molecule2cdxml

Simple utility to convert molecules to CDXML format using Indigo toolkit

Dependencies

• C++ compiler with support for C++14
• CMake of version 3.4 or higher
• Git
• Indigo cheminformatics toolkit

Instructions:

1. Install system requirements (example for Ubuntu):

   sudo apt update
   sudo apt install -y cmake g++ git make

2. Clone Indigo repository:

   git clone https://github.com/epam/indigo

3. Create CMake build folder and prepare build scripts

   mkdir build
   cd build
   cmake ..

4. Build utility

   cmake --build . --target molecule2cdxml --config Release 

   On Linux you may add additional parameters to parallelize and speed up the compilation:

   cmake --build . --target molecule2cdxml --config Release -- -j $(nproc)

5. Check that utility works fine:

   $ ./molecule2cdxml c1ccccc1
   <?xml version="1.0" encoding="UTF-8"?>
   <!DOCTYPE CDXML SYSTEM "http://www.cambridgesoft.com/xml/cdxml.dtd">
   <CDXML BondLength="30.000000" LabelFont="3" CaptionFont="4">
       <fonttable>
           <font id="1" charset="utf-8" name="Arial"/>
           <font id="2" charset="utf-8" name="Times New Roman"/>
       </fonttable>
       <colortable>
           <color r="1" g="1" b="1"/>
           <color r="0" g="0" b="0"/>
           <color r="1" g="0" b="0"/>
           <color r="1" g="1" b="0"/>
           <color r="0" g="1" b="0"/>
           <color r="0" g="1" b="1"/>
           <color r="0" g="0" b="1"/>
           <color r="1" g="0" b="1"/>
           <color r="0.5" g="0.5" b="0.5"/>
       </colortable>
       <page HeightPages="1" WidthPages="1">
           <fragment>
               <n id="1" Element="6">
                   <t p="0.000000 -0.000000" Justification="Center">
                       <s font="3" size="10" face="96">CH4</s>
                   </t>
               </n>
           </fragment>
       </page>
   </CDXML>