packmol-memgen-minimal 1.1.16__py3-none-any.whl

packmol_memgen_minimal-1.1.16.dist-info/METADATA

@@ -0,0 +1,664 @@
+Metadata-Version: 2.4
+Name: packmol-memgen-minimal
+Version: 1.1.16
+Summary: A fork of packmol_memgen from AmberTools, a PACKMOL wrapper for packing proteins into membranes, aimed to be minimal, mordernized and self-contained.
+Project-URL: Homepage, https://github.com/xiaoxuan-yu/packmol_memgen_minimal/
+Author-email: Xiaoxuan Yu <xiaoxuan_yu@pku.edu.cn>
+License:  GNU GENERAL PUBLIC LICENSE
+                               Version 2, June 1991
+        
+         Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
+         <https://fsf.org/>
+         Everyone is permitted to copy and distribute verbatim copies
+         of this license document, but changing it is not allowed.
+        
+                                    Preamble
+        
+          The licenses for most software are designed to take away your
+        freedom to share and change it.  By contrast, the GNU General Public
+        License is intended to guarantee your freedom to share and change free
+        software--to make sure the software is free for all its users.  This
+        General Public License applies to most of the Free Software
+        Foundation's software and to any other program whose authors commit to
+        using it.  (Some other Free Software Foundation software is covered by
+        the GNU Lesser General Public License instead.)  You can apply it to
+        your programs, too.
+        
+          When we speak of free software, we are referring to freedom, not
+        price.  Our General Public Licenses are designed to make sure that you
+        have the freedom to distribute copies of free software (and charge for
+        this service if you wish), that you receive source code or can get it
+        if you want it, that you can change the software or use pieces of it
+        in new free programs; and that you know you can do these things.
+        
+          To protect your rights, we need to make restrictions that forbid
+        anyone to deny you these rights or to ask you to surrender the rights.
+        These restrictions translate to certain responsibilities for you if you
+        distribute copies of the software, or if you modify it.
+        
+          For example, if you distribute copies of such a program, whether
+        gratis or for a fee, you must give the recipients all the rights that
+        you have.  You must make sure that they, too, receive or can get the
+        source code.  And you must show them these terms so they know their
+        rights.
+        
+          We protect your rights with two steps: (1) copyright the software, and
+        (2) offer you this license which gives you legal permission to copy,
+        distribute and/or modify the software.
+        
+          Also, for each author's protection and ours, we want to make certain
+        that everyone understands that there is no warranty for this free
+        software.  If the software is modified by someone else and passed on, we
+        want its recipients to know that what they have is not the original, so
+        that any problems introduced by others will not reflect on the original
+        authors' reputations.
+        
+          Finally, any free program is threatened constantly by software
+        patents.  We wish to avoid the danger that redistributors of a free
+        program will individually obtain patent licenses, in effect making the
+        program proprietary.  To prevent this, we have made it clear that any
+        patent must be licensed for everyone's free use or not licensed at all.
+        
+          The precise terms and conditions for copying, distribution and
+        modification follow.
+        
+                            GNU GENERAL PUBLIC LICENSE
+           TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+        
+          0. This License applies to any program or other work which contains
+        a notice placed by the copyright holder saying it may be distributed
+        under the terms of this General Public License.  The "Program", below,
+        refers to any such program or work, and a "work based on the Program"
+        means either the Program or any derivative work under copyright law:
+        that is to say, a work containing the Program or a portion of it,
+        either verbatim or with modifications and/or translated into another
+        language.  (Hereinafter, translation is included without limitation in
+        the term "modification".)  Each licensee is addressed as "you".
+        
+        Activities other than copying, distribution and modification are not
+        covered by this License; they are outside its scope.  The act of
+        running the Program is not restricted, and the output from the Program
+        is covered only if its contents constitute a work based on the
+        Program (independent of having been made by running the Program).
+        Whether that is true depends on what the Program does.
+        
+          1. You may copy and distribute verbatim copies of the Program's
+        source code as you receive it, in any medium, provided that you
+        conspicuously and appropriately publish on each copy an appropriate
+        copyright notice and disclaimer of warranty; keep intact all the
+        notices that refer to this License and to the absence of any warranty;
+        and give any other recipients of the Program a copy of this License
+        along with the Program.
+        
+        You may charge a fee for the physical act of transferring a copy, and
+        you may at your option offer warranty protection in exchange for a fee.
+        
+          2. You may modify your copy or copies of the Program or any portion
+        of it, thus forming a work based on the Program, and copy and
+        distribute such modifications or work under the terms of Section 1
+        above, provided that you also meet all of these conditions:
+        
+            a) You must cause the modified files to carry prominent notices
+            stating that you changed the files and the date of any change.
+        
+            b) You must cause any work that you distribute or publish, that in
+            whole or in part contains or is derived from the Program or any
+            part thereof, to be licensed as a whole at no charge to all third
+            parties under the terms of this License.
+        
+            c) If the modified program normally reads commands interactively
+            when run, you must cause it, when started running for such
+            interactive use in the most ordinary way, to print or display an
+            announcement including an appropriate copyright notice and a
+            notice that there is no warranty (or else, saying that you provide
+            a warranty) and that users may redistribute the program under
+            these conditions, and telling the user how to view a copy of this
+            License.  (Exception: if the Program itself is interactive but
+            does not normally print such an announcement, your work based on
+            the Program is not required to print an announcement.)
+        
+        These requirements apply to the modified work as a whole.  If
+        identifiable sections of that work are not derived from the Program,
+        and can be reasonably considered independent and separate works in
+        themselves, then this License, and its terms, do not apply to those
+        sections when you distribute them as separate works.  But when you
+        distribute the same sections as part of a whole which is a work based
+        on the Program, the distribution of the whole must be on the terms of
+        this License, whose permissions for other licensees extend to the
+        entire whole, and thus to each and every part regardless of who wrote it.
+        
+        Thus, it is not the intent of this section to claim rights or contest
+        your rights to work written entirely by you; rather, the intent is to
+        exercise the right to control the distribution of derivative or
+        collective works based on the Program.
+        
+        In addition, mere aggregation of another work not based on the Program
+        with the Program (or with a work based on the Program) on a volume of
+        a storage or distribution medium does not bring the other work under
+        the scope of this License.
+        
+          3. You may copy and distribute the Program (or a work based on it,
+        under Section 2) in object code or executable form under the terms of
+        Sections 1 and 2 above provided that you also do one of the following:
+        
+            a) Accompany it with the complete corresponding machine-readable
+            source code, which must be distributed under the terms of Sections
+            1 and 2 above on a medium customarily used for software interchange; or,
+        
+            b) Accompany it with a written offer, valid for at least three
+            years, to give any third party, for a charge no more than your
+            cost of physically performing source distribution, a complete
+            machine-readable copy of the corresponding source code, to be
+            distributed under the terms of Sections 1 and 2 above on a medium
+            customarily used for software interchange; or,
+        
+            c) Accompany it with the information you received as to the offer
+            to distribute corresponding source code.  (This alternative is
+            allowed only for noncommercial distribution and only if you
+            received the program in object code or executable form with such
+            an offer, in accord with Subsection b above.)
+        
+        The source code for a work means the preferred form of the work for
+        making modifications to it.  For an executable work, complete source
+        code means all the source code for all modules it contains, plus any
+        associated interface definition files, plus the scripts used to
+        control compilation and installation of the executable.  However, as a
+        special exception, the source code distributed need not include
+        anything that is normally distributed (in either source or binary
+        form) with the major components (compiler, kernel, and so on) of the
+        operating system on which the executable runs, unless that component
+        itself accompanies the executable.
+        
+        If distribution of executable or object code is made by offering
+        access to copy from a designated place, then offering equivalent
+        access to copy the source code from the same place counts as
+        distribution of the source code, even though third parties are not
+        compelled to copy the source along with the object code.
+        
+          4. You may not copy, modify, sublicense, or distribute the Program
+        except as expressly provided under this License.  Any attempt
+        otherwise to copy, modify, sublicense or distribute the Program is
+        void, and will automatically terminate your rights under this License.
+        However, parties who have received copies, or rights, from you under
+        this License will not have their licenses terminated so long as such
+        parties remain in full compliance.
+        
+          5. You are not required to accept this License, since you have not
+        signed it.  However, nothing else grants you permission to modify or
+        distribute the Program or its derivative works.  These actions are
+        prohibited by law if you do not accept this License.  Therefore, by
+        modifying or distributing the Program (or any work based on the
+        Program), you indicate your acceptance of this License to do so, and
+        all its terms and conditions for copying, distributing or modifying
+        the Program or works based on it.
+        
+          6. Each time you redistribute the Program (or any work based on the
+        Program), the recipient automatically receives a license from the
+        original licensor to copy, distribute or modify the Program subject to
+        these terms and conditions.  You may not impose any further
+        restrictions on the recipients' exercise of the rights granted herein.
+        You are not responsible for enforcing compliance by third parties to
+        this License.
+        
+          7. If, as a consequence of a court judgment or allegation of patent
+        infringement or for any other reason (not limited to patent issues),
+        conditions are imposed on you (whether by court order, agreement or
+        otherwise) that contradict the conditions of this License, they do not
+        excuse you from the conditions of this License.  If you cannot
+        distribute so as to satisfy simultaneously your obligations under this
+        License and any other pertinent obligations, then as a consequence you
+        may not distribute the Program at all.  For example, if a patent
+        license would not permit royalty-free redistribution of the Program by
+        all those who receive copies directly or indirectly through you, then
+        the only way you could satisfy both it and this License would be to
+        refrain entirely from distribution of the Program.
+        
+        If any portion of this section is held invalid or unenforceable under
+        any particular circumstance, the balance of the section is intended to
+        apply and the section as a whole is intended to apply in other
+        circumstances.
+        
+        It is not the purpose of this section to induce you to infringe any
+        patents or other property right claims or to contest validity of any
+        such claims; this section has the sole purpose of protecting the
+        integrity of the free software distribution system, which is
+        implemented by public license practices.  Many people have made
+        generous contributions to the wide range of software distributed
+        through that system in reliance on consistent application of that
+        system; it is up to the author/donor to decide if he or she is willing
+        to distribute software through any other system and a licensee cannot
+        impose that choice.
+        
+        This section is intended to make thoroughly clear what is believed to
+        be a consequence of the rest of this License.
+        
+          8. If the distribution and/or use of the Program is restricted in
+        certain countries either by patents or by copyrighted interfaces, the
+        original copyright holder who places the Program under this License
+        may add an explicit geographical distribution limitation excluding
+        those countries, so that distribution is permitted only in or among
+        countries not thus excluded.  In such case, this License incorporates
+        the limitation as if written in the body of this License.
+        
+          9. The Free Software Foundation may publish revised and/or new versions
+        of the General Public License from time to time.  Such new versions will
+        be similar in spirit to the present version, but may differ in detail to
+        address new problems or concerns.
+        
+        Each version is given a distinguishing version number.  If the Program
+        specifies a version number of this License which applies to it and "any
+        later version", you have the option of following the terms and conditions
+        either of that version or of any later version published by the Free
+        Software Foundation.  If the Program does not specify a version number of
+        this License, you may choose any version ever published by the Free Software
+        Foundation.
+        
+          10. If you wish to incorporate parts of the Program into other free
+        programs whose distribution conditions are different, write to the author
+        to ask for permission.  For software which is copyrighted by the Free
+        Software Foundation, write to the Free Software Foundation; we sometimes
+        make exceptions for this.  Our decision will be guided by the two goals
+        of preserving the free status of all derivatives of our free software and
+        of promoting the sharing and reuse of software generally.
+        
+                                    NO WARRANTY
+        
+          11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+        FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
+        OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+        PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+        OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+        MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  THE ENTIRE RISK AS
+        TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU.  SHOULD THE
+        PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+        REPAIR OR CORRECTION.
+        
+          12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+        WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
+        REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+        INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+        OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+        TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+        YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+        PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+        POSSIBILITY OF SUCH DAMAGES.
+        
+                             END OF TERMS AND CONDITIONS
+        
+                    How to Apply These Terms to Your New Programs
+        
+          If you develop a new program, and you want it to be of the greatest
+        possible use to the public, the best way to achieve this is to make it
+        free software which everyone can redistribute and change under these terms.
+        
+          To do so, attach the following notices to the program.  It is safest
+        to attach them to the start of each source file to most effectively
+        convey the exclusion of warranty; and each file should have at least
+        the "copyright" line and a pointer to where the full notice is found.
+        
+            <one line to give the program's name and a brief idea of what it does.>
+            Copyright (C) <year>  <name of author>
+        
+            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, see <https://www.gnu.org/licenses/>.
+        
+        Also add information on how to contact you by electronic and paper mail.
+        
+        If the program is interactive, make it output a short notice like this
+        when it starts in an interactive mode:
+        
+            Gnomovision version 69, Copyright (C) year name of author
+            Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+            This is free software, and you are welcome to redistribute it
+            under certain conditions; type `show c' for details.
+        
+        The hypothetical commands `show w' and `show c' should show the appropriate
+        parts of the General Public License.  Of course, the commands you use may
+        be called something other than `show w' and `show c'; they could even be
+        mouse-clicks or menu items--whatever suits your program.
+        
+        You should also get your employer (if you work as a programmer) or your
+        school, if any, to sign a "copyright disclaimer" for the program, if
+        necessary.  Here is a sample; alter the names:
+        
+          Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+          `Gnomovision' (which makes passes at compilers) written by James Hacker.
+        
+          <signature of Moe Ghoul>, 1 April 1989
+          Moe Ghoul, President of Vice
+        
+        This General Public License does not permit incorporating your program into
+        proprietary programs.  If your program is a subroutine library, you may
+        consider it more useful to permit linking proprietary applications with the
+        library.  If this is what you want to do, use the GNU Lesser General
+        Public License instead of this License.
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.11
+Requires-Dist: hatch-vcs>=0.5.0
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: pdb2pqr>=3.7.1
+Requires-Dist: scipy
+Requires-Dist: tqdm
+Provides-Extra: full
+Requires-Dist: mdtraj; extra == 'full'
+Requires-Dist: mempro; extra == 'full'
+Requires-Dist: packmol; extra == 'full'
+Requires-Dist: vermouth; extra == 'full'
+Provides-Extra: martini
+Requires-Dist: mdtraj; extra == 'martini'
+Requires-Dist: vermouth; extra == 'martini'
+Provides-Extra: mempro
+Requires-Dist: mempro; extra == 'mempro'
+Provides-Extra: packmol
+Requires-Dist: packmol; extra == 'packmol'
+Description-Content-Type: text/x-rst
+
+#############################################################
+                 PACKMOL MEMGEN MINIMAL  2026.1.8
+#############################################################
+Xiaoxuan Yu
+2026-01-08
+
+################
+THIS FORK NOTES
+################
+
+This repository is a fork of packmol-memgen. The original README content is
+preserved below; this section summarizes the changes and current behavior.
+
+- Packaging: this fork is published on PyPI (sdist/wheel). The Python wheel aims to
+  avoid system-level dependencies (e.g., no AmberTools requirement). Some features 
+  include SIRAH coarse-graining support, minimization, parametrization and protonation
+  using reduce are not available in this fork.
+
+- Packmol: packing is performed by the external PACKMOL command-line tool. This
+  package does not bundle PACKMOL; it is expected to be available on PATH. For
+  convenience, it can be installed via an optional dependency (extra).
+
+- Membrane orientation: membrane alignment/orientation is performed via MemPrO
+  (Python + JAX) instead of the upstream memembed/ppm3 workflow. MemPrO is invoked
+  via subprocess as an external command-line tool. MemPrO is not bundled into this
+  package but can be installed via an optional dependency for convenience.
+
+- Protonation: protonation uses pdb2pqr when needed.
+- Output location: use ``--outdir DIR`` to write all generated files (final ``--output``, ``--log``, ``--packlog`` scripts/logs, intermediate structures) into a single directory.
+
+###########################################
+Martini Auto-Mapping (MemPrO/Insane4MemPrO)
+###########################################
+
+When ``--martini`` is enabled, the script can auto-build ``--insane_args`` for
+MemPrO/Insane4MemPrO with the following behavior:
+
+- Lipids: ``--lipids`` + ``--ratio`` map to Insane ``-l/-u``. ``//`` syntax is
+  supported for lower/upper leaflets. Two ``--lipids`` entries are supported and
+  map to Insane ``-l/-u`` (inner membrane) and ``-lo/-uo`` (outer membrane).
+- Box size: ``--dims`` is converted from Angstrom to nm and passed as ``-x/-y/-z``.
+- Curvature: ``--curvature`` or ``--curv_radius`` maps to ``-curv c0,0,dir``
+  where ``c0 = abs(curvature)``, ``dir = sign(curvature)``.
+- Solvents: ``--solvents`` + ``--solvent_ratio`` map to ``-sol`` entries. The
+  only automatic name mapping is ``WAT -> W``, which emits a warning once. All
+  other solvent names must match Insane solventParticles (see
+  ``packmol_memgen/data/insane_solvents.txt``).
+- Salts: ``--salt``, ``--salt_c``, ``--salt_a`` map to ``-posi_c0/1/2`` and
+  ``-negi_c0/1/2`` using ion tokens stripped to letters (e.g. ``Na+`` -> ``NA``).
+  ``--saltcon`` maps to ``-ion_conc`` with the value replicated for all three
+  compartments.
+
+The following options are *not* supported in Martini auto-mapping and will emit
+warnings: ``--distxy_fix``, ``--dist``, ``--dist_wat``, ``--xygauss``,
+``--apl_offset``, ``--lip_offset``, ``--pbc``, ``--nocounter``,
+``--charge_imbalance``, ``--imbalance_ion``. You can still supply custom
+``--insane_args`` to override or extend the auto-generated arguments.
+
+############
+Installation
+############
+Minimal installation (this fork without PACKMOL or MemPrO):
+
+``pip install packmol-memgen-minimal``
+
+With optional packmol as a dependency:
+
+``pip install packmol-memgen-minimal[packmol]``
+
+With optional mempro as a dependency:
+
+``pip install packmol-memgen-minimal[mempro]``
+
+With both optional dependencies:
+
+``pip install packmol-memgen-minimal[full]``
+
+You may prefer mordern Python packaging tools such as `uv` to install 
+
+``uv tool install packmol-memgen-minimal``
+
+extras are supported in `uv` as well. Other tools may work similarly.
+
+
+############
+LICENSE NOTE
+############
+
+This fork is distributed under GPL-2.0-only, inherited from the upstream project.
+
+MemPrO is an optional external command-line tool distributed under the GNU GPL v3.
+This project interacts with MemPrO via subprocess calls; MemPrO is not bundled into
+this package and its license applies to MemPrO itself.
+
+The martini force field parameter file `packmol_memgen/data/martini_v3.0.0.itp` is 
+sourced from https://github.com/Martini-Force-Field-Initiative/martini-forcefields 
+and is distributed under the Apache License 2.0. The full Apache 2.0 license text 
+is provided at `packmol_memgen/data/LICENSE.Apache-2.0`.
+
+##########
+CREDITS
+##########
+
+This project depends on and/or interoperates with the following open-source
+software. Please refer to each project for license terms.
+
+Core dependencies (installed via PyPI):
+
+- NumPy (https://github.com/numpy/numpy)
+- SciPy (https://github.com/scipy/scipy)
+- pandas (https://github.com/pandas-dev/pandas)
+- tqdm (https://github.com/tqdm/tqdm)
+- matplotlib (https://github.com/matplotlib/matplotlib)
+- PDB2PQR (https://github.com/Electrostatics/pdb2pqr)
+- docopt (https://github.com/docopt/docopt)
+
+Optional external tools (installed separately; invoked via subprocess):
+
+- PACKMOL (MIT License, https://github.com/m3g/packmol)
+- MemPrO (GNU GPL v3, https://github.com/ShufflerBardOnTheEdge/MemPrO)
+
+Additional utilities used by this workflow:
+
+- PDBREMIX (MIT License, https://github.com/boscoh/pdbremix)
+- charmmlipid2amber (GPL-2.0, from `AmberTools 2025`, https://ambermd.org/AmberTools.php)
+- Martini 3 force field parameters (Apache-2.0, https://github.com/Martini-Force-Field-Initiative/martini-forcefields)
+
+
+#############################################################
+                 PACKMOL MEMGEN  2023.8.8 
+#############################################################
+Stephan N. Schott V.
+2016-11-07
+
+
+
+############ 
+INSTALLATION
+############
+
+The main installation of Packmol Memgen is intended to be installed within AmberTools20. If that is not the case
+the following instructions could be follow to make it run as a stand-alone, though it is not officially supported.
+
+Dependencies:
+Boost (tested with 1.54 or above)
+gfortran & gcc (tested with 4.8 and above)
+python 2.7 (or above)
+
+The script should work as is. Includes a setup.py script which should work as usual:
+
+``python setup.py install``
+
+or
+
+``pip install .``
+
+You can specify a custom installation location with --home=<FOLDER> or --prefix=<FOLDER>, respectively.
+Testing of the software can be performed in the example folder, by executing "./example.sh".
+This folder can be easily cleaned by executing "./example.sh clean"
+
+
+
+##############
+CHANGELOG 
+##############
+2025.3.22
+ - Added initial functionality to support Packmol's PBC option
+2025.3.17
+ - Added onlyleapin flag to generate a template leap input without parametrizing.
+ - Modified memembed with Claude 3.7 suggestions to stop using boost.
+ - Updated packmol to 20.16
+2025.2.10
+ - Force using propka for titration with_ph in pdb2pqr
+2025.1.29
+ - Bugfix calculating center of PDB. This could have caused issues in calculating volumes, mainly in solvated systems.
+2024.3.27
+ - Changed MEMEMBED to push TER to output file
+2024.3.18:
+ - Separation of function in classes
+ - Better management of ppm3 alignment function
+2024.2.9:
+ - Fixed help typo
+ - PACKMOL Update to fix FORCED output
+2023.8.8:
+ - Added siWT4 COM to avoid overlaps
+ - Fixed deprecated np.float calls
+ - Added ppm3 support and code
+ - Shift water box if --dims is used to add at least 5A water on membrane surface
+ - Add packmol finetuning parameters
+2023.2.24:
+ - Changed versioning to CalVer
+ - Updated packmol
+ - Added all amber supported ions and OPC3
+ - Added option to generate HMR systems
+ - Added control for minimization function and pmemd.cuda
+ - Added option to use pdb2pqr to protonate, if available
+ - Multiple small changes and cleanup
+v1.2.3:
+ - Added support for Lipid21 sphingolipids
+ - Add channel_plug flag and fix 2LPG head atoms in memgen.parm
+ - Add function to identify sterol lipid piercing within packed box
+ - Limit packing of sterols in the rim under some conditions
+v1.2.1:
+ - Fixed using %v/v concentrations for solutes.
+v1.2.0:
+ - Added sterols ergosterol, stigmasterol, sitosterol, campesterol
+ - Reformated and cleaned FF parameter files
+ - Fixed bogus packing params
+ - Added functionality for using alternate solvents
+ - User provided memgen.parm or solvent.parm extend and not only replace parameters used by default
+ - Added support for coarse graining systems with SIRAH 
+ - Fixed bug that caused charmmlipid2amber to fail when packing a single residue molecule
+ - Support for Lipid21 / Lipid17 can be selected.
+v1.1.0:
+ - Added parameters for cardiolipin headgroup
+ - New PDBs generated with stereocenter constraints
+ - Added --solute_prot_dist to set free diffusion simulations with ligands starting at a distance of a potential target.
+ - Fixed rounding error for solute placement in water compartments
+ - Added flags --apl_offset --self_assembly 
+ - Small code changes
+v1.0.8:
+ - Added preliminary code for --double_span option for proteins with two transmembrane regions. Can be used with --preoriented given proper MEM atoms
+ - Added preliminary code for using different surface geometries
+ - Added --tight_box to use dimensions calculated during the packing process in the leap parametrization
+v1.0.7:
+ - Added APL values derived from Lipid17 DOPC:X 4:1 300K 1 bar. Flag to use old APL values added.
+ - Allow to pass custom memgen.parm file with --memgen_parm
+v1.0.5:
+ - Changed pdb file distro
+ - Added experimental pdbs for all possible combinations
+ - Added PI & multiple protonation states parameters
+ - memgen.parm to all missing lipids
+v1.0.2:
+ - Fixed the way dims and solute_inmem are handled
+ - Included parameters for lysophospholipid heads PE PG PC // BETA! (pdbs and memgen.parm)
+ - Fixed and updated internal charmmlipid2amber.csv
+ - Added missing MG pdb
+v1.0.1:
+ - Added flags dims, gaff2 and solute_charge
+ - Possible to specify concentrations as percentages. Depends on pdbremix at the moment! 
+v1.0.0:
+ - Modified POPC pdb to avoid bug that apparently caused it to be stuck in a maxima
+ - Fixed bug while trying to find lipid APL with the same headgroup
+ - Newest packmol version 18.169
+ - Inclusion of boost 1.69 // compatible with gcc 8 compilers  // AmberTools19 includes boost!
+ - Mac compatible compilation code 
+v0.9.95:
+ - Added writeout flag to control intermediate saves. Allows shorter nloops.
+ - Adapted code to Leandro's nloop_all. 
+ - New packmol version with bug fixes (18.104). Should fix isues with Windows WSL.
+ - Python 3 friendly code.
+ - Added cubic flag for solvating. reducebuild for protonating HIS.
+ - Fixed multi bilayer z-dim size bug.
+ - Changed solute_con to accept either number of molecules or concentrations.
+v0.9.9:
+ - Possibility to build stacked membrane systems by calling --lipids multiple times. PDB files to be embeded have to be included with --pdb now, to make possible to specify multiple inputs.
+ - A charge imbalance can be specified between compartments (CompEL!)
+ - If desired, a specific per leaflet composition can be specified.
+ - The orientation by MEMEMBED is with the N-terminus to the "inside" (or to lower z values). Added flag (--n_ter) to set this per protein in case of multiple bilayers.
+v0.9.8:
+ - Modified print commands for logging statements.
+ - Added optional grid building command (testing!)
+ - Added functions that allow minimization and parametrization, given that AMBERHOME is defined
+ - Added option to keep ligands after protein alignment
+v0.9.7:
+ - Check if ions are required before adding the line to packmol (avoids "bug" that adds one molecule even when the number is 0)
+v0.9.6:
+ - Possible to add solutes in water based on PDB input
+ - Modified sigterm command for runs
+ - Reduced the verbosity. Can be called with --verbose
+v0.9.5:
+ - Changed parsing system to argparse
+ - Adapted to work with Wooey
+ - Implemented charmmlipid2amber as a module // charmm and amber outputs
+v0.9.1:
+ - Now is possible to create membranes without proteins by setting the PDB as None
+ - The xy dimensions can be set with the flag -distxy_fix. This flag is required if no PDB is given
+v0.9:
+ - Multiple lipids available! (-available_lipids for a list)
+ - Detection of neutralization / salt concentration included
+v0.7:
+ - Volume estimation by building grid based on PDBREMIX
+ - Search for AMBERHOME definition, using reduce if available
+ - Automated alignment available based on MEMEMBED
+ - Tiny code clean-up
+v0.3:
+ - Distance is measured considering worst case scenario (max x and y considered to be on the diagonal)
+ - Added progress bar for all-together packing step
+ - Filter for non-defined arguments