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Warnings

 

/home/jesus/devel/php/pear/Science/Chemistry/PDBFile.php

1 Warning(s).
 
[class] Science_Chemistry_PDBFile mismatch
PHPDoc found 1 syntax error(s) in the tag list. Tag: '@see Science_Chemistry_PDBParser' - Could not understand all references. Use function() to referr to functions and to referr to variables - don't know what 'Science_Chemistry_PDBParser' referrs to.. Syntax: '([^\s]+(?:::))?([^:][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*\(\s*\))' (function), '([^\s]+(?:::))?([$][^:][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*)' (variable), '([^\s]+)' (module or class)..
 
 

/home/jesus/devel/php/pear/Science/Chemistry/PDBParser.php

2 Warning(s).
 
[class] Science_Chemistry_PDBParser mismatch
PHPDoc found 1 syntax error(s) in the tag list. Tag: '@see Science_Chemistry_PDBFile' - Could not understand all references. Use function() to referr to functions and to referr to variables - don't know what 'Science_Chemistry_PDBFile' referrs to.. Syntax: '([^\s]+(?:::))?([^:][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*\(\s*\))' (function), '([^\s]+(?:::))?([$][^:][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*)' (variable), '([^\s]+)' (module or class)..
 
[variable] $date mismatch
PHPDoc found 1 syntax error(s) in the tag list. Tag: '@var date' - General syntax error, syntax: '@var (object objectname|type) [$varname]'./(string|integer|int|long|real|double|float|boolean|bool|mixed|array|object)(?:\s+([a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*))?(?:\s+([&]?[$][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*))?\s*(.*)?/is.
 
 

/home/jesus/devel/php/pear/Science/Chemistry/Atom_PDB.php

4 Warning(s).
 
[functions] $valid mismatch
@see referrs to the function 'initAtom()' which is not defined in the class. Entry gets ignored.
 
[function] science_chemistry_atom_pdb missing
1st parameter '$atomrec' is not documented add '@param (object objectname|type) [description]' to the end of the @param[eter] list.
 
[function] science_chemistry_atom_pdb missing
2nd parameter '$residue' is not documented add '@param string [description]' to the end of the @param[eter] list.
 
[function] getfield missing
1st parameter '$field' is not documented add '@param (object objectname|type) [description]' to the end of the @param[eter] list.
 
 

/home/jesus/devel/php/pear/Science/Chemistry/Atom.php

2 Warning(s).
 
[function] science_chemistry_atom mismatch
2nd parameter type '$coords' does match the the documented type 'array', possible error consider an update to '@param string $coords array of coordinates (x, y, z)' or '@param string array of coordinates (x, y, z)', the variable name is optional.
 
[function] tocml mismatch
1st parameter type '$id' does match the the documented type 'string', possible error consider an update to '@param integer $id (description)' or '@param integer (description)', the variable name is optional.
 
 

/home/jesus/devel/php/pear/Science/Chemistry/Macromolecule_PDB.php

2 Warning(s).
 
[variables] science_chemistry_macromolecule_pdb mismatch
@see referrs to the variable '$pdb' which is not defined in the class. Entry gets ignored.
 
[function] science_chemistry_macromolecule_pdb mismatch
3th parameter type '$pdbfile' does match the the documented type 'object PDBFile', possible error consider an update to '@param string $pdbfile reference to the PDB file object' or '@param string reference to the PDB file object', the variable name is optional.
 
 

/home/jesus/devel/php/pear/Science/Chemistry/Macromolecule.php

5 Warning(s).
 
[function] science_chemistry_macromolecule mismatch
2nd parameter type '$molecules' does match the the documented type 'array', possible error consider an update to '@param string $molecules (description)' or '@param string (description)', the variable name is optional.
 
[function] tocml mismatch
1st parameter '$title' does not match the documented name '$id', update the tag to '@param string $title (description)' or '@param string (description)', the variable name is optional.
 
[function] tocml mismatch
2nd parameter type '$id' does match the the documented type 'boolean', possible error consider an update to '@param string $id (description)' or '@param string (description)', the variable name is optional.
 
[function] tocml mismatch
2nd parameter '$id' does not match the documented name '$connect', update the tag to '@param string $id (description)' or '@param string (description)', the variable name is optional.
 
[function] tocml missing
3th parameter '$connect' is not documented add '@param boolean [description]' to the end of the @param[eter] list.
 
 

/home/jesus/devel/php/pear/Science/Chemistry/Residue_PDB.php

2 Warning(s).
 
[function] science_chemistry_residue_pdb mismatch
3th parameter type '$macromol' does match the the documented type 'object Science_Chemistry_Macromolecule_PDB', possible error consider an update to '@param string $macromol reference to the containing macromolecule' or '@param string reference to the containing macromolecule', the variable name is optional.
 
[function] getgeomparams missing
1st parameter '$param' is not documented add '@param (object objectname|type) [description]' to the end of the @param[eter] list.
 
 

/home/jesus/devel/php/pear/Science/Chemistry/Molecule.php

5 Warning(s).
 
[function] science_chemistry_molecule mismatch
2nd parameter type '$atoms' does match the the documented type 'array', possible error consider an update to '@param string $atoms (description)' or '@param string (description)', the variable name is optional.
 
[function] tocml mismatch
1st parameter '$title' does not match the documented name '$id', update the tag to '@param string $title (description)' or '@param string (description)', the variable name is optional.
 
[function] tocml mismatch
2nd parameter type '$id' does match the the documented type 'boolean', possible error consider an update to '@param string $id (description)' or '@param string (description)', the variable name is optional.
 
[function] tocml mismatch
2nd parameter '$id' does not match the documented name '$connect', update the tag to '@param string $id (description)' or '@param string (description)', the variable name is optional.
 
[function] tocml missing
3th parameter '$connect' is not documented add '@param boolean [description]' to the end of the @param[eter] list.
 
 

/home/jesus/devel/php/pear/Science/Chemistry/PDBFile.php

2 Warning(s).
 
[functions] science_chemistry_pdbfile mismatch
@see referrs to the function 'mkArrays()' which is not defined in the class. Entry gets ignored.
 
[functions] parsefile mismatch
@see referrs to the function 'Science_Chemistry_Macromolecule_PDB()' which is not defined in the class. Entry gets ignored.
 
 

/home/jesus/devel/php/pear/Science/Chemistry/PDBParser.php

3 Warning(s).
 
[functions] parseresidues mismatch
@see referrs to the function 'parseFile()' which is not defined in the class. Entry gets ignored.
 
[function] parseatom missing
3th parameter '&$atomname' is not documented add '@param (object objectname|type) [description]' to the end of the @param[eter] list.
 
[function] getresiduelist mismatch
2nd parameter '$resname' does not match the documented name '$resnam', update the tag to '@param string $resname Residue name, e.g. HIS, CYS, etc.' or '@param string Residue name, e.g. HIS, CYS, etc.', the variable name is optional.
 

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