gemmi-protools 0.1.6__py3-none-any.whl → 0.1.7__py3-none-any.whl
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- gemmi_protools/utils/fixer.py +15 -1
- {gemmi_protools-0.1.6.dist-info → gemmi_protools-0.1.7.dist-info}/METADATA +1 -1
- {gemmi_protools-0.1.6.dist-info → gemmi_protools-0.1.7.dist-info}/RECORD +6 -6
- {gemmi_protools-0.1.6.dist-info → gemmi_protools-0.1.7.dist-info}/WHEEL +1 -1
- {gemmi_protools-0.1.6.dist-info → gemmi_protools-0.1.7.dist-info}/licenses/LICENSE +0 -0
- {gemmi_protools-0.1.6.dist-info → gemmi_protools-0.1.7.dist-info}/top_level.txt +0 -0
gemmi_protools/utils/fixer.py
CHANGED
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@@ -50,7 +50,9 @@ def clean_structure(input_file: Union[str, pathlib.Path],
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add_missing_atoms: str = "heavy",
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keep_heterogens: str = "all",
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replace_nonstandard: bool = True,
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-
ph: Union[float, int] = 7.0
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+
ph: Union[float, int] = 7.0,
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check_mode: bool = True,
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threshold: float = 0.3,
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):
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"""
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@@ -69,6 +71,9 @@ def clean_structure(input_file: Union[str, pathlib.Path],
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none: remove all heterogens
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:param replace_nonstandard: default True, replace all non-standard residues to standard ones
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:param ph: default 7.0, ph values to add missing hydrogen atoms
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+
:param check_mode: default True to check the ratio of residues with missing atoms
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:param threshold: float, default 0.3, only use when check_mode=True
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:return:
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str, status message of fixing
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if successful, return Finish, otherwise message of error
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@@ -82,6 +87,15 @@ def clean_structure(input_file: Union[str, pathlib.Path],
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######################################################
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fixer = _load_by_pbdfixer(input_file)
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######################################################
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# check
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######################################################
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fixer.findMissingResidues()
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fixer.findMissingAtoms()
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ratio = len(fixer.missingAtoms) / fixer.topology.getNumResidues()
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if ratio > threshold:
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return dict(input=input_file, msg="Too many residues with missing atoms: %.2f" % ratio)
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######################################################
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# replace non-standard residues
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######################################################
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@@ -11,10 +11,10 @@ gemmi_protools/io/struct_info.py,sha256=9nBj1Zer03S8_Wks7L7uRlc9PlbfCKzoaT32pKR5
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gemmi_protools/utils/__init__.py,sha256=F6e1xNT_7lZAWQgNIneH06o2qtWYrHNr_xPUPTwwx5E,29
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gemmi_protools/utils/align.py,sha256=CZcrvjy-ZbX2u7OAn-YGblbxaj9YFUDX4CFZcpbpnB8,6959
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gemmi_protools/utils/dockq.py,sha256=XmMwVEy-H4p6sH_HPcDWA3TP77OWdih0fE_BQJDr4pU,4189
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-
gemmi_protools/utils/fixer.py,sha256=
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+
gemmi_protools/utils/fixer.py,sha256=WUiIoK8dFPGUkXlK-wiiWyorYD8T71rN7WDE2psGSiE,9061
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gemmi_protools/utils/ppi.py,sha256=VWYsdxWwQoS1xwEYj5KB96Zz3F8r5Eyuw6NT3ReD-wc,2330
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gemmi_protools-0.1.
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gemmi_protools-0.1.
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gemmi_protools-0.1.
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gemmi_protools-0.1.
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-
gemmi_protools-0.1.
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gemmi_protools-0.1.7.dist-info/licenses/LICENSE,sha256=JuQvKcgj6n11y5y6nXr9rABv3gJSswc4eTCd5WZBtSY,1062
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gemmi_protools-0.1.7.dist-info/METADATA,sha256=tsp4fzE0T7lTsmPaRYK5UzgqS4OjrvOSfESFMqbkk0Y,567
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gemmi_protools-0.1.7.dist-info/WHEEL,sha256=zaaOINJESkSfm_4HQVc5ssNzHCPXhJm0kEUakpsEHaU,91
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gemmi_protools-0.1.7.dist-info/top_level.txt,sha256=P12mYJi5O5EKIn5u-RFaWxuix431CgLacSRD7rBid_U,15
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gemmi_protools-0.1.7.dist-info/RECORD,,
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File without changes
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File without changes
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