uffutils 0.2.0

A set of commandline tools for manipulating UFF files.

UFF Utils

This library contains a set of pipeline tools for manipulating UFF files. It works a bit like this:

uffutils modify my_original_file.uff my_subset_file.uff --node-step 100 --node-count 1000
$nodes = $(uffutils inspect my_subset_file.uff --nodes-only)
uffutils modify my_file.uff my_output.uff `
    --node-selection $nodes `
    --scale-length 1000 `
    --to-global-frame `
    --rotate 90,90,90 `
    --translate 100,100,100

Installing

The inspect command

The inspect command allows you to view the contents of a UFF file. Example usage:

uffutils inspect my_file.uff  # Print nice overview 
uffutils inspect my_file.uff --nodes # Print full list of nodes

The modify command

The modify command allows you to modify a UFF file. For example, you can create a file with a subset of nodes in various ways:

uffutils modify my_file.uff list_of_nodes.uff --node-selection "1, 2, 3"
uffutils modify my_file.uff first_ten_nodes.uff --node-count 10 
uffutils modify my_file.uff every_tenth_node.uff --node-step 10 

You can scale length:

uffutils modify my_file.uff m_to_mm.uff --scale-length 1000 

And do various other operations:

uffutils modify my_file.uff in_global_frame.uff --to-global-frame 
uffutils modify my_file.uff rotated_euler_xyz.uff --rotate "90,90,90" 
uffutils modify my_file.uff translated_xyz.uff --translate "10,20,30"

And you do all these things at once:

uffutils modify my_file.uff my_output.uff `
    --node-selection "1,2,3" `
    --scale-length 1000 `
    --to-global-frame `
    --rotate 90,90,90 `
    --translate 100,100,100

Alternative implementation

I considered doing something with piping, but got stuck in the fact the the PyUFF library I'm using can't handle streams. It would've looking something like this:

uffutils subset my_original_file.uff my_subset_file.uff --step 100 
uffutils subset my_file.uff - --nodes $(uffutils describe my_subset_file.uff --nodes) | 
uffutils scale - my_output.uff --length 1000