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moved hybrid methods back to dynamics
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jamesmkrieger committed Feb 18, 2021
1 parent ff2fd5e commit 7ca495d
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Showing 6 changed files with 30 additions and 46 deletions.
5 changes: 0 additions & 5 deletions prody/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -115,11 +115,6 @@ def turnonDepracationWarnings(action='always'):
__all__.extend(dynamics.__all__)
__all__.append('dynamics')

from . import hybrid
from .hybrid import *
__all__.extend(hybrid.__all__)
__all__.append('hybrid')

from . import ensemble
from .ensemble import *
__all__.extend(ensemble.__all__)
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17 changes: 17 additions & 0 deletions prody/dynamics/__init__.py
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Expand Up @@ -339,8 +339,25 @@
from .signature import *
__all__.extend(signature.__all__)

from . import adaptive
from .adaptive import *
__all__.extend(adaptive.__all__)

from . import hybrid
from .hybrid import *
__all__.extend(hybrid.__all__)

from . import clustenm
from .clustenm import *
__all__.extend(clustenm.__all__)

from . import essa
from .essa import *
__all__.extend(essa.__all__)


# workaround for circular dependency to accommodate original design style
from prody.ensemble import functions
functions.Hybrid = Hybrid
functions.ClustENM = ClustENM
functions.AdaptiveHybrid = AdaptiveHybrid
6 changes: 3 additions & 3 deletions prody/hybrid/adaptive.py → prody/dynamics/adaptive.py
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Expand Up @@ -26,9 +26,9 @@
from prody.ensemble.ensemble import Ensemble
from prody.proteins.pdbfile import writePDBStream, parsePDBStream

from prody.dynamics.functions import calcENM
from prody.dynamics.modeset import ModeSet
from prody.dynamics.nma import NMA
from .functions import calcENM
from .modeset import ModeSet
from .nma import NMA

from .hybrid import Hybrid

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14 changes: 7 additions & 7 deletions prody/hybrid/clustenm.py → prody/dynamics/clustenm.py
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Expand Up @@ -36,13 +36,13 @@
from scipy.cluster.hierarchy import fcluster, linkage

from prody import LOGGER
from prody.dynamics.anm import ANM
from prody.dynamics.gnm import GNM, ZERO
from prody.dynamics.rtb import RTB
from prody.dynamics.imanm import imANM
from prody.dynamics.exanm import exANM
from prody.dynamics.editing import extendModel
from prody.dynamics.sampling import sampleModes
from .anm import ANM
from .gnm import GNM, ZERO
from .rtb import RTB
from .imanm import imANM
from .exanm import exANM
from .editing import extendModel
from .sampling import sampleModes

from prody.measure.transform import calcTransformation, applyTransformation, calcRMSD
from prody.proteins.pdbfile import writePDB, writePDBStream, parsePDBStream
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6 changes: 3 additions & 3 deletions prody/hybrid/hybrid.py → prody/dynamics/hybrid.py
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Expand Up @@ -37,9 +37,9 @@

from prody import LOGGER

from prody.dynamics.anm import ANM
from prody.dynamics.gnm import GNM, ZERO
from prody.dynamics.editing import extendModel
from .anm import ANM
from .gnm import GNM, ZERO
from .editing import extendModel

from prody.measure.transform import calcTransformation, applyTransformation, calcRMSD
from prody.ensemble.ensemble import Ensemble
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28 changes: 0 additions & 28 deletions prody/hybrid/__init__.py

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