Output files

This section aims to provide the user with a complete description of all the files returned as output of a GPathFinder calculation. To learn how to perform different analysis over this data, you can check the tutorial Analyzing GPathFinder results.

The results of the calculation will be saved inside a folder on the path indicated in the output.path parameter of the .yaml input file. This folder will contain:

  • A `.gaudi-log` file: contains the log information of the calculation, with data about the time employed in the execution, the evolution of the scores along the calculation and possible errors/warnings.
  • A `.yaml` file: contains a replica of the .yaml input file employed in the calculation.
  • A `.gpath-output` file: contains a summary of the obtained results, with data about their scores and name of the file that actually has the pathway. Can be used to get an overview of the quality of the solutions.
  • A `summary.csv` file: contains a summary of the scoring of all obtained results, detailed by frame. Also contains the coordinates of every solution (considering the center of mass of the ligand at every frame of the pathway). Can be used to see at a frame detail the quality of a concrete solution and differences between solutions.
  • A set of `.zip` files: contain the different pathways obtained from the calculation. The number of solutions will be equal to the population size if output.pareto was set to False or equal to the size of the pareto frontier (i.e. dominant solutions) otherwise.

Optional files

  • A `.nmd` file: contains the information about the prody modes calculated in Normal Mode Analysis of the receptor molecule. This file only will be present if gaudi.genes.path_normalmodes.write_modes was set to True.
  • A `.samples` file: contains the information about all the samples generated during Normal Mode Analysis of the receptor molecule. This file only will be present if gaudi.genes.path_normalmodes.write_samples was set to True.

Contents of the .zip corresponding to each solution

Each .zip file contains all the necessary information to reproduce at atomic level the pathway proposed by GPathFinder as a solution for your problem. Inside the file there are the following contents:

  • Two `.mol2` files with the original 3D structures of the ligand and the receptor.
  • A `.gaudi` file with the summary of the files.
  • Another `.zip` file which contains a set of .pdb files with all the frames of the pathway (each one has a conformation of the ligand and receptor molecules). You can open these .pdb files in any visualization tool like a MD-movie and work with them and analyze each frame. An example of a pathway that represents a GPathFinder solution can be found here.

Moreover, an allele.txt and a scores.txt files are present with all the necessary information to reconstruct the pathway from the original structures and the score information for every frame. These additional files can be used by your own scripts to analyze the results in further detail.

Finally, a trajectory.pdb file which contains the route that follows the ligand, as a set of points that represent the center of the ligand at each step of the trajectory. This can be used to easily compare the trajectory of different solutions obtained from GPathFinder calculations.