protein_orientation
python protein_orientation.py -husage: protein_orientation.py [-h] -c GRO_FILE_LIST -f XTC_FILE_LIST -com_sel
COM_SELECTION [-method METHOD] -n
NUM_OF_PROTEINS [-skip SKIP]
[-vtraj VECTOR_TRAJ]
[-res_vector_sel RES_VECTOR_SEL]
[-stride STRIDE_FILE] [-pa_only PA_SINGLE]
[-nprocs NPROCS] [-ref_option REF_OPTION]
[-sec_struc_choice SEC_STRUC_CHOICE]
Calculates the orientation of a user defined region of a protein
optional arguments:
-h, --help show this help message and exit
-c GRO_FILE_LIST The list of coordinate files [.gro], this takes the
form of a text file with each file location starting
on a new line.
-f XTC_FILE_LIST The list of corrected trajectory files: pbc artifacts
removed, no jumping across PBC. This takes the form of
a text file with each file location starting on a new
line.
-com_sel COM_SELECTION
The range of resids to use for centre of mass
calculation, in the form of A:B, where A and B are
integers.
-method METHOD The vectors can be calculated by 1) a set of user
defined vectors based on the centre of mass of the
main selection and the alpha carbon (CA) of a
specified residue OR 2) the method can be used in
combination with (1) and use the principal axes of
inertia. In either (1) or (2) the user must define a
set of vectors that roughly correspond to the
principal axes - this ensures that when calculated
they always point in the direction specified by the
users vectors. Options: user or user_pa. Default =
user_pa
-n NUM_OF_PROTEINS Number of protein copies in the system, default 1.
-skip SKIP The number of frames to skip, default 1.
-vtraj VECTOR_TRAJ Set to True if you want a trajectory of the vectors,
default False.
-res_vector_sel RES_VECTOR_SEL
The resids of the residues to use for the roll, pitch,
and yaw calculation respectively: in the form A, B, C.
-stride STRIDE_FILE The name of the stride file to read, a .txt file. This
will be used in combination with the -com_sel
selection to only choose those residues involved in
secondary structure. If using the 'user_pa' method
(see -method) this option must be supplied.
-pa_only PA_SINGLE If set to True a principal component calculation will
be carried out and written to a .pdb file, this is to
help in selecting the appropriate residues for a run.
Default False
-nprocs NPROCS Number of processes to use, default=1.
-ref_option REF_OPTION
Choice of what basis of vectors to use as a reference,
from which the Euler angles will be calcualted.
Permitted chocies are: 'first_frame', angles will be
calculated in reference to the PAs calculated in the
first frame. 'user', angles will be calculated in
reference to a user defined set of vectors. 'standard'
where the standard is x, y, z = [1,0,0], [0,1,0],
[0,0,1]. default = 'standard'.
-ref_basis REF_BASIS To be used in combination with 'user' if used (see
-ref_option). The basis vectors to be used as a
reference, if not passed the default will be used (see
-ref_option). This should be a .txt file with the x,
y, z coordinates on each line.
-sec_struc_choice SEC_STRUC_CHOICE
A file containing the choice of secondary structure to
use in the calculation of the centre of mass. If using
the 'user_pa' method (see -method) this option must be
supplied. Valid choices include: 'strand', '310helix',
or 'alphahelix'. In the file these must be comma
separated and have no whitespace between them. e.g.
strand,310helix
python protein_orientation.py -c gro_file_list.txt -f xtc_file_list.txt -com_sel 1:123 -n 1 -method user_pa -res_vector_sel 102,69,5 -stride stride_file.txt -nprocs 10 -skip 10 -ref_option standard -sec_struc_choice sec_struc.txt