bpforms 0.0.16

Description:

bpforms 0.0.16

BpForms: toolkit for concretely describing non-canonical DNA, RNA, and proteins
BpForms is a set of tools for concretely representing the primary
structures of non-canonical forms of biopolymers, such as oxidized DNA,
methylated RNA, and acetylated proteins, and calculating properties of
non-canonical biopolymers.
BpForms encompasses five tools:

A grammar for concretely describing the primary structures of
non-canonical biopolymers. See the
documentation for more
information. For example, the following text represents a modified
DNA molecule that contains a deoxyinosine monomeric form at the
fourth position.
ACG[id: "dI" | structure: "[H][C@]1(O)C[C@@]([H])(O[C@]1([H])CO)N1C=NC2=C1N=CN=C2O"]T

This concrete representation enables the BpForms software tools to
calculate properties of non-canonical biopolymers.

Tools for calculating properties of non-canonical biopolymers
including their chemical formulae, molecular weights, charges, and
major protonation and tautomerization states.
A web app: https://bpforms.org
A JSON REST API: https://bpforms.org/api
A command line interface. See the
documentation
for more information.
A Python API. See the
documentation
for more information.

BpForms was motivated by the need to concretely represent the
biochemistry of DNA modification, DNA repair, post-transcriptional
processing, and post-translational processing in whole-cell
computational models. BpForms is also
a valuable tool for experimental proteomics and synthetic biology. In
particular, we developed BpForms because there were no notations,
schemas, data models, or file formats for concretely representing
non-canonical forms of biopolymers, despite the existence of several
databases and ontologies of DNA, RNA, and protein modifications, the
ProForma Proteoform
Notation, and
the MOMODICS codes for modified RNA
bases.
BpForms can be combined with *BcForms*
to concretely describe the primary structure of complexes.

Installation
The following is a brief guide to installing BpForms. The
Dockerfile in the repository contains detailed
instructions for how to install BpForms in Ubuntu Linux.

Install the third-party dependencies listed below.

ChemAxon Marvin:
optional to calculate major protonation and tautomerization states
and draw molecules
Java >= 1.8
Open Babel
Pip >= 19.0
Python >= 3.6


To use Marvin to calculate major protonation and tautomerization
states, set JAVA_HOME to the path to your Java virtual machine
(JVM) export JAVA_HOME=/usr/lib/jvm/default-java
To use Marvin to calculate major protonation and tautomerization
states, add Marvin to the Java class path
export CLASSPATH=$CLASSPATH:/opt/chemaxon/marvinsuite/lib/MarvinBeans.jar
Install this package

Install the latest release from PyPI: pip install bpforms
Install the latest revision from GitHub:
pip install git+https://github.com/KarrLab/pkg_utils.git#egg=pkg_utils pip install git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils[chem] pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms
To calculate major protonation and tautomerization states,
BpForms must be installed with the [protontation] option:
pip install bpforms[protontation] pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms[protontation]
To draw molecules, BpForms must be installed with the
[draw] option:
pip install bpforms[draw] pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms[draw]
To export the alphabets in OBO format, BpForms must be
installed with the [onto_export] option:
pip install bpforms[onto_export] pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms[onto_export]
To install the rest API, BpForms must be installed with the
[rest_api] option:
pip install bpforms[rest_api] pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms[rest_api]





Examples, tutorial, and documentation
Please see the documentation. An
interactive
tutorial
is also available in the whole-cell modeling sandbox.


License
The package is released under the MIT license.


Citing BpForms
Lang PF, Chebaro Y & Jonathan R. Karr. BpForms: a toolkit for concretely
describing modified DNA, RNA and proteins. arXiv:1903.10042.
:link:


Development team
This package was developed by the Karr Lab
at the Icahn School of Medicine at Mount Sinai in New York, USA.

Jonathan Karr
Yassmine
Chebaro
Paul Lang



Questions and comments
Please contact the Karr Lab with any
questions or comments.