Dihedral Angles and Cis/Trans [1]

Dihedral

This analyzer computes dihedral angles along the backbone of each (selected) connected subgraph. The angles are rounded to integer degrees and binned into 1-degree bins.

Command Line Input

-d
--dihedral
Calculate dihedral angles. Optionally provide a base output filename.
Default: dihedrals.csv

--dihedral-range {abs,nonabs}
abs gives 0-180 degrees (absolute angles), nonabs gives -179-180 degrees.
Default: abs

--special-dihedral
Take only certain dihedrals into account.
Provide the atom types of the four consecutive elements along the backbone you want to calculate the dihedral angles for.
Usage example: -d –special-dihedral OCCO

By default, the filenames are dihedrals.csv, dihedrals_list.csv, and cisTrans.csv. The basename for the first two files can be changed by providing the desired name after the -d or --dihedral flag.

Example

MakroLyzer -xyz polymer.xyz -d --dihedral-range nonabs

Outputs

The dihedral analyzer writes three files:

  • dihedrals.csv: Dihedral angle counts per frame. The first column is Angle and each additional column is Frame <idx>.

  • dihedrals_list.csv: One row per subgraph and frame with the angle list sorted along the backbone.

  • CisTrans.csv: Cis/trans counts per frame, plus longest consecutive cis and trans passages. Column order: Frame, Cis count, Trans count, Longest consecutive cis, Longest consecutive trans.

Cis/trans classification uses \(|\theta| \le 90\) degrees for cis and \(90 < |\theta| \le 180\) degrees for trans.