4.1.4. propka.conformation_container¶
4.1.4.1. Molecular data structures¶
Container data structure for molecular conformations.
Module Attributes
A large number that gets multipled with the integer obtained from applying |
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A number that gets mutiplied with an atom’s residue number. |
Classes
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Container for molecular conformations |
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class
propka.conformation_container.
ConformationContainer
(name='', parameters=None, molecular_container=None)[source]¶ Container for molecular conformations
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calculate_charge
(parameters, ph=None)[source]¶ Calculate charge for folded and unfolded states.
- Parameters
parameters – parameters for calculation
ph – pH for calculation
- Returns
charge for unfolded state
charge for folded state
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calculate_folding_energy
(ph=None, reference=None)[source]¶ Calculate folding energy over all groups in conformation container.
- Parameters
ph – pH for calculation
reference – reference state
- Returns
folding energy TODO - need units
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calculate_pka
(version, options)[source]¶ Calculate pKas for conformation container.
- Parameters
version – version object
options – option object
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copy_atom
(atom)[source]¶ Add a copy of the atom to container.
- Parameters
atom – atom to copy and add
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coupling_effects
()[source]¶ Penalize groups based on coupling effects.
Bases: The group with the highest pKa (the most stable one in the charged form) will be the first one to adopt a proton as pH is lowered and this group is allowed to titrate. The remaining groups are penalised.
Acids: The group with the highest pKa (the least stable one in the charged form) will be the last group to loose the proton as pH is raised and will be penalised. The remaining groups are allowed to titrate.
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find_bonded_titratable_groups
(atom, num_bonds, original_atom)[source]¶ Find bonded titrable groups.
- Parameters
atom – atom to check for bonds
num_bonds – number of bonds for coupling
original_atom – another atom to check for bonds
- Returns
a set of bonded atom groups
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find_covalently_coupled_groups
()[source]¶ Find covalently coupled groups and set common charge centres.
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find_group
(group)[source]¶ Find a group in the container.
- Parameters
group – group to find
- Returns
False (if group not found) or group
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find_non_covalently_coupled_groups
(verbose=False)[source]¶ Find non-covalently coupled groups and set common charge centres.
- Parameters
verbose – verbose output
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get_a_coupled_system_of_groups
(new_group, coupled_groups, get_coupled_groups)[source]¶ Set up coupled systems of groups.
- Parameters
new_group – added to coupled_groups
coupled_groups – existing coupled groups
get_coupled_groups – TODO - I don’t know what this
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get_backbone_co_groups
()[source]¶ Get CO backbone groups needed for pKa calculations.
- Returns
list of groups
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get_backbone_groups
()[source]¶ Get backbone groups needed for the pKa calculations.
- Returns
list of groups
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get_backbone_nh_groups
()[source]¶ Get NH backbone groups needed for pKa calculations.
- Returns
list of groups
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get_backbone_reorganisation_groups
()[source]¶ Get groups involved with backbone reorganization.
- Returns
list of groups
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get_chain
(chain)[source]¶ Get atoms associated with a specific chain.
- Parameters
chain – chain to select
- Returns
list of atoms
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get_coupled_systems
(groups, get_coupled_groups)[source]¶ A generator that yields covalently coupled systems.
- Parameters
groups – groups for generating coupled systems
get_coupled_groups – TODO - I don’t know what this is
- Yields
covalently coupled systems
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get_covalently_coupled_groups
()[source]¶ Get covalently coupled groups needed for pKa calculations.
- Returns
list of groups
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get_group_names
(group_list)[source]¶ Get names of groups in list.
- Parameters
group_list – list to check
- Returns
list of groups
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get_groups_for_calculations
()[source]¶ Get a list of groups that should be included in results report.
If –titrate_only option is specified, only residues that are titratable and are in that list are included; otherwise all titratable residues and CYS residues are included.
- Returns
list of groups
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get_groups_in_residue
(residue)[source]¶ Get residue groups needed for pKa calculations.
- Parameters
residue – specific residue with groups
- Returns
list of groups
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get_non_covalently_coupled_groups
()[source]¶ Get non-covalently coupled groups needed for pKa calculations.
- Returns
list of groups
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get_sidechain_groups
()[source]¶ Get sidechain groups needed for the pKa calculations.
- Returns
list of groups
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get_titratable_groups
()[source]¶ Get all titratable groups needed for pKa calculations.
- Returns
list of groups
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init_group
(group)[source]¶ Initialize the given Group object.
- Parameters
group – group object to initialize
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setup_and_add_group
(group)[source]¶ Check if we want to include this group in the calculations.
- Parameters
group – group to check
Share sidechain, backbone, and Coloumb determinants between groups.
- Parameters
groups – groups to share between
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propka.conformation_container.
RESIDUE_MULTIPLIER
= 1000¶ A number that gets mutiplied with an atom’s residue number. Used in calculating keys for atom sorting.
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propka.conformation_container.
UNICODE_MULTIPLIER
= 10000000.0¶ A large number that gets multipled with the integer obtained from applying
ord()
to the atom chain ID. Used in calculating atom keys for sorting.