java.io.Serializable
public class FileParsingParameters
extends java.lang.Object
implements java.io.Serializable
setParseCAOnly(boolean)
- parse only the Atom records for C-alpha atomssetParseSecStruc(boolean)
- a flag if the secondary structure information from the PDB file (author's assignment) should be parsed.
If true the assignment can be accessed through AminoAcid
.getSecStruc(); setAlignSeqRes(boolean)
- should the AminoAcid sequences from the SEQRES
and ATOM records of a PDB file be aligned? (default:yes)setHeaderOnly(boolean)
- parse only the PDB/mmCIF file header, ignoring coordinates
setCreateAtomBonds(boolean)
- create atom bonds from parsed bonds in PDB/mmCIF files and chemical component files
Modifier and Type | Field | Description |
---|---|---|
static int |
ATOM_CA_THRESHOLD |
The maximum number of atoms that will be parsed before the parser switches to a CA-only
representation of the PDB file.
|
static int |
MAX_ATOMS |
The maximum number of atoms we will add to a structure,
this protects from memory overflows in the few really big protein structures.
|
Constructor | Description |
---|---|
FileParsingParameters() |
Modifier and Type | Method | Description |
---|---|---|
java.lang.String[] |
getAcceptedAtomNames() |
By default the parser will read in all atoms (unless using the CAonly switch).
|
int |
getAtomCaThreshold() |
The maximum number of atoms that will be parsed before the parser switches to a CA-only
representation of the PDB file.
|
int |
getMaxAtoms() |
The maximum numbers of atoms to load in a protein structure (prevents memory overflows)
|
boolean |
isAlignSeqRes() |
Flag if the SEQRES amino acids should be aligned with the ATOM amino acids.
|
boolean |
isHeaderOnly() |
Parse only the PDB file header out of the files
|
boolean |
isParseBioAssembly() |
Should the biological assembly info (REMARK 350) be parsed from the PDB file?
|
boolean |
isParseCAOnly() |
The flag if only the C-alpha atoms of the structure should be parsed.
|
boolean |
isParseSecStruc() |
Is secondary structure assignment being parsed from the file?
default is null
|
boolean |
isUpdateRemediatedFiles() |
Deprecated.
Properties which impact downloading and caching behavior
have been moved to the
StructureIOFile implementations.
See LocalPDBDirectory#getFetchBehavior(LocalPDBDirectory.FetchBehavior) |
boolean |
isUseInternalChainId() |
Should we use internal (asym_id) or public facing (author) chain ids
|
void |
setAcceptedAtomNames(java.lang.String[] fullAtomNames) |
By default the parser will read in all atoms (unless using the CAonly switch).
|
void |
setAlignSeqRes(boolean alignSeqRes) |
Define if the SEQRES in the structure should be aligned with the ATOM records
if yes, the AminoAcids in structure.getSeqRes will have the coordinates set.
|
void |
setAtomCaThreshold(int atomCaThreshold) |
The maximum number of atoms that will be parsed before the parser switches to a CA-only
representation of the PDB file.
|
void |
setCreateAtomBonds(boolean createAtomBonds) |
Should we create bonds between atoms when parsing a file.
|
void |
setCreateAtomCharges(boolean createAtomCharges) |
Should we create charges on atoms when parsing a file?
|
void |
setDefault() |
|
void |
setHeaderOnly(boolean headerOnly) |
Parse only the PDB file header out of the files
|
void |
setMaxAtoms(int maxAtoms) |
The maximum numbers of atoms to load in a protein structure (prevents memory overflows)
|
void |
setParseBioAssembly(boolean parseBioAssembly) |
Should the biological assembly info (REMARK 350) be parsed from the PDB file?
|
void |
setParseCAOnly(boolean parseCAOnly) |
Flag if only the C-alpha atoms of the structure should be parsed.
|
void |
setParseSecStruc(boolean parseSecStruc) |
A flag to tell the parser to parse the Author's secondary structure assignment from the file
default is set to false, i.e.
|
void |
setUpdateRemediatedFiles(boolean updateRemediatedFiles) |
Deprecated.
Properties which impact downloading and caching behavior
have been moved to the
StructureIOFile implementations.
See LocalPDBDirectory.setFetchBehavior(LocalPDBDirectory.FetchBehavior) |
void |
setUseInternalChainId(boolean useInternalChainId) |
Set the useInternalChainId parsing mode.
|
boolean |
shouldCreateAtomBonds() |
Should we create bonds between atoms when parsing a file?
|
boolean |
shouldCreateAtomCharges() |
Should we create charges on atoms when parsing a file?
|
public static final int ATOM_CA_THRESHOLD
public static final int MAX_ATOMS
public void setDefault()
public boolean isParseSecStruc()
public void setParseSecStruc(boolean parseSecStruc)
parseSecStruc
- if HELIX STRAND and TURN fields are being parsedpublic boolean isHeaderOnly()
public void setHeaderOnly(boolean headerOnly)
headerOnly
- flagpublic boolean isParseCAOnly()
public void setParseCAOnly(boolean parseCAOnly)
parseCAOnly
- boolean flag to enable or disable C-alpha only parsingpublic boolean isAlignSeqRes()
public void setAlignSeqRes(boolean alignSeqRes)
alignSeqRes
- @Deprecated public boolean isUpdateRemediatedFiles()
StructureIOFile
implementations.
See LocalPDBDirectory#getFetchBehavior(LocalPDBDirectory.FetchBehavior)
@Deprecated public void setUpdateRemediatedFiles(boolean updateRemediatedFiles)
StructureIOFile
implementations.
See LocalPDBDirectory.setFetchBehavior(LocalPDBDirectory.FetchBehavior)
updateRemediatedFiles
- public java.lang.String[] getAcceptedAtomNames()
public void setAcceptedAtomNames(java.lang.String[] fullAtomNames)
accepted
- atom names, or null if all atoms are accepted. default nullpublic int getMaxAtoms()
public void setMaxAtoms(int maxAtoms)
maxAtoms
- maximun nr of atoms to loadpublic int getAtomCaThreshold()
public void setAtomCaThreshold(int atomCaThreshold)
atomCaThreshold
- maximum number of atoms for all atom representation.public boolean isParseBioAssembly()
public void setParseBioAssembly(boolean parseBioAssembly)
parseBioAssembly
- boolean flag yes/nopublic boolean shouldCreateAtomBonds()
public void setCreateAtomBonds(boolean createAtomBonds)
createAtomBonds
- true if we should create the bonds, false if notBondMaker
public boolean shouldCreateAtomCharges()
public void setCreateAtomCharges(boolean createAtomCharges)
createAtomCharges
- true if we should create the charges, false if notpublic boolean isUseInternalChainId()
public void setUseInternalChainId(boolean useInternalChainId)
useInternalChainId
-