Macs in Chemistry

Insanely Great Science

RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry

 

The first announcement of a meeting to be held next year.

RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry Friday, 15th June 2018 Royal Society of Chemistry at Burlington House, London, UK.
Twitter hashtag - #RSC_AIChem

AIfirst_announcement

Artificial Intelligence is presently experiencing a renaissance in development of new methods and practical applications to ongoing challenges in Chemistry. We are pleased to announce that the Biological & Medicinal Chemistry Sector (BMCS) and Chemical Information & Computer Applications Group (CICAG) of the Royal Society of Chemistry are organising a one-day conference entitled Artificial Intelligence in Chemistry to present the current efforts in applying these new methods. We will combine aspects of artificial intelligence and deep machine learning methods to applications in chemistry.

Applications for oral and poster presentations are welcomed. Posters will be displayed throughout the day and applicants will be asked if they would like to provide a two-minute flash oral presentation when submitting their abstract. Closing dates are 31st January for oral and 13th April for poster submissions.

More details here http://www.maggichurchouseevents.co.uk/bmcs/AI-2018.htm.


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RSC CICAG Membership

 

Royal Society of Chemistry members will be getting their annual subscription details around now. Can I remind people that your membership entitles you to membership of up to THREE Interest Groups.

Scan3

I'd urge you to make use of them, in particular:-

86 Chemical Information and Computer Applications Group

Update

Currently it seems Members who wish to change/join interest groups and divisions currently need to request this via email (membership@rsc.org) or telephone (01223 432141).

The Chemical Information and Computer Applications Group (CICAG) is one of the RSC’s many member-led Interest Groups, which exist to benefit RSC members and the wider chemical science community, and to meet the requirements of the RSC’s strategy and charter.

Scope and Aims

The storage, retrieval, analysis and preservation of chemical information and data are of critical importance for research, development and education in the chemical sciences. All chemists, and everybody else who works with chemical substances, need tools and techniques for handling chemical information.

CICAG works to:

  • Support users of chemical information, data and computer applications and advance excellence in the chemical sciences
  • Inform RSC members and others of the latest developments in these rapidly evolving areas
  • Promote the wider recognition of excellence in chemical information and computer applications at this level.

CICAG also organises a number of meetings each year at which members get reduced rates. Details of previous meetings are here.

You can also follow CICAG on Twitter https://twitter.com/RSC_CICAG or LinkedIn https://www.linkedin.com/groups/1989945.

twitterCICAG


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Python and compchem

 

Python seems to becoming the lingua franca for scientific scripting/progamming and it is perhaps not surprising that we now see increasing support for computational chemistry.

Chemtools is a set of modules that is intended to help with more advanced computations using common electronic structure methods/ programs. Currently the is some limited support for Gamess-US and MolPro program packages but other codes can be easily interfaced. It requires:

  • Python works with Python 2.7.x and 3.x
  • numba
  • numpy
  • mendeleev
  • scipy
  • setuptools

Chemtools is NOT hosted on pypi yet but in can be installed by pip from the bibbucket repository with:

pip install https://bitbucket.org/lukaszmentel/chemtools/get/tip.tar.gz

Pygamess is a GAMESS wrapper for Python, it requires:

  • Python 2.6 or later (not support 3.x)
  • RDKit
  • GAMESS

It can be installed using pip

pip install pygamess

Usage

single point calculation with RDKit

from pygamess import Gamess
from rdkit import Chem
from rdkit.Chem import AllChem
m = Chem.MolFromSmiles("CC")
m = Chem.AddHs(m)
AllChem.EmbedMolecule(m)
0
AllChem.UFFOptimizeMolecule(m,maxIters=200)
0
g = Gamess()
nm = g.run(m)
nm.GetProp("total_energy")
'-78.302511990200003'

PyQuante: Python Quantum Chemistry, an open-source suite of programs for developing quantum chemistry methods, it currently supports

  • Hartree-Fock: Restricted closed-shell HF and unrestricted open-shell HF;
  • DFT: LDA (SVWN, Xalpha) and GGA (BLYP) functionals;
  • Optimized-effective potential DFT;
  • Two electron integrals computed using Huzinaga, Rys, or Head-Gordon/Pople techniques; C and Python interfaces to all of these programs;
  • MINDO/3 semiempirical energies and forces;
  • CI-Singles excited states;
  • DIIS convergence acceleration;
  • Second-order Moller-Plesset (MP2) perturbation theory.

cclib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages. The goals of cclib are centered around the reuse of data obtained from these programs and contained in output files, specifically

  • ADF (versions 2007 and 2013)
  • DALTON (versions 2013 and 2015)
  • Firefly, formerly known as PC GAMESS (version 8.0)
  • GAMESS (US) (version 2012)
  • GAMESS-UK (version 7.0)
  • Gaussian (versions 03 and 09)
  • Jaguar (versions 7.0 and 8.3)
  • Molpro (versions 2006 and 2012)
  • NWChem (versions 6.0 and 6.5)
  • ORCA (versions 2.9 and 3.0)
  • Psi (versions 3.4 and 4.0)
  • Q-Chem (version 4.2)

FragBuilder a tool to create, setup and analyse QM calculations on peptides. DOI.

Update

And of course there is OpenBabel that can be used create input files for a variety of computational chemistry packages.

If I've missed anything please feel free to let me know.


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LiteMol

 

The LiteMol suite consists of three components, data delivery services (CoordinateServer and DensityServer), the BinaryCIF compression format, and a new lightweight 3D molecular viewer (LiteMol Viewer) https://www.nature.com/articles/nmeth.4499.epdf?.

You can try it out at https://www.litemol.org/.

litemol

The LiteMol suite works on all modern web browsers and mobile devices.

LiteMol Viewer is an HTML5 web application for 3D visualization of molecules and other related data. LiteMol is written in TypeScript, a typed extension of JavaScript and uses WebGL for 3D visualization.

Among other things, LiteMol provides:

  • Standard visualizations: cartoons, surface, balls and sticks, etc.
  • Assemblies and symmetry mates.
  • Electron Density and CryoEM maps.
  • Integration with PDBe API: view and explore validation and annotation data.
  • Integration with the Coordinate Server: download only parts of structures you are interested in.
  • Support for the BinaryCIF format that reduces the amount of data that needs to be sent to the client several times.

Comments

Collaborative Computational Project No. 4 for Macromolecular X-Ray Crystallography

 

CCP4 exists to produce and support a world-leading, integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques.

update 047 is out and contains updates to:

Component Description Mac OS 64-bit Linux 32-bit Linux 64-bit Windows 32-bit Windows 64-bit
panddas update to 2.11 yes yes yes - -
Molrep PFMOD correction yes yes yes yes yes
pointless 1.11.6 yes yes yes yes yes
pointless1.11.5 bug fix for multi lattice data yes yes yes yes yes
ccp4i2 fixes in molrep interface yes yes yes yes yes
edstats new version yes yes yes yes yes
ccp4i lorestr: fix for interface yes yes yes yes yes
monomers add 0WD,2Q5,6G6,6ZL,79F,7K9,8LL, 9Q8,FJI,OMZ,QUJ,QVE,RU2,YY9 yes yes yes yes yes
monomers Format fix: CPN,CPO,DEF,GCR,IMF,QPT yes yes yes yes yes
monomers Replace: UAP yes yes yes yes yes
ccp4mg fixes bug which causes MG/MrBUMP to not work for many sequences yes yes yes yes yes
ccp4mg update for https access to PDBe yes yes yes yes yes
mmdb2 False "duplicate sequence number" error in case of short residue names yes yes yes yes yes
numpy update to 1.12.1 yes yes yes - -
scipy update to 1.16.1 yes yes yes - -

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