diff --git a/modules/img/alg/src/dft.hh b/modules/img/alg/src/dft.hh
index 32dcf022ea747211bf6a69b78e6b7cc2a239dc0c..9e8d8c6748fd0080dce445fff81db8a6abba8a62 100644
--- a/modules/img/alg/src/dft.hh
+++ b/modules/img/alg/src/dft.hh
@@ -30,7 +30,7 @@ namespace ost { namespace img { namespace alg {
/// \brief Computes Fourier Trasnform honoring the origin of the image
///
/// \sa \ref view_phase_diff.py "View Phase Diference Example"
-/// \sa \ref fft_li.py "View Fourier Transform Example"
+/// \sa \ref code_fragments/img/fft_li.py "View Fourier Transform Example"
class DLLEXPORT_IMG_ALG DFT: public ConstModOPAlgorithm {
public:
DFT();
diff --git a/modules/io/doc/io.dox b/modules/io/doc/io.dox
index e89777217a2d449f1c91edbf0e4c52946fc22609..3c864b38b7b8232f1d4314fa2a8529318b3efb9c 100644
--- a/modules/io/doc/io.dox
+++ b/modules/io/doc/io.dox
@@ -6,7 +6,7 @@ namespace ost { namespace io {
The io module deals with input and output of \ref mol::EntityHandle "entities",
\ref seq::AlignmentHandle "multiple sequence alignments" and
-\ref iplt::ImageHandle "map data". Importers for common file formats such as PDB,
+\ref ost::img::ImageHandle "map data". Importers for common file formats such as PDB,
SDF, FASTA, CLUSTAL W, DX and the CHARMM files are available.
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 85751e6970310949aafbea427ca97733f4934e8f..58b592b01fe12438b2f4d8e3b5ee603a612ac615 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -210,7 +210,7 @@ except ImportError:
pass
## loads several images and puts them in an ImageList
- # \sa \ref fft_li.py "View Fourier Transform Example"
+ # \sa \ref code_fragments/img/fft_li.py "View Fourier Transform Example"
def LoadImageList (files):
image_list=img.ImageList()
for file in files:
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index 593fed6f2b70e25c777454bd3e8d95db8554ef56..832bfdc7684e2b1a6557a842739950af501767df 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -180,7 +180,9 @@ public:
/// \brief Set the translational vector
///
- /// \param
+ /// \param x
+ /// \param y
+ /// \param z
void SetVector(Real x, Real y, Real z)
{
translation_.SetX(x);
@@ -194,7 +196,15 @@ public:
/// \brief Set the rotational matrix
///
- /// \param
+ /// \param i00
+ /// \param i01
+ /// \param i02
+ /// \param i10
+ /// \param i11
+ /// \param i12
+ /// \param i20
+ /// \param i21
+ /// \param i22
void SetMatrix(Real i00, Real i01, Real i02,
Real i10, Real i11, Real i12,
Real i20, Real i21, Real i22)
@@ -266,7 +276,7 @@ public:
/// \brief Set method details
///
- /// \param method details
+ /// \param method_details
void SetMethodDetails(String method_details) {
method_details_ = method_details;
}
@@ -435,7 +445,7 @@ public:
/// \brief Set the start page for a publication
///
- /// \param start
+ /// \param first
void SetPageFirst(String first) { page_first_ = first; }
/// \brief Get the start page of a publication
@@ -445,7 +455,7 @@ public:
/// \brief Set the end page for a publication
///
- /// \param end
+ /// \param last
void SetPageLast(String last) { page_last_ = last; }
/// \brief Get the last page of a publication
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index 15cc727ad76d4a86b2952970bbfb3c4321fbb733..a8e35f52cf543ca6f744224d88723caef4d16b42 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -61,18 +61,22 @@ public:
/// \brief create a MMCifReader
///
/// \param stream input stream
+ /// \param ent_handle
+ /// \param profile
+
MMCifReader(std::istream& stream, mol::EntityHandle& ent_handle,
const IOProfile& profile);
/// \brief create a MMCifReader
///
/// \param filename input file
+ /// \param ent_handle
+ /// \param profile
MMCifReader(const String& filename, mol::EntityHandle& ent_handle,
const IOProfile& profile);
/// \brief Initialise the reader.
///
- /// \param loc Location of the file
void Init();
/// \brief Set up a fresh instance
@@ -193,8 +197,9 @@ protected:
/// \brief fetch values identifying atoms
///
/// \param[in] columns data row
- /// \param[out] chain_name takes atom_site.label_asym_id or, if
+ /// \param[out] auth_chain_name takes atom_site.label_asym_id or, if
/// auth_chain_id_ is set, atom_site.auth_asym_id as a chain name
+ /// \param[out] cif_chain_name
/// \param[out] res_name fetches atom_site.label_comp_id
/// \param[out] resnum gets atom_site.label_seq_id if available, consecutive
/// numbers, otherwise
diff --git a/modules/mol/alg/src/distance_rmsd_test.hh b/modules/mol/alg/src/distance_rmsd_test.hh
index 12e4ec86646d7241aa6649f19b512f54cb95df17..bd583ed0210a8f3e276432ba5e75162d6f3ffc85 100644
--- a/modules/mol/alg/src/distance_rmsd_test.hh
+++ b/modules/mol/alg/src/distance_rmsd_test.hh
@@ -52,7 +52,7 @@ namespace ost { namespace mol { namespace alg {
/// If a string is provided as an argument to the function, residue-per-residue statistics are stored as
/// residue properties. Specifically, the local residue-based Distance RMSD score is stored in a float property
/// as the provided string, while the residue-based sum of squared distances and the number of distances checked
-/// are saved in two properties named <string>_sum (a float property) and <string>_count (an int property).
+/// are saved in two properties named [string]_sum (a float property) and [string]_count (an int property).
std::pair<Real,long int> DLLEXPORT_OST_MOL_ALG
DistanceRMSDTest(const EntityView& mdl,
const GlobalRDMap& glob_dist_list,
diff --git a/modules/mol/alg/src/local_dist_diff_test.hh b/modules/mol/alg/src/local_dist_diff_test.hh
index f9013c97566e4edb261bb3ee4e0a2b8be90f53a4..9dd2f230617ac1b0b795ec6a7e467a80c1485655 100644
--- a/modules/mol/alg/src/local_dist_diff_test.hh
+++ b/modules/mol/alg/src/local_dist_diff_test.hh
@@ -45,7 +45,7 @@ namespace ost { namespace mol { namespace alg {
/// If a string is provided as an argument to the function, residue-per-residue statistics are stored as
/// residue properties. Specifically, the local residue-based lddt score is stored in a float property named
/// as the provided string, while the residue-based number of conserved and total distances are saved in two
-/// int properties named <string>_conserved and <string>_total.
+/// int properties named [string]_conserved and [string]_total.
std::pair<long int,long int> DLLEXPORT_OST_MOL_ALG
LocalDistDiffTest(const EntityView& mdl, const GlobalRDMap& dist_list,
std::vector<Real> cutoff_list, int sequence_separation = 0,
@@ -67,7 +67,7 @@ LocalDistDiffTest(const EntityView& mdl, const GlobalRDMap& dist_list,
/// If a string is provided as an argument to the function, residue-per-residue statistics are stored as
/// residue properties. Specifically, the local residue-based lddt score is stored in a float property named
/// as the provided string, while the residue-based number of conserved and total distances are saved in two
-/// int properties named <string>_conserved and <string>_total.
+/// int properties named [string]_conserved and [string]_total.
Real DLLEXPORT_OST_MOL_ALG LocalDistDiffTest(const EntityView& mdl,
const EntityView& target,
Real cutoff,
diff --git a/modules/mol/base/src/atom_base.hh b/modules/mol/base/src/atom_base.hh
index 4ddc13f2f46cea4c19c0e0372bb313b936d51386..c3ec3777d53e836b43d16b9ddd7dfe83f2886226 100644
--- a/modules/mol/base/src/atom_base.hh
+++ b/modules/mol/base/src/atom_base.hh
@@ -33,10 +33,6 @@ namespace ost { namespace mol {
///
/// Groups common functionality for AtomView and AtomHandle.
///
-/// Most of the atom properties such as temperature factor, element, radius
-/// and charge can be accessed with #GetAtomProps() that returns an object of
-/// type AtomProp.
-///
/// Like \ref ResidueBase residues, \ref ChainBase "chains" and
/// \ref EntityBase "entities" atoms are generic property containers and may as
/// such store \ref generic_properties "custom properties".
diff --git a/modules/mol/base/src/coord_group.hh b/modules/mol/base/src/coord_group.hh
index c9ea57e4efef9f7e07a5f9e868220f50587d050b..754330d6c3b703809ee734e79e53f2afe58558bc 100644
--- a/modules/mol/base/src/coord_group.hh
+++ b/modules/mol/base/src/coord_group.hh
@@ -64,7 +64,7 @@ public:
/// \brief start time in ps, default 0.0
float GetStartTime() const;
- /// \rbrief set start time in ps
+ /// \brief set start time in ps
void SetStartTime(float t);
/// \brief assign positions to the given frame - order and count must match
diff --git a/modules/mol/base/src/editor_base.hh b/modules/mol/base/src/editor_base.hh
index a53391767bfb006b7670b3922f9c8ae23872008a..c45036072670958e5eeef9cadb9f23c6def955be 100644
--- a/modules/mol/base/src/editor_base.hh
+++ b/modules/mol/base/src/editor_base.hh
@@ -153,7 +153,11 @@ public:
/// algorithms as well as most builders in the conop module rely on proper
/// naming.
/// \param pos is the position of the atom in global coordinates
- AtomHandle InsertAtom(ResidueHandle residue, const String& name,
+ /// \param ele
+ /// \param occupancy
+ /// \param b_factor
+ /// \param is_hetatm
+ AtomHandle InsertAtom(ResidueHandle residue, const String& name,
const geom::Vec3& pos, const String& ele="",
Real occupancy=1.0, Real b_factor=0.0,
bool is_hetatm=false);
@@ -194,6 +198,8 @@ public:
/// Error will be thrown.
/// \param position
/// is the alternative position
+ /// \param occ
+ /// \param b_factor
/// \sa EditorBase::InsertAltAtom(), ResidueHandle
void AddAltAtomPos(const String& group, const AtomHandle& atom,
const geom::Vec3& position, Real occ=1.0,
@@ -301,7 +307,7 @@ public:
/// \brief renumber residues of one chain
///
- /// \param name
+ /// \param chain
/// All residues of this chain will be renumbered according to the
/// parameters start and keep_spacing
///
diff --git a/modules/mol/base/src/entity_base.hh b/modules/mol/base/src/entity_base.hh
index fb23974d1e346f51862c9ec998d92e7d80049c27..b00ac720e9847e18419786a929d5e869735b0724 100644
--- a/modules/mol/base/src/entity_base.hh
+++ b/modules/mol/base/src/entity_base.hh
@@ -41,7 +41,7 @@ public:
/// \brief Set entity name
///
- /// \param entity_name is the new entity name.
+ /// \param ent_name is the new entity name.
///
/// \sa EntityBase::GetName
void SetName(const String& ent_name);
diff --git a/modules/mol/base/src/entity_handle.hh b/modules/mol/base/src/entity_handle.hh
index 5cb26134bb181c3055bc73bed2a71ac23c0a45a4..cb0ab5f0f2f6d694daac83694df3dc3af10d83a1 100644
--- a/modules/mol/base/src/entity_handle.hh
+++ b/modules/mol/base/src/entity_handle.hh
@@ -250,11 +250,9 @@ public:
void FixTransform();
/// \brief get complete list of residues
- /// \sa #ResiduesBegin, #ResiduesEnd
ResidueHandleList GetResidueList() const;
/// \brief get complete list of atoms
- /// \sa #AtomsBegin, #AtomsEnd
AtomHandleList GetAtomList() const;
/// \brief get complete list of atom positions
diff --git a/modules/mol/base/src/residue_base.hh b/modules/mol/base/src/residue_base.hh
index 993683cb223aaf661704ce0c08c81d16f55f1bbf..30e174b24f80da16914b740e946f54c28f38e6ca 100644
--- a/modules/mol/base/src/residue_base.hh
+++ b/modules/mol/base/src/residue_base.hh
@@ -62,8 +62,6 @@ namespace ost { namespace mol {
/// amino acids, co-enzymes, water coordinated ions, drugs, solvents) as obtained
/// from the PDB.
///
-/// When loading an entity from file, the one-letter and chemical class of a
-/// residue are assigned by the \ref conop::Builder "default builder".
class DLLEXPORT_OST_MOL ResidueBase:
public GenericPropContainer<ResidueBase> {
public:
diff --git a/modules/mol/base/src/view_op.hh b/modules/mol/base/src/view_op.hh
index 1774b289dc7689166f075500f2ee3c96026e3a35..dea7c29ab58f11f2f70c9c864554c69884592c89 100644
--- a/modules/mol/base/src/view_op.hh
+++ b/modules/mol/base/src/view_op.hh
@@ -73,7 +73,7 @@ EntityView DLLEXPORT_OST_MOL CreateViewFromAtomList(const AtomViewList& atoms);
/// \throw IntegrityError if trying to compare two views that do not point to
/// the same entity.
/// \return a pair of views. \c first contains the elements that are in \p view1,
-/// but not in \p view2, \second contains the elements that are in \p view2
+/// but not in \p view2, \c second contains the elements that are in \p view2
/// but not in \p view1
std::pair<EntityView, EntityView> DLLEXPORT_OST_MOL
CompareViews(const EntityView& view1, const EntityView& view2);
diff --git a/modules/seq/alg/src/merge_pairwise_alignments.hh b/modules/seq/alg/src/merge_pairwise_alignments.hh
index 6a825d2e036af65c03d191fee1064367fbd71a6e..04bc8832d4e6f40dc10084439a3d5bb38eb6a7f6 100644
--- a/modules/seq/alg/src/merge_pairwise_alignments.hh
+++ b/modules/seq/alg/src/merge_pairwise_alignments.hh
@@ -37,7 +37,7 @@ namespace ost { namespace seq { namespace alg {
/// The method does not produce the optimal multiple sequence alignemnt for all
/// the sequences.
///
-/// \param pairwise_alignments is a list of AlignmentHandles, each containing
+/// \param pairwise_alns is a list of AlignmentHandles, each containing
/// two sequences
/// \param ref_seq is the reference sequence. The reference sequence must not
/// contain any gaps.