Merge pull request #54 from alanwilter/failing_cases new_release

Prepared for different user's scenarios

Dockerfile

@@ -29,9 +29,11 @@ RUN apt-get update && apt-get install -y \
     python3-openbabel \
     libgfortran5 \
     libarpack++2-dev \
+    python3-ipython \
     && apt-get autoremove -y && apt-get autoclean -y && apt-get clean -y \
     && rm -rf /var/lib/apt/lists/*
 
 COPY run_acpype.py /home
 COPY acpype_lib /home/acpype_lib
-RUN ln -s /home/run_acpype.py /usr/local/bin/acpype
+RUN ln -s /home/run_acpype.py /usr/local/bin/acpype
+ENV PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/amber21/bin" 

README.md

@@ -1,12 +1,17 @@
 # ACPYPE
 
-![GitHub](https://img.shields.io/github/license/alanwilter/acpype?style=social)
-![GitHub All Releases](https://img.shields.io/github/downloads/alanwilter/acpype/total?style=social)
-![Docker Pulls](https://img.shields.io/docker/pulls/acpype/acpype?style=social&logo=docker)
-![Docker Image Size (tag)](https://img.shields.io/docker/image-size/lpkagami/acpype/latest?style=social&logo=docker)
-![GitHub Relase](https://img.shields.io/github/release-date/alanwilter/acpype?style=social)
-![Conda Version](https://img.shields.io/conda/vn/conda-forge/acpype.svg)
-![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/acpype.svg)
+![GitHub](https://img.shields.io/github/license/alanwilter/acpype?style=plastic)
+![GitHub release (latest by date)](https://img.shields.io/github/v/release/alanwilter/acpype?display_name=tag&logo=github&style=plastic)
+![GitHub Relase](https://img.shields.io/github/release-date/alanwilter/acpype?style=plastic&logo=github)<!-- ![GitHub All Releases](https://img.shields.io/github/downloads/alanwilter/acpype/total?style=plastic) -->
+![Docker Pulls](https://img.shields.io/docker/pulls/acpype/acpype?style=plastic&logo=docker)
+![Docker Image Size (tag)](https://img.shields.io/docker/image-size/acpype/acpype/latest?style=plastic&logo=docker)
+![Conda Version](https://img.shields.io/conda/vn/conda-forge/acpype.svg?style=plastic&logo=conda-forge)
+![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/acpype.svg?style=plastic&logo=conda-forge)<!-- ![Conda](https://img.shields.io/conda/pn/conda-forge/acpype?logo=conda-forge&style=plastic) -->
+![PyPI](https://img.shields.io/pypi/v/acpype?style=plastic&logo=pypi)
+![PyPI - Downloads](https://img.shields.io/pypi/dm/acpype?style=plastic&logo=pypi)
+![GitHub Workflow Status](https://img.shields.io/github/workflow/status/alanwilter/acpype/check_acpype)
+<!-- ![Scrutinizer code quality (GitHub/Bitbucket)](https://img.shields.io/scrutinizer/quality/g/alanwilter/acpype) -->
+<!-- ![Scrutinizer coverage (GitHub/BitBucket)](https://img.shields.io/scrutinizer/coverage/g/alanwilter/acpype) -->
 
 ## AnteChamber PYthon Parser interfacE
 
@@ -87,21 +92,33 @@ There are several ways of obtaining `acpype`:
 
 1. Via **[CONDA](https://anaconda.org/search?q=acpype)**:
 
+   *(It should be wholesome, fully funcional, all batteries included)*
+
    ```bash
    conda install -c conda-forge acpype
    ```
 
 2. Via **[PyPI](https://pypi.org/project/acpype/)**:
 
+   *(Make sure you  have `AmberTools` and, optionally but highly recommended, `OpenBabel` )*
+
    ```bash
+   # You can use conda to get the needed 3rd parties for example
+   conda create -n acpype --channel conda-forge ambertools openbabel
+
+   pip install acpype
+
+   # or if you feel daring
+
    pip install git+https://github.com/alanwilter/acpype.git
    ```
 
-   note that `pip install acpype`, unfortunately, is not *yet* picking the original one.
-
 3. By downloading it via `git`:
 
+   *(Make sure you  have `AmberTools` and, optionally but highly recommended, `OpenBabel` )*
+
    ```bash
+   # You can use conda to get the needed 3rd parties for example
    conda create -n acpype --channel conda-forge ambertools openbabel
    git clone https://github.com/alanwilter/acpype.git
    ```
@@ -110,39 +127,37 @@ There are several ways of obtaining `acpype`:
 
 4. Via **[Docker](https://hub.docker.com/repository/docker/acpype/acpype/)**:
 
-   If you have Docker installed, you can run `acpype` by:
-
-   ```bash
-   docker pull acpype/acpype:latest
-   ```
+   *(It should be wholesome, fully funcional, all batteries included)*
+
+   If you have Docker installed, you can run `acpype_docker.sh` by:
 
-   Then, on Linux / MacOS choose a folder where to work (e.g. contains your PDB, MOL2 or inpcrd/prmtop files) and do:
+   NOTE: first time may take some time as it pulls the `acpype` docker image.
+
+   On Linux / MacOS:
 
    ```bash
-
-   # it opens a terminal inside docker with access to your working folder
-   docker run -i -t --rm -v ${PWD}:/wdir -w /wdir acpype/acpype bash
-
-   # use acpype 
-   acpype -i CCCC
-   acpype -i DDD.pdb -c gas # if you have a DDD.pdb file there in "wdir" ($PWD)
-   exit # and your output files will be at your working directory ($PWD)
+   ln -fsv "$PWD/acpype_docker.sh" /usr/local/bin/acpype_docker
+
    ```
 
    On Windows:
    Using Command Prompt:
 
+    In the directory where the `acpype_docker.bat` file is found:
+
    ```bash
-   docker run -i -t --rm -v%cd%:/wdir -w /wdir acpype bash
+   setx /M path "%path%;%cd%"
    ```
-
-   Using PowerShell:
-
+   Commands:
    ```bash
-   docker run -i -t --rm -v ${PWD}:/wdir -w /wdir acpype bash
+   acpype_docker -i CCCC
+
+   acpype_docker -i tests/DDD.pdb -c gas
    ```
+**NB:**
 
-**NB:** Installing via `conda` or via `pip/git` you get `AmberTools v.21.11` and `OpenBabel v3.11`. Our `AmberTools v.21.11` comes with binary `charmmgen` from `AmberTools17` in order to generate CHARMM topologies.
+- By installing via `conda` or using via `docker` you get `AmberTools v.21.11` and `OpenBabel v3.1.1`. Our `AmberTools v.21.11` comes with binary `charmmgen` from `AmberTools17` in order to generate CHARMM topologies.
+- By installing via `pip` you get `AmberTools` (as described above) embeded. However, the included binaries may not work in your system (library dependecies issues) and with only provide binaries for Linux (Ubuntu20) and Mac OSX.
 
 ##### To Test, if doing via `git`
 
@@ -174,7 +189,7 @@ To get help and more information, type:
 At folder `acpype/`, type:
 
 ```bash
-  ln -s $PWD/run_acpype.py /usr/local/bin/acpype
+  ln -fsv "$PWD/run_acpype.py" /usr/local/bin/acpype
 ```
 
 Then re-login or start another shell session.
@@ -241,4 +256,4 @@ cns < FFF_CNS.inp
 
 #### To Verify with NAMD
 
-- see [TutorialNAMD]
+- see [TutorialNAMD](../../wiki/Tutorial-NAMD)

acpype_docker.bat

@@ -0,0 +1,2 @@
+@echo on
+docker run -i -t -v %cd%:/wdir -w /wdir acpype/acpype acpype %*

acpype_docker.sh

@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+
+docker run -i -t -v "${PWD}":/wdir -w /wdir acpype/acpype acpype "$@"

acpype_lib/__init__.py

@@ -1,3 +1,4 @@
 # from https://packaging.python.org/guides/single-sourcing-package-version/
 # using option 2
-__version__ = "2021.11.27"
+# updated automatically via pre-commit git-hook
+__version__ = "2021.11.29"

acpype_lib/acpype.py

@@ -59,36 +59,43 @@
 import time
 import os
 import sys
-import sysconfig
 from shutil import rmtree, which
 from acpype_lib.topol import MolTopol, ACTopol, header
 from acpype_lib.parser_args import get_option_parser
-from acpype_lib.utils import while_replace
-from acpype_lib.utils import checkSmiles, elapsedTime
+from acpype_lib.utils import while_replace, elapsedTime
+from acpype_lib.params import binaries
 
-# For pip package
-if which("antechamber") is None:
-    LOCAL_PATH = sysconfig.get_paths()["purelib"]
-    if sys.platform == "linux":
-        os.environ["PATH"] += os.pathsep + LOCAL_PATH + "/amber21-11_linux/bin:" + LOCAL_PATH + "/amber21-11_linux/dat/"
-        os.environ["AMBERHOME"] = LOCAL_PATH + "/amber21-11_linux/"
-        os.environ["ACHOME"] = LOCAL_PATH + "/amber21-11_linux/bin/"
-        os.environ["LD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_linux/lib/"
-    elif sys.platform == "darwin":
-        os.environ["PATH"] += os.pathsep + LOCAL_PATH + "/amber21-11_os/bin:" + LOCAL_PATH + "/amber21-11_os/dat/"
-        os.environ["AMBERHOME"] = LOCAL_PATH + "/amber21-11_os/"
-        os.environ["ACHOME"] = LOCAL_PATH + "/amber21-11_os/bin/"
-        os.environ["LD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_os/lib/"
 
-if sys.version_info < (3, 6):
-    raise Exception("Sorry, you need python 3.6 or higher")
+def set_for_pip():
+    # For pip package
+    if which(binaries["ac_bin"]) is None:
+        try:
+            LOCAL_PATH = os.path.dirname(os.path.dirname(__file__))
+            if sys.platform == "linux":
+                os.environ["PATH"] += os.pathsep + LOCAL_PATH + "/amber21-11_linux/bin"
+                os.environ["AMBERHOME"] = LOCAL_PATH + "/amber21-11_linux/"
+                os.environ["LD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_linux/lib/"
+            elif sys.platform == "darwin":
+                os.environ["PATH"] += os.pathsep + LOCAL_PATH + "/amber21-11_os/bin"
+                os.environ["AMBERHOME"] = LOCAL_PATH + "/amber21-11_os/"
+                os.environ["LD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_os/lib/"
+                os.environ["DYLD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_os/lib/"
+        except Exception:
+            print("ERROR: AmberTools NOT FOUND")
 
 
-def init_main(argv=None):
+def chk_py_ver():
+    if sys.version_info < (3, 6):
+        raise Exception("Sorry, you need python 3.6 or higher")
+
+
+def init_main(binaries=binaries, argv=None):
 
     """
     Main function, to satisfy Conda
     """
+    chk_py_ver()
+    set_for_pip()
     if argv is None:
         argv = sys.argv[1:]
 
@@ -141,6 +148,7 @@ def init_main(argv=None):
         else:
             molecule = ACTopol(
                 args.input,
+                binaries=binaries,
                 chargeType=args.charge_method,
                 chargeVal=args.net_charge,
                 debug=args.debug,
@@ -196,8 +204,8 @@ def init_main(argv=None):
     except Exception:
         pass
 
-    if not amb2gmxF and molecule.babelExe:
-        if checkSmiles(args.input):
+    if not amb2gmxF and molecule.obabelExe:
+        if molecule.checkSmiles():
             afile = "smiles_molecule.mol2"
             if os.path.exists(afile):
                 os.remove(afile)

acpype_lib/params.py

@@ -1,3 +1,5 @@
+binaries = {"ac_bin": "antechamber", "obabel_bin": "obabel"}
+
 MAXTIME = 3 * 3600
 cal = 4.184
 Pi = 3.141593

acpype_lib/parser_args.py

@@ -3,6 +3,7 @@
 
 
 def get_option_parser():
+    # not used yet: -e -l -r
     parser = argparse.ArgumentParser(usage=usage + epilog)
     group = parser.add_mutually_exclusive_group()
     parser.add_argument(