Welcome to COSMOpy’s documentation!¶
Introduction¶
COSMOpy is a Python interface to the BIOVIA Solvation Chemistry software.
COSMOlogic is now part of Dassault Systèmes the 3DEXPERIENCE (R) Company, and its BIOVIA brand.
BIOVIA COSMOtherm - Predictive property calculation of liquids by the COSMO-RS theory
BIOVIA COSMObase - High quality collections of pre-calculated compound information
BIOVIA COSMOconf - Flexible conformer generation toolbox for the most relevant conformers
BIOVIA COSMOquick - Quick and powerful toolbox removing the need for costly quantum chemistry
TURBOMOLE - General purpose, fast and robust quantum chemistry program package
Note: Not to be confused with the astronomy related theoretical cosmology module called CosmoPy: http://ifa.hawaii.edu/cosmopy/
Indices and tables¶
Download and installation¶
Please take a look at BIOVIA PipelinePilot to create workflows.
Pre-requisites:
COSMOthermX installation
Python 3 (Python 2.7 libraries exist, but not being updated any more, starting with August 2019)
RDkit (optional)
Getting started¶
The general module to handle all COSMOpy objects is the module COSMOpy and its class CosmoPy
Dealing with compounds and mixtures
Supports conformer sets, ionic liquids and mixture compositions
Storage of compound or mixture properties
Handling of COSMOtherm, COSMObase, COSMOconf, COSMOquick, MOPAC and TURBOMOLE
Search compounds in the COSMObase
Compute new compounds by COSMOconf and TURBOMOLE
Predict thermodynamic values by COSMOtherm: activity coefficients, vapor pressures, partitioning, … etc.
Apply COSMOquick models
Open compound files
.sdf, .smi, .xyz, …
.cosmo files and conformer sets
Chemoinformatics routines (using RDKit or CDK), e.g.,
Generate 3D structures from SMILES
Substructure searches
Initialize CosmoPy object
The CosmoPy object is a general class to handle COSMOlogic software. It is initialized in the following way (more details on the initialition see COSMOpy.COSMOpy.CosmoPy):
- Example
>>> from COSMOpy import *
>>> cp = CosmoPy() # Initialize CosmoPy main object
Working with COSMOlogic software
The following example shows how to:
Search the COSMObase at TZVP level
Define COSMOtherm job types and compute jobs
Get properties from COSMOtherm calculations
- Example
>>> cp.cosmotherm.setLevel("TZVP") # Set level of calculation "SVP", "TZVP", "TZVPD-FINE"
>>> ethanol = cp.cosmotherm.searchName("ethanol")[0] # Search name in the COSMObase used for COSMOtherm calculations - index 0 returns 1st compound in list
>>> cp.cosmotherm.define(ethanol, "Henry constant") # Define a calculation type - here: "Henry constant" (= equivalent to panel name in COSMOthermX)
>>> cp.cosmotherm.compute() # Run COSMOtherm calculations
>>> ethanol.getProperty("H") # Henry constant (the property name is parsed from the .tab result file)
0.051
>>> cp.cosmotherm.define(ethanol, "Henry constant", T = 350) # Now, define a temperature
>>> cp.cosmotherm.compute() # Run COSMOtherm calculations
>>> ethanol.getProperty("H", "log(kPa)", T = 350) # Return Henry constant in unit of interest (automatic unit conversion!)
4.11
In addition to the cosmotherm instance, there are also cosmoconf, cosmoquick, turbomole etc. instances to the CosmoPy object. More details on accessing the COSMOlogic software packages from Python is presented in the documentation to the individual calculation classes:
Functions: Unit conversion
A general unit conversion function is part of the COSMOpy library, the conversion factors based on NIST or IUPAC recommendations:
convertUnit:
COSMOcompound.convertUnit()convertConcentration:
COSMOcompound.convertConcentration()
- Example
>>> convertUnit(5, "kcal/mol", "kJ/mol")
20.92
>>> convertUnit(5, "kcal/mol", "kJ/kg", mol_weight = 88.0) # Conversion of mol --> kg units
237.73
>>> convertUnit(5, "bar", "log(kPa)") # Logarithmic units (note: log = log10; ln = ln)
2.70
>>> convertConcentration(0.5, "mol/l") # Conversion of 0.5 mol/l (solute/water) to molar fraction in water
[0.0089, 0.9911]
>>> convertConcentration(14, "mg/ml", mol_weight = 151.06, T = 293) # Water solubility of paracetamol (at 293 K) = 14 mg/ml
[0.0017, 0.9983]
Objects: Compound handling
The COSMOpy library works with different objects related to compounds and mixtures:
Type |
Class |
Explanation |
|---|---|---|
Compound |
Single conformer |
|
ConformerSet |
Conformer set |
|
CompoundList |
Collection of compounds or conformer sets |
|
IonicLiquid |
Ionic liquids composite of cations and antions |
|
Mixture |
Mixtures of compounds or conformer sets of a defined composition |
|
Micelle |
Micelle or membrane including components and specific properties |
- Example
>>> isopropanol = Compound("iso-Propanol", "CC(O)C") # Compound (defined by compound name and SMILES)
>>>
>>> mixture = Mixture("Alcohols") # Mixture (mixture name will be used by COSMOtherm as input file name)
>>> mixture.addCompound(ethanol, x = 0.3)
>>> mixture.addCompound(isopropanol, x = 0.7)
Objects: Opening .sdf .smi or .cosmo files
Type |
Class |
Explanation |
|---|---|---|
CompoundReader |
.sdf, .smi, .xyz, .cosmo |
|
ConformerSetReader |
_c0.cosmo, _c1.cosmo, … |
|
MicelleReader |
.mic |
- Example
>>> cosmo = ConformerSetReader("/home/somewhere/ethanol_c0.cosmo") # Read cosmo conformer sets (specify first conformer _c0 here)
>>> ethanol = cosmo.getCompound() # Reads all conformers for ethanol (_c0.cosmo, _c1.cosmo, ...)
>>> cosmo.close()
>>>
>>> sdf = CompoundReader("/home/somewhere/solutes.sdf") # Read sdf files
>>> solute = sdf.getCompound(0) # Multi-SMI/SDF: compound 1,2,3,...
>>> sdf.close()
>>>
>>> mic = CompoundReader("/home/somewhere/dmpc.mic") # Read mic micelle or membrane files
>>> dmpc = mic.getMicelle(0) # Get dmpc system and all components
>>> mic.close()
Cheminformatics
COSMOpy.COSMOcheminf.Cheminf(requires: RDKit)
- Example
>>> ethanol = Compound("ethanol", "CCO")
>>> ethanol.cheminf.getFormalCharge()
0
>>> ethanol.cheminf.getCoordinates()
[[0.00, 0.00, 0.00], [-0.68, 0.87, -0.09], ...]
>>> ethanol.cheminf.getSmartsCount("[CH2,H3]")
2