UManSysProp

UManSysProp is an online facility for calculating the properties of individual organic molecules and ensemble mixtures. Built using open source chemical informatics, the facilities provided are divided according to broad applications.

The code is licensed under the GPL v2 or above. Packages can be downloaded from PyPI. The source code can be obtained from GitHub, which also hosts the bug tracker. The documentation (which includes installation and quick start examples) can be read on ReadTheDocs.

Table of Contents

Client Installation

The client component of UManSysProp can be installed on any machine with Python available. On Ubuntu, the waveform PPA can be used for simple installation:

$ sudo add-apt-repository ppa:waveform/ppa
$ sudo apt-get update
$ sudo apt-get install python-umansysprop

On other platforms, the package can be installed from PyPI. Specify the client option to pull in all dependencies required by the client component:

$ sudo pip install "umansysprop[client]"

Server Installation

The server component of UManSysProp is only tested on Linux platforms, although it should theoretically work on others. The application uses the WSGI architecture for communication with web-servers; integration with your web-server depends on understanding WSGI applications. The Flask deployment guide may be helpful in this case.

The server component can be installed from PyPI. Specify the server option to pull in all dependencies required by the server component:

$ sudo pip install "umansysprop[server]"

Please be aware that OpenBabel is a requirement of the server component. As this is SWIG based you will need a C/C++ build environment installed, along with the necessary Python and OpenBabel headers. The following command should suffice for this on Ubuntu:

$ sudo apt-get install build-essential python-dev libopenbabel-dev

Quick Start

It is strongly recommended that you use UManSysProp from within the IPython shell. The API is designed with documentation built-in which can be queried “live” from within the environment, and this is considerably easier from within the IPython shell. The rest of this guide will include tips for usage within IPython, but examples will be given in the syntax of the regular Python shell.

The first step in using the UManSysProp system is creating a UManSysProp instance. This requires the URL of the UManSysProp server which defaults to http://umansysprop.seaes.manchester.ac.uk/:

>>> import umansysprop.client
>>> client = umansysprop.client.UManSysProp()

Once you have a client instance, you can query it to find out what methods are available from the web API. Within the IPython shell this can be done simply by entering client. and pressing the Tab key twice. Alternatively, the following one-liner in the regular Python shell can be used to query non-private methods:

>>> [m for m in dir(client) if not m.startswith('_')]
['CCN_potential_inorg',
 'CCN_potential_inorg_org',
 'CCN_potential_org',
 'absorptive_partitioning',
 'absorptive_partitioning_no_ions',
 'activity_coefficient_inorg_org',
 'activity_coefficient_org',
 'critical_property',
 'hygroscopic_growth_factor_inorg',
 'hygroscopic_growth_factor_inorg_org',
 'hygroscopic_growth_factor_org',
 'sub_cooled_density',
 'vapour_pressure']

Once you’ve selected a method to call you can discover what parameters it takes and what it expects in those parameters by querying the method’s documentation. Within the IPython shell this can be viewed simply by appending ? to the method name. Alternatively, the help() function can be used in a regular Python shell:

>>> help(client.vapour_pressure)
Help on method vapour_pressure in module umansysprop.client:

vapour_pressure(self, compounds, temperatures, vp_method, bp_method)...
    Calculates vapour pressures for all specified *compounds* (given as a
    sequence of SMILES strings) at all given *temperatures* (a sequence of
    floating point values giving temperatures in degrees Kelvin). The
    *vp_method* parameter is one of the strings:

    * 'nannoolal'
    * 'myrdal_and_yalkowsky'
    * 'evaporation'
    ...

The various methods are not included within this documentation (which only covers the framework) simply because they are defined by the server API (not by this package). The documentation for each tool can viewed on the UManSysProp API documentation page.

Calling any of the methods will (in the event of success) return a Result instance. This is simply a list() which contains a sequence of Table instances. Each table has a name and this can be used to access the table in the owning Result list. For example:

>>> result = client.vapour_pressure(
... ['CCCC', 'C(CC(=O)O)C(=O)O', 'C(=O)(C(=O)O)O',
... 'CCCCC/C=C/C/C=C/CC/C=C/CCCC(=O)O'],
... [298.15, 299.15, 300.15, 310.15],
... vp_method='nannoolal', bp_method='nannoolal')
>>> result
[<Table name="pressures">]
>>> result.pressures
<Table name="pressures">

Table instances have a friendly string representation which can be used at the command line for quick evaluation of the contents:

>>> print(result.pressures)
       |           CCCC | C(CC(=O)O)C(=O)O | C(=O)(C(=O)O)O | CCCCC/C=C/C/C=C/CC/C=C/CCCC(=O)O
-------+----------------+------------------+----------------+---------------------------------
298.15 | 0.220914923012 |   -6.33293991048 | -5.19636054531 |                   -9.66033139516
299.15 | 0.235479319348 |   -6.28117761855 | -5.15170377256 |                   -9.58901500825
300.15 | 0.249933657549 |   -6.22986499517 | -5.10742877511 |                   -9.51835276669
310.15 | 0.388688301563 |   -5.74023509659 | -4.68464352888 |                   -8.84581513627

The Table class also provides several attributes which can be used to access the data in a variety of common extension formats, specifically numpy ndarrays and pandas DataFrames:

>>> result.pressures.as_dataframe
Compound         CCCC  C(CC(=O)O)C(=O)O  C(=O)(C(=O)O)O  \
Temperature
298.15       0.220915         -6.332940       -5.196361
299.15       0.235479         -6.281178       -5.151704
300.15       0.249934         -6.229865       -5.107429
310.15       0.388688         -5.740235       -4.684644

Compound     CCCCC/C=C/C/C=C/CC/C=C/CCCC(=O)O
Temperature
298.15                              -9.660331
299.15                              -9.589015
300.15                              -9.518353
310.15                              -8.845815

API Reference

The API reference below is primarily geared towards those users that wish to use the UManSysProp client component.

umansysprop.client Module

This module contains the client library for interacting with the UManSysProp server. Only one user-accessible class is defined in the module:

UManSysProp
class umansysprop.client.UManSysProp(base_url='http://umansysprop.seaes.manchester.ac.uk/')[source]

Provides a simple Python interface to the methods provided via the JSON API on the UManSysProp website. Constructing an instance of this class will cause the new instance to query the server for all available methods. Each method will be exposed as a method of the instance, with docstrings obtained from the server. For example:

>>> import umansysprop.client
>>> client = umansysprop.client.UManSysProp()
>>> client.vapour_pressure
<bound method ?.vapour_pressure of <umansysprop.client.UManSysProp object at 0x7f80fbae7b50>>
>>> client.vapour_pressure.__doc__
u"\nCalculates vapour pressures for all specified *compounds* (given..."

The class can be constructed with an alternative base_url if you wish to point it a different server. The base_url parameter defaults to the UManSysProp website.

Methods can be called like a normal Python method, but will result in a request being sent to the web-server, processed, and the JSON-formatted results being re-constructed as a Result list on the client. For example:

>>> result = client.vapour_pressure([
... 'CCCC', 'C(CC(=O)O)C(=O)O', 'C(=O)(C(=O)O)O',
... 'CCCCC/C=C/C/C=C/CC/C=C/CCCC(=O)O'],
... [298.15, 299.15, 300.15, 310.15],
... 'nannoolal', 'nannoolal')
>>> result
[<Table name="pressures">]
>>> result.pressures
<Table name="pressures">
>>> result.pressures.data
{(298.15, u'C(=O)(C(=O)O)O'): -5.196360545314141,
 (298.15, u'C(CC(=O)O)C(=O)O'): -6.33293991047814,
 (298.15, u'CCCC'): 0.22091492301164387,
 (298.15, u'CCCCC/C=C/C/C=C/CC/C=C/CCCC(=O)O'): -9.660331395164858,
 (299.15, u'C(=O)(C(=O)O)O'): -5.151703772558254,
 (299.15, u'C(CC(=O)O)C(=O)O'): -6.281177618554678,
 (299.15, u'CCCC'): 0.2354793193478599,
 (299.15, u'CCCCC/C=C/C/C=C/CC/C=C/CCCC(=O)O'): -9.58901500825095,
 (300.15, u'C(=O)(C(=O)O)O'): -5.107428775107059,
 (300.15, u'C(CC(=O)O)C(=O)O'): -6.229864995169396,
 (300.15, u'CCCC'): 0.24993365754879804,
 (300.15, u'CCCCC/C=C/C/C=C/CC/C=C/CCCC(=O)O'): -9.518352766693454,
 (310.15, u'C(=O)(C(=O)O)O'): -4.684643528880829,
 (310.15, u'C(CC(=O)O)C(=O)O'): -5.74023509658808,
 (310.15, u'CCCC'): 0.38868830156274703,
 (310.15, u'CCCCC/C=C/C/C=C/CC/C=C/CCCC(=O)O'): -8.845815136269506}

Please refer to the reference for Result and Table for more information on accessing the result data.

umansysprop.results Module

This module defines the classes used to encapsulate results returned by the UManSysProp server. Each tool method on the client will return an instance of the Result class which in turn contains one or more Table instances.

Result
class umansysprop.results.Result(*tables)[source]

Represents a list of named Table objects.

The result of a method is represented as a sequence of tables. This class contains a list of Table objects each of which may be retrieved by name, or by index in the list (tables with identical names are not ignored, but only the first table may be retrieved by name).

Note

This class has an extended string representation intended for easy command line debugging. Simply print an instance of the class to view a dump of all the tables contained within it.

Table
class umansysprop.results.Table(name, rows, cols, func=None, data=None, title='', rows_title=None, cols_title=None, rows_unit=None, cols_unit=None)[source]

Represents a single table in a Result.

A tool is expected to return a sequence of Table objects in a Result object. Each table has a name (which can be used to access it in the Result object), an ordered list of keys for rows and cols, and a function which is used to derive the data for each cell. The function accepts two arguments, the row and column key in that order, and is expected to return a scalar value. The reason for constructing a table in this manner (lazy evaluation) is that it enables renderers to query the table structure and layout without necessarily calculating anything. Calculated data is cached on the assumption that such calculations are expensive.

The row and column keys can be any immutable value (immutability is required as they will form keys in a dict at evaluation time). Keys which are tuples will be treated specially as renderers. For example, if each row key is a 2-tuple, then each row in the resulting table will have two row headers in two separate columns at the left of the table. This can aid in representing data with more than 2 dimensions in a table.

Consider a result set keyed by values A, B, and C. The table can be constructed with a series of 2-tuple row keys (A, B), while the column can be scalar C values. The resulting table will be rendered as follows:

    C1 C2 C3
A1 B1 data data data
B2 data data data
A2 B1 data data data
B2 data data data

Optional attributes also exist for title, rows_title, cols_title, rows_unit, and cols_unit (these all default to an empty string if omitted). In the case that tuples are used for row or column keys, the corresponding title and unit values must be tuples as well.

Note

Like Result, this class has an extended string representation intended for easy command line debugging. Printing an instance of this class will produce a human readable string representation of the table’s row and column keys along with the calculated data.

as_ndarray

Returns the content of the table as a numpy ndarray with the shape (rows, cols). Rows and columns will be in the order given by the rows and cols attributes. Please note that row and column keys are not included in the resulting array (as ndarrays purposely do not support heterogeneous data types).

Warning

Accessing this property will implicitly import the numpy module. This is not done during module import to avoid creating an explicit dependency on numpy.

as_dataframe

Returns the content of the table as a pandas DataFrame. The rows and cols attributes will be included as the index and columns of the resulting DataFrame.

Warning

Accessing this property will implicitly import the pandas module. This is not done during module import to avoid creating an explicit dependency on pandas.

col_dims

The number of dimensions within the column keys. If this is greater than one, then cols is a sequence of tuples.

col_titles

Returns cols_title as a tuple, regardless. This property is intended to make renderers simpler.

cols

An ordered sequence of keys for the columns of the table. If col_dims is greater than one, this this is a sequence of tuples. These values, combined with rows can be used to index data in display order like so:

for row in table.rows:
    for col in table.cols:
        print(table.data[(row, col)])
cols_iter

Returns an iterator over cols where each key is returned as a tuple, regardless.

cols_title

A string or tuple of strings giving the title of each column dimension. Note that if col_dims is 1, this may be either a string or a 1-tuple containing a string. The associated col_titles attribute may be easier to work with.

cols_unit

A string or tuple of strings giving the units of each column dimension. Note that if col_dims is 1, this may be either a string or a 1-tuple containing a string. The associated col_units attribute may be easier to work with.

data

The data contained within the table. This is presented as a dict keyed by (row_key, col_key) tuples. To retrieve data in the same order as it should be presented, iterate over the rows and cols attributes.

data_iter

Returns an iterator over data where each key, value combination is returned as a tuple of (row_key, col_key, value), and each row and column key is returned as a tuple, regardless of the number of row and column dimensions. Furthermore, items are returned in declared row then column order. This property is intended to make renderers simpler.

name

The name of the table. This is intended for scripting usage and as such will only ever contain a string beginning with an alphabetic character followed by zero or more alphanumeric characters or underscores.

row_dims

The number of dimensions within the row keys. If this is greater than one, then rows is a sequence of tuples.

row_titles

Returns rows_title as a tuple, regardless. This property is intended to make renderers simpler.

rows

An ordered sequence of keys for the rows of the table. If row_dims is greater than one, then this is a sequence of tuples. These values, combined with cols can be used to index data in display order like so:

for row in table.rows:
    for col in table.cols:
        print(table.data[(row, col)])
rows_iter

Returns an iterator over rows where each key is returned as a tuple, regardless. This property is intended to make renderers simpler.

rows_title

A string or tuple of strings giving the title of each row dimension. Note that if row_dims is 1, this may be either a string or a 1-tuple containing a string. The associated row_titles attribute may be easier to work with.

rows_unit

A string or tuple of strings giving the units of each row dimension. Note that if row_dims is 1, this may be either a string or a 1-tuple containing a string. The associated row_units attribute may be easier to work with.

title

The human readable title of the table, typically rendered in the web interface as the table’s caption.

Change log

Release 0.1 (2015-08-07)

Initial release

License

GNU General Public License

Version 2, June 1991 Copyright © 1989, 1991 Free Software Foundation, Inc. 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA

Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.

Preamble

The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software–to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation’s software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Lesser General Public License instead.) You can apply it to your programs, too.

When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things.

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The precise terms and conditions for copying, distribution and modification follow.

TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION

0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The “Program”, below, refers to any such program or work, and a “work based on the Program” means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term “modification”.) Each licensee is addressed as “you”.

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1. You may copy and distribute verbatim copies of the Program’s source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program.

You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee.

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In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License.

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NO WARRANTY

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END OF TERMS AND CONDITIONS

How to Apply These Terms to Your New Programs

If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.

To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to where the full notice is found.

::

<one line to give the program’s name and a brief idea of what it does.> Copyright (C) <year> <name of author>

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

Also add information on how to contact you by electronic and paper mail.

If the program is interactive, make it output a short notice like this when it starts in an interactive mode:

Gnomovision version 69, Copyright (C) year name of author
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.

The hypothetical commands show w and show c should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than show w’ and `show c; they could even be mouse-clicks or menu items–whatever suits your program.

You should also get your employer (if you work as a programmer) or your school, if any, to sign a “copyright disclaimer” for the program, if necessary. Here is a sample; alter the names:

Yoyodyne, Inc., hereby disclaims all copyright interest in the program
`Gnomovision' (which makes passes at compilers) written by James Hacker.

<signature of Ty Coon>, 1 April 1989
Ty Coon, President of Vice

This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License.

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