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update print instructions in the documentation #58

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1 change: 1 addition & 0 deletions docs/source/guide/contribute.rst
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Expand Up @@ -18,6 +18,7 @@ Contributors
- |ghi| `llazzaro <https://github.com/llazzaro>`_ (Leonardo Lazzaro)
- |ghi| `bjodah <https://github.com/bjodah>`_ (Björn Dahlgren)
- |ghi| `RickardSjogren <https://github.com/RickardSjogren>`_ (Rickard Sjögren)
- |ghi| `nbehrnd <https://github.com/nbehrnd>`_ (Norwid Behrnd)

.. _`source code`: https://github.com/mcs07/PubChemPy
.. _`Issue Tracker`: https://github.com/mcs07/PubChemPy/issues
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23 changes: 10 additions & 13 deletions docs/source/guide/gettingstarted.rst
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Expand Up @@ -22,17 +22,17 @@ Let's get the Compound with `CID 5090`_::
Now we have a :class:`~pubchempy.Compound` object called ``c``. We can get all the information we need from this
object::

>>> print c.molecular_formula
>>> print(c.molecular_formula)
C17H14O4S
>>> print c.molecular_weight
314.35566
>>> print c.isomeric_smiles
>>> print(c.molecular_weight)
314.4
>>> print(c.isomeric_smiles)
CS(=O)(=O)C1=CC=C(C=C1)C2=C(C(=O)OC2)C3=CC=CC=C3
>>> print c.xlogp
>>> print(c.xlogp)
2.3
>>> print c.iupac_name
>>> print(c.iupac_name)
3-(4-methylsulfonylphenyl)-4-phenyl-2H-furan-5-one
>>> print c.synonyms
>>> print(c.synonyms)
[u'rofecoxib', u'Vioxx', u'Ceoxx', u'162011-90-7', u'MK 966', ... ]

.. note::
Expand All @@ -51,19 +51,16 @@ What if you don't know the PubChem CID of the Compound you want? Just use the :f
function::

>>> results = pcp.get_compounds('Glucose', 'name')
>>> print results
[Compound(79025), Compound(5793), Compound(64689), Compound(206)]
>>> print(results)
[Compound(5793)]

The first argument is the identifier, and the second argument is the identifier type, which must be one of ``name``,
``smiles``, ``sdf``, ``inchi``, ``inchikey`` or ``formula``. It looks like there are 4 compounds in the PubChem
Database that have the name Glucose associated with them. Let's take a look at them in more detail::

>>> for compound in results:
... print compound.isomeric_smiles
C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)O
... print(compound.isomeric_smiles)
C([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)O)O)O)O
C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O)O
C(C1C(C(C(C(O1)O)O)O)O)O

It looks like they all have different stereochemistry information.

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12 changes: 6 additions & 6 deletions docs/source/guide/substance.rst
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Expand Up @@ -17,18 +17,18 @@ Retrieving substances
Retrieve Substances using the :func:`~pubchempy.get_substances` function::

>>> results = pcp.get_substances('Coumarin 343', 'name')
>>> print results
[Substance(24864499), Substance(85084977), Substance(126686397), Substance(143491255), Substance(152243230), Substance(162092514), Substance(162189467), Substance(186021999), Substance(206257050)]
>>> print(results)
[Substance(24864499), Substance(85084977), Substance(126686397), Substance(143491255), Substance(152243230), Substance(162092514), Substance(162189467), Substance(186021999), Substance(206257050), ... ]


You can also instantiate a Substance directly from its SID::

>>> substance = pcp.Substance.from_sid(223766453)
>>> print substance.synonyms
>>> print(substance.synonyms)
['2-(Acetyloxy)-benzoic acid', '2-(acetyloxy)benzoic acid', '2-acetoxy benzoic acid', '2-acetoxy-benzoic acid', '2-acetoxybenzoic acid', '2-acetyloxybenzoic acid', 'BSYNRYMUTXBXSQ-UHFFFAOYSA-N', 'acetoxybenzoic acid', 'acetyl salicylic acid', 'acetyl-salicylic acid', 'acetylsalicylic acid', 'aspirin', 'o-acetoxybenzoic acid']
>>> print substance.source_id
>>> print(substance.source_id)
BSYNRYMUTXBXSQ-UHFFFAOYSA-N
>>> print substance.standardized_cid
>>> print(substance.standardized_cid)
2244
>>> print substance.standardized_compound
>>> print(substance.standardized_compound)
Compound(2244)
12 changes: 6 additions & 6 deletions docs/source/index.rst
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Expand Up @@ -13,15 +13,15 @@ retrieval of chemical properties.
Here's a quick example showing how to search for a compound by name::

for compound in get_compounds('glucose', 'name'):
print compound.cid
print compound.isomeric_smiles
print(compound.cid)
print(compound.isomeric_smiles)

Here's how you get calculated properties for a specific compound::

vioxx = Compound.from_cid(5090)
print vioxx.molecular_formula
print vioxx.molecular_weight
print vioxx.xlogp
print(vioxx.molecular_formula)
print(vioxx.molecular_weight)
print(vioxx.xlogp)

All the heavy lifting is done by PubChem's servers, using their database and chemical toolkits.

Expand All @@ -37,7 +37,7 @@ Features
- Download compound records as XML, ASNT/B, JSON, SDF and depiction as a PNG image.
- Construct property tables using *pandas* DataFrames.
- A complete Python wrapper around the `PubChem PUG REST web service`_.
- Supports Python versions 2.7 – 3.4.
- Supports Python versions 2.7 – 3.9.


Useful links
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