schrodinger.protein.nonstandard_residues module¶
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schrodinger.protein.nonstandard_residues.
get_residue_database
(*, load_saved=True)¶ Get the global nonstandard residue database.
If there is an error loading the saved database file, an empty (default) database will be returned.
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schrodinger.protein.nonstandard_residues.
get_default_user_dbfile
()¶ Return the path to the default user DB file.
- Returns
Default path to user DB file.
- Return type
str
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schrodinger.protein.nonstandard_residues.
get_saved_db_file
()¶ Return the path to the database file that is saved in Maestro’s prefs or, if no preference is specified, a default location in the user’s userdata directory.,
- Returns
Saved DB filepath to be used
- Return type
str
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schrodinger.protein.nonstandard_residues.
strip_caps
(st)¶ Strip any ACE & NMA caps, and add an OXT cap.
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schrodinger.protein.nonstandard_residues.
find_atom
(st, name)¶ Find the atom with the given PDB name. None is returned if no such atom is present.
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schrodinger.protein.nonstandard_residues.
flip_isomer
(st)¶ Invert the isomerism of the alpha carbon. So D residue gets converted to L and vice versa.
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schrodinger.protein.nonstandard_residues.
generate_smiles
(st, use_annotations=False)¶ Generate the SMILES string for the given structure.
- Parameters
use_annotations (bool) – Whether to use annotations instead of 3D geometry (set if the structure is 2D).
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class
schrodinger.protein.nonstandard_residues.
ResidueDatabase
(db_file=None)¶ Bases:
PyQt5.QtCore.QObject
A collection of AminoAcid objects. Included built-in residues. For now, just a collection of database-related functions.
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residuesChanged
¶
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__init__
(db_file=None)¶ Initialize self. See help(type(self)) for accurate signature.
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property
amino_acids
¶
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classmethod
get_built_in_residues
()¶ Return a list of built-in residues AminoAcid objects from the installation.
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readDatabaseFile
(db_file)¶ Read the specified database file, and return a ResidueDatabase (which is basically a list of AminoAcid objects, including built-in residues). Raises RuntimeError on failure.
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reset
()¶
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saveDatabase
(amino_acids, db_file=None)¶
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static
exportDatabase
(amino_acids, db_file)¶ Export the amino acids database.
- Parameters
amino_acids (list[AminoAcid]) – Amino acids to export.
db_file (str) – Database file path.
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blockSignals
(self, bool) → bool¶
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childEvent
(self, QChildEvent)¶
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children
(self) → List[QObject]¶
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connectNotify
(self, QMetaMethod)¶
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customEvent
(self, QEvent)¶
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deleteLater
(self)¶
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destroyed
¶ destroyed(self, object: QObject = None) [signal]
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disconnect
(self)¶
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disconnectNotify
(self, QMetaMethod)¶
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dumpObjectInfo
(self)¶
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dumpObjectTree
(self)¶
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dynamicPropertyNames
(self) → List[QByteArray]¶
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event
(self, QEvent) → bool¶
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eventFilter
(self, QObject, QEvent) → bool¶
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findChild
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶ findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject
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findChildren
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶ findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]
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inherits
(self, str) → bool¶
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installEventFilter
(self, QObject)¶
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isSignalConnected
(self, QMetaMethod) → bool¶
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isWidgetType
(self) → bool¶
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isWindowType
(self) → bool¶
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killTimer
(self, int)¶
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metaObject
(self) → QMetaObject¶
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moveToThread
(self, QThread)¶
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objectName
(self) → str¶
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objectNameChanged
¶ objectNameChanged(self, str) [signal]
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parent
(self) → QObject¶
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property
(self, str) → Any¶
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pyqtConfigure
(...)¶ Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.
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receivers
(self, PYQT_SIGNAL) → int¶
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removeEventFilter
(self, QObject)¶
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sender
(self) → QObject¶
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senderSignalIndex
(self) → int¶
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setObjectName
(self, str)¶
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setParent
(self, QObject)¶
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setProperty
(self, str, Any) → bool¶
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signalsBlocked
(self) → bool¶
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startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
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staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
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thread
(self) → QThread¶
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timerEvent
(self, QTimerEvent)¶
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tr
(self, str, disambiguation: str = None, n: int = - 1) → str¶
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class
schrodinger.protein.nonstandard_residues.
AminoAcid
(st, built_in=False, standard=False)¶ Bases:
object
Class representing an amino acid (residue) row in the table.
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__init__
(st, built_in=False, standard=False)¶ Initialize self. See help(type(self)) for accurate signature.
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property
name
¶ AminoAcid.name will return the PDB residue name for this AA.
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property
code
¶ AminoAcid.code will return the 1-letter code for this residue.
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property
aligns_with
¶
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property
description
¶ AminoAcid.description will return the title of the CT.
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property
locked
¶ AminoAcid.code will return whether the residue is locked from editing.
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st_changed
()¶ Must be called every time the structure is modified. Will update the SMILES string and the .isomer property.
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property
identifier
¶ Return an ID string for this residue, which includes the residue name, isomer, and description.
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is_editable
()¶
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