trajectory_asl_monitor.py Command Help
Command: $SCHRODINGER/run trajectory_asl_monitor.py
usage: trajectory_asl_monitor.py [-v] [-h] [-distance DISTANCE] [-byatom]
[-sidechain_sasa] [-report_min_dist]
[-report_center_dist] [-within_all]
[-coordfile]
input_cms output_basename asl1 asl2
[asl2 ...]
Monitors the number of atom groups within a specified distance of another atom
group during a trajectory.
The output of this script is the number of atom groups that fall within this
threshold over each frame of the trajectory and the results are written as one
line per frame to a CSV file.
Copyright Schrodinger, LLC. All rights reserved.
positional arguments:
input_cms Input cms file.
output_basename Basename for output files.
asl1 ASL expression to specify the first group of atoms. The
script will monitor the number of these groups within a
specified distance of a second group of atoms. For
instance, to monitor the number of water molecules near
a residue, set this ASL to 'water.
asl2 ASL expression to specify the second group of atoms.
The script will track the number of atoms that match
the first group that are near this group of atoms. For
instance, to monitor the number of water molecules near
a residue, set this ASL to the residue and asl1 to
'water'. This flag can be specified multiple times.
Each time indicates another independent group to
monitor. The results for each group will be written to
a separate output file named output_basename_x.csv,
where _x indicates the order of groups specified on the
command line.
options:
-v, -version Show the program's version and exit.
-h, -help Show this help message and exit.
-distance DISTANCE Threshold distance between group 1 and 2. The default
is 5.0 Angstoms.
-byatom Report the total number of atoms (not residues) within
the threshold distance. This is useful when in some
frames only part of a residue or molecule specified by
-asl1 may be within the threshold distance of the
second group. The default action is to count any
residue with at least one atom within the threshold
distance and report the total number of residues.
-sidechain_sasa For each frame, report the total SASA for all side
chain atoms in the groups specified by -asl2.
-report_min_dist For each frame, report the minimum distance between the
two groups of atoms.
-report_center_dist For each frame, report the distance between the centers
of masses of the two atom groups.
-within_all If more than one -asl2 group is supplied and
-within_all is specified, then only one output file
will be produced and it will contain information for
first group members that are within the specified
distance of ALL -asl2 groups. The default behavior is
to produce an output file for each -asl2 group, and
each output file contains data for first group members
that are within the specified distance of just that
-asl2 group.
-coordfile Write out a file with the coordinates of matching
analyzed frame. Each line in the file will either be an
ASL line indicating which -asl2 group the data is for,
a Frame designator, a blank line to indicate the end of
a group of atoms, or a line with the atom number,
element, and XYZ coordinates of an atom in the group.
The file will have the same base name as the output
file with -coords.txt added on to it.