDR information of the col’th index in the sequence under a given antibody CDR numbering scheme.

Parameters:
  • col (int) – index into the sequence
  • scheme (AntibodyCDRScheme) – The antibody CDR numbering scheme to use
Returns:

Antibody CDR label, start, and end positions
Return type:

AntibodyCDR, which is a named tuple of (AntibodyCDRLabel, int, int) if col is in a CDR, otherwise (AntibodyCDRLabel.NotCDR, None, None)
getAntibodyCDRs(scheme)

Returns a list of antibody CDR information for the entire sequence.

Parameters:scheme (AntibodyCDRScheme) – The antibody CDR numbering scheme to use
Returns:A list of Antibody CDR labels, starts, and end positions
Return type:list(AntibodyCDR)
isAntibodyChain()
Returns:Whether the sequence described is an antibody chain
Return type:bool
getSparseRescodes(modulo)
ligand_contacts
ligands
onStructureChanged()
resetAnnotation(ann)

Force a reset of an annotation’s cache.

clearAllCaching()
getSSBondPartner(index)

Return the residue’s intra-sequence disulfide bond partner, if any.

If the residue is not involved in a disulfide bond, its partner has been deleted, or its partner is in another sequence, it will return None.

Parameters:index (int) – Index of the residue to check
Returns:the other Residue in the disulfide bond or None
Return type:schrodinger.protein.residue.Residue or None
inscode
resnum
class schrodinger.protein.annotation.NucleicAcidSequenceAnnotations(seq)

Bases: schrodinger.protein.annotation.ProteinSequenceAnnotations

class schrodinger.protein.annotation.ProteinAlignmentAnnotations(aln)

Bases: object

Knows how to annotate an alignment (a collection of aligned sequences)

class ANNOTATION_TYPES

Bases: object

consensus_freq = 6
consensus_seq = 5
consensus_symbols = 4
indices = 1
mean_hydrophobicity = 2
mean_isoelectric_point = 3
alignment
indices

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

mean_hydrophobicity

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

mean_isoelectric_point

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

consensus_seq

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

consensus_freq

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

consensus_symbols

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

clearAllCaching()