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Chemical Data Processing Library Python API - Version 1.4.0
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Chemical Data Processing Library Python API - Version 1.4.0
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Provides keys for built-in control-parameters. More...
Inheritance diagram for CDPL.Biomol.ControlParameter:Static Public Attributes | |
| STRICT_ERROR_CHECKING = CDPL.Base.LookupKey('STRICT_ERROR_CHECKING') | |
| Specifies whether non-fatal recoverable I/O errors should be ignored or cause an I/O operation to fail. More... | |
| CHECK_LINE_LENGTH = CDPL.Base.LookupKey('CHECK_LINE_LENGTH') | |
| Specifies whether to check if data lines exceed the maximum allowed line length when reading or writing data in PDB [PDB] format. More... | |
| RESIDUE_DICTIONARY = CDPL.Base.LookupKey('RESIDUE_DICTIONARY') | |
| Specifies the residue dictionary consulted during PDB and mmCIF I/O when looking up canonical residue atom names, bonding, atom types, or formal charges. More... | |
| APPLY_DICT_FORMAL_CHARGES = CDPL.Base.LookupKey('APPLY_DICT_FORMAL_CHARGES') | |
| Specifies whether to apply the formal atom charges provided by the residue dictionary during input data postprocessing. More... | |
| APPLY_DICT_ATOM_TYPES = CDPL.Base.LookupKey('APPLY_DICT_ATOM_TYPES') | |
| Specifies whether to apply the atom types provided by the residue dictionary during input data postprocessing. More... | |
| CALC_MISSING_FORMAL_CHARGES = CDPL.Base.LookupKey('CALC_MISSING_FORMAL_CHARGES') | |
| Specifies whether to calculate formal atomic charges for atoms whose charge could not be obtained from the input data or the residue dictionary. More... | |
| PERCEIVE_MISSING_BOND_ORDERS = CDPL.Base.LookupKey('PERCEIVE_MISSING_BOND_ORDERS') | |
| Specifies whether to perceive bond orders for bonds whose order could not be obtained from the input data or the residue dictionary. More... | |
| COMBINE_INTERFERING_RESIDUE_COORDINATES = CDPL.Base.LookupKey('COMBINE_INTERFERING_RESIDUE_COORDINATES') | |
| Specifies whether to merge alternative residue conformers whose atoms overlap in space (see Biomol.combineInterferingResidueCoordinates()). More... | |
| PDB_APPLY_DICT_ATOM_BONDING_TO_NON_STD_RESIDUES = CDPL.Base.LookupKey('PDB_APPLY_DICT_ATOM_BONDING_TO_NON_STD_RESIDUES') | |
| Specifies whether to use the residue dictionary to derive atom-bonding for atoms of non-standard residues when reading PDB data. More... | |
| PDB_APPLY_DICT_ATOM_BONDING_TO_STD_RESIDUES = CDPL.Base.LookupKey('PDB_APPLY_DICT_ATOM_BONDING_TO_STD_RESIDUES') | |
| Specifies whether to use the residue dictionary to derive atom-bonding for atoms of standard residues when reading PDB data. More... | |
| PDB_APPLY_DICT_BOND_ORDERS_TO_NON_STD_RESIDUES = CDPL.Base.LookupKey('PDB_APPLY_DICT_BOND_ORDERS_TO_NON_STD_RESIDUES') | |
| Specifies whether to apply the residue dictionary bond orders to bonds of non-standard residues when reading PDB data. More... | |
| PDB_IGNORE_CONECT_RECORDS = CDPL.Base.LookupKey('PDB_IGNORE_CONECT_RECORDS') | |
Specifies whether to skip CONECT records when reading PDB data. More... | |
| PDB_DEDUCE_BOND_ORDERS_FROM_CONECT_RECORDS = CDPL.Base.LookupKey('PDB_DEDUCE_BOND_ORDERS_FROM_CONECT_RECORDS') | |
Specifies whether to deduce bond orders from the duplication pattern of bonded atom pairs in CONECT records when reading PDB data. More... | |
| PDB_IGNORE_FORMAL_CHARGE_FIELD = CDPL.Base.LookupKey('PDB_IGNORE_FORMAL_CHARGE_FIELD') | |
Specifies whether to ignore the formal charge field of ATOM/HETATM records when reading PDB data. More... | |
| PDB_EVALUATE_MASTER_RECORD = CDPL.Base.LookupKey('PDB_EVALUATE_MASTER_RECORD') | |
Specifies whether to verify the record counts in the PDB MASTER record against the actual numbers observed during input. More... | |
| PDB_TRUNCATE_LINES = CDPL.Base.LookupKey('PDB_TRUNCATE_LINES') | |
| Specifies whether to truncate output PDB data lines that exceed the maximum allowed line length instead of failing the write operation. More... | |
| PDB_WRITE_FORMAL_CHARGES = CDPL.Base.LookupKey('PDB_OUTPUT_FORMAL_CHARGES') | |
| PDB_OUTPUT_CONECT_RECORDS = CDPL.Base.LookupKey('PDB_OUTPUT_CONECT_RECORDS') | |
Specifies whether to write CONECT records when generating PDB output. More... | |
| PDB_OUTPUT_CONECT_RECORDS_FOR_ALL_BONDS = CDPL.Base.LookupKey('PDB_OUTPUT_CONECT_RECORDS_FOR_ALL_BONDS') | |
Specifies whether CONECT records shall be written for all bonds (and not only for non-standard ones) when generating PDB output. More... | |
| PDB_OUTPUT_CONECT_RECORDS_REFLECTING_BOND_ORDER = CDPL.Base.LookupKey('PDB_OUTPUT_CONECT_RECORDS_REFLECTING_BOND_ORDER') | |
Specifies whether CONECT records shall encode the bond order via the duplication count of bonded atom pairs when generating PDB output. More... | |
| PDB_FORMAT_VERSION = CDPL.Base.LookupKey('PDB_FORMAT_VERSION') | |
| Specifies the PDB format version to use when generating PDB output (see Biomol.PDBFormatVersion). More... | |
| MMCIF_APPLY_DICT_ATOM_BONDING = CDPL.Base.LookupKey('MMCIF_APPLY_DICT_ATOM_BONDING') | |
| Specifies whether to use the residue dictionary to derive atom-bonding when reading mmCIF data. More... | |
| MMCIF_APPLY_DICT_BOND_ORDERS = CDPL.Base.LookupKey('MMCIF_APPLY_DICT_BOND_ORDERS') | |
| Specifies whether to apply the residue dictionary bond orders when reading mmCIF data. More... | |
| MMCIF_OUTPUT_BIOPOLYMERS_AS_CHEM_COMP = CDPL.Base.LookupKey('MMCIF_OUTPUT_BIOPOLYMERS_AS_CHEM_COMP') | |
Specifies whether or not residue structures shall be emitted as chem_comp category data when generating mmCIF output. More... | |
| MMCIF_OUTPUT_DATA_POSTPROC_FUNCTION = CDPL.Base.LookupKey('MMCIF_OUTPUT_DATA_POSTPROC_FUNCTION') | |
| Specifies a postprocessing function that is applied to the constructed mmCIF data record before it is written to the output stream. More... | |
Provides keys for built-in control-parameters.
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Specifies whether non-fatal recoverable I/O errors should be ignored or cause an I/O operation to fail.
If the control-parameter is set to True, not only severe errors cause an I/O operation to fail, but also non-fatal errors from which a recovery would be possible. If the control-parameter is set to False, I/O operations will proceed even if a non-fatal error has been detected.
Value Type: bool
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Specifies whether to check if data lines exceed the maximum allowed line length when reading or writing data in PDB [PDB] format.
If the control-parameter is set to True, the length of data lines that were read from or have to be written to data encoded in one of the above mentioned formats will be checked against the maximum allowed line length. Lines that exceeded the line length limit are considered as an error condition and cause the input or output operation to fail. If CHECK_LINE_LENGTH is False, the length of data lines will not be checked and has no impact on the success of the performed I/O operation.
Value Type: bool
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Specifies the residue dictionary consulted during PDB and mmCIF I/O when looking up canonical residue atom names, bonding, atom types, or formal charges.
Value Type: Biomol.ResidueDictionary.SharedPointer
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Specifies whether to apply the formal atom charges provided by the residue dictionary during input data postprocessing.
Value Type: bool
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Specifies whether to apply the atom types provided by the residue dictionary during input data postprocessing.
Value Type: bool
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Specifies whether to calculate formal atomic charges for atoms whose charge could not be obtained from the input data or the residue dictionary.
Value Type: bool
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Specifies whether to perceive bond orders for bonds whose order could not be obtained from the input data or the residue dictionary.
Value Type: bool
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Specifies whether to merge alternative residue conformers whose atoms overlap in space (see Biomol.combineInterferingResidueCoordinates()).
Value Type: bool
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Specifies whether to use the residue dictionary to derive atom-bonding for atoms of non-standard residues when reading PDB data.
Value Type: bool
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Specifies whether to use the residue dictionary to derive atom-bonding for atoms of standard residues when reading PDB data.
Value Type: bool
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Specifies whether to apply the residue dictionary bond orders to bonds of non-standard residues when reading PDB data.
Value Type: bool
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Specifies whether to skip CONECT records when reading PDB data.
Value Type: bool
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Specifies whether to deduce bond orders from the duplication pattern of bonded atom pairs in CONECT records when reading PDB data.
Value Type: bool
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Specifies whether to ignore the formal charge field of ATOM/HETATM records when reading PDB data.
Value Type: bool
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Specifies whether to verify the record counts in the PDB MASTER record against the actual numbers observed during input.
Value Type: bool
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Specifies whether to truncate output PDB data lines that exceed the maximum allowed line length instead of failing the write operation.
Value Type: bool
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Specifies whether to write CONECT records when generating PDB output.
Value Type: bool
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Specifies whether CONECT records shall be written for all bonds (and not only for non-standard ones) when generating PDB output.
Value Type: bool
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Specifies whether CONECT records shall encode the bond order via the duplication count of bonded atom pairs when generating PDB output.
Value Type: bool
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Specifies the PDB format version to use when generating PDB output (see Biomol.PDBFormatVersion).
Value Type: unsigned int
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Specifies whether to use the residue dictionary to derive atom-bonding when reading mmCIF data.
Value Type: bool
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Specifies whether to apply the residue dictionary bond orders when reading mmCIF data.
Value Type: bool
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Specifies whether or not residue structures shall be emitted as chem_comp category data when generating mmCIF output.
Value Type: bool
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Specifies a postprocessing function that is applied to the constructed mmCIF data record before it is written to the output stream.
Value Type: Biomol.MMCIFDataProcessingFunction
1.9.1