OEChem -- Python Theory Manual

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24 Chapter 5. Properties of MoleculesIf you wish to store a numeric value, use <strong>Python</strong>’s “str()” method to convert it to a string and then use “int()” or“float()” on the value when retrieving the data.The following functions provide access to the PDB data.Storing PDB Data on a MoleculeUse OESetPDBData to set a tag and value data pair. Both tag and value must be strings. If an item with the sametag already exists, it is replaced. The second form is the same as the first but uses an OESDDataPair instance.OESetPDBData ( mol , tag , value )OESetPDBData ( mol , dp )Use OEAddPDBData to add a tag and value data pair. Both tag and value must be strings. If an item with the sametag already exists, another one is added. The second form is the same as the first but uses an OESDDataPairinstance.Note that for PDB header items like REMARK, each line is treated as a separate instance, so to add multipleREMARK lines be sure to use this form instead of OESetPDBData.OEAddPDBData ( mol , tag , value )OEAddPDBData ( mol , dp )Retrieving PDB Data from a MoleculeTo determine if a molecule has an item with tag:OEHasPDBData ( mol , tag )Use OEGetPDBData to get the value for the given tag. If the molecule does not have that tag, an empty string isreturned. Note that if there are multiple parts with the same tag, this will only return the first instance. Using theiterator access show below will allow retrieving multiple tags.OEGetPDBData ( mol , tag )To get access to all PDB data, an iterator of OEBPDBDataPair can be used.OEGetPDBDataPairs ( mol )Copying PDB DataTo copy the entire set of PDB data from a source (src) molecule to a destination (dst) molecule, useOECopyPDBData.OECopyPDBData ( dest , src )Deleting PDB Data from a MoleculeUse OEDeletePDBData to delete a tagged data item. All data items with the specified tag will be deleted.OEDeletePDBData ( mol , tag )To clear all PDB data from a molecule, use OEClearPDBData.OEClearPDBData ( mol )
5.4. Manipulation of Tagged Data 255.4.3 Multi-conformer moleculesFor using tag data with multi-conformer molecules, see ‘Dude, where’s my SD Data?’ on page 31.
Page 1 and 2: OEChem - Python Theory Manualversio
Page 3 and 4: CONTENTS1 Python 11.1 A Bit About L
Page 5 and 6: 15.1 Atom Stereochemistry . . . . .
Page 8: 230.1 Normalization . . . . . . . .
Page 11 and 12: 1.4. Installing Python from Source
Page 13 and 14: 2.3. Getting Started with OEChem Mo
Page 15 and 16: CHAPTERTHREEManipulating Molecules3
Page 17 and 18: 3.4. Generating a SMILES from a Mol
Page 19 and 20: CHAPTERFOURReading and Writing Mole
Page 21 and 22: 4.3. Molecular File Formats 13Note
Page 24 and 25: 16 Chapter 4. Reading and Writing M
Page 26 and 27: CHAPTERFIVEProperties of Molecules5
Page 28 and 29: 20 Chapter 5. Properties of Molecul
Page 30 and 31: 22 Chapter 5. Properties of Molecul
Page 34 and 35: CHAPTERSIXOEMols and OEGraphMols6.1
Page 36 and 37: 28 Chapter 6. OEMols and OEGraphMol
Page 42 and 43: 34 Chapter 7. Traversing the Atoms
Page 44 and 45: 36 Chapter 7. Traversing the Atoms
Page 46 and 47: CHAPTEREIGHTProperties of Atoms8.1
Page 48 and 49: 40 Chapter 8. Properties of Atoms8.
Page 50 and 51: 42 Chapter 8. Properties of Atoms8.
Page 52 and 53: CHAPTERNINEProperties of Bonds9.1 S
Page 54 and 55: CHAPTERTENAtom, Bond and Conformer
Page 56 and 57: 48 Chapter 11. Creating Atoms, Bond
Page 58 and 59: 50 Chapter 11. Creating Atoms, Bond
Page 60 and 61: CHAPTERTWELVEConnectivity Processin
Page 62 and 63: CHAPTERTHIRTEENRing Processing13.1
Page 64 and 65: 56 Chapter 13. Ring Processing13.6
Page 66 and 67: CHAPTERFOURTEENAromaticity Processi
Page 68 and 69: 60 Chapter 15. Stereochemistry Proc
Page 70 and 71: 62 Chapter 16. Atom and Bond Typing
Page 72 and 73: 64 Chapter 16. Atom and Bond Typing
Page 74 and 75: 66 Chapter 17. Formal and Partial C
Page 76 and 77: CHAPTEREIGHTEENPattern MatchingOECh
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74 Chapter 18. Pattern MatchingScor
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76 Chapter 18. Pattern MatchingFigu
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82 Chapter 19. Coordinate HandlingI
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84 Chapter 19. Coordinate Handling1
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86 Chapter 19. Coordinate HandlingO
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88 Chapter 20. Logging and Error Ha
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90 Chapter 21. Periodic Table Funct
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CHAPTERTWENTYTWOPredicate Functions
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94 Chapter 22. Predicate Functions2
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CHAPTERTWENTYTHREEMolecular File Fo
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98 Chapter 23. Molecular File Forma
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100 Chapter 23. Molecular File Form
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102 Chapter 24. Miscellaneous Utili
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104 Chapter 25. The SMILES Line Not
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106 Chapter 26. Biopolymer Residues
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CHAPTERTWENTYSEVENValence ModelsThi
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114 Chapter 27. Valence ModelsNitro
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CHAPTERTWENTYEIGHTSMARTS Pattern Ma
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118 Chapter 29. SMARTS Pattern Matc
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120 Chapter 30. Reactionsethanediam
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122 Chapter 30. Reactions1 #!/usr/b
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CHAPTERTHIRTYONELicense handlingWit
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126 Chapter 32. OEChem Class Hierar
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CHAPTERTHIRTYTHREEBibliography1. Sh
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CHAPTERTHIRTYFOURRelease Notes34.1
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132 Chapter 34. Release Notes2. The
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134 Chapter 34. Release Notes6. Mem
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136 Chapter 34. Release Notes34.2.3
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INDEXAAddContraint, 71API, 26, 27,
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