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.. _gettingstarted:
Getting started
===============
This page gives a introduction on how to get started with CIRpy. Before we start, make sure you have
:ref:`installed CIRpy <install>`.
Basic usage
-----------
The simplest way to use CIRpy is with the ``resolve`` function::
>>> import cirpy
>>> cirpy.resolve('Aspirin', 'smiles')
'C1=CC=CC(=C1C(O)=O)OC(C)=O'
The first parameter is the input string and the second parameter is the desired output representation. The main
output representations for the second parameter are::
stdinchi
stdinchikey
inchi
smiles
ficts
ficus
uuuuu
hashisy
sdf
names
iupac_name
cas
formula
All return a string, apart from ``names`` and ``cas``, which return a list of strings.
File formats
------------
Output can additionally be returned in a variety of file formats that are specified using the second parameter in the
same way::
>>> cirpy.resolve('c1ccccc1', 'cif')
"data_C6H6\n#\n_chem_comp.id\t'C6H6'\n#\nloop_\n_chem_comp_atom.comp_id\n..."
The full list of file formats::
alc # Alchemy format
cdxml # CambridgeSoft ChemDraw XML format
cerius # MSI Cerius II format
charmm # Chemistry at HARvard Macromolecular Mechanics file format
cif # Crystallographic Information File
cml # Chemical Markup Language
ctx # Gasteiger Clear Text format
gjf # Gaussian input data file
gromacs # GROMACS file format
hyperchem # HyperChem file format
jme # Java Molecule Editor format
maestro # Schroedinger MacroModel structure file format
mol # Symyx molecule file
mol2 # Tripos Sybyl MOL2 format
mrv # ChemAxon MRV format
pdb # Protein Data Bank
sdf3000 # Symyx Structure Data Format 3000
sln # SYBYL Line Notation
xyz # xyz file format
Properties
----------
A number of calculated structure-based properties can be returned, also specified using the second parameter::
>>> cirpy.resolve('coumarin 343', 'h_bond_acceptor_count')
'5'
The full list of properties::
mw # (Molecular weight)
h_bond_donor_count
h_bond_acceptor_count
h_bond_center_count
rule_of_5_violation_count
rotor_count
effective_rotor_count
ring_count
ringsys_count
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