BeadWeaver 0.0.3

Bead weaver is a package for manipulating .itp files

BeadWeaver

Beadweaver is a software for manipulating itps of coarse-grained biological molecules.

Quick start

Create a virtual environment

python -m venv beadweaver

source beadweaver/bin/activate

Install beadweaver package

cd BeadWeaver

pip install . (This will not be editable)

or

pip install -e . (This will be editable and will make adjustments anytime the github is changed)

Activate Beadweaver GUI

BWGUI

GUI Button Functions

Delete Bond: Click on two beads, then click the delete button to remove the bond between molecules.

Add Bond: Click on two beads, then click the add bond button to remove the bond between molecules.

Library: The library is a drop-down menu of molecules that Beadweaver can access. You can select the molecule of interest, and that molecule will be loaded.

Select: First, select the beads from the current structure by clicking them. Then click the select button. A menu will appear; type in the name of the new structure. That new structure can be used in New Molecule and will be added to the Library.

New Molecule: Allows the user to insert a new molecule into the GUI using a string format. First, click Delete Molecule, then click New Molecule. Enter the name of the new molecule and click OK. A second command box will appear; enter the new molecule string.

Format: bond#<molecule name>bond#-bond#<molecule name>bond# or bond#(bond molecule#(bond#<molecule name>bond#-bond#<letters>bond#

Example: 0<KDO>1-2<KDO>0 or 0<KDO>1-2<KDO>1-1(1(3<KDO>0

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