cuiksamples2atoms.c File Reference

Detailed Description

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A tool to create files with atom coordinates from sample files. The pdb files typically include low reliable atom positions, i.e. atom positions that do not fullfill the rigid geometry hypothesis (each pair of atoms is at a different distance, and each bond angle is also different). Moreover, the PDB standard defines the atom positions wiht low accuracy (4 digits only). For these reasons, when defining worlds from PDB files using cuikpdb2world the atom positions can be taken from an .atoms file, if available. This applications generates this .atoms files from a world and a valid sample.

Moreover, the atom positions can be used to transfer samples from automatically generated worlds to user-defined ones, both describing the same molecule. The world generated with cuikpdb2world is the one that can be used, for instance, to evaluate energies since it is "syncronized" with a given PDB. The automatically generated world has reference frames for each link that can be different from those in the user-generated world. Thus, files with samples can not be direclty shared between the user and the generated worlds. However, we can generate the atom positions from the user-generated world (with cuiksamples2atoms) and then recover the sample for the automatically generated world (with cuikatoms2samples).

Note that this process reads sample or dof files according the parameters. Thus, this could be also called cuikdofs2atoms.

Definition in file cuiksamples2atoms.c.

Functions

int main (int argc, char **arg)
 Main body of the cuiksamples2atoms application. More...
 

Function Documentation

int main ( int  argc,
char **  arg 
)

Main body of the cuiksamples2atoms application.

A tool to create files with atom coordinates from sample files. The pdb files typically include low reliable atom positions, i.e. atom positions that do not fullfill the rigid geometry hypothesis (each pair of atoms is at a different distance, and each bond angle is also different). Moreover, the pdb standard defines the atom positions wiht low accuracy (4 digits only). For these reasons, when defining worlds from pdb files using cuikpdb2world the atom positions can be taken not from the pdb but from an .atoms file, if available. This applications generates this .atoms files from a world and a valid sample.

Moreover, the atom positions can be used to transfer samples from automatically generated worlds to user-defined ones, both describing the same molecule. The world generated with cuikpdb2world is the one that can be used, for instance, to evaluate energies since it is "syncronized" with a given PDB. The automatically generated world has reference frames for each link that can be different from those in the user-generated world. Thus, files with samples can not be direclty shared between the user and the generated worlds. However, we can generate the atom positions from the user-generated world (with cuiksamples2atoms) and then recover the sample for the automatically generated world (with cuikatoms2samples).

Note that this process reads sample or dof files according the parameters. Thus, this could be also called cuikdofs2atoms.

CAUTION: This only works for carefully defined worlds where the atoms are in the same order as in the PDB. This is NOT the case for automatically generated world (as those generated for protein loops).

Use:

  • cuiksamples2atoms problem_name out_name

where

  • problem_name is used to generate the input and output file names.
  • out_name [optional] The output atom file.

The extension are optional.

Parameters
argcNumber of elements in the command line that starts the application (i.e., the cuiksamples2atoms command itself and its arguments).
argStrings with the arguments.
Returns
EXIT_SUCCESS (0) if the execution worked out fine and EXIT_FAILURE if not.

Definition at line 111 of file cuiksamples2atoms.c.

References ATOM_EXT, CreateFileName(), CT_REPRESENTATION, DeleteFileName(), DeleteParameters(), DeleteWorld(), Error(), FALSE, GetFileFullName(), GetParameter(), GetWorldNumSystemVariables(), InitParametersFromFile(), InitWorldFromFile(), IsMechanismInWorldAllSpheres(), JOINTS_EXT, LINKS_EXT, NEW, PARAM_EXT, REP_JOINTS, TRUE, Warning(), and WorldPrintAtoms().