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OpenStructure
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OpenStructure
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Inherits object.
Public Member Functions | |
| def | __init__ |
| def | GetName |
| def | SetName |
| def | ca_entity |
| def | ca_chains |
| def | GetAlignment |
| def | chem_groups |
| def | GetAngles |
| def | GetAxis |
| def | contacts |
| def | contacts |
| def | contacts_ca |
| def | contacts_ca |
Data Fields | |
| original_name | |
| calpha_only | |
| is_valid | |
Entity with cached entries for QS scoring. Any known / precomputed information can be filled into the appropriate attribute here as long as they are labelled as read/write. Otherwise the quantities are computed on first access and cached (lazy evaluation). The heaviest load is expected when computing :attr:`contacts` and :attr:`contacts_ca`. :param ent: Entity to be used for QS scoring. A copy of it will be processed. :type ent: :class:`~ost.mol.EntityHandle` or :class:`~ost.mol.EntityView` .. attribute:: is_valid True, if successfully initialized. False, if input structure is monomer or has less than 2 protein chains with >= 20 residues. :type: :class:`bool` .. attribute:: original_name Name set for *ent* when object was created. :type: :class:`str` .. attribute:: ent Cleaned version of *ent* passed at construction. Hydrogens are removed, the entity is processed with a :class:`~ost.conop.RuleBasedProcessor` and chains listed in :attr:`removed_chains` have been removed. The name of this entity might change during scoring (see :func:`GetName`). Otherwise, this will be fixed. :type: :class:`~ost.mol.EntityHandle` .. attribute:: removed_chains Chains removed from *ent* passed at construction. These are ligand and water chains as well as small (< 20 res.) peptides or chains with no amino acids (determined by chem. type, which is set by rule based processor). :type: :class:`list` of :class:`str` .. attribute:: calpha_only Whether entity is CA-only (i.e. it has 0 CB atoms) :type: :class:`bool`
Definition at line 581 of file qsscoring.py.
| def __init__ | ( | self, | |
| ent | |||
| ) |
Definition at line 630 of file qsscoring.py.
| def ca_chains | ( | self | ) |
Map of chain names in :attr:`ent` to sequences with attached view to CA-only chains (into :attr:`ca_entity`). Useful for alignments and superpositions. :getter: Computed on first use (cached) :type: :class:`dict` (key = :class:`str`, value = :class:`~ost.seq.SequenceHandle`)
Definition at line 688 of file qsscoring.py.
| def ca_entity | ( | self | ) |
Reduced representation of :attr:`ent` with only CA atoms. This guarantees that each included residue has exactly one atom. :getter: Computed on first use (cached) :type: :class:`~ost.mol.EntityHandle`
Definition at line 675 of file qsscoring.py.
| def chem_groups | ( | self | ) |
Intra-complex group of chemically identical (seq. id. > 95%) polypeptide chains as extracted from :attr:`ca_chains`. First chain in group is the one with the longest sequence. :getter: Computed on first use (cached) :type: :class:`list` of :class:`list` of :class:`str` (chain names)
Definition at line 720 of file qsscoring.py.
| def contacts | ( | self | ) |
Connectivity dictionary (**read/write**).
As given by :func:`GetContacts` with *calpha_only* = False on :attr:`ent`.
:getter: Computed on first use (cached)
:setter: Uses :func:`FilterContacts` to ensure that we only keep contacts
for chains in the cleaned entity.
:type: See return type of :func:`GetContacts`
Definition at line 766 of file qsscoring.py.
| def contacts | ( | self, | |
| new_contacts | |||
| ) |
Definition at line 781 of file qsscoring.py.
| def contacts_ca | ( | self | ) |
CA-only connectivity dictionary (**read/write**). Like :attr:`contacts` but with *calpha_only* = True in :func:`GetContacts`.
Definition at line 786 of file qsscoring.py.
| def contacts_ca | ( | self, | |
| new_contacts | |||
| ) |
Definition at line 796 of file qsscoring.py.
| def GetAlignment | ( | self, | |
| c1, | |||
| c2 | |||
| ) |
Get sequence alignment of chain *c1* with chain *c2*. Computed on first use based on :attr:`ca_chains` (cached). :param c1: Chain name for first chain to align. :type c1: :class:`str` :param c2: Chain name for second chain to align. :type c2: :class:`str` :rtype: :class:`~ost.seq.AlignmentHandle` or None if it failed.
Definition at line 704 of file qsscoring.py.
| def GetAngles | ( | self, | |
| c1, | |||
| c2 | |||
| ) |
Get Euler angles from superposition of chain *c1* with chain *c2*. Computed on first use based on :attr:`ca_chains` (cached). :param c1: Chain name for first chain to superpose. :type c1: :class:`str` :param c2: Chain name for second chain to superpose. :type c2: :class:`str` :return: 3 Euler angles (may contain nan if something fails). :rtype: :class:`numpy.array`
Definition at line 735 of file qsscoring.py.
| def GetAxis | ( | self, | |
| c1, | |||
| c2 | |||
| ) |
Get axis of symmetry from superposition of chain *c1* with chain *c2*. Computed on first use based on :attr:`ca_chains` (cached). :param c1: Chain name for first chain to superpose. :type c1: :class:`str` :param c2: Chain name for second chain to superpose. :type c2: :class:`str` :return: Rotational axis (may contain nan if something fails). :rtype: :class:`numpy.array`
Definition at line 750 of file qsscoring.py.
| def GetName | ( | self | ) |
Wrapper to :func:`~ost.mol.EntityHandle.GetName` of :attr:`ent`. This is used to uniquely identify the entity while scoring. The name may therefore change while :attr:`original_name` remains fixed.
Definition at line 659 of file qsscoring.py.
| def SetName | ( | self, | |
| new_name | |||
| ) |
Wrapper to :func:`~ost.mol.EntityHandle.SetName` of :attr:`ent`. Use this to change unique identifier while scoring (see :func:`GetName`).
Definition at line 667 of file qsscoring.py.
| calpha_only |
Definition at line 638 of file qsscoring.py.
| is_valid |
Definition at line 643 of file qsscoring.py.
| original_name |
Definition at line 632 of file qsscoring.py.
1.8.5