Révision 0969983f docs/source/inp_ref_manual.rst
| b/docs/source/inp_ref_manual.rst | ||
|---|---|---|
| 7 | 7 |
``dockonsurf/examples/dockonsurf.inp``. |
| 8 | 8 |
|
| 9 | 9 |
Keywords must be specified under one of the four existing |
| 10 |
sections: ``Global``, ``Isolated``, ``Screening`` and ``Refinement``, the last
|
|
| 11 |
three corresponding to the stages DockOnSurf consist on. Keywords can be
|
|
| 12 |
classified in three categories: |
|
| 10 |
sections: :ref:`global`, :ref:`isolated`, :ref:`screening` and :ref:`refinement`
|
|
| 11 |
, the last three corresponding to the stages DockOnSurf consist on. Keywords can
|
|
| 12 |
beclassified in three categories:
|
|
| 13 | 13 |
|
| 14 | 14 |
* *mandatory*, for which its value must always be provided (eg. **run_type**) |
| 15 | 15 |
* *keyword-dependent*, for which specification is only mandatory depending on |
| ... | ... | |
| 29 | 29 |
elements around parentheses-like characters: "()", "[]" or "{}". (eg. "(a1,
|
| 30 | 30 |
a2,a3) [b1 b2 b3] {c1;c2; c3}").
|
| 31 | 31 |
|
| 32 |
.. _global: |
|
| 33 |
|
|
| 32 | 34 |
Global |
| 33 | 35 |
^^^^^^ |
| 34 | 36 |
Parameters in this section have an effect on the entire DockOnSurf execution. |
| ... | ... | |
| 83 | 85 |
| Mandatory if *batch_q_sys* is not set to "False". |
| 84 | 86 |
| Accepted values: The name/path of the file. |
| 85 | 87 |
|
| 88 |
.. _isolated: |
|
| 89 |
|
|
| 86 | 90 |
Isolated |
| 87 | 91 |
^^^^^^^^ |
| 88 | 92 |
Parameters in this section have an effect on the Isolated stage. |
| ... | ... | |
| 106 | 110 |
unreasonable geometries. |
| 107 | 111 |
| Accepted values: "MMFF", "UFF" or "False". Default value: MMFF |
| 108 | 112 |
|
| 113 |
.. _screening: |
|
| 114 |
|
|
| 109 | 115 |
Screening |
| 110 | 116 |
^^^^^^^^^ |
| 111 | 117 |
Parameters in this section have an effect on the Screening stage. |
| ... | ... | |
| 239 | 245 |
| Accepted values: The name/path of the file. |
| 240 | 246 |
|
| 241 | 247 |
| **select_magns** (*mandatory*): Which magnitudes/quantities should be used to |
| 242 |
select the conformers generated at the ``Isolated`` stage.
|
|
| 248 |
select the conformers generated at the :ref:`isolated` stage.
|
|
| 243 | 249 |
| Accepted values: "energy" or "MOI". |
| 244 | 250 |
|
| 245 | 251 |
| **set_angles** (*mandatory*): Which set of angles must be used to perform the |
| ... | ... | |
| 284 | 290 |
| Accepted values: a three-dimensional vector (eg. "(1, -2, 4)"), "x", "y", "z", |
| 285 | 291 |
"-x", "-y", "-z" or "auto". Default value: auto. |
| 286 | 292 |
|
| 287 |
| **use_molec_file** (*optional*): Instead of carrying out the ``Screening``
|
|
| 288 |
stage using the molecules obtained in ``Isolated``. It uses a single conformer
|
|
| 289 |
provided with a coordinates file. |
|
| 293 |
| **use_molec_file** (*optional*): Instead of carrying out the :ref:`screening`
|
|
| 294 |
stage using the molecules obtained in :ref:`isolated`. It uses a single
|
|
| 295 |
conformer provided with a coordinates file.
|
|
| 290 | 296 |
| Accepted values: The name/path of the file. Default value: False. |
| 291 | 297 |
|
| 298 |
.. _refinement: |
|
| 299 |
|
|
| 292 | 300 |
Refinement |
| 293 | 301 |
^^^^^^^^^^ |
| 294 | 302 |
Parameters in this section have an effect on the Refinement stage. |
Formats disponibles : Unified diff