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I want to install this package under a conda environment but have been encountering syntax errors when I try to run the scripts.
I first attempted to install with the following commands: conda create -n pdbtools python=2.7 conda activate pdbtools pip install git+git://github.com/harmslab/pdbtools
However when I then try and run a command from the package I get the following error:
pdb_bfactor
Traceback (most recent call last): File "/Users/samuelhaysom/opt/anaconda3/envs/pdbtools/bin/pdb_bfactor", line 19, in <module> from pdbtools.helper import cmdline File "/Users/samuelhaysom/opt/anaconda3/envs/pdbtools/lib/python2.7/site-packages/pdbtools/__init__.py", line 1, in <module> from . import addH, atom_renumber, bfactor, centerasu, centermass, clean, closecontacts, contact, contactplot, coulomb, dist_filter, disulfide, download, exper, iondist, ligand, moment, mutator, neighbors, offset, oligomer, param, residue_renumber, sasa, satk, seq, splitnmr, subset, torsion, watercontact, helper File "/Users/samuelhaysom/opt/anaconda3/envs/pdbtools/lib/python2.7/site-packages/pdbtools/addH.py", line 14, in <module> from .helper import container, cmdline, geometry ImportError: No module named helper
I then tried to install as in the instructions for this repo, after first creating and activating a conda environment as follows: conda create -n pdbtools python=2.7 conda activate pdbtools git clone https://github.com/harmslab/pdbtools cd pdbtools pip install -e .
I then got a different error: Traceback (most recent call last): File "/Users/samuelhaysom/opt/anaconda3/envs/pdbtools/bin/pdb_bfactor", line 7, in <module> exec(compile(f.read(), __file__, 'exec')) File "/Users/samuelhaysom/pdbtools/scripts/pdb_bfactor", line 19, in <module> from pdbtools.helper import cmdline File "/Users/samuelhaysom/pdbtools/pdbtools/__init__.py", line 1, in <module> from . import addH, atom_renumber, bfactor, centerasu, centermass, clean, closecontacts, contact, contactplot, coulomb, dist_filter, disulfide, download, exper, iondist, ligand, moment, mutator, neighbors, offset, oligomer, param, residue_renumber, sasa, satk, seq, splitnmr, subset, torsion, watercontact, helper File "/Users/samuelhaysom/pdbtools/pdbtools/addH.py", line 16, in <module> from .disulfide import pdbDisulfide File "/Users/samuelhaysom/pdbtools/pdbtools/disulfide.py", line 19, in <module> from .clean import stripACS File "/Users/samuelhaysom/pdbtools/pdbtools/clean.py", line 269 print(log[-1], end=' ') ^ SyntaxError: invalid syntax
Not sure if there is a simple solution here but can I suggest that at some point it would be good to make this package compatible with either PYPI or anaconda to make installation easier and the package more accessible.
The text was updated successfully, but these errors were encountered:
I want to install this package under a conda environment but have been encountering syntax errors when I try to run the scripts.
I first attempted to install with the following commands:
conda create -n pdbtools python=2.7 conda activate pdbtools pip install git+git://github.com/harmslab/pdbtools
However when I then try and run a command from the package I get the following error:
pdb_bfactor
Traceback (most recent call last): File "/Users/samuelhaysom/opt/anaconda3/envs/pdbtools/bin/pdb_bfactor", line 19, in <module> from pdbtools.helper import cmdline File "/Users/samuelhaysom/opt/anaconda3/envs/pdbtools/lib/python2.7/site-packages/pdbtools/__init__.py", line 1, in <module> from . import addH, atom_renumber, bfactor, centerasu, centermass, clean, closecontacts, contact, contactplot, coulomb, dist_filter, disulfide, download, exper, iondist, ligand, moment, mutator, neighbors, offset, oligomer, param, residue_renumber, sasa, satk, seq, splitnmr, subset, torsion, watercontact, helper File "/Users/samuelhaysom/opt/anaconda3/envs/pdbtools/lib/python2.7/site-packages/pdbtools/addH.py", line 14, in <module> from .helper import container, cmdline, geometry ImportError: No module named helper
I then tried to install as in the instructions for this repo, after first creating and activating a conda environment as follows:
conda create -n pdbtools python=2.7 conda activate pdbtools git clone https://github.com/harmslab/pdbtools cd pdbtools pip install -e .
I then got a different error:
Traceback (most recent call last): File "/Users/samuelhaysom/opt/anaconda3/envs/pdbtools/bin/pdb_bfactor", line 7, in <module> exec(compile(f.read(), __file__, 'exec')) File "/Users/samuelhaysom/pdbtools/scripts/pdb_bfactor", line 19, in <module> from pdbtools.helper import cmdline File "/Users/samuelhaysom/pdbtools/pdbtools/__init__.py", line 1, in <module> from . import addH, atom_renumber, bfactor, centerasu, centermass, clean, closecontacts, contact, contactplot, coulomb, dist_filter, disulfide, download, exper, iondist, ligand, moment, mutator, neighbors, offset, oligomer, param, residue_renumber, sasa, satk, seq, splitnmr, subset, torsion, watercontact, helper File "/Users/samuelhaysom/pdbtools/pdbtools/addH.py", line 16, in <module> from .disulfide import pdbDisulfide File "/Users/samuelhaysom/pdbtools/pdbtools/disulfide.py", line 19, in <module> from .clean import stripACS File "/Users/samuelhaysom/pdbtools/pdbtools/clean.py", line 269 print(log[-1], end=' ') ^ SyntaxError: invalid syntax
Not sure if there is a simple solution here but can I suggest that at some point it would be good to make this package compatible with either PYPI or anaconda to make installation easier and the package more accessible.
The text was updated successfully, but these errors were encountered: