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MolMod is a collection of molecular modelling tools for python.

Home Page: http://molmod.github.io/molmod

License: GNU General Public License v3.0

Python 96.52% C 3.48%

molmod's Introduction

MolMod is a collection of molecular modelling tools for python. It is used by other software developed at the CMM, including Yaff, TAMkin and Zeobuilder.

More information about MolMod can be found on the CMM Code website: http://molmod.ugent.be/software

MolMod is distributed as open source software under the conditions of the GPL license version 3. Read the file COPYING for more details, or visit http://www.gnu.org/licenses/

Installation

MolMod can be installed with pip (system wide or in a virtual environment):

pip install Cython numpy
pip install molmod

Alternatively, you can install MolMod in your home directory:

pip install Cython numpy --user
pip install molmod --user

Lastly, you can also install MolMod with conda. (See https://www.continuum.io/downloads)

# Using the builds from Travis-CI ...
conda install -c molmod molmod
# ... or using the packages on conda-force
conda install -c conda-forge molmod

Testing

The tests can be executed as follows:

pytest molmod

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molmod's Issues

Pattern examples

The documentation lists examples for finding rings and other patterns, but the examples appear to be missing. Do you have the zeolite, or other, examples for using NRingPattern?

https://molmod.github.io/molmod/tutorial/patterns.html

Update installation instructions with releases on conda-forge

For most users, packages on conda-forge would be a little easier to install. See https://github.com/conda-forge/molmod-feedstock and https://anaconda.org/conda-forge/molmod. (E.g. this channel also has packages for Windows.)

Hello, we are new to both Python and MolMod, we would like to parse the molecules
in a xyz trajectory file using MolMod and calculated related proproperties. We found
that the Molecule.from_file only reads the first structure, is it possible to read in
multiple structures?

thank you

Tests fail: No module named ext

Tests fail in the FreeBSD port:

$ nosetests molmod
E
======================================================================
ERROR: Failure: ImportError (No module named ext)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/ports/science/py-molmod/work-py27/molmod-1.4.4/molmod/__init__.py", line 67, in <module>
    from molmod.similarity import *
  File "/usr/ports/science/py-molmod/work-py27/molmod-1.4.4/molmod/similarity.py", line 45, in <module>
    from molmod.ext import similarity_table_labels, similarity_table_distances, \
ImportError: No module named ext

----------------------------------------------------------------------
Ran 1 test in 0.002s

molmod 1.4.8: Failing tests

I'm using Python 3.8.6 and matplot lib 3.3.3.
GCC is 10.2.0.

The compilation is done with:
export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;python setup.py build_ext -i; nosetests -v

While building MolMod 1.4.8 with Python 3.8.6, I get the following error:

======================================================================
ERROR: test_fingerprint_collisions (molmod.test.test_molecular_graphs.MolecularGraphTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/dev/shm/build/molmod/1.4.8/foss-2020b/molmod-1.4.8/molmod/test/test_molecular_graphs.py", line 387, in test_fingerprint_collisions
    g0 = Molecule.from_file(pkg_resources.resource_filename("../data/test/" + fn0))
TypeError: resource_filename() missing 1 required positional argument: 'resource_name'

======================================================================
FAIL: test_check_anagrad_full_prec (molmod.test.test_minimizer.MinimizerTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/dev/shm/build/molmod/1.4.8/foss-2020b/molmod-1.4.8/molmod/test/test_minimizer.py", line 243, in test_check_anagrad_full_prec
    check_anagrad(prec_fun, x_init, 1e-5, 1e-4)
  File "/dev/shm/build/molmod/1.4.8/foss-2020b/molmod-1.4.8/molmod/minimizer.py", line 1608, in check_anagrad
    raise AssertionError("Error in the analytical gradient, component %i, got %s, should be about %s" % (i, ana_grad[i], num_grad_comp))
AssertionError: Error in the analytical gradient, component 1, got 0.3081499243346107, should be about -0.3733645133952023

======================================================================
FAIL: test_shortest_vector (molmod.test.test_unit_cells.UnitCellTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/dev/shm/build/molmod/1.4.8/foss-2020b/molmod-1.4.8/molmod/test/test_unit_cells.py", line 175, in test_shortest_vector
    assert np.dot(change, r0) <= 0
AssertionError

----------------------------------------------------------------------

Get atom order

Hello,

First of all, great tool thanks for sharing!

I am parsing some SDF files downloaded from RCSB PDB using SDFReader.

I would like to be able to access the numbering of the atoms found in the original SDF e.g. (N1, C3, O3, etc).
Looking at the attributes of the graph and molecule classes I haven't found anything that seems to do the job.

Could it be that the ordering of the nodes can be used to retrieve the atom ordering in the original file?

Thanks!

Change NumPy dependency to >= 1.16.0

See molmod/tamkin#23

Deprecate graph searching algorithms

They occasionally fail and should be tested more thoroughly, which is I cannot make a priority in short term.

version.py not available

The file version.py is listed in .gitignore, so it is not available, but it is needed to build the docs.

$ make html
mkdir -p _build/html _static
sphinx-build -b html -d _build/doctrees   . _build/html
Running Sphinx v1.6.3

Exception occurred:
  File "conf.py", line 62, in <module>
    with open('../molmod/version.py', 'r') as fh:
IOError: [Errno 2] No such file or directory: '../molmod/version.py'

Is it possible to calculate per Residue Energy decomposition from MD simulation trajectories?

Molecular Dynamics Simulation programs calculate the potential energy of the system each frame in trajectory, but what I want is how much of each residual share in all potential energy? So, i am wondering is it possible to calculate with molmod each residue share from dcd or any kind of trajectories.

nosetests 1 test failed

I downloaded and installed molmod using pip install molmod -user. After installation when i run nosetests -v molmod, i get the following error. Please help me to solve this:

======================================================================
FAIL: test_example_001 (molmod.test.test_meta.MetaTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/molmod/test/test_meta.py", line 49, in test_example_001
    self.check_example("001_molecules", "a_convert.py")
  File "/usr/local/lib/python2.7/dist-packages/molmod/test/test_meta.py", line 41, in check_example
    self.assertEqual(retcode, 0)
AssertionError: 256 != 0
-------------------- >> begin captured stdout << ---------------------
cd /usr/local/share/molmod/examples/001_molecules; PYTHONPATH=/home/minhaj/[email protected]/Temp_TAMUQ_Working_folder/NPRP-EP/DFT_Studies/CALCULATIONS/RAAD2/111Cu_FullML/Coadsorption/CplusO/AfterGeoms-3/004_DymMat_TS:${PYTHONPATH} ./a_convert.py 1> /dev/null 2> /dev/null

--------------------- >> end captured stdout << ----------------------

----------------------------------------------------------------------
Ran 277 tests in 40.623s

FAILED (SKIP=3, failures=1)

incompatibel to newer python versions?

Hi,

installing molmod in anaconda using conda install -c molmod molmod gives some errors

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

molmod -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0']

Your python: python=3.10

molmod not work with newer python versions?

Creating complete graph

Hi,

I'd like to create a complete graph. I have tried, for example,
MolecularGraph.from_geometry(mol, scaling=1.5)
and even
MolecularGraph.from_geometry(mol, scaling=150000.).
Can you please explain how to create a complete graph in your system?

Thanks!

Missing version.py

Trying to get the version from git describe
fatal: No names found, cannot describe anything.
Trying to get the version from molmod/version.py
Could not determine version. Giving up.

when launching python setup.py

molmod / molmod Goto Github PK

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