Metadata-Version: 2.4
Name: packmol-memgen-minimal
Version: 1.1.19
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==21.1.4; 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==21.1.14; 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
