Molecule Building Utilities

This module implements workflows related to the building of geometries or building geometries as starting points of simulations.

mol2box

The tag parameter should be a semicolon-separated list of SMILES strings, with the number of molecules indicated by a number, separated with comma. For example, o,64 means a box with 64 water molecule, and O,32;COO,32 means an equimolar mixture of water and ethonol.

The box parameter can be a single float for a cubic box, a semicolon-separated list for an orthogonal cell.

The seed parameter specified the random number generator used in packmol.

The 3D conformation will be build and hydrogen atoms added by openbabel. The molecules will then be packed into the specified box with packmol.

Input channels

Channel	Type	i/o[idx]	Note
`name`	`val`	`in[0]`	an id to identify the process
`tag`	`val`	`in[1]`	a string specifying the geometry
`box`	`val`	`in[2]`	a string specifying the box size
`seed`	`val`	`in[3]`	random number generator seed
`name`	`val`	`out.*[0]`	same as input
`geo`	`file`	`out.geo[1]`	the geometry packed with packmol
`log`	`file`	`out.log[1]`	packmol input and logs

Source code

nextflow.enable.dsl=2

params.publish = "."

process mol2box {
  label 'molutils'
  publishDir "$params.publish/molutils/$name"

  input:
    tuple val(name), val(tags), val(box), val(seed)

  output:
    tuple val(name), path("${name}.xyz"), emit: geo
    tuple val(name), path("packmol.{in,log}"), emit: logs

  shell:
  '''
  rm -rf packmol.in

  cat << EOF >> packmol.in
  tolerance 2.0
  filetype xyz
  output !{name}.xyz
  seed !{seed}
  EOF

  mols=$(echo "!{tags}" | tr ";" "\\n")
  for mol in $mols
  do
    IFS=, read smiles number <<< "$mol"
    obabel -h --gen3d -oxyz -:"$smiles" -O $smiles.xyz
    cat << EOF >> packmol.in
  structure $smiles.xyz
    number $number
    inside cube 0. 0. 0. !{box-2.0}
  end structure
  EOF
  done

  packmol < packmol.in > packmol.log
  sed -i '2s/.*/Lattice="!{box} 0.0 0.0 0.0 !{box} 0.0 0.0 0.0 !{box}"/' !{name}.xyz
  '''
}