Standard Data File Options
Write
[invert] [noxcol] [noheader] [square2d] [nosquare2d]
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).
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.
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>
Read
[index <col>] [read2d] [vector] [mat3x3]
index <col> Use column <col> (starting from 1) as index column (1D data only).
read1d Read data as 1D data sets (default).
read2d Read data as 2D square matrix.
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).
By default, standard data files 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.