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Setup will fail if .mol2 atom substructure ID matches filename
See original GitHub issueThis is very likely a niche issue (my very sloppy work found this error), but it may be worth sanitizing .mol2 files during setup–
If the substructure id for a atom in a mol2 file matches the filename, e.g.
20G.mol2
47 48 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 C09 -2.7090 -4.5890 6.9990 C.2 203 20G 0.2532
2 N10 -3.6170 -5.6600 6.6290 N.am 203 20G -0.2986
3 C11 -4.8540 -5.3500 5.9460 C.3 203 20G 0.0164
....
Then setup will fail with the following:
2017-06-27 11:00:19,824: Setting CUDA platform to use precision model 'mixed'.
2017-06-27 11:00:19,828: Single node: executing <function _check_resume at 0x7f745d8cbe60>
2017-06-27 11:00:19,828: Single node: executing <function _setup_experiments at 0x7f745d8d1140>
2017-06-27 11:00:19,828: Setting up the systems for 4LUC, 20G and pme
2017-06-27 11:02:09,738: Single node: executing <function _safe_makedirs at 0x7f745d8d1320>
2017-06-27 11:02:09,738: Single node: executing <bound method YamlBuilder._generate_yaml of <yank.yamlbuild.YamlBuilder object at 0x7f745ccaaf50>>
2017-06-27 11:02:09,748: DSL string for the ligand: "resname 20G"
2017-06-27 11:02:09,748: DSL string for the solvent: "auto"
2017-06-27 11:02:09,749: Reading phase complex
2017-06-27 11:02:09,749: prmtop: ./setup/systems/4LUC/complex.prmtop
2017-06-27 11:02:09,749: inpcrd: ./setup/systems/4LUC/complex.inpcrd
Traceback (most recent call last):
File "/home/yanker/miniconda2/bin/yank", line 11, in <module>
load_entry_point('yank==0.16.1', 'console_scripts', 'yank')()
File "/home/yanker/miniconda2/lib/python2.7/site-packages/yank/cli.py", line 71, in main
dispatched = getattr(commands, command).dispatch(command_args)
File "/home/yanker/miniconda2/lib/python2.7/site-packages/yank/commands/script.py", line 100, in dispatch
yaml_builder.run_experiments()
File "/home/yanker/miniconda2/lib/python2.7/site-packages/yank/yamlbuild.py", line 1462, in run_experiments
for experiment_index, experiment in enumerate(self._build_experiments()):
File "/home/yanker/miniconda2/lib/python2.7/site-packages/yank/yamlbuild.py", line 2392, in _build_experiments
yield self._build_experiment(combination, output_dir)
File "/home/yanker/miniconda2/lib/python2.7/site-packages/yank/yamlbuild.py", line 2654, in _build_experiment
solvent_atoms=solvent_dsl)
File "/home/yanker/miniconda2/lib/python2.7/site-packages/yank/yank.py", line 90, in __init__
self.ligand_atoms = ligand_atoms
File "/home/yanker/miniconda2/lib/python2.7/site-packages/yank/yank.py", line 113, in ligand_atoms
self._ligand_atoms = self._resolve_atom_indices(value)
File "/home/yanker/miniconda2/lib/python2.7/site-packages/yank/yank.py", line 215, in _resolve_atom_indices
atoms_description = self._topology.select(atoms_description).tolist()
File "/home/yanker/miniconda2/lib/python2.7/site-packages/mdtraj/core/topology.py", line 933, in select
filter_func = parse_selection(selection_string).expr
File "/home/yanker/miniconda2/lib/python2.7/site-packages/mdtraj/core/selection.py", line 354, in __call__
raise ValueError('\n'.join(lines))
ValueError: Expected end of text (at char 10), (line:1, col:11): resname 20G
^^^
This occurs with the following:
yanker@hopper:~/yank_files/kras$ conda list
# packages in environment at /home/yanker/miniconda2:
#
alabaster 0.7.9 py27_0
alchemy 1.2.3 py27_0 omnia
ambermini 16.16.0 6 omnia
babel 2.3.4 py27_0
cairo 1.14.8 0
cffi 1.9.1 py27_0
click 6.7 <pip>
clusterutils 0.1.2 py27_0 omnia
conda 4.3.22 py27_0
conda-env 2.6.0 0
cryptography 1.7.1 py27_0
curl 7.49.0 1
cycler 0.10.0 py27_0
cython 0.25.2 py27_0
dbus 1.10.10 0
docopt 0.6.2 py27_1 omnia
docutils 0.12 py27_2
enum34 1.1.6 py27_0
expat 2.1.0 0
fftw3f 3.3.4 2 omnia
Flask 0.12 <pip>
fontconfig 2.12.1 3
freetype 2.5.5 2
functools32 3.2.3.2 py27_0
glib 2.50.2 1
gst-plugins-base 1.8.0 0
gstreamer 1.8.0 0
hdf4 4.2.12 0
hdf5 1.8.17 1
icu 54.1 0
idna 2.1 py27_0
imagesize 0.7.1 py27_0
ipaddress 1.0.17 py27_0
itsdangerous 0.24 <pip>
jinja2 2.8.1 py27_0
jpeg 8d 2
latexcodec 1.0.1 py27_0 omnia
libffi 3.2.1 1
libgcc 5.2.0 0
libgfortran 3.0.0 1
libiconv 1.14 0
libnetcdf 4.4.1 0
libpng 1.6.27 0
libxcb 1.12 1
libxml2 2.9.4 0
markupsafe 0.23 py27_2
matplotlib 2.0.0 np111py27_0
mdtraj 1.8.0 np111py27_1 omnia
mkl 2017.0.1 0
mpi4py 2.0.0 py27_2
mpich2 1.4.1p1 0
netcdf4 1.2.4 np111py27_0
nose 1.3.7 py27_1
numexpr 2.6.1 np111py27_2
numpy 1.11.3 py27_0
numpydoc 0.6.0 py27_0
openmm 7.2.0 py27_0 omnia/label/dev
openmmtools 0.11.0 py27_0 omnia
openmoltools 0.7.4 py27_0 omnia
openssl 1.0.2j 0
oset 0.1.3 py27_1 omnia
pandas 0.19.2 np111py27_1
parmed 2.7.1 py27_0 omnia
pcre 8.39 1
pip 8.1.2 py27_0
pixman 0.34.0 0
pyasn1 0.1.9 py27_0
pybtex 0.18 py27_0 omnia
pybtex-docutils 0.2.1 py27_1 omnia
pycairo 1.10.0 py27_0
pycosat 0.6.1 py27_1
pycparser 2.17 py27_0
pycrypto 2.6.1 py27_4
pygments 2.1.3 py27_0
pymbar 3.0.0.beta2 np111py27_0 omnia
pyopenssl 16.2.0 py27_0
pyparsing 2.1.4 py27_0
pyqt 5.6.0 py27_2
pytables 3.3.0 np111py27_0
python 2.7.12 1
python-dateutil 2.6.0 py27_0
pytz 2016.10 py27_0
pyyaml 3.12 py27_0
qt 5.6.2 2
readline 6.2 2
redis 2.10.5 <pip>
requests 2.12.4 py27_0
rq 0.7.1 <pip>
ruamel_yaml 0.11.14 py27_0
schema 0.6.2 py27_0 omnia
scipy 0.18.1 np111py27_1
setuptools 27.2.0 py27_0
sip 4.18 py27_0
six 1.10.0 py27_0
snowballstemmer 1.2.1 py27_0
sphinx 1.5.1 py27_0
sphinxcontrib-bibtex 0.3.2 py27_0 omnia
sqlite 3.13.0 0
subprocess32 3.2.6 py27_0 omnia
tk 8.5.18 0
Werkzeug 0.11.15 <pip>
wheel 0.29.0 py27_0
yaml 0.1.6 0
yank 0.16.1 py27_0 omnia
zlib 1.2.8 3
Issue Analytics
- State:
- Created 6 years ago
- Comments:13 (12 by maintainers)
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DOES have such problems.
I see—the problem is that we create the
Topographyfrom theTopologyread in from the AMBERprmtopfile in these lines, so we would have to