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Commit 11019a26 by Maarten L. Hekkelman
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Merge branch 'sugar-tests' into develop

parents 291ef737 6f8909dc
Showing with 442 additions and 20 deletions
CMakeLists.txt
...@@ -394,6 +394,7 @@ if(CIFPP_BUILD_TESTS) ...@@ -394,6 +394,7 @@ if(CIFPP_BUILD_TESTS)
# pdb2cif # pdb2cif
rename-compound rename-compound
structure structure
sugar
unit) unit)
foreach(CIFPP_TEST IN LISTS CIFPP_tests) foreach(CIFPP_TEST IN LISTS CIFPP_tests)
......
data/ccd-subset.cif
...@@ -2394,3 +2394,189 @@ VAL "Create component" 1999-07-08 RCSB ...@@ -2394,3 +2394,189 @@ VAL "Create component" 1999-07-08 RCSB
VAL "Modify descriptor" 2011-06-04 RCSB VAL "Modify descriptor" 2011-06-04 RCSB
# #
data_NAG
#
_chem_comp.id NAG
_chem_comp.name 2-acetamido-2-deoxy-beta-D-glucopyranose
_chem_comp.type "D-saccharide, beta linking"
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C8 H15 N O6"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
;N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE
;
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2020-07-17
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 221.208
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code NAG
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 8PCH
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
# #
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 NAG N-acetyl-beta-D-glucosamine PDB ?
2 NAG 2-acetamido-2-deoxy-beta-D-glucose PDB ?
3 NAG 2-acetamido-2-deoxy-D-glucose PDB ?
4 NAG 2-acetamido-2-deoxy-glucose PDB ?
5 NAG N-ACETYL-D-GLUCOSAMINE PDB ?
# #
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
NAG C1 C1 C 0 1 N N R 7.396 28.163 26.662 0.185 1.082 -0.421 C1 NAG 1
NAG C2 C2 C 0 1 N N R 6.973 29.233 27.644 0.790 -0.220 0.112 C2 NAG 2
NAG C3 C3 C 0 1 N N R 7.667 29.055 29.000 -0.124 -1.390 -0.265 C3 NAG 3
NAG C4 C4 C 0 1 N N S 7.573 27.588 29.490 -1.526 -1.129 0.294 C4 NAG 4
NAG C5 C5 C 0 1 N N R 7.902 26.592 28.373 -2.042 0.207 -0.246 C5 NAG 5
NAG C6 C6 C 0 1 N N N 7.599 25.173 28.797 -3.417 0.504 0.355 C6 NAG 6
NAG C7 C7 C 0 1 N N N 6.291 31.299 26.595 3.197 0.157 0.076 C7 NAG 7
NAG C8 C8 C 0 1 N N N 6.684 32.649 26.036 4.559 -0.052 -0.533 C8 NAG 8
NAG N2 N2 N 0 1 N N N 7.268 30.545 27.089 2.114 -0.422 -0.480 N2 NAG 9
NAG O1 O1 O 0 1 N Y N 6.676 28.363 25.419 1.003 2.185 -0.024 O1 NAG 10
NAG O3 O3 O 0 1 N N N 7.038 29.909 29.947 0.395 -2.600 0.291 O3 NAG 11
NAG O4 O4 O 0 1 N N N 8.494 27.358 30.574 -2.405 -2.180 -0.114 O4 NAG 12
NAG O5 O5 O 0 1 N N N 7.104 26.875 27.206 -1.130 1.248 0.113 O5 NAG 13
NAG O6 O6 O 0 1 N N N 6.232 25.040 29.165 -3.949 1.691 -0.236 O6 NAG 14
NAG O7 O7 O 0 1 N N N 5.114 30.936 26.562 3.074 0.845 1.067 O7 NAG 15
NAG H1 H1 H 0 1 N N N 8.477 28.257 26.481 0.133 1.040 -1.509 H1 NAG 16
NAG H2 H2 H 0 1 N N N 5.888 29.146 27.803 0.879 -0.163 1.197 H2 NAG 17
NAG H3 H3 H 0 1 N N N 8.729 29.321 28.892 -0.174 -1.478 -1.350 H3 NAG 18
NAG H4 H4 H 0 1 N N N 6.544 27.403 29.831 -1.483 -1.091 1.382 H4 NAG 19
NAG H5 H5 H 0 1 N N N 8.971 26.674 28.128 -2.123 0.154 -1.332 H5 NAG 20
NAG H61 H61 H 0 1 N N N 7.816 24.492 27.961 -4.088 -0.333 0.157 H61 NAG 21
NAG H62 H62 H 0 1 N N N 8.232 24.910 29.657 -3.320 0.645 1.431 H62 NAG 22
NAG H81 H81 H 0 1 N N N 5.791 33.159 25.646 4.560 0.320 -1.558 H81 NAG 23
NAG H82 H82 H 0 1 N N N 7.136 33.258 26.833 5.305 0.490 0.050 H82 NAG 24
NAG H83 H83 H 0 1 N N N 7.411 32.511 25.222 4.799 -1.115 -0.532 H83 NAG 25
NAG HN2 HN2 H 0 1 N N N 8.210 30.881 27.079 2.212 -0.973 -1.273 HN2 NAG 26
NAG HO1 HO1 H 0 1 N Y N 6.933 27.696 24.793 0.679 3.044 -0.328 HO1 NAG 27
NAG HO3 HO3 H 0 1 N Y N 7.459 29.809 30.793 -0.135 -3.384 0.091 HO3 NAG 28
NAG HO4 HO4 H 0 1 N Y N 8.425 26.456 30.863 -3.312 -2.079 0.206 HO4 NAG 29
NAG HO6 HO6 H 0 1 N Y N 6.060 24.143 29.428 -4.822 1.940 0.099 HO6 NAG 30
# #
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
NAG C1 C2 SING N N 1
NAG C1 O1 SING N N 2
NAG C1 O5 SING N N 3
NAG C1 H1 SING N N 4
NAG C2 C3 SING N N 5
NAG C2 N2 SING N N 6
NAG C2 H2 SING N N 7
NAG C3 C4 SING N N 8
NAG C3 O3 SING N N 9
NAG C3 H3 SING N N 10
NAG C4 C5 SING N N 11
NAG C4 O4 SING N N 12
NAG C4 H4 SING N N 13
NAG C5 C6 SING N N 14
NAG C5 O5 SING N N 15
NAG C5 H5 SING N N 16
NAG C6 O6 SING N N 17
NAG C6 H61 SING N N 18
NAG C6 H62 SING N N 19
NAG C7 C8 SING N N 20
NAG C7 N2 SING N N 21
NAG C7 O7 DOUB N N 22
NAG C8 H81 SING N N 23
NAG C8 H82 SING N N 24
NAG C8 H83 SING N N 25
NAG N2 HN2 SING N N 26
NAG O1 HO1 SING N N 27
NAG O3 HO3 SING N N 28
NAG O4 HO4 SING N N 29
NAG O6 HO6 SING N N 30
# #
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
NAG SMILES ACDLabs 12.01 "O=C(NC1C(O)C(O)C(OC1O)CO)C"
NAG InChI InChI 1.03 "InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1"
NAG InChIKey InChI 1.03 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NAG SMILES_CANONICAL CACTVS 3.370 "CC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]1O"
NAG SMILES CACTVS 3.370 "CC(=O)N[CH]1[CH](O)O[CH](CO)[CH](O)[CH]1O"
NAG SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@H]1O)CO)O)O"
NAG SMILES "OpenEye OEToolkits" 1.7.6 "CC(=O)NC1C(C(C(OC1O)CO)O)O"
# #
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
NAG "SYSTEMATIC NAME" ACDLabs 12.01 "2-(acetylamino)-2-deoxy-beta-D-glucopyranose"
NAG "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "N-[(2R,3R,4R,5S,6R)-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]ethanamide"
NAG "CONDENSED IUPAC CARBOHYDRATE SYMBOL" GMML 1.0 DGlcpNAcb
NAG "COMMON NAME" GMML 1.0 N-acetyl-b-D-glucopyranosamine
NAG "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 b-D-GlcpNAc
NAG "SNFG CARBOHYDRATE SYMBOL" GMML 1.0 GlcNAc
# #
loop_
_pdbx_chem_comp_feature.comp_id
_pdbx_chem_comp_feature.type
_pdbx_chem_comp_feature.value
_pdbx_chem_comp_feature.source
_pdbx_chem_comp_feature.support
NAG "CARBOHYDRATE ISOMER" D PDB ?
NAG "CARBOHYDRATE RING" pyranose PDB ?
NAG "CARBOHYDRATE ANOMER" beta PDB ?
NAG "CARBOHYDRATE PRIMARY CARBONYL GROUP" aldose PDB ?
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
NAG "Create component" 1999-07-08 RCSB
NAG "Modify descriptor" 2011-06-04 RCSB
NAG "Modify leaving atom flag" 2011-07-01 RCSB
NAG "Modify leaving atom flag" 2012-11-26 RCSB
NAG "Other modification" 2019-08-12 RCSB
NAG "Other modification" 2019-12-19 RCSB
NAG "Other modification" 2020-07-03 RCSB
NAG "Modify name" 2020-07-17 RCSB
NAG "Modify synonyms" 2020-07-17 RCSB
##
\ No newline at end of file
include/cif++/Cif++.hpp
...@@ -176,6 +176,7 @@ class Item ...@@ -176,6 +176,7 @@ class Item
, mValue(rhs.mValue) , mValue(rhs.mValue)
{ {
} }
Item(Item &&rhs) noexcept Item(Item &&rhs) noexcept
: mName(std::move(rhs.mName)) : mName(std::move(rhs.mName))
, mValue(std::move(rhs.mValue)) , mValue(std::move(rhs.mValue))
......
include/cif++/Structure.hpp
...@@ -214,6 +214,10 @@ class Atom ...@@ -214,6 +214,10 @@ class Atom
std::string pdbID() const; // auth_comp_id + '_' + auth_asym_id + '_' + auth_seq_id + pdbx_PDB_ins_code std::string pdbID() const; // auth_comp_id + '_' + auth_asym_id + '_' + auth_seq_id + pdbx_PDB_ins_code
bool operator==(const Atom &rhs) const; bool operator==(const Atom &rhs) const;
bool operator!=(const Atom &rhs) const
{
return not operator==(rhs);
}
// access data in compound for this atom // access data in compound for this atom
...@@ -238,6 +242,13 @@ class Atom ...@@ -238,6 +242,13 @@ class Atom
friend std::ostream &operator<<(std::ostream &os, const Atom &atom); friend std::ostream &operator<<(std::ostream &os, const Atom &atom);
/// \brief Synchronize data with underlying cif data
void sync()
{
if (mImpl)
mImpl->prefetch();
}
private: private:
friend class Structure; friend class Structure;
...@@ -289,6 +300,13 @@ typedef std::vector<Atom> AtomView; ...@@ -289,6 +300,13 @@ typedef std::vector<Atom> AtomView;
// -------------------------------------------------------------------- // --------------------------------------------------------------------
enum class EntityType
{
Polymer, NonPolymer, Macrolide, Water, Branched
};
// --------------------------------------------------------------------
class Residue class Residue
{ {
public: public:
...@@ -316,10 +334,7 @@ class Residue ...@@ -316,10 +334,7 @@ class Residue
AtomView &atoms(); AtomView &atoms();
const AtomView &atoms() const; const AtomView &atoms() const;
void addAtom(const Atom &atom) void addAtom(Atom &atom);
{
mAtoms.push_back(atom);
}
/// \brief Unique atoms returns only the atoms without alternates and the first of each alternate atom id. /// \brief Unique atoms returns only the atoms without alternates and the first of each alternate atom id.
AtomView unique_atoms() const; AtomView unique_atoms() const;
...@@ -336,6 +351,8 @@ class Residue ...@@ -336,6 +351,8 @@ class Residue
int seqID() const { return mSeqID; } int seqID() const { return mSeqID; }
std::string entityID() const; std::string entityID() const;
EntityType entityType() const;
std::string authAsymID() const; std::string authAsymID() const;
std::string authSeqID() const; std::string authSeqID() const;
std::string authInsCode() const; std::string authInsCode() const;
...@@ -457,6 +474,11 @@ class Monomer : public Residue ...@@ -457,6 +474,11 @@ class Monomer : public Residue
// for LEU and VAL // for LEU and VAL
float chiralVolume() const; float chiralVolume() const;
bool operator==(const Monomer &rhs) const
{
return mPolymer == rhs.mPolymer and mIndex == rhs.mIndex;
}
private: private:
const Polymer *mPolymer; const Polymer *mPolymer;
size_t mIndex; size_t mIndex;
...@@ -508,10 +530,14 @@ class Sugar : public Residue ...@@ -508,10 +530,14 @@ class Sugar : public Residue
int num() const { return std::stoi(mAuthSeqID); } int num() const { return std::stoi(mAuthSeqID); }
std::string name() const; std::string name() const;
// Sugar & /// \brief Return the atom the C1 is linked to
Atom getLink() const { return mLink; }
void setLink(Atom link) { mLink = link; }
private: private:
const Branch &mBranch; const Branch &mBranch;
Atom mLink;
}; };
class Branch : public std::vector<Sugar> class Branch : public std::vector<Sugar>
...@@ -519,6 +545,8 @@ class Branch : public std::vector<Sugar> ...@@ -519,6 +545,8 @@ class Branch : public std::vector<Sugar>
public: public:
Branch(Structure &structure, const std::string &asymID); Branch(Structure &structure, const std::string &asymID);
void linkAtoms();
std::string name() const; std::string name() const;
float weight() const; float weight() const;
std::string asymID() const { return mAsymID; } std::string asymID() const { return mAsymID; }
...@@ -532,6 +560,8 @@ class Branch : public std::vector<Sugar> ...@@ -532,6 +560,8 @@ class Branch : public std::vector<Sugar>
private: private:
friend Sugar; friend Sugar;
std::string name(const Sugar &s) const;
Structure *mStructure; Structure *mStructure;
std::string mAsymID; std::string mAsymID;
}; };
...@@ -602,6 +632,9 @@ class Structure ...@@ -602,6 +632,9 @@ class Structure
const AtomView &atoms() const { return mAtoms; } const AtomView &atoms() const { return mAtoms; }
// AtomView &atoms() { return mAtoms; } // AtomView &atoms() { return mAtoms; }
EntityType getEntityTypeForEntityID(const std::string entityID) const;
EntityType getEntityTypeForAsymID(const std::string asymID) const;
AtomView waters() const; AtomView waters() const;
const std::list<Polymer> &polymers() const { return mPolymers; } const std::list<Polymer> &polymers() const { return mPolymers; }
...@@ -683,6 +716,18 @@ class Structure ...@@ -683,6 +716,18 @@ class Structure
void changeResidue(Residue &res, const std::string &newCompound, void changeResidue(Residue &res, const std::string &newCompound,
const std::vector<std::tuple<std::string, std::string>> &remappedAtoms); const std::vector<std::tuple<std::string, std::string>> &remappedAtoms);
/// \brief Remove a residue, can be monomer or nonpoly
///
/// \param asym_id The asym ID
/// \param seq_id The sequence ID
void removeResidue(const std::string &asym_id, int seq_id, const std::string &auth_seq_id)
{
removeResidue(getResidue(asym_id, seq_id, auth_seq_id));
}
/// \brief Remove residue \a res, can be monomer or nonpoly
void removeResidue(Residue &res);
/// \brief Create a new non-polymer entity, returns new ID /// \brief Create a new non-polymer entity, returns new ID
/// \param mon_id The mon_id for the new nonpoly, must be an existing and known compound from CCD /// \param mon_id The mon_id for the new nonpoly, must be an existing and known compound from CCD
/// \return The ID of the created entity /// \return The ID of the created entity
...@@ -704,17 +749,20 @@ class Structure ...@@ -704,17 +749,20 @@ class Structure
/// \return The newly create asym ID /// \return The newly create asym ID
std::string createNonpoly(const std::string &entity_id, std::vector<std::vector<cif::Item>> &atom_info); std::string createNonpoly(const std::string &entity_id, std::vector<std::vector<cif::Item>> &atom_info);
/// \brief Create a new (sugar) branch with one first NAG containing atoms \a nag_atoms /// \brief Create a new (sugar) branch with one first NAG containing atoms constructed from \a nag_atom_info
Branch &createBranch(std::vector<std::vector<cif::Item>> &nag_atoms); Branch &createBranch(std::vector<std::vector<cif::Item>> &nag_atom_info);
/// \brief Extend an existing (sugar) branch identified by \a asymID with one sugar containing atoms \a atoms /// \brief Extend an existing (sugar) branch identified by \a asymID with one sugar containing atoms constructed from \a atom_info
Branch &extendBranch(const std::string &asym_id, std::vector<std::vector<cif::Item>> &atoms);
/// \brief Remove a residue, can be monomer or nonpoly
/// ///
/// \param asym_id The asym ID /// \param asym_id The asym id of the branch to extend
/// \param seq_id The sequence ID /// \param atom_info Array containing the info for the atoms to construct for the new sugar
void removeResidue(const std::string &asym_id, int seq_id); /// \param link_sugar The sugar to link to, note: this is the sugar number (1 based)
/// \param link_atom The atom id of the atom linked in the sugar
Branch &extendBranch(const std::string &asym_id, std::vector<std::vector<cif::Item>> &atom_info,
int link_sugar, const std::string &link_atom);
/// \brief Remove \a branch
void removeBranch(Branch &branch);
/// \brief Remove residue \a res /// \brief Remove residue \a res
/// ///
......
src/BondMap.cpp
...@@ -276,11 +276,17 @@ BondMap::BondMap(const Structure &p) ...@@ -276,11 +276,17 @@ BondMap::BondMap(const Structure &p)
continue; continue;
} }
auto c = atomMapByAsymSeqAndAtom.at(make_tuple(asymID, lastSeqID, "C", lastAuthSeqID)); auto kc = make_tuple(asymID, lastSeqID, "C", lastAuthSeqID);
auto n = atomMapByAsymSeqAndAtom.at(make_tuple(asymID, seqID, "N", authSeqID)); auto kn = make_tuple(asymID, seqID, "N", authSeqID);
if (atomMapByAsymSeqAndAtom.count(kc) and atomMapByAsymSeqAndAtom.count(kn))
{
auto c = atomMapByAsymSeqAndAtom.at(kc);
auto n = atomMapByAsymSeqAndAtom.at(kn);
if (not(c.empty() or n.empty()))
bindAtoms(c, n); bindAtoms(c, n);
}
// if (not(c.empty() or n.empty()))
lastSeqID = seqID; lastSeqID = seqID;
lastAuthSeqID = authSeqID; lastAuthSeqID = authSeqID;
...@@ -298,10 +304,21 @@ BondMap::BondMap(const Structure &p) ...@@ -298,10 +304,21 @@ BondMap::BondMap(const Structure &p)
"ptnr1_label_seq_id", "ptnr2_label_seq_id", "ptnr1_label_seq_id", "ptnr2_label_seq_id",
"ptnr1_auth_seq_id", "ptnr2_auth_seq_id"); "ptnr1_auth_seq_id", "ptnr2_auth_seq_id");
std::string a = atomMapByAsymSeqAndAtom.at(make_tuple(asym1, seqId1, atomId1, authSeqId1)); auto ka = make_tuple(asym1, seqId1, atomId1, authSeqId1);
std::string b = atomMapByAsymSeqAndAtom.at(make_tuple(asym2, seqId2, atomId2, authSeqId2)); auto kb = make_tuple(asym2, seqId2, atomId2, authSeqId2);
if (not(a.empty() or b.empty()))
if (atomMapByAsymSeqAndAtom.count(ka) and atomMapByAsymSeqAndAtom.count(kb))
{
auto a = atomMapByAsymSeqAndAtom.at(ka);
auto b = atomMapByAsymSeqAndAtom.at(kb);
linkAtoms(a, b); linkAtoms(a, b);
}
// std::string a = atomMapByAsymSeqAndAtom.at(make_tuple(asym1, seqId1, atomId1, authSeqId1));
// std::string b = atomMapByAsymSeqAndAtom.at(make_tuple(asym2, seqId2, atomId2, authSeqId2));
// if (not(a.empty() or b.empty()))
// linkAtoms(a, b);
} }
// then link all atoms in the compounds // then link all atoms in the compounds
......
test/sugar-test.cpp 0 → 100644
/*-
* SPDX-License-Identifier: BSD-2-Clause
*
* Copyright (c) 2021 NKI/AVL, Netherlands Cancer Institute
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#define BOOST_TEST_ALTERNATIVE_INIT_API
#include <boost/test/included/unit_test.hpp>
#include <stdexcept>
#include "cif++/Cif++.hpp"
#include "cif++/Structure.hpp"
#include "cif++/CifValidator.hpp"
// --------------------------------------------------------------------
cif::File operator""_cf(const char* text, size_t length)
{
struct membuf : public std::streambuf
{
membuf(char* text, size_t length)
{
this->setg(text, text, text + length);
}
} buffer(const_cast<char*>(text), length);
std::istream is(&buffer);
return cif::File(is);
}
// --------------------------------------------------------------------
std::filesystem::path gTestDir = std::filesystem::current_path();
bool init_unit_test()
{
cif::VERBOSE = 1;
// not a test, just initialize test dir
if (boost::unit_test::framework::master_test_suite().argc == 2)
gTestDir = boost::unit_test::framework::master_test_suite().argv[1];
// do this now, avoids the need for installing
cif::addFileResource("mmcif_pdbx_v50.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx_v50.dic");
// initialize CCD location
cif::addFileResource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
mmcif::CompoundFactory::instance().pushDictionary(gTestDir / "HEM.cif");
return true;
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(sugar_name_1)
{
using namespace cif::literals;
const std::filesystem::path example(gTestDir / "1juh.cif.gz");
mmcif::File file(example.string());
mmcif::Structure s(file);
auto &db = s.datablock();
auto &entity = db["entity"];
auto &branches = s.branches();
BOOST_CHECK_EQUAL(branches.size(), 4);
for (auto &branch : branches)
{
auto entityID = branch.front().entityID();
auto name = entity.find1<std::string>("id"_key == entityID, "pdbx_description");
BOOST_CHECK_EQUAL(branch.name(), name);
}
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(create_sugar_1)
{
using namespace cif::literals;
const std::filesystem::path example(gTestDir / "1juh.cif.gz");
mmcif::File file(example.string());
mmcif::Structure s(file);
// collect atoms from asym L first
auto &NAG = s.getResidue("L");
auto nagAtoms = NAG.atoms();
s.removeResidue(NAG);
std::vector<std::vector<cif::Item>> ai;
auto &db = s.datablock();
auto &as = db["atom_site"];
for (auto r : as.find("label_asym_id"_key == "L"))
ai.emplace_back(r.begin(), r.end());
auto &branch = s.createBranch(ai);
BOOST_CHECK_EQUAL(branch.name(), "2-acetamido-2-deoxy-beta-D-glucopyranose");
BOOST_CHECK_EQUAL(branch.size(), 1);
BOOST_CHECK_EQUAL(branch[0].atoms().size(), nagAtoms.size());
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(create_sugar_2)
{
using namespace cif::literals;
const std::filesystem::path example(gTestDir / "1juh.cif.gz");
mmcif::File file(example.string());
mmcif::Structure s(file);
// Get branch for H
auto &bH = s.getBranchByAsymID("H");
BOOST_CHECK_EQUAL(bH.size(), 2);
std::vector<std::vector<cif::Item>> ai[2];
auto &db = s.datablock();
auto &as = db["atom_site"];
for (size_t i = 0; i < 2; ++i)
{
for (auto r : as.find("label_asym_id"_key == "H" and "auth_seq_id"_key == i + 1))
ai[i].emplace_back(r.begin(), r.end());
}
s.removeBranch(bH);
auto &bN = s.createBranch(ai[0]);
s.extendBranch(bN.asymID(), ai[1], 1, "O4");
BOOST_CHECK_EQUAL(bN.name(), "2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose");
BOOST_CHECK_EQUAL(bN.size(), 2);
file.save(gTestDir / "test-create_sugar_2.cif");
}
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