Standard Data File Options
Write
write [invert] [noxcol] [groupby <type>] [noheader] [square2d|nosquare2d] [nosparse|sparse [cut <cutoff>]]
invert Normally, data is written out with X-values pertaining to frames (i.e. data over all trajectories is printed in columns). This command flips that behavior so that X-values pertain to data sets (i.e. data over all trajectories is printed in rows).
groupby <type> (1D) group data sets by <type>:
name Group by name.
aspect Group by aspect.
idx Group by index.
ens Group by ensemble number.
dim Group by dimension.
xcol Write indices for the specified datafile. This is usually the default behavior.
noxcol Prevent printing of indices (i.e. the #Frame column in most datafiles) for the specified datafile. Useful e.g. if one would like a 2D plot such as phi vs psi. For example, given the input:
dihedral phi :1@C :2@N :2@CA :2@C out phipsi.dat dihedral psi :2@N :2@CA :2@C :3@N out phipsi.dat datafile phipsi.dat noxcol
CPPTRAJ will write a 2 column datafile containing only phi and psi, no frame numbers will be written.
header Write header line at beginning of data file. This is usually the default behavior.
noheader Prevent printing of header line (e.g. ’#Frame D1’) at the beginning of data file.
square2d Write 2D data as a square matrix, e.g.:
| <1,1> | <2,1> | <3,1> |
| <1,2> | <2,2> | <3,2> |
nosquare2d Write 2D data in 3 columns as: <X> <Y> <Value>
sparse Only write 3D grid voxels with value > cutoff (default 0).
cut <cut> Cutoff for ‘sparse’; default 0.
nosparse Write all 3D voxels (default).
Read
read [prec {flt|dbl}]
{[read1d [index <col>] [onlycols <range>] [floatcols <range>]
[intcols <range>] [stringcols <range>]] |
[read2d [{square2d|nosquare2d}]] |
[vector] |
[mat3x3] |
[read3d [dims <nx>,<ny>,<nz>] [origin <ox>,<oy>,<oz>]
[delta <dx>,<dy>,dz>] [prec {dbl|flt}] [bin {center|corner} ]
}
prec {flt|dbl} Read 2d/3d data as single (flt) or double (dbl, default) precision.
read1d Read data as 1D data sets (default).
index <col> Use column <col> (starting from 1) as index column (1D data only).
onlycols <range> Only read columns in range.
floatcols <range> Force specified columns to be read as single-precision floats.
intcols <range> Force specified columns to be read as integers.
stringcols <range> Force specified columns to be read as strings.
read2d Read data as 2D matrix.
square2d Read data as square matrix (default).
nosquare2d Read data as XYZ matrix (i.e. each line contains ‘<column> <row> <data>’).
vector Read data as vector. If indices are present they will be skipped. Assume first 3 columns after the index volumn are vector X, Y, and Z, and (if present) the next 3 columns contain vector origin X, Y, and Z.
mat3x3 Read data as 3×3 matrix. If indices are present they will be skipped. Assume matrices are in row major order on each line, i.e. M(1,1) M(1,2) …M(3,2) M(3,3).
read3d Read data as 3D grid. If no dimension data in file must also speify ‘dims’.
dims <dx>,<dy>,<dz> Grid dimensions.
origin <ox>,<oy>,<oz> Grid origins (default 0,0,0).
delta <dx>,<dy>,dz> Grid spacings (default 1,1,1).
prec {dbl | flt} Grid precision, double or float (default float).
bin {center | corner} Coords specify bin centers or corners (default corners).
By default, standard data les are assumed to contain 1D data in columns. Data set legends will be read in if the file has a header line (denoted by ‘#’). Columns labeled ‘#Frame’ are automatically considered the ‘index’ column and skipped. Data sets are stored as <name>:<idx> where <name> is the given data set name (the file name if not specified) and <idx> corresponds to the column the data was read from starting from 1. CPPTRAJ assumes the data increases monotonically and will automatically attempt to determine the dimensions of the data set(s); a warning will be printed if this is not successful.
If a file contains the header: #F1 F2 <name> CPPTRAJ will assume the file contains pairwise distances for clustering, where the F1 and F2 columns contain the frame numbers, and the <name> column contains the distance.