First commit

Author: abartesaghi

FrealignEulerAnglesConvention.txt

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+From ccp.f
+C - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+C  Below is the standard Eulerian rotation ZYZ
+C    The model or its transform is rotated first by PHI around Z, then 
+C    by THETA about the new Y, and thirdly by PSI about the new Z.
+C
+C    The rotation matrix used is  R=R(psi)*R(theta)*R(phi) as in Spider
+C
+C                 c  s  0          c  0 -s          c  s  0
+C                -s  c  0     *    0  1  0     *   -s  c  0
+C                 0  0  1          s  0  c          0  0  1
+C
+C                 about Z          about Y          about Z
+C - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+
+DM(1) = CPHI * CTHE * CPSI - SPHI * SPSI
+DM(2) = SPHI * CTHE * CPSI + CPHI * SPSI
+DM(3) = - STHE * CPSI
+DM(4) = - CPHI * CTHE * SPSI - SPHI * CPSI
+DM(5) = - SPHI * CTHE * SPSI + CPHI * CPSI
+DM(6) = STHE * SPSI
+DM(7) = STHE * CPHI
+DM(8) = STHE * SPHI
+DM(9) = CTHE

INSTALL

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+Installing CSP
+--------------
+
+1. Run the configuration script 
+   ./configure.sh. /PATH/TO/FREALIGN/EXECUTABLE/frealign_v8.exe
+   
+   This creates the ./bin/ folder, runs cmake to create the Makefile,
+   and link the FREALIGN executable where CSP needed it.
+
+2. Run ./make_csp.sh to build the framework, the executable is
+   ./bin/csp
+
+3. Link the frealign executable frealign_v8.exe in the FREALIGN
+   folder. See next section and read the output of the configure.sh
+
+To run an experiment, set the configuration in parameters.config,
+prepare the data files and run it with run_csp_experiment.sh. Read
+README for more information.
+
+
+FREALING installation
+---------------------
+
+The scripts to run FREALING are included in this release and are
+located in the ./frealign/ folder (${CSP_DIR}/frealign).
+
+The scripts have variations with respect to their last version. I'd
+tried to reduce the amount of these variations to maintain "backwards
+compatibility". The main change is that SPA_DIR should be the folder
+where this folder, i.e. the folder where the CSP scripts are located,
+CSP_DIR as is referred in the README file.
+
+In order to be able to run FREALING, CSP expected to find the
+executable in the ${CSP_DIR}/frealign folder. Then it must be linked
+or copied to this folder. The full path to the executable is given as
+the parameter to the configuration script.
+
+Also CSP_DIR is redefined in the run_usp_experiment.sh and
+run_frealign_*.sh scripts. This is done automatically.

LICENSE

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+Copyright (c) 2023, Bartesaghi Lab
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+    list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+    this list of conditions and the following disclaimer in the documentation
+    and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+    contributors may be used to endorse or promote products derived from
+    this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.