First commit of Flexutils-Scripts

Author: DavidHerreros

.gitignore

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+# Python compilation files
+*.pyc
+
+# Ignore temporary packaging folder
+*.egg-info
+toolkit/*.egg-info
+
+# IDE files
+.idea

CHANGES.txt

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+include LICENSE
+include requirement/*.yml
+include icon_square.png
+include scripts/*.py
+include socket/*.py
+include viewers/*.py
+include *.sh
+include *.rst
+include *.txt
+include *.py

LICENSE

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+=======================
+Flexutils Scripts
+=======================
+
+This package provides a the environment and scripts needed by `scipion-em-flexutils <https://github.com/scipion-em/scipion-em-flexutils>`_ plugin

MANIFEST.in

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+# **************************************************************************
+# *
+# * Authors:     David Herreros Calero ([email protected])
+# *
+# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
+# *
+# * This program is free software; you can redistribute it and/or modify
+# * it under the terms of the GNU General Public License as published by
+# * the Free Software Foundation; either version 2 of the License, or
+# * (at your option) any later version.
+# *
+# * This program 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 General Public License for more details.
+# *
+# * You should have received a copy of the GNU General Public License
+# * along with this program; if not, write to the Free Software
+# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
+# * 02111-1307  USA
+# *
+# *  All comments concerning this program package may be sent to the
+# *  e-mail address '[email protected]'
+# *
+# **************************************************************************
+
+
+import os
+import sys
+import subprocess
+
+
+__version__ = "1.0.0"
+
+
+def getImagePath(image_name):
+    """Returns the absolute path to an image within the package."""
+    module_dir = os.path.dirname(__file__)  # Get the directory of this module
+    image_path = os.path.join(module_dir, 'media', image_name)
+    return image_path
+
+def getCondaBase():
+    try:
+        conda_base = subprocess.check_output("conda info --base", shell=True, text=True).strip()
+        return conda_base
+    except subprocess.CalledProcessError as e:
+        print(f"Error finding Conda base: {e}")
+        return None
+
+def getCondaSourceFile():
+    conda_source_file = f"{getCondaBase()}/etc/profile.d/conda.sh"
+    return conda_source_file
+
+def getProgram(program, env_name=None):
+    env_name = env_name if env_name is not None else f"flexutils-{__version__}"
+    return f"source {getCondaSourceFile()} && conda activate {env_name} && python {program}"
+
+def runProgram(program, args, env=None, cwd=None):
+    command = program + " " + args
+    subprocess.check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
+                          env=env, cwd=cwd)

README.rst

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+# **************************************************************************
+# *
+# * Authors:     David Herreros Calero ([email protected])
+# *
+# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
+# *
+# * This program is free software; you can redistribute it and/or modify
+# * it under the terms of the GNU General Public License as published by
+# * the Free Software Foundation; either version 2 of the License, or
+# * (at your option) any later version.
+# *
+# * This program 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 General Public License for more details.
+# *
+# * You should have received a copy of the GNU General Public License
+# * along with this program; if not, write to the Free Software
+# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
+# * 02111-1307  USA
+# *
+# *  All comments concerning this program package may be sent to the
+# *  e-mail address '[email protected]'
+# *
+# **************************************************************************
+

flexutils_scripts/__init__.py

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+# **************************************************************************
+# *
+# * Authors:  David Herreros Calero ([email protected])
+# *
+# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
+# *
+# * This program is free software; you can redistribute it and/or modify
+# * it under the terms of the GNU General Public License as published by
+# * the Free Software Foundation; either version 2 of the License, or
+# * (at your option) any later version.
+# *
+# * This program 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 General Public License for more details.
+# *
+# * You should have received a copy of the GNU General Public License
+# * along with this program; if not, write to the Free Software
+# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
+# * 02111-1307  USA
+# *
+# *  All comments concerning this program package may be sent to the
+# *  e-mail address '[email protected]'
+# *
+# **************************************************************************
+
+
+from flexutils_scripts import utils as utl
+
+
+def alignMaps(file_input, file_target, file_output, global_search=None):
+    # Align maps in ChimeraX using fitmap
+    _ = utl.alignMapsChimeraX(file_input, file_target, global_search=global_search,
+                              output_map=file_output)
+
+
+if __name__ == '__main__':
+    import argparse
+
+    # Input parameters
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--i', type=str, required=True)
+    parser.add_argument('--r', type=str, required=True)
+    parser.add_argument('--o', type=str, required=True)
+    parser.add_argument('--gs', type=int)
+
+    args = parser.parse_args()
+
+    if args.gs is None:
+        gs = None
+    else:
+        gs = args.gs
+
+    # Initialize volume slicer
+    alignMaps(args.i, args.r, args.o, gs)