From c0a4dd1dde9ca09787823bc06c7efd6fda643758 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 10 May 2022 15:39:40 +0200
Subject: [PATCH] enable nucleotide as query prop =>
prot.Select("nucleotide=true")
---
modules/mol/base/doc/query.rst | 3 +++
modules/mol/base/src/property_id.cc | 5 ++++-
modules/mol/base/src/property_id.hh | 6 +++---
modules/mol/base/src/query_state.cc | 4 ++++
4 files changed, 14 insertions(+), 4 deletions(-)
diff --git a/modules/mol/base/doc/query.rst b/modules/mol/base/doc/query.rst
index 16e9a3a02..99c2392fe 100644
--- a/modules/mol/base/doc/query.rst
+++ b/modules/mol/base/doc/query.rst
@@ -219,6 +219,9 @@ This index is the same for views and handles.
**peptide** (bool): Whether the residue is :attr:`peptide linking
<ResidueHandle.peptide_linking>`.
+**nucleotide** (bool): Whether the residue is :attr:`nucleotide linking
+<ResidueHandle.nucleotide_linking>`.
+
**protein** (bool): Whether the residue is considered to be
:attr:`part of a connected protein <ResidueHandle.is_protein>`.
diff --git a/modules/mol/base/src/property_id.cc b/modules/mol/base/src/property_id.cc
index 467227294..ad2f90333 100644
--- a/modules/mol/base/src/property_id.cc
+++ b/modules/mol/base/src/property_id.cc
@@ -50,6 +50,7 @@ struct Properties : public boost::spirit::symbols<Prop> {
("abfac", Prop(Prop::ABFAC, Prop::FLOAT, Prop::ATOM))
("rbfac", Prop(Prop::RBFAC, Prop::FLOAT, Prop::RESIDUE))
("peptide", Prop(Prop::PEPTIDE, Prop::INT, Prop::RESIDUE))
+ ("nucleotide", Prop(Prop::NUCLEOTIDE, Prop::INT, Prop::RESIDUE))
("rindex", Prop(Prop::RINDEX, Prop::INT, Prop::RESIDUE))
("protein", Prop(Prop::PROTEIN, Prop::INT, Prop::RESIDUE))
("ligand", Prop(Prop::LIGAND, Prop::INT, Prop::RESIDUE))
@@ -111,7 +112,9 @@ String Prop::GetName() const
case ABFAC:
return "abfac";
case PEPTIDE:
- return "peptide";
+ return "peptide";
+ case NUCLEOTIDE:
+ return "nucleotide";
case ACHARGE:
return "acharge";
case RINDEX:
diff --git a/modules/mol/base/src/property_id.hh b/modules/mol/base/src/property_id.hh
index 7fec20853..a3b24ac42 100644
--- a/modules/mol/base/src/property_id.hh
+++ b/modules/mol/base/src/property_id.hh
@@ -39,9 +39,9 @@ public:
/// the GenericProp 'propname' at the atom, residue and chain level
/// respectively.
typedef enum {
- RNAME, ANAME, CNAME, ELE, RNUM, ANUM, AX, AY, AZ, OCC, AINDEX, RTYPE, ISHETATM,
- RBFAC, ABFAC, PEPTIDE, ACHARGE, RINDEX, PROTEIN, LIGAND, WATER, WITHIN,
- UNDEF, CUSTOM
+ RNAME, ANAME, CNAME, ELE, RNUM, ANUM, AX, AY, AZ, OCC, AINDEX, RTYPE,
+ ISHETATM, RBFAC, ABFAC, PEPTIDE, NUCLEOTIDE, ACHARGE, RINDEX, PROTEIN,
+ LIGAND, WATER, WITHIN, UNDEF, CUSTOM
} ID;
typedef enum {
diff --git a/modules/mol/base/src/query_state.cc b/modules/mol/base/src/query_state.cc
index 2b18845d3..40e09a53d 100644
--- a/modules/mol/base/src/query_state.cc
+++ b/modules/mol/base/src/query_state.cc
@@ -204,6 +204,10 @@ boost::logic::tribool QueryState::EvalResidue(const ResidueImplPtr& r) {
case Prop::PEPTIDE:
int_value=r->GetChemClass().IsPeptideLinking();
s_[*i] = cmp_num<int>(ss.comp_op,int_value,boost::get<int>(ss.param));
+ break;
+ case Prop::NUCLEOTIDE:
+ int_value=r->GetChemClass().IsNucleotideLinking();
+ s_[*i] = cmp_num<int>(ss.comp_op,int_value,boost::get<int>(ss.param));
break;
case Prop::RBFAC:
// This is ugly! Outcome is the same for a prefiltered view as it is for
--
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