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This is the version 0.7.6.7 (JUL 2022).

There are only a few small changes to the previous version:
1) Support for installation on the Apple Silicon chips
2) Removal of two rare, but potentially segmentation faul causing bugs.

NOTE: This version did not have the tests run, thus the expected values may have changes a little.
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Michal Tykac authored and Michal Tykac committed Jul 25, 2022
2 parents 6b40215 + 949ed6d commit 856637e
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2 changes: 1 addition & 1 deletion README.md
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ProSHADE
========

Protein Shape Description and Symmetry Detection version 0.7.6.6 (JUL 2022)
Protein Shape Description and Symmetry Detection version 0.7.6.7 (JUL 2022)

# Introduction

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14 changes: 11 additions & 3 deletions proshade/CMakeLists.txt
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Expand Up @@ -47,7 +47,7 @@ endif ( ${PRODUCE_PYTHON_BINDINGS} MATCHES 1 )

##########################################################################################
################################### Set project name
project ( proshade VERSION 0.7.6.6 LANGUAGES CXX C )
project ( proshade VERSION 0.7.6.7 LANGUAGES CXX C )

##########################################################################################
################################### Force C++11
Expand Down Expand Up @@ -270,10 +270,18 @@ if ( "${CMAKE_SYSTEM_NAME}" STREQUAL "Windows" )
COMMAND type nul > ${PROJECT_SOURCE_DIR}/extern/buildSOFT2
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/extern/soft-2.0
)
else ( "${CMAKE_SYSTEM_NAME}" STREQUAL "Windows" )
else ( "${CMAKE_SYSTEM_NAME}" STREQUAL "Windows" )
SET ( CHIPSET_ARCHITECTURE_SOFT_COMMAND "uname" )
SET ( CHIPSET_ARCHITECTURE_SOFT_COMMAND_ARGS "-m" )
execute_process ( COMMAND ${CHIPSET_ARCHITECTURE_SOFT_COMMAND} ${CHIPSET_ARCHITECTURE_SOFT_COMMAND_ARGS}
WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
RESULT_VARIABLE SOFT_ARCH_BUILD_RESULT
OUTPUT_VARIABLE SOFT_ARCH_BUILD
OUTPUT_STRIP_TRAILING_WHITESPACE )
message ( STATUS "SOFT library architecture : " ${SOFT_ARCH_BUILD} )
add_custom_command (
OUTPUT ${PROJECT_SOURCE_DIR}/extern/buildSOFT2
COMMAND make lib FFTWINC=-I${FFTW3_INC_PATH} FFTWLIB1=-L${FFTW3_LIB_PATH} FFTWLIB2=-lfftw3 > ${CMAKE_SOURCE_DIR}/extern/soft-2.0/install.log.txt 2> ${CMAKE_SOURCE_DIR}/extern/soft-2.0/install.err.txt
COMMAND make lib SOFTLIBARCH=${SOFT_ARCH_BUILD} FFTWINC=-I${FFTW3_INC_PATH} FFTWLIB1=-L${FFTW3_LIB_PATH} FFTWLIB2=-lfftw3 > ${CMAKE_SOURCE_DIR}/extern/soft-2.0/install.log.txt 2> ${CMAKE_SOURCE_DIR}/extern/soft-2.0/install.err.txt
COMMAND touch ${PROJECT_SOURCE_DIR}/extern/buildSOFT2
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/extern/soft-2.0
)
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2 changes: 1 addition & 1 deletion proshade/extern/soft-2.0/Makefile
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Expand Up @@ -33,7 +33,7 @@
## CFLAGS = -O3 -pg
## CFLAGS = -O3
## CFLAGS = -Wall -g -I./include $(FFTWINC)
CFLAGS = -Wall -O3 -g -I./include $(FFTWINC) -fPIC -std=c99
CFLAGS = -Wall -O3 -g -I./include $(FFTWINC) -fPIC -std=c99 -arch $(SOFTLIBARCH)

FFTWLIB := $(FFTWLIB1) $(FFTWLIB2)

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4 changes: 2 additions & 2 deletions proshade/interfacedCodes/EMDA/symmetryPredictions/getMaskedSymmetryPredictions.py
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Expand Up @@ -83,7 +83,7 @@
outputFileName = "V29_results_allKnownEMDB_COM_resol-"
EMDBDataPath = "/Users/mysak/BioCEV/proshade/xx_EMDBSymmetry"
unreleasedIDsList = [ "EMD-10163", "EMD-10165", "EMD-10166", "EMD-10168", "EMD-10169", "EMD-10170", "EMD-10174", "EMD-21320", "EMD-4320", "EMD-4522", "EMD-4523", "EMD-4524", "EMD-4606", "EMD-4607", "EMD-4718", "EMD-5039", "EMD-6758", "EMD-8144", "EMD-8145", "EMD-1300" ]
tooLargeIDsList = [ "EMD-0174", "EMD-11111", "EMD-20091", "EMD-21648", "EMD-0880", "EMD-11008", "EMD-0436", "EMD-11040", "EMD-0618", "EMD-10768", "EMD-10926", "EMD-1610", "EMD-23042" ]
tooLargeIDsList = [ "EMD-0174", "EMD-11111", "EMD-20091", "EMD-21648", "EMD-0880", "EMD-11008", "EMD-0436", "EMD-11040", "EMD-0618", "EMD-10768", "EMD-10926", "EMD-1610", "EMD-23042", "EMD-1472" ]

### 2047 causes segfault and I have no idea why ...

Expand All @@ -95,7 +95,7 @@
### no user manipulation is required.
###

startFrom = 382
startFrom = 782
resolutionFilename = resolution
outResCondensed = 0
outResAxes = 0
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151 changes: 100 additions & 51 deletions ...de/interfacedCodes/EMDA/symmetryPredictions_centre/getMaskedSymmetryPredictions_centre.py
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4 changes: 2 additions & 2 deletions proshade/src/bin/bin.cpp
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Expand Up @@ -19,15 +19,15 @@
\author Michal Tykac
\author Garib N. Murshudov
\version 0.7.6.6
\version 0.7.6.7
\date JUL 2022
*/

//==================================================== DOxygen main page specifications

/*! \mainpage ProSHADE Documentation
*
* Protein Shape Description and Symmetry Detection version 0.7.6.6 (JUL 2022)
* Protein Shape Description and Symmetry Detection version 0.7.6.7 (JUL 2022)
*
* \section intro Introduction
*
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2 changes: 1 addition & 1 deletion proshade/src/proshade/ProSHADE.cpp
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Expand Up @@ -18,7 +18,7 @@
\author Michal Tykac
\author Garib N. Murshudov
\version 0.7.6.6
\version 0.7.6.7
\date JUL 2022
*/

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2 changes: 1 addition & 1 deletion proshade/src/proshade/ProSHADE.hpp
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Expand Up @@ -18,7 +18,7 @@
\author Michal Tykac
\author Garib N. Murshudov
\version 0.7.6.6
\version 0.7.6.7
\date JUL 2022
*/

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27 changes: 15 additions & 12 deletions proshade/src/proshade/ProSHADE_data.cpp
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Expand Up @@ -17,7 +17,7 @@
\author Michal Tykac
\author Garib N. Murshudov
\version 0.7.6.6
\version 0.7.6.7
\date JUL 2022
*/

Expand Down Expand Up @@ -667,7 +667,8 @@ void ProSHADE_internal_data::ProSHADE_data::readInMAP ( ProSHADE_settings* setti
}

//================================================ Apply Fourier weights
ProSHADE_internal_io::applyWeights ( this->internalMap, settings->fourierWeightsFileName, this->xDimIndices, this->yDimIndices, this->zDimIndices, settings->verbose, settings->messageShift,
ProSHADE_internal_io::applyWeights ( this->internalMap, settings->fourierWeightsFileName,
this->xDimIndices, this->yDimIndices, this->zDimIndices, settings->verbose, settings->messageShift,
weightsArr, weigXDim, weigYDim, weigZDim );

//================================================ Remove negative values if so required
Expand Down Expand Up @@ -728,7 +729,7 @@ void ProSHADE_internal_data::ProSHADE_data::readInPDB ( ProSHADE_settings* setti
{
settings->setResolution ( 8.0 );
}

//================================================ Open PDB file for reading
gemmi::Structure pdbFile = gemmi::read_structure ( gemmi::MaybeGzipped ( this->fileName ) );

Expand Down Expand Up @@ -1488,33 +1489,36 @@ void ProSHADE_internal_data::ProSHADE_data::reSampleMap ( ProSHADE_settings* set
//================================================ Now re-sample the map
if ( settings->changeMapResolution )
{
ProSHADE_internal_mapManip::reSampleMapToResolutionFourier ( this->internalMap, settings->requestedResolution * settings->resolutionOversampling, this->xDimIndices, this->yDimIndices, this->zDimIndices,
ProSHADE_internal_mapManip::reSampleMapToResolutionFourier ( this->internalMap, settings->requestedResolution * settings->resolutionOversampling,
this->xDimIndices, this->yDimIndices, this->zDimIndices,
this->xDimSize, this->yDimSize, this->zDimSize, changeVals );

if ( settings->changeMapResolutionTriLinear )
{
ProSHADE_internal_messages::printWarningMessage ( settings->verbose, "!!! ProSHADE WARNING !!! Requested both Fourier-space and real-space map re-sampling. Defaulting to only Fourier space re-samplling.", "WM00049" );
}
}

if ( settings->changeMapResolutionTriLinear && !settings->changeMapResolution )
{
ProSHADE_internal_mapManip::reSampleMapToResolutionTrilinear ( this->internalMap, settings->requestedResolution * settings->resolutionOversampling, this->xDimIndices, this->yDimIndices, this->zDimIndices,
ProSHADE_internal_mapManip::reSampleMapToResolutionTrilinear ( this->internalMap, settings->requestedResolution * settings->resolutionOversampling,
this->xDimIndices, this->yDimIndices, this->zDimIndices,
this->xDimSize, this->yDimSize, this->zDimSize, changeVals );

}

//================================================ Set the internal values to reflect the new map size
this->xDimIndices += static_cast<proshade_unsign> ( changeVals[0] );
this->yDimIndices += static_cast<proshade_unsign> ( changeVals[1] );
this->zDimIndices += static_cast<proshade_unsign> ( changeVals[2] );
this->xDimIndices = static_cast< proshade_unsign > ( static_cast< proshade_signed > ( this->xDimIndices ) + static_cast< proshade_signed > ( changeVals[0] ) );
this->yDimIndices = static_cast< proshade_unsign > ( static_cast< proshade_signed > ( this->yDimIndices ) + static_cast< proshade_signed > ( changeVals[1] ) );
this->zDimIndices = static_cast< proshade_unsign > ( static_cast< proshade_signed > ( this->zDimIndices ) + static_cast< proshade_signed > ( changeVals[2] ) );

this->xGridIndices = this->xDimIndices;
this->yGridIndices = this->yDimIndices;
this->zGridIndices = this->zDimIndices;

this->xTo += static_cast<proshade_unsign> ( changeVals[0] );
this->yTo += static_cast<proshade_unsign> ( changeVals[1] );
this->zTo += static_cast<proshade_unsign> ( changeVals[2] );
this->xTo += static_cast< proshade_signed > ( changeVals[0] );
this->yTo += static_cast< proshade_signed > ( changeVals[1] );
this->zTo += static_cast< proshade_signed > ( changeVals[2] );

this->xDimSize = changeVals[3];
this->yDimSize = changeVals[4];
Expand All @@ -1532,7 +1536,6 @@ void ProSHADE_internal_data::ProSHADE_data::reSampleMap ( ProSHADE_settings* set
//================================================ Move by indices (this should be sufficient)
ProSHADE_internal_mapManip::moveMapByIndices ( &xMov, &yMov, &zMov, this->xDimSize, this->yDimSize, this->zDimSize, &this->xFrom, &this->xTo,
&this->yFrom, &this->yTo, &this->zFrom, &this->zTo, &this->xAxisOrigin, &this->yAxisOrigin, &this->zAxisOrigin );

ProSHADE_internal_mapManip::moveMapByFourier ( this->internalMap, xMov, yMov, zMov, this->xDimSize, this->yDimSize, this->zDimSize,
static_cast< proshade_signed > ( this->xDimIndices ), static_cast< proshade_signed > ( this->yDimIndices ), static_cast< proshade_signed > ( this->zDimIndices ) );

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2 changes: 1 addition & 1 deletion proshade/src/proshade/ProSHADE_data.hpp
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Expand Up @@ -17,7 +17,7 @@
\author Michal Tykac
\author Garib N. Murshudov
\version 0.7.6.6
\version 0.7.6.7
\date JUL 2022
*/

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2 changes: 1 addition & 1 deletion proshade/src/proshade/ProSHADE_distances.cpp
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Expand Up @@ -16,7 +16,7 @@
\author Michal Tykac
\author Garib N. Murshudov
\version 0.7.6.6
\version 0.7.6.7
\date JUL 2022
*/

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2 changes: 1 addition & 1 deletion proshade/src/proshade/ProSHADE_distances.hpp
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Expand Up @@ -16,7 +16,7 @@
\author Michal Tykac
\author Garib N. Murshudov
\version 0.7.6.6
\version 0.7.6.7
\date JUL 2022
*/

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2 changes: 1 addition & 1 deletion proshade/src/proshade/ProSHADE_exceptions.cpp
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Expand Up @@ -15,7 +15,7 @@
\author Michal Tykac
\author Garib N. Murshudov
\version 0.7.6.6
\version 0.7.6.7
\date JUL 2022
*/

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2 changes: 1 addition & 1 deletion proshade/src/proshade/ProSHADE_exceptions.hpp
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Expand Up @@ -16,7 +16,7 @@
\author Michal Tykac
\author Garib N. Murshudov
\version 0.7.6.6
\version 0.7.6.7
\date JUL 2022
*/

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2 changes: 1 addition & 1 deletion proshade/src/proshade/ProSHADE_io.cpp
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Expand Up @@ -15,7 +15,7 @@
\author Michal Tykac
\author Garib N. Murshudov
\version 0.7.6.6
\version 0.7.6.7
\date JUL 2022
*/

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2 changes: 1 addition & 1 deletion proshade/src/proshade/ProSHADE_io.hpp
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Expand Up @@ -15,7 +15,7 @@
\author Michal Tykac
\author Garib N. Murshudov
\version 0.7.6.6
\version 0.7.6.7
\date JUL 2022
*/

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2 changes: 1 addition & 1 deletion proshade/src/proshade/ProSHADE_mapManip.cpp
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Expand Up @@ -15,7 +15,7 @@
\author Michal Tykac
\author Garib N. Murshudov
\version 0.7.6.6
\version 0.7.6.7
\date JUL 2022
*/

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2 changes: 1 addition & 1 deletion proshade/src/proshade/ProSHADE_mapManip.hpp
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Expand Up @@ -15,7 +15,7 @@
\author Michal Tykac
\author Garib N. Murshudov
\version 0.7.6.6
\version 0.7.6.7
\date JUL 2022
*/

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7 changes: 3 additions & 4 deletions proshade/src/proshade/ProSHADE_maths.cpp
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Expand Up @@ -16,7 +16,7 @@

\author Michal Tykac
\author Garib N. Murshudov
\version 0.7.6.6
\version 0.7.6.7
\date JUL 2022
*/

Expand Down Expand Up @@ -1308,7 +1308,6 @@ void ProSHADE_internal_maths::getRotationMatrixFromEulerZYZAngles ( proshade_sin
//============================================ Run LAPACK ZGESDD
dgeev_ ( &jobLeftEigs, &jobRightEigs, &dim, matrixToDecompose, &dim, eigValReal, eigValImag, leftEigVectors, &dim,
rightEigVectors, &dim, work, &workSize, &returnValue );

//============================================ Check for errors
if ( returnValue != 0 )
{
Expand Down Expand Up @@ -1402,7 +1401,7 @@ void ProSHADE_internal_maths::getRotationMatrixFromEulerZYZAngles ( proshade_sin
*z *= -1.0;
*ang *= -1.0;
}

//================================================ Free memory
delete[] eigValReal;
delete[] eigValImag;
Expand Down Expand Up @@ -1441,7 +1440,7 @@ void ProSHADE_internal_maths::getRotationMatrixFromEulerZYZAngles ( proshade_sin

//================================================ Standardise angle to range 0 to 2pi
if ( *ang < 0.0 ) { *ang = ( 2.0 * M_PI ) + *ang; }

//================================================ Done
return ;

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2 changes: 1 addition & 1 deletion proshade/src/proshade/ProSHADE_maths.hpp
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Expand Up @@ -16,7 +16,7 @@
\author Michal Tykac
\author Garib N. Murshudov
\version 0.7.6.6
\version 0.7.6.7
\date JUL 2022
*/

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2 changes: 1 addition & 1 deletion proshade/src/proshade/ProSHADE_messages.cpp
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Expand Up @@ -15,7 +15,7 @@
\author Michal Tykac
\author Garib N. Murshudov
\version 0.7.6.6
\version 0.7.6.7
\date JUL 2022
*/

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2 changes: 1 addition & 1 deletion proshade/src/proshade/ProSHADE_messages.hpp
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Expand Up @@ -15,7 +15,7 @@
\author Michal Tykac
\author Garib N. Murshudov
\version 0.7.6.6
\version 0.7.6.7
\date JUL 2022
*/

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2 changes: 1 addition & 1 deletion proshade/src/proshade/ProSHADE_misc.cpp
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Expand Up @@ -15,7 +15,7 @@
\author Michal Tykac
\author Garib N. Murshudov
\version 0.7.6.6
\version 0.7.6.7
\date JUL 2022
*/

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2 changes: 1 addition & 1 deletion proshade/src/proshade/ProSHADE_misc.hpp
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Expand Up @@ -16,7 +16,7 @@
\author Michal Tykac
\author Garib N. Murshudov
\version 0.7.6.6
\version 0.7.6.7
\date JUL 2022
*/

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