propka.conformation_container¶
Molecular data structures¶
Container data structure for molecular conformations.
Module Attributes
A large number that gets multipled with the integer obtained from applying 

A number that gets mutiplied with an atom's residue number. 
Classes

Container for molecular conformations 
 class propka.conformation_container.ConformationContainer(name='', parameters=None, molecular_container=None)[source]¶
Container for molecular conformations
Changed in version 3.4.0: Removed
additional_setup_when_reading_input_files()
as reading PROPKA inputs is no longer supported. 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
 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
 calculate_pka(version, options)[source]¶
Calculate pKas for conformation container.
 Parameters
version – version object
options – option object
 copy_atom(atom)[source]¶
Add a copy of the atom to container.
 Parameters
atom – atom to copy and add
 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.
 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
 find_covalently_coupled_groups()[source]¶
Find covalently coupled groups and set common charge centres.
 find_group(group)[source]¶
Find a group in the container.
 Parameters
group – group to find
 Returns
False (if group not found) or group
 find_non_covalently_coupled_groups(verbose=False)[source]¶
Find noncovalently coupled groups and set common charge centres.
 Parameters
verbose – verbose output
 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
 get_backbone_co_groups()[source]¶
Get CO backbone groups needed for pKa calculations.
 Returns
list of groups
 get_backbone_groups()[source]¶
Get backbone groups needed for the pKa calculations.
 Returns
list of groups
 get_backbone_nh_groups()[source]¶
Get NH backbone groups needed for pKa calculations.
 Returns
list of groups
 get_backbone_reorganisation_groups()[source]¶
Get groups involved with backbone reorganization.
 Returns
list of groups
 get_chain(chain)[source]¶
Get atoms associated with a specific chain.
 Parameters
chain – chain to select
 Returns
list of atoms
 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
 get_covalently_coupled_groups()[source]¶
Get covalently coupled groups needed for pKa calculations.
 Returns
list of groups
 get_group_names(group_list)[source]¶
Get names of groups in list.
 Parameters
group_list – list to check
 Returns
list of groups
 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
 get_groups_in_residue(residue)[source]¶
Get residue groups needed for pKa calculations.
 Parameters
residue – specific residue with groups
 Returns
list of groups
 get_non_covalently_coupled_groups()[source]¶
Get noncovalently coupled groups needed for pKa calculations.
 Returns
list of groups
 get_sidechain_groups()[source]¶
Get sidechain groups needed for the pKa calculations.
 Returns
list of groups
 get_titratable_groups()[source]¶
Get all titratable groups needed for pKa calculations.
 Returns
list of groups
 init_group(group)[source]¶
Initialize the given Group object.
 Parameters
group – group object to initialize
 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
 propka.conformation_container.RESIDUE_MULTIPLIER = 1000¶
A number that gets mutiplied with an atom’s residue number. Used in calculating keys for atom sorting.