#include <rule_based_builder.hh>
Inherits Builder.
Additional Inherited Members | |
 Static Public Member Functions inherited from Builder | |
| static String | GuessAtomElement (const String &atom_name, bool hetatm) |
| static bool | AreResiduesConsecutive (const mol::ResidueHandle &r1, const mol::ResidueHandle &r2) |
Detailed Description
Use library of chemical compounds to derive bonds and clean-up structural problems.
- Todo:
- Sorting of the residues directly uses impl layer of the base module. Would be much nicer if the order could be assigned in the public interface and then tell the residues to sort the atoms in ascending order.
Definition at line 40 of file rule_based_builder.hh.
Constructor & Destructor Documentation
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inline |
Definition at line 42 of file rule_based_builder.hh.
Member Function Documentation
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virtual |
requires chemical types
Reimplemented from Builder.
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assign named torsions to single residue
Reimplemented from Builder.
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Check residue completeness.
By using the description of the chemical compound, the completeness of the residue is verified. The method distinguishes between required atoms and atoms that are optional, like OXT that is only present, if not peptide bond is formed. Whenever an unknown atom is encountered, OnUnknownAtom() is invoked. Subclasses of the RuleBasedBuilder may implement some additional logic to deal with unknown atom. Likewise, whenever a required atom is missing, OnMissingAtom() is invoked. Hydrogen atoms are not considered as required by default
Reimplemented from Builder.
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add any missing atoms to the residue based on its key, with coordinates set to zero
Reimplemented from Builder.
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connect atoms of one residue
Connects atoms of residue based on residue and atom name. This method does not establish inter-residue bonds. To connect atoms that belong to different residues, use ConnectResidueToPrev(), or ConnectResidueToNext().
Reimplemented from Builder.
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virtual |
Connects the two residues together.
Connections are established if both of the residues are peptide-linking components and when PeptideBondExists() returns true.
- Parameters:
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rh is the N-terminal partner donating the C and O for the peptide bond. next is the C-terminal partner, donating the nitrogen to the bond.
Reimplemented from Builder.
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fill atom properties such as element and radius
Reimplemented from Builder.
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Fill in missing information based on atom name.
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Set residue properties such as chemical class.
Reimplemented from Builder.
| bool HasUnknownAtoms | ( | mol::ResidueHandle | res | ) |
whether the residue has unknown atoms
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Identify residue by name.
Looks-up the residue in the database of chemical compounds and returns the name of the residue or "UNK" if the residue has not been found in the library.
Reimplemented from Builder.
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Check whether the residue has all required atoms. This does not include hydrogens and leaving atoms such as the terminal OXT.
Reimplemented from Builder.
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Invoked whenever an atom is missing.
It is up to the overloaded method to deal with the missing atom, either by ignoring it or by inserting a dummy atom.
Definition at line 110 of file rule_based_builder.hh.
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Invoked whenever an unkknown atom has been encountered during a residue completeness check.
The default implementation guesses the atom properties based on the name and returns false, meaning that it should be treated as an unknown atom.
Custom implementations of this method may delete the atom, or modify it.
- Todo:
- what should be done when the atom name is changed? it would be neccessary to rerun CheckResidueCompleteness().
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inlinevirtual |
Reimplemented from Builder.
Definition at line 46 of file rule_based_builder.hh.
The documentation for this class was generated from the following file:
- stage/include/ost/conop/rule_based_builder.hh
