diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..a2bf2de --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +/.project +/.pydevproject diff --git a/.settings/.gitignore b/.settings/.gitignore new file mode 100644 index 0000000..b012ade --- /dev/null +++ b/.settings/.gitignore @@ -0,0 +1 @@ +/org.eclipse.core.resources.prefs diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..b033e5f --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,216 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = _build + +# User-friendly check for sphinx-build +ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) +$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) +endif + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . + +.PHONY: help +help: + @echo "Please use \`make ' where is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " applehelp to make an Apple Help Book" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " xml to make Docutils-native XML files" + @echo " pseudoxml to make pseudoxml-XML files for display purposes" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + @echo " coverage to run coverage check of the documentation (if enabled)" + +.PHONY: clean +clean: + rm -rf $(BUILDDIR)/* + +.PHONY: html +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +.PHONY: dirhtml +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +.PHONY: singlehtml +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." + +.PHONY: pickle +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +.PHONY: json +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +.PHONY: htmlhelp +htmlhelp: + $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + @echo + @echo "Build finished; now you can run HTML Help Workshop with the" \ + ".hhp project file in $(BUILDDIR)/htmlhelp." + +.PHONY: qthelp +qthelp: + $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp + @echo + @echo "Build finished; now you can run "qcollectiongenerator" with the" \ + ".qhcp project file in $(BUILDDIR)/qthelp, like this:" + @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/FESetup12.qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/FESetup12.qhc" + +.PHONY: applehelp +applehelp: + $(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp + @echo + @echo "Build finished. The help book is in $(BUILDDIR)/applehelp." + @echo "N.B. You won't be able to view it unless you put it in" \ + "~/Library/Documentation/Help or install it in your application" \ + "bundle." + +.PHONY: devhelp +devhelp: + $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp + @echo + @echo "Build finished." + @echo "To view the help file:" + @echo "# mkdir -p $$HOME/.local/share/devhelp/FESetup12" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/FESetup12" + @echo "# devhelp" + +.PHONY: epub +epub: + $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub + @echo + @echo "Build finished. The epub file is in $(BUILDDIR)/epub." + +.PHONY: latex +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make' in that directory to run these through (pdf)latex" \ + "(use \`make latexpdf' here to do that automatically)." + +.PHONY: latexpdf +latexpdf: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through pdflatex..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +.PHONY: latexpdfja +latexpdfja: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through platex and dvipdfmx..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +.PHONY: text +text: + $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text + @echo + @echo "Build finished. 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The message catalogs are in $(BUILDDIR)/locale." + +.PHONY: changes +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +.PHONY: linkcheck +linkcheck: + $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." + +.PHONY: doctest +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." + +.PHONY: coverage +coverage: + $(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage + @echo "Testing of coverage in the sources finished, look at the " \ + "results in $(BUILDDIR)/coverage/python.txt." + +.PHONY: xml +xml: + $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml + @echo + @echo "Build finished. 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these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +#sys.path.insert(0, os.path.abspath('.')) + +# -- General configuration ------------------------------------------------ + +# If your documentation needs a minimal Sphinx version, state it here. +#needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [ + 'sphinx.ext.autodoc', + 'sphinx.ext.doctest', + 'sphinx.ext.todo', +] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +# source_suffix = ['.rst', '.md'] +source_suffix = '.rst' + +# The encoding of source files. +#source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = u'FESetup1.2' +copyright = u'2018, Hannes Loeffler' +author = u'Hannes Loeffler' + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# +# The short X.Y version. +version = u'1.2' +# The full version, including alpha/beta/rc tags. +release = u'1.2.1' + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# +# This is also used if you do content translation via gettext catalogs. +# Usually you set "language" from the command line for these cases. +language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +#today = '' +# Else, today_fmt is used as the format for a strftime call. +#today_fmt = '%B %d, %Y' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = ['_build'] + +# The reST default role (used for this markup: `text`) to use for all +# documents. +#default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +#add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +#add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +#show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# A list of ignored prefixes for module index sorting. +#modindex_common_prefix = [] + +# If true, keep warnings as "system message" paragraphs in the built documents. +#keep_warnings = False + +# If true, `todo` and `todoList` produce output, else they produce nothing. +todo_include_todos = True + + +# -- Options for HTML output ---------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# html_theme = 'alabaster' (default) +html_theme = 'sphinx_rtd_theme' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +#html_theme_options = {} + +# Add any paths that contain custom themes here, relative to this directory. +#html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# " v documentation". +#html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +#html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +#html_logo = None + +# The name of an image file (relative to this directory) to use as a favicon of +# the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +#html_favicon = None + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + +# Add any extra paths that contain custom files (such as robots.txt or +# .htaccess) here, relative to this directory. These files are copied +# directly to the root of the documentation. +#html_extra_path = [] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +#html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +#html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +#html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +#html_additional_pages = {} + +# If false, no module index is generated. +#html_domain_indices = True + +# If false, no index is generated. +#html_use_index = True + +# If true, the index is split into individual pages for each letter. +#html_split_index = False + +# If true, links to the reST sources are added to the pages. +#html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +#html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +#html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +#html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +#html_file_suffix = None + +# Language to be used for generating the HTML full-text search index. +# Sphinx supports the following languages: +# 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja' +# 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr' +#html_search_language = 'en' + +# A dictionary with options for the search language support, empty by default. +# Now only 'ja' uses this config value +#html_search_options = {'type': 'default'} + +# The name of a javascript file (relative to the configuration directory) that +# implements a search results scorer. If empty, the default will be used. +#html_search_scorer = 'scorer.js' + +# Output file base name for HTML help builder. +htmlhelp_basename = 'FESetup12doc' + +# -- Options for LaTeX output --------------------------------------------- + +latex_elements = { +# The paper size ('letterpaper' or 'a4paper'). +#'papersize': 'letterpaper', + +# The font size ('10pt', '11pt' or '12pt'). +#'pointsize': '10pt', + +# Additional stuff for the LaTeX preamble. +#'preamble': '', + +# Latex figure (float) alignment +#'figure_align': 'htbp', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, +# author, documentclass [howto, manual, or own class]). +latex_documents = [ + (master_doc, 'FESetup12.tex', u'FESetup1.2 Documentation', + u'Hannes Loeffler', 'manual'), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +#latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +#latex_use_parts = False + +# If true, show page references after internal links. +#latex_show_pagerefs = False + +# If true, show URL addresses after external links. +#latex_show_urls = False + +# Documents to append as an appendix to all manuals. +#latex_appendices = [] + +# If false, no module index is generated. +#latex_domain_indices = True + + +# -- Options for manual page output --------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + (master_doc, 'fesetup12', u'FESetup1.2 Documentation', + [author], 1) +] + +# If true, show URL addresses after external links. +#man_show_urls = False + + +# -- Options for Texinfo output ------------------------------------------- + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + (master_doc, 'FESetup12', u'FESetup1.2 Documentation', + author, 'FESetup12', 'One line description of project.', + 'Miscellaneous'), +] + +# Documents to append as an appendix to all manuals. +#texinfo_appendices = [] + +# If false, no module index is generated. +#texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +#texinfo_show_urls = 'footnote' + +# If true, do not generate a @detailmenu in the "Top" node's menu. +#texinfo_no_detailmenu = False diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 0000000..1d1f4ca --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,25 @@ +.. FESetup1.2 documentation master file, created by + sphinx-quickstart on Wed May 9 13:51:48 2018. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to FESetup1.2's documentation! +====================================== + +Contents: + +.. toctree:: + :maxdepth: 2 + + introduction + installation + running-fesetup + input-options + +Indices and tables +================== + +.. * :ref:`genindex` +.. * :ref:`modindex` +.. * :ref:`search` + diff --git a/docs/input-options.rst b/docs/input-options.rst new file mode 100644 index 0000000..f0bdc02 --- /dev/null +++ b/docs/input-options.rst @@ -0,0 +1,216 @@ +============= +Input Options +============= + +---------------- +Full option list +---------------- + +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Options unique to each section +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +The following tables list all options unique to each section. Note that empty strings (denoted as 'none' in the table) means that the user has to use appropriate values. 'molecules' will be overwritten i.e. ignored when 'morph_pairs' are used in [ligand]. The default for complex building is to combine every protein with every ligand. If you do no want that, you must explicitly list all pairs using the 'pairs' key. Please note that your file and directory names must not contain the characters ':' (colon), '>' (right angle bracket), '"' (double quote) and '~' (tilde). The comma ',' is permited as long as the filename is enclosed in double quotes, e.g. + + morph_pairs = "1,2-dichloroethane" > E-dichloroethene, + E-dichloroethene > "1,2-dichloroethane" + +[globals] + ++-----------------------+---------------------+---------+-------------------------------+ +| Key | Values, default | Type | Explanation | +| | listed first | | | ++=======================+=====================+=========+===============================+ +| AFE.type | Sire, sander/dummy, | string | free energy type, determines | +| | sander/softcore, | | which MD package the input | +| | gromacs, | | files are created for (for | +| | pmemd/softcore, | | backwards compatability | +| | pmemd/dummy | | AMBER = sander/dummy and | +| | charmm/pert | | AMBER/softcore = | +| | | | sander/softcore) | ++-----------------------+---------------------+---------+-------------------------------+ +| AFE.separate_vdw_elec | True, False | bool | separate the Coulomb (charge) | +| | | | transformation from the | +| | | | vdW+bonded transformation | ++-----------------------+---------------------+---------+-------------------------------+ +| forcefield | amber, ff14SB, | list of | ff family, subtype of ff, | +| | tip3p, hfe | strings | water ff, divalent ion set | ++-----------------------+---------------------+---------+-------------------------------+ +| ff_addons | empty | list of | additional force fields like | +| | | strings | GLYCAM_06j-1 or lipid14 | ++-----------------------+---------------------+---------+-------------------------------+ +| gaff | gaff1, gaff2 | string | Choice for the small | +| | | | molecules forcefield, either | +| | | | GAFF 1.x or GAFF2.x | ++-----------------------+---------------------+---------+-------------------------------+ +| logfile | dGprep.log | string | name of the debug log file | ++-----------------------+---------------------+---------+-------------------------------+ +| mdengine | amber, sander; | list of | program for minimisation and | +| | amber,pmemd; | 2 | MD, the first in the list is | +| | gromacs, mdrun | strings | the MD package, the second is | +| | namd, namd2 | | the actual binary | ++-----------------------+---------------------+---------+-------------------------------+ +| mdengine.prefix | empty | string | the string preceding the | +| | | | mdengine binary command, | +| | | | e.g. mpirun -np 4 (for MPI | +| | | | programs) | ++-----------------------+---------------------+---------+-------------------------------+ +| mdengine.postfix | empty | string | the string following the | +| | | | mdengine binary command, | +| | | | e.g. +p2 +isomalloc_sync | +| | | | (for namd multicore) | ++-----------------------+---------------------+---------+-------------------------------+ +| parmchk_version | 2, 1 | integer | parmchk version | ++-----------------------+---------------------+---------+-------------------------------+ +| mcs.timeout | 60.0 | float | timeout in seconds for fmcs, | +| | | | 0 means no timeout | ++-----------------------+---------------------+---------+-------------------------------+ +| remake | False, True | bool | remake already done | +| | | | molecules (excluding morphs) | ++-----------------------+---------------------+---------+-------------------------------+ +| overwrite | False, True | bool | by default no files are ever | +| | | | overwritten in the _ | +| | | | directories, use this to | +| | | | change this behaviour | ++-----------------------+---------------------+---------+-------------------------------+ +| user_params | False, True | bool | read user force field | +| | | | parameter files, i.e. all | +| | | | .frmod, .preb and .lib (OFF | +| | | | format) files are read in | ++-----------------------+---------------------+---------+-------------------------------+ + +[ligand] + ++-------------------------+-----------------------+---------+------------------------------------------------------+ +| Key | Values, default | Type | Explanation | +| | listed first | | | ++=========================+=======================+=========+======================================================+ +| basedir | none, | string | base directory to find ligands | +| | must be set by user | | | ++-------------------------+-----------------------+---------+------------------------------------------------------+ +| file.name | ligand.pdb | string | ligand input file name | ++-------------------------+-----------------------+---------+------------------------------------------------------+ +| file.format | none, determined from | string | format of file.name, can be used to overwrite if | +| | extension of filename | | file extension is different from actual file format | ++-------------------------+-----------------------+---------+------------------------------------------------------+ +| ions.conc | 0.0 | float | sets the NaCl concentration in mol/l | ++-------------------------+-----------------------+---------+------------------------------------------------------+ +| ions.dens | 1.0 | float | density for which the ion concentration is wanted | ++-------------------------+-----------------------+---------+------------------------------------------------------+ +| calc_charge | False, True | bool | Force calculation of molecule's formal charge, | +| | | | required e.g. for mol2 format for which Openbabel | +| | | | computes the charge only in select cases. | ++-------------------------+-----------------------+---------+------------------------------------------------------+ +| conf_search.conj_econv | 1e-06 | float | conformation search option | ++-------------------------+-----------------------+---------+------------------------------------------------------+ +| conf_search.conj_steps | 250 | integer | conformation search option | ++-------------------------+-----------------------+---------+------------------------------------------------------+ +| conf_search.ffield | mmff94 | string | conformation search option | ++-------------------------+-----------------------+---------+------------------------------------------------------+ +| conf_search.geomsteps | 5 | integer | conformation search option | ++-------------------------+-----------------------+---------+------------------------------------------------------+ +| conf_search.numconf | 0 | integer | conformation search option | ++-------------------------+-----------------------+---------+------------------------------------------------------+ +| conf_search.steep_econv | 0.0001 | float | conformation search option | ++-------------------------+-----------------------+---------+------------------------------------------------------+ +| conf_search.steep_steps | 100 | integer | conformation search option | ++-------------------------+-----------------------+---------+------------------------------------------------------+ +| molecules | none, | list of | list of molecules | +| | must be set by user | strings | | ++-------------------------+-----------------------+---------+------------------------------------------------------+ +| morph.absolute | False, True | bool | write absolute transformation MORPH.pert | +| | | | files for Sire | ++-------------------------+-----------------------+---------+------------------------------------------------------+ +| morph_pairs | none, | list of | list of pairs in the form lig1 > lig2, overwrites | +| | must be set by user | strings | 'molecules', do not use '>' in file names | ++-------------------------+-----------------------+---------+------------------------------------------------------+ +| neutralize | False, True | bool | neutralize the solvation box by adding minimum | +| | | | couterions required | ++-------------------------+-----------------------+---------+------------------------------------------------------+ +| skip_param | False, True | bool | skip the parameterisation step, useful in | +| | | | conjunction with user_params or ff_addons | +| | | | see [globals] | ++-------------------------+-----------------------+---------+------------------------------------------------------+ + +[protein] + ++----------------------+--------------------------+---------+------------------------------------------------------+ +| Key | Values, default | Type | Explanation | +| | listed first | | | ++======================+==========================+=========+======================================================+ +| align_axes | False, True | bool | align protein along principal axes before hydrating | ++----------------------+--------------------------+---------+------------------------------------------------------+ +| basedir | none, | string | base directory to proteins | +| | must be set by user | | | ++----------------------+--------------------------+---------+------------------------------------------------------+ +| ions.conc | 0.0 | float | sets the NaCl concentration in mol/l | ++----------------------+--------------------------+---------+------------------------------------------------------+ +| ions.dens | 1.0 | float | density for which the ion concentration is wanted | ++----------------------+--------------------------+---------+------------------------------------------------------+ +| molecules | none, | list of | list of molecules | +| | must be set by user | strings | | ++----------------------+--------------------------+---------+------------------------------------------------------+ +| neutralize | False, True | bool | neutralize the solvation box by adding minimum | +| | | | couterions required | ++----------------------+--------------------------+---------+------------------------------------------------------+ +| propka | False, True | bool | use ProPKA to protonate protein | ++----------------------+--------------------------+---------+------------------------------------------------------+ +| propka.pH | 7.0 | float | pH for ProPKA | ++----------------------+--------------------------+---------+------------------------------------------------------+ + +[complex] + ++----------------------+--------------------------+---------+------------------------------------------------------+ +| Key | Values, default | Type | Explanation | +| | listed first | | | ++======================+==========================+=========+======================================================+ +| align_axes | False, True | bool | align protein along principal axes before hydrating | ++----------------------+--------------------------+---------+------------------------------------------------------+ +| ions.conc | 0.0 | float | sets the NaCl concentration in mol/l | ++----------------------+--------------------------+---------+------------------------------------------------------+ +| ions.dens | 1.0 | float | density for which the ion concentration is wanted | ++----------------------+--------------------------+---------+------------------------------------------------------+ +| neutralize | False, True | bool | neutralize the solvation box by adding minimum | +| | | | couterions required | ++----------------------+--------------------------+---------+------------------------------------------------------+ +| flatten_rings | False, True | bool | make aromatic rings fully planar, for MC with Sire | ++----------------------+--------------------------+---------+------------------------------------------------------+ +| pairs | none, must be set by | list of | list of pairs in the form protein:ligand, do not use | +| | user | strings | ':' in file names | ++----------------------+--------------------------+---------+------------------------------------------------------+ + +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +The minimisation and MD options +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +The following options are the minimsation and MD options for molecule setup common to ligands, proteins and complexes. To allow minimisation and MD 'box.type' has to be set explicilty which also creates a water box. If 'box.type' is not set by the user then no box will be created and minimisation or MD will not be carried out. To actually run a minimsation or simulation you will need to set any of the '.nsteps' keys to a value larger than 0. The only difference is relaxation where setting 'md.relax.nrestr' to a value larger than 0 will trigger restraint relaxation. The order of simulation protocols is fixed as heating (md.heat.*), constant volume and temperature (md.constT.*), pressurising = density adjustment (md.press.*), relaxation at NpT conditions (md.relax.*). If any of those steps are not needed set '.nsteps' to 0 but be aware that there are no further sanity checks. The MD protocol can be preceded by a minimisation step (min.*). + + ++-----------------+------------------------------+---------+--------------------------------------------------------+ +| Key | Values, default listed first | Type | Explanation | ++=================+==============================+=========+========================================================+ +| box.type | empty string = no box | string | creates a box of water | +| | created, rectangular, | | | +| | octahedron (limited support) | | | ++-----------------+------------------------------+---------+--------------------------------------------------------+ +| box.length | 10.0 | float | the distance in Ångström between solute and the box | +| | | | edges, NOTE: the TIP3P box will create a system of low | +| | | | density and thus this distance will decrease on | +| | | | pressuring the sytem. | ++-----------------+------------------------------+---------+--------------------------------------------------------+ +| min.ncyc | 0 | integer | number of steepest decent steps in minimisation | ++-----------------+------------------------------+---------+--------------------------------------------------------+ +| .nsteps | 0 | integer | number of steps; e.g. min.nsteps | ++-----------------+------------------------------+---------+--------------------------------------------------------+ +| .restr_force | 10.0 | float | restraint force; e.g. md.heat.restr_force | ++-----------------+------------------------------+---------+--------------------------------------------------------+ +| .restraint | protein, backbone, heavy, | string | restraint type, if other string then in the list it is | +| | notligand, notsolvent | | the restraintmask for sander; e.g. md.constT.restraint | ++-----------------+------------------------------+---------+--------------------------------------------------------+ +| .T | 300.0 | float | temperature; e.g. md.press.T | ++-----------------+------------------------------+---------+--------------------------------------------------------+ +| .p | 1.0 | float | pressure; e.g. md.relax.p | ++-----------------+------------------------------+---------+--------------------------------------------------------+ +| md.relax.nrestr | 0 | integer | number of relaxation steps, needed to trigger | +| | | | restraint relaxation | ++-----------------+------------------------------+---------+--------------------------------------------------------+ diff --git a/docs/installation.rst b/docs/installation.rst new file mode 100644 index 0000000..6e53c75 --- /dev/null +++ b/docs/installation.rst @@ -0,0 +1,36 @@ +============ +Installation +============ + +Linux, Intel 32bit and 64bit + + Run the installer package from www.ccpbiosim.ac.uk/software in a convenient location (N will stand for the release you have downloaded). You can run the installer with "--help" to see further options. Here we describe interactive installation i.e. when run without any command line options. The installer requires the xz compression tool to be installed on your system. + + > cd /where/I/want/it # replace the path to whatever you like + > ./FESetupN_Linux.sh # extract all files into FESetupN/ + + The installer will automatically detect which version to extract (either 32 or 64 bit). You will be asked to provide paths to AMBER, GROMACS, NAMD and DL_POLY. It is strongly recommended to choose 'N' (the default, so just press Enter) when the first question suggests to use your existing $AMBERHOME. Choose the internal path as suggested in the following question to avoid modifications to the original AmberTools installation. Press Enter to accept defaults or to set an empty path if you do not have a certain MD package. You will also be asked for a Python 2.7 interpreter (the default is "python", assumed to be located in the $PATH but read the note below). You will find the FESetup script in ./FESetupN/FesetupMM/bin after successful installation (MM is either 32 or 64 depending on your hardware). + Check that FESetup is working. You can do this by running the test set from our first tutorial or just run the FESetup script without any command line parameters. This will write the default input parameters to your terminal. + You can copy/link the FESetup script to your PATH e.g. /usr/local/bin if you like, or create an alias to point to the script. + +Our packages are self-contained and come with all relevant tools from AmberTools 16 including sander (pmemd still requires a full AMBER license). To carry out standard MD simulations, in particular equilibration of your system, the abstract MD engine supports AMBER (both sander and pmemd), NAMD, GROMACS and DL_POLY. Please note that currently we do not directly support NAMD's alchemical free energy methods though there is support for dual topology runs with AMBER inputs in NAMD (an additional PDB file is required to mark appearing/vanishing atoms, see NAMD manual). Standard MD is supported for NAMD though. + +Also note that you should use the standard Python interpreter (e.g. the one that comes as a package with your OS distribution or you download and compile from python.org). Python versions that come with a package management systems of their own may break the assumptions that our installer makes with regards to shared libraries. Specifially, anaconda appears to mess with the library search path and seems to disregard the setup in the FESetup script. + +------------ +Dependencies +------------ + +FESetup depends on various third-party software. All of these are included in the installer package. Here a list of dependencies for those who want to compile everything +themselves. Not listed are some dependencies which can be installed through the operating sytem's package management software. Some secondary dependencies are listed too. +Debian based systems have most libraries, toolkits and tools pre-compiled and ready to install through their package managment system. + +Python 2.7 + +Sire/corelib 0.0.1, Sire/Python2 0.0.1: Qt4, Boost, GSL, BLAS/LAPACK, pcre3 + +Ambertools 16 + +OpenBabel 2.3.x: eigen, swig, xml2 + +RDKit 2016: numpy, Boost diff --git a/docs/introduction.rst b/docs/introduction.rst new file mode 100644 index 0000000..4ab8995 --- /dev/null +++ b/docs/introduction.rst @@ -0,0 +1,70 @@ +============ +Introduction +============ + +FESetup automates the setup of relative alchemical free energy (AFE) simulations such as thermodynamic integration (TI) and free energy perturbation (FEP). Post–processing methods like MM–PBSA and LIE are supported as well. FESetup can also be used for general simulation setup ("equilibration") through an abstract MD engine (currently supported MD engines are AMBER, GROMACS, NAMD and DL_POLY). For relative AFE simulation the mapping of corresponding atoms between the two free energy states, that is their topological similarity, is computed via a maximum common substructure search (MCSS). This enables a maximal single topology description of the perturbed molecule pair. Ligand molecules can automatically be parameterised using the AMBER GAFF/AM1-BCC method. Supported force fields for biomolecules are all the modern AMBER force fields. + +The AFE simulation packages that are currently supported are Sire, AMBER, GROMACS and CHARMM/PERT. All these codes implement AFE simulation by making use of a hybrid single/dual topology description of the perturbed region i.e. the mapped region (single topology) can be used simultaneously with an un–mapped, duplicated region (dual topology) from each state. There is also some support for NAMD's purely dual topology implementation but this requires an additional PDB file to mark appearing/vanishing atoms and possibly relative restraints to keep ligands spatially in place and/or together. + +FESetup particularly aims at automation where it makes sense and is possible, ease of use and robustness of the code. Users are very welcome to discuss on our forum, report issues and request new features. The software is licensed under the GPL2 and such is a community effort: user contributions in any form are highly encouraged! + +The basis of the current code was a collection of Python and shell scripts written previously by Julien Michel and Christopher Woods. The FESetup1.2 code base was mainly developed by Hannes Loeffler (STFC) with contributions from the original developers. + +Please cite DOI: 10.1021/acs.jcim.5b00368 when you use FESetup. + +---------------------------- +Capabilities and Description +---------------------------- + +The sections here give a brief overview of FESetup from a general point of view i.e. topics like background information, concepts, implementation ideas and philosophies, etc. but also the limits of the current software. + +------- +General +------- + +FESetup is currently (July 2017) mainly geared at automated setup for receptor-ligand simulations. But in principle any biomolecular system can be set up for simulation provided the system is supported by the force field (AMBER and AMBER/GAFF) and the ligand is not covalently bound and can reasonably be parameterised with AM1/BCC. The latter implies that the ligand is a relatively "small" organic molecule as typically considered in the drug development process. + +Core functionality of FESetup are the parameterisation of (possibly large numbers of) ligands and the "morphing" of a pair of ligands. Morphing describes how a molecule's force field parameters are transformed (or "perturbed") into a set of parameters descriptive for a second, topological related molecule. As such FESetup is a perturbed topology creator. Ligand parameterisation enables standard MD simulation including post-processing methods like MM-PBSA for simplified free energy estimates. The topology file describing the morphing of the ligand pair enables alchemical free energy simulation like Thermodynamic Integration (TI) or Free Energy Perturbation (FEP, also called EXP for exponential formula). Currently, FESetup supports such simulation setups for Sire, AMBER, Gromacs and the PERT module in CHARMM. In the case of AMBER the dual topology softcore approach as well as the older explicit dummy atom approach, as implemented in both sander and pmemd, are supported. + +FESetup reads a series of coordinates for ligands and proteins. The ligands can then be parameterised with the AM1/BCC method and can be combined with a protein (or other molecule supported by the AMBER force fields or with user supplied parameters) into a complex. This requires the complex to be set up properly beforehand, e.g. the complex may have been created via a previous docking run or by any other suitable method. Protein and ligand coordinates must be supplied separately. While the protein is expected in PDB format the ligand can be in any format supported by OpenBabel (but must have 3D coordinates). A caveat though is that OpenBabel does not read total charge information from all file formats that support this and thus the most suitable formats are either PDB or SDF for the ligand if a charge other than zero is needed. Internally the coordinates will be converted to the mol2 format. If morph pairs are requested, FESetup will compute the "difference" between the two ligand molecules using a maximum common substructure search (MCSS) algorithm (from RDKit) as a distance metric and use this information to create appropriate topology files and control files for alchemical free energy simulation. + +---------- +MD engines +---------- + +FESetup makes use of an abstract MD engine, currently for the purpose of "equilibration" of simulation systems. This means that various popular MD simulation software packages (at the moment: AMBER, DL_POLY, NAMD and GROMACS) can be used in a transparent fashion, that is without the need to know the specific control and command structures of a particular simulation software. This is, of course, somewhat limited by MD software not always providing fully equivalent features as in other software packages. But for the general purpose of carrying out setup processes like minimization, heating, pressurizing, restraint release, etc. this is sufficient and sensible starting structures for production MD simulation can be obtained without problems. + +The MD engine mechanism allows the user to choose the specific binary (program) to be used for MD/minimisation, e.g. with AMBER that could be any variant of sander or pmemd, with GROMACS any variant of mdrun, etc. Parallel versions are supported to a certain extent too as described in the following. Multi-threaded binaries like mdrun with thread-MPI or the multi-core version of NAMD will run on any single machine or "node". MPI versions like the AMBER binaries do also work but currently there is no support for job schedulers like PBS, LSF, etc. + +Some of the limitations of abstraction are that software like GROMACS or NAMD appear to always need a minimization step of a solvated system prior to MD whereas AMBER is less sensitive to this. FESetup currently includes standard input configuration settings for minimization, random velocity assignment, heating, constant T and pressurizing. For all these, restraints can be defined by either keyword or an AMBER mask. All corresponding run-time control parameters are created through templates and each of these steps is carried out as an individual simulation run. This is also done for NAMD despite it having full scripting capabilities of its own. However, the abstract interface hides the details of the actual MD engine away and thus is much easier to use. In addition, the interface is unified i.e. it appears the same independent of the MD engine chosen. AMBER and GROMACS do no have built-in scripting facilities and thus the separate steps are needed especially the step-wise release of restraints. + +---------------------------------- +Maximum Common Substructure Search +---------------------------------- + +Morph pairs are generated through a graph based maximum common substructure search (MCSS) algorithm, in particular the implementation in RDKit. By comparing the graphs of two ligands the maximum match between their atoms, based on the topology i.e. connectivity, are found. Currently we do not distinguish between atom types or bond types, i.e. the graph is unlabeled. Rings, on the other hand, are required to match other rings and cannot be broken. All atoms not part of the MCS mapping (equivalent atoms between the two ligands are recorded), are considered to be dummy atoms and coordinates are created accordingly from internal coordinates (this is not needed in the AMBER dual topology softcore apprach). + +There are, however, a few caveats to keep in mind. First, the comparison is carried out in graph space which is essentially only two dimensional. Thus 3D features are not retained unless otherwise specified. This includes the substitution patterns of stereogenic centres, e.g. the absolute configuration can be reverted with the scheme described above. Symmetry related issues, e.g. molecules may have multiple MCSs but a "random" one is assigned to a given morph pair, may appear too. Retaining specific binding modes is another problem which may be caused by symmetry but other origins, e.g. flipping by 180 degrees or parts of a molecules preferring another binding pocket when decorated differently, are possible too. FESetup allows the user to provide explicit atom tagging of individual atoms to overcome these problems albeit at the expense of automation. Tagging however allows the user to overwrite the default behaviour of FESetup and can thus guide the mapping to their own preferences. + +Second, the time behaviour of MCSS algorithms may pose problems. In the worst case a search would be exponential in time due to the need of an exhaustive search (in practice, the MCSS algorithms have clever shortcuts but there is no universal algorithm available because NP-complete) which implies that for every additional atom the search time would be doubled. We have found several examples where the MCS search can range from many minutes to hours to days (in a very large system of a molecular weight of nearly 1500 with the old Python implementation of fmcs). In practice, however, the MCS appears to be found within just a minute or so (more careful testing needed) and we have not found any problem cases yet where the MCS would not be as expected from visual inspection. FESetup provides a setting to limit the time spend on the MCS search. + +---------------- +Adding hydrogens +---------------- + +This is a particular serious matter and attitudes among researchers vary. We strongly recommend that the user makes sure that hydrogens are added to the ligand and protonation state as well as tautomeric state are fully determined before FESetup is run. It is the user's responsibility to get the chemistry right. + +In principle, there is a setting in FESetup to allow addition of hydrogens in a simple valence filling fashion. But we have found that this does not always work properly with OpenBabel, e.g. the N9 (binding to the ribose) in nucleosides appears to be always perceived as being located within a double-bonded or aromatic ring. This results in addition of a hydrogen and a charge of +1 on N9. However, charge parameterisation is achieved through sqm, a semi-empirical tool in the AmberTools, which crucially depends on having the charge properly assigned, or otherwise may terminate with an error or compute grossly wrong results. + +Finding protonation and tautomeric states is even much more difficult because they depend strongly on the environment. There is currently no support for assignment of such states in FESetup. Any future work in this direction will have to await very thorough investigations into what is possible and what not. + +----------------------- +Charge parameterisation +----------------------- + +The parameterisation steps in FESetup currently carries out charge calculation for the AMBER/GAFF force field at the AM1/BCC level with the help of the AmberTools toolchain antechamber. This method derives Mulliken charges at the semiempirical AM1 level of theory (via sqm) and then applies bond charge corrections (BCC) to these Mulliken charges to finally obtain charges almost equivalent to the higher level HF 6-31G* RESP charge derivation scheme. A subsequent run through parmchk(2) will assign missing bonded parameters through a similarity search in the first attempt or, if this cannot be achieved, an empirical approach is followed. If both methods fail the correpsonding force field parameters will be set to zero. This is actually exploited in the case of the dummy atoms as the corresponding atom type does not have an equivalent in the data base (the code relies on zero force field parameters for identifying dummy atoms at various places). Lennard-Jones parameters and mixing rules will be applied as per the initial perception of GAFF atom types (atomtype and bondtype tools). + +There are a few notable limitations. Sqm carries out geometry minimizations in vacuum. This can lead to distorted structures when highly charged groups are present, e.g. zwitterions. We have also found proton "shifts" between the two ends of a molecule and "decarboxylation", both in very rare cases. FESetup provides a (undocumented) option to carry out geometry minimizations with the help of an implicit solvent model (through the QM/MM feature in sander without an actual MM part). But we did not really find an improvement for the aforementioned problems except for more stable SCF convergence and a smoother geometry optimisation. + +Larger molecules should probably be considered to be broken into sensible smaller fragments similar to how the biomolecules force field has been parameterised. This is beyond the scope of FESetup currently, however. More elaborate schemes, on the other hand. like the original RESP method or possibly specialised software like R.E.D. may be incorporated in the future. + diff --git a/docs/running-fesetup.rst b/docs/running-fesetup.rst new file mode 100644 index 0000000..9acbee0 --- /dev/null +++ b/docs/running-fesetup.rst @@ -0,0 +1,94 @@ +=============== +Running FESetup +=============== + +The script FESetup in the release is the command line tool for the end-user. This shell script sets a few environment variables and eventually calls dGprep.py. dGprep.py is the actually code running the routines for AFE setup. + +Note: this manual describes options used as of Release 1.2. + +------------ +Command line +------------ + +Default values for all key–value pairs are written to stdout for each of the four sections when FESetup is called without any command-line parameters. Calling FESetup with '--help' gives information of all possible command line parameters. Currently all options are for information purposes only so will not affect the setup in any way. The option --tracebacklimit is really only of use for debugging. As noted above FESetup is the front-end script to the Python code dGprep.py. :: + + > FESetup --help + + usage: dGprep.py [-h] [-v] [--tracebacklimit N] [infile] + + positional arguments: + infile input file in INI format, if not given then just output defaults + + optional arguments: + -h, --help show this help message and exit + -v, --version full version information + --tracebacklimit N set the Python traceback limit (for debugging) + +------------ +Input format +------------ + +The input file format for the FESetup script (dGprep.py) is an INI like format, popular in the MS-DOS/Windows world. It is not exactly the same format but a simplified version of it. + +The input file may contain four sections where the section names are delimited with brackets: + +The four sections of the INI file + +#. [globals] global settings, the section name is optional if it is the first section in the file + +#. [ligand] settings for the ligand + +#. [protein] settings for the protein + +#. [complex] settings for the complex + + +Each section consists of various key-value pairs which are two strings separated with an equal sign ("="). The key must not contain any whitespace.:: + + # a typical key-value pair + morph_pairs = p-aminophenol > o-cresol + +Lines may be continued with an initial whitespace (normal space, TAB) on the following line:: + + # multiple continuation lines + morph_pairs = ethane > methanol, ethane > tbutane, ethane > propane, + tbutane > propane, tbutane > acetone, + propane > acetone, propane > methane + +However, list pairs must always appear on the same line because each line is parsed individually. So the following will cause an error:: + + # this will result in an error + morph_pairs = ethane > methanol, ethane > tbutane, ethane > + propane, # the string "propane" must appear in the previous line! + + +Comments are either empty lines or lines starting with '#' or ';' (leading whitespace is removed). Inline comments are allowed too provided the comment character is preceded by a space. Otherwise the string is part of the preceding string, e.g:: + + basedir = smallmols # this is an inline comment + basedir = smallmol#foo # the valid string and directory name 'smallmol#foo' + +-------------------------- +Explicit tagging mechanism +-------------------------- + +In some cases it may be necessary to explicitly map certain atoms to one another e.g. to preserve a certain spatial rearrangment as for binding modes. This means that the default mapping algorithm (maximum common substructure search, MCSS) can be given additional hints. In the following example the benzofuran is oriented in the way outlined by forcing a certain mapping. As should be evident there are twelve ways of mapping the two molecules but if e.g. the binding mode is known a prior the user has here a chance to preserve it!:: + + [ligand] + basedir = smallmols + morph_pairs = benzol > benzofuran /1=3/2=2 # indices start from 1 + +An alternative mechanism is to create a special file in basedir (as set in the [ligand] section). The name of the file must be in the form ligand1~ligand2.map, e.g. if the input reads:: + + [ligand] + basedir = smallmols + morph_pairs = benzol > benzofuran + +then the map file must be in smallmols i.e. smallmols/benzol~benzofuran.map . + +The map file has a two column format indicating which atom index in the initial state maps to which atom index in the final state. Atom indexes start from 1:: + + # example mapping file benzol~benzofuran.map in the basedir smallmols/ + # explicitly map the following atom indexes onto each other + 1 3 # this mapping and... + 2 2 # ...this one will fix the orientation of benzofuran in space + diff --git a/docs/temp-theme.css b/docs/temp-theme.css new file mode 100644 index 0000000..7be9339 --- /dev/null +++ b/docs/temp-theme.css @@ -0,0 +1,5 @@ +*{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box}article,aside,details,figcaption,figure,footer,header,hgroup,nav,section{display:block}audio,canvas,video{display:inline-block;*display:inline;*zoom:1}audio:not([controls]){display:none}[hidden]{display:none}*{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box}html{font-size:100%;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%}body{margin:0}a:hover,a:active{outline:0}abbr[title]{border-bottom:1px 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