topology
¶
Parser for topology XML files.
Code author: Nathan Baker
Code author: Yong Huang
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class
pdb2pqr.topology.
Topology
(topology_file)[source]¶ Contains the structured definitions of residue reference coordinates as well as alternate titration, conformer, and tautomer states.
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class
pdb2pqr.topology.
TopologyAtom
(parent)[source]¶ A class for atom topology information.
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__init__
(parent)[source]¶ Initialize with an upper-level class that contains an atom array.
For example, initialize with
TopologyReference
orTopologyConformerAddition
Parameters: parent – parent object with atom array
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class
pdb2pqr.topology.
TopologyConformer
(topology_tautomer)[source]¶ A class for topology conformer information.
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__init__
(topology_tautomer)[source]¶ Initialize object.
Parameters: topology_tautomer (TopologyTautomer) – tautomer for which to evaluate conformers
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class
pdb2pqr.topology.
TopologyConformerAdd
(topology_conformer)[source]¶ A class for adding atoms to a conformer.
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__init__
(topology_conformer)[source]¶ Initialize object.
Parameters: topology_conformer (TopologyConformer) – conformer to which to add atoms
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class
pdb2pqr.topology.
TopologyConformerRemove
(topology_conformer)[source]¶ A class for removing atoms from a conformer.
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__init__
(topology_conformer)[source]¶ Initialize object.
Parameters: topology_conformer (TopologyConformer) – conformer to which to add atoms
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class
pdb2pqr.topology.
TopologyDihedral
(parent)[source]¶ A class for dihedral angle topology information.
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class
pdb2pqr.topology.
TopologyHandler
[source]¶ Handler for XML-based topology files.
Assumes the following hierarchy of tags:
- topology
- residue
- reference
- titrationstate
- tautomer
- conformer
- tautomer
- residue
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characters
(text)[source]¶ Parse characters in topology XML file.
Parameters: text (str) – XML character data
- topology
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class
pdb2pqr.topology.
TopologyReference
(topology_residue)[source]¶ A class for the reference structure of a residue.
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__init__
(topology_residue)[source]¶ Initialize object.
Parameters: topology_residue (TopologyResidue) – reference residue
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class
pdb2pqr.topology.
TopologyResidue
(topology_)[source]¶ A class for residue topology information.
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class
pdb2pqr.topology.
TopologyTautomer
(topology_titration_state)[source]¶ A class for topology tautomer information.
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__init__
(topology_titration_state)[source]¶ Initialize object.
Parameters: topology_titration_state (TopologyTitrationState) – titration state of this residue
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class
pdb2pqr.topology.
TopologyTitrationState
(topology_residue)[source]¶ A class for the titration state of a residue.
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__init__
(topology_residue)[source]¶ Initialize object.
Parameters: topology_residue (TopologyResidue) – residue topology
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