From 72428138ea28cad225515231b6df9a6807eb9ea7 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed, 22 Nov 2023 09:50:57 +0100
Subject: [PATCH] document internal processor functions
---
modules/conop/src/processor.cc | 13 +++++++++++--
1 file changed, 11 insertions(+), 2 deletions(-)
diff --git a/modules/conop/src/processor.cc b/modules/conop/src/processor.cc
index e3206b0b4..39b393381 100644
--- a/modules/conop/src/processor.cc
+++ b/modules/conop/src/processor.cc
@@ -259,7 +259,10 @@ void Processor::ConnectResidues(mol::ResidueHandle rh,
}
}
-
+/// \brief Return the AtomHandle corresponding to AtomSpecList[ordinal]
+/// This function assumes that the State of the AtomImpl has been set to the
+/// index on the AtomSpec of the compound (see ReorderAtoms).
+/// Returns an Invalid AtomHandle if the atom is not present.
mol::AtomHandle Processor::LocateAtom(const mol::AtomHandleList& ahl,
int ordinal) const
{
@@ -318,7 +321,13 @@ void Processor::ConnectAtomsOfResidue(mol::ResidueHandle rh,
}
}
-
+/// \brief Reorder atoms to follow the order in the compound AtomSpecs
+///
+/// This function reorders atoms so that atom names appear in the same order as
+/// the atoms in the compound's AtomSpec. Unknown atoms (ie atoms not in the
+/// compound) are sorted to the back.
+/// Side effect: sets the State on the AtomImpl to the index of the Atom
+/// on the AtomSpecs list.
void Processor::ReorderAtoms(mol::ResidueHandle residue,
CompoundPtr compound,
bool fix_element) const
--
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