drawVectors.py¶
drawVectors represents dipole and hydrophobicity vectors over a protein’s structure. Opens a ChimeraX GUI.
- Usage:
$ chimera –script “drawVectors.py 1abc.pdb”
-
drawVectors.main(proteinfile)¶ Reads protein file to create structure. Visualizes protein structure, dipole vector and hydrophobic vector in Chimera X.
- Parameters
proteinfile (str) – PDB File
-
drawVectors.generateStructure(proteinfile)¶ Creates protein structure from Builder from metrics module.
- Parameters
proteinfile (Path) – File path to PDB file.
- Returns
Protein structure
-
drawVectors.createcoordinates(proteinfile)¶ Creates coordinates for the center of mass, the dipole vector and th hydrophobic vector.
- Parameters
proteinfile (Path) – File path to PDB file.
- Returns
Coordinates of the center of mass, dipole vector and hydrophobic vector
- Return type
tuple
-
drawVectors.generateVectorFile(proteinfile)¶ Creates vector files for dipole and hydrophobic vector.
- Parameters
proteinfile (Path) – File path to PDB file.
- Returns
Vectorfiles for dipole and hydrophobic vector.
- Return type
str
-
drawVectors.drawProtein(session, proteinfile)¶ Displays protein structure in ChimeraX session.
- Parameters
session – Global variable pointing to program instance, known to Chimera environment.
proteinfile – File path to PDB file.
-
drawVectors.drawVectors(session, *vectorfiles)¶ Consume as many files as fed.
- Parameters
session – Global variable pointing to program instance, known to Chimera environment.
vectorfile – File to create vector in Chimera X.
-
drawVectors.angles(session, proteinfile)¶ Defines markers for the center of mass and the tip of the hydrophobic and dipole vector. Calculates the angle between the both vectors. Based on: https://rbvi.github.io/chimerax-recipes/mark_blobs/mark_blobs.html
- Parameters
session – Global variable pointing to program instance, known to Chimera environment.
proteinfile (Path) – File path to PDB file.
-
drawVectors.drawArc(session, proteinfile)¶ Draws arc between both vectors.
- Parameters
session – Global variable pointing to program instance, known to Chimera environment.
proteinfile (Path) – File path to PDB file.
-
drawVectors.labels(session, proteinfile)¶ Creates labels for hydrophobic vector, dipole vector and protein name.
- Parameters
session – Global variable pointing to program instance, known to Chimera environment.
proteinfile (Path) – File path to PDB file.