Data Type: Molecule Trajectory Bundle ()

Description:

An object of type Molecule Trajectory Bundle represents a set of Molecule Trajectory.

Commands:

getNumTrajectories
Returns the number of trajectories in the bundle.

getTrajectoryIx <name>
Returns index of trajectory with given name. 0 if no such trajectory.

setTrajectoryName <index> <name>
Renames the index'th trajectory with the given name. No return value.

findDuplicates
Searches for identical topologies within the bundle. Prints a list which shows for each trajectory the list of trajectories that have an identical topology. If no duplicates were found in the bundle, 0 is returned.

Editing:

addTrajectory <object-name>
Adds the trajectory with the given name in the Project View to the bundle. Removes all trajectories with the given indices. No return value.

replaceWithTrajectory <index> <object-name>
Repalces the index'th trajectory with the trajectory with the given name in the Project View. No return value.

removeIx <indices>
Removes all trajectories with the given indices. The list of indices needs to be seperated by white space and enclosed in curly brackets. No return value. Example:

•  removeIx {1 5 6}
  

removeDuplicatesByData <name>
If several trajectories have the same value for the given data field, this command will keep only the first occurence and remove the others. If a trajectory has no field of the given name it will not be considered in the operation (i.e., it will always be kept regardless whether there are other ones without this field).

copyIx <indices>
Copies the trajectories with the given indices into a new bundle, which will be added to the Project View. The order of the trajectories in the new bundle will be as given by the indices. The list of indices needs to be seperated by white space and enclosed in curly brackets. Returns label of new object in Project View.

removeNames <names>
Removes all trajectories of the given names. The list of names needs to be seperated by whitespace and enclosed in curly brackets. No return value.

restrictToIx <indices>
Removes all trajectories in the bundle except the ones with the given indices. The indices need to be seperated by a white space and enclosed in curly brackets. No return value.

restrictToNmes <names>
Removes all trajectories in the bundle except the ones with the given namess. The names need to be seperated by a white space and enclosed in curly brackets. No return value.

restrictRandom <number>
Restricts the bundle to a random set of <number> trajectories. No return value.

applyTransform <matrix>
Applies given 4x4 transformation matrix to all trajectories in the bundle. No return value.

addHydrogens
Adds hydrogens to all trajectories in the bundle. No return value.

removeHydrogens
Removes hydrogens for all trajectories in the bundle. No return value.

addMMFFParameterization
Adds MMFF94 parameterization for all trajectories in the bundle. No return value.

computeBonds
Computes bonds based on an average bond length table for all trajectories in the bundle. No return value.

loadIntoMemory
For some file types containing trajectories, only the currently used timestep is used in memory. This means that most of the editing commands will not work. This command allows each trajectory in the bundle to be loaded into memory. No return value.

alignBySmartsMatching
Aligns each trajectory in the bundle to <mol2> by first matching the given smarts string to both molecules and then using this matching for computing the transformation yielding the lowest rmsd between the matched groups. If either of the molecules did not have a matching nothing will be done. No return value.

Sorting:

sortByName
Sorts trajectories in bundle by the name. No return value.

sortByData <name> <type>
Sort the trajectories in the bundle by the given data entry. Type may be "string", "float" or "int". No return value.

reverseOrder
Reverses order of trajectories in bundle. No return value.

Searching:

match <atomexpression>
Returns a list of indices of trajectories for which at least one atom matches the given atom expression.

Importing/exporting data entries:

readData <filename> <dataname> <datatype>
Reads data entry from a file. Each data value needs to be in a seperate line and the number of lines must be the same as the number of trajectories in the bundle. No return value.

writeData <filename> <dataname>
Writes data entry to a file. There will be one line per trajectory containing the data value for the trajectory. No return value.

writeAllData <filename>
Writes all data entries to a csv file. There will be one line per trajectory containing first the index of the trajectory and then the data values for the trajectory, all comma separated. The first line will contain the field names. No return value.