diff --git a/CMakeLists.txt b/CMakeLists.txt
index 552aae0c891874ff9771e522e0df7c11899fcc84..c5a7f82a84892190623d18f200922d01fa694ae6 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -46,6 +46,7 @@ option(ENABLE_STATIC "whether static libraries should be compiled" OFF)
option(UBUNTU_LAYOUT "whether Debian/Ubuntu's lib and libexec directory layout should be used" OFF)
option(HIDDEN_VISIBILITY "on gcc, use -fvisibility=hidden" OFF)
option(ENABLE_MM "whether openmm support is added" OFF)
+option(ENABLE_PARASAIL, "whether parasail alignment library should be included" OFF)
if (CXX)
set(CMAKE_CXX_COMPILER ${CXX})
@@ -130,6 +131,11 @@ if(ENABLE_MM)
else()
set(_OPENMM OFF)
endif()
+if(ENABLE_PARASAIL)
+ set(_PARASAIL ON)
+else()
+ set(_PARASAIL OFF)
+endif()
if (UBUNTU_LAYOUT)
@@ -228,6 +234,10 @@ else(ENABLE_MM)
set(_OPENMM_PLUGINS "NONE")
endif(ENABLE_MM)
+if(ENABLE_PARASAIL)
+ find_package(Parasail REQUIRED)
+endif(ENABLE_PARASAIL)
+
if (ENABLE_STATIC)
set(Boost_LIBRARIES)
set(Boost_USE_STATIC_LIBS ON)
@@ -290,7 +300,7 @@ include_directories(${Boost_INCLUDE_DIRS}
${PNG_INCLUDE_DIRS}
${OPEN_MM_INCLUDE_DIRS}
${SQLITE3_INCLUDE_DIRS}
- )
+ ${PARASAIL_INCLUDE_DIR})
if (UNIX)
SET(CMAKE_SKIP_BUILD_RPATH FALSE)
@@ -342,6 +352,7 @@ message(STATUS
" SpaceNav Device support (-DENABLE_SPNAV) : ${_SPNAV}\n"
" OpenMM support (-DENABLE_MM) : ${_OPENMM}\n"
" OpenMM plugins (-DOPEN_MM_PLUGIN_DIR) : ${_OPENMM_PLUGINS}\n"
+ " Parasail alignment library (-DENABLE_PARASAIL) : ${_PARASAIL}\n"
" Optimize (-DOPTIMIZE) : ${_OPT}\n"
" Profiling support (-DPROFILE) : ${_PROFILE}\n"
" Double Precision (-DUSE_DOUBLE_PRECISION) : ${_DOUBLE_PREC}\n"
diff --git a/cmake_support/FindParasail.cmake b/cmake_support/FindParasail.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..40db27a15956429f31a3fce5508f433a91f7ffe9
--- /dev/null
+++ b/cmake_support/FindParasail.cmake
@@ -0,0 +1,11 @@
+# Try to find Parasail
+#
+# Find the native Parasail include and library. Sets:
+#
+# PARASAIL_INCLUDE_DIR - Parasail include dir.
+# PARASAIL_LIBRARY - Parasail library.
+
+find_path(PARASAIL_INCLUDE_DIR parasail.h HINTS PARASAIL_INCLUDE_DIR REQUIRED)
+find_library(PARASAIL_LIBRARY NAMES parasail HINTS PARASAIL_LIBRARY REQUIRED)
+
+mark_as_advanced (PARASAIL_LIBRARY PARASAIL_INCLUDE_DIR)
diff --git a/modules/bindings/doc/bindings.rst b/modules/bindings/doc/bindings.rst
index 06df24a3074a0b8c602e69763a1f7e68aefc3f24..9b2106fc6bc8b170f5acdd349e34e2342bb66aaf 100644
--- a/modules/bindings/doc/bindings.rst
+++ b/modules/bindings/doc/bindings.rst
@@ -25,3 +25,4 @@ So far, the binding module includes:
lga
cadscore
dockq
+ parasail
diff --git a/modules/bindings/doc/parasail.rst b/modules/bindings/doc/parasail.rst
new file mode 100644
index 0000000000000000000000000000000000000000..1750163aa68b0c7b91191d540ad0774b2001851c
--- /dev/null
+++ b/modules/bindings/doc/parasail.rst
@@ -0,0 +1,74 @@
+Parasail - Pairwise sequence alignments
+================================================================================
+
+Basic access to pairwise sequence alignment functionality in
+`parasail <https://github.com/jeffdaily/parasail/>`_ from
+within OpenStructure.
+
+Citation:
+
+ Jeff Daily. Parasail: SIMD C library for global, semi-global,
+ and local pairwise sequence alignments. (2016) BMC Bioinformatics
+
+Parasail support must be enabled at compile time - see installation
+instructions. Parasail allows to choose from various strategies but
+for the sake of simplicity, this Python binding always calls
+``parasail_<mode>_trace_scan_sat`` which seems reasonably fast
+across the global, semi-global and local modes.
+See parasail documentation for more information. Example usage:
+
+.. code-block:: python
+
+ from ost import bindings
+
+ print("parasail available?", bindings.ParasailAvailable())
+
+ s1 = seq.CreateSequence("A", "HEAGAWGHEE")
+ s2 = seq.CreateSequence("B", "PAWHEA")
+
+ aln = bindings.ParaGlobalAlign(s1, s2, gap_open_penalty=11,
+ gap_extension_penalty=1,
+ matrix="blosum62")
+
+ print(aln.ToString())
+
+
+.. method:: ParasailAvailable()
+
+ returns if OpenStructure has been compiled with parasail support
+
+.. method:: ParaGlobalAlign(s1, s2, gap_open_penalty=11, \
+ gap_extension_penalty=1, matrix="blosum62")
+
+ Calls parasail_nw_trace_scan_sat to perform a Needleman-Wunsch global
+ alignment.
+
+ :param s1: First sequence
+ :type s1: :class:`ost.seq.SequenceHandle`
+ :param s2: Second sequence
+ :type s2: :class:`ost.seq.SequenceHandle`
+ :param gap_open_penalty: Gap opening penalty for dynamic programming table
+ :type gap_open_penalty: :class:`int`
+ :param gap_extension_penalty: Gap extension penalty for dynamic programming
+ table
+ :type gap_extension_penalty: :class:`int`
+ :param matrix: Substution matrix - Anything that can be resolved by parasail.
+ E.g. pretty much the full BLOSUM/PAM families of matrices
+ ("blosum62", "pam100",...) for protein sequences, or
+ "nuc44"/"dnafull" for nucleotides.
+ :returns: :class:`ost.seq.AlignmentHandle`
+
+
+.. method:: ParaSemiGlobalAlign(s1, s2, gap_open_penalty=11, \
+ gap_extension_penalty=1, matrix="blosum62")
+
+ Same as :meth:`ParaGlobalAlign` but calling parasail_sg_trace_scan_sat to
+ perform a semi-global alignment.
+
+
+.. method:: ParaLocalAlign(s1, s2, gap_open_penalty=11, \
+ gap_extension_penalty=1, matrix="blosum62")
+
+ Same as :meth:`ParaGlobalAlign` but calling parasail_sw_trace_scan_sat to
+ perform a Smith-Waterman local alignment. The sequences in the returned
+ alignment might be subsequences of *s1*/*s2* but have offsets set.
diff --git a/modules/bindings/pymod/CMakeLists.txt b/modules/bindings/pymod/CMakeLists.txt
index 5e3f670ad285bd8a1a4910f70fa27323595cd9f6..afe90d392dae584309fdf8aa70a6d1b167f17c98 100644
--- a/modules/bindings/pymod/CMakeLists.txt
+++ b/modules/bindings/pymod/CMakeLists.txt
@@ -21,6 +21,7 @@ dockq.py
set(OST_BINDINGS_PYMOD_SOURCES
export_tmalign.cc
+ export_parasail.cc
wrap_bindings.cc
)
diff --git a/modules/bindings/pymod/export_parasail.cc b/modules/bindings/pymod/export_parasail.cc
new file mode 100644
index 0000000000000000000000000000000000000000..ea8a987c230f763d57bda2b29dda49cfa56652ed
--- /dev/null
+++ b/modules/bindings/pymod/export_parasail.cc
@@ -0,0 +1,42 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2020 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <boost/python.hpp>
+#include <ost/bindings/wrap_parasail.hh>
+using namespace boost::python;
+
+void export_parasail() {
+
+ def("ParaLocalAlign", &ost::bindings::ParaLocalAlign, (arg("s1"), arg("s2"),
+ arg("gap_open_penalty")=11,
+ arg("gap_extension_penalty")=1,
+ arg("matrix")="blosum62"));
+
+ def("ParaGlobalAlign", &ost::bindings::ParaGlobalAlign, (arg("s1"), arg("s2"),
+ arg("gap_open_penalty")=11,
+ arg("gap_extension_penalty")=1,
+ arg("matrix")="blosum62"));
+
+ def("ParaSemiGlobalAlign", &ost::bindings::ParaSemiGlobalAlign, (arg("s1"), arg("s2"),
+ arg("gap_open_penalty")=11,
+ arg("gap_extension_penalty")=1,
+ arg("matrix")="blosum62"));
+
+ def("ParasailAvailable", &ost::bindings::ParasailAvailable);
+}
diff --git a/modules/bindings/pymod/wrap_bindings.cc b/modules/bindings/pymod/wrap_bindings.cc
index c60893f21d62ca6082c5d57529ef46ccb40a88f3..c41157fc7a718e0778e5c8cab3319179caef51aa 100644
--- a/modules/bindings/pymod/wrap_bindings.cc
+++ b/modules/bindings/pymod/wrap_bindings.cc
@@ -24,8 +24,10 @@ using namespace boost::python;
void export_TMAlign();
+void export_parasail();
BOOST_PYTHON_MODULE(_ost_bindings)
{
export_TMAlign();
+ export_parasail();
}
diff --git a/modules/bindings/src/CMakeLists.txt b/modules/bindings/src/CMakeLists.txt
index 2ae1b882de59efa1ccb99947d4c7c44c99678098..fa8e8d3961efa374afdf007d3316cb94f7e88683 100644
--- a/modules/bindings/src/CMakeLists.txt
+++ b/modules/bindings/src/CMakeLists.txt
@@ -5,11 +5,13 @@ if (COMPILE_TMTOOLS)
endif()
set(OST_BINDINGS_SOURCES
-wrap_tmalign.cc)
+wrap_tmalign.cc
+wrap_parasail.cc)
set(OST_BINDINGS_HEADERS
-wrap_tmalign.hh)
+wrap_tmalign.hh
+wrap_parasail.hh)
module(NAME bindings SOURCES ${OST_BINDINGS_SOURCES}
HEADERS ${OST_BINDINGS_HEADERS} HEADER_OUTPUT_DIR ost/bindings
- DEPENDS_ON ost_geom ost_mol ost_seq)
+ DEPENDS_ON ost_geom ost_mol ost_seq LINK ${PARASAIL_LIBRARY})
diff --git a/modules/bindings/src/wrap_parasail.cc b/modules/bindings/src/wrap_parasail.cc
new file mode 100644
index 0000000000000000000000000000000000000000..34e9fe1ec8ba7fc348feb698f93c0405d811a337
--- /dev/null
+++ b/modules/bindings/src/wrap_parasail.cc
@@ -0,0 +1,195 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2024 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <ost/bindings/wrap_parasail.hh>
+
+#if OST_PARASAIL_ENABLED
+
+#include <parasail.h> // include for external parasail
+
+typedef parasail_result_t* (*parasail_aln_fn)(const char*, int, const char*,
+ int, int, int,
+ const parasail_matrix_t *);
+
+namespace{
+
+ost::seq::AlignmentHandle Align(const ost::seq::SequenceHandle& s1,
+ const ost::seq::SequenceHandle& s2,
+ int gap_open_penalty, int gap_extension_penalty,
+ const parasail_matrix_t* matrix,
+ parasail_aln_fn aln_fn,
+ bool set_offset) {
+
+ parasail_result_t *r = NULL;
+ parasail_traceback_t *traceback_r = NULL;
+
+ String s1_str = s1.GetGaplessString();
+ String s2_str = s2.GetGaplessString();
+
+ const char* s1_c_str = s1_str.c_str();
+ int s1_len = s1_str.size();
+ const char* s2_c_str = s2_str.c_str();
+ int s2_len = s2_str.size();
+
+ r = aln_fn(s1_c_str, s1_len, s2_c_str, s2_len, 11, 1, matrix);
+ traceback_r = parasail_result_get_traceback(r, s1_c_str, s1_len,
+ s2_c_str, s2_len, matrix,
+ '|', ':', '.');
+
+ ost::seq::AlignmentHandle aln = ost::seq::CreateAlignment();
+ ost::seq::SequenceHandle aln_s1 =
+ ost::seq::CreateSequence(s1.GetName(), String(traceback_r->query));
+
+ ost::seq::SequenceHandle aln_s2 =
+ ost::seq::CreateSequence(s2.GetName(), String(traceback_r->ref));
+
+ if(set_offset) {
+
+ /*
+ Tried the code below to set offsets but observed wrongly reported
+ offset which can be triggered from Python:
+
+ from ost import io
+ from ost import seq
+ from ost import bindings
+
+ test_seq = seq.CreateSequence("s", "MMDKHKYRVEIQQMMFVSGEINDPPVETTSLIEDIVRGQVIEILLQSNKTAHLRGSRSIL"
+ "PEDVIFLIRHDKAKVNRLRTYLSWKDLRKNAKDQDASAGVASGTGNPGAGGEDDLKKAGG"
+ "GEKDEKDGGNMMKVKKSQIKLPWELQFMFNEHPLENNDDNDDMDEDEREANIVTLKRLKM"
+ "ADDRTRNMTKEEYVHWSDCRQASFTFRKNKRFKDWSGISQLTEGKPHDDVIDILGFLTFE"
+ "IVCSLTETALKIKQREQVLQTQKDKSQQSSQDNTNFEFASSTLHRKKRLFDGPENVINPL"
+ "KPRHIEEAWRVLQTIDMRHRALTNFKGGRLSSKPIIM")
+
+
+ s = seq.CreateSequence("asdf", "MTKSIYIIIGYMLHDEEFFYFFFISFYTLWIVFFLLHLSFFSTLSFGIFHDFDTDVYIKVGNYIL"
+ "HFLELSKNSNLLKNSSEMLKHFRLASLMYMYVYTQMICPSLLGIRN")
+
+
+ aln = bindings.ParaLocalAlign(test_seq, s)
+
+ print(aln.ToString())
+ print(aln.GetSequence(0).offset)
+ print(aln.GetSequence(1).offset)
+
+
+
+
+ // Not sure if this is the most efficient way to set offsets,
+ // i.e. the index of start characters which are actually
+ // present in returned alignments
+ parasail_cigar_t* cigar = parasail_result_get_cigar(r, s1_c_str, s1_len,
+ s2_c_str, s2_len,
+ matrix);
+
+ aln_s1.SetOffset(cigar->beg_query);
+ aln_s2.SetOffset(cigar->beg_ref);
+ parasail_cigar_free(cigar);
+ */
+
+ // this is far from optimal but doesn't have the issue described above
+ aln_s1.SetOffset(s1.GetString().find(aln_s1.GetGaplessString()));
+ aln_s2.SetOffset(s2.GetString().find(aln_s2.GetGaplessString()));
+ }
+ aln.AddSequence(aln_s1);
+ aln.AddSequence(aln_s2);
+
+ parasail_result_free(r);
+ parasail_traceback_free(traceback_r);
+
+ return aln;
+}
+
+}
+
+namespace ost{ namespace bindings{
+
+ost::seq::AlignmentHandle ParaLocalAlign(const ost::seq::SequenceHandle& s1,
+ const ost::seq::SequenceHandle& s2,
+ int gap_open_penalty,
+ int gap_extension_penalty,
+ const String& matrix) {
+ const parasail_matrix_t* m = parasail_matrix_lookup(matrix.c_str());
+ return Align(s1, s2, gap_open_penalty, gap_extension_penalty,
+ m, parasail_sw_trace_scan_sat, true);
+}
+
+ost::seq::AlignmentHandle ParaGlobalAlign(const ost::seq::SequenceHandle& s1,
+ const ost::seq::SequenceHandle& s2,
+ int gap_open_penalty,
+ int gap_extension_penalty,
+ const String& matrix) {
+ const parasail_matrix_t* m = parasail_matrix_lookup(matrix.c_str());
+ return Align(s1, s2, gap_open_penalty, gap_extension_penalty,
+ m, parasail_nw_trace_scan_sat, false);
+}
+
+ost::seq::AlignmentHandle ParaSemiGlobalAlign(const ost::seq::SequenceHandle& s1,
+ const ost::seq::SequenceHandle& s2,
+ int gap_open_penalty,
+ int gap_extension_penalty,
+ const String& matrix) {
+ const parasail_matrix_t* m = parasail_matrix_lookup(matrix.c_str());
+ return Align(s1, s2, gap_open_penalty, gap_extension_penalty,
+ m, parasail_sg_trace_scan_sat, false);
+}
+
+bool ParasailAvailable() {
+ return true;
+}
+
+}} // ns
+
+#else
+
+namespace ost{ namespace bindings{
+
+ost::seq::AlignmentHandle ParaLocalAlign(const ost::seq::SequenceHandle& s1,
+ const ost::seq::SequenceHandle& s2,
+ int gap_open_penalty,
+ int gap_extension_penalty,
+ const String& matrix) {
+ throw ost::Error("Must enable Parasail when compiling OpenStructure to use "
+ "ParaLocalAlign");
+}
+
+ost::seq::AlignmentHandle ParaGlobalAlign(const ost::seq::SequenceHandle& s1,
+ const ost::seq::SequenceHandle& s2,
+ int gap_open_penalty,
+ int gap_extension_penalty,
+ const String& matrix) {
+ throw ost::Error("Must enable Parasail when compiling OpenStructure to use "
+ "ParaGlobalAlign");
+}
+
+ost::seq::AlignmentHandle ParaSemiGlobalAlign(const ost::seq::SequenceHandle& s1,
+ const ost::seq::SequenceHandle& s2,
+ int gap_open_penalty,
+ int gap_extension_penalty,
+ const String& matrix) {
+ throw ost::Error("Must enable Parasail when compiling OpenStructure to use "
+ "ParaSemiGlobalAlign");
+}
+
+bool ParasailAvailable() {
+ return false;
+}
+
+}} // ns
+
+#endif
diff --git a/modules/bindings/src/wrap_parasail.hh b/modules/bindings/src/wrap_parasail.hh
new file mode 100644
index 0000000000000000000000000000000000000000..785965467778b3925f20d39982862f27d4322194
--- /dev/null
+++ b/modules/bindings/src/wrap_parasail.hh
@@ -0,0 +1,49 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2024 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#ifndef OST_BINDINGS_PARASAIL_H
+#define OST_BINDINGS_PARASAIL_H
+
+#include <ost/seq/sequence_handle.hh>
+#include <ost/seq/alignment_handle.hh>
+
+namespace ost { namespace bindings {
+
+ost::seq::AlignmentHandle ParaLocalAlign(const ost::seq::SequenceHandle& s1,
+ const ost::seq::SequenceHandle& s2,
+ int gap_open_penalty = 11,
+ int gap_extension_penalty = 1,
+ const String& matrix="blosum62");
+
+ost::seq::AlignmentHandle ParaGlobalAlign(const ost::seq::SequenceHandle& s1,
+ const ost::seq::SequenceHandle& s2,
+ int gap_open_penalty = 11,
+ int gap_extension_penalty = 1,
+ const String& matrix="blosum62");
+
+ost::seq::AlignmentHandle ParaSemiGlobalAlign(const ost::seq::SequenceHandle& s1,
+ const ost::seq::SequenceHandle& s2,
+ int gap_open_penalty = 11,
+ int gap_extension_penalty = 1,
+ const String& matrix="blosum62");
+
+bool ParasailAvailable();
+
+}} //ns
+
+#endif
diff --git a/modules/config/CMakeLists.txt b/modules/config/CMakeLists.txt
index 826de455f14d4ce06edc720108634b9c1b5ab9f4..91d92232034d71c75657957a163111e1c7dcbd8c 100644
--- a/modules/config/CMakeLists.txt
+++ b/modules/config/CMakeLists.txt
@@ -50,6 +50,11 @@ if (ENABLE_INFO)
else()
set(info_enabled 0)
endif()
+if (ENABLE_PARASAIL)
+ set(parasail_enabled 1)
+else()
+ set(parasail_enabled 0)
+endif()
set(config_hh_generator "CMake")
set(CONFIG_HH_FILE "${CMAKE_CURRENT_SOURCE_DIR}/config.hh")
diff --git a/modules/config/config.hh.in b/modules/config/config.hh.in
index e48f750d40af524b7d7850773b510e1f9e926935..d84ca3b689e662ae4de739dadf9381b92570928d 100644
--- a/modules/config/config.hh.in
+++ b/modules/config/config.hh.in
@@ -31,5 +31,6 @@
#define OST_FFT_USE_THREADS @fftw_use_threads@
#define OST_UBUNTU_LAYOUT @ubuntu_layout@
#define OST_INFO_ENABLED @info_enabled@
+#define OST_PARASAIL_ENABLED @parasail_enabled@
#endif
diff --git a/modules/doc/install.rst b/modules/doc/install.rst
index 1fc703dd90c59bb4d5d338cdf623d030c062c105..42cf59b918bcc27161421c9ff6cbd36bb4407e05 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -57,6 +57,11 @@ If you would like to use the :mod:`molecular mechanics <ost.mol.mm>` module:
* `OpenMM <https://simtk.org/home/openmm>`_ (7.7.0)
+If you would like to do pairwise sequence alignments with parasail
+in the :mod:`bindings <ost.bindings>` module:
+
+* `parasail <https://github.com/jeffdaily/parasail/>`_ (2.6.2)
+
We do not provide backwards compatibility to Python 2.7. The last
release supporting Python 2.7 is 1.11.0.
@@ -187,6 +192,13 @@ can influence it.
* `OPEN_MM_PLUGIN_DIR`: the path for OpenMM plugins
* see example below for commonly used paths
+* `ENABLE_PARASAIL` controls whether parasail should be enabled. By default,
+ this is switched off. If it is turned on, you must also set the paths
+ to your parasail installation:
+
+ * `PARASAIL_INCLUDE_DIR`: the include path containing the file parasail.h
+ * `PARASAIL_LIBRARY`: the parasail library
+
* Several paths to other libraries can be set if they are not in the expected
locations: