RInChI Master Script¶

Contains all of the action of the RInChI module! Uses a system of subparsers which can be called independently.

Modifications:

D.F. Hampshire 2017

Usage: rinchi.py [-h] {search,convert,db,changes,addition,stats} ...

RInChI Module Command Line Tools. Can execute each of the other functions, allowing
for a complete command line program navigation.

positional arguments:
  {search,convert,db,changes,addition,stats}
                        Main Function
    search              Search for RInChIs, InChIs & their components or
                        RInChI Keys in a RInChI SQL Database / Flat File
    convert             RInChI Conversion to/from other formats
    db                  RInChI SQL Database Manipulation Tools
    changes             RInChI Changes Analysis
    addition            RInChI Addition
    stats               RInChI Statistical analysis

optional arguments:
  -h, --help            show this help message and exit

RInChI Addition Script¶

This script adds together flat files of RInChIs separated by newlines.

Modifications:

C.H.G. Allen 2012

D.F. Hampshire 2016

Rewritten to use argparse module and Python3

rinchi_add.add_addition(subparser)¶

Adds the arguments for the addition operation to the ArgumentParser object.

Parameters:	subparser – An `ArgumentParser` object

rinchi_add.addition_ops(args, parser)¶

Executes the addition operations.

Parameters:	args – The output of the `parser.parse_args()`. The command line arguments. parser – An `ArgumentParser` object

usage: rinchi_add.py [-h] [-o [OUTPUT]] input_path

This script combines seperate RInChIs representing the steps of a multi-step
reaction into a total RInChI representing the overall reaction.

The input RInChI file should contain the RInChIs representing the steps of the
reaction IN ORDER and seperated by line breaks.

positional arguments:
  input_path            Path of file to input

optional arguments:
  -h, --help            show this help message and exit
  -o [OUTPUT], --output [OUTPUT]
                        Output the result to a file. Optionally specify the
                        file output name

RInChI Changes Analysis Script¶

This script analyses RInChI(s) for changes in properties.

Modifications:

Allen

Hammond 2014

D.F. Hampshire 2017

Interface completely rewritten. New features added. Based on prior work.

rinchi_changes.add_changes(subparser)¶

Adds the arguments for the changes operation to the ArgumentParser object.

Parameters:	subparser – An `ArgumentParser` object

rinchi_changes.changes_ops(args, parser)¶

Executes the changes operations.

Parameters:	args – The output of the `parser.parse_args()`. The command line arguments. parser – An `ArgumentParser` object

usage: rinchi_changes.py [-h] (-b | -r | -k) [--list] [--filein] [--ringcount]
                         [--formula] [--valence] [--hybrid]
                         [--ringcountelements] [--ringcountold]
                         [--stereoold [STEREOOLD]]
                         input

RInChI Analysis and Manipulation

positional arguments:
  input                 The file or string containing RInChI(s) or Long Key to
                        be processed

optional arguments:
  -h, --help            show this help message and exit
  -b, --batch           Process multiple RInChIs
  -r, --rinchi          Process a single RInChI
  -k, --key             Process a RInChI key

File options:
  --list                List RInChIs along with results. Otherwise returns
                        count populations
  --filein              Assert that the input is a file

Operation:
  --ringcount           Change in ring populations by size
  --formula             Change in formula across a reaction
  --valence             Change in valence across reaction
  --hybrid              Change in hybridisation of C atoms across reaction
  --ringcountelements   Change in ring populations by ring elements
  --ringcountold        Change in ring populations. Old method
  --stereoold [STEREOOLD]
                        Change stereocentres. Old method. Takes an argument as
                        a dictionary such as
                        {'sp2':True,'sp3':False,'wd':True} for options to 1.
                        Count sp2 centres 2. Count sp3 centre 3. Well defined
                        stereocentres only

RInChI Conversion Script¶

Converts RInChIs to and from various chemical reaction file formats.

Modifications:

Allen 2012

D.F. Hampshire 2016

Code rewritten for Python 3 using the argparse module, and major structural and procedural changes.

rinchi_convert.add_convert(subparser)¶

Adds the arguments for the conversion operation to the ArgumentParser object.

Parameters:	subparser – An `ArgumentParser` object

rinchi_convert.convert_ops(args, parser)¶

Executes the conversion operations.

Parameters:	args – The output of the `parser.parse_args()`. The command line arguments. parser – An `ArgumentParser` object

usage: rinchi_convert.py [-h]
                         (--rxn2rinchi | --rdf2rinchi | --rinchi2file | --rinchi2key | --rdf2csv | --dir2csv | --svg)
                         [-o [FILEOUT]] [-i] [-e] [-ra] [-l] [-s] [-w] [-r]
                         [-ordf] [-orxn]
                         input

RInChI Conversion tools

positional arguments:
  input                 The path of the file or folder to be converted, or the
                        input string

optional arguments:
  -h, --help            show this help message and exit

Conversion Type:
  --rxn2rinchi          RXN to RInChI conversion
  --rdf2rinchi          RDF to RInChI conversion
  --rinchi2file         RInChI-to-File conversion. Accepts any file containing
                        a rinchi and optionally rauxinfo. The RAuxInfo must
                        immediately follow the RInChI
  --rinchi2key          RInChi to RInChI-Key conversion
  --rdf2csv             Create or append a .csv with an rdfile
  --dir2csv             Convert a directory of rdfiles to a single csv file
  --svg                 Convert a RInChI to a collection of .svg files

All operations:
  -o [FILEOUT], --fileout [FILEOUT]
                        Save the output to disk.
  -i, --filein          Assert that the input is a file

Conversion to RInChI file:
  -e, --equilibrium     Force output to be an equilibrium reaction
  -ra, --rauxinfo       Generate and return RAuxInfo
  -l, --longkey         Generate and return the Long-RInChIKey
  -s, --shortkey        Generate and return the Short-RInChIKey
  -w, --webkey          Generate and return the Web-RInChIKey

Converting RInChIs to Keys:
  -r, --include_rinchi  Include original RInChI in the output

Converting to a RXN/RDF:
  -ordf, --rdfileoutput
                        Output as RDFile. Otherwise RXN file(s) are produced
  -orxn, --rxnfileoutput
                        Output as RXNFile

RInChI Databasing Tools Script¶

Converts, creates, and removes from SQL databases

Modifications:

Hammond 2014

D.F. Hampshire 2016

Major features added

rinchi_database.add_db(subparser)¶

Parameters:	subparser –

rinchi_database.db_ops(args)¶

Executes the database operations.

Parameters:	args – The output of the `parser.parse_args()`. The command line arguments.

usage: rinchi_database.py [-h] [-o [OUTPUT]] [--rdf2db] [--csv2db]
                          [--ufingerprints] [--rfingerprints]
                          [--cfingerprints] [--convert2_to_3]
                          [--generate_rauxinfo] [-k [{L,S,W}]]
                          [database] [input]

Database Tools Module

positional arguments:
  database              The existing database to manipulate, or the name of
                        database to be created
  input                 The name of the input data file or table

optional arguments:
  -h, --help            show this help message and exit
  -o [OUTPUT], --output [OUTPUT]
                        The output table name or something else to output

Adding Data to a database:
  --rdf2db              Convert and add an rdfile to an SQL database
  --csv2db              Add the contents of a rinchi .csv file to an SQL
                        database

Fingerprints:
  --ufingerprints       Adds new entries to the fpts table containing
                        fingerprint data
  --rfingerprints       Returns the fingerprint of a given key
  --cfingerprints       Returns all RInChIs containing the given InChI to
                        STDOUT

Converting operations:
  --convert2_to_3       Creates a new table of v.03 rinchis from a table of
                        v.02 rinchis
  --generate_rauxinfo   Generate RAuxInfos from rinchis within a SQL database
  -k [{L,S,W}], --key [{L,S,W}]
                        Returns the RInChI corresponding to a given key.
                        Optionally accepts an argument denoting the type of
                        key to lookup

RInChI Searching Script¶

Searches an SQL database for InChIs.

Modifications:

Hammond 2014

D.F. Hampshire 2017

Rewrote search function completely

rinchi_search.add_search(subparser)¶

Adds the arguments for the search operation to the ArgumentParser object.

Parameters:	subparser – An `ArgumentParser` object

rinchi_search.search_ops(args)¶

Executes the search operations.

Parameters:	args – The output of the `parser.parse_args()`

usage: rinchi_search.py [-h] (-k [{L,S,W,N}] | -i | -l) [-db]
                        [-o {list,file,stats}] [-hb HYBRIDISATION]
                        [-v VALENCE] [-r RINGS] [-f FORMULA] [-re RINGELEMENT]
                        [-iso] [-rct] [-pdt] [-agt] [-n NUMBER]
                        search_term file [table_name]

Search for RInChIs, InChIs & their components or RInChI Keys in a RInChI SQL
Database / Flat File

positional arguments:
  search_term           The search_term to find
  file                  The database or flat file to search
  table_name            The table name for the search to be performed on.
                        Providing this argument asserts that the input file is
                        an SQL database

optional arguments:
  -h, --help            show this help message and exit

Action:
  -k [{L,S,W,N}], --key [{L,S,W,N}]
                        Returns the RInChI corresponding to a given key.
                        Optionally accepts an argument denoting the type of
                        key to lookup
  -i, --inchi           Returns all RInChIs containing the given InChI with
                        filters
  -l, --layer           Search for a component of an InChI in a database

Input / Output Options:
  -db, --is_database    Assert that the input is a database. If the table_name
                        argument is not provided then the default value of
                        'rinchis03' is used
  -o {list,file,stats}, --output_format {list,file,stats}
                        The format of the output - must be one of 'list',
                        'file', 'stats'

Filters - the changes should be of the form 'sp2=1,sp3=-1,...':
  -hb HYBRIDISATION, --hybridisation HYBRIDISATION
                        The changes in hybridisation sought
  -v VALENCE, --valence VALENCE
                        The changes in valence sought
  -r RINGS, --rings RINGS
                        The changes in ring numbers sought by size
  -f FORMULA, --formula FORMULA
                        The changes in the formula sought by element
  -re RINGELEMENT, --ringelement RINGELEMENT
                        Search for reactions containing a certain ring type
  -iso, --isotopic      Search for reactions containing defined isotopic
                        layers
  -rct, --reactant      Search for the InChI in the reactants
  -pdt, --product       Search for the InChI in the products
  -agt, --agent         Search for the InChI in the agents
  -n NUMBER, --number NUMBER
                        Limit the number of initial search results. A value of
                        0 means no limit

RInChI Statictics Script¶

Calculates summary statistics for a flat file of RInChIs.

Modifications:

D.F. Hampshire 2017

rinchi_stats.add_stats(subparser)¶

Adds the arguments for the stats operation to the ArgumentParser object.

Parameters:	subparser – An `ArgumentParser` object

rinchi_stats.stats_ops(args)¶

Executes the statitics operations.

Parameters:	args – The output of the `parser.parse_args()`. The command line arguments.

usage: rinchi_stats.py [-h] [-all] [-r] [-p] [-a] [-d] [-u] [-m [MOSTCOMMON]]
                       input

RInChI Statistical analysis

positional arguments:
  input                 The flat file of rinchis to generate statistics from

optional arguments:
  -h, --help            show this help message and exit
  -all                  return all information
  -r, --reactants       Include information about the reactants
  -p, --products        Include Information about the products
  -a, --agents          Include information about the agents
  -d, --directions      Include information about the directions
  -u, --unknownstructs  Include information about unknown structures
  -m [MOSTCOMMON], --mostcommon [MOSTCOMMON]
                        Only include information about the most commonly
                        occuring items

RInChI Extended Toolkit command line scripts documentation

RInChI Master Script¶

RInChI Addition Script¶

RInChI Changes Analysis Script¶

RInChI Conversion Script¶

RInChI Databasing Tools Script¶

RInChI Searching Script¶

RInChI Statictics Script¶

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