[Debichem-devel] Bug#1030491: prody: FTBFS: AssertionError: 3205 != 3211 : selection 'abs(x) == sqrt(sq(x))' for Selection 'all' failed, expected 3211, selected 3205
Lucas Nussbaum
lucas at debian.org
Sat Feb 4 07:57:42 GMT 2023
Source: prody
Version: 2.3.1+dfsg-3
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20230203 ftbfs-bookworm
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> debian/rules binary
> dh binary --buildsystem pybuild --with numpy3,python3
> dh_update_autotools_config -O--buildsystem=pybuild
> dh_autoreconf -O--buildsystem=pybuild
> dh_auto_configure -O--buildsystem=pybuild
> I: pybuild base:240: python3.11 setup.py config
> running config
> dh_auto_build -O--buildsystem=pybuild
> I: pybuild base:240: /usr/bin/python3 setup.py build
> running build
> running build_py
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody
> copying prody/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/hierview.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/segment.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/chain.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/atommap.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/flags.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/selection.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/residue.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/atomic.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/donor.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/bond.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/subset.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/dihedral.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/nbexclusion.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/pointer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/acceptor.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/atomgroup.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/angle.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/select.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/improper.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/crossterm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/functions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/fields.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> copying prody/atomic/atom.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/database
> copying prody/database/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/database
> copying prody/database/quartataweb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/database
> copying prody/database/uniprot.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/database
> copying prody/database/goa.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/database
> copying prody/database/pfam.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/database
> copying prody/database/cath.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/database
> copying prody/database/dali.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/database
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/essa.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/exgnm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/rtb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/sampling.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/adaptive.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/vmdfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/compare.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/bbenm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/exanm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/signature.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/heatmapper.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/nma.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/gamma.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/pca.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/imanm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/nmdfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/modeset.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/editing.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/mechstiff.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/gnm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/plotting.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/functions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/entropy.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/anm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/mode.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/perturb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/clustenm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> copying prody/dynamics/analysis.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/ensemble
> copying prody/ensemble/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/ensemble
> copying prody/ensemble/ensemble.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/ensemble
> copying prody/ensemble/conformation.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/ensemble
> copying prody/ensemble/pdbensemble.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/ensemble
> copying prody/ensemble/functions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/ensemble
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/kdtree
> copying prody/kdtree/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/kdtree
> copying prody/kdtree/kdtree.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/kdtree
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/measure
> copying prody/measure/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/measure
> copying prody/measure/transform.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/measure
> copying prody/measure/measure.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/measure
> copying prody/measure/contacts.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/measure
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/proteins
> copying prody/proteins/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/proteins
> copying prody/proteins/wwpdb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/proteins
> copying prody/proteins/compare.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/proteins
> copying prody/proteins/emdfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/proteins
> copying prody/proteins/ciffile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/proteins
> copying prody/proteins/cifheader.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/proteins
> copying prody/proteins/dssp.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/proteins
> copying prody/proteins/starfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/proteins
> copying prody/proteins/stride.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/proteins
> copying prody/proteins/pdbclusters.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/proteins
> copying prody/proteins/header.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/proteins
> copying prody/proteins/blastpdb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/proteins
> copying prody/proteins/functions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/proteins
> copying prody/proteins/pdbfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/proteins
> copying prody/proteins/localpdb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/proteins
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/sequence
> copying prody/sequence/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/sequence
> copying prody/sequence/msafile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/sequence
> copying prody/sequence/msa.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/sequence
> copying prody/sequence/plotting.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/sequence
> copying prody/sequence/sequence.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/sequence
> copying prody/sequence/analysis.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/sequence
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/trajectory
> copying prody/trajectory/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/trajectory
> copying prody/trajectory/dcdfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/trajectory
> copying prody/trajectory/psffile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/trajectory
> copying prody/trajectory/trajfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/trajectory
> copying prody/trajectory/trajbase.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/trajectory
> copying prody/trajectory/trajectory.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/trajectory
> copying prody/trajectory/frame.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/trajectory
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/chromatin
> copying prody/chromatin/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/chromatin
> copying prody/chromatin/norm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/chromatin
> copying prody/chromatin/hic.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/chromatin
> copying prody/chromatin/cluster.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/chromatin
> copying prody/chromatin/functions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/chromatin
> copying prody/chromatin/straw.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/chromatin
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/compounds
> copying prody/compounds/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/compounds
> copying prody/compounds/ccd.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/compounds
> copying prody/compounds/pdbligands.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/compounds
> copying prody/compounds/functions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/compounds
> copying prody/compounds/bird.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/compounds
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/domain_decomposition
> copying prody/domain_decomposition/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/domain_decomposition
> copying prody/domain_decomposition/spectrus.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/domain_decomposition
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/utilities
> copying prody/utilities/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/utilities
> copying prody/utilities/logger.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/utilities
> copying prody/utilities/settings.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/utilities
> copying prody/utilities/legacy.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/utilities
> copying prody/utilities/pathtools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/utilities
> copying prody/utilities/drawtools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/utilities
> copying prody/utilities/eigtools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/utilities
> copying prody/utilities/doctools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/utilities
> copying prody/utilities/seqtools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/utilities
> copying prody/utilities/misctools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/utilities
> copying prody/utilities/checkers.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/utilities
> copying prody/utilities/laptools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/utilities
> copying prody/utilities/TreeConstruction.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/utilities
> copying prody/utilities/catchall.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/utilities
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps
> copying prody/apps/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps
> copying prody/apps/apptools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps
> copying prody/apps/prody_apps/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps
> copying prody/apps/prody_apps/prody_energy.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps
> copying prody/apps/prody_apps/prody_anm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps
> copying prody/apps/prody_apps/prody_catdcd.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps
> copying prody/apps/prody_apps/prody_contacts.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps
> copying prody/apps/prody_apps/prody_pca.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps
> copying prody/apps/prody_apps/prody_gnm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps
> copying prody/apps/prody_apps/nmaoptions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps
> copying prody/apps/prody_apps/prody_select.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps
> copying prody/apps/prody_apps/prody_blast.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps
> copying prody/apps/prody_apps/prody_eda.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps
> copying prody/apps/prody_apps/prody_fetch.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps
> copying prody/apps/prody_apps/prody_align.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps
> copying prody/apps/prody_apps/prody_biomol.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps
> copying prody/apps/evol_apps/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps
> copying prody/apps/evol_apps/evol_filter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps
> copying prody/apps/evol_apps/evol_conserv.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps
> copying prody/apps/evol_apps/evol_coevol.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps
> copying prody/apps/evol_apps/evol_occupancy.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps
> copying prody/apps/evol_apps/evol_merge.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps
> copying prody/apps/evol_apps/evol_refine.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps
> copying prody/apps/evol_apps/evol_fetch.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps
> copying prody/apps/evol_apps/evol_search.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps
> copying prody/apps/evol_apps/evol_rankorder.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests
> copying prody/tests/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/apps
> copying prody/tests/apps/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/apps
> copying prody/tests/apps/test_prody_anm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/apps
> copying prody/tests/apps/test_prody_pca.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/apps
> copying prody/tests/apps/test_prody_gnm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/apps
> copying prody/tests/apps/test_prody_examples.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/apps
> copying prody/tests/apps/test_prody_catdcd.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/apps
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic
> copying prody/tests/atomic/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic
> copying prody/tests/atomic/test_subset.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic
> copying prody/tests/atomic/test_fragment.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic
> copying prody/tests/atomic/test_atommap.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic
> copying prody/tests/atomic/test_atomic.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic
> copying prody/tests/atomic/test_hierview.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic
> copying prody/tests/atomic/test_select.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics
> copying prody/tests/dynamics/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics
> copying prody/tests/dynamics/test_enms.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics
> copying prody/tests/dynamics/test_editing.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics
> copying prody/tests/dynamics/test_pca.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics
> copying prody/tests/dynamics/test_signature.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/ensemble
> copying prody/tests/ensemble/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/ensemble
> copying prody/tests/ensemble/test_conformation.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/ensemble
> copying prody/tests/ensemble/test_functions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/ensemble
> copying prody/tests/ensemble/test_pdbensemble.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/ensemble
> copying prody/tests/ensemble/test_ensemble.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/ensemble
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/kdtree
> copying prody/tests/kdtree/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/kdtree
> copying prody/tests/kdtree/test_kdtree.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/kdtree
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/measure
> copying prody/tests/measure/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/measure
> copying prody/tests/measure/test_measure.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/measure
> copying prody/tests/measure/test_transform.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/measure
> copying prody/tests/measure/test_contacts.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/measure
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins
> copying prody/tests/proteins/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins
> copying prody/tests/proteins/test_localpdb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins
> copying prody/tests/proteins/test_ciffile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins
> copying prody/tests/proteins/test_header.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins
> copying prody/tests/proteins/test_dssp.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins
> copying prody/tests/proteins/test_wwpdb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins
> copying prody/tests/proteins/test_pdbfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence
> copying prody/tests/sequence/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence
> copying prody/tests/sequence/test_sequence.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence
> copying prody/tests/sequence/test_msafile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence
> copying prody/tests/sequence/test_msa.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence
> copying prody/tests/sequence/test_analysis.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/trajectory
> copying prody/tests/trajectory/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/trajectory
> copying prody/tests/trajectory/test_dcdfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/trajectory
> copying prody/tests/trajectory/test_frame.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/trajectory
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/utilities
> copying prody/tests/utilities/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/utilities
> copying prody/tests/utilities/test_pathtools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/utilities
> copying prody/tests/utilities/test_checkers.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/utilities
> copying prody/tests/utilities/test_misctools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/utilities
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/utilities/datafiles
> copying prody/utilities/datafiles/saxs_water.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/utilities/datafiles
> copying prody/utilities/datafiles/mod_res_map.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/utilities/datafiles
> copying prody/tests/datafiles/pdb1ubi_ca.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/pdb1ubi.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/pdb2nwl-opm.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/pdb1r19_dssp.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/pdb3o21.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/pdb2gb1_truncated.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/pdb2k39_ca.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/pdbRTER.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/pdb2k39_truncated.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/pdb1tw7_step3_charmm2namd_doubled_hex.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/pdb1tw7_step3_charmm2namd.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/pdb1ejg.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/pdb3p3w.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/pdb3hsy.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/pdb3mht.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/pdb1tw7_step3_charmm2namd_doubled_h36.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/pdb1ejg_oneatom.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/exanm2nwl_evalues.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/gnm1ubi_vectors.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/pca2k39_vectors.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/exanm2nwl_vectors.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/msa_Cys_knot_di.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/hit1ubi.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/gnm1ubi_evalues.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/anm1ubi_vectors.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/msa_Cys_knot_sca.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/commute1ubi.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/anm1ubi_evalues.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/pca2k39_evalues.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/mmcif_6zu5.cif -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/mmcif_6yfy.cif -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/anm1ubi_hessian.coo -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/pca2k39_cov.coo -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/exanm2nwl_hessian.coo -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/rtb2gb1_hessian.coo -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/rtb2gb1_project.coo -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/gnm1ubi_kirchhoff.coo -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/dcd2k39_truncated.dcd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/xmlSTI.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/msa_Cys_knot.slx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/msa_Cys_knot.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> copying prody/tests/datafiles/msa_Cys_knot.sth -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles
> running build_ext
> building 'prody.dynamics.rtbtools' extension
> creating build
> creating build/temp.linux-x86_64-cpython-311
> creating build/temp.linux-x86_64-cpython-311/prody
> creating build/temp.linux-x86_64-cpython-311/prody/dynamics
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c prody/dynamics/rtbtools.c -o build/temp.linux-x86_64-cpython-311/prody/dynamics/rtbtools.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/prody/dynamics/rtbtools.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics/rtbtools.cpython-311-x86_64-linux-gnu.so
> building 'prody.dynamics.smtools' extension
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c prody/dynamics/smtools.c -o build/temp.linux-x86_64-cpython-311/prody/dynamics/smtools.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/prody/dynamics/smtools.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/dynamics/smtools.cpython-311-x86_64-linux-gnu.so
> building 'prody.sequence.msatools' extension
> creating build/temp.linux-x86_64-cpython-311/prody/sequence
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c prody/sequence/msatools.c -o build/temp.linux-x86_64-cpython-311/prody/sequence/msatools.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/prody/sequence/msatools.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/sequence/msatools.cpython-311-x86_64-linux-gnu.so
> building 'prody.sequence.msaio' extension
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c prody/sequence/msaio.c -o build/temp.linux-x86_64-cpython-311/prody/sequence/msaio.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/prody/sequence/msaio.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/sequence/msaio.cpython-311-x86_64-linux-gnu.so
> building 'prody.sequence.seqtools' extension
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c prody/sequence/seqtools.c -o build/temp.linux-x86_64-cpython-311/prody/sequence/seqtools.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/prody/sequence/seqtools.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/sequence/seqtools.cpython-311-x86_64-linux-gnu.so
> building 'prody.kdtree._CKDTree' extension
> creating build/temp.linux-x86_64-cpython-311/prody/kdtree
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c prody/kdtree/KDTree.c -o build/temp.linux-x86_64-cpython-311/prody/kdtree/KDTree.o
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c prody/kdtree/KDTreemodule.c -o build/temp.linux-x86_64-cpython-311/prody/kdtree/KDTreemodule.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/prody/kdtree/KDTree.o build/temp.linux-x86_64-cpython-311/prody/kdtree/KDTreemodule.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/kdtree/_CKDTree.cpython-311-x86_64-linux-gnu.so
> building 'prody.proteins.ccealign' extension
> creating build/temp.linux-x86_64-cpython-311/prody/proteins
> creating build/temp.linux-x86_64-cpython-311/prody/proteins/ccealign
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iprody/utilities/tnt -I/usr/include/python3.11 -c prody/proteins/ccealign/ccealignmodule.cpp -o build/temp.linux-x86_64-cpython-311/prody/proteins/ccealign/ccealignmodule.o
> x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/prody/proteins/ccealign/ccealignmodule.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/proteins/ccealign.cpython-311-x86_64-linux-gnu.so
> dh_auto_test -O--buildsystem=pybuild
> I: pybuild base:240: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build; python3.11 -m unittest discover -v
> /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
> warnings.warn(
> testANMCommand (prody.tests.apps.test_prody_anm.TestANMCommand.testANMCommand) ... skipped 'prody command not found'
> testAlignConcat (prody.tests.apps.test_prody_catdcd.TestCatdcdCommand.testAlignConcat) ... skipped 'prody command not found'
> testAlignException (prody.tests.apps.test_prody_catdcd.TestCatdcdCommand.testAlignException) ... skipped 'prody command is not found'
> testIOException (prody.tests.apps.test_prody_catdcd.TestCatdcdCommand.testIOException) ... skipped 'prody command is not found'
> testSelectConcat (prody.tests.apps.test_prody_catdcd.TestCatdcdCommand.testSelectConcat) ... skipped 'prody command not found'
> testSelectException (prody.tests.apps.test_prody_catdcd.TestCatdcdCommand.testSelectException) ... skipped 'prody command is not found'
> testSelectException2 (prody.tests.apps.test_prody_catdcd.TestCatdcdCommand.testSelectException2) ... skipped 'prody command is not found'
> testSimpleConcat (prody.tests.apps.test_prody_catdcd.TestCatdcdCommand.testSimpleConcat) ... skipped 'prody command not found'
> testCommandExample1 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample1)
> Test example: $ prody anm 1p38 ... skipped 'prody command not found'
> testCommandExample10 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample10)
> Test example: $ prody align 2k39 --select "backbone and resnum < 71" ... skipped 'prody command not found'
> testCommandExample11 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample11)
> Test example: $ prody align --select "resnum < 300" 1p38 1r39 1zz2 ... skipped 'prody command not found'
> testCommandExample12 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample12)
> Test example: $ prody align --select "resnum 1 to 70" 1aar 2k39 ... skipped 'prody command not found'
> testCommandExample13 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample13)
> Test example: $ prody align --select "noh heme and chain A" 1hrc 1fi7 ... skipped 'prody command not found'
> testCommandExample14 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample14)
> Test example: $ prody biomol 2bfu ... skipped 'prody command not found'
> testCommandExample15 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample15)
> Test example: $ prody select -o B11 "resname B11" 1zz2 $ prody select -o BOG "resname BOG" 1zz2 $ prody contacts -r 4.0 -t residue -s protein 1zz2 B11.pdb BOG.pdb ... skipped 'prody command not found'
> testCommandExample16 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample16)
> Test example: $ prody fetch 1mkp 1p38 ... skipped 'prody command not found'
> testCommandExample17 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample17)
> Test example: $ prody select backbone 1p38 1r39 ... skipped 'prody command not found'
> testCommandExample18 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample18)
> Test example: $ prody energy 1p38 1r39 ... skipped 'prody command not found'
> testCommandExample2 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample2)
> Test example: $ prody anm 1aar -s "calpha and chain A and resnum < 70" -A ... skipped 'prody command not found'
> testCommandExample3 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample3)
> Test example: $ prody gnm 1p38 ... skipped 'prody command not found'
> testCommandExample4 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample4)
> Test example: $ prody gnm 1aar -c 7 -s "calpha and chain A and resnum < 70" -A ... skipped 'prody command not found'
> testCommandExample5 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample5)
> Test example: $ prody pca 2k39 ... skipped 'prody command not found'
> testCommandExample6 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample6)
> Test example: $ prody pca 2k39 --select "backbone and resnum < 71" -a -A ... skipped 'prody command not found'
> testCommandExample7 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample7)
> Test example: $ prody pca 2k39 ... skipped 'prody command not found'
> testCommandExample8 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample8)
> Test example: $ prody pca 2k39 --select "backbone and resnum < 71" -a -A ... skipped 'prody command not found'
> testCommandExample9 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample9)
> Test example: $ prody align 2k39 ... skipped 'prody command not found'
> testGNMCommand (prody.tests.apps.test_prody_gnm.TestGNMCommand.testGNMCommand) ... skipped 'prody command not found'
> testPCACommandDCD (prody.tests.apps.test_prody_pca.TestPCACommand.testPCACommandDCD) ... skipped 'prody command not found'
> testPCACommandPDB (prody.tests.apps.test_prody_pca.TestPCACommand.testPCACommandPDB) ... skipped 'prody command not found'
> testAtomGroup (prody.tests.atomic.test_atomic.TestAtomIterations.testAtomGroup) ... ok
> testAtomMap (prody.tests.atomic.test_atomic.TestAtomIterations.testAtomMap) ... ok
> testChain (prody.tests.atomic.test_atomic.TestAtomIterations.testChain) ... ok
> testResidue (prody.tests.atomic.test_atomic.TestAtomIterations.testResidue) ... ok
> testSelection (prody.tests.atomic.test_atomic.TestAtomIterations.testSelection) ... ok
> testAtom (prody.tests.atomic.test_atomic.TestPickling.testAtom) ... ok
> testAtomGroup (prody.tests.atomic.test_atomic.TestPickling.testAtomGroup) ... ok
> testSelection (prody.tests.atomic.test_atomic.TestPickling.testSelection) ... ok
> testSaveLoad (prody.tests.atomic.test_atomic.TestSaveLoad.testSaveLoad) ... ok
> testInstantiation (prody.tests.atomic.test_atommap.TestInstantiation.testInstantiation) ... ok
> testAllSelection (prody.tests.atomic.test_atommap.TestSelection.testAllSelection) ... ok
> testChainSelection (prody.tests.atomic.test_atommap.TestSelection.testChainSelection) ... ok
> testGetBoolArray (prody.tests.atomic.test_atommap.TestSelection.testGetBoolArray) ... ok
> testNameSelection (prody.tests.atomic.test_atommap.TestSelection.testNameSelection) ... ok
> testSplit (prody.tests.atomic.test_fragment.TestFragment.testSplit) ... ok
> testSplitCopy (prody.tests.atomic.test_fragment.TestFragment.testSplitCopy) ... ok
> testSplitNoh (prody.tests.atomic.test_fragment.TestFragment.testSplitNoh) ... ok
> testSplitNohCopy (prody.tests.atomic.test_fragment.TestFragment.testSplitNohCopy) ... ok
> testWhole (prody.tests.atomic.test_fragment.TestFragment.testWhole) ... ok
> testWhole2 (prody.tests.atomic.test_fragment.TestFragment.testWhole2) ... ok
> testWholeAll (prody.tests.atomic.test_fragment.TestFragment.testWholeAll) ... ok
> testWholeCopy (prody.tests.atomic.test_fragment.TestFragment.testWholeCopy) ... ok
> testWholeNoh (prody.tests.atomic.test_fragment.TestFragment.testWholeNoh) ... ok
> testWholeNohCopy (prody.tests.atomic.test_fragment.TestFragment.testWholeNohCopy) ... ok
> testCA (prody.tests.atomic.test_hierview.TestShuffled.testCA) ... ok
> testProtein (prody.tests.atomic.test_hierview.TestShuffled.testProtein) ... ok
> testNumResidues (prody.tests.atomic.test_hierview.TestTerRecord.testNumResidues) ... ok
> testResidueIndexing (prody.tests.atomic.test_hierview.TestTerRecord.testResidueIndexing) ... ok
> testSelectionResidueIndexing (prody.tests.atomic.test_hierview.TestTerRecord.testSelectionResidueIndexing) ... ok
> testSelectionResidueIndexing2 (prody.tests.atomic.test_hierview.TestTerRecord.testSelectionResidueIndexing2) ... ok
> testMacro1 (prody.tests.atomic.test_select.TestMacros.testMacro1)
> Test macro *cacb*: 'name CA CB' ... ok
> testMacro2 (prody.tests.atomic.test_select.TestMacros.testMacro2)
> Test macro *donors*: '(protein) and (name N NE NH2 ND2 NE2 ND1 OG OH NH1 SG OG1 NE2 NZ NE1 ND1 NE2)' ... ok
> testMacroFunctions (prody.tests.atomic.test_select.TestMacros.testMacroFunctions) ... ok
> testBondedtoSelection1 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection1)
> Test bondedto selections 'bonded to index 0' for imatinib ... ok
> testBondedtoSelection10 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection10)
> Test bondedto selections "bonded 2 to index 0" ... ok
> testBondedtoSelection11 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection11)
> Test bondedto selections 'bonded 0 to index 0' for imatinib ... ok
> testBondedtoSelection12 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection12)
> Test bondedto selections "bonded 0 to index 0" ... ok
> testBondedtoSelection13 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection13)
> Test bondedto selections 'bonded 3 to index 0' for imatinib ... ok
> testBondedtoSelection14 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection14)
> Test bondedto selections "bonded 3 to index 0" ... ok
> testBondedtoSelection15 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection15)
> Test bondedto selections 'bonded 4 to index 0' for imatinib ... ok
> testBondedtoSelection16 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection16)
> Test bondedto selections "bonded 4 to index 0" ... ok
> testBondedtoSelection17 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection17)
> Test bondedto selections 'bonded 4 to index 0' for imatinib ... ok
> testBondedtoSelection18 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection18)
> Test bondedto selections "bonded 4 to index 0" ... ok
> testBondedtoSelection19 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection19)
> Test bondedto selections 'bonded 4 to index 0' for imatinib ... ok
> testBondedtoSelection2 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection2)
> Test bondedto selections "bonded to index 0" ... ok
> testBondedtoSelection20 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection20)
> Test bondedto selections "bonded 4 to index 0" ... ok
> testBondedtoSelection21 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection21)
> Test bondedto selections 'exbonded 1 to index 0' for imatinib ... ok
> testBondedtoSelection22 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection22)
> Test bondedto selections "exbonded 1 to index 0" ... ok
> testBondedtoSelection23 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection23)
> Test bondedto selections 'exbonded 2 to index 0' for imatinib ... ok
> testBondedtoSelection24 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection24)
> Test bondedto selections "exbonded 2 to index 0" ... ok
> testBondedtoSelection25 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection25)
> Test bondedto selections 'exbonded 3 to index 0' for imatinib ... ok
> testBondedtoSelection26 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection26)
> Test bondedto selections "exbonded 3 to index 0" ... ok
> testBondedtoSelection27 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection27)
> Test bondedto selections 'bonded 20 to index 0' for imatinib ... ok
> testBondedtoSelection28 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection28)
> Test bondedto selections "bonded 20 to index 0" ... ok
> testBondedtoSelection29 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection29)
> Test bondedto selections 'bonded 20 to index 10' for imatinib ... ok
> testBondedtoSelection3 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection3)
> Test bondedto selections 'exbonded to index 0' for imatinib ... ok
> testBondedtoSelection30 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection30)
> Test bondedto selections "bonded 20 to index 10" ... ok
> testBondedtoSelection31 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection31)
> Test bondedto selections 'bonded to index 1000' for imatinib ... ok
> testBondedtoSelection32 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection32)
> Test bondedto selections "bonded to index 1000" ... ok
> testBondedtoSelection33 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection33)
> Test bondedto selections 'fragment 0' for imatinib ... ok
> testBondedtoSelection34 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection34)
> Test bondedto selections "fragment 0" ... ok
> testBondedtoSelection35 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection35)
> Test bondedto selections 'fragment 1' for imatinib ... ok
> testBondedtoSelection36 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection36)
> Test bondedto selections "fragment 1" ... ok
> testBondedtoSelection37 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection37)
> Test bondedto selections 'fragment 0 1 2' for imatinib ... ok
> testBondedtoSelection38 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection38)
> Test bondedto selections "fragment 0 1 2" ... ok
> testBondedtoSelection39 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection39)
> Test bondedto selections 'fragindex 0 1 2' for imatinib ... ok
> testBondedtoSelection4 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection4)
> Test bondedto selections "exbonded to index 0" ... ok
> testBondedtoSelection40 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection40)
> Test bondedto selections "fragindex 0 1 2" ... ok
> testBondedtoSelection41 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection41)
> Test bondedto selections 'fragindex 0:2' for imatinib ... ok
> testBondedtoSelection42 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection42)
> Test bondedto selections "fragindex 0:2" ... ok
> testBondedtoSelection5 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection5)
> Test bondedto selections 'bonded to index 67' for imatinib ... ok
> testBondedtoSelection6 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection6)
> Test bondedto selections "bonded to index 67" ... ok
> testBondedtoSelection7 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection7)
> Test bondedto selections 'exbonded to index 67' for imatinib ... ok
> testBondedtoSelection8 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection8)
> Test bondedto selections "exbonded to index 67" ... ok
> testBondedtoSelection9 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection9)
> Test bondedto selections 'bonded 2 to index 0' for imatinib ... ok
> testComparisonsSelection1 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection1)
> Test comparisons selections 'x = -51.659' for pdb3mht ... ok
> testComparisonsSelection10 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection10)
> Test comparisons selections "beta > 10" ... ok
> testComparisonsSelection11 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection11)
> Test comparisons selections 'beta < 10' for pdb3mht ... ok
> testComparisonsSelection12 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection12)
> Test comparisons selections "beta < 10" ... ok
> testComparisonsSelection13 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection13)
> Test comparisons selections 'occupancy > 0.999999' for pdb3mht ... ok
> testComparisonsSelection14 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection14)
> Test comparisons selections "occupancy > 0.999999" ... ok
> testComparisonsSelection15 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection15)
> Test comparisons selections '-10 <= x < 0' for pdb3mht ... ok
> testComparisonsSelection16 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection16)
> Test comparisons selections "-10 <= x < 0" ... ok
> testComparisonsSelection17 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection17)
> Test comparisons selections '11 > 10' for pdb3mht ... ok
> testComparisonsSelection18 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection18)
> Test comparisons selections "11 > 10" ... ok
> testComparisonsSelection19 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection19)
> Test comparisons selections 'radius > 10' for pdb3mht ... ok
> testComparisonsSelection2 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection2)
> Test comparisons selections "x = -51.659" ... ok
> testComparisonsSelection20 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection20)
> Test comparisons selections "radius > 10" ... ok
> testComparisonsSelection21 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection21)
> Test comparisons selections 'chain = A' for pdb3mht ... ok
> testComparisonsSelection22 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection22)
> Test comparisons selections "chain = A" ... ok
> testComparisonsSelection23 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection23)
> Test comparisons selections 'x x < 1' for pdb3mht ... ok
> testComparisonsSelection24 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection24)
> Test comparisons selections "x x < 1" ... ok
> testComparisonsSelection25 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection25)
> Test comparisons selections 'name < 1' for pdb3mht ... ok
> testComparisonsSelection26 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection26)
> Test comparisons selections "name < 1" ... ok
> testComparisonsSelection3 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection3)
> Test comparisons selections 'x != -51.659' for pdb3mht ... ok
> testComparisonsSelection4 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection4)
> Test comparisons selections "x != -51.659" ... ok
> testComparisonsSelection5 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection5)
> Test comparisons selections 'z >= 82.813' for pdb3mht ... ok
> testComparisonsSelection6 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection6)
> Test comparisons selections "z >= 82.813" ... ok
> testComparisonsSelection7 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection7)
> Test comparisons selections 'z < 82.813' for pdb3mht ... ok
> testComparisonsSelection8 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection8)
> Test comparisons selections "z < 82.813" ... ok
> testComparisonsSelection9 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection9)
> Test comparisons selections 'beta > 10' for pdb3mht ... ok
> testCompositeSelection1 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection1)
> Test composite selections 'chain x y z C and x 10' for pdb3mht ... ok
> testCompositeSelection10 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection10)
> Test composite selections "water and within 5 of not protein" ... ok
> testCompositeSelection11 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection11)
> Test composite selections 'backbone and sqrt((x - 25)**2 + (y - 74)**2 + (z - 13)**2) <= 500' for pdb3mht ... ok
> testCompositeSelection12 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection12)
> Test composite selections "backbone and sqrt((x - 25)**2 + (y - 74)**2 + (z - 13)**2) <= 500" ... ok
> testCompositeSelection13 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection13)
> Test composite selections '(not resname SAH) and (protein and name CA) or (nucleic and name P)' for pdb3mht ... ok
> testCompositeSelection14 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection14)
> Test composite selections "(not resname SAH) and (protein and name CA) or (nucleic and name P)" ... ok
> testCompositeSelection15 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection15)
> Test composite selections 'protein and (backbone or name H)' for pdb3mht ... ok
> testCompositeSelection16 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection16)
> Test composite selections "protein and (backbone or name H)" ... ok
> testCompositeSelection17 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection17)
> Test composite selections 'same residue as within 4 of and resname SAH' for pdb3mht ... ok
> testCompositeSelection18 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection18)
> Test composite selections "same residue as within 4 of and resname SAH" ... ok
> testCompositeSelection19 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection19)
> Test composite selections 'protein and name CA CB and same residue as ((x+21.2)**2 + (y-35.9)**2 + (z-80.0)**2)**0.5 < 10' for pdb3mht ... ok
> testCompositeSelection2 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection2)
> Test composite selections "chain x y z C and x 10" ... ok
> testCompositeSelection20 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection20)
> Test composite selections "protein and name CA CB and same residue as ((x+21.2)**2 + (y-35.9)**2 + (z-80.0)**2)**0.5 < 10" ... ok
> testCompositeSelection3 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection3)
> Test composite selections 'resnum `1` `2`' for pdb3mht ... ok
> testCompositeSelection4 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection4)
> Test composite selections "resnum `1` `2`" ... ok
> testCompositeSelection5 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection5)
> Test composite selections 'same residue as within 4 of resname SAH' for pdb3mht ... ok
> testCompositeSelection6 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection6)
> Test composite selections "same residue as within 4 of resname SAH" ... ok
> testCompositeSelection7 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection7)
> Test composite selections 'name CA and same residue as within 4 of resname SAH' for pdb3mht ... ok
> testCompositeSelection8 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection8)
> Test composite selections "name CA and same residue as within 4 of resname SAH" ... ok
> testCompositeSelection9 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection9)
> Test composite selections 'water and within 5 of not protein' for pdb3mht ... ok
> testDocexamplesSelection1 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection1)
> Test docexamples selections 'serial 1 2 3' for pdb3mht ... ok
> testDocexamplesSelection10 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection10)
> Test docexamples selections "beta 555.55" ... ok
> testDocexamplesSelection11 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection11)
> Test docexamples selections 'beta 1 to 500' for pdb3mht ... ok
> testDocexamplesSelection12 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection12)
> Test docexamples selections "beta 1 to 500" ... ok
> testDocexamplesSelection13 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection13)
> Test docexamples selections 'beta 1:500' for pdb3mht ... ok
> testDocexamplesSelection14 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection14)
> Test docexamples selections "beta 1:500" ... ok
> testDocexamplesSelection15 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection15)
> Test docexamples selections 'beta < 500' for pdb3mht ... ok
> testDocexamplesSelection16 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection16)
> Test docexamples selections "beta < 500" ... ok
> testDocexamplesSelection17 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection17)
> Test docexamples selections 'resnum 120A 120B' for pdb3mht ... ok
> testDocexamplesSelection18 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection18)
> Test docexamples selections "resnum 120A 120B" ... ok
> testDocexamplesSelection19 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection19)
> Test docexamples selections 'icode A' for pdb3mht ... ok
> testDocexamplesSelection2 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection2)
> Test docexamples selections "serial 1 2 3" ... ok
> testDocexamplesSelection20 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection20)
> Test docexamples selections "icode A" ... ok
> testDocexamplesSelection21 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection21)
> Test docexamples selections 'icode _' for pdb3mht ... ok
> testDocexamplesSelection22 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection22)
> Test docexamples selections "icode _" ... ok
> testDocexamplesSelection23 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection23)
> Test docexamples selections 'charge 1' for pdb3mht ... ok
> testDocexamplesSelection24 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection24)
> Test docexamples selections "charge 1" ... ok
> testDocexamplesSelection25 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection25)
> Test docexamples selections 'abs(charge) == 1' for pdb3mht ... ok
> testDocexamplesSelection26 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection26)
> Test docexamples selections "abs(charge) == 1" ... ok
> testDocexamplesSelection27 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection27)
> Test docexamples selections 'charge < 0' for pdb3mht ... ok
> testDocexamplesSelection28 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection28)
> Test docexamples selections "charge < 0" ... ok
> testDocexamplesSelection29 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection29)
> Test docexamples selections '0 < mass < 500' for pdb3mht ... ok
> testDocexamplesSelection3 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection3)
> Test docexamples selections 'serial 1 to 10' for pdb3mht ... ok
> testDocexamplesSelection30 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection30)
> Test docexamples selections "0 < mass < 500" ... ok
> testDocexamplesSelection31 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection31)
> Test docexamples selections 'abs(mass) <= mass <= 10' for pdb3mht ... ok
> testDocexamplesSelection32 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection32)
> Test docexamples selections "abs(mass) <= mass <= 10" ... ok
> testDocexamplesSelection4 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection4)
> Test docexamples selections "serial 1 to 10" ... ok
> testDocexamplesSelection5 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection5)
> Test docexamples selections 'serial 1:10:2' for pdb3mht ... ok
> testDocexamplesSelection6 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection6)
> Test docexamples selections "serial 1:10:2" ... ok
> testDocexamplesSelection7 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection7)
> Test docexamples selections 'serial < 10' for pdb3mht ... ok
> testDocexamplesSelection8 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection8)
> Test docexamples selections "serial < 10" ... ok
> testDocexamplesSelection9 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection9)
> Test docexamples selections 'beta 555.55' for pdb3mht ... ok
> testEquivalentSelection1 (prody.tests.atomic.test_select.TestSelect.testEquivalentSelection1)
> Test equivalent selections 'chain C' for pdb3mht ... ok
> testEquivalentSelection2 (prody.tests.atomic.test_select.TestSelect.testEquivalentSelection2)
> Test equivalent selections "chain C" ... ok
> testEquivalentSelection3 (prody.tests.atomic.test_select.TestSelect.testEquivalentSelection3)
> Test equivalent selections 'chain C' for pdb3mht ... ok
> testEquivalentSelection4 (prody.tests.atomic.test_select.TestSelect.testEquivalentSelection4)
> Test equivalent selections "chain C" ... ok
> testEquivalentSelection5 (prody.tests.atomic.test_select.TestSelect.testEquivalentSelection5)
> Test equivalent selections 'nucleic' for pdb3mht ... ok
> testEquivalentSelection6 (prody.tests.atomic.test_select.TestSelect.testEquivalentSelection6)
> Test equivalent selections "nucleic" ... ok
> testFlagsSelection1 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection1)
> Test flags selections 'none' for pdb3mht ... ok
> testFlagsSelection10 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection10)
> Test flags selections "aliphatic" ... ok
> testFlagsSelection100 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection100)
> Test flags selections "bridge" ... ok
> testFlagsSelection101 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection101)
> Test flags selections 'bend' for pdb3mht ... ok
> testFlagsSelection102 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection102)
> Test flags selections "bend" ... ok
> testFlagsSelection103 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection103)
> Test flags selections 'coil' for pdb3mht ... ok
> testFlagsSelection104 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection104)
> Test flags selections "coil" ... ok
> testFlagsSelection11 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection11)
> Test flags selections 'aromatic' for pdb3mht ... ok
> testFlagsSelection12 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection12)
> Test flags selections "aromatic" ... ok
> testFlagsSelection13 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection13)
> Test flags selections 'at' for pdb3mht ... ok
> testFlagsSelection14 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection14)
> Test flags selections "at" ... ok
> testFlagsSelection15 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection15)
> Test flags selections 'basic' for pdb3mht ... ok
> testFlagsSelection16 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection16)
> Test flags selections "basic" ... ok
> testFlagsSelection17 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection17)
> Test flags selections 'buried' for pdb3mht ... ok
> testFlagsSelection18 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection18)
> Test flags selections "buried" ... ok
> testFlagsSelection19 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection19)
> Test flags selections 'cg' for pdb3mht ... ok
> testFlagsSelection2 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection2)
> Test flags selections "none" ... ok
> testFlagsSelection20 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection20)
> Test flags selections "cg" ... ok
> testFlagsSelection21 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection21)
> Test flags selections 'charged' for pdb3mht ... ok
> testFlagsSelection22 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection22)
> Test flags selections "charged" ... ok
> testFlagsSelection23 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection23)
> Test flags selections 'cyclic' for pdb3mht ... ok
> testFlagsSelection24 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection24)
> Test flags selections "cyclic" ... ok
> testFlagsSelection25 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection25)
> Test flags selections 'heme' for pdb3mht ... ok
> testFlagsSelection26 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection26)
> Test flags selections "heme" ... ok
> testFlagsSelection27 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection27)
> Test flags selections 'hydrophobic' for pdb3mht ... ok
> testFlagsSelection28 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection28)
> Test flags selections "hydrophobic" ... ok
> testFlagsSelection29 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection29)
> Test flags selections 'ion' for pdb3mht ... ok
> testFlagsSelection3 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection3)
> Test flags selections 'all' for pdb3mht ... ok
> testFlagsSelection30 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection30)
> Test flags selections "ion" ... ok
> testFlagsSelection31 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection31)
> Test flags selections 'large' for pdb3mht ... ok
> testFlagsSelection32 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection32)
> Test flags selections "large" ... ok
> testFlagsSelection33 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection33)
> Test flags selections 'lipid' for pdb3mht ... ok
> testFlagsSelection34 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection34)
> Test flags selections "lipid" ... ok
> testFlagsSelection35 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection35)
> Test flags selections 'medium' for pdb3mht ... ok
> testFlagsSelection36 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection36)
> Test flags selections "medium" ... ok
> testFlagsSelection37 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection37)
> Test flags selections 'neutral' for pdb3mht ... ok
> testFlagsSelection38 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection38)
> Test flags selections "neutral" ... ok
> testFlagsSelection39 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection39)
> Test flags selections 'nucleic' for pdb3mht ... ok
> testFlagsSelection4 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection4)
> Test flags selections "all" ... ok
> testFlagsSelection40 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection40)
> Test flags selections "nucleic" ... ok
> testFlagsSelection41 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection41)
> Test flags selections 'nucleotide' for pdb3mht ... ok
> testFlagsSelection42 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection42)
> Test flags selections "nucleotide" ... ok
> testFlagsSelection43 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection43)
> Test flags selections 'nucleobase' for pdb3mht ... ok
> testFlagsSelection44 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection44)
> Test flags selections "nucleobase" ... ok
> testFlagsSelection45 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection45)
> Test flags selections 'nucleoside' for pdb3mht ... ok
> testFlagsSelection46 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection46)
> Test flags selections "nucleoside" ... ok
> testFlagsSelection47 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection47)
> Test flags selections 'polar' for pdb3mht ... ok
> testFlagsSelection48 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection48)
> Test flags selections "polar" ... ok
> testFlagsSelection49 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection49)
> Test flags selections 'protein' for pdb3mht ... ok
> testFlagsSelection5 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection5)
> Test flags selections 'acidic' for pdb3mht ... ok
> testFlagsSelection50 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection50)
> Test flags selections "protein" ... ok
> testFlagsSelection51 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection51)
> Test flags selections 'stdaa' for pdb3mht ... ok
> testFlagsSelection52 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection52)
> Test flags selections "stdaa" ... ok
> testFlagsSelection53 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection53)
> Test flags selections 'nonstdaa' for pdb3mht ... ok
> testFlagsSelection54 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection54)
> Test flags selections "nonstdaa" ... ok
> testFlagsSelection55 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection55)
> Test flags selections 'purine' for pdb3mht ... ok
> testFlagsSelection56 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection56)
> Test flags selections "purine" ... ok
> testFlagsSelection57 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection57)
> Test flags selections 'pyrimidine' for pdb3mht ... ok
> testFlagsSelection58 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection58)
> Test flags selections "pyrimidine" ... ok
> testFlagsSelection59 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection59)
> Test flags selections 'small' for pdb3mht ... ok
> testFlagsSelection6 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection6)
> Test flags selections "acidic" ... ok
> testFlagsSelection60 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection60)
> Test flags selections "small" ... ok
> testFlagsSelection61 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection61)
> Test flags selections 'sugar' for pdb3mht ... ok
> testFlagsSelection62 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection62)
> Test flags selections "sugar" ... ok
> testFlagsSelection63 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection63)
> Test flags selections 'surface' for pdb3mht ... ok
> testFlagsSelection64 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection64)
> Test flags selections "surface" ... ok
> testFlagsSelection65 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection65)
> Test flags selections 'water' for pdb3mht ... ok
> testFlagsSelection66 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection66)
> Test flags selections "water" ... ok
> testFlagsSelection67 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection67)
> Test flags selections 'hetero' for pdb3mht ... ok
> testFlagsSelection68 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection68)
> Test flags selections "hetero" ... ok
> testFlagsSelection69 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection69)
> Test flags selections 'hetatm' for pdb3mht ... ok
> testFlagsSelection7 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection7)
> Test flags selections 'acyclic' for pdb3mht ... ok
> testFlagsSelection70 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection70)
> Test flags selections "hetatm" ... ok
> testFlagsSelection71 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection71)
> Test flags selections 'calpha' for pdb3mht ... ok
> testFlagsSelection72 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection72)
> Test flags selections "calpha" ... ok
> testFlagsSelection73 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection73)
> Test flags selections 'backbone' for pdb3mht ... ok
> testFlagsSelection74 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection74)
> Test flags selections "backbone" ... ok
> testFlagsSelection75 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection75)
> Test flags selections 'backbonefull' for pdb3mht ... ok
> testFlagsSelection76 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection76)
> Test flags selections "backbonefull" ... ok
> testFlagsSelection77 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection77)
> Test flags selections 'sidechain' for pdb3mht ... ok
> testFlagsSelection78 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection78)
> Test flags selections "sidechain" ... ok
> testFlagsSelection79 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection79)
> Test flags selections 'carbon' for pdb3mht ... ok
> testFlagsSelection8 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection8)
> Test flags selections "acyclic" ... ok
> testFlagsSelection80 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection80)
> Test flags selections "carbon" ... ok
> testFlagsSelection81 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection81)
> Test flags selections 'hydrogen' for pdb3mht ... ok
> testFlagsSelection82 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection82)
> Test flags selections "hydrogen" ... ok
> testFlagsSelection83 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection83)
> Test flags selections 'noh' for pdb3mht ... ok
> testFlagsSelection84 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection84)
> Test flags selections "noh" ... ok
> testFlagsSelection85 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection85)
> Test flags selections 'nitrogen' for pdb3mht ... ok
> testFlagsSelection86 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection86)
> Test flags selections "nitrogen" ... ok
> testFlagsSelection87 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection87)
> Test flags selections 'oxygen' for pdb3mht ... ok
> testFlagsSelection88 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection88)
> Test flags selections "oxygen" ... ok
> testFlagsSelection89 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection89)
> Test flags selections 'sulfur' for pdb3mht ... ok
> testFlagsSelection9 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection9)
> Test flags selections 'aliphatic' for pdb3mht ... ok
> testFlagsSelection90 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection90)
> Test flags selections "sulfur" ... ok
> testFlagsSelection91 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection91)
> Test flags selections 'extended' for pdb3mht ... ok
> testFlagsSelection92 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection92)
> Test flags selections "extended" ... ok
> testFlagsSelection93 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection93)
> Test flags selections 'helix' for pdb3mht ... ok
> testFlagsSelection94 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection94)
> Test flags selections "helix" ... ok
> testFlagsSelection95 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection95)
> Test flags selections 'helix310' for pdb3mht ... ok
> testFlagsSelection96 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection96)
> Test flags selections "helix310" ... ok
> testFlagsSelection97 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection97)
> Test flags selections 'turn' for pdb3mht ... ok
> testFlagsSelection98 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection98)
> Test flags selections "turn" ... ok
> testFlagsSelection99 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection99)
> Test flags selections 'bridge' for pdb3mht ... ok
> testFloatSelection1 (prody.tests.atomic.test_select.TestSelect.testFloatSelection1)
> Test float selections 'beta 5.0 41.15 11.85' for pdb3mht ... ok
> testFloatSelection10 (prody.tests.atomic.test_select.TestSelect.testFloatSelection10)
> Test float selections "z 115.246 45.784" ... ok
> testFloatSelection11 (prody.tests.atomic.test_select.TestSelect.testFloatSelection11)
> Test float selections 'charge 0' for pdb3mht ... ok
> testFloatSelection12 (prody.tests.atomic.test_select.TestSelect.testFloatSelection12)
> Test float selections "charge 0" ... ok
> testFloatSelection13 (prody.tests.atomic.test_select.TestSelect.testFloatSelection13)
> Test float selections 'mass 1' for pdb3mht ... ok
> testFloatSelection14 (prody.tests.atomic.test_select.TestSelect.testFloatSelection14)
> Test float selections "mass 1" ... ok
> testFloatSelection15 (prody.tests.atomic.test_select.TestSelect.testFloatSelection15)
> Test float selections 'radius 0' for pdb3mht ... ok
> testFloatSelection16 (prody.tests.atomic.test_select.TestSelect.testFloatSelection16)
> Test float selections "radius 0" ... ok
> testFloatSelection17 (prody.tests.atomic.test_select.TestSelect.testFloatSelection17)
> Test float selections 'beta "1."' for pdb3mht ... ok
> testFloatSelection18 (prody.tests.atomic.test_select.TestSelect.testFloatSelection18)
> Test float selections "beta "1."" ... ok
> testFloatSelection19 (prody.tests.atomic.test_select.TestSelect.testFloatSelection19)
> Test float selections 'beta = "1."' for pdb3mht ... ok
> testFloatSelection2 (prody.tests.atomic.test_select.TestSelect.testFloatSelection2)
> Test float selections "beta 5.0 41.15 11.85" ... ok
> testFloatSelection20 (prody.tests.atomic.test_select.TestSelect.testFloatSelection20)
> Test float selections "beta = "1."" ... ok
> testFloatSelection3 (prody.tests.atomic.test_select.TestSelect.testFloatSelection3)
> Test float selections 'occupancy 1.0' for pdb3mht ... ok
> testFloatSelection4 (prody.tests.atomic.test_select.TestSelect.testFloatSelection4)
> Test float selections "occupancy 1.0" ... ok
> testFloatSelection5 (prody.tests.atomic.test_select.TestSelect.testFloatSelection5)
> Test float selections 'x 6.665' for pdb3mht ... ok
> testFloatSelection6 (prody.tests.atomic.test_select.TestSelect.testFloatSelection6)
> Test float selections "x 6.665" ... ok
> testFloatSelection7 (prody.tests.atomic.test_select.TestSelect.testFloatSelection7)
> Test float selections 'y 69.99 13.314' for pdb3mht ... ok
> testFloatSelection8 (prody.tests.atomic.test_select.TestSelect.testFloatSelection8)
> Test float selections "y 69.99 13.314" ... ok
> testFloatSelection9 (prody.tests.atomic.test_select.TestSelect.testFloatSelection9)
> Test float selections 'z 115.246 45.784' for pdb3mht ... ok
> testFunctionSelection1 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection1)
> Test function selections 'sqrt(x**2 + y**2 + z**2) < 100' for pdb3mht ... ok
> testFunctionSelection10 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection10)
> Test function selections "ceil(beta) == 10" ... ok
> testFunctionSelection11 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection11)
> Test function selections 'floor(beta) == 10' for pdb3mht ... ok
> testFunctionSelection12 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection12)
> Test function selections "floor(beta) == 10" ... ok
> testFunctionSelection13 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection13)
> Test function selections 'abs(x) == sqrt(sq(x))' for pdb3mht ... FAIL
> testFunctionSelection14 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection14)
> Test function selections "abs(x) == sqrt(sq(x))" ... FAIL
> testFunctionSelection15 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection15)
> Test function selections 'sq(x-5)+sq(y+4)+sq(z) > sq(100)' for pdb3mht ... ok
> testFunctionSelection16 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection16)
> Test function selections "sq(x-5)+sq(y+4)+sq(z) > sq(100)" ... ok
> testFunctionSelection17 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection17)
> Test function selections '1 > sq(occ)' for pdb3mht ... ok
> testFunctionSelection18 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection18)
> Test function selections "1 > sq(occ)" ... ok
> testFunctionSelection19 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection19)
> Test function selections 'sq(x x) > 1' for pdb3mht ... ok
> testFunctionSelection2 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection2)
> Test function selections "sqrt(x**2 + y**2 + z**2) < 100" ... ok
> testFunctionSelection20 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection20)
> Test function selections "sq(x x) > 1" ... ok
> testFunctionSelection3 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection3)
> Test function selections 'sqrt(x**2 + y**2 + z**2) == (x**2 + y**2 + z**2) ** 0.5' for pdb3mht ... ok
> testFunctionSelection4 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection4)
> Test function selections "sqrt(x**2 + y**2 + z**2) == (x**2 + y**2 + z**2) ** 0.5" ... ok
> testFunctionSelection5 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection5)
> Test function selections 'beta % 3 < 1' for pdb3mht ... ok
> testFunctionSelection6 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection6)
> Test function selections "beta % 3 < 1" ... ok
> testFunctionSelection7 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection7)
> Test function selections 'beta % 4 % 3 < 1' for pdb3mht ... ok
> testFunctionSelection8 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection8)
> Test function selections "beta % 4 % 3 < 1" ... ok
> testFunctionSelection9 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection9)
> Test function selections 'ceil(beta) == 10' for pdb3mht ... ok
> testIntegerSelection1 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection1)
> Test integer selections 'index 10 20 10000' for pdb3mht ... ok
> testIntegerSelection10 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection10)
> Test integer selections "resnum 100 105" ... ok
> testIntegerSelection11 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection11)
> Test integer selections 'resid 0' for pdb3mht ... ok
> testIntegerSelection12 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection12)
> Test integer selections "resid 0" ... ok
> testIntegerSelection13 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection13)
> Test integer selections 'resid 100 105' for pdb3mht ... ok
> testIntegerSelection14 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection14)
> Test integer selections "resid 100 105" ... ok
> testIntegerSelection15 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection15)
> Test integer selections 'resid 100 A 105' for pdb3mht ... ok
> testIntegerSelection16 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection16)
> Test integer selections "resid 100 A 105" ... ok
> testIntegerSelection17 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection17)
> Test integer selections 'fragindex 0' for pdb3mht ... ok
> testIntegerSelection18 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection18)
> Test integer selections "fragindex 0" ... ok
> testIntegerSelection19 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection19)
> Test integer selections 'fragment 0' for pdb3mht ... ok
> testIntegerSelection2 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection2)
> Test integer selections "index 10 20 10000" ... ok
> testIntegerSelection20 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection20)
> Test integer selections "fragment 0" ... ok
> testIntegerSelection3 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection3)
> Test integer selections 'serial 0' for pdb3mht ... ok
> testIntegerSelection4 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection4)
> Test integer selections "serial 0" ... ok
> testIntegerSelection5 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection5)
> Test integer selections 'serial 1 2' for pdb3mht ... ok
> testIntegerSelection6 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection6)
> Test integer selections "serial 1 2" ... ok
> testIntegerSelection7 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection7)
> Test integer selections 'resnum 0' for pdb3mht ... ok
> testIntegerSelection8 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection8)
> Test integer selections "resnum 0" ... ok
> testIntegerSelection9 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection9)
> Test integer selections 'resnum 100 105' for pdb3mht ... ok
> testInvalidSelection1 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection1)
> Test invalid selections 'chain C and and chain C' for pdb3mht ... ok
> testInvalidSelection10 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection10)
> Test invalid selections "sqr(x-5)+sqr(y+4)+sqr(z) > sqr(100)" ... ok
> testInvalidSelection11 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection11)
> Test invalid selections 'x > sq(calpha)' for pdb3mht ... ok
> testInvalidSelection12 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection12)
> Test invalid selections "x > sq(calpha)" ... ok
> testInvalidSelection13 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection13)
> Test invalid selections 'x > sq(name CA and resname ALA)' for pdb3mht ... ok
> testInvalidSelection14 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection14)
> Test invalid selections "x > sq(name CA and resname ALA)" ... ok
> testInvalidSelection15 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection15)
> Test invalid selections 'resname ALA and +1' for pdb3mht ... ok
> testInvalidSelection16 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection16)
> Test invalid selections "resname ALA and +1" ... ok
> testInvalidSelection2 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection2)
> Test invalid selections "chain C and and chain C" ... ok
> testInvalidSelection3 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection3)
> Test invalid selections 'chain C or or chain D' for pdb3mht ... ok
> testInvalidSelection4 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection4)
> Test invalid selections "chain C or or chain D" ... ok
> testInvalidSelection5 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection5)
> Test invalid selections 'chain C or not or chain D' for pdb3mht ... ok
> testInvalidSelection6 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection6)
> Test invalid selections "chain C or not or chain D" ... ok
> testInvalidSelection7 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection7)
> Test invalid selections 'chain C + 3' for pdb3mht ... ok
> testInvalidSelection8 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection8)
> Test invalid selections "chain C + 3" ... ok
> testInvalidSelection9 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection9)
> Test invalid selections 'sqr(x-5)+sqr(y+4)+sqr(z) > sqr(100)' for pdb3mht ... ok
> testKwargsSelection1 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection1)
> Test kwargs selections 'within 100 of origin' for pdb3mht ... ok
> testKwargsSelection10 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection10)
> Test kwargs selections "within 100 of none" ... ok
> testKwargsSelection2 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection2)
> Test kwargs selections "within 100 of origin" ... ok
> testKwargsSelection3 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection3)
> Test kwargs selections 'within 100 of origin' for pdb3mht ... ok
> testKwargsSelection4 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection4)
> Test kwargs selections "within 100 of origin" ... ok
> testKwargsSelection5 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection5)
> Test kwargs selections 'within 100 of origin' for pdb3mht ... ok
> testKwargsSelection6 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection6)
> Test kwargs selections "within 100 of origin" ... ok
> testKwargsSelection7 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection7)
> Test kwargs selections 'within 100 of origin' for pdb3mht ... ok
> testKwargsSelection8 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection8)
> Test kwargs selections "within 100 of origin" ... ok
> testKwargsSelection9 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection9)
> Test kwargs selections 'within 100 of none' for pdb3mht ... ok
> testLogicalSelection1 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection1)
> Test logical selections 'name or name' for pdb3mht ... ok
> testLogicalSelection10 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection10)
> Test logical selections "index 0 or index 1 " ... ok
> testLogicalSelection11 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection11)
> Test logical selections 'not not not not index 1' for pdb3mht ... ok
> testLogicalSelection12 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection12)
> Test logical selections "not not not not index 1" ... ok
> testLogicalSelection13 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection13)
> Test logical selections 'index 0 or index 1 or index 2' for pdb3mht ... ok
> testLogicalSelection14 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection14)
> Test logical selections "index 0 or index 1 or index 2" ... ok
> testLogicalSelection15 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection15)
> Test logical selections 'index 0 or index 1 or index 2 or index 4' for pdb3mht ... ok
> testLogicalSelection16 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection16)
> Test logical selections "index 0 or index 1 or index 2 or index 4" ... ok
> testLogicalSelection17 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection17)
> Test logical selections 'index 0 and index 1 ' for pdb3mht ... ok
> testLogicalSelection18 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection18)
> Test logical selections "index 0 and index 1 " ... ok
> testLogicalSelection19 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection19)
> Test logical selections 'index < 50 and index < 5' for pdb3mht ... ok
> testLogicalSelection2 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection2)
> Test logical selections "name or name" ... ok
> testLogicalSelection20 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection20)
> Test logical selections "index < 50 and index < 5" ... ok
> testLogicalSelection21 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection21)
> Test logical selections 'index < 50 and index < 25 and index < 5' for pdb3mht ... ok
> testLogicalSelection22 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection22)
> Test logical selections "index < 50 and index < 25 and index < 5" ... ok
> testLogicalSelection23 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection23)
> Test logical selections 'index < 5 and index < 25 and index < 50' for pdb3mht ... ok
> testLogicalSelection24 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection24)
> Test logical selections "index < 5 and index < 25 and index < 50" ... ok
> testLogicalSelection25 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection25)
> Test logical selections 'index 0 to 5 and index 0 to 25 and index 0 to 50' for pdb3mht ... ok
> testLogicalSelection26 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection26)
> Test logical selections "index 0 to 5 and index 0 to 25 and index 0 to 50" ... ok
> testLogicalSelection27 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection27)
> Test logical selections 'index < 5 and index < 25 and index < 50 or index < 50 or index < 5' for pdb3mht ... ok
> testLogicalSelection28 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection28)
> Test logical selections "index < 5 and index < 25 and index < 50 or index < 50 or index < 5" ... ok
> testLogicalSelection3 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection3)
> Test logical selections 'name and name' for pdb3mht ... ok
> testLogicalSelection4 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection4)
> Test logical selections "name and name" ... ok
> testLogicalSelection5 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection5)
> Test logical selections 'name CA and name CA' for pdb3mht ... ok
> testLogicalSelection6 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection6)
> Test logical selections "name CA and name CA" ... ok
> testLogicalSelection7 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection7)
> Test logical selections 'name CA or name CA' for pdb3mht ... ok
> testLogicalSelection8 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection8)
> Test logical selections "name CA or name CA" ... ok
> testLogicalSelection9 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection9)
> Test logical selections 'index 0 or index 1 ' for pdb3mht ... ok
> testOperationSelection1 (prody.tests.atomic.test_select.TestSelect.testOperationSelection1)
> Test operation selections 'x ** 2 < 10' for pdb3mht ... ok
> testOperationSelection10 (prody.tests.atomic.test_select.TestSelect.testOperationSelection10)
> Test operation selections "x**2 + y**2 + z**2 < 10000" ... ok
> testOperationSelection2 (prody.tests.atomic.test_select.TestSelect.testOperationSelection2)
> Test operation selections "x ** 2 < 10" ... ok
> testOperationSelection3 (prody.tests.atomic.test_select.TestSelect.testOperationSelection3)
> Test operation selections 'x ** 2 ** 2 ** 2 < 10' for pdb3mht ... ok
> testOperationSelection4 (prody.tests.atomic.test_select.TestSelect.testOperationSelection4)
> Test operation selections "x ** 2 ** 2 ** 2 < 10" ... ok
> testOperationSelection5 (prody.tests.atomic.test_select.TestSelect.testOperationSelection5)
> Test operation selections 'x ** (+2 ** (+2 ** +2)) < 10' for pdb3mht ... ok
> testOperationSelection6 (prody.tests.atomic.test_select.TestSelect.testOperationSelection6)
> Test operation selections "x ** (+2 ** (+2 ** +2)) < 10" ... ok
> testOperationSelection7 (prody.tests.atomic.test_select.TestSelect.testOperationSelection7)
> Test operation selections 'occupancy % 2 == 1' for pdb3mht ... ok
> testOperationSelection8 (prody.tests.atomic.test_select.TestSelect.testOperationSelection8)
> Test operation selections "occupancy % 2 == 1" ... ok
> testOperationSelection9 (prody.tests.atomic.test_select.TestSelect.testOperationSelection9)
> Test operation selections 'x**2 + y**2 + z**2 < 10000' for pdb3mht ... ok
> testRangeSelection1 (prody.tests.atomic.test_select.TestSelect.testRangeSelection1)
> Test range selections 'index 0:10' for pdb3mht ... ok
> testRangeSelection10 (prody.tests.atomic.test_select.TestSelect.testRangeSelection10)
> Test range selections "resnum 10to15" ... ok
> testRangeSelection11 (prody.tests.atomic.test_select.TestSelect.testRangeSelection11)
> Test range selections 'resnum 10:16:1' for pdb3mht ... ok
> testRangeSelection12 (prody.tests.atomic.test_select.TestSelect.testRangeSelection12)
> Test range selections "resnum 10:16:1" ... ok
> testRangeSelection13 (prody.tests.atomic.test_select.TestSelect.testRangeSelection13)
> Test range selections 'resnum `-3:16:1`' for pdb3mht ... ok
> testRangeSelection14 (prody.tests.atomic.test_select.TestSelect.testRangeSelection14)
> Test range selections "resnum `-3:16:1`" ... ok
> testRangeSelection15 (prody.tests.atomic.test_select.TestSelect.testRangeSelection15)
> Test range selections 'resid 10to15' for pdb3mht ... ok
> testRangeSelection16 (prody.tests.atomic.test_select.TestSelect.testRangeSelection16)
> Test range selections "resid 10to15" ... ok
> testRangeSelection17 (prody.tests.atomic.test_select.TestSelect.testRangeSelection17)
> Test range selections 'resid 10:16:1' for pdb3mht ... ok
> testRangeSelection18 (prody.tests.atomic.test_select.TestSelect.testRangeSelection18)
> Test range selections "resid 10:16:1" ... ok
> testRangeSelection19 (prody.tests.atomic.test_select.TestSelect.testRangeSelection19)
> Test range selections 'x `-10:20`' for pdb3mht ... ok
> testRangeSelection2 (prody.tests.atomic.test_select.TestSelect.testRangeSelection2)
> Test range selections "index 0:10" ... ok
> testRangeSelection20 (prody.tests.atomic.test_select.TestSelect.testRangeSelection20)
> Test range selections "x `-10:20`" ... ok
> testRangeSelection21 (prody.tests.atomic.test_select.TestSelect.testRangeSelection21)
> Test range selections 'x 0:20:1' for pdb3mht ... ok
> testRangeSelection22 (prody.tests.atomic.test_select.TestSelect.testRangeSelection22)
> Test range selections "x 0:20:1" ... ok
> testRangeSelection23 (prody.tests.atomic.test_select.TestSelect.testRangeSelection23)
> Test range selections 'beta 13.02:13.01' for pdb3mht ... ok
> testRangeSelection24 (prody.tests.atomic.test_select.TestSelect.testRangeSelection24)
> Test range selections "beta 13.02:13.01" ... ok
> testRangeSelection3 (prody.tests.atomic.test_select.TestSelect.testRangeSelection3)
> Test range selections 'index 0to10' for pdb3mht ... ok
> testRangeSelection4 (prody.tests.atomic.test_select.TestSelect.testRangeSelection4)
> Test range selections "index 0to10" ... ok
> testRangeSelection5 (prody.tests.atomic.test_select.TestSelect.testRangeSelection5)
> Test range selections 'serial 0:10:2' for pdb3mht ... ok
> testRangeSelection6 (prody.tests.atomic.test_select.TestSelect.testRangeSelection6)
> Test range selections "serial 0:10:2" ... ok
> testRangeSelection7 (prody.tests.atomic.test_select.TestSelect.testRangeSelection7)
> Test range selections 'serial 0:10:10' for pdb3mht ... ok
> testRangeSelection8 (prody.tests.atomic.test_select.TestSelect.testRangeSelection8)
> Test range selections "serial 0:10:10" ... ok
> testRangeSelection9 (prody.tests.atomic.test_select.TestSelect.testRangeSelection9)
> Test range selections 'resnum 10to15' for pdb3mht ... ok
> testRegexpSelection1 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection1)
> Test regexp selections 'resname "S.."' for pdb3mht ... ok
> testRegexpSelection10 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection10)
> Test regexp selections "name "C((A|B)"" ... ok
> testRegexpSelection2 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection2)
> Test regexp selections "resname "S.."" ... ok
> testRegexpSelection3 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection3)
> Test regexp selections 'name "C.*"' for pdb3mht ... ok
> testRegexpSelection4 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection4)
> Test regexp selections "name "C.*"" ... ok
> testRegexpSelection5 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection5)
> Test regexp selections 'name ".*\'"' for pdb3mht ... ok
> testRegexpSelection6 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection6)
> Test regexp selections "name ".*'"" ... ok
> testRegexpSelection7 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection7)
> Test regexp selections 'name "C(A|B)"' for pdb3mht ... ok
> testRegexpSelection8 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection8)
> Test regexp selections "name "C(A|B)"" ... ok
> testRegexpSelection9 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection9)
> Test regexp selections 'name "C((A|B)"' for pdb3mht ... ok
> testSameasSelection1 (prody.tests.atomic.test_select.TestSelect.testSameasSelection1)
> Test sameas selections 'same residue as index 0' for pdb3mht ... ok
> testSameasSelection10 (prody.tests.atomic.test_select.TestSelect.testSameasSelection10)
> Test sameas selections "same chain as chain C" ... ok
> testSameasSelection11 (prody.tests.atomic.test_select.TestSelect.testSameasSelection11)
> Test sameas selections 'same residue as chain X' for pdb3mht ... ok
> testSameasSelection12 (prody.tests.atomic.test_select.TestSelect.testSameasSelection12)
> Test sameas selections "same residue as chain X" ... ok
> testSameasSelection13 (prody.tests.atomic.test_select.TestSelect.testSameasSelection13)
> Test sameas selections 'same none as chain C' for pdb3mht ... ok
> testSameasSelection14 (prody.tests.atomic.test_select.TestSelect.testSameasSelection14)
> Test sameas selections "same none as chain C" ... ok
> testSameasSelection15 (prody.tests.atomic.test_select.TestSelect.testSameasSelection15)
> Test sameas selections 'same residue as same residue as same residue as index 0' for pdb3mht ... ok
> testSameasSelection16 (prody.tests.atomic.test_select.TestSelect.testSameasSelection16)
> Test sameas selections "same residue as same residue as same residue as index 0" ... ok
> testSameasSelection2 (prody.tests.atomic.test_select.TestSelect.testSameasSelection2)
> Test sameas selections "same residue as index 0" ... ok
> testSameasSelection3 (prody.tests.atomic.test_select.TestSelect.testSameasSelection3)
> Test sameas selections 'same chain as index 0' for pdb3mht ... ok
> testSameasSelection4 (prody.tests.atomic.test_select.TestSelect.testSameasSelection4)
> Test sameas selections "same chain as index 0" ... ok
> testSameasSelection5 (prody.tests.atomic.test_select.TestSelect.testSameasSelection5)
> Test sameas selections 'same segment as index 0' for pdb3mht ... ok
> testSameasSelection6 (prody.tests.atomic.test_select.TestSelect.testSameasSelection6)
> Test sameas selections "same segment as index 0" ... ok
> testSameasSelection7 (prody.tests.atomic.test_select.TestSelect.testSameasSelection7)
> Test sameas selections 'same residue as resname DG ALA' for pdb3mht ... ok
> testSameasSelection8 (prody.tests.atomic.test_select.TestSelect.testSameasSelection8)
> Test sameas selections "same residue as resname DG ALA" ... ok
> testSameasSelection9 (prody.tests.atomic.test_select.TestSelect.testSameasSelection9)
> Test sameas selections 'same chain as chain C' for pdb3mht ... ok
> testSequenceSelection1 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection1)
> Test sequence selections 'sequence al' for pdb3mht ... ok
> testSequenceSelection10 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection10)
> Test sequence selections "sequence FKPY" ... ok
> testSequenceSelection11 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection11)
> Test sequence selections 'sequence "SS."' for pdb3mht ... ok
> testSequenceSelection12 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection12)
> Test sequence selections "sequence "SS."" ... ok
> testSequenceSelection13 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection13)
> Test sequence selections 'sequence "S[A-Z]{2}G"' for pdb3mht ... ok
> testSequenceSelection14 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection14)
> Test sequence selections "sequence "S[A-Z]{2}G"" ... ok
> testSequenceSelection15 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection15)
> Test sequence selections 'sequence "S.S.S"' for pdb3mht ... ok
> testSequenceSelection16 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection16)
> Test sequence selections "sequence "S.S.S"" ... ok
> testSequenceSelection17 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection17)
> Test sequence selections 'sequence "."' for pdb3mht ... ok
> testSequenceSelection18 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection18)
> Test sequence selections "sequence "."" ... ok
> testSequenceSelection2 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection2)
> Test sequence selections "sequence al" ... ok
> testSequenceSelection3 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection3)
> Test sequence selections 'sequence A' for pdb3mht ... ok
> testSequenceSelection4 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection4)
> Test sequence selections "sequence A" ... ok
> testSequenceSelection5 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection5)
> Test sequence selections 'sequence MIEIK' for pdb3mht ... ok
> testSequenceSelection6 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection6)
> Test sequence selections "sequence MIEIK" ... ok
> testSequenceSelection7 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection7)
> Test sequence selections 'sequence VLNAL' for pdb3mht ... ok
> testSequenceSelection8 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection8)
> Test sequence selections "sequence VLNAL" ... ok
> testSequenceSelection9 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection9)
> Test sequence selections 'sequence FKPY' for pdb3mht ... ok
> testSpecialcharSelection1 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection1)
> Test specialchar selections 'altloc ` `' for pdb3mht ... ok
> testSpecialcharSelection2 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection2)
> Test specialchar selections "altloc ` `" ... ok
> testSpecialcharSelection3 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection3)
> Test specialchar selections 'name A` `CA`' for pdb3mht ... ok
> testSpecialcharSelection4 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection4)
> Test specialchar selections "name A` `CA`" ... ok
> testSpecialcharSelection5 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection5)
> Test specialchar selections 'name `A``' for pdb3mht ... ok
> testSpecialcharSelection6 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection6)
> Test specialchar selections "name `A``" ... ok
> testSpecialcharSelection7 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection7)
> Test specialchar selections 'z `+100.291`' for pdb3mht ... ok
> testSpecialcharSelection8 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection8)
> Test specialchar selections "z `+100.291`" ... ok
> testStringSelection1 (prody.tests.atomic.test_select.TestSelect.testStringSelection1)
> Test string selections 'name P' for pdb3mht ... ok
> testStringSelection10 (prody.tests.atomic.test_select.TestSelect.testStringSelection10)
> Test string selections "chain x" ... ok
> testStringSelection11 (prody.tests.atomic.test_select.TestSelect.testStringSelection11)
> Test string selections 'chain x y' for pdb3mht ... ok
> testStringSelection12 (prody.tests.atomic.test_select.TestSelect.testStringSelection12)
> Test string selections "chain x y" ... ok
> testStringSelection13 (prody.tests.atomic.test_select.TestSelect.testStringSelection13)
> Test string selections 'chain x y z' for pdb3mht ... ok
> testStringSelection14 (prody.tests.atomic.test_select.TestSelect.testStringSelection14)
> Test string selections "chain x y z" ... ok
> testStringSelection15 (prody.tests.atomic.test_select.TestSelect.testStringSelection15)
> Test string selections 'chain x y z C' for pdb3mht ... ok
> testStringSelection16 (prody.tests.atomic.test_select.TestSelect.testStringSelection16)
> Test string selections "chain x y z C" ... ok
> testStringSelection17 (prody.tests.atomic.test_select.TestSelect.testStringSelection17)
> Test string selections 'chain C D' for pdb3mht ... ok
> testStringSelection18 (prody.tests.atomic.test_select.TestSelect.testStringSelection18)
> Test string selections "chain C D" ... ok
> testStringSelection19 (prody.tests.atomic.test_select.TestSelect.testStringSelection19)
> Test string selections 'chain CD' for pdb3mht ... ok
> testStringSelection2 (prody.tests.atomic.test_select.TestSelect.testStringSelection2)
> Test string selections "name P" ... ok
> testStringSelection20 (prody.tests.atomic.test_select.TestSelect.testStringSelection20)
> Test string selections "chain CD" ... ok
> testStringSelection21 (prody.tests.atomic.test_select.TestSelect.testStringSelection21)
> Test string selections 'resname DG' for pdb3mht ... ok
> testStringSelection22 (prody.tests.atomic.test_select.TestSelect.testStringSelection22)
> Test string selections "resname DG" ... ok
> testStringSelection23 (prody.tests.atomic.test_select.TestSelect.testStringSelection23)
> Test string selections 'resname DG ALA' for pdb3mht ... ok
> testStringSelection24 (prody.tests.atomic.test_select.TestSelect.testStringSelection24)
> Test string selections "resname DG ALA" ... ok
> testStringSelection25 (prody.tests.atomic.test_select.TestSelect.testStringSelection25)
> Test string selections 'altloc A' for pdb3mht ... ok
> testStringSelection26 (prody.tests.atomic.test_select.TestSelect.testStringSelection26)
> Test string selections "altloc A" ... ok
> testStringSelection27 (prody.tests.atomic.test_select.TestSelect.testStringSelection27)
> Test string selections 'altloc _' for pdb3mht ... ok
> testStringSelection28 (prody.tests.atomic.test_select.TestSelect.testStringSelection28)
> Test string selections "altloc _" ... ok
> testStringSelection29 (prody.tests.atomic.test_select.TestSelect.testStringSelection29)
> Test string selections 'secondary H' for pdb3mht ... ok
> testStringSelection3 (prody.tests.atomic.test_select.TestSelect.testStringSelection3)
> Test string selections 'name P CA' for pdb3mht ... ok
> testStringSelection30 (prody.tests.atomic.test_select.TestSelect.testStringSelection30)
> Test string selections "secondary H" ... ok
> testStringSelection31 (prody.tests.atomic.test_select.TestSelect.testStringSelection31)
> Test string selections 'secondary H E' for pdb3mht ... ok
> testStringSelection32 (prody.tests.atomic.test_select.TestSelect.testStringSelection32)
> Test string selections "secondary H E" ... ok
> testStringSelection33 (prody.tests.atomic.test_select.TestSelect.testStringSelection33)
> Test string selections 'secondary _' for pdb3mht ... ok
> testStringSelection34 (prody.tests.atomic.test_select.TestSelect.testStringSelection34)
> Test string selections "secondary _" ... ok
> testStringSelection35 (prody.tests.atomic.test_select.TestSelect.testStringSelection35)
> Test string selections 'segment _' for pdb3mht ... ok
> testStringSelection36 (prody.tests.atomic.test_select.TestSelect.testStringSelection36)
> Test string selections "segment _" ... ok
> testStringSelection4 (prody.tests.atomic.test_select.TestSelect.testStringSelection4)
> Test string selections "name P CA" ... ok
> testStringSelection5 (prody.tests.atomic.test_select.TestSelect.testStringSelection5)
> Test string selections 'name `A 1`' for pdb3mht ... ok
> testStringSelection6 (prody.tests.atomic.test_select.TestSelect.testStringSelection6)
> Test string selections "name `A 1`" ... ok
> testStringSelection7 (prody.tests.atomic.test_select.TestSelect.testStringSelection7)
> Test string selections 'chain C' for pdb3mht ... ok
> testStringSelection8 (prody.tests.atomic.test_select.TestSelect.testStringSelection8)
> Test string selections "chain C" ... ok
> testStringSelection9 (prody.tests.atomic.test_select.TestSelect.testStringSelection9)
> Test string selections 'chain x' for pdb3mht ... ok
> testSynonymsSelection1 (prody.tests.atomic.test_select.TestSelect.testSynonymsSelection1)
> Test synonyms selections 'chain C' for pdb3mht ... ok
> testSynonymsSelection2 (prody.tests.atomic.test_select.TestSelect.testSynonymsSelection2)
> Test synonyms selections "chain C" ... ok
> testSynonymsSelection3 (prody.tests.atomic.test_select.TestSelect.testSynonymsSelection3)
> Test synonyms selections 'chain C D' for pdb3mht ... ok
> testSynonymsSelection4 (prody.tests.atomic.test_select.TestSelect.testSynonymsSelection4)
> Test synonyms selections "chain C D" ... ok
> testUnintendedSelection1 (prody.tests.atomic.test_select.TestSelect.testUnintendedSelection1)
> Test unintended selections 'abs beta = beta' for pdb3mht ... ok
> testUnintendedSelection2 (prody.tests.atomic.test_select.TestSelect.testUnintendedSelection2)
> Test unintended selections "abs beta = beta" ... ok
> testUserdataSelection1 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection1)
> Test userdata selections 'temp < 10' for pdb3mht ... ok
> testUserdataSelection10 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection10)
> Test userdata selections "occ" ... ok
> testUserdataSelection11 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection11)
> Test userdata selections 'occ and occupancy == 1' for pdb3mht ... ok
> testUserdataSelection12 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection12)
> Test userdata selections "occ and occupancy == 1" ... ok
> testUserdataSelection13 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection13)
> Test userdata selections 'occ and occupancy == 1 and oc10 - 9 == 1' for pdb3mht ... ok
> testUserdataSelection14 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection14)
> Test userdata selections "occ and occupancy == 1 and oc10 - 9 == 1" ... ok
> testUserdataSelection15 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection15)
> Test userdata selections 'occ and occupancy == 1 and temp < 10' for pdb3mht ... ok
> testUserdataSelection16 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection16)
> Test userdata selections "occ and occupancy == 1 and temp < 10" ... ok
> testUserdataSelection17 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection17)
> Test userdata selections 'occ > 0' for pdb3mht ... ok
> testUserdataSelection18 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection18)
> Test userdata selections "occ > 0" ... ok
> testUserdataSelection2 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection2)
> Test userdata selections "temp < 10" ... ok
> testUserdataSelection3 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection3)
> Test userdata selections 'temp < 10 and chain D' for pdb3mht ... ok
> testUserdataSelection4 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection4)
> Test userdata selections "temp < 10 and chain D" ... ok
> testUserdataSelection5 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection5)
> Test userdata selections 'oc10 - 9 == 1' for pdb3mht ... ok
> testUserdataSelection6 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection6)
> Test userdata selections "oc10 - 9 == 1" ... ok
> testUserdataSelection7 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection7)
> Test userdata selections 'temp < 10' for pdb3mht ... ok
> testUserdataSelection8 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection8)
> Test userdata selections "temp < 10" ... ok
> testUserdataSelection9 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection9)
> Test userdata selections 'occ' for pdb3mht ... ok
> testWithinSelection1 (prody.tests.atomic.test_select.TestSelect.testWithinSelection1)
> Test within selections 'within 10 of index 0' for pdb3mht ... ok
> testWithinSelection10 (prody.tests.atomic.test_select.TestSelect.testWithinSelection10)
> Test within selections "within 5 of within 5 of within 5 of index 0" ... ok
> testWithinSelection11 (prody.tests.atomic.test_select.TestSelect.testWithinSelection11)
> Test within selections 'exwithin 5 of exwithin 5 of exwithin 5 of index 0' for pdb3mht ... ok
> testWithinSelection12 (prody.tests.atomic.test_select.TestSelect.testWithinSelection12)
> Test within selections "exwithin 5 of exwithin 5 of exwithin 5 of index 0" ... ok
> testWithinSelection13 (prody.tests.atomic.test_select.TestSelect.testWithinSelection13)
> Test within selections 'within 1 of pdb' for pdb3mht ... ok
> testWithinSelection14 (prody.tests.atomic.test_select.TestSelect.testWithinSelection14)
> Test within selections "within 1 of pdb" ... ok
> testWithinSelection15 (prody.tests.atomic.test_select.TestSelect.testWithinSelection15)
> Test within selections 'exwithin 1 of pdb' for pdb3mht ... ok
> testWithinSelection16 (prody.tests.atomic.test_select.TestSelect.testWithinSelection16)
> Test within selections "exwithin 1 of pdb" ... ok
> testWithinSelection17 (prody.tests.atomic.test_select.TestSelect.testWithinSelection17)
> Test within selections 'exwithin 1 of ag' for pdb3mht ... ok
> testWithinSelection18 (prody.tests.atomic.test_select.TestSelect.testWithinSelection18)
> Test within selections "exwithin 1 of ag" ... ok
> testWithinSelection19 (prody.tests.atomic.test_select.TestSelect.testWithinSelection19)
> Test within selections 'within 100 of index 10000' for pdb3mht ... ok
> testWithinSelection2 (prody.tests.atomic.test_select.TestSelect.testWithinSelection2)
> Test within selections "within 10 of index 0" ... ok
> testWithinSelection20 (prody.tests.atomic.test_select.TestSelect.testWithinSelection20)
> Test within selections "within 100 of index 10000" ... ok
> testWithinSelection3 (prody.tests.atomic.test_select.TestSelect.testWithinSelection3)
> Test within selections 'exwithin 100 of index 0' for pdb3mht ... ok
> testWithinSelection4 (prody.tests.atomic.test_select.TestSelect.testWithinSelection4)
> Test within selections "exwithin 100 of index 0" ... ok
> testWithinSelection5 (prody.tests.atomic.test_select.TestSelect.testWithinSelection5)
> Test within selections 'exwithin 4 of resname SAH' for pdb3mht ... ok
> testWithinSelection6 (prody.tests.atomic.test_select.TestSelect.testWithinSelection6)
> Test within selections "exwithin 4 of resname SAH" ... ok
> testWithinSelection7 (prody.tests.atomic.test_select.TestSelect.testWithinSelection7)
> Test within selections '(within 4 of water) and not water' for pdb3mht ... ok
> testWithinSelection8 (prody.tests.atomic.test_select.TestSelect.testWithinSelection8)
> Test within selections "(within 4 of water) and not water" ... ok
> testWithinSelection9 (prody.tests.atomic.test_select.TestSelect.testWithinSelection9)
> Test within selections 'within 5 of within 5 of within 5 of index 0' for pdb3mht ... ok
> testWithout_AndSelection1 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection1)
> Test without_and selections 'coil protein' for pdb3mht ... ok
> testWithout_AndSelection10 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection10)
> Test without_and selections "(protein nucleic)" ... ok
> testWithout_AndSelection11 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection11)
> Test without_and selections 'noh hetero water' for pdb3mht ... ok
> testWithout_AndSelection12 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection12)
> Test without_and selections "noh hetero water" ... ok
> testWithout_AndSelection13 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection13)
> Test without_and selections 'ca occupancy > 0' for pdb3mht ... ok
> testWithout_AndSelection14 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection14)
> Test without_and selections "ca occupancy > 0" ... ok
> testWithout_AndSelection15 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection15)
> Test without_and selections 'ca occupancy - 0 > 0' for pdb3mht ... ok
> testWithout_AndSelection16 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection16)
> Test without_and selections "ca occupancy - 0 > 0" ... ok
> testWithout_AndSelection17 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection17)
> Test without_and selections 'ca occupancy - 0 > 0 + 0' for pdb3mht ... ok
> testWithout_AndSelection18 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection18)
> Test without_and selections "ca occupancy - 0 > 0 + 0" ... ok
> testWithout_AndSelection19 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection19)
> Test without_and selections 'occupancy > ca 0' for pdb3mht ... ok
> testWithout_AndSelection2 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection2)
> Test without_and selections "coil protein" ... ok
> testWithout_AndSelection20 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection20)
> Test without_and selections "occupancy > ca 0" ... ok
> testWithout_AndSelection21 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection21)
> Test without_and selections 'noh hetero (water)' for pdb3mht ... ok
> testWithout_AndSelection22 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection22)
> Test without_and selections "noh hetero (water)" ... ok
> testWithout_AndSelection23 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection23)
> Test without_and selections 'noh hetero not (water)' for pdb3mht ... ok
> testWithout_AndSelection24 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection24)
> Test without_and selections "noh hetero not (water)" ... ok
> testWithout_AndSelection25 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection25)
> Test without_and selections '(water) hetero' for pdb3mht ... ok
> testWithout_AndSelection26 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection26)
> Test without_and selections "(water) hetero" ... ok
> testWithout_AndSelection27 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection27)
> Test without_and selections 'ca abs(beta) = beta + abs(0)' for pdb3mht ... ok
> testWithout_AndSelection28 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection28)
> Test without_and selections "ca abs(beta) = beta + abs(0)" ... ok
> testWithout_AndSelection3 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection3)
> Test without_and selections 'sidechain sc protein' for pdb3mht ... ok
> testWithout_AndSelection4 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection4)
> Test without_and selections "sidechain sc protein" ... ok
> testWithout_AndSelection5 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection5)
> Test without_and selections 'bbfull bb' for pdb3mht ... ok
> testWithout_AndSelection6 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection6)
> Test without_and selections "bbfull bb" ... ok
> testWithout_AndSelection7 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection7)
> Test without_and selections '(charged basic)' for pdb3mht ... ok
> testWithout_AndSelection8 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection8)
> Test without_and selections "(charged basic)" ... ok
> testWithout_AndSelection9 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection9)
> Test without_and selections '(protein nucleic)' for pdb3mht ... ok
> testSetData (prody.tests.atomic.test_subset.TestUserData.testSetData) ... ok
> testDatafile_1ejg (prody.tests.datafiles.TestDatafiles.testDatafile_1ejg)
> Test presence of "pdb1ejg.pdb" ... ok
> testDatafile_1ubi (prody.tests.datafiles.TestDatafiles.testDatafile_1ubi)
> Test presence of "pdb1ubi.pdb" ... ok
> testDatafile_1ubi_ca (prody.tests.datafiles.TestDatafiles.testDatafile_1ubi_ca)
> Test presence of "pdb1ubi_ca.pdb" ... ok
> testDatafile_2gb1_truncated (prody.tests.datafiles.TestDatafiles.testDatafile_2gb1_truncated)
> Test presence of "pdb2gb1_truncated.pdb" ... ok
> testDatafile_2k39_ca (prody.tests.datafiles.TestDatafiles.testDatafile_2k39_ca)
> Test presence of "pdb2k39_ca.pdb" ... ok
> testDatafile_2nwl (prody.tests.datafiles.TestDatafiles.testDatafile_2nwl)
> Test presence of "pdb2nwl-opm.pdb" ... ok
> testDatafile_3hsy (prody.tests.datafiles.TestDatafiles.testDatafile_3hsy)
> Test presence of "pdb3hsy.pdb" ... ok
> testDatafile_3mht (prody.tests.datafiles.TestDatafiles.testDatafile_3mht)
> Test presence of "pdb3mht.pdb" ... ok
> testDatafile_3o21 (prody.tests.datafiles.TestDatafiles.testDatafile_3o21)
> Test presence of "pdb3o21.pdb" ... ok
> testDatafile_3p3w (prody.tests.datafiles.TestDatafiles.testDatafile_3p3w)
> Test presence of "pdb3p3w.pdb" ... ok
> testDatafile_DI (prody.tests.datafiles.TestDatafiles.testDatafile_DI)
> Test presence of "msa_Cys_knot_di.dat" ... ok
> testDatafile_Fasta (prody.tests.datafiles.TestDatafiles.testDatafile_Fasta)
> Test presence of "msa_Cys_knot.fasta" ... ok
> testDatafile_RTER (prody.tests.datafiles.TestDatafiles.testDatafile_RTER)
> Test presence of "pdbRTER.pdb" ... ok
> testDatafile_SCA (prody.tests.datafiles.TestDatafiles.testDatafile_SCA)
> Test presence of "msa_Cys_knot_sca.dat" ... ok
> testDatafile_Selex (prody.tests.datafiles.TestDatafiles.testDatafile_Selex)
> Test presence of "msa_Cys_knot.slx" ... ok
> testDatafile_Stockholm (prody.tests.datafiles.TestDatafiles.testDatafile_Stockholm)
> Test presence of "msa_Cys_knot.sth" ... ok
> testDatafile_anm1ubi_evalues (prody.tests.datafiles.TestDatafiles.testDatafile_anm1ubi_evalues)
> Test presence of "anm1ubi_evalues.dat" ... ok
> testDatafile_anm1ubi_hessian (prody.tests.datafiles.TestDatafiles.testDatafile_anm1ubi_hessian)
> Test presence of "anm1ubi_hessian.coo" ... ok
> testDatafile_anm1ubi_vectors (prody.tests.datafiles.TestDatafiles.testDatafile_anm1ubi_vectors)
> Test presence of "anm1ubi_vectors.dat" ... ok
> testDatafile_commute1ubi (prody.tests.datafiles.TestDatafiles.testDatafile_commute1ubi)
> Test presence of "commute1ubi.dat" ... ok
> testDatafile_dcd (prody.tests.datafiles.TestDatafiles.testDatafile_dcd)
> Test presence of "dcd2k39_truncated.dcd" ... ok
> testDatafile_dssp (prody.tests.datafiles.TestDatafiles.testDatafile_dssp)
> Test presence of "pdb1r19_dssp.pdb" ... ok
> testDatafile_five_digits (prody.tests.datafiles.TestDatafiles.testDatafile_five_digits)
> Test presence of "pdb1tw7_step3_charmm2namd.pdb" ... ok
> testDatafile_gnm1ubi_evalues (prody.tests.datafiles.TestDatafiles.testDatafile_gnm1ubi_evalues)
> Test presence of "gnm1ubi_evalues.dat" ... ok
> testDatafile_gnm1ubi_kirchhoff (prody.tests.datafiles.TestDatafiles.testDatafile_gnm1ubi_kirchhoff)
> Test presence of "gnm1ubi_kirchhoff.coo" ... ok
> testDatafile_gnm1ubi_vectors (prody.tests.datafiles.TestDatafiles.testDatafile_gnm1ubi_vectors)
> Test presence of "gnm1ubi_vectors.dat" ... ok
> testDatafile_h36 (prody.tests.datafiles.TestDatafiles.testDatafile_h36)
> Test presence of "pdb1tw7_step3_charmm2namd_doubled_h36.pdb" ... ok
> testDatafile_hex (prody.tests.datafiles.TestDatafiles.testDatafile_hex)
> Test presence of "pdb1tw7_step3_charmm2namd_doubled_hex.pdb" ... ok
> testDatafile_hit1ubi (prody.tests.datafiles.TestDatafiles.testDatafile_hit1ubi)
> Test presence of "hit1ubi.dat" ... ok
> testDatafile_long_chid_cif (prody.tests.datafiles.TestDatafiles.testDatafile_long_chid_cif)
> Test presence of "mmcif_6zu5.cif" ... ok
> testDatafile_multi_model_cif (prody.tests.datafiles.TestDatafiles.testDatafile_multi_model_cif)
> Test presence of "mmcif_6yfy.cif" ... ok
> testDatafile_multi_model_truncated (prody.tests.datafiles.TestDatafiles.testDatafile_multi_model_truncated)
> Test presence of "pdb2k39_truncated.pdb" ... ok
> testDatafile_oneatom (prody.tests.datafiles.TestDatafiles.testDatafile_oneatom)
> Test presence of "pdb1ejg_oneatom.pdb" ... ok
> testDatafile_pca2k39_cov (prody.tests.datafiles.TestDatafiles.testDatafile_pca2k39_cov)
> Test presence of "pca2k39_cov.coo" ... ok
> testDatafile_pca2k39_evalues (prody.tests.datafiles.TestDatafiles.testDatafile_pca2k39_evalues)
> Test presence of "pca2k39_evalues.dat" ... ok
> testDatafile_pca2k39_vectors (prody.tests.datafiles.TestDatafiles.testDatafile_pca2k39_vectors)
> Test presence of "pca2k39_vectors.dat" ... ok
> testDatafile_rtb2gb1_hessian (prody.tests.datafiles.TestDatafiles.testDatafile_rtb2gb1_hessian)
> Test presence of "rtb2gb1_hessian.coo" ... ok
> testDatafile_rtb2gb1_project (prody.tests.datafiles.TestDatafiles.testDatafile_rtb2gb1_project)
> Test presence of "rtb2gb1_project.coo" ... ok
> testDatafile_sti (prody.tests.datafiles.TestDatafiles.testDatafile_sti)
> Test presence of "xmlSTI.xml" ... ok
> testMode1d (prody.tests.dynamics.test_editing.TestExtending.testMode1d) ... ok
> testMode3d (prody.tests.dynamics.test_editing.TestExtending.testMode3d) ... ok
> testModel1d (prody.tests.dynamics.test_editing.TestExtending.testModel1d) ... ok
> testModel3d (prody.tests.dynamics.test_editing.TestExtending.testModel3d) ... ok
> testVector1d (prody.tests.dynamics.test_editing.TestExtending.testVector1d) ... ok
> testVector3d (prody.tests.dynamics.test_editing.TestExtending.testVector3d) ... ok
> testBuildHessianSlow (prody.tests.dynamics.test_enms.TestANM.testBuildHessianSlow) ... ok
> testBuildMatrixCoordsArray (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixCoordsArray)
> Test output when *coords* is an array. ... ok
> testBuildMatrixCoordsWrongType (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixCoordsWrongType)
> Test response to wrong type *coords* argument. ... ok
> testBuildMatrixCutoffInvalidValue (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixCutoffInvalidValue)
> Test response to wrong *cutoff* argument. ... ok
> testBuildMatrixCutoffWrongType (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixCutoffWrongType)
> Test response to cutoff of wrong type. ... ok
> testBuildMatrixInvalidGamma (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixInvalidGamma)
> Test response to invalid *gamma* argument. ... ok
> testBuildMatrixWrongCoords (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixWrongCoords)
> Test response to wrong coords.dtype. ... ok
> testBuildMatrixWrongGamma (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixWrongGamma)
> Test response to wrong *gamma* argument. ... ok
> testSetHessianWrongShape (prody.tests.dynamics.test_enms.TestANM.testSetHessianWrongShape)
> Test response to wrong shape *hessian* argument. ... ok
> testSetMatrixAcceptableDtype (prody.tests.dynamics.test_enms.TestANM.testSetMatrixAcceptableDtype)
> Test response to acceptable matrix.dtype. ... ok
> testSetMatrixNonSquare (prody.tests.dynamics.test_enms.TestANM.testSetMatrixNonSquare)
> Test response to non-square matrix. ... ok
> testSetMatrixWrongDim (prody.tests.dynamics.test_enms.TestANM.testSetMatrixWrongDim)
> Test response to wrong dim *kirchhoff* argument. ... ok
> testSetMatrixWrongDtype (prody.tests.dynamics.test_enms.TestANM.testSetMatrixWrongDtype)
> Test response to wrong matrix.dtype. ... ok
> testSetMatrixWrongType (prody.tests.dynamics.test_enms.TestANM.testSetMatrixWrongType)
> Test response to wrong matrix type argument. ... ok
> testEigenvalues (prody.tests.dynamics.test_enms.TestANMResults.testEigenvalues)
> Test eigenvalues. ... ok
> testEigenvectors (prody.tests.dynamics.test_enms.TestANMResults.testEigenvectors)
> Test eigenvectors. ... ok
> testGetCutoff (prody.tests.dynamics.test_enms.TestANMResults.testGetCutoff)
> Testing return type of :meth:`~.GNMBase.getCutoff`. ... ok
> testGetGamma (prody.tests.dynamics.test_enms.TestANMResults.testGetGamma)
> Testing return type of :meth:`~.GNMBase.getGamma`. ... ok
> testGetHessian (prody.tests.dynamics.test_enms.TestANMResults.testGetHessian) ... ok
> testHessian (prody.tests.dynamics.test_enms.TestANMResults.testHessian)
> Test Hessian matrix. ... ok
> testHessianSums (prody.tests.dynamics.test_enms.TestANMResults.testHessianSums) ... ok
> testHessianSymmetry (prody.tests.dynamics.test_enms.TestANMResults.testHessianSymmetry) ... ok
> testVariances (prody.tests.dynamics.test_enms.TestANMResults.testVariances)
> Test variances. ... ok
> testEigenvalues (prody.tests.dynamics.test_enms.TestEXANMResults.testEigenvalues)
> Test eigenvalues. ... ok
> testEigenvectors (prody.tests.dynamics.test_enms.TestEXANMResults.testEigenvectors)
> Test eigenvectors. ... ok
> testGetCutoff (prody.tests.dynamics.test_enms.TestEXANMResults.testGetCutoff)
> Testing return type of :meth:`~.GNMBase.getCutoff`. ... ok
> testGetGamma (prody.tests.dynamics.test_enms.TestEXANMResults.testGetGamma)
> Testing return type of :meth:`~.GNMBase.getGamma`. ... ok
> testGetHessian (prody.tests.dynamics.test_enms.TestEXANMResults.testGetHessian) ... ok
> testHessian (prody.tests.dynamics.test_enms.TestEXANMResults.testHessian)
> Test Hessian matrix. ... ok
> testHessianSums (prody.tests.dynamics.test_enms.TestEXANMResults.testHessianSums) ... ok
> testHessianSymmetry (prody.tests.dynamics.test_enms.TestEXANMResults.testHessianSymmetry) ... ok
> testVariances (prody.tests.dynamics.test_enms.TestEXANMResults.testVariances)
> Test variances. ... ok
> testBuildMatrixCoordsArray (prody.tests.dynamics.test_enms.TestGNM.testBuildMatrixCoordsArray)
> Test output when *coords* is an array. ... ok
> testBuildMatrixCoordsWrongType (prody.tests.dynamics.test_enms.TestGNM.testBuildMatrixCoordsWrongType)
> Test response to wrong type *coords* argument. ... ok
> testBuildMatrixCutoffInvalidValue (prody.tests.dynamics.test_enms.TestGNM.testBuildMatrixCutoffInvalidValue)
> Test response to wrong *cutoff* argument. ... ok
> testBuildMatrixCutoffWrongType (prody.tests.dynamics.test_enms.TestGNM.testBuildMatrixCutoffWrongType)
> Test response to cutoff of wrong type. ... ok
> testBuildMatrixInvalidGamma (prody.tests.dynamics.test_enms.TestGNM.testBuildMatrixInvalidGamma)
> Test response to invalid *gamma* argument. ... ok
> testBuildMatrixWrongCoords (prody.tests.dynamics.test_enms.TestGNM.testBuildMatrixWrongCoords)
> Test response to wrong coords.dtype. ... ok
> testBuildMatrixWrongGamma (prody.tests.dynamics.test_enms.TestGNM.testBuildMatrixWrongGamma)
> Test response to wrong *gamma* argument. ... ok
> testSetMatrixAcceptableDtype (prody.tests.dynamics.test_enms.TestGNM.testSetMatrixAcceptableDtype)
> Test response to acceptable matrix.dtype. ... ok
> testSetMatrixNonSquare (prody.tests.dynamics.test_enms.TestGNM.testSetMatrixNonSquare)
> Test response to non-square matrix. ... ok
> testSetMatrixWrongDim (prody.tests.dynamics.test_enms.TestGNM.testSetMatrixWrongDim)
> Test response to wrong dim *kirchhoff* argument. ... ok
> testSetMatrixWrongDtype (prody.tests.dynamics.test_enms.TestGNM.testSetMatrixWrongDtype)
> Test response to wrong matrix.dtype. ... ok
> testSetMatrixWrongType (prody.tests.dynamics.test_enms.TestGNM.testSetMatrixWrongType)
> Test response to wrong matrix type argument. ... ok
> testBuildKirchoffSlow (prody.tests.dynamics.test_enms.TestGNMResults.testBuildKirchoffSlow) ... ok
> testCommuteTime (prody.tests.dynamics.test_enms.TestGNMResults.testCommuteTime) ... ok
> testEigenvalues (prody.tests.dynamics.test_enms.TestGNMResults.testEigenvalues) ... ok
> testEigenvectors (prody.tests.dynamics.test_enms.TestGNMResults.testEigenvectors) ... ok
> testGetCutoff (prody.tests.dynamics.test_enms.TestGNMResults.testGetCutoff)
> Testing return type of :meth:`~.GNMBase.getCutoff`. ... ok
> testGetGamma (prody.tests.dynamics.test_enms.TestGNMResults.testGetGamma)
> Testing return type of :meth:`~.GNMBase.getGamma`. ... ok
> testGetKirchoff (prody.tests.dynamics.test_enms.TestGNMResults.testGetKirchoff) ... ok
> testKirchhoff (prody.tests.dynamics.test_enms.TestGNMResults.testKirchhoff) ... ok
> testKirchhoffSums (prody.tests.dynamics.test_enms.TestGNMResults.testKirchhoffSums) ... ok
> testKirchhoffSymmetry (prody.tests.dynamics.test_enms.TestGNMResults.testKirchhoffSymmetry) ... ok
> testCalcModes (prody.tests.dynamics.test_enms.TestRTB.testCalcModes) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/utilities/eigtools.py:41: DeprecationWarning: Keyword argument 'eigvals' is deprecated in favour of 'subset_by_index' keyword instead and will be removed in SciPy 1.12.0.
> values, vectors = linalg.eigh(M, turbo=turbo, eigvals=eigvals)
> ok
> testHessian (prody.tests.dynamics.test_enms.TestRTB.testHessian) ... ok
> testProjection (prody.tests.dynamics.test_enms.TestRTB.testProjection) ... ok
> testGetCutoff (prody.tests.dynamics.test_enms.testGNMBase.testGetCutoff)
> Testing return type of :meth:`~.GNMBase.getCutoff`. ... ok
> testGetGamma (prody.tests.dynamics.test_enms.testGNMBase.testGetGamma)
> Testing return type of :meth:`~.GNMBase.getGamma`. ... ok
> testBuildMatrixCoordsArray (prody.tests.dynamics.test_pca.TestPCA.testBuildMatrixCoordsArray)
> Test output when *coords* is an array. ... ok
> testBuildMatrixCoordsWrongType (prody.tests.dynamics.test_pca.TestPCA.testBuildMatrixCoordsWrongType)
> Test response to wrong type *coords* argument. ... ok
> testBuildMatrixWrongCoords (prody.tests.dynamics.test_pca.TestPCA.testBuildMatrixWrongCoords)
> Test response to wrong coords.dtype. ... ok
> testSetMatrixAcceptableDtype (prody.tests.dynamics.test_pca.TestPCA.testSetMatrixAcceptableDtype)
> Test response to acceptable matrix.dtype. ... ok
> testSetMatrixNonSquare (prody.tests.dynamics.test_pca.TestPCA.testSetMatrixNonSquare)
> Test response to non-square matrix. ... ok
> testSetMatrixWrongDim (prody.tests.dynamics.test_pca.TestPCA.testSetMatrixWrongDim)
> Test response to wrong dim *kirchhoff* argument. ... ok
> testSetMatrixWrongDtype (prody.tests.dynamics.test_pca.TestPCA.testSetMatrixWrongDtype)
> Test response to wrong matrix.dtype. ... ok
> testSetMatrixWrongType (prody.tests.dynamics.test_pca.TestPCA.testSetMatrixWrongType)
> Test response to wrong matrix type argument. ... ok
> testBuildMatrixCoordsArray (prody.tests.dynamics.test_pca.TestPCAResults.testBuildMatrixCoordsArray)
> Test output when *coords* is an array. ... ok
> testBuildMatrixCoordsWrongType (prody.tests.dynamics.test_pca.TestPCAResults.testBuildMatrixCoordsWrongType)
> Test response to wrong type *coords* argument. ... ok
> testBuildMatrixWrongCoords (prody.tests.dynamics.test_pca.TestPCAResults.testBuildMatrixWrongCoords)
> Test response to wrong coords.dtype. ... ok
> testCovariance (prody.tests.dynamics.test_pca.TestPCAResults.testCovariance) ... ok
> testCovarianceSymmetry (prody.tests.dynamics.test_pca.TestPCAResults.testCovarianceSymmetry) ... ok
> testEigenvalues (prody.tests.dynamics.test_pca.TestPCAResults.testEigenvalues) ... ok
> testEigenvectors (prody.tests.dynamics.test_pca.TestPCAResults.testEigenvectors) ... ok
> testNumModesAll (prody.tests.dynamics.test_pca.TestPCAResults.testNumModesAll) ... ok
> testNumModesSet (prody.tests.dynamics.test_pca.TestPCAResults.testNumModesSet) ... ok
> testSetMatrixAcceptableDtype (prody.tests.dynamics.test_pca.TestPCAResults.testSetMatrixAcceptableDtype)
> Test response to acceptable matrix.dtype. ... ok
> testSetMatrixNonSquare (prody.tests.dynamics.test_pca.TestPCAResults.testSetMatrixNonSquare)
> Test response to non-square matrix. ... ok
> testSetMatrixWrongDim (prody.tests.dynamics.test_pca.TestPCAResults.testSetMatrixWrongDim)
> Test response to wrong dim *kirchhoff* argument. ... ok
> testSetMatrixWrongDtype (prody.tests.dynamics.test_pca.TestPCAResults.testSetMatrixWrongDtype)
> Test response to wrong matrix.dtype. ... ok
> testSetMatrixWrongType (prody.tests.dynamics.test_pca.TestPCAResults.testSetMatrixWrongType)
> Test response to wrong matrix type argument. ... ok
> testSlicing (prody.tests.dynamics.test_signature.TestSDArray.testSlicing) ... ok
> testCoordinates (prody.tests.ensemble.test_conformation.TestConformation.testCoordinates) ... ok
> testCoordinatesForAll (prody.tests.ensemble.test_conformation.TestConformation.testCoordinatesForAll) ... ok
> testGetIndex (prody.tests.ensemble.test_conformation.TestConformation.testGetIndex)
> Test get index function. ... ok
> testGetNumAtoms (prody.tests.ensemble.test_conformation.TestConformation.testGetNumAtoms)
> Test get index function. ... ok
> testWeights (prody.tests.ensemble.test_conformation.TestConformation.testWeights) ... ok
> testCoordinates (prody.tests.ensemble.test_conformation.TestPDBConformation.testCoordinates) ... ok
> testCoordinatesForAll (prody.tests.ensemble.test_conformation.TestPDBConformation.testCoordinatesForAll) ... ok
> testGetIndex (prody.tests.ensemble.test_conformation.TestPDBConformation.testGetIndex) ... ok
> testGetNumAtoms (prody.tests.ensemble.test_conformation.TestPDBConformation.testGetNumAtoms) ... ok
> testWeights (prody.tests.ensemble.test_conformation.TestPDBConformation.testWeights) ... ok
> testWeightsForAll (prody.tests.ensemble.test_conformation.TestPDBConformation.testWeightsForAll) ... ok
> testConcatenation (prody.tests.ensemble.test_ensemble.TestEnsemble.testConcatenation)
> Test concatenation of ensembles without weights. ... ok
> testConcatenationNoweightsWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testConcatenationNoweightsWeights)
> Test concatenation of ensembles without and with weights. ... ok
> testConcatenationWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testConcatenationWeights)
> Test concatenation of ensembles with weights. ... ok
> testConcatenationWeightsNoweights (prody.tests.ensemble.test_ensemble.TestEnsemble.testConcatenationWeightsNoweights)
> Test concatenation of ensembles with and without weights. ... ok
> testDelCoordsetAll (prody.tests.ensemble.test_ensemble.TestEnsemble.testDelCoordsetAll) ... ok
> testDelCoordsetMiddle (prody.tests.ensemble.test_ensemble.TestEnsemble.testDelCoordsetMiddle) ... ok
> testGetCoordinates (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetCoordinates)
> Test correctness of reference coordinates. ... ok
> testGetCoordsets (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetCoordsets)
> Test correctness of all coordinates. ... ok
> testGetNumAtoms (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetNumAtoms) ... ok
> testGetNumCsets (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetNumCsets) ... ok
> testGetRMSDs (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetRMSDs) ... ok
> testGetRMSDsWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetRMSDsWeights) ... ok
> testGetWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetWeights)
> Test correctness of all weights. ... ok
> testIterCoordsets (prody.tests.ensemble.test_ensemble.TestEnsemble.testIterCoordsets)
> Test coordinate iteration. ... ok
> testSelection (prody.tests.ensemble.test_ensemble.TestEnsemble.testSelection)
> Test atom selection of ensemble. ... ok
> testSlicing (prody.tests.ensemble.test_ensemble.TestEnsemble.testSlicing)
> Test slicing operation. ... ok
> testSlicingCopy (prody.tests.ensemble.test_ensemble.TestEnsemble.testSlicingCopy)
> Test making a copy by slicing operation. ... ok
> testSlicingList (prody.tests.ensemble.test_ensemble.TestEnsemble.testSlicingList)
> Test slicing with a list. ... ok
> testSlicingWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testSlicingWeights)
> Test slicing operation with weights. ... ok
> testSuperpose (prody.tests.ensemble.test_ensemble.TestEnsemble.testSuperpose) ... ok
> testSuperposeWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testSuperposeWeights) ... ok
> testResults (prody.tests.ensemble.test_functions.TestBuildPDBEnsemble.testResults) ... ok
> testInvalidType (prody.tests.ensemble.test_functions.TestCalcOccupancies.testInvalidType) ... ok
> testResults (prody.tests.ensemble.test_functions.TestCalcOccupancies.testResults) ... ok
> testWeightsNone (prody.tests.ensemble.test_functions.TestCalcOccupancies.testWeightsNone) ... ok
> testResults (prody.tests.ensemble.test_functions.TestTrimPDBEnsemble.testResults) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/sequence/sequence.py:52: DeprecationWarning: tostring() is deprecated. Use tobytes() instead.
> return self._array.tostring().decode()
> ok
> testAddCoordsets (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testAddCoordsets) ... ok
> testConcatenation (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testConcatenation)
> Test concatenation of PDB ensembles. ... ok
> testDelCoordsetAll (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testDelCoordsetAll)
> Test consequences of deleting all coordinate sets. ... ok
> testDelCoordsetMiddle (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testDelCoordsetMiddle) ... ok
> testDelCoordsetMiddleTrans (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testDelCoordsetMiddleTrans) ... ok
> testGetCoordinates (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetCoordinates) ... ok
> testGetCoordsets (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetCoordsets) ... ok
> testGetNumAtoms (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetNumAtoms) ... ok
> testGetNumCsets (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetNumCsets) ... ok
> testGetWeights (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetWeights) ... ok
> testIterCoordsets (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testIterCoordsets) ... ok
> testSlicing (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testSlicing) ... ok
> testSlicingCopy (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testSlicingCopy) ... ok
> testSlicingList (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testSlicingList) ... ok
> testSlicingWeights (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testSlicingWeights) ... ok
> testAllSearch (prody.tests.kdtree.test_kdtree.TestKDTree.testAllSearch) ... ok
> testSearch (prody.tests.kdtree.test_kdtree.TestKDTree.testSearch) ... ok
> testPairNoPBC (prody.tests.kdtree.test_kdtree.TestKDTreePBC.testPairNoPBC) ... ok
> testPairPBC (prody.tests.kdtree.test_kdtree.TestKDTreePBC.testPairPBC) ... ok
> testPointNoPBC (prody.tests.kdtree.test_kdtree.TestKDTreePBC.testPointNoPBC) ... ok
> testPointPBC (prody.tests.kdtree.test_kdtree.TestKDTreePBC.testPointPBC) ... ok
> testMINvsMAX (prody.tests.measure.test_contacts.TestContacts.testMINvsMAX) ... ok
> testPBCvsNONE (prody.tests.measure.test_contacts.TestContacts.testPBCvsNONE) ... ok
> testAtomicArgumentSwitching (prody.tests.measure.test_contacts.TestNeighbors.testAtomicArgumentSwitching) ... ok
> testCoordArgumentSwitching (prody.tests.measure.test_contacts.TestNeighbors.testCoordArgumentSwitching) ... ok
> testNoPBC (prody.tests.measure.test_contacts.TestNeighbors.testNoPBC) ... ok
> testPBC (prody.tests.measure.test_contacts.TestNeighbors.testPBC) ... ok
> testPBCAtomicArgumentSwitching (prody.tests.measure.test_contacts.TestNeighbors.testPBCAtomicArgumentSwitching) ... ok
> testPBCCoordArgumentSwitching (prody.tests.measure.test_contacts.TestNeighbors.testPBCCoordArgumentSwitching) ... ok
> testCenter (prody.tests.measure.test_measure.TestCenter.testCenter) ... ok
> testCenterWithWeights (prody.tests.measure.test_measure.TestCenter.testCenterWithWeights) ... ok
> testMultiCoordsets (prody.tests.measure.test_measure.TestCenter.testMultiCoordsets) ... ok
> testMultiCoordsetsWithWeights (prody.tests.measure.test_measure.TestCenter.testMultiCoordsetsWithWeights) ... ok
> testCTerPhi (prody.tests.measure.test_measure.TestDihedrals.testCTerPhi) ... ok
> testCTerPsi (prody.tests.measure.test_measure.TestDihedrals.testCTerPsi) ... ok
> testCalcPhi (prody.tests.measure.test_measure.TestDihedrals.testCalcPhi) ... ok
> testCalcPsi (prody.tests.measure.test_measure.TestDihedrals.testCalcPsi) ... ok
> testNTerPhi (prody.tests.measure.test_measure.TestDihedrals.testNTerPhi) ... ok
> testNTerPsi (prody.tests.measure.test_measure.TestDihedrals.testNTerPsi) ... ok
> testPBC (prody.tests.measure.test_measure.TestDistances.testPBC) ... ok
> testPBCSymmetry (prody.tests.measure.test_measure.TestDistances.testPBCSymmetry) ... ok
> testMSF (prody.tests.measure.test_measure.TestMSF.testMSF) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/trajectory/dcdfile.py:273: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
> xyz = fromstring(self._file.read(self._itemsize * n_floats),
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/trajectory/dcdfile.py:320: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
> data = fromstring(data, self._dtype)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/trajectory/dcdfile.py:294: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
> unitcell = fromstring(self._file.read(48), dtype=np.float64)
> ok
> testMSFfloat (prody.tests.measure.test_measure.TestMSF.testMSFfloat) ... ok
> testByArgument (prody.tests.measure.test_transform.TestMoveAtoms.testByArgument) ... ok
> testToArgument (prody.tests.measure.test_transform.TestMoveAtoms.testToArgument) ... ok
> testTransformation (prody.tests.measure.test_transform.TestMoveAtoms.testTransformation) ... ok
> testWrap (prody.tests.measure.test_transform.TestWrapAtoms.testWrap) ... ok
> testAgArgMultiModel (prody.tests.proteins.test_ciffile.TestParseMMCIF.testAgArgMultiModel)
> Test number of coordinate sets when using *ag* arguments. ... ok
> testAgArgument (prody.tests.proteins.test_ciffile.TestParseMMCIF.testAgArgument)
> Test outcome of valid and invalid *ag* arguments. ... /usr/lib/python3.11/traceback.py:240: ResourceWarning: unclosed file <_io.TextIOWrapper name='/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles/mmcif_6yfy.cif' mode='rt' encoding='UTF-8'>
> tb.tb_frame.clear()
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> ok
> testChainArgument (prody.tests.proteins.test_ciffile.TestParseMMCIF.testChainArgument)
> Test outcome of valid and invalid *chain* arguments. ... ok
> testLongChainArgument (prody.tests.proteins.test_ciffile.TestParseMMCIF.testLongChainArgument)
> Test outcome of valid and invalid *chain* arguments. ... /usr/lib/python3.11/traceback.py:240: ResourceWarning: unclosed file <_io.TextIOWrapper name='/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles/mmcif_6zu5.cif' mode='rt' encoding='UTF-8'>
> tb.tb_frame.clear()
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> ok
> testModelArgument (prody.tests.proteins.test_ciffile.TestParseMMCIF.testModelArgument)
> Test outcome of valid and invalid *model* arguments. ... ok
> testPDBArgument (prody.tests.proteins.test_ciffile.TestParseMMCIF.testPDBArgument)
> Test outcome of invalid *pdb* arguments. ... ok
> testSubsetArgument (prody.tests.proteins.test_ciffile.TestParseMMCIF.testSubsetArgument)
> Test outcome of valid and invalid *subset* arguments. ... ok
> testTitleArgument (prody.tests.proteins.test_ciffile.TestParseMMCIF.testTitleArgument)
> Test outcome of *title* argument. ... ok
> testUsualCase (prody.tests.proteins.test_ciffile.TestParseMMCIF.testUsualCase)
> Test the outcome of a simple parsing scenario. ... ok
> testDSSPBridgePartners (prody.tests.proteins.test_dssp.TestDSSPFunctions.testDSSPBridgePartners)
> Check if the DSSP bridge-partners were correctly parsed and ... skipped 'dssp is not found'
> testHeaderContent (prody.tests.proteins.test_header.TestParsePDBHeaderOnly.testHeaderContent) ... ok
> testHeaderType (prody.tests.proteins.test_header.TestParsePDBHeaderOnly.testHeaderType) ... ok
> testCompressedArgument (prody.tests.proteins.test_localpdb.TestFetchPDB.testCompressedArgument)
> Test decompressing fetched PDB files. ... skipped 'Not running tests needing network access.'
> testFetchingMultipleFiles (prody.tests.proteins.test_localpdb.TestFetchPDB.testFetchingMultipleFiles)
> Test the outcome of fetching multiple PDB files. ... skipped 'Not running tests needing network access.'
> testFetchingSingleFile (prody.tests.proteins.test_localpdb.TestFetchPDB.testFetchingSingleFile)
> Test the outcome of fetching a single PDB file. ... skipped 'Not running tests needing network access.'
> testInvalidPDBIdentifier (prody.tests.proteins.test_localpdb.TestFetchPDB.testInvalidPDBIdentifier)
> Test outcome of passing invalid PDB identifiers. ... ok
> testAgArgMultiModel (prody.tests.proteins.test_pdbfile.TestParsePDB.testAgArgMultiModel)
> Test number of coordinate sets when using *ag* arguments. ... ok
> testAgArgSingleModel (prody.tests.proteins.test_pdbfile.TestParsePDB.testAgArgSingleModel)
> Test number of coordinate sets when using *ag* arguments. ... ok
> testAgArgument (prody.tests.proteins.test_pdbfile.TestParsePDB.testAgArgument)
> Test outcome of valid and invalid *ag* arguments. ... /usr/lib/python3.11/traceback.py:240: ResourceWarning: unclosed file <_io.TextIOWrapper name='/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles/pdb2k39_truncated.pdb' mode='rt' encoding='UTF-8'>
> tb.tb_frame.clear()
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> ok
> testChainArgument (prody.tests.proteins.test_pdbfile.TestParsePDB.testChainArgument)
> Test outcome of valid and invalid *chain* arguments. ... ok
> testFiveDigitResnum (prody.tests.proteins.test_pdbfile.TestParsePDB.testFiveDigitResnum)
> Test parsing PDB files with five digit resnums ... ok
> testHexResnum (prody.tests.proteins.test_pdbfile.TestParsePDB.testHexResnum)
> Test parsing PDB files with hexadecimal resnums ... ok
> testHexSerial (prody.tests.proteins.test_pdbfile.TestParsePDB.testHexSerial)
> Test parsing PDB files with hexadecimal serial numbers ... ok
> testHybrid36Resnum (prody.tests.proteins.test_pdbfile.TestParsePDB.testHybrid36Resnum)
> Test parsing PDB files with Hybrid36 resnums ... ok
> testHybrid36Serial (prody.tests.proteins.test_pdbfile.TestParsePDB.testHybrid36Serial)
> Test parsing PDB files with Hybrid36 serial numbers ... ok
> testModelArgument (prody.tests.proteins.test_pdbfile.TestParsePDB.testModelArgument)
> Test outcome of valid and invalid *model* arguments. ... ok
> testPDBArgument (prody.tests.proteins.test_pdbfile.TestParsePDB.testPDBArgument)
> Test outcome of invalid *pdb* arguments. ... ok
> testSubsetArgument (prody.tests.proteins.test_pdbfile.TestParsePDB.testSubsetArgument)
> Test outcome of valid and invalid *subset* arguments. ... ok
> testTitleArgument (prody.tests.proteins.test_pdbfile.TestParsePDB.testTitleArgument)
> Test outcome of *title* argument. ... ok
> testUsualCase (prody.tests.proteins.test_pdbfile.TestParsePDB.testUsualCase)
> Test the outcome of a simple parsing scenario. ... ok
> testAltlocA (prody.tests.proteins.test_pdbfile.TestParsePDBAltloc.testAltlocA) ... ok
> testAltlocB (prody.tests.proteins.test_pdbfile.TestParsePDBAltloc.testAltlocB) ... ok
> testAltlocC (prody.tests.proteins.test_pdbfile.TestParsePDBAltloc.testAltlocC) ... ok
> testAltlocNone (prody.tests.proteins.test_pdbfile.TestParsePDBAltloc.testAltlocNone) ... ok
> testAtomGroupContent (prody.tests.proteins.test_pdbfile.TestParsePDBHeaderAndAllModels.testAtomGroupContent) ... ok
> testAtomGroupType (prody.tests.proteins.test_pdbfile.TestParsePDBHeaderAndAllModels.testAtomGroupType) ... ok
> testModelArgument (prody.tests.proteins.test_pdbfile.TestWritePDB.testModelArgument)
> Test valid and invalid model arguments. ... /usr/lib/python3.11/traceback.py:240: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/test.pdb' mode='wt' encoding='UTF-8'>
> tb.tb_frame.clear()
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> ok
> testParsingOutput (prody.tests.proteins.test_pdbfile.TestWritePDB.testParsingOutput)
> Test if parsing output is the same as parsing original file. ... ok
> testWritingHex (prody.tests.proteins.test_pdbfile.TestWritePDB.testWritingHex)
> Test if output from writing hexadecimal is as expected. ... ok
> testWritingHybrid36 (prody.tests.proteins.test_pdbfile.TestWritePDB.testWritingHybrid36)
> Test if output from writing Hybrid36 is as expected. ... ok
> testCompressed (prody.tests.proteins.test_wwpdb.TestFTP.testCompressed) ... skipped 'Not running tests needing network access.'
> testDecompressed (prody.tests.proteins.test_wwpdb.TestFTP.testDecompressed) ... skipped 'Not running tests needing network access.'
> testCompressed (prody.tests.proteins.test_wwpdb.TestHTTP.testCompressed) ... skipped 'Not running tests needing network access.'
> testDecompressed (prody.tests.proteins.test_wwpdb.TestHTTP.testDecompressed) ... skipped 'Not running tests needing network access.'
> testResidueCount (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testResidueCount) ... ok
> testResidueOccupancy (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testResidueOccupancy) ... ok
> testSequenceCount (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testSequenceCount) ... ok
> testSequenceOccupancy (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testSequenceOccupancy) ... ok
> testMATLAB (prody.tests.sequence.test_analysis.TestCalcMeff.testMATLAB) ... ok
> testTwenty (prody.tests.sequence.test_analysis.TestCalcMeff.testTwenty) ... ok
> testTwentyReversed (prody.tests.sequence.test_analysis.TestCalcMeff.testTwentyReversed) ... ok
> testZero1 (prody.tests.sequence.test_analysis.TestCalcMeff.testZero1) ... ok
> testZero2 (prody.tests.sequence.test_analysis.TestCalcMeff.testZero2) ... ok
> testAmbiguity (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity) ... ok
> testAmbiguity2 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity2) ... ok
> testAmbiguity3 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity3) ... ok
> testAmbiguity4 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity4) ... ok
> testAmbiguity5 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity5) ... ok
> testAmbiguity6 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity6) ... ok
> testAmbiguity7 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity7) ... ok
> testInf (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testInf) ... ok
> testNoAmbiguity (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testNoAmbiguity) ... ok
> testNorm (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testNorm) ... ok
> testNorm2 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testNorm2) ... ok
> testSixSequences (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testSixSequences) ... ok
> testTwenty (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testTwenty) ... ok
> testTwentyReversed (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testTwentyReversed) ... ok
> testAmbiguity (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity) ... ok
> testAmbiguity2 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity2) ... ok
> testAmbiguity3 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity3) ... ok
> testAmbiguity4 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity4) ... ok
> testAmbiguity5 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity5) ... ok
> testAmbiguity6 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity6) ... ok
> testAmbiguity7 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity7) ... ok
> testFourSequences (prody.tests.sequence.test_analysis.TestCalcOMES.testFourSequences) ... ok
> testInf (prody.tests.sequence.test_analysis.TestCalcOMES.testInf) ... ok
> testNoAmbiguity (prody.tests.sequence.test_analysis.TestCalcOMES.testNoAmbiguity) ... ok
> testTwenty (prody.tests.sequence.test_analysis.TestCalcOMES.testTwenty) ... ok
> testTwentyReversed (prody.tests.sequence.test_analysis.TestCalcOMES.testTwentyReversed) ... ok
> testZero (prody.tests.sequence.test_analysis.TestCalcOMES.testZero) ... ok
> testMATLAB (prody.tests.sequence.test_analysis.TestCalcSCA.testMATLAB) ... ok
> testZero (prody.tests.sequence.test_analysis.TestCalcSCA.testZero) ... ok
> testAmbiguous (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testAmbiguous) ... ok
> testGapDividend (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testGapDividend) ... ok
> testSixSequences (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testSixSequences) ... ok
> testSmallProbability (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testSmallProbability) ... ok
> testTwenty (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testTwenty) ... ok
> testMATLAB10 (prody.tests.sequence.test_analysis.TestDirectInfo.testMATLAB10) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/sequence/analysis.py:592: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
> c = matrix.dot(matrix(zeros((length*q, 1), float)),
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/sequence/analysis.py:593: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
> matrix(zeros((1, length*q), float)))
> /usr/lib/python3/dist-packages/numpy/matrixlib/defmatrix.py:69: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
> return matrix(data, dtype=dtype, copy=False)
> ok
> testMATLAB8 (prody.tests.sequence.test_analysis.TestDirectInfo.testMATLAB8) ... ok
> testTwenty (prody.tests.sequence.test_analysis.TestDirectInfo.testTwenty) ... ok
> testTwentyReversed (prody.tests.sequence.test_analysis.TestDirectInfo.testTwentyReversed) ... ok
> testZero (prody.tests.sequence.test_analysis.TestDirectInfo.testZero) ... ok
> testZero1 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero1) ... ok
> testZero2 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero2) ... ok
> testZero3 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero3) ... ok
> testZero4 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero4) ... ok
> testIdentityMatrix (prody.tests.sequence.test_analysis.TestIdentity.testIdentityMatrix) ... ok
> testIdentityMatrixNonTurbo (prody.tests.sequence.test_analysis.TestIdentity.testIdentityMatrixNonTurbo) ... ok
> testUnique (prody.tests.sequence.test_analysis.TestUnique.testUnique) ... ok
> testUnique2 (prody.tests.sequence.test_analysis.TestUnique.testUnique2) ... ok
> testMerge (prody.tests.sequence.test_msa.TestMerging.testMerge) ... ok
> testAddition (prody.tests.sequence.test_msa.TestRefinement.testAddition) ... ok
> testAll (prody.tests.sequence.test_msa.TestRefinement.testAll) ... ok
> testColocc (prody.tests.sequence.test_msa.TestRefinement.testColocc) ... ok
> testExtension (prody.tests.sequence.test_msa.TestRefinement.testExtension) ... ok
> testLabel (prody.tests.sequence.test_msa.TestRefinement.testLabel) ... ok
> testRowCol (prody.tests.sequence.test_msa.TestRefinement.testRowCol) ... ok
> testRowocc (prody.tests.sequence.test_msa.TestRefinement.testRowocc) ... ok
> testSeqid (prody.tests.sequence.test_msa.TestRefinement.testSeqid) ... ok
> testSeqidLabel (prody.tests.sequence.test_msa.TestRefinement.testSeqidLabel) ... ok
> testMSAFile (prody.tests.sequence.test_msafile.TestMSAFile.testMSAFile) ... ok
> testWriteFasta (prody.tests.sequence.test_msafile.TestMSAFile.testWriteFasta) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/sequence/sequence.py:32: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
> self._seq = fromstring(one, '|S1')
> ok
> testWriteSelex (prody.tests.sequence.test_msafile.TestMSAFile.testWriteSelex) ... ok
> testWriteStockholm (prody.tests.sequence.test_msafile.TestMSAFile.testWriteStockholm) ... ok
> testArray (prody.tests.sequence.test_msafile.TestParseMSA.testArray) ... ok
> testIterator (prody.tests.sequence.test_msafile.TestParseMSA.testIterator) ... ok
> testMapping (prody.tests.sequence.test_msafile.TestParseMSA.testMapping) ... ok
> testFasta (prody.tests.sequence.test_msafile.TestWriteMSA.testFasta) ... ok
> testSelex (prody.tests.sequence.test_msafile.TestWriteMSA.testSelex) ... ok
> testStringConversion (prody.tests.sequence.test_sequence.TestSequence.testStringConversion) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/sequence/sequence.py:36: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
> self._seq = fromstring(args[0], '|S1')
> ok
> testParseDCD (prody.tests.trajectory.test_dcdfile.TestDCDFile.testParseDCD) ... ok
> testWrite (prody.tests.trajectory.test_dcdfile.TestDCDFile.testWrite) ... ok
> testWriteDCD (prody.tests.trajectory.test_dcdfile.TestDCDFile.testWriteDCD) ... ok
> testWriteModeAppend (prody.tests.trajectory.test_dcdfile.TestDCDFile.testWriteModeAppend) ... ok
> testAll (prody.tests.trajectory.test_frame.TestSuperpose.testAll) ... ok
> testCarbon (prody.tests.trajectory.test_frame.TestSuperpose.testCarbon) ... ok
> testCoords (prody.tests.utilities.test_checkers.TestCheckCoords.testCoords) ... ok
> testCoordset (prody.tests.utilities.test_checkers.TestCheckCoords.testCoordset) ... ok
> testCoordsetNatoms (prody.tests.utilities.test_checkers.TestCheckCoords.testCoordsetNatoms) ... ok
> testInvalidCoords (prody.tests.utilities.test_checkers.TestCheckCoords.testInvalidCoords) ... ok
> testCorrectMonotypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testCorrectMonotypeOneArg) ... ok
> testCorrectMonotypeTwoArgs (prody.tests.utilities.test_checkers.testCheckTypes.testCorrectMonotypeTwoArgs) ... ok
> testCorrectMultitypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testCorrectMultitypeOneArg) ... ok
> testWrongMonotypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testWrongMonotypeOneArg) ... ok
> testWrongMonotypeTwoArgs (prody.tests.utilities.test_checkers.testCheckTypes.testWrongMonotypeTwoArgs) ... ok
> testWrongMultitypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testWrongMultitypeOneArg) ... ok
> testContinuous (prody.tests.utilities.test_misctools.TestRangeString.testContinuous) ... ok
> testGapped (prody.tests.utilities.test_misctools.TestRangeString.testGapped) ... ok
> testNegative (prody.tests.utilities.test_misctools.TestRangeString.testNegative) ... ok
> testRepeated (prody.tests.utilities.test_misctools.TestRangeString.testRepeated) ... ok
> testBuffer (prody.tests.utilities.test_pathtools.TestGunzip.testBuffer) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/utilities/test_pathtools.py:34: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/compressed.txt.gz'>
> buff = open(self.gzfn, 'rb').read()
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> ok
> testFile (prody.tests.utilities.test_pathtools.TestGunzip.testFile) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/utilities/test_pathtools.py:29: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/compressed.txt' mode='r' encoding='UTF-8'>
> text = open(fn).read()
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> ok
>
> ======================================================================
> FAIL: testFunctionSelection13 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection13)
> Test function selections 'abs(x) == sqrt(sq(x))' for pdb3mht
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic/test_select.py", line 442, in func
> self.assertEqual(len(sel), natoms,
> AssertionError: 3205 != 3211 : selection 'abs(x) == sqrt(sq(x))' for AtomGroup 3mht failed, expected 3211, selected 3205
>
> ======================================================================
> FAIL: testFunctionSelection14 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection14)
> Test function selections "abs(x) == sqrt(sq(x))"
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic/test_select.py", line 483, in func
> self.assertEqual(len(sel), natoms,
> AssertionError: 3205 != 3211 : selection 'abs(x) == sqrt(sq(x))' for Selection 'all' failed, expected 3211, selected 3205
>
> ----------------------------------------------------------------------
> Ran 954 tests in 50.511s
>
> FAILED (failures=2, skipped=37)
> E: pybuild pybuild:388: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build; python3.11 -m unittest discover -v
> dh_auto_test: error: pybuild --test -i python{version} -p 3.11 returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2023/02/03/prody_2.3.1+dfsg-3_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20230203;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230203&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
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