ChemWiz

Program for manipulations with molecules and performing computations with them

This program is pre-alpha and doesn't do anything useful yet

In order to build ChemWiz, you first need to clone it with submodules:

git clone --recurse-submodules https://github.com/yurivict/ChemWiz.git

Then you need to install all dependencies listed below.

Boost: for some container types and string formatting
C++ Bitmap Library: to support the "Image" type (https://github.com/ArashPartow/bitmap)
PicoSHA2: to compute cryptographic hashes (https://github.com/okdshin/PicoSHA2)
Cblas: headers used by the rmsd++ headers, actual functions come from OpenBlas
Lapacke: headers used by the rmsd++ headers
nlohmann-json: for parsing of the periodic table json, etc.
rang: to print colored and styled text to the terminal (https://github.com/agauniyal/rang)
(optional) mmtf-cpp: for parsing chemical structures in the MMTF format (https://github.com/rcsb/mmtf-cpp)
MiniDNN: the neural network library
Eigen3: the linear algebra library

MuJS: for running JavaScript code that is used for scripting (https://mujs.com/)
OpenSSL: for crypto used to access https:// URLs
OpenBLAS: used by the 'rmsd' code for matrix computations
SQLite3: to save results and persistent state across runs. The library is loaded dynamically by the JS code, the executable isn't linked with it.
Qhull: to compute convex hulls of molecules (https://github.com/qhull/qhull)
(optional) OpenBabel: for parsing molecules in SMILES format (http://openbabel.org/wiki/Main_Page)
(optional) libdsrpdb: for parsing proteins in the PDB format (or perhaps any large and complex molecules) (https://graphics.stanford.edu/~drussel/pdb/)
Qt5 components: core and webenginewidgets (used only by the browser in qt5-QtWebEngine-browser/)

(optional) Jmol: for converting molecules to 3-D images, the executable 'jmoldata' is run from the scripts (http://jmol.sourceforge.net/)
(optional) ffmpeg: for converting frames (images) to movies, the executable 'ffmpeg' is run from the scripts (https://www.ffmpeg.org/)

All optional library dependencies have corresponding build switches in the form USE_xx.

rmsd library (https://github.com/charnley/rmsd, BSD 2-Clause licensed): Jimmy Charnley Kromann's rmsd library for Root-Mean-Square-Deviation calculation

Jmol produces invalid (not entirely valid) PNGs: https://sourceforge.net/p/jmol/bugs/604/

Name		Name	Last commit message	Last commit date
Latest commit History 455 Commits
.unused/WebGL-in-app		.unused/WebGL-in-app
apps		apps
contrib		contrib
modules		modules
molecules/Amino_Acids		molecules/Amino_Acids
qa		qa
qt5-QtWebEngine-browser		qt5-QtWebEngine-browser
.gitmodules		.gitmodules
BUGS		BUGS
LICENSE		LICENSE
Makefile		Makefile
Mat3.h		Mat3.h
README.md		README.md
Vec3-ext.cpp		Vec3-ext.cpp
Vec3-ext.h		Vec3-ext.h
Vec3.h		Vec3.h
binary.cpp		binary.cpp
common.cpp		common.cpp
common.h		common.h
float-array.cpp		float-array.cpp
image.cpp		image.cpp
js-binding.cpp		js-binding.cpp
js-binding.h		js-binding.h
js-support.cpp		js-support.cpp
js-support.h		js-support.h
linear-algebra.cpp		linear-algebra.cpp
main.cpp		main.cpp
misc.h		misc.h
molecule-dsrpdb.cpp		molecule-dsrpdb.cpp
molecule-mmtf.cpp		molecule-mmtf.cpp
molecule-ob.cpp		molecule-ob.cpp
molecule-pdb.cpp		molecule-pdb.cpp
molecule-qhull.cpp		molecule-qhull.cpp
molecule-xyz.cpp		molecule-xyz.cpp
molecule.cpp		molecule.cpp
molecule.h		molecule.h
mytypes.h		mytypes.h
neural-network.cpp		neural-network.cpp
obj.cpp		obj.cpp
obj.h		obj.h
op-rmsd.cpp		op-rmsd.cpp
op-rmsd.h		op-rmsd.h
pdb.cpp		pdb.cpp
periodic-table-data.cpp		periodic-table-data.cpp
periodic-table-data.h		periodic-table-data.h
process.cpp		process.cpp
process.h		process.h
stl-ext.h		stl-ext.h
structure-db.cpp		structure-db.cpp
structure-db.h		structure-db.h
temp-file.cpp		temp-file.cpp
temp-file.h		temp-file.h
tm.cpp		tm.cpp
tm.h		tm.h
util.cpp		util.cpp
util.h		util.h
web-io.cpp		web-io.cpp
web-io.h		web-io.h
xerror.h		xerror.h