Add more VDW radii and efficiency improvements

[menoliu]

Added:

• VDW radii for ions, metals, etc. according to the CRC Handbook of Chemistry and Physics, 82nd Ed
• Acceptance and automated processing of proteins with a membrane built from PPM v3 and CHARMM-GUI's bilayer builder
• Automated clash-checking of multiple IDR fragments with each other
• Automatic identification of multiple-chains in a PDB file and input sequence
• Automatic processing and building of dynamic complexes (multiple chains) given template and sequence

Improved:

• Use multiprocessing for merge sub-client
• Increase clash-checking efficiency by at least 75x (e.g. previously clash-checking for 80,000 conformers took 9.5hrs, now it takes 20-30 minutes)

Changed:

• Change the default values for backbone -etbb energy to 100 kJ and sidechain -etss to 250 kJ

[menoliu]

@joaomcteixeira I've made some (a lot) of improvements to LDRS and some IDPConfGen functions. As promised we can do everything we did via scripts internally now with just a single command in the ldrs subclient. Just wondering if you could check out the documentation I've added and any other comments before I merge. I've also built the foundations for multi-chain processing here

Edit 1: I have also tested the supplemental scripts from LDRS paper with this branch and they are working