3.1. bcforms package¶

3.1.1. Submodules¶

3.1.2. bcforms.main module¶

bcforms command line interface

Author: Jonathan Karr <karr@mssm.edu>
Date: 2019-06-25
Copyright: 2019, Karr Lab
License: MIT

class bcforms.__main__.App(label=None, **kw)[source]¶

Bases: cement.core.foundation.App

Command line application

class Meta[source]¶

Bases: object

base_controller = 'base'[source]¶

handlers = [<class 'bcforms.__main__.BaseController'>, <class 'bcforms.__main__.ValidateController'>, <class 'bcforms.__main__.GetFormulaController'>, <class 'bcforms.__main__.GetMolWtController'>, <class 'bcforms.__main__.GetChargeController'>][source]¶

label = 'bcforms'[source]¶

class bcforms.__main__.BaseController(*args, **kw)[source]¶

Bases: cement.ext.ext_argparse.ArgparseController

Base controller for command line application

class Meta[source]¶

Bases: object

arguments = [(['-v', '--version'], {'action': 'version', 'version': '0.0.9'})][source]¶

description = 'bcforms'[source]¶

help = 'bcforms'[source]¶

label = 'base'[source]¶

class bcforms.__main__.GetChargeController(*args, **kw)[source]¶

Bases: cement.ext.ext_argparse.ArgparseController

Calculate the total charge of a BcForm

Example:

bcforms get-charge 'abc_a + abc_b' '{abc_a:+1, abc_b:-1}'

class Meta[source]¶

Bases: object

arguments = [(['form'], {'type': <class 'str'>, 'help': 'input BcForm'}), (['subunit_charges'], {'type': <class 'str'>, 'help': 'dictionary of subunit charge'})][source]¶

description = 'Calculate the total charge of a BcForm'[source]¶

help = 'Calculate the total charge of a BcForm'[source]¶

label = 'get-charge'[source]¶

stacked_on = 'base'[source]¶

stacked_type = 'nested'[source]¶

class bcforms.__main__.GetFormulaController(*args, **kw)[source]¶

Bases: cement.ext.ext_argparse.ArgparseController

Calculate the chemical formula of a BcForm

Example:

bcforms get-formula 'abc_a + abc_b' '{abc_a:C5H10O, abc_b:C3H5O}'

class Meta[source]¶

Bases: object

arguments = [(['form'], {'type': <class 'str'>, 'help': 'input BcForm'}), (['subunit_formulas'], {'type': <class 'str'>, 'help': 'dictionary of subunit formulas'})][source]¶

description = 'Calculate the chemical formula of a BcForm'[source]¶

help = 'Calculate the chemical formula of a BcForm'[source]¶

label = 'get-formula'[source]¶

stacked_on = 'base'[source]¶

stacked_type = 'nested'[source]¶

class bcforms.__main__.GetMolWtController(*args, **kw)[source]¶

Bases: cement.ext.ext_argparse.ArgparseController

Calculate the molecular weight of a BcForm

Example

bcforms get-molwt ‘abc_a + abc_b’ ‘{abc_a:86, abc_b:57}’

class Meta[source]¶

Bases: object

arguments = [(['form'], {'type': <class 'str'>, 'help': 'input BcForm'}), (['subunit_mol_wts'], {'type': <class 'str'>, 'help': 'dictionary of subunit molecular weights'})][source]¶

description = 'Calculate the molecular weight of a BcForm'[source]¶

help = 'Calculate the molecular weight of a BcForm'[source]¶

label = 'get-molwt'[source]¶

stacked_on = 'base'[source]¶

stacked_type = 'nested'[source]¶

class bcforms.__main__.ValidateController(*args, **kw)[source]¶

Bases: cement.ext.ext_argparse.ArgparseController

Validate a biopolymer form

Example:

bcforms validate 'abc_a + abc_b'

class Meta[source]¶

Bases: object

arguments = [(['form'], {'type': <class 'str'>, 'help': 'BcForm to validate'})][source]¶

description = 'Validate a biocomplex form'[source]¶

help = 'Validate a biocomplex form'[source]¶

label = 'validate'[source]¶

stacked_on = 'base'[source]¶

stacked_type = 'nested'[source]¶

bcforms.__main__.main()[source]¶

3.1.3. bcforms._version module¶

3.1.4. bcforms.core module¶

BcForms

Author: Mike Zheng <xzheng20@colby.edu>
Author: Jonathan Karr <karr@mssm.edu>
Date: 2019-06-25
Copyright: 2019, Karr Lab
License: MIT

class bcforms.core.Atom(subunit, element, position, monomer, charge=0, subunit_idx=None, component_type=None)[source]¶

Bases: object

Atom in a crosslink

subunit[source]¶

id of subunit

Type: str

subunit_idx[source]¶

index of the subunit for homomers

Type: int

element[source]¶

code of the element

Type: str

position[source]¶

SMILES position of the atom within the compound

Type: int

monomer[source]¶

index of parent monomer

Type: int

charge[source]¶

charge of the atom

Type: int

component_type[source]¶

type of component the atom belongs to: either ‘monomer’ or ‘backbone’

Type: str

__str__()[source]¶

Generate a string representation

Returns: string representation
Return type: str

property charge[source]

Get the charge of the atom

Returns: charge
Return type: int

property component_type[source]

Get the type of component the atom belongs to

Returns: component type
Return type: str

property element[source]

Get the element of the atom

Returns: element
Return type: str

is_equal(other)[source]¶

Check if two atoms are semantically equal (belong to the same subunit/monomer and have the same element, position, and charge)

Parameters: other (Atom) – another atom
Returns: True, if the atoms are semantically equal
Return type: bool

property monomer[source]

Get the position in the subunit of the monomer that the atom belongs to

Returns: monomer position
Return type: int

property position[source]

Get the position of the atom in the compound

Returns: position
Return type: int

property subunit[source]

Get the subunit that the atom belongs to

Returns: subunit
Return type: str

property subunit_idx[source]

Get the index of the homomer of the subunit that the atom belongs to

Returns: subunit_idx or None
Return type: int

class bcforms.core.BcForm(subunits=None, crosslinks=None)[source]¶

Bases: object

A form of a macromolecular complex

subunits[source]¶

subunit composition of the complex

Type: list of Subunit

crosslinks[source]¶

crosslinks in the complex

Type: list Crosslink

__str__()[source]¶

Generate a string representation

Returns: string representation of complex
Return type: str

clean()[source]¶

Clean up the subunits and the crosslinks

For example, convert 1 * a + 1 * a to 2 * a

property crosslinks[source]

Get the crosslinks

Returns: crosslinks
Return type: list of Crosslink

export(format='smiles', options=[])[source]¶

Export the structure to string

Parameters

format (str, optional) – export format
options (list, optional) – export options

Returns

exported string representation of the structure

Return type

str

file = <_io.TextIOWrapper name='/root/project/bcforms/grammar.lark' mode='r' encoding='UTF-8'>[source]¶

from_set(subunits)[source]¶

Set the subunits from a list of subunits

Note: this method does not support crosslinks

Parameters

subunits –

(list): list representation of a complex. For example:

[
    {'id': 'ABC_A', 'stoichiometry': 2},
    {'id': 'ABC_B', 'stoichiometry': 3},
]

Returns

this complex

Return type

BcForm

Raises

ValueError – subunit has no ‘id’ key
ValueError – subunit has no ‘stoichiometry’ key

from_str(string)[source]¶

Set a complex from a string representation

Parameters: string (str) – string representation of a complex
Returns: structured BcForm representation of the string
Return type: BcForm

get_charge(subunit_charges=None)[source]¶

Get the total charge

If user wants to calculate charge of nested BcForm, where some subunits are BcForm objects, then the subunit BcForms must be able to calculate its own charge through structure

Parameters

subunit_formulas (dict or None) – dictionary of subunit ids and charges

Returns

the total charge of the BcForm

Return type

int

Raises

ValueError – subunit_charges does not include all subunits
ValueError – Not all subunits have defined charge

get_formula(subunit_formulas=None)[source]¶

Get the empirical formula

If user wants to calculate formula of nested BcForm, where some subunits are BcForm objects, then the subunit BcForms must be able to calculate its own formula through structure

Parameters

subunit_formulas (dict or None) – dictionary of subunit ids and empirical formulas

Returns

the empirical formula of the BcForm

Return type

EmpiricalFormula

Raises

ValueError – subunit formulas does not include all subunits
ValueError – Not all subunits have defined formula

get_genomic_image(seq_features=None, width=1200, cols=2, nt_per_track=80, **kwargs)[source]¶

Get a genomic visualization of the BpForm

Parameters

seq_features (dict) –
list of features each represented by a dictionary with three keys
- label (str): description of the type of feature
- color (str): color
- positions (list of list of int): list of position ranges of the type of feature
width (int, optional) – width
cols (int, optional) – number of columns of polymers
nt_per_track (int, optional) – number of nucleotides per track

The method also accepts the same arguments as: bpforms.util.gen_genomic_viz.

Returns: SVG image
Return type: str

get_mol_wt(subunit_mol_wts=None)[source]¶

Get the molecular weight

If user wants to calculate molecular weight of nested BcForm, where some subunits are BcForm objects, then the subunit BcForms must be able to calculate its own molecular weight through structure

Parameters

subunit_formulas (dict or None) – dictionary of subunit ids and molecular weights

Returns

the molecular weight of the BcForm

Return type

float

Raises

ValueError – subunit_mol_wts does not include all subunits
ValueError – Not all subunits have defined molecular weight

get_structure()[source]¶

Get an Open Babel molecule of the structure

Returns: Open Babel molecule of the structure
Return type: openbabel.OBMol

get_subunit_attribute(subunit_id, attribute)[source]¶

Set attribute (stoichiometry, structure) of subunit by id

Parameters

subunit_id (str) – id of subunit
attribute (str) – attribute to set

Returns

int for stoichiometry, bpforms.BpForm, openbabel.OBMol, or None for structure

Raises

ValueError – No Subunit with subunit_id
ValueError – Invalid attribute

is_equal(other)[source]¶

Check if two complexes are semantically equal (same subunits and crosslinks)

Parameters: other (BcForm) – another complex
Returns: True, if the complexes are semantically equal
Return type: bool

set_subunit_attribute(subunit_id, attribute, value)[source]¶

Set attribute (stoichiometry, structure) of subunit by id

Parameters

subunit_id (str) – id of subunit
attribute (str) – attribute to set
value (int for stoichiometry, bpforms.BpForm, openbabel.OBMol, or None for structure) – value

Raises

ValueError – No Subunit with subunit_id
ValueError – Invalid attribute

property subunits[source]

Get the subunits

Returns: subunits
Return type: list of Subunit or BcForm

validate()[source]¶

Check if the BcForm is valid

Check if the crosslinking subunit is in the subunit list and if the subunit_idx is valid

Returns: list of errors, if any
Return type: list of str

class bcforms.core.Crosslink[source]¶

Bases: abc.ABC

Abstract class of a crosslink between subunits

abstract __str__()[source]¶

Generate a string representation

Returns: string representation
Return type: str

abstract get_l_bond_atoms()[source]¶

Get the left bond atoms

Returns: left bond atoms
Return type: list of Atom

abstract get_l_displaced_atoms()[source]¶

Get the left displaced atoms

Returns: left displaced atoms
Return type: list of Atom

abstract get_order()[source]¶

Get the order

Returns: order
Return type: BondOrder

abstract get_r_bond_atoms()[source]¶

Get the right bond atoms

Returns: right bond atoms
Return type: list of Atom

abstract get_r_displaced_atoms()[source]¶

Get the right displaced atoms

Returns: right displaced atoms
Return type: list of Atom

abstract get_stereo()[source]¶

Get the stereochemistry

Returns: stereochemistry
Return type: BondStereo

is_equal(other)[source]¶

Check if two crosslinks are semantically equal (have the same bond atoms)

Parameters: other (Crosslink) – another crosslink
Returns: True, if the crosslinks are semantically equal
Return type: bool

class bcforms.core.InlineCrosslink(l_bond_atoms=None, r_bond_atoms=None, l_displaced_atoms=None, r_displaced_atoms=None, order=<BondOrder.single: 1>, stereo=None, comments=None)[source]¶

Bases: bcforms.core.Crosslink

A crosslink between subunits defined inline

l_bond_atoms[source]¶

atoms from the left subunit that bond with the right subunit

Type: list of Atom

r_bond_atoms[source]¶

atoms from the right subunit that bond with the left subunit

Type: list of Atom

l_displaced_atoms[source]¶

atoms from the left subunit displaced by the crosslink

Type: list of Atom

r_displaced_atoms[source]¶

atoms from the right subunit displaced by the crosslink

Type: list of Atom

order[source]¶

order

Type: BondOrder

stereo[source]¶

stereochemistry

Type: BondStereo

comments[source]¶

comments

Type: str

__str__()[source]¶

Generate a string representation

Returns: string representation
Return type: str

property comments[source]

Get comments

Returns: comments
Return type: str

get_l_bond_atoms()[source]¶

Get the left bond atoms

Returns: left bond atoms
Return type: list of Atom

get_l_displaced_atoms()[source]¶

Get the left displaced atoms

Returns: left displaced atoms
Return type: list of Atom

get_order()[source]¶

Get the order

Returns: order
Return type: BondOrder

get_r_bond_atoms()[source]¶

Get the right bond atoms

Returns: right bond atoms
Return type: list of Atom

get_r_displaced_atoms()[source]¶

Get the right displaced atoms

Returns: right displaced atoms
Return type: list of Atom

get_stereo()[source]¶

Get the stereochemistry

Returns: stereochemistry
Return type: BondStereo

property l_bond_atoms[source]

Get the left bond atoms

Returns: left bond atoms
Return type: list of Atom

property l_displaced_atoms[source]

Get the left displaced atoms

Returns: left displaced atoms
Return type: list of Atom

property order[source]

Get the order

Returns: order
Return type: BondOrder

property r_bond_atoms[source]

Get the right bond atoms

Returns: right bond atoms
Return type: list of Atom

property r_displaced_atoms[source]

Get the right displaced atoms

Returns: right displaced atoms
Return type: list of Atom

property stereo[source]

Get the stereochemistry

Returns: stereochemistry
Return type: BondStereo

class bcforms.core.OntologyCrosslink(type, l_subunit, l_monomer, r_subunit, r_monomer, l_subunit_idx=None, r_subunit_idx=None)[source]¶

Bases: bcforms.core.Crosslink

A pre-defined crosslink between subunits

type[source]¶

type of the pre-defined crosslink

Type: str

l_subunit[source]¶

name of the left subunit

Type: str

l_subunit_idx[source]¶

index of the left subunit, optional if only one copy of the subunit

Type: int, optional

l_monomer[source]¶

index of the monomer from the left subunit

Type: int

r_subunit[source]¶

name of the left subunit

Type: str

r_subunit_idx[source]¶

index of the left subunit, optional if only one copy of the subunit

Type: int, optional

r_monomer[source]¶

index of the monomer from the right subunit

Type: int

xlink_details[source]¶

detailed information about the abstracted crosslink

Type: tuple

_xlink_atom_parser[source]¶

lark grammar parser used to parse atom strings

Type: lark.Lark

class ParseTreeTransformer(visit_tokens=False)[source]¶

Bases: lark.visitors.Transformer

atom_charge(*args)[source]¶

atom_element(*args)[source]¶

atom_position(*args)[source]¶

start(*args)[source]¶

__str__()[source]¶

Generate a string representation

Returns: string representation
Return type: str

get_details()[source]¶

Get the full details of the crosslink in a dictionary

Returns: detailed information of the crosslink
Return type: dict
Raises: KeyError – Unknown abstracted crosslink type

get_l_bond_atoms()[source]¶

Get the left bond atoms

Returns: left bond atoms
Return type: list of Atom

get_l_displaced_atoms()[source]¶

Get the left displaced atoms

Returns: left displaced atoms
Return type: list of Atom

get_order()[source]¶

Get the order

Returns: order
Return type: BondOrder

get_r_bond_atoms()[source]¶

Get the right bond atoms

Returns: right bond atoms
Return type: list of Atom

get_r_displaced_atoms()[source]¶

Get the right displaced atoms

Returns: right displaced atoms
Return type: list of Atom

get_stereo()[source]¶

Get the stereochemistry

Returns: stereochemistry
Return type: BondStereo

property l_monomer[source]

Get the index of the left monomer in the crosslink

Returns: index of the left monomer
Return type: int

property l_subunit[source]

Get the name of the left subunit in the crosslink

Returns: name of the left subunit
Return type: str

property l_subunit_idx[source]

Get the index of the left subunit in the crosslink

Returns: index of the left subunit
Return type: int

property r_monomer[source]

Get the index of the right monomer in the crosslink

Returns: index of the right monomer
Return type: int

property r_subunit[source]

Get the name of the right subunit in the crosslink

Returns: name of the right subunit
Return type: str

property r_subunit_idx[source]

Get the index of the right subunit in the crosslink

Returns: index of the right subunit
Return type: int

property type[source]

Get the type of the abstracted crosslink

Returns: type of the crosslink
Return type: str

class bcforms.core.Subunit(id, stoichiometry, structure=None, formula=None, mol_wt=None, charge=None)[source]¶

Bases: object

Subunit in a BcForm macromolecular complex

id[source]¶

id of the subunit

Type: str

stoichiometry[source]¶

stoichiometry of the subunit

Type: int

structure[source]¶

structure of the subunit

Type: bpforms.BpForm or openbabel.OBMol, optional

formula[source]¶

formula of the subunit

Type: EmpiricalFormula, optional

mol_wt[source]¶

molecular weight of the subunit

Type: float, optional

charge[source]¶

charge of the subunit

Type: int, optional

property charge[source]

Get the charge of the subunit

Returns: charge of the subunit
Return type: int or None

export(format='smiles', options=[])[source]¶

Export the structure to string

Parameters

format (str, optional) – export format
options (list, optional) – export options

Returns

exported string representation of the structure

Return type

str

property formula[source]

Get the empirical formula of the subunit

Returns: formula of the subunit
Return type: EmpiricalFormula or None

get_charge(charge=None)[source]¶

Get the total charge

Parameters: charge (int or None) – Subunit charge per copy
Returns: the total charge of the Subunit
Return type: int or None

get_formula(formula=None)[source]¶

Get the empirical formula

Parameters: formula (EmpiricalFormula or None) – Subunit empirical formula per copy
Returns: the empirical formula of the Subunit
Return type: EmpiricalFormula or None

get_mol_wt(mol_wt=None)[source]¶

Get the molecular weight

Parameters: mol_wt (float or None) – Subunit molecular weight per copy
Returns: the molecular weight of the Subunit
Return type: float or None

get_structure()[source]¶

Get an Open Babel molecule of the structure

Returns

openbabel.OBMol: Open Babel molecule of the structure
dict of obj:dict: dictionary which maps subunit_idx to
atom_maps

Return type

tuple

Raises

ValueError – Subunit structure is None

property id[source]

Get the id of the subunit

Returns: id of the subunit
Return type: str

is_equal(other)[source]¶

Check if two Subunits are semantically equal

Check id and stoichiometry; do not check structure yet

Parameters: other (Subunit) – another Subunit
Returns: True, if the Subunits are semantically equal
Return type: bool

property mol_wt[source]

Get the molecular weight of the subunit

Returns: molecular weight of the subunit
Return type: float or None

property stoichiometry[source]

Get the stoichiometry of the subunit

Returns: stoichiometry of the subunit
Return type: int

property structure[source]

Get the structure of the subunit

Returns: structure of the subunit
Return type: bpforms.BpForm or openbabel.OBMol or None

bcforms.core.draw_xlink(xlink_name, include_all_hydrogens=False, remove_hydrogens=True, show_atom_nums=False, l_color=59982, r_color=44527, bond_color=15352320, width=300, height=200, atom_label_font_size=0.6, image_format='png', include_xml_header=False)[source]¶

Generate an image of a crosslink

Parameters

xlink_name (str) – name of xlink
include_all_hydrogens (bool, optional) – if True, show all hydrogens
remove_hydrogens (bool, optional) – if True, remove all hydrogens
show_atom_nums (bool, optional) – if True, show atom numbers
l_color (int, optional) – color of left monomer
r_color (int, optional) – color of right monomer
bond_color (int, optional) – color of crosslinking bond
width (int, optional) – width
height (int, optional) – height
atom_label_font_size (float, optional) – relative font size of atom labels
image_format (str, optional) – format of image
include_xml_header (bool, optional) – if True, include XML header for SVG image

Returns

image

Return type

object

Raises

KeyError – Unknown crosslink id
ValueError – Unknown monomer alphabet

bcforms.core.get_hydrogen_atom(parent_atom, bonding_hydrogens, i_monomer)[source]¶

Get a hydrogen atom attached to a parent atom :param parent_atom: parent atom :type parent_atom: openbabel.OBAtom :param bonding_hydrogens: hydrogens that have already been gotten :type bonding_hydrogens: list :param i_monomer: index of parent monomer in sequence :type i_monomer: int

Returns: hydrogen atom
Return type: openbabel.OBAtom

bcforms.core.parse_yaml(path)[source]¶

Read a YAML file

Parameters: path (str) – path to YAML file which defines alphabet
Returns: content of file
Return type: object

3.1.5. bcforms.rest module¶

REST JSON API

Author: Mike Zheng <xzheng20@colby.edu>
Author: Jonathan Karr <karr@mssm.edu>
Date: 2019-07-03
License: MIT

class bcforms.rest.Bcform(api=None, *args, **kwargs)[source]¶

Bases: flask_restplus.resource.Resource

endpoint = 'bcform_bcform'[source]¶

mediatypes()[source]¶

methods = {'POST'}[source]¶

post()[source]¶

class bcforms.rest.CrosslinkResource(api=None, *args, **kwargs)[source]¶

Bases: flask_restplus.resource.Resource

Get crosslinks

endpoint = 'crosslink_crosslink_resource'[source]¶

get()[source]¶

Get crosslinks

Returns: dictionary representation of all crosslinks
Return type: dict

mediatypes()[source]¶

methods = {'GET'}[source]¶

class bcforms.rest.PrefixMiddleware(app, prefix='')[source]¶: Bases: object

bcforms.rest.get_crosslinks()[source]¶

Get an alphabet

Returns: dictionary representation of crosslinks
Return type: dict

3.1. bcforms package¶

3.1.1. Submodules¶

3.1.2. bcforms.__main__ module¶

3.1.3. bcforms._version module¶

3.1.4. bcforms.core module¶

3.1.5. bcforms.rest module¶

3.1.6. Module contents¶

3.1.2. bcforms.main module¶