From cf3fb6f065491ecc82086ea08ae3b60e4ebf400f Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Thu, 11 May 2023 15:59:58 +0200
Subject: [PATCH] feat: SCHWED-5913 setup compound lib with import ost
This sets up the compound lib upon calling import ost.
It simplifies the ost_startup.py script accordingly.
It is now possible to override the compound lib with
an environment variable: OST_COMPOUNDS_CHEMLIB
---
modules/base/pymod/__init__.py.in | 75 ++++++++++++++++++++++++++++++-
modules/conop/doc/compoundlib.rst | 15 +++++--
modules/doc/install.rst | 16 +++++++
scripts/ost_config.in | 1 +
scripts/ost_startup.py.in | 13 ------
5 files changed, 102 insertions(+), 18 deletions(-)
diff --git a/modules/base/pymod/__init__.py.in b/modules/base/pymod/__init__.py.in
index 7b39730af..2d6f85a73 100644
--- a/modules/base/pymod/__init__.py.in
+++ b/modules/base/pymod/__init__.py.in
@@ -16,12 +16,13 @@
# along with this library; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
#------------------------------------------------------------------------------
-
+import os
__all__=['CharList','Correl', 'FileLogSink', 'FloatList', 'FloatMatrix', 'FloatMatrix3', 'FloatMatrix4', 'GetCurrentLogSink', 'GetPrefixPath', 'GetSharedDataPath', 'GetVerbosityLevel', 'Histogram', 'IntList', 'LogDebug', 'LogError', 'LogInfo', 'LogScript', 'LogSink', 'LogTrace', 'LogVerbose', 'LogWarning', 'Max', 'Mean', 'Median', 'Min', 'MultiLogSink', 'PopLogSink', 'PopVerbosityLevel', 'PushLogSink', 'PushVerbosityLevel', 'Range', 'SetPrefixPath', 'StdDev', 'StreamLogSink', 'StringList', 'StringLogSink', 'Units', 'VERSION', 'VERSION_MAJOR', 'VERSION_MINOR', 'VERSION_PATCH', 'WITH_NUMPY', 'conop', 'geom', 'io', 'mol', 'seq', 'stutil' @ALL_ADDITIONAL_MODULES@]
from ._ost_base import *
from .stutil import *
+from ost import conop
class StreamLogSink(LogSink):
def __init__(self, stream):
@@ -29,3 +30,75 @@ class StreamLogSink(LogSink):
self._stream=stream
def LogMessage(self, message, level):
self._stream.write(message)
+
+
+def _SetupOstPrefix():
+ """ This function attempts to set the OST prefix path if $OST_ROOT was not
+ set already.
+
+ It does so by assuming that the __init__.py file is located under
+ $OST_ROOT/lib(64)?/pythonX.XX/site-packages/ost. This might not be the case
+ in all settings (conda, pip?). In that case this function should be
+ adapted.
+ """
+
+ try:
+ # $OST_ROOT was set
+ GetPrefixPath()
+ except RuntimeError:
+ # Setup from this file's path
+ prefix_path = __file__
+ for _ in range(5):
+ prefix_path = os.path.dirname(prefix_path)
+ SetPrefixPath(prefix_path)
+
+
+def _TrySetCompoundsLib(path):
+ """Tries to set the compound lib to 'path', or raises a ValueError."""
+ if path is not None and os.path.exists(path):
+ compound_lib = conop.CompoundLib.Load(path)
+ if compound_lib is not None:
+ conop.SetDefaultLib(compound_lib)
+ return
+ raise ValueError("Could not load %s" % path)
+
+
+def _SetupCompoundsLib():
+ """ This function sets up the compound lib.
+
+ By order of priority, the following heuristics are used:
+
+ 1. The $OST_COMPOUNDS_CHEMLIB environment variable
+ 2. The 'compounds.chemlib' file in the shared path under the folder pointed
+ by the $OST_ROOT environment variable
+
+ If no compound library can be loaded with any of these strategies, a warning
+ message is issued.
+
+ """
+ # Try with the $OST_COMPOUNDS_CHEMLIB environment variable
+ compound_lib_path = os.getenv("OST_COMPOUNDS_CHEMLIB")
+ try:
+ _TrySetCompoundsLib(compound_lib_path)
+ except ValueError:
+ pass
+ else:
+ return
+
+ # Try from GetSharedDataPath() - requires $OST_ROOT to be set.
+ try:
+ compound_lib_path = os.path.join(GetSharedDataPath(), 'compounds.chemlib')
+ _TrySetCompoundsLib(compound_lib_path)
+ except (RuntimeError, ValueError):
+ pass
+ else:
+ return
+
+ LogWarning("Compound library not available. Some functionality may not " \
+ "work as expected.")
+
+
+# Setup OST
+PushVerbosityLevel(LogLevel.Script)
+_SetupOstPrefix()
+_SetupCompoundsLib()
diff --git a/modules/conop/doc/compoundlib.rst b/modules/conop/doc/compoundlib.rst
index b454ff98d..fed70b637 100644
--- a/modules/conop/doc/compoundlib.rst
+++ b/modules/conop/doc/compoundlib.rst
@@ -21,10 +21,17 @@ build the compound library manually.
.. function:: GetDefaultLib()
- :return: Default compound library set by :func:`SetDefaultLib`. If you got
- OpenStructure as a bundle or you :ref:`compiled <cmake-flags>` it
- with a specified ``COMPOUND_LIB`` flag, this will return a compound
- library when executing scripts with ``ost``.
+ Get the default compound library. This is set by :func:`SetDefaultLib`.
+
+ If you obtained OpenStructure as a container or you
+ :ref:`compiled <cmake-flags>` it with a specified ``COMPOUND_LIB`` flag,
+ this function will return a compound library.
+
+ You can override the default compound library by pointing the
+ ``OST_COMPOUNDS_CHEMLIB`` environment variable to a valid compound library
+ file.
+
+ :return: Default compound library.
:rtype: :class:`CompoundLib` or None if no library set
.. function:: SetDefaultLib(lib)
diff --git a/modules/doc/install.rst b/modules/doc/install.rst
index d840eeab2..dd4d4d5e1 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -420,6 +420,22 @@ or, to start the command-line interpreter:
If you repeatedly use OpenStructure, it is recommended to add
/path/to/ost/stage/bin to your path.
+You can also import OpenStructure directly into your existing python scripts,
+jupyter notebooks etc. Simply make sure to point the following environment
+variables to the right folders:
+
+.. code-block:: bash
+
+ export OST_ROOT=/path/to/ost/stage
+ export PYTHONPATH=$OST_ROOT/lib64/python3.10/site-packages/:$PYTHONPATH
+ python
+
+And then you can simply import ost as a module:
+
+.. code-block:: python
+
+ import ost
+
Getting the newest changes
--------------------------------------------------------------------------------
diff --git a/scripts/ost_config.in b/scripts/ost_config.in
index d0ba65da0..69e792960 100644
--- a/scripts/ost_config.in
+++ b/scripts/ost_config.in
@@ -25,6 +25,7 @@ export DNG_ROOT=`cd "$BIN_DIR/..";pwd`
export DNG_BINDIR="$DNG_ROOT/bin"
export DNG_LIBDIR="$DNG_ROOT/@LIBDIR@"
export DNG_INITDIR="$DNG_LIBDIR/@PYTHON_MODULE_PATH@/ost/"
+export OST_ROOT="$DNG_ROOT"
export PATH="$DNG_BINDIR:${PATH}"
export DYLD_FRAMEWORK_PATH="$DNG_LIBDIR:${DYLD_FRAMEWORK_PATH}"
diff --git a/scripts/ost_startup.py.in b/scripts/ost_startup.py.in
index 3d22c7e7e..c451bec38 100644
--- a/scripts/ost_startup.py.in
+++ b/scripts/ost_startup.py.in
@@ -44,23 +44,10 @@ parser.disable_interspersed_args()
_site_packs='python%d.%d/site-packages' % sys.version_info[0:2]
_base_dir=os.getenv('DNG_ROOT')
sys.path.insert(0, os.path.join(_base_dir, '@LIBDIR@', _site_packs))
-
-from ost import SetPrefixPath, GetSharedDataPath, conop
-SetPrefixPath(_base_dir)
-
-def _InitRuleBasedProcessor():
- compound_lib_path=os.path.join(GetSharedDataPath(), 'compounds.chemlib')
- if os.path.exists(compound_lib_path):
- compound_lib=conop.CompoundLib.Load(compound_lib_path)
- conop.SetDefaultLib(compound_lib)
-
-# switch to rule-based processor, if compound library is available
-_InitRuleBasedProcessor()
from ost import *
import ost
-import os.path
HistoryFile=os.path.expanduser('~/.ost_history')
# we are not in GUI mode.
--
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