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OpenStructure
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OpenStructure
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Public Member Functions | |
| def | __init__ |
| def | view |
| def | contact_mode |
| def | contact_d |
| def | chain_names |
| def | interacting_chains |
| def | contacts |
| def | hr_contacts |
| def | interface_residues |
| def | hr_interface_residues |
| def | GetChain |
| def | GetSequence |
Data Fields | |
| contact_mode | |
Helper object for Contact-score computation
Definition at line 9 of file contact_score.py.
| def __init__ | ( | self, | |
| ent, | |||
contact_d = 5.0, |
|||
contact_mode = "aa" |
|||
| ) |
Definition at line 12 of file contact_score.py.
| def chain_names | ( | self | ) |
Chain names in :attr:`~view` Names are sorted :type: :class:`list` of :class:`str`
Definition at line 96 of file contact_score.py.
| def contact_d | ( | self | ) |
Pairwise distance of residues to be considered as contacts Given at :class:`ContactScorer` construction :type: :class:`float`
Definition at line 86 of file contact_score.py.
| def contact_mode | ( | self | ) |
The contact mode Can either be "aa", meaning that all atoms are considered to identify contacts, or "repr" which only considers distances between representative atoms. For peptides thats CB (CA for GLY), for nucleotides thats C3'. :type: :class:`str`
Definition at line 73 of file contact_score.py.
| def contacts | ( | self | ) |
Interchain contacts Organized as :class:`dict` with key (cname1, cname2) and values being a set of tuples with the respective residue indices. cname1 < cname2 evaluates to True.
Definition at line 118 of file contact_score.py.
| def GetChain | ( | self, | |
| chain_name | |||
| ) |
Get chain by name :param chain_name: Chain in :attr:`~view` :type chain_name: :class:`str`
Definition at line 165 of file contact_score.py.
| def GetSequence | ( | self, | |
| chain_name | |||
| ) |
Get sequence of chain Returns sequence of specified chain as raw :class:`str` :param chain_name: Chain in :attr:`~view` :type chain_name: :class:`str`
Definition at line 176 of file contact_score.py.
| def hr_contacts | ( | self | ) |
Human readable interchain contacts Human readable version of :attr:`~contacts`. Simple list with tuples containing two strings specifying the residues in contact. Format: <cname>.<rnum>.<ins_code>
Definition at line 130 of file contact_score.py.
| def hr_interface_residues | ( | self | ) |
Human readable interface residues Human readable version of :attr:`interface_residues`. :class:`list` of strings specifying the interface residues in format: <cname>.<rnum>.<ins_code>
Definition at line 154 of file contact_score.py.
| def interacting_chains | ( | self | ) |
Pairs of chains in :attr:`~view` with at least one contact :type: :class:`list` of :class:`tuples`
Definition at line 108 of file contact_score.py.
| def interface_residues | ( | self | ) |
Interface residues Residues in each chain that are in contact with any other chain. Organized as :class:`dict` with key cname and values the respective residue indices in a :class:`set`.
Definition at line 142 of file contact_score.py.
| def view | ( | self | ) |
The structure depending on *contact_mode* Full view in case of "aa", view that only contains representative atoms in case of "repr". :type: :class:`ost.mol.EntityView`
Definition at line 62 of file contact_score.py.
| contact_mode |
Definition at line 44 of file contact_score.py.
1.8.5