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Unverified Commit 8dd60914 authored by Tristan Croll's avatar Tristan Croll Committed by GitHub
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Merge pull request #3 from openmm/master 

Sync with official repo
parents 3475b790 75c1fcb6
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wrappers/python/simtk/openmm/app/simulation.py
View file @ 8dd60914
......@@ -196,10 +196,11 @@ class Simulation(object):
while stepsToGo > 10:
self.integrator.step(10) # Only take 10 steps at a time, to give Python more chances to respond to a control-c.
stepsToGo -= 10
self.currentStep += 10
if endTime is not None and datetime.now() >= endTime:
return
self.integrator.step(stepsToGo)
self.currentStep += nextSteps
self.currentStep += stepsToGo
if anyReport:
# One or more reporters are ready to generate reports. Organize them into three
# groups: ones that want wrapped positions, ones that want unwrapped positions,
......
wrappers/python/simtk/unit/unit_definitions.py
View file @ 8dd60914
......@@ -237,6 +237,8 @@ joules = joule = Unit({joule_base_unit: 1.0})
define_prefixed_units(joule_base_unit, module = sys.modules[__name__])
erg_base_unit = ScaledUnit(1.0, dyne * centimeter, "erg", "erg")
erg = ergs = Unit({erg_base_unit: 1.0})
hartree_base_unit = ScaledUnit(4.3597447222071e-18, joule, "hartree", "Ha")
hartree = hartrees = Unit({hartree_base_unit: 1.0})
# In molecular simulations, "kilojoules" are in microscopic units
# And you really only want to use kilojoules/mole.
......
wrappers/python/src/swig_doxygen/doxygen/Doxyfile deleted 100644 → 0
View file @ 3475b790
# Doxyfile 1.5.9
# This file describes the settings to be used by the documentation system
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SHORT_NAMES = NO
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IMAGE_PATH =
# The INPUT_FILTER tag can be used to specify a program that doxygen should
# invoke to filter for each input file. Doxygen will invoke the filter program
# by executing (via popen()) the command <filter> <input-file>, where <filter>
# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
# input file. Doxygen will then use the output that the filter program writes
# to standard output.
# If FILTER_PATTERNS is specified, this tag will be
# ignored.
INPUT_FILTER =
# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
# basis.
# Doxygen will compare the file name with each pattern and apply the
# filter if there is a match.
# The filters are a list of the form:
# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER
# is applied to all files.
FILTER_PATTERNS =
# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
# INPUT_FILTER) will be used to filter the input files when producing source
# files to browse (i.e. when SOURCE_BROWSER is set to YES).
FILTER_SOURCE_FILES = NO
#---------------------------------------------------------------------------
# configuration options related to source browsing
#---------------------------------------------------------------------------
# If the SOURCE_BROWSER tag is set to YES then a list of source files will
# be generated. Documented entities will be cross-referenced with these sources.
# Note: To get rid of all source code in the generated output, make sure also
# VERBATIM_HEADERS is set to NO.
SOURCE_BROWSER = NO
# Setting the INLINE_SOURCES tag to YES will include the body
# of functions and classes directly in the documentation.
INLINE_SOURCES = NO
# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
# doxygen to hide any special comment blocks from generated source code
# fragments. Normal C and C++ comments will always remain visible.
STRIP_CODE_COMMENTS = YES
# If the REFERENCED_BY_RELATION tag is set to YES
# then for each documented function all documented
# functions referencing it will be listed.
REFERENCED_BY_RELATION = NO
# If the REFERENCES_RELATION tag is set to YES
# then for each documented function all documented entities
# called/used by that function will be listed.
REFERENCES_RELATION = NO
# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
# link to the source code.
# Otherwise they will link to the documentation.
REFERENCES_LINK_SOURCE = YES
# If the USE_HTAGS tag is set to YES then the references to source code
# will point to the HTML generated by the htags(1) tool instead of doxygen
# built-in source browser. The htags tool is part of GNU's global source
# tagging system (see http://www.gnu.org/software/global/global.html). You
# will need version 4.8.6 or higher.
USE_HTAGS = NO
# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
# will generate a verbatim copy of the header file for each class for
# which an include is specified. Set to NO to disable this.
VERBATIM_HEADERS = YES
#---------------------------------------------------------------------------
# configuration options related to the alphabetical class index
#---------------------------------------------------------------------------
# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
# of all compounds will be generated. Enable this if the project
# contains a lot of classes, structs, unions or interfaces.
ALPHABETICAL_INDEX = NO
# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
# in which this list will be split (can be a number in the range [1..20])
COLS_IN_ALPHA_INDEX = 5
# In case all classes in a project start with a common prefix, all
# classes will be put under the same header in the alphabetical index.
# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
# should be ignored while generating the index headers.
IGNORE_PREFIX =
#---------------------------------------------------------------------------
# configuration options related to the HTML output
#---------------------------------------------------------------------------
# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
# generate HTML output.
GENERATE_HTML = YES
# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
# If a relative path is entered the value of OUTPUT_DIRECTORY will be
# put in front of it. If left blank `html' will be used as the default path.
HTML_OUTPUT = html
# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
# doxygen will generate files with .html extension.
HTML_FILE_EXTENSION = .html
# The HTML_HEADER tag can be used to specify a personal HTML header for
# each generated HTML page. If it is left blank doxygen will generate a
# standard header.
HTML_HEADER =
# The HTML_FOOTER tag can be used to specify a personal HTML footer for
# each generated HTML page. If it is left blank doxygen will generate a
# standard footer.
HTML_FOOTER =
# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
# style sheet that is used by each HTML page. It can be used to
# fine-tune the look of the HTML output. If the tag is left blank doxygen
# will generate a default style sheet. Note that doxygen will try to copy
# the style sheet file to the HTML output directory, so don't put your own
# stylesheet in the HTML output directory as well, or it will be erased!
HTML_STYLESHEET =
# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
# files or namespaces will be aligned in HTML using tables. If set to
# NO a bullet list will be used.
HTML_ALIGN_MEMBERS = YES
# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
# documentation will contain sections that can be hidden and shown after the
# page has loaded. For this to work a browser that supports
# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox
# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
HTML_DYNAMIC_SECTIONS = NO
# If the GENERATE_DOCSET tag is set to YES, additional index files
# will be generated that can be used as input for Apple's Xcode 3
# integrated development environment, introduced with OSX 10.5 (Leopard).
# To create a documentation set, doxygen will generate a Makefile in the
# HTML output directory. Running make will produce the docset in that
# directory and running "make install" will install the docset in
# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
# it at startup.
# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html for more information.
GENERATE_DOCSET = NO
# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
# feed. A documentation feed provides an umbrella under which multiple
# documentation sets from a single provider (such as a company or product suite)
# can be grouped.
DOCSET_FEEDNAME = "Doxygen generated docs"
# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
# should uniquely identify the documentation set bundle. This should be a
# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
# will append .docset to the name.
DOCSET_BUNDLE_ID = org.doxygen.Project
# If the GENERATE_HTMLHELP tag is set to YES, additional index files
# will be generated that can be used as input for tools like the
# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
# of the generated HTML documentation.
GENERATE_HTMLHELP = NO
# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
# be used to specify the file name of the resulting .chm file. You
# can add a path in front of the file if the result should not be
# written to the html output directory.
CHM_FILE =
# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
# be used to specify the location (absolute path including file name) of
# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
# the HTML help compiler on the generated index.hhp.
HHC_LOCATION =
# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
# controls if a separate .chi index file is generated (YES) or that
# it should be included in the master .chm file (NO).
GENERATE_CHI = NO
# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
# is used to encode HtmlHelp index (hhk), content (hhc) and project file
# content.
CHM_INDEX_ENCODING =
# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
# controls whether a binary table of contents is generated (YES) or a
# normal table of contents (NO) in the .chm file.
BINARY_TOC = NO
# The TOC_EXPAND flag can be set to YES to add extra items for group members
# to the contents of the HTML help documentation and to the tree view.
TOC_EXPAND = NO
# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and QHP_VIRTUAL_FOLDER
# are set, an additional index file will be generated that can be used as input for
# Qt's qhelpgenerator to generate a Qt Compressed Help (.qch) of the generated
# HTML documentation.
GENERATE_QHP = NO
# If the QHG_LOCATION tag is specified, the QCH_FILE tag can
# be used to specify the file name of the resulting .qch file.
# The path specified is relative to the HTML output folder.
QCH_FILE =
# The QHP_NAMESPACE tag specifies the namespace to use when generating
# Qt Help Project output. For more information please see
# http://doc.trolltech.com/qthelpproject.html#namespace
QHP_NAMESPACE =
# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating
# Qt Help Project output. For more information please see
# http://doc.trolltech.com/qthelpproject.html#virtual-folders
QHP_VIRTUAL_FOLDER = doc
# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to add.
# For more information please see
# http://doc.trolltech.com/qthelpproject.html#custom-filters
QHP_CUST_FILTER_NAME =
# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the custom filter to add.For more information please see
# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">Qt Help Project / Custom Filters</a>.
QHP_CUST_FILTER_ATTRS =
# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this project's
# filter section matches.
# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">Qt Help Project / Filter Attributes</a>.
QHP_SECT_FILTER_ATTRS =
# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can
# be used to specify the location of Qt's qhelpgenerator.
# If non-empty doxygen will try to run qhelpgenerator on the generated
# .qhp file.
QHG_LOCATION =
# The DISABLE_INDEX tag can be used to turn on/off the condensed index at
# top of each HTML page. The value NO (the default) enables the index and
# the value YES disables it.
DISABLE_INDEX = NO
# This tag can be used to set the number of enum values (range [1..20])
# that doxygen will group on one line in the generated HTML documentation.
ENUM_VALUES_PER_LINE = 4
# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
# structure should be generated to display hierarchical information.
# If the tag value is set to FRAME, a side panel will be generated
# containing a tree-like index structure (just like the one that
# is generated for HTML Help). For this to work a browser that supports
# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+,
# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are
# probably better off using the HTML help feature. Other possible values
# for this tag are: HIERARCHIES, which will generate the Groups, Directories,
# and Class Hierarchy pages using a tree view instead of an ordered list;
# ALL, which combines the behavior of FRAME and HIERARCHIES; and NONE, which
# disables this behavior completely. For backwards compatibility with previous
# releases of Doxygen, the values YES and NO are equivalent to FRAME and NONE
# respectively.
GENERATE_TREEVIEW = NONE
# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
# used to set the initial width (in pixels) of the frame in which the tree
# is shown.
TREEVIEW_WIDTH = 250
# Use this tag to change the font size of Latex formulas included
# as images in the HTML documentation. The default is 10. Note that
# when you change the font size after a successful doxygen run you need
# to manually remove any form_*.png images from the HTML output directory
# to force them to be regenerated.
FORMULA_FONTSIZE = 10
#---------------------------------------------------------------------------
# configuration options related to the LaTeX output
#---------------------------------------------------------------------------
# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
# generate Latex output.
GENERATE_LATEX = NO
# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
# If a relative path is entered the value of OUTPUT_DIRECTORY will be
# put in front of it. If left blank `latex' will be used as the default path.
LATEX_OUTPUT = latex
# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
# invoked. If left blank `latex' will be used as the default command name.
LATEX_CMD_NAME = latex
# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
# generate index for LaTeX. If left blank `makeindex' will be used as the
# default command name.
MAKEINDEX_CMD_NAME = makeindex
# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
# LaTeX documents. This may be useful for small projects and may help to
# save some trees in general.
COMPACT_LATEX = NO
# The PAPER_TYPE tag can be used to set the paper type that is used
# by the printer. Possible values are: a4, a4wide, letter, legal and
# executive. If left blank a4wide will be used.
PAPER_TYPE = a4wide
# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
# packages that should be included in the LaTeX output.
EXTRA_PACKAGES =
# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
# the generated latex document. The header should contain everything until
# the first chapter. If it is left blank doxygen will generate a
# standard header. Notice: only use this tag if you know what you are doing!
LATEX_HEADER =
# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
# is prepared for conversion to pdf (using ps2pdf). The pdf file will
# contain links (just like the HTML output) instead of page references
# This makes the output suitable for online browsing using a pdf viewer.
PDF_HYPERLINKS = YES
# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
# plain latex in the generated Makefile. Set this option to YES to get a
# higher quality PDF documentation.
USE_PDFLATEX = YES
# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
# command to the generated LaTeX files. This will instruct LaTeX to keep
# running if errors occur, instead of asking the user for help.
# This option is also used when generating formulas in HTML.
LATEX_BATCHMODE = NO
# If LATEX_HIDE_INDICES is set to YES then doxygen will not
# include the index chapters (such as File Index, Compound Index, etc.)
# in the output.
LATEX_HIDE_INDICES = NO
# If LATEX_SOURCE_CODE is set to YES then doxygen will include source code with syntax highlighting in the LaTeX output. Note that which sources are shown also depends on other settings such as SOURCE_BROWSER.
LATEX_SOURCE_CODE = NO
#---------------------------------------------------------------------------
# configuration options related to the RTF output
#---------------------------------------------------------------------------
# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
# The RTF output is optimized for Word 97 and may not look very pretty with
# other RTF readers or editors.
GENERATE_RTF = NO
# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
# If a relative path is entered the value of OUTPUT_DIRECTORY will be
# put in front of it. If left blank `rtf' will be used as the default path.
RTF_OUTPUT = rtf
# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
# RTF documents. This may be useful for small projects and may help to
# save some trees in general.
COMPACT_RTF = NO
# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
# will contain hyperlink fields. The RTF file will
# contain links (just like the HTML output) instead of page references.
# This makes the output suitable for online browsing using WORD or other
# programs which support those fields.
# Note: wordpad (write) and others do not support links.
RTF_HYPERLINKS = NO
# Load stylesheet definitions from file. Syntax is similar to doxygen's
# config file, i.e. a series of assignments. You only have to provide
# replacements, missing definitions are set to their default value.
RTF_STYLESHEET_FILE =
# Set optional variables used in the generation of an rtf document.
# Syntax is similar to doxygen's config file.
RTF_EXTENSIONS_FILE =
#---------------------------------------------------------------------------
# configuration options related to the man page output
#---------------------------------------------------------------------------
# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
# generate man pages
GENERATE_MAN = NO
# The MAN_OUTPUT tag is used to specify where the man pages will be put.
# If a relative path is entered the value of OUTPUT_DIRECTORY will be
# put in front of it. If left blank `man' will be used as the default path.
MAN_OUTPUT = man
# The MAN_EXTENSION tag determines the extension that is added to
# the generated man pages (default is the subroutine's section .3)
MAN_EXTENSION = .3
# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
# then it will generate one additional man file for each entity
# documented in the real man page(s). These additional files
# only source the real man page, but without them the man command
# would be unable to find the correct page. The default is NO.
MAN_LINKS = NO
#---------------------------------------------------------------------------
# configuration options related to the XML output
#---------------------------------------------------------------------------
# If the GENERATE_XML tag is set to YES Doxygen will
# generate an XML file that captures the structure of
# the code including all documentation.
GENERATE_XML = YES
# The XML_OUTPUT tag is used to specify where the XML pages will be put.
# If a relative path is entered the value of OUTPUT_DIRECTORY will be
# put in front of it. If left blank `xml' will be used as the default path.
XML_OUTPUT = xml
# The XML_SCHEMA tag can be used to specify an XML schema,
# which can be used by a validating XML parser to check the
# syntax of the XML files.
XML_SCHEMA =
# The XML_DTD tag can be used to specify an XML DTD,
# which can be used by a validating XML parser to check the
# syntax of the XML files.
XML_DTD =
# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
# dump the program listings (including syntax highlighting
# and cross-referencing information) to the XML output. Note that
# enabling this will significantly increase the size of the XML output.
XML_PROGRAMLISTING = NO
#---------------------------------------------------------------------------
# configuration options for the AutoGen Definitions output
#---------------------------------------------------------------------------
# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
# generate an AutoGen Definitions (see autogen.sf.net) file
# that captures the structure of the code including all
# documentation. Note that this feature is still experimental
# and incomplete at the moment.
GENERATE_AUTOGEN_DEF = NO
#---------------------------------------------------------------------------
# configuration options related to the Perl module output
#---------------------------------------------------------------------------
# If the GENERATE_PERLMOD tag is set to YES Doxygen will
# generate a Perl module file that captures the structure of
# the code including all documentation. Note that this
# feature is still experimental and incomplete at the
# moment.
GENERATE_PERLMOD = NO
# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
# the necessary Makefile rules, Perl scripts and LaTeX code to be able
# to generate PDF and DVI output from the Perl module output.
PERLMOD_LATEX = NO
# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
# nicely formatted so it can be parsed by a human reader.
# This is useful
# if you want to understand what is going on.
# On the other hand, if this
# tag is set to NO the size of the Perl module output will be much smaller
# and Perl will parse it just the same.
PERLMOD_PRETTY = YES
# The names of the make variables in the generated doxyrules.make file
# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
# This is useful so different doxyrules.make files included by the same
# Makefile don't overwrite each other's variables.
PERLMOD_MAKEVAR_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the preprocessor
#---------------------------------------------------------------------------
# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
# evaluate all C-preprocessor directives found in the sources and include
# files.
ENABLE_PREPROCESSING = YES
# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
# names in the source code. If set to NO (the default) only conditional
# compilation will be performed. Macro expansion can be done in a controlled
# way by setting EXPAND_ONLY_PREDEF to YES.
MACRO_EXPANSION = NO
# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
# then the macro expansion is limited to the macros specified with the
# PREDEFINED and EXPAND_AS_DEFINED tags.
EXPAND_ONLY_PREDEF = NO
# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
# in the INCLUDE_PATH (see below) will be search if a #include is found.
SEARCH_INCLUDES = YES
# The INCLUDE_PATH tag can be used to specify one or more directories that
# contain include files that are not input files but should be processed by
# the preprocessor.
INCLUDE_PATH =
# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
# patterns (like *.h and *.hpp) to filter out the header-files in the
# directories. If left blank, the patterns specified with FILE_PATTERNS will
# be used.
INCLUDE_FILE_PATTERNS =
# The PREDEFINED tag can be used to specify one or more macro names that
# are defined before the preprocessor is started (similar to the -D option of
# gcc). The argument of the tag is a list of macros of the form: name
# or name=definition (no spaces). If the definition and the = are
# omitted =1 is assumed. To prevent a macro definition from being
# undefined via #undef or recursively expanded use the := operator
# instead of the = operator.
PREDEFINED =
# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
# this tag can be used to specify a list of macro names that should be expanded.
# The macro definition that is found in the sources will be used.
# Use the PREDEFINED tag if you want to use a different macro definition.
EXPAND_AS_DEFINED =
# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
# doxygen's preprocessor will remove all function-like macros that are alone
# on a line, have an all uppercase name, and do not end with a semicolon. Such
# function macros are typically used for boiler-plate code, and will confuse
# the parser if not removed.
SKIP_FUNCTION_MACROS = YES
#---------------------------------------------------------------------------
# Configuration::additions related to external references
#---------------------------------------------------------------------------
# The TAGFILES option can be used to specify one or more tagfiles.
# Optionally an initial location of the external documentation
# can be added for each tagfile. The format of a tag file without
# this location is as follows:
#
# TAGFILES = file1 file2 ...
# Adding location for the tag files is done as follows:
#
# TAGFILES = file1=loc1 "file2 = loc2" ...
# where "loc1" and "loc2" can be relative or absolute paths or
# URLs. If a location is present for each tag, the installdox tool
# does not have to be run to correct the links.
# Note that each tag file must have a unique name
# (where the name does NOT include the path)
# If a tag file is not located in the directory in which doxygen
# is run, you must also specify the path to the tagfile here.
TAGFILES =
# When a file name is specified after GENERATE_TAGFILE, doxygen will create
# a tag file that is based on the input files it reads.
GENERATE_TAGFILE =
# If the ALLEXTERNALS tag is set to YES all external classes will be listed
# in the class index. If set to NO only the inherited external classes
# will be listed.
ALLEXTERNALS = NO
# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
# in the modules index. If set to NO, only the current project's groups will
# be listed.
EXTERNAL_GROUPS = YES
# The PERL_PATH should be the absolute path and name of the perl script
# interpreter (i.e. the result of `which perl').
PERL_PATH = /usr/bin/perl
#---------------------------------------------------------------------------
# Configuration options related to the dot tool
#---------------------------------------------------------------------------
# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
# or super classes. Setting the tag to NO turns the diagrams off. Note that
# this option is superseded by the HAVE_DOT option below. This is only a
# fallback. It is recommended to install and use dot, since it yields more
# powerful graphs.
CLASS_DIAGRAMS = YES
# You can define message sequence charts within doxygen comments using the \msc
# command. Doxygen will then run the mscgen tool (see
# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the
# documentation. The MSCGEN_PATH tag allows you to specify the directory where
# the mscgen tool resides. If left empty the tool is assumed to be found in the
# default search path.
MSCGEN_PATH =
# If set to YES, the inheritance and collaboration graphs will hide
# inheritance and usage relations if the target is undocumented
# or is not a class.
HIDE_UNDOC_RELATIONS = YES
# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
# available from the path. This tool is part of Graphviz, a graph visualization
# toolkit from AT&T and Lucent Bell Labs. The other options in this section
# have no effect if this option is set to NO (the default)
HAVE_DOT = NO
# By default doxygen will write a font called FreeSans.ttf to the output
# directory and reference it in all dot files that doxygen generates. This
# font does not include all possible unicode characters however, so when you need
# these (or just want a differently looking font) you can specify the font name
# using DOT_FONTNAME. You need need to make sure dot is able to find the font,
# which can be done by putting it in a standard location or by setting the
# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory
# containing the font.
DOT_FONTNAME = FreeSans
# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
# The default size is 10pt.
DOT_FONTSIZE = 10
# By default doxygen will tell dot to use the output directory to look for the
# FreeSans.ttf font (which doxygen will put there itself). If you specify a
# different font using DOT_FONTNAME you can set the path where dot
# can find it using this tag.
DOT_FONTPATH =
# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
# will generate a graph for each documented class showing the direct and
# indirect inheritance relations. Setting this tag to YES will force the
# the CLASS_DIAGRAMS tag to NO.
CLASS_GRAPH = YES
# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
# will generate a graph for each documented class showing the direct and
# indirect implementation dependencies (inheritance, containment, and
# class references variables) of the class with other documented classes.
COLLABORATION_GRAPH = YES
# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
# will generate a graph for groups, showing the direct groups dependencies
GROUP_GRAPHS = YES
# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
# collaboration diagrams in a style similar to the OMG's Unified Modeling
# Language.
UML_LOOK = NO
# If set to YES, the inheritance and collaboration graphs will show the
# relations between templates and their instances.
TEMPLATE_RELATIONS = NO
# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
# tags are set to YES then doxygen will generate a graph for each documented
# file showing the direct and indirect include dependencies of the file with
# other documented files.
INCLUDE_GRAPH = YES
# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
# documented header file showing the documented files that directly or
# indirectly include this file.
INCLUDED_BY_GRAPH = YES
# If the CALL_GRAPH and HAVE_DOT options are set to YES then
# doxygen will generate a call dependency graph for every global function
# or class method. Note that enabling this option will significantly increase
# the time of a run. So in most cases it will be better to enable call graphs
# for selected functions only using the \callgraph command.
CALL_GRAPH = NO
# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
# doxygen will generate a caller dependency graph for every global function
# or class method. Note that enabling this option will significantly increase
# the time of a run. So in most cases it will be better to enable caller
# graphs for selected functions only using the \callergraph command.
CALLER_GRAPH = NO
# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
# will graphical hierarchy of all classes instead of a textual one.
GRAPHICAL_HIERARCHY = YES
# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
# then doxygen will show the dependencies a directory has on other directories
# in a graphical way. The dependency relations are determined by the #include
# relations between the files in the directories.
DIRECTORY_GRAPH = YES
# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
# generated by dot. Possible values are png, jpg, or gif
# If left blank png will be used.
DOT_IMAGE_FORMAT = png
# The tag DOT_PATH can be used to specify the path where the dot tool can be
# found. If left blank, it is assumed the dot tool can be found in the path.
DOT_PATH =
# The DOTFILE_DIRS tag can be used to specify one or more directories that
# contain dot files that are included in the documentation (see the
# \dotfile command).
DOTFILE_DIRS =
# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
# nodes that will be shown in the graph. If the number of nodes in a graph
# becomes larger than this value, doxygen will truncate the graph, which is
# visualized by representing a node as a red box. Note that doxygen if the
# number of direct children of the root node in a graph is already larger than
# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note
# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
DOT_GRAPH_MAX_NODES = 50
# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
# graphs generated by dot. A depth value of 3 means that only nodes reachable
# from the root by following a path via at most 3 edges will be shown. Nodes
# that lay further from the root node will be omitted. Note that setting this
# option to 1 or 2 may greatly reduce the computation time needed for large
# code bases. Also note that the size of a graph can be further restricted by
# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
MAX_DOT_GRAPH_DEPTH = 0
# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
# background. This is disabled by default, because dot on Windows does not
# seem to support this out of the box. Warning: Depending on the platform used,
# enabling this option may lead to badly anti-aliased labels on the edges of
# a graph (i.e. they become hard to read).
DOT_TRANSPARENT = NO
# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
# files in one run (i.e. multiple -o and -T options on the command line). This
# makes dot run faster, but since only newer versions of dot (>1.8.10)
# support this, this feature is disabled by default.
DOT_MULTI_TARGETS = NO
# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
# generate a legend page explaining the meaning of the various boxes and
# arrows in the dot generated graphs.
GENERATE_LEGEND = YES
# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
# remove the intermediate dot files that are used to generate
# the various graphs.
DOT_CLEANUP = YES
#---------------------------------------------------------------------------
# Options related to the search engine
#---------------------------------------------------------------------------
# The SEARCHENGINE tag specifies whether or not a search engine should be
# used. If set to NO the values of all tags below this one will be ignored.
SEARCHENGINE = NO
wrappers/python/src/swig_doxygen/doxygen/Doxyfile.in
View file @ 8dd60914
......@@ -588,7 +588,7 @@ INPUT_ENCODING = UTF-8
# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx
# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90
FILE_PATTERNS =
FILE_PATTERNS = *.h
# The RECURSIVE tag can be used to turn specify whether or not subdirectories
# should be searched for input files as well. Possible values are YES and NO.
......
wrappers/python/src/swig_doxygen/swigInputBuilder.py
View file @ 8dd60914
......@@ -446,6 +446,7 @@ class SwigInputBuilder:
#write only non Constructor and Destructor methods and python mods
self.fOut.write("\n")
methodsWithOutputArgs = set()
for items in methodList:
clearOutput=""
(shortClassName, memberNode,
......@@ -479,6 +480,7 @@ class SwigInputBuilder:
(INDENT, simpleType, pType, pName))
clearOutput = "%s%s%%clear %s %s;\n" \
% (clearOutput, INDENT, pType, pName)
methodsWithOutputArgs.add((shortClassName, methName))
mArgsstring = getText("argsstring", memberNode)
try:
......@@ -503,7 +505,10 @@ class SwigInputBuilder:
paramList = findNodes(memberNode, 'param')
# write pythonprepend blocks
mArgsstring = getText("argsstring", memberNode)
if isConstructors:
mArgsstring = '' # specifying args to constructors seems to prevent append and prepend from working
else:
mArgsstring = getText("argsstring", memberNode)
if self.fOutPythonprepend and \
len(paramList) and \
mArgsstring.find('=0') < 0:
......@@ -523,6 +528,28 @@ class SwigInputBuilder:
s = ("the %s object does not own its corresponding OpenMM object"
% self.__class__.__name__)
raise Exception(s)'''.format(argName=argName)
# Convert input arguments to the proper units, if specified.
if key not in methodsWithOutputArgs:
if key in self.configModule.UNITS:
argUnits=self.configModule.UNITS[key][1]
elif ("*", methName) in self.configModule.UNITS:
argUnits=self.configModule.UNITS[("*", methName)][1]
else:
argUnits = ()
if len(argUnits) > 0 and (self.SWIG_COMPACT_ARGUMENTS or isConstructors):
textInside += '''
args = list(args)'''
for i, units in enumerate(argUnits):
if units is not None:
if self.SWIG_COMPACT_ARGUMENTS or isConstructors:
argName = 'args[%s]' % i
else:
argName = getText('declname', paramList[i])
textInside += '''
if unit.is_quantity({argName}):
{argName} = {argName}.value_in_unit({units})'''.format(argName=argName, units=units)
for argNum in self.configModule.REQUIRE_ORDERED_SET.get(key, []):
if self.SWIG_COMPACT_ARGUMENTS:
argName = 'args[%s]' % argNum
......@@ -568,7 +595,7 @@ class SwigInputBuilder:
% (addText, INDENT, valueUnits[0])
for vUnit in valueUnits[1]:
if vUnit is not None:
if vUnit is not None and key in methodsWithOutputArgs:
addText = "%s%sval[%s]=unit.Quantity(val[%s], %s)\n" \
% (addText, INDENT, index, index, vUnit)
index+=1
......
wrappers/python/src/swig_doxygen/swigInputConfig.py
View file @ 8dd60914
......@@ -117,9 +117,6 @@ SKIP_METHODS = [('State', 'getPositions'),
# The build script assumes method args that are non-const references are
# used to output values. This list gives excpetions to this rule.
NO_OUTPUT_ARGS = [('LocalEnergyMinimizer', 'minimize', 'context'),
('System', 'getDefaultPeriodicBoxVectors', 'a'),
('System', 'getDefaultPeriodicBoxVectors', 'b'),
('System', 'getDefaultPeriodicBoxVectors', 'c'),
('Platform', 'setPropertyValue', 'context'),
('AmoebaTorsionTorsionForce', 'setTorsionTorsionGrid', 'grid'),
('AmoebaVdwForce', 'setParticleExclusions', 'exclusions'),
......@@ -175,8 +172,14 @@ UNITS = {
("*", "getDefaultPressureX") : ("unit.bar", ()),
("*", "getDefaultPressureY") : ("unit.bar", ()),
("*", "getDefaultPressureZ") : ("unit.bar", ()),
("*", "setDefaultPressure") : (None, ("unit.bar",)),
("*", "setDefaultPressureX") : (None, ("unit.bar",)),
("*", "setDefaultPressureY") : (None, ("unit.bar",)),
("*", "setDefaultPressureZ") : (None, ("unit.bar",)),
("*", "getDefaultSurfaceTension") : ("unit.bar*unit.nanometer", ()),
("*", "setDefaultSurfaceTension") : (None, ("unit.bar*unit.nanometer",)),
("*", "getDefaultTemperature") : ("unit.kelvin", ()),
("*", "setDefaultTemperature") : (None, ("unit.kelvin",)),
("*", "getErrorTolerance") : (None, ()),
("*", "getEwaldErrorTolerance") : (None, ()),
("*", "getFriction") : ("1/unit.picosecond", ()),
......@@ -205,6 +208,7 @@ UNITS = {
("*", "getSoluteDielectric") : (None, ()),
("*", "getSolventDielectric") : (None, ()),
("*", "getStepSize") : ("unit.picosecond", ()),
("*", "getMaximumStepSize") : ("unit.picosecond", ()),
("*", "getSystem") : (None, ()),
("*", "getTabulatedFunction") : (None, ()),
("*", "getUseDispersionCorrection") : (None, ()),
......@@ -309,15 +313,14 @@ UNITS = {
("AmoebaTorsionTorsionForce", "getTorsionTorsionParameters") : ( None, ()),
("AmoebaTorsionTorsionForce", "getTorsionTorsionGrid") : ( None, ()),
# LPW 2012-10 : Is this a duplicate entry?
#("AmoebaVdwForce", "getParticleParameters") : ( None, (None, None, None, 'unit.nanometer', 'unit.kilojoule_per_mole', None)),
("AmoebaVdwForce", "getSigmaCombiningRule") : ( None, ()),
("AmoebaVdwForce", "getEpsilonCombiningRule") : ( None, ()),
("AmoebaVdwForce", "getParticleExclusions") : ( None, ()),
("AmoebaVdwForce", "getAlchemicalMethod") : ( None, ()),
("AmoebaVdwForce", "getSoftcorePower") : ( None, ()),
("AmoebaVdwForce", "getSoftcoreAlpha") : ( None, ()),
("AmoebaVdwForce", "getCutoff") : ( 'unit.nanometer', ()),
# LPW 2012-10 Modified because it no longer returns ivIndex and classIndex.
# ("AmoebaVdwForce", "getParticleParameters") : ( None, (None, None, 'unit.nanometer', 'unit.kilojoule_per_mole', None)),
("AmoebaVdwForce", "getParticleParameters") : ( None, (None, 'unit.nanometer', 'unit.kilojoule_per_mole', None)),
("AmoebaVdwForce", "getParticleParameters") : ( None, (None, 'unit.nanometer', 'unit.kilojoule_per_mole', None, None)),
("AmoebaWcaDispersionForce", "getParticleParameters") : ( None, ('unit.nanometer', 'unit.kilojoule_per_mole')),
("AmoebaWcaDispersionForce", "getAwater") : ( '1/(unit.nanometer*unit.nanometer*unit.nanometer)',()),
......@@ -459,6 +462,7 @@ UNITS = {
("System", "getVirtualSite") : (None, ()),
("DrudeLangevinIntegrator", "getDrudeTemperature") : ("unit.kelvin", ()),
("DrudeLangevinIntegrator", "getMaxDrudeDistance") : ("unit.nanometer", ()),
("MonteCarloMembraneBarostat", "MonteCarloMembraneBarostat") : (None, ("unit.bar", "unit.bar*unit.nanometer", "unit.kelvin", None, None, None)),
("MonteCarloMembraneBarostat", "getXYMode") : (None, ()),
("MonteCarloMembraneBarostat", "getZMode") : (None, ()),
("DrudeLangevinIntegrator", "getDrudeFriction") : ("1/unit.picosecond", ()),
......
wrappers/python/src/swig_doxygen/swig_lib/python/header.i
View file @ 8dd60914
......@@ -20,6 +20,16 @@ PyObject *copyVVec3ToList(std::vector<Vec3> vVec3) {
return pyList;
}
int isNumpyAvailable() {
static bool initialized = false;
static bool available = false;
if (!initialized) {
initialized = true;
available = (_import_array() >= 0);
}
return available;
}
} // namespace OpenMM
%}
......
wrappers/python/src/swig_doxygen/swig_lib/python/typemaps.i
View file @ 8dd60914
......@@ -156,13 +156,49 @@ OpenMM::Vec3 Py_SequenceToVec3(PyObject* obj, int& status) {
%fragment("Py_SequenceToVecDouble", "header", fragment="Py_StripOpenMMUnits") {
int Py_SequenceToVecDouble(PyObject* obj, std::vector<double>& out) {
PyObject* stripped = NULL;
PyObject* stripped = Py_StripOpenMMUnits(obj);
PyObject* item = NULL;
PyObject* item1 = NULL;
PyObject* iterator = NULL;
stripped = Py_StripOpenMMUnits(obj);
iterator = PyObject_GetIter(stripped);
if (isNumpyAvailable()) {
if (PyArray_Check(stripped) && PyArray_ISCARRAY_RO(stripped) && PyArray_NDIM(stripped) == 1) {
int type = PyArray_TYPE(stripped);
int length = PyArray_SIZE(stripped);
void* data = PyArray_DATA((PyArrayObject*) stripped);
if (type == NPY_DOUBLE) {
out.resize(length);
memcpy(&out[0], data, sizeof(double)*length);
Py_DECREF(stripped);
return SWIG_OK;
}
if (type == NPY_FLOAT) {
out.resize(length);
float* floatData = (float*) data;
for (int i = 0; i < length; i++)
out[i] = floatData[i];
Py_DECREF(stripped);
return SWIG_OK;
}
if (type == NPY_INT32) {
out.resize(length);
int* intData = (int*) data;
for (int i = 0; i < length; i++)
out[i] = intData[i];
Py_DECREF(stripped);
return SWIG_OK;
}
if (type == NPY_INT64) {
out.resize(length);
long long* longData = (long long*) data;
for (int i = 0; i < length; i++)
out[i] = longData[i];
Py_DECREF(stripped);
return SWIG_OK;
}
}
}
PyObject* iterator = PyObject_GetIter(stripped);
if (iterator == NULL) {
Py_DECREF(stripped);
return SWIG_ERROR;
......@@ -194,16 +230,6 @@ int Py_SequenceToVecDouble(PyObject* obj, std::vector<double>& out) {
}
%fragment("Py_SequenceToVecVec3", "header", fragment="Py_SequenceToVec3") {
int isNumpyAvailable() {
static bool initialized = false;
static bool available = false;
if (!initialized) {
initialized = true;
available = (_import_array() >= 0);
}
return available;
}
int Py_SequenceToVecVec3(PyObject* obj, std::vector<Vec3>& out) {
PyObject* stripped = Py_StripOpenMMUnits(obj); // new reference
if (isNumpyAvailable()) {
......
wrappers/python/tests/TestAPIUnits.py
View file @ 8dd60914
......@@ -969,7 +969,7 @@ class TestAPIUnits(unittest.TestCase):
self.assertEqual(force.getNumParticles(), 3)
p, sig, eps, scale = force.getParticleParameters(0)
p, sig, eps, scale, alchemical = force.getParticleParameters(0)
self.assertEqual(p, 0)
self.assertEqual(sig, 0.1*nanometers)
self.assertIs(sig.unit, nanometers)
......@@ -977,7 +977,7 @@ class TestAPIUnits(unittest.TestCase):
self.assertIs(eps.unit, kilojoules_per_mole)
self.assertEqual(scale, 1.0)
p, sig, eps, scale = force.getParticleParameters(1)
p, sig, eps, scale, alchemical = force.getParticleParameters(1)
self.assertEqual(p, 1)
self.assertEqual(sig, 1.0*angstroms)
self.assertIs(sig.unit, nanometers)
......@@ -985,7 +985,7 @@ class TestAPIUnits(unittest.TestCase):
self.assertIs(eps.unit, kilojoules_per_mole)
self.assertEqual(scale, 0.5)
p, sig, eps, scale = force.getParticleParameters(2)
p, sig, eps, scale, alchemical = force.getParticleParameters(2)
self.assertEqual(p, 1)
self.assertAlmostEqualUnit(sig, 0.8*angstroms)
self.assertIs(sig.unit, nanometers)
......@@ -1176,6 +1176,28 @@ class TestAPIUnits(unittest.TestCase):
self.assertEqual(force.getDefaultTemperature(), 298.15*kelvin)
self.assertAlmostEqualUnit(force.getDefaultCollisionFrequency(), 1/picosecond)
def testMonteCarloMembraneBarostat(self):
""" Tests the MonteCarloMembraneBarostat API features """
force = MonteCarloMembraneBarostat(1.0, 1.5, 300, MonteCarloMembraneBarostat.XYAnisotropic, MonteCarloMembraneBarostat.ZFixed, 25)
self.assertEqual(force.getDefaultPressure(), 1.0*bar)
self.assertEqual(force.getDefaultSurfaceTension(), 1.5*bar*nanometer)
self.assertEqual(force.getDefaultTemperature(), 300*kelvin)
self.assertEqual(force.getXYMode(), MonteCarloMembraneBarostat.XYAnisotropic)
self.assertEqual(force.getZMode(), MonteCarloMembraneBarostat.ZFixed)
self.assertEqual(force.getFrequency(), 25)
force = MonteCarloMembraneBarostat(1.1*bar, 2.0*bar*nanometer, 350*kelvin, MonteCarloMembraneBarostat.XYAnisotropic, MonteCarloMembraneBarostat.ZFixed, 25)
self.assertEqual(force.getDefaultPressure(), 1.1*bar)
self.assertEqual(force.getDefaultSurfaceTension(), 2.0*bar*nanometer)
self.assertEqual(force.getDefaultTemperature(), 350*kelvin)
force.setDefaultPressure(1.2*bar)
force.setDefaultSurfaceTension(2.5*bar*nanometer)
force.setDefaultTemperature(298.15)
self.assertEqual(force.getDefaultPressure(), 1.2*bar)
self.assertEqual(force.getDefaultSurfaceTension(), 2.5*bar*nanometer)
self.assertEqual(force.getDefaultTemperature(), 298.15*kelvin)
def testDrudeSCFIntegrator(self):
""" Tests the DrudeSCFIntegrator API features """
integrator = DrudeSCFIntegrator(0.002)
......
wrappers/python/tests/TestAmberPrmtopFile.py
View file @ 8dd60914
......@@ -127,6 +127,14 @@ class TestAmberPrmtopFile(unittest.TestCase):
self.assertTrue(found_matching_solvent_dielectric and
found_matching_solute_dielectric)
def test_ImplicitSolventZeroSA(self):
"""Test that requesting gbsaModel=None yields a surface area energy of 0 when
prmtop.createSystem produces a GBSAOBCForce"""
system = prmtop2.createSystem(implicitSolvent=OBC2, gbsaModel=None)
for force in system.getForces():
if isinstance(force, GBSAOBCForce):
self.assertEqual(force.getSurfaceAreaEnergy(), 0*kilojoule/(nanometer**2*mole))
def test_HydrogenMass(self):
"""Test that altering the mass of hydrogens works correctly."""
......@@ -376,5 +384,21 @@ class TestAmberPrmtopFile(unittest.TestCase):
self.assertRaises(ValueError, lambda: f.addParticle([0, 0.9, 0.5]))
self.assertRaises(ValueError, lambda: f.addParticle([0, 0.21, 0.5]))
def testNucleicGBParametes(self):
"""Test that correct GB parameters are used for nucleic acids."""
prmtop = AmberPrmtopFile('systems/DNA_mbondi3.prmtop')
inpcrd = AmberInpcrdFile('systems/DNA_mbondi3.inpcrd')
sanderEnergy = [-19223.87993545, -19527.40433175, -19788.1070698]
for solvent, expectedEnergy in zip([OBC2, GBn, GBn2], sanderEnergy):
system = prmtop.createSystem(implicitSolvent=solvent, gbsaModel=None)
for f in system.getForces():
if isinstance(f, CustomGBForce) or isinstance(f, GBSAOBCForce):
f.setForceGroup(1)
integrator = VerletIntegrator(0.001)
context = Context(system, integrator, Platform.getPlatformByName('Reference'))
context.setPositions(inpcrd.positions)
energy = context.getState(getEnergy=True, groups={1}).getPotentialEnergy().value_in_unit(kilojoules_per_mole)
self.assertAlmostEqual(energy, expectedEnergy, delta=5e-4*abs(energy))
if __name__ == '__main__':
unittest.main()
wrappers/python/tests/TestCharmmFiles.py
View file @ 8dd60914
......@@ -5,7 +5,13 @@ from simtk.openmm import *
from simtk.unit import *
import simtk.openmm.app.element as elem
import math
import os
import tempfile
import warnings
if sys.version_info >= (3,0):
from io import StringIO
else:
from cStringIO import StringIO
class TestCharmmFiles(unittest.TestCase):
......@@ -93,12 +99,10 @@ class TestCharmmFiles(unittest.TestCase):
def test_NBFIX(self):
"""Tests CHARMM systems with NBFIX Lennard-Jones modifications"""
warnings.filterwarnings('ignore', category=CharmmPSFWarning)
psf = CharmmPsfFile('systems/ala3_solv.psf')
psf = CharmmPsfFile('systems/ala3_solv.psf', unitCellDimensions=Vec3(32.7119500, 32.9959600, 33.0071500)*angstroms)
crd = CharmmCrdFile('systems/ala3_solv.crd')
params = CharmmParameterSet('systems/par_all36_prot.prm',
'systems/toppar_water_ions.str')
# Box dimensions (found from bounding box)
psf.setBox(32.7119500*angstroms, 32.9959600*angstroms, 33.0071500*angstroms)
# Turn off charges so we only test the Lennard-Jones energies
for a in psf.atom_list:
......@@ -114,7 +118,7 @@ class TestCharmmFiles(unittest.TestCase):
state = con.getState(getEnergy=True, enforcePeriodicBox=True)
ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(ene, 15490.0033559, delta=0.05)
self.assertAlmostEqual(ene, 15559.71602, delta=0.05)
def test_Drude(self):
"""Test CHARMM systems with Drude force field"""
......@@ -127,14 +131,14 @@ class TestCharmmFiles(unittest.TestCase):
# Now compute the full energy
plat = Platform.getPlatformByName('Reference')
system = psf.createSystem(params, nonbondedMethod=PME)
system = psf.createSystem(params, nonbondedMethod=PME, ewaldErrorTolerance=0.00005)
integrator = DrudeLangevinIntegrator(300*kelvin, 1.0/picosecond, 1*kelvin, 10/picosecond, 0.001*picoseconds)
con = Context(system, integrator, plat)
con.setPositions(crd.positions)
state = con.getState(getEnergy=True, enforcePeriodicBox=True)
ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(ene, -1831.54, delta=0.5)
self.assertAlmostEqual(ene, -1788.36644, delta=1.0)
def test_Lonepair(self):
"""Test the lonepair facilities, in particular the colinear type of lonepairs"""
......@@ -169,12 +173,11 @@ class TestCharmmFiles(unittest.TestCase):
def testSystemOptions(self):
""" Test various options in CharmmPsfFile.createSystem """
warnings.filterwarnings('ignore', category=CharmmPSFWarning)
psf = CharmmPsfFile('systems/ala3_solv.psf')
psf = CharmmPsfFile('systems/ala3_solv.psf',
periodicBoxVectors=(Vec3(32.7119500, 0, 0)*angstroms, Vec3(0, 32.9959600, 0)*angstroms, Vec3(0, 0, 33.0071500)*angstroms))
crd = CharmmCrdFile('systems/ala3_solv.crd')
params = CharmmParameterSet('systems/par_all36_prot.prm',
'systems/toppar_water_ions.str')
# Box dimensions (found from bounding box)
psf.setBox(32.7119500*angstroms, 32.9959600*angstroms, 33.0071500*angstroms)
# Check some illegal options
self.assertRaises(ValueError, lambda:
......@@ -275,6 +278,77 @@ class TestCharmmFiles(unittest.TestCase):
dtheta = math.pi-angle
self.assertAlmostEqual(energy, dtheta**2, delta=1e-5)
def test_Residues(self):
"""Test that residues are read correctly, even if they have the same RESID while being in separate segments."""
m14 = (["C{}".format(i) for i in range(1,14)]
+ ["H{}".format(i) for i in range(1,12)]
+ ["N{}".format(i) for i in range(1,4)]
)
tip3 = ["OH2", "H1", "H2"]
pot = ["POT"]
cla = ["CLA"]
psf = CharmmPsfFile('systems/charmm-solvated/isa_wat.3_kcl.m14.psf')
for residue in psf.topology.residues():
atoms = [atom.name for atom in residue.atoms()]
if residue.name == "M14":
self.assertEqual(sorted(m14), sorted(atoms))
elif residue.name == "TIP3":
self.assertEqual(sorted(tip3), sorted(atoms))
elif residue.name == "POT":
self.assertEqual(sorted(pot), sorted(atoms))
elif residue.name == "CLA":
self.assertEqual(sorted(cla), sorted(atoms))
else:
self.assertTrue(False)
def test_NoLongRangeCorrection(self):
"""Test that long range correction is disabled."""
parameters = CharmmParameterSet(
'systems/charmm-solvated/envi.str',
'systems/charmm-solvated/m14.rtf',
'systems/charmm-solvated/m14.prm'
)
psf = CharmmPsfFile('systems/charmm-solvated/isa_wat.3_kcl.m14.psf')
psf.setBox(3.0584*nanometers,3.0584*nanometers,3.0584*nanometers)
system = psf.createSystem(parameters, nonbondedMethod=PME)
for force in system.getForces():
if isinstance(force, CustomNonbondedForce):
self.assertFalse(force.getUseLongRangeCorrection())
if isinstance(force, NonbondedForce):
self.assertFalse(force.getUseDispersionCorrection())
def test_NoPsfWarning(self):
"""Test that PSF warning is not thrown."""
parameters = CharmmParameterSet(
'systems/charmm-solvated/envi.str',
'systems/charmm-solvated/m14.rtf',
'systems/charmm-solvated/m14.prm'
)
with warnings.catch_warnings():
warnings.simplefilter("error", CharmmPSFWarning)
psf = CharmmPsfFile('systems/charmm-solvated/isa_wat.3_kcl.m14.psf')
psf.setBox(3.0584*nanometers,3.0584*nanometers,3.0584*nanometers)
psf.createSystem(parameters, nonbondedMethod=PME)
def test_NBXMod(self):
"""Test that all values of NBXMod are interpreted correctly."""
crd = CharmmCrdFile('systems/ala_ala_ala.crd')
with open('systems/charmm22.par') as parfile:
par = parfile.read()
# The following values were computed with CHARMM.
modeEnergy = {0: 754318.20507, 1: 754318.20507, 2: 908.35224, 3: 59.65279, 4: -241.12856, 5: 39.13169}
for nbxmod in range(-5, 6):
with tempfile.NamedTemporaryFile(suffix='.par', mode='w', delete=False) as parfile:
parfile.write(par.replace('nbxmod 5', 'nbxmod %d' % nbxmod))
parfile.close()
params = CharmmParameterSet('systems/charmm22.rtf', parfile.name)
os.remove(parfile.name)
system = self.psf_c.createSystem(params, nonbondedMethod=NoCutoff)
context = Context(system, VerletIntegrator(1*femtoseconds), Platform.getPlatformByName('Reference'))
context.setPositions(crd.positions)
energy = context.getState(getEnergy=True).getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(energy, modeEnergy[abs(nbxmod)], delta=1e-3*abs(energy))
if __name__ == '__main__':
unittest.main()
......
wrappers/python/tests/TestForceField.py
View file @ 8dd60914
......@@ -6,6 +6,7 @@ from simtk.unit import *
import simtk.openmm.app.element as elem
import simtk.openmm.app.forcefield as forcefield
import math
import textwrap
try:
from cStringIO import StringIO
except ImportError:
......@@ -50,16 +51,77 @@ class TestForceField(unittest.TestCase):
for f in forces))
def test_DispersionCorrection(self):
"""Test to make sure the nonbondedCutoff parameter is passed correctly."""
for useDispersionCorrection in [True, False]:
system = self.forcefield1.createSystem(self.pdb1.topology,
nonbondedCutoff=2*nanometer,
useDispersionCorrection=useDispersionCorrection)
"""Test to make sure that the dispersion/long-range correction is set properly."""
top = Topology()
chain = top.addChain()
for lrc in (True, False):
xml = textwrap.dedent(
"""
<ForceField>
<LennardJonesForce lj14scale="0.3" useDispersionCorrection="{lrc}">
<Atom type="A" sigma="1" epsilon="0.1"/>
<Atom type="B" sigma="2" epsilon="0.2"/>
<NBFixPair type1="A" type2="B" sigma="2.5" epsilon="1.1"/>
</LennardJonesForce>
<NonbondedForce coulomb14scale="0.833333" lj14scale="0.5" useDispersionCorrection="{lrc2}">
<Atom type="A" sigma="0.315" epsilon="0.635"/>
</NonbondedForce>
</ForceField>
"""
)
ff = ForceField(StringIO(xml.format(lrc=lrc, lrc2=lrc)))
system = ff.createSystem(top)
checked_nonbonded = False
checked_custom = False
for force in system.getForces():
if isinstance(force, NonbondedForce):
self.assertEqual(useDispersionCorrection, force.getUseDispersionCorrection())
self.assertEqual(force.getUseDispersionCorrection(), lrc)
checked_nonbonded = True
elif isinstance(force, CustomNonbondedForce):
self.assertEqual(force.getUseLongRangeCorrection(), lrc)
checked_custom = True
self.assertTrue(checked_nonbonded and checked_custom)
# check that the keyword argument overwrites xml input
lrc_kwarg = not lrc
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
system2 = ff.createSystem(top, useDispersionCorrection=lrc_kwarg)
self.assertTrue(len(w) == 2)
assert "conflict" in str(w[-1].message).lower()
checked_nonbonded = False
checked_custom = False
for force in system2.getForces():
if isinstance(force, NonbondedForce):
self.assertEqual(force.getUseDispersionCorrection(), lrc_kwarg)
checked_nonbonded = True
elif isinstance(force, CustomNonbondedForce):
self.assertEqual(force.getUseLongRangeCorrection(), lrc_kwarg)
checked_custom = True
self.assertTrue(checked_nonbonded and checked_custom)
# check that no warning is generated when useDispersionCorrection is not in the xml file
xml = textwrap.dedent(
"""
<ForceField>
<LennardJonesForce lj14scale="0.3">
<Atom type="A" sigma="1" epsilon="0.1"/>
<Atom type="B" sigma="2" epsilon="0.2"/>
<NBFixPair type1="A" type2="B" sigma="2.5" epsilon="1.1"/>
</LennardJonesForce>
<NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
<Atom type="A" sigma="0.315" epsilon="0.635"/>
</NonbondedForce>
</ForceField>
"""
)
ff = ForceField(StringIO(xml))
system = ff.createSystem(top)
for lrc_kwarg in [True, False]:
with warnings.catch_warnings():
warnings.simplefilter("error")
system2 = ff.createSystem(top, useDispersionCorrection=lrc_kwarg)
def test_Cutoff(self):
"""Test to make sure the nonbondedCutoff parameter is passed correctly."""
......@@ -227,7 +289,7 @@ class TestForceField(unittest.TestCase):
angles = forcefield.HarmonicAngleGenerator(ff)
angles.registerAngle({'class1':'HW', 'class2':'OW', 'class3':'HW', 'angle':1.82421813418*radians, 'k':836.8*kilojoules_per_mole/radian})
ff.registerGenerator(angles)
nonbonded = forcefield.NonbondedGenerator(ff, 0.833333, 0.5)
nonbonded = forcefield.NonbondedGenerator(ff, 0.833333, 0.5, True)
nonbonded.registerAtom({'type':'tip3p-O', 'charge':-0.834, 'sigma':0.31507524065751241*nanometers, 'epsilon':0.635968*kilojoules_per_mole})
nonbonded.registerAtom({'type':'tip3p-H', 'charge':0.417, 'sigma':1*nanometers, 'epsilon':0*kilojoules_per_mole})
ff.registerGenerator(nonbonded)
......@@ -415,7 +477,7 @@ class TestForceField(unittest.TestCase):
self.assertEqual(unmatched_residues[0].chain.id, 'X')
self.assertEqual(unmatched_residues[0].id, '1')
def test_ggenerateTemplatesForUnmatchedResidues(self):
def test_generateTemplatesForUnmatchedResidues(self):
"""Test generation of blank forcefield residue templates for unmatched residues."""
#
# Test where we generate parameters for only a ligand.
......@@ -712,7 +774,7 @@ class TestForceField(unittest.TestCase):
<Atom name="SOD" type="SOD"/>
</Residue>
</Residues>
<LennardJonesForce lj14scale="1.0">
<LennardJonesForce lj14scale="1.0" useDispersionCorrection="False">
<Atom type="CLA" sigma="0.404468018036" epsilon="0.6276"/>
<Atom type="SOD" sigma="0.251367073323" epsilon="0.1962296"/>
<NBFixPair type1="CLA" type2="SOD" sigma="0.33239431" epsilon="0.350933"/>
......@@ -852,6 +914,33 @@ class TestForceField(unittest.TestCase):
forcefield = ForceField(ff)
system = forcefield.createSystem(pdb.topology)
def test_IdenticalTemplates(self):
"""Test a case where patches produce two identical templates."""
ff = ForceField('charmm36.xml')
pdb = PDBFile(StringIO("""
ATOM 1 N HIS 1A -2.670 -0.476 0.475 1.00 0.00 N
ATOM 2 HT1 HIS 1A -2.645 -1.336 1.036 1.00 0.00 H
ATOM 3 HT2 HIS 1A -2.859 -0.751 -0.532 1.00 0.00 H
ATOM 4 HT3 HIS 1A -3.415 0.201 0.731 1.00 0.00 H
ATOM 5 CA HIS 1A -1.347 0.163 0.471 1.00 0.00 C
ATOM 6 HA HIS 1A -1.111 0.506 1.479 1.00 0.00 H
ATOM 7 CB HIS 1A -0.352 -0.857 -0.040 1.00 0.00 C
ATOM 8 HB1 HIS 1A -0.360 -1.741 0.636 1.00 0.00 H
ATOM 9 HB2 HIS 1A -0.640 -1.175 -1.046 1.00 0.00 H
ATOM 10 CG HIS 1A 1.003 -0.275 -0.063 1.00 0.00 C
ATOM 11 CD2 HIS 1A 2.143 -0.931 -0.476 1.00 0.00 C
ATOM 12 HD2 HIS 1A 2.217 -1.952 -0.840 1.00 0.00 H
ATOM 13 NE2 HIS 1A 3.137 -0.024 -0.328 1.00 0.00 N
ATOM 14 HE2 HIS 1A 4.132 -0.238 -0.565 1.00 0.00 H
ATOM 15 CE1 HIS 1A 2.649 1.130 0.150 1.00 0.00 C
ATOM 16 HE1 HIS 1A 3.233 2.020 0.360 1.00 0.00 H
ATOM 17 ND1 HIS 1A 1.323 0.973 0.314 1.00 0.00 N
ATOM 18 C HIS 1A -1.465 1.282 -0.497 1.00 0.00 C
ATOM 19 OT1 HIS 1A -2.108 2.309 -0.180 1.00 0.00 O
ATOM 20 OT2 HIS 1A -0.864 1.172 -1.737 1.00 0.00 O
END"""))
# If the check is not done correctly, this will throw an exception.
ff.createSystem(pdb.topology)
class AmoebaTestForceField(unittest.TestCase):
"""Test the ForceField.createSystem() method with the AMOEBA forcefield."""
......@@ -940,5 +1029,6 @@ class AmoebaTestForceField(unittest.TestCase):
diff = norm(f1-f2)
self.assertTrue(diff < 0.1 or diff/norm(f1) < 1e-3)
if __name__ == '__main__':
unittest.main()
wrappers/python/tests/TestGromacsTopFile.py
View file @ 8dd60914
......@@ -172,6 +172,13 @@ class TestGromacsTopFile(unittest.TestCase):
top = GromacsTopFile('systems/bnz.top')
gro = GromacsGroFile('systems/bnz.gro')
for atom in top.topology.atoms():
if atom.name.startswith('C'):
self.assertEqual(elem.carbon, atom.element)
elif atom.name.startswith('H'):
self.assertEqual(elem.hydrogen, atom.element)
else:
self.assertIsNone(atom.element)
system = top.createSystem()
self.assertEqual(26, system.getNumParticles())
......
wrappers/python/tests/TestMetadynamics.py 0 → 100644
View file @ 8dd60914
import unittest
from simtk.openmm import *
from simtk.openmm.app import *
from simtk.unit import *
class TestMetadynamics(unittest.TestCase):
"""Test the Metadynamics class"""
def testHarmonicOscillator(self):
"""Test running metadynamics on a harmonic oscillator."""
system = System()
system.addParticle(1.0)
system.addParticle(1.0)
force = HarmonicBondForce()
force.addBond(0, 1, 1.0, 100000.0)
system.addForce(force)
cv = CustomBondForce('r')
cv.addBond(0, 1)
bias = BiasVariable(cv, 0.94, 1.06, 0.02)
meta = Metadynamics(system, [bias], 300*kelvin, 2.0, 5.0, 10)
integrator = LangevinIntegrator(300*kelvin, 10/picosecond, 0.001*picosecond)
topology = Topology()
chain = topology.addChain()
residue = topology.addResidue('H2', chain)
topology.addAtom('H1', element.hydrogen, residue)
topology.addAtom('H2', element.hydrogen, residue)
simulation = Simulation(topology, system, integrator, Platform.getPlatformByName('Reference'))
simulation.context.setPositions([Vec3(0, 0, 0), Vec3(1, 0, 0)])
meta.step(simulation, 200000)
fe = meta.getFreeEnergy()
center = bias.gridWidth//2
fe -= fe[center]
# Energies should be reasonably well converged over the central part of the range.
for i in range(center-3, center+4):
r = bias.minValue + i*(bias.maxValue-bias.minValue)/(bias.gridWidth-1)
e = 0.5*100000.0*(r-1.0)**2*kilojoules_per_mole
assert abs(fe[i]-e) < 1.0*kilojoules_per_mole
\ No newline at end of file
wrappers/python/tests/TestModeller.py
View file @ 8dd60914
from collections import defaultdict
import unittest
import math
import sys
from validateModeller import *
from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
from collections import defaultdict
if sys.version_info >= (3, 0):
from io import StringIO
else:
......@@ -593,6 +597,51 @@ class TestModeller(unittest.TestCase):
validate_equivalence(self, topology_start, topology_after)
def test_addHydrogensPdb3_keepPositions(self):
""" Test addHydrogens() does not change existing Hs positions """
# build the Modeller
topology_start = self.topology_start3
positions = self.positions3.value_in_unit(nanometers)
modeller = Modeller(topology_start, positions)
# Record original hydrogen positions
oriH = [atom.index for atom in modeller.topology.atoms() if atom.element == element.hydrogen]
oriH_pos = [positions[i] for i in oriH]
# Remove hydrogens from last residue
res_list = list(topology_start.residues())
toDelete = [atom for atom in res_list[-1].atoms() if atom.element == element.hydrogen]
modeller.delete(toDelete)
n_deleted = len(toDelete)
# Add hydrogen atoms back.
modeller.addHydrogens(self.forcefield)
topology_after = modeller.getTopology()
# Fetch 'new' positions
new_positions = modeller.positions.value_in_unit(nanometers)
newH = [atom.index for atom in topology_after.atoms() if atom.element == element.hydrogen]
newH_pos = [new_positions[i] for i in newH]
# Did we add all Hs back in correctly?
self.assertEqual(len(newH), len(oriH))
# Are the old ones at the same position?
# Negative control
oriH_fixed = oriH_pos[:-1*n_deleted]
newH_fixed = newH_pos[:-1*n_deleted]
xyz_diff = any([norm(o-n) > 1e-6 for o, n in zip(oriH_fixed, newH_fixed)])
self.assertEqual(xyz_diff, False)
# Were the new ones optimized?
# Positive control
oriH_added = oriH_pos[-1*n_deleted:]
newH_added = newH_pos[-1*n_deleted:]
xyz_diff = all([norm(o-n) > 1e-6 for o, n in zip(oriH_added, newH_added)])
self.assertEqual(xyz_diff, True)
def test_addHydrogensASH(self):
""" Test of addHydrogens() in which we force ASH to be a variant using the variants parameter. """
......@@ -1078,27 +1127,50 @@ class TestModeller(unittest.TestCase):
def test_addMembrane(self):
"""Test adding a membrane."""
pdb = PDBFile('systems/alanine-dipeptide-implicit.pdb')
modeller = Modeller(pdb.topology, pdb.positions)
"""Test adding a membrane to a realistic system."""
mol = PDBxFile('systems/gpcr.cif')
modeller = Modeller(mol.topology, mol.positions)
ff = ForceField('amber14-all.xml', 'amber14/tip3p.xml')
# Add a membrane around alanine dipeptide??? I know, it's a silly thing to do,
# but it's fast, and all we care about is whether it works!
# Add a membrane around the GPCR
modeller.addMembrane(ff, minimumPadding=1.1*nanometers, ionicStrength=1*molar)
modeller.addMembrane(ff, minimumPadding=0.5*nanometers, ionicStrength=1*molar)
# Make sure we added everything correctly
resCount = defaultdict(int)
for res in modeller.topology.residues():
resCount[res.name] += 1
self.assertTrue(resCount['POP'] > 1)
self.assertEqual(16, resCount['ALA'])
self.assertEqual(226, resCount['POP']) # 2x128 - overlapping
self.assertTrue(resCount['HOH'] > 1)
self.assertTrue(resCount['CL'] > 1)
self.assertEqual(resCount['CL'], resCount['NA'])
self.assertEqual(1, resCount['ALA'])
originalSize = max(pdb.positions) - min(pdb.positions)
deltaQ = resCount['CL'] - resCount['NA']
self.assertEqual(deltaQ, 10) # protein net q: +10
# Check _addIons did the right thing.
expected_ion_fraction = 1.0*molar/(55.4*molar)
total_water = resCount['HOH']
total_water_ions = resCount['HOH'] + resCount['CL'] + resCount['NA']
# total_water_ions - protein charge
expected_sodium = math.floor((total_water_ions-10)*expected_ion_fraction+0.5)
expected_chlorine = expected_sodium + 10
self.assertEqual(resCount['CL'], expected_chlorine)
self.assertEqual(resCount['NA'], expected_sodium)
# Check lipid numbering for repetitions
lipidIdList = [(r.chain.id, r.id) for r in modeller.topology.residues()
if r.name == 'POP']
self.assertEqual(len(lipidIdList), len(set(lipidIdList)))
# Check dimensions to see if padding was respected
originalSize = max(mol.positions) - min(mol.positions)
newSize = modeller.topology.getUnitCellDimensions()
for i in range(3):
self.assertTrue(newSize[i] >= originalSize[i]+0.5*nanometers)
self.assertTrue(newSize[i] >= originalSize[i]+1.1*nanometers)
def assertVecAlmostEqual(self, p1, p2, tol=1e-7):
......
wrappers/python/tests/TestPdbxFile.py
View file @ 8dd60914
......@@ -11,7 +11,29 @@ else:
class TestPdbxFile(unittest.TestCase):
"""Test the PDBx/mmCIF file parser"""
def test_FormatConversion(self):
"""Test conversion from PDB to PDBx"""
mol = PDBFile('systems/ala_ala_ala.pdb')
# Write to 'file'
output = StringIO()
PDBxFile.writeFile(mol.topology, mol.positions, output,
keepIds=True)
# Read from 'file'
input = StringIO(output.getvalue())
try:
pdbx = PDBxFile(input)
except Exception:
self.fail('Parser failed to read PDBx/mmCIF file')
# Close file handles
output.close()
input.close()
def test_Triclinic(self):
"""Test parsing a file that describes a triclinic box."""
pdb = PDBxFile('systems/triclinic.pdbx')
......
wrappers/python/tests/TestSimulatedTempering.py 0 → 100644
View file @ 8dd60914
import unittest
from simtk.openmm import *
from simtk.openmm.app import *
from simtk.unit import *
class TestSimulatedTempering(unittest.TestCase):
"""Test the SimulatedTempering class"""
def testHarmonicOscillator(self):
"""Test running simulated tempering on a harmonic oscillator."""
system = System()
system.addParticle(1.0)
system.addParticle(1.0)
force = HarmonicBondForce()
force.addBond(0, 1, 1.0, 1000.0)
system.addForce(force)
integrator = LangevinIntegrator(300*kelvin, 10/picosecond, 0.001*picosecond)
topology = Topology()
chain = topology.addChain()
residue = topology.addResidue('H2', chain)
topology.addAtom('H1', element.hydrogen, residue)
topology.addAtom('H2', element.hydrogen, residue)
simulation = Simulation(topology, system, integrator, Platform.getPlatformByName('Reference'))
st = SimulatedTempering(simulation, numTemperatures=10, minTemperature=200*kelvin, maxTemperature=400*kelvin, tempChangeInterval=5, reportInterval=10000)
self.assertEqual(10, len(st.temperatures))
self.assertEqual(200*kelvin, st.temperatures[0])
self.assertEqual(400*kelvin, st.temperatures[-1])
simulation.context.setPositions([Vec3(0, 0, 0), Vec3(1, 0, 0)])
# Run for a little while to let the weights stabilize.
st.step(10000)
# Run for a while and record the temperatures and distances.
distances = [[] for i in range(10)]
count = 0
for i in range(7000):
st.step(5)
pos = simulation.context.getState(getPositions=True).getPositions().value_in_unit(nanometers)
r = norm(pos[0]-pos[1])
distances[st.currentTemperature].append(r)
count += 1
# Check that it spent roughly equal time at each temperature, and that the distributions
# are correct.
for d, t in zip(distances, st.temperatures):
n = len(d)
assert count/20 < n < count/5
meanDist = sum(d)/n
assert 0.97 < meanDist < 1.03
meanEnergy = sum([0.5*1000*(r-1)**2 for r in d])/n
expectedEnergy = (0.5*MOLAR_GAS_CONSTANT_R*t).value_in_unit(kilojoules_per_mole)
self.assertAlmostEqual(expectedEnergy, meanEnergy, delta=expectedEnergy*0.3)
\ No newline at end of file
wrappers/python/tests/TestSimulation.py
View file @ 8dd60914
......@@ -146,6 +146,12 @@ class TestSimulation(unittest.TestCase):
self.assertTrue(endTime >= startTime+timedelta(seconds=5))
self.assertTrue(endTime < startTime+timedelta(seconds=10))
# Check that the time and step count are consistent.
time = simulation.context.getState().getTime().value_in_unit(picoseconds)
expectedTime = simulation.currentStep*integrator.getStepSize().value_in_unit(picoseconds)
self.assertAlmostEqual(expectedTime, time)
# Load the checkpoint and state and make sure they are both correct.
......
wrappers/python/tests/systems/DNA_mbondi3.inpcrd 0 → 100644
View file @ 8dd60914
default_name
628
-1.0164436 9.7204202 -1.3496514 -1.5620000 8.9700000 -1.1030000
-2.3800000 8.3410000 -2.1080000 -1.7179782 7.9601325 -2.8856681
-3.0821711 9.0510193 -2.5449544 -3.1520000 7.1860000 -1.5010000
-4.0109994 7.0112223 -2.1488220 -2.4040000 5.9370000 -1.5420000
-2.4650000 5.3370000 -0.2560000 -3.3042020 4.6425056 -0.2170330
-1.2970000 4.4760000 -0.1030000 0.0080000 4.8710000 0.0720000
0.2697674 5.9181807 0.1079058 0.8370000 3.8690000 0.1800000
0.0320000 2.7420000 0.0700000 0.3670000 1.3650000 0.1110000
1.4810000 0.8470000 0.2580000 -0.7570000 0.5590000 -0.0400000
-0.6224177 -0.4317938 -0.0253663 -2.0390000 1.0200000 -0.2090000
-2.9910000 0.0830000 -0.3390000 -2.8621932 -0.9187515 -0.3370285
-3.9355033 0.4149725 -0.4724460 -2.3650000 2.3010000 -0.2490000
-1.2880000 3.1010000 -0.1050000 -3.5320000 7.3410000 -0.0280000
-3.5123763 8.3641638 0.3473002 -2.5000000 6.5010000 0.7270000
-1.7984795 7.1599851 1.2385736 -3.0074918 5.8728140 1.4590750
-4.8180000 6.7680000 0.1780000 -5.8420000 7.9490000 1.9600000
-6.6600000 9.0120000 1.3350000 -5.0280000 8.3570000 3.1270000
-6.7800000 6.7170000 2.3660000 -7.0690000 5.7060000 1.3810000
-6.3331501 5.7993265 0.5823041 -8.0811551 5.8464212 1.0016260
-6.9570000 4.3290000 2.0030000 -7.5464700 3.6571448 1.3791130
-5.6030000 3.7970000 1.9340000 -5.2520000 3.3030000 3.2170000
-5.4904599 2.2410471 3.2760949 -3.7870000 3.3370000 3.3330000
-3.1070000 4.5160000 3.4680000 -3.6473914 5.4507935 3.4911987
-1.7720000 4.5350000 3.5730000 -1.2564625 5.4892729 3.6810955
-1.0930000 3.2840000 3.5380000 0.2390000 3.2410000 3.6390000
0.6830222 2.3343046 3.6098747 0.7696948 4.0943254 3.7404903
-1.7470000 2.1280000 3.4070000 -3.0960000 2.1240000 3.3020000
-3.7380000 1.0700000 3.1790000 -7.3140000 4.2390000 3.4870000
-7.9144987 5.0655961 3.8667881 -5.9660000 4.2150000 4.2080000
-5.8013377 5.1717774 4.7035427 -5.9646181 3.4169155 4.9504011
-7.9760000 3.0020000 3.7260000 -9.3240000 3.6410000 5.5670000
-10.6180000 4.0540000 4.9780000 -8.8450000 4.4470000 6.7120000
-9.3940000 2.0990000 5.9870000 -9.0950000 1.0920000 5.0010000
-8.5645733 1.5750459 4.1803818 -10.0221846 0.6359194 4.6539843
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-3.0000000 -7.1870000 1.5330000 -3.8598665 -7.0147340 2.1803433
-2.2590000 -5.9330000 1.5690000 -2.3230000 -5.3400000 0.2810000
-3.1663490 -4.6507105 0.2392668 -1.1520000 -4.4660000 0.1230000
0.1050000 -4.9780000 -0.0430000 0.2532187 -6.0476423 -0.0602193
1.1660000 -4.1730000 -0.1860000 2.1558360 -4.6096997 -0.3187345
0.9330000 -2.7680000 -0.1580000 1.9520000 -1.9160000 -0.2970000
1.7446019 -0.9278532 -0.2714544 2.8921980 -2.2629310 -0.4225705
-0.2910000 -2.2580000 0.0030000 -1.3530000 -3.0840000 0.1460000
-2.5040000 -2.6480000 0.2980000 -3.3790000 -7.3490000 0.0600000
-3.3542540 -8.3737211 -0.3107197 -2.3520000 -6.5080000 -0.6980000
-1.6479131 -7.1657806 -1.2075935 -2.8626471 -5.8846952 -1.4320509
-4.6690000 -6.7840000 -0.1480000 -4.9947625 -6.8385221 -1.0493905
wrappers/python/tests/systems/DNA_mbondi3.prmtop 0 → 100644
View file @ 8dd60914
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