# SOME DESCRIPTIVE TITLE.
# Copyright (C) 2018, UIBCDF Lab at the Mexico City Childrens Hospital
# Federico Gomez and authors
# This file is distributed under the same license as the MolSysMT package.
# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
#
#, fuzzy
msgid ""
msgstr ""
"Project-Id-Version: MolSysMT \n"
"Report-Msgid-Bugs-To: \n"
"POT-Creation-Date: 2019-10-16 15:55-0500\n"
"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
"Language-Team: LANGUAGE <LL@li.org>\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=utf-8\n"
"Content-Transfer-Encoding: 8bit\n"
"Generated-By: Babel 2.7.0\n"

#: ../api/_autosummary/molsysmt.add_missing_hydrogens.rst:2
msgid "molsysmt.add\\_missing\\_hydrogens"
msgstr ""

#: molsysmt.add_missing_hydrogens:2 of
msgid ""
"The missing hydrogens of a molecular model are added. This method does "
"not remove any hydrogen already present."
msgstr ""

#: molsysmt.add_missing_hydrogens:5 of
msgid ""
"Regarding the protonation states of the aminoacids the documentation "
"corresponding to the chosen engine should be checked for further details."
msgstr ""

#: molsysmt.add_missing_hydrogens:8 of
msgid ""
"OpenMM: The protonation state is determined according the frequency of "
"the variant at the specified pH, and the participation of Cysteines in "
"disulfide bonds or Histidines in hydrogen bonds. This engine needs the "
"specification of a forcefield. See the `OpenMM User Manual "
"<http://docs.openmm.org/7.0.0/userguide/application.html#adding-"
"hydrogens>`_ or the `OpenMM Api Guide <http://docs.openmm.org/development"
"/api-"
"python/generated/simtk.openmm.app.modeller.Modeller.html#simtk.openmm.app.modeller.Modeller.addHydrogens>`_."
msgstr ""

#: molsysmt.add_missing_hydrogens:10 of
msgid ""
"PDBFixer: The protonation state is determined according to the frequency "
"of the variant at the specified pH. See the `PDBFixer Manual "
"<http://htmlpreview.github.io/?https://raw.github.com/pandegroup/pdbfixer/master/Manual.html>`_."
msgstr ""

#: molsysmt.add_missing_hydrogens of
msgid "Parameters"
msgstr ""

#: molsysmt.add_missing_hydrogens:15 of
msgid "**item: Molecular model in accepted form.**"
msgstr ""

#: molsysmt.add_missing_hydrogens:15 of
msgid "Molecular model in any of the accepted forms by MolSysMT."
msgstr ""

#: molsysmt.add_missing_hydrogens:18 of
msgid "**pH: float, default: 7.4**"
msgstr ""

#: molsysmt.add_missing_hydrogens:18 of
msgid "The pH based on which to determine the aminoacids protonation states."
msgstr ""

#: molsysmt.add_missing_hydrogens:21 of
msgid "**forcefield: str, default: 'AMBER99SB-ILDN'**"
msgstr ""

#: molsysmt.add_missing_hydrogens:21 of
msgid ""
"Name of the forcefield to be used by OpenMM ([check the list of names "
"accepted here]())"
msgstr ""

#: molsysmt.add_missing_hydrogens:30 of
msgid "**engine: str ('OpenMM' or 'PDBFixer'), default: 'OpenMM'**"
msgstr ""

#: molsysmt.add_missing_hydrogens:30 of
msgid ""
"Name of the engine used to add the missing hydrogens. The following "
"options are available:"
msgstr ""

#: molsysmt.add_missing_hydrogens:25 of
msgid ""
"'OpenMM': The method openmm.app.modeller.Modeller.addHydrogens is "
"included in the workflow. See the `OpenMM User Manual "
"<http://docs.openmm.org/7.0.0/userguide/application.html#adding-"
"hydrogens>`_ or the `OpenMM Api Guide <http://docs.openmm.org/development"
"/api-"
"python/generated/simtk.openmm.app.modeller.Modeller.html#simtk.openmm.app.modeller.Modeller.addHydrogens>`_."
msgstr ""

#: molsysmt.add_missing_hydrogens:30 of
msgid ""
"'PDBFixer': The method pdbfixer.PDBFixer.addMissingHydrogens() is "
"included in the workflow. See the `PDBFixer Manual "
"<http://htmlpreview.github.io/?https://raw.github.com/pandegroup/pdbfixer/master/Manual.html>`_."
msgstr ""

#: molsysmt.add_missing_hydrogens:33 of
msgid "**verbose: bool, default: False**"
msgstr ""

#: molsysmt.add_missing_hydrogens:33 of
msgid "The method prints out useful information if verbose=`True`."
msgstr ""

#: molsysmt.add_missing_hydrogens of
msgid "Returns"
msgstr ""

#: molsysmt.add_missing_hydrogens:51 of
msgid "**item** : Molecular model in the same form as input `item`."
msgstr ""

#: molsysmt.add_missing_hydrogens:38 of
msgid ""
"A new molecular model with the missing hydrogens added is returned. The "
"form will be the same as the input model."
msgstr ""

