From 9c8d226f0d939ef2427cb94ba040bf271c5357e4 Mon Sep 17 00:00:00 2001 From: karolamik13 Date: Mon, 9 Oct 2023 21:42:26 +0200 Subject: [PATCH 1/6] Changes in ImportError for hpb.so --- prody/proteins/interactions.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/prody/proteins/interactions.py b/prody/proteins/interactions.py index d0d5a4cd3..95d1d7067 100644 --- a/prody/proteins/interactions.py +++ b/prody/proteins/interactions.py @@ -181,7 +181,7 @@ def calcHydrophobicOverlapingAreas(atoms, **kwargs): import hpb imported_hpb = True except ImportError: - raise ImportError('Please provide hpb.so file into the directory.') + raise ImportError('Please provide hpb.so file.') if imported_hpb: selection = kwargs.pop('selection', 'protein and noh') @@ -254,7 +254,7 @@ def calcSASA(atoms, **kwargs): import hpb imported_hpb = True except ImportError: - raise ImportError('Please provide hpb.so file into the directory.') + raise ImportError('Please provide hpb.so file.') if imported_hpb: selection = kwargs.pop('selection', 'protein and noh') @@ -317,7 +317,7 @@ def calcVolume(atoms, **kwargs): import hpb imported_hpb = True except ImportError: - raise ImportError('Please provide hpb.so file into the directory.') + raise ImportError('Please provide hpb.so file.') if imported_hpb: selection = kwargs.pop('selection', 'protein and noh') @@ -1066,7 +1066,7 @@ def calcHydrophobic(atoms, **kwargs): try: hpb_overlaping_results = calcHydrophobicOverlapingAreas(atoms_hydrophobic, cumulative_values='pairs') except: - LOGGER.info('Please provide hpb.so file into the directory to obtain additional data.') + LOGGER.info('Please provide hpb.so file to obtain additional data.') LOGGER.info('Calculating hydrophobic interactions.') Hydrophobic_calculations = [] @@ -1137,7 +1137,7 @@ def calcHydrophobic(atoms, **kwargs): import hpb imported_hpb = True except ImportError: - LOGGER.info('Please provide hpb.so file into the directory.') + LOGGER.info('Please provide hpb.so file.') if imported_hpb: Hydrophobic_calculations = sorted(Hydrophobic_calculations, key=lambda x : x[-2]) From 5b12908efefe8d511114561510a5b3f707dc4d45 Mon Sep 17 00:00:00 2001 From: karolamik13 Date: Mon, 9 Oct 2023 22:07:32 +0200 Subject: [PATCH 2/6] hpb description in the main ProDy README --- README.rst | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/README.rst b/README.rst index 773b828c8..b833599bb 100644 --- a/README.rst +++ b/README.rst @@ -72,3 +72,15 @@ with ProDy. The original CE method was developed by Ilya Shindyalov and Philip Bourne. The Python version which is used by ProDy is developed by Jason Vertrees and available under the New BSD license. +Hbp module: The calculation of hydrophobic interactions, solvent accessible surface +area (SASA) and volume for each residue is using geometric methods based on the +information of the atoms in the molecule. The methods have been programmed in C++ +and can be compiled as a python module “hpb.so” which is then used by ProDy. +Files for compilation are localized at ~/prody/proteins/hpbmodule folder and +required C++ and Fortran compiler. After compilation hpb.so file can be +storage in ~/prody/proteins folder in ProDy or in the local directory which +is used to perform calulations. +C++ code was developed by Xin Cao and Fortran code by Xin Cao, Michelle H. Hummel, +Bihua Yu, and Evangelos A. Coutsias (License in ~/prody/proteins/hpbmodule +folder). Details of the method can be found in the Supplementary Material of +InSty manuscript (soon will be submited for publication). \ No newline at end of file From 5911002f57f6350c1bbf0fec8698c129c211623d Mon Sep 17 00:00:00 2001 From: karolamik13 Date: Tue, 10 Oct 2023 08:20:07 +0200 Subject: [PATCH 3/6] More information in README (main ProDy) --- README.rst | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/README.rst b/README.rst index b833599bb..6a70871bb 100644 --- a/README.rst +++ b/README.rst @@ -79,8 +79,12 @@ and can be compiled as a python module “hpb.so” which is then used by ProDy. Files for compilation are localized at ~/prody/proteins/hpbmodule folder and required C++ and Fortran compiler. After compilation hpb.so file can be storage in ~/prody/proteins folder in ProDy or in the local directory which -is used to perform calulations. -C++ code was developed by Xin Cao and Fortran code by Xin Cao, Michelle H. Hummel, -Bihua Yu, and Evangelos A. Coutsias (License in ~/prody/proteins/hpbmodule -folder). Details of the method can be found in the Supplementary Material of -InSty manuscript (soon will be submited for publication). \ No newline at end of file +is used to perform calulations. The precompiled versions for Python 2.7, +3.8, 3.9, and 3.10 are availabe in ~/prody/proteins/hpbmodule. The user can +choose the correct version of hpb.so and copy to the ~/prody/proteins or +local directory. +C++ code of hpb.so was developed by Xin Cao and Fortran code by Xin Cao, +Michelle H. Hummel, Bihua Yu, and Evangelos A. Coutsias (License in +~/prody/proteins/hpbmodule folder). Details of the method can be found +in the Supplementary Material of InSty manuscript +(soon will be submited for publication). \ No newline at end of file From 7f2d9cbffd3ae0d455ab3eb6e1f22f2c1b6fe788 Mon Sep 17 00:00:00 2001 From: karolamik13 Date: Tue, 10 Oct 2023 10:32:37 +0200 Subject: [PATCH 4/6] Fixing typos in README (main ProDy) --- README.rst | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.rst b/README.rst index 6a70871bb..f4752f2b1 100644 --- a/README.rst +++ b/README.rst @@ -76,15 +76,15 @@ Hbp module: The calculation of hydrophobic interactions, solvent accessible surf area (SASA) and volume for each residue is using geometric methods based on the information of the atoms in the molecule. The methods have been programmed in C++ and can be compiled as a python module “hpb.so” which is then used by ProDy. -Files for compilation are localized at ~/prody/proteins/hpbmodule folder and +Files for compilation are stored at /prody/proteins/hpbmodule folder and required C++ and Fortran compiler. After compilation hpb.so file can be storage in ~/prody/proteins folder in ProDy or in the local directory which is used to perform calulations. The precompiled versions for Python 2.7, -3.8, 3.9, and 3.10 are availabe in ~/prody/proteins/hpbmodule. The user can -choose the correct version of hpb.so and copy to the ~/prody/proteins or +3.8, 3.9, and 3.10 are availabe in /prody/proteins/hpbmodule. The user can +choose the correct version of hpb.so and copy to the /prody/proteins or local directory. C++ code of hpb.so was developed by Xin Cao and Fortran code by Xin Cao, Michelle H. Hummel, Bihua Yu, and Evangelos A. Coutsias (License in -~/prody/proteins/hpbmodule folder). Details of the method can be found +/prody/proteins/hpbmodule folder). Details of the method can be found in the Supplementary Material of InSty manuscript -(soon will be submited for publication). \ No newline at end of file +(soon will be submitted for publication). \ No newline at end of file From 34ec4905cd031ff43e49244f0e5b74f3920a8db6 Mon Sep 17 00:00:00 2001 From: karolamik13 Date: Tue, 10 Oct 2023 10:49:35 +0200 Subject: [PATCH 5/6] Last typos in README (main ProDy) --- README.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.rst b/README.rst index f4752f2b1..c89ffc904 100644 --- a/README.rst +++ b/README.rst @@ -76,15 +76,15 @@ Hbp module: The calculation of hydrophobic interactions, solvent accessible surf area (SASA) and volume for each residue is using geometric methods based on the information of the atoms in the molecule. The methods have been programmed in C++ and can be compiled as a python module “hpb.so” which is then used by ProDy. -Files for compilation are stored at /prody/proteins/hpbmodule folder and +Files for compilation are stored at prody/proteins/hpbmodule folder and required C++ and Fortran compiler. After compilation hpb.so file can be storage in ~/prody/proteins folder in ProDy or in the local directory which is used to perform calulations. The precompiled versions for Python 2.7, -3.8, 3.9, and 3.10 are availabe in /prody/proteins/hpbmodule. The user can -choose the correct version of hpb.so and copy to the /prody/proteins or +3.8, 3.9, and 3.10 are availabe in prody/proteins/hpbmodule. The user can +choose the correct version of hpb.so and copy to the prody/proteins or local directory. C++ code of hpb.so was developed by Xin Cao and Fortran code by Xin Cao, Michelle H. Hummel, Bihua Yu, and Evangelos A. Coutsias (License in -/prody/proteins/hpbmodule folder). Details of the method can be found +prody/proteins/hpbmodule folder). Details of the method can be found in the Supplementary Material of InSty manuscript (soon will be submitted for publication). \ No newline at end of file From c32fcfa6d8c2f4596380b2b8b79ccda7326c25eb Mon Sep 17 00:00:00 2001 From: karolamik13 Date: Tue, 10 Oct 2023 10:57:46 +0200 Subject: [PATCH 6/6] Removed typo in README (~/) --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index c89ffc904..d628bfbbd 100644 --- a/README.rst +++ b/README.rst @@ -78,7 +78,7 @@ information of the atoms in the molecule. The methods have been programmed in C+ and can be compiled as a python module “hpb.so” which is then used by ProDy. Files for compilation are stored at prody/proteins/hpbmodule folder and required C++ and Fortran compiler. After compilation hpb.so file can be -storage in ~/prody/proteins folder in ProDy or in the local directory which +storage in prody/proteins folder in ProDy or in the local directory which is used to perform calulations. The precompiled versions for Python 2.7, 3.8, 3.9, and 3.10 are availabe in prody/proteins/hpbmodule. The user can choose the correct version of hpb.so and copy to the prody/proteins or