Metadata-Version: 2.1
Name: bpforms
Version: 0.0.4
Summary: Unambiguous representation of modified DNA, RNA, and proteins
Home-page: https://www.bpforms.org
Author: Karr Lab
Author-email: karr@mssm.com
License: MIT
Download-URL: https://github.com/KarrLab/bpforms
Description: |PyPI package| |Documentation| |Test results| |Test coverage| |Code
        analysis| |License| |Analytics|
        
        BpForms: unambiguous representation of modified DNA, RNA, and proteins
        ======================================================================
        
        BpForms is a set of tools for unambiguously representing the structures
        of modified forms of biopolymers such as DNA, RNA, and protein.
        
        -  The BpForms notation can unambiguously represent the structure of
           modified forms of biopolymers. For example, the following represents
           a modified DNA molecule that contains a deoxyinosine monomer at the
           fourth position.
           ``ACG[id: "dI"    | structure: InChI=1S       /C10H12N4O4       /c15-2-6-5(16)1-7(18-6)14-4-13-8-9(14)11-3-12-10(8)17       /h3-7,15-16H,1-2H2,(H,11,12,17)       /t5-,6+,7+       /m0       /s1       ]T``
        -  This concrete representation of modified biopolymers enables the
           BpForms software tools to calculate the chemical formulae, molecular
           weights, and charges of biopolymers, as well as to automatically
           calculate the major protonation and tautomerization state of
           biopolymers at specific pHs.
        
        BpForms encompasses five tools:
        
        -  `Notation for describing
           biopolymers <https://docs.karrlab.org/bpforms/>`__
        -  Web-based graphical interface: https://bpforms.org
        -  `REST JSON
           API <https://docs.karrlab.org/bpforms/master/0.0.1/rest_api.html#rest-api>`__
        -  `Command line
           interface <https://docs.karrlab.org/bpforms/master/0.0.1/cli.html>`__
        -  `Python
           API <https://docs.karrlab.org/bpforms/master/0.0.1/python_api.html>`__
        
        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 <https://www.wholecell.org>`__. In addition,
        BpForms are a valuable tool for experimental proteomics. In particular,
        we developed BpForms because there were no notations, schemas, data
        models, or file formats for concretely representing modified forms of
        biopolymers, despite the existence of several databases and ontologies
        of DNA, RNA, and protein modifications and the `ProForma Proteoform
        Notation <https://www.topdownproteomics.org/resources/proforma/>`__.
        
        The BpForms syntax was inspired by the ProForma Proteoform Notation.
        BpForms improves upon this syntax in several ways:
        
        -  BpForms separates the representation of modified biopolymers from the
           chemical processes which generate them.
        -  BpForms clarifies the representation of multiply modified monomers.
           This is necessary to represent the combinatorial complexity of
           modified DNA, RNA, and proteins.
        -  BpForms can be customized to represent any modification and,
           therefore, is not limited to previously enumerated modifications.
           This is also necessary to represent the combinatorial complexity of
           modified DNA, RNA, and proteins.
        -  BpForms supports two additional types of uncertainty in the
           structures of biopolymers: uncertainty in the position of a modified
           nucleotide/amino acid within the polymer sequence, and uncertainty in
           the chemical identity of modified nucleotide/amino acid as deviation
           from its expected mass or charge.
        -  BpForms has a concrete grammar. This enables error checking, as well
           the calculation of chemical formulae, masses, and charges, which is
           essential for modeling.
        
        Installation
        ------------
        
        1. Install the third-party dependencies listed below. Detailed
           installation instructions are available in `An Introduction to
           Whole-Cell
           Modeling <http://docs.karrlab.org/intro_to_wc_modeling/master/0.0.1/installation.html>`__.
        
           -  `ChemAxon Marvin <https://chemaxon.com/products/marvin>`__:
              optional to calculate major protonation and tautomerization states
           -  `Java <https://www.java.com>`__ >= 1.8
           -  `Open Babel <http://openbabel.org>`__
           -  `Pip <https://pip.pypa.io>`__ >= 18.0
           -  `Python <https://www.python.org>`__ >= 3.6
        
        2. 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``
        
        3. 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``
        
        4. Install this package
        
           -  Install the latest release from PyPI. ``pip install bpforms[all]``
        
           -  Install the latest revision from GitHub.
              ``pip install git+https://github.com/KarrLab/log.git#egg=log   pip install git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils[all]   pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms[all]``
        
        Examples, tutorial, and documentation
        -------------------------------------
        
        Please see the `documentation <https://docs.karrlab.org/bpforms>`__. An
        `interactive
        tutorial <https://sandbox.karrlab.org/notebooks/bpforms/Tutorial.ipynb>`__
        is also available in the whole-cell modeling sandbox.
        
        License
        -------
        
        The package is released under the `MIT license <LICENSE>`__.
        
        Development team
        ----------------
        
        This package was developed by the `Karr Lab <https://www.karrlab.org>`__
        at the Icahn School of Medicine at Mount Sinai in New York, USA.
        
        -  `Jonathan Karr <https://www.karrlab.org>`__
        -  `Yassmine
           Chebaro <https://www.linkedin.com/in/yassmine-chebaro-6bb8a05/>`__
        -  `Paul Lang <http://www.dtc.ox.ac.uk/people/17/langp/>`__
        
        Questions and comments
        ----------------------
        
        Please contact the `Karr Lab <https://www.karrlab.org>`__ with any
        questions or comments.
        
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Keywords: DNA,RNA,protein,post-transcriptional modification,post-translational modification,proteoform,phosphorylation,methylation
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Provides-Extra: docs
Provides-Extra: all
Provides-Extra: rest_api
Provides-Extra: tests
