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3
.gitignore
vendored
3
.gitignore
vendored
@@ -11,4 +11,5 @@ data/components.cif*
|
||||
CMakeSettings.json
|
||||
msvc/
|
||||
Testing/
|
||||
|
||||
rsrc/feature-request.txt
|
||||
test/1cbs.cif
|
||||
|
||||
@@ -25,7 +25,7 @@
|
||||
cmake_minimum_required(VERSION 3.16)
|
||||
|
||||
# set the project name
|
||||
project(cifpp VERSION 3.0.2 LANGUAGES CXX)
|
||||
project(cifpp VERSION 4.0.0 LANGUAGES CXX)
|
||||
|
||||
list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
|
||||
|
||||
@@ -43,9 +43,6 @@ set(CXX_EXTENSIONS OFF)
|
||||
set(CMAKE_CXX_STANDARD 17)
|
||||
set(CMAKE_CXX_STANDARD_REQUIRED ON)
|
||||
|
||||
# https://stackoverflow.com/questions/63902528/program-crashes-when-filesystempath-is-destroyed
|
||||
find_package(Filesystem REQUIRED)
|
||||
|
||||
if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
|
||||
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers")
|
||||
elseif(MSVC)
|
||||
@@ -73,6 +70,8 @@ if(BUILD_FOR_CCP4)
|
||||
set(BUILD_SHARED_LIBS ON)
|
||||
endif()
|
||||
endif("$ENV{CCP4}" STREQUAL "" OR NOT EXISTS $ENV{CCP4})
|
||||
|
||||
add_definitions(-DCCP4=1)
|
||||
endif()
|
||||
|
||||
# Check if CCP4 is available
|
||||
@@ -395,6 +394,7 @@ if(CIFPP_BUILD_TESTS)
|
||||
# pdb2cif
|
||||
rename-compound
|
||||
structure
|
||||
sugar
|
||||
unit)
|
||||
|
||||
foreach(CIFPP_TEST IN LISTS CIFPP_tests)
|
||||
|
||||
15
changelog
15
changelog
@@ -1,3 +1,15 @@
|
||||
Version 4.0.0
|
||||
- getResidue in mmcif::Structure now requires both a
|
||||
sequence ID and an auth sequence ID. As a result the code was cleaned
|
||||
up considerably.
|
||||
|
||||
Version 3.0.5
|
||||
- mmcif::Structure redesign. It is now a wrapper around a cif::Datablock.
|
||||
|
||||
Version 3.0.4
|
||||
- Fix in mmCIF parser, now correctly handles the unquoted
|
||||
string ??
|
||||
|
||||
Version 3.0.3
|
||||
- Better configuration checks, for atomic e.g.
|
||||
- Fixed a problem introduced in refactoring mmcif::Atom
|
||||
@@ -17,6 +29,9 @@ Version 3.0.0
|
||||
- Upgraded mmcif::Structure
|
||||
- various other small fixes
|
||||
|
||||
Version 2.0.5
|
||||
- Backporting updated CMakeLists.txt file
|
||||
|
||||
Version 2.0.4
|
||||
- Reverted a too strict test when reading cif files.
|
||||
|
||||
|
||||
@@ -2394,3 +2394,189 @@ VAL "Create component" 1999-07-08 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
|
||||
##
|
||||
@@ -172,19 +172,26 @@ enum AtomType : uint8_t
|
||||
// --------------------------------------------------------------------
|
||||
// AtomTypeInfo
|
||||
|
||||
enum RadiusType
|
||||
enum class RadiusType
|
||||
{
|
||||
eRadiusCalculated,
|
||||
eRadiusEmpirical,
|
||||
eRadiusCovalentEmpirical,
|
||||
Calculated,
|
||||
Empirical,
|
||||
CovalentEmpirical,
|
||||
|
||||
eRadiusSingleBond,
|
||||
eRadiusDoubleBond,
|
||||
eRadiusTripleBond,
|
||||
SingleBond,
|
||||
DoubleBond,
|
||||
TripleBond,
|
||||
|
||||
eRadiusVanderWaals,
|
||||
VanderWaals,
|
||||
|
||||
eRadiusTypeCount
|
||||
TypeCount
|
||||
};
|
||||
|
||||
constexpr size_t RadiusTypeCount = static_cast<size_t>(RadiusType::TypeCount);
|
||||
|
||||
enum class IonicRadiusType
|
||||
{
|
||||
Effective, Crystal
|
||||
};
|
||||
|
||||
struct AtomTypeInfo
|
||||
@@ -194,7 +201,7 @@ struct AtomTypeInfo
|
||||
std::string symbol;
|
||||
float weight;
|
||||
bool metal;
|
||||
float radii[eRadiusTypeCount];
|
||||
float radii[RadiusTypeCount];
|
||||
};
|
||||
|
||||
extern const AtomTypeInfo kKnownAtoms[];
|
||||
@@ -218,11 +225,32 @@ class AtomTypeTraits
|
||||
static bool isElement(const std::string &symbol);
|
||||
static bool isMetal(const std::string &symbol);
|
||||
|
||||
float radius(RadiusType type = eRadiusSingleBond) const
|
||||
float radius(RadiusType type = RadiusType::SingleBond) const
|
||||
{
|
||||
if (type >= eRadiusTypeCount)
|
||||
if (type >= RadiusType::TypeCount)
|
||||
throw std::invalid_argument("invalid radius requested");
|
||||
return mInfo->radii[type] / 100.f;
|
||||
return mInfo->radii[static_cast<size_t>(type)] / 100.f;
|
||||
}
|
||||
|
||||
/// \brief Return the radius for a charged version of this atom in a solid crystal
|
||||
///
|
||||
/// \param charge The charge of the ion
|
||||
/// \return The radius of the ion
|
||||
float crystal_ionic_radius(int charge) const;
|
||||
|
||||
/// \brief Return the radius for a charged version of this atom in a non-solid environment
|
||||
///
|
||||
/// \param charge The charge of the ion
|
||||
/// \return The radius of the ion
|
||||
float effective_ionic_radius(int charge) const;
|
||||
|
||||
/// \brief Return the radius for a charged version of this atom, returns the effective radius by default
|
||||
///
|
||||
/// \param charge The charge of the ion
|
||||
/// \return The radius of the ion
|
||||
float ionic_radius(int charge, IonicRadiusType type = IonicRadiusType::Effective) const
|
||||
{
|
||||
return type == IonicRadiusType::Effective ? effective_ionic_radius(charge) : crystal_ionic_radius(charge);
|
||||
}
|
||||
|
||||
// data type encapsulating the Waasmaier & Kirfel scattering factors
|
||||
|
||||
@@ -176,6 +176,7 @@ class Item
|
||||
, mValue(rhs.mValue)
|
||||
{
|
||||
}
|
||||
|
||||
Item(Item &&rhs) noexcept
|
||||
: mName(std::move(rhs.mName))
|
||||
, mValue(std::move(rhs.mValue))
|
||||
@@ -1183,6 +1184,9 @@ struct Empty
|
||||
{
|
||||
};
|
||||
|
||||
/// \brief A helper to make it possible to have conditions like ("id"_key == cif::null)
|
||||
inline constexpr Empty null = Empty();
|
||||
|
||||
struct Key
|
||||
{
|
||||
explicit Key(const std::string &itemTag)
|
||||
@@ -2169,17 +2173,21 @@ class File
|
||||
File();
|
||||
File(std::istream &is, bool validate = false);
|
||||
File(const std::filesystem::path &path, bool validate = false);
|
||||
File(const char *data, size_t length); // good luck trying to find out what it is...
|
||||
|
||||
File(File &&rhs);
|
||||
File(const File &rhs) = delete;
|
||||
File &operator=(const File &rhs) = delete;
|
||||
|
||||
~File();
|
||||
virtual ~File();
|
||||
|
||||
void load(const std::filesystem::path &p);
|
||||
void save(const std::filesystem::path &p);
|
||||
virtual void load(const std::filesystem::path &p);
|
||||
virtual void save(const std::filesystem::path &p);
|
||||
|
||||
void load(std::istream &is);
|
||||
void save(std::ostream &os);
|
||||
virtual void load(std::istream &is);
|
||||
virtual void save(std::ostream &os);
|
||||
|
||||
virtual void load(const char *data, std::size_t length);
|
||||
|
||||
/// \brief Load only the data block \a datablock from the mmCIF file
|
||||
void load(std::istream &is, const std::string &datablock);
|
||||
@@ -2211,6 +2219,12 @@ class File
|
||||
|
||||
void append(Datablock *e);
|
||||
|
||||
Datablock &emplace(std::string_view name)
|
||||
{
|
||||
append(new Datablock(name));
|
||||
return back();
|
||||
}
|
||||
|
||||
Datablock *get(std::string_view name) const;
|
||||
Datablock &operator[](std::string_view name);
|
||||
|
||||
@@ -2248,6 +2262,9 @@ class File
|
||||
iterator begin() const;
|
||||
iterator end() const;
|
||||
|
||||
Datablock &front();
|
||||
Datablock &back();
|
||||
|
||||
bool empty() const { return mHead == nullptr; }
|
||||
|
||||
const Validator &getValidator() const;
|
||||
|
||||
@@ -1,17 +1,17 @@
|
||||
/*-
|
||||
* SPDX-License-Identifier: BSD-2-Clause
|
||||
*
|
||||
*
|
||||
* Copyright (c) 2020 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
|
||||
@@ -82,16 +82,7 @@ inline bool isAnyPrint(int ch)
|
||||
(ch >= 0x20 and ch <= 0x7f and (kCharTraitsTable[ch - 0x20] & kAnyPrintMask) != 0);
|
||||
}
|
||||
|
||||
inline bool isUnquotedString(const char *s)
|
||||
{
|
||||
bool result = isOrdinary(*s++);
|
||||
while (result and *s != 0)
|
||||
{
|
||||
result = isNonBlank(*s);
|
||||
++s;
|
||||
}
|
||||
return result;
|
||||
}
|
||||
bool isUnquotedString(const char *s);
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
@@ -139,7 +130,7 @@ class SacParser
|
||||
int getNextChar();
|
||||
|
||||
void retract();
|
||||
void restart();
|
||||
int restart(int start);
|
||||
|
||||
CIFToken getNextToken();
|
||||
void match(CIFToken token);
|
||||
@@ -181,8 +172,9 @@ class SacParser
|
||||
eStateTextField,
|
||||
eStateFloat = 100,
|
||||
eStateInt = 110,
|
||||
// eStateNumericSuffix = 200,
|
||||
eStateValue = 300
|
||||
eStateValue = 300,
|
||||
eStateDATA,
|
||||
eStateSAVE
|
||||
};
|
||||
|
||||
std::istream &mData;
|
||||
@@ -191,7 +183,6 @@ class SacParser
|
||||
bool mValidate;
|
||||
uint32_t mLineNr;
|
||||
bool mBol;
|
||||
int mState, mStart;
|
||||
CIFToken mLookahead;
|
||||
std::string mTokenValue;
|
||||
CIFValueType mTokenType;
|
||||
|
||||
@@ -221,7 +221,7 @@ struct PointF
|
||||
|
||||
FType length() const
|
||||
{
|
||||
return sqrt(mX * mX + mY * mY + mZ * mZ);
|
||||
return std::sqrt(mX * mX + mY * mY + mZ * mZ);
|
||||
}
|
||||
};
|
||||
|
||||
@@ -285,7 +285,7 @@ inline double DistanceSquared(const PointF<F> &a, const PointF<F> &b)
|
||||
template <typename F>
|
||||
inline double Distance(const PointF<F> &a, const PointF<F> &b)
|
||||
{
|
||||
return sqrt(
|
||||
return std::sqrt(
|
||||
(a.mX - b.mX) * (a.mX - b.mX) +
|
||||
(a.mY - b.mY) * (a.mY - b.mY) +
|
||||
(a.mZ - b.mZ) * (a.mZ - b.mZ));
|
||||
@@ -332,10 +332,10 @@ double DihedralAngle(const PointF<F> &p1, const PointF<F> &p2, const PointF<F> &
|
||||
double result = 360;
|
||||
if (u > 0 and v > 0)
|
||||
{
|
||||
u = DotProduct(p, x) / sqrt(u);
|
||||
v = DotProduct(p, y) / sqrt(v);
|
||||
u = DotProduct(p, x) / std::sqrt(u);
|
||||
v = DotProduct(p, y) / std::sqrt(v);
|
||||
if (u != 0 or v != 0)
|
||||
result = atan2(v, u) * 180 / kPI;
|
||||
result = std::atan2(v, u) * 180 / kPI;
|
||||
}
|
||||
|
||||
return result;
|
||||
@@ -351,7 +351,7 @@ double CosinusAngle(const PointF<F> &p1, const PointF<F> &p2, const PointF<F> &p
|
||||
|
||||
double x = DotProduct(v12, v12) * DotProduct(v34, v34);
|
||||
if (x > 0)
|
||||
result = DotProduct(v12, v34) / sqrt(x);
|
||||
result = DotProduct(v12, v34) / std::sqrt(x);
|
||||
|
||||
return result;
|
||||
}
|
||||
@@ -378,7 +378,9 @@ Point Nudge(Point p, float offset);
|
||||
|
||||
Quaternion Normalize(Quaternion q);
|
||||
|
||||
Quaternion ConstructFromAngleAxis(float angle, Point axis);
|
||||
std::tuple<double, Point> QuaternionToAngleAxis(Quaternion q);
|
||||
|
||||
Point Centroid(const std::vector<Point> &Points);
|
||||
Point CenterPoints(std::vector<Point> &Points);
|
||||
|
||||
@@ -436,9 +438,9 @@ class SphericalDots
|
||||
double lat = std::asin((2.0 * i) / P);
|
||||
double lon = std::fmod(i, kGoldenRatio) * 2 * kPI / kGoldenRatio;
|
||||
|
||||
p->mX = sin(lon) * cos(lat);
|
||||
p->mY = cos(lon) * cos(lat);
|
||||
p->mZ = sin(lat);
|
||||
p->mX = std::sin(lon) * std::cos(lat);
|
||||
p->mY = std::cos(lon) * std::cos(lat);
|
||||
p->mZ = std::sin(lat);
|
||||
|
||||
++p;
|
||||
}
|
||||
|
||||
@@ -1,17 +1,17 @@
|
||||
/*-
|
||||
* SPDX-License-Identifier: BSD-2-Clause
|
||||
*
|
||||
*
|
||||
* Copyright (c) 2020 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
|
||||
@@ -34,16 +34,16 @@
|
||||
#include "cif++/Point.hpp"
|
||||
|
||||
/*
|
||||
To modify a structure, you will have to use actions.
|
||||
|
||||
The currently supported actions are:
|
||||
|
||||
To modify a structure, you will have to use actions.
|
||||
|
||||
The currently supported actions are:
|
||||
|
||||
// - Move atom to new location
|
||||
- Remove atom
|
||||
- Remove atom
|
||||
// - Add new atom that was formerly missing
|
||||
// - Add alternate Residue
|
||||
-
|
||||
|
||||
-
|
||||
|
||||
*/
|
||||
|
||||
namespace mmcif
|
||||
@@ -61,7 +61,6 @@ class File;
|
||||
class Atom
|
||||
{
|
||||
private:
|
||||
|
||||
struct AtomImpl : public std::enable_shared_from_this<AtomImpl>
|
||||
{
|
||||
AtomImpl(cif::Datablock &db, const std::string &id, cif::Row row);
|
||||
@@ -77,6 +76,8 @@ class Atom
|
||||
|
||||
bool getAnisoU(float anisou[6]) const;
|
||||
|
||||
int charge() const;
|
||||
|
||||
void moveTo(const Point &p);
|
||||
|
||||
const Compound &comp() const;
|
||||
@@ -99,7 +100,7 @@ class Atom
|
||||
int mRefcount;
|
||||
cif::Row mRow;
|
||||
|
||||
mutable std::vector<std::tuple<std::string,cif::detail::ItemReference>> mCachedRefs;
|
||||
mutable std::vector<std::tuple<std::string, cif::detail::ItemReference>> mCachedRefs;
|
||||
|
||||
mutable const Compound *mCompound = nullptr;
|
||||
|
||||
@@ -110,14 +111,17 @@ class Atom
|
||||
};
|
||||
|
||||
public:
|
||||
|
||||
Atom() {}
|
||||
|
||||
Atom(std::shared_ptr<AtomImpl> impl)
|
||||
: mImpl(impl) {}
|
||||
: mImpl(impl)
|
||||
{
|
||||
}
|
||||
|
||||
Atom(const Atom &rhs)
|
||||
: mImpl(rhs.mImpl) {}
|
||||
: mImpl(rhs.mImpl)
|
||||
{
|
||||
}
|
||||
|
||||
Atom(cif::Datablock &db, cif::Row &row);
|
||||
|
||||
@@ -152,10 +156,10 @@ class Atom
|
||||
set_property(name, std::to_string(value));
|
||||
}
|
||||
|
||||
const std::string &id() const { return impl().mID; }
|
||||
AtomType type() const { return impl().mType; }
|
||||
const std::string &id() const { return impl().mID; }
|
||||
AtomType type() const { return impl().mType; }
|
||||
|
||||
Point location() const { return impl().mLocation; }
|
||||
Point location() const { return impl().mLocation; }
|
||||
void location(Point p)
|
||||
{
|
||||
if (not mImpl)
|
||||
@@ -176,33 +180,33 @@ class Atom
|
||||
void translateRotateAndTranslate(Point t1, Quaternion q, Point t2);
|
||||
|
||||
// for direct access to underlying data, be careful!
|
||||
const cif::Row getRow() const { return impl().mRow; }
|
||||
const cif::Row getRow() const { return impl().mRow; }
|
||||
const cif::Row getRowAniso() const;
|
||||
|
||||
bool isSymmetryCopy() const { return impl().mSymmetryCopy; }
|
||||
std::string symmetry() const { return impl().mSymmetryOperator; }
|
||||
bool isSymmetryCopy() const { return impl().mSymmetryCopy; }
|
||||
std::string symmetry() const { return impl().mSymmetryOperator; }
|
||||
|
||||
const Compound &comp() const { return impl().comp(); }
|
||||
bool isWater() const { return impl().mCompID == "HOH" or impl().mCompID == "H2O" or impl().mCompID == "WAT"; }
|
||||
const Compound &comp() const { return impl().comp(); }
|
||||
bool isWater() const { return impl().mCompID == "HOH" or impl().mCompID == "H2O" or impl().mCompID == "WAT"; }
|
||||
int charge() const;
|
||||
|
||||
float uIso() const;
|
||||
bool getAnisoU(float anisou[6]) const { return impl().getAnisoU(anisou); }
|
||||
bool getAnisoU(float anisou[6]) const { return impl().getAnisoU(anisou); }
|
||||
float occupancy() const;
|
||||
|
||||
// specifications
|
||||
const std::string& labelAtomID() const { return impl().mAtomID; }
|
||||
const std::string& labelCompID() const { return impl().mCompID; }
|
||||
const std::string& labelAsymID() const { return impl().mAsymID; }
|
||||
const std::string &labelAtomID() const { return impl().mAtomID; }
|
||||
const std::string &labelCompID() const { return impl().mCompID; }
|
||||
const std::string &labelAsymID() const { return impl().mAsymID; }
|
||||
std::string labelEntityID() const;
|
||||
int labelSeqID() const { return impl().mSeqID; }
|
||||
const std::string& labelAltID() const { return impl().mAltID; }
|
||||
bool isAlternate() const { return not impl().mAltID.empty(); }
|
||||
int labelSeqID() const { return impl().mSeqID; }
|
||||
const std::string &labelAltID() const { return impl().mAltID; }
|
||||
bool isAlternate() const { return not impl().mAltID.empty(); }
|
||||
|
||||
std::string authAtomID() const;
|
||||
std::string authCompID() const;
|
||||
std::string authAsymID() const;
|
||||
const std::string& authSeqID() const { return impl().mAuthSeqID; }
|
||||
const std::string &authSeqID() const { return impl().mAuthSeqID; }
|
||||
std::string pdbxAuthInsCode() const;
|
||||
std::string pdbxAuthAltID() const;
|
||||
|
||||
@@ -210,6 +214,10 @@ class Atom
|
||||
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
|
||||
{
|
||||
return not operator==(rhs);
|
||||
}
|
||||
|
||||
// access data in compound for this atom
|
||||
|
||||
@@ -225,7 +233,7 @@ class Atom
|
||||
std::swap(mImpl, b.mImpl);
|
||||
}
|
||||
|
||||
int compare(const Atom &b) const { return impl().compare(*b.mImpl); }
|
||||
int compare(const Atom &b) const { return impl().compare(*b.mImpl); }
|
||||
|
||||
bool operator<(const Atom &rhs) const
|
||||
{
|
||||
@@ -234,11 +242,16 @@ class 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:
|
||||
friend class Structure;
|
||||
|
||||
void setID(int id);
|
||||
|
||||
const AtomImpl &impl() const
|
||||
{
|
||||
if (not mImpl)
|
||||
@@ -287,12 +300,19 @@ typedef std::vector<Atom> AtomView;
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
enum class EntityType
|
||||
{
|
||||
Polymer, NonPolymer, Macrolide, Water, Branched
|
||||
};
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
class Residue
|
||||
{
|
||||
public:
|
||||
// constructor
|
||||
Residue(const Structure &structure, const std::string &compoundID,
|
||||
const std::string &asymID, int seqID = 0, const std::string &authSeqID = {})
|
||||
const std::string &asymID, int seqID, const std::string &authSeqID)
|
||||
: mStructure(&structure)
|
||||
, mCompoundID(compoundID)
|
||||
, mAsymID(asymID)
|
||||
@@ -310,12 +330,11 @@ class Residue
|
||||
virtual ~Residue();
|
||||
|
||||
const Compound &compound() const;
|
||||
|
||||
AtomView &atoms();
|
||||
const AtomView &atoms() const;
|
||||
|
||||
void addAtom(const Atom &atom)
|
||||
{
|
||||
mAtoms.push_back(atom);
|
||||
}
|
||||
void addAtom(Atom &atom);
|
||||
|
||||
/// \brief Unique atoms returns only the atoms without alternates and the first of each alternate atom id.
|
||||
AtomView unique_atoms() const;
|
||||
@@ -332,6 +351,8 @@ class Residue
|
||||
int seqID() const { return mSeqID; }
|
||||
std::string entityID() const;
|
||||
|
||||
EntityType entityType() const;
|
||||
|
||||
std::string authAsymID() const;
|
||||
std::string authSeqID() const;
|
||||
std::string authInsCode() const;
|
||||
@@ -369,6 +390,16 @@ class Residue
|
||||
|
||||
friend Structure;
|
||||
|
||||
bool operator==(const mmcif::Residue &rhs) const
|
||||
{
|
||||
return this == &rhs or (
|
||||
mStructure == rhs.mStructure and
|
||||
mSeqID == rhs.mSeqID and
|
||||
mAsymID == rhs.mAsymID and
|
||||
mCompoundID == rhs.mCompoundID and
|
||||
mAuthSeqID == rhs.mAuthSeqID);
|
||||
}
|
||||
|
||||
protected:
|
||||
Residue() {}
|
||||
|
||||
@@ -377,9 +408,6 @@ class Residue
|
||||
const Structure *mStructure = nullptr;
|
||||
std::string mCompoundID, mAsymID;
|
||||
int mSeqID = 0;
|
||||
|
||||
// Watch out, this is used only to label waters... The rest of the code relies on
|
||||
// MapLabelToAuth to get this info. Perhaps we should rename this member field.
|
||||
std::string mAuthSeqID;
|
||||
AtomView mAtoms;
|
||||
};
|
||||
@@ -446,6 +474,11 @@ class Monomer : public Residue
|
||||
// for LEU and VAL
|
||||
float chiralVolume() const;
|
||||
|
||||
bool operator==(const Monomer &rhs) const
|
||||
{
|
||||
return mPolymer == rhs.mPolymer and mIndex == rhs.mIndex;
|
||||
}
|
||||
|
||||
private:
|
||||
const Polymer *mPolymer;
|
||||
size_t mIndex;
|
||||
@@ -483,35 +516,87 @@ class Polymer : public std::vector<Monomer>
|
||||
cif::RowSet mPolySeq;
|
||||
};
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
// Sugar and Branch, to describe glycosylation sites
|
||||
|
||||
class Branch;
|
||||
|
||||
class Sugar : public Residue
|
||||
{
|
||||
public:
|
||||
Sugar(const Branch &branch, const std::string &compoundID,
|
||||
const std::string &asymID, int authSeqID);
|
||||
|
||||
int num() const { return std::stoi(mAuthSeqID); }
|
||||
std::string name() const;
|
||||
|
||||
/// \brief Return the atom the C1 is linked to
|
||||
Atom getLink() const { return mLink; }
|
||||
void setLink(Atom link) { mLink = link; }
|
||||
|
||||
private:
|
||||
|
||||
const Branch &mBranch;
|
||||
Atom mLink;
|
||||
};
|
||||
|
||||
class Branch : public std::vector<Sugar>
|
||||
{
|
||||
public:
|
||||
Branch(Structure &structure, const std::string &asymID);
|
||||
|
||||
void linkAtoms();
|
||||
|
||||
std::string name() const;
|
||||
float weight() const;
|
||||
std::string asymID() const { return mAsymID; }
|
||||
|
||||
Structure &structure() { return *mStructure; }
|
||||
const Structure &structure() const { return *mStructure; }
|
||||
|
||||
Sugar &getSugarByNum(int nr);
|
||||
const Sugar &getSugarByNum(int nr) const;
|
||||
|
||||
private:
|
||||
friend Sugar;
|
||||
|
||||
std::string name(const Sugar &s) const;
|
||||
|
||||
Structure *mStructure;
|
||||
std::string mAsymID;
|
||||
};
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
// file is a reference to the data stored in e.g. the cif file.
|
||||
// This object is not copyable.
|
||||
|
||||
class File : public std::enable_shared_from_this<File>
|
||||
class File : public cif::File
|
||||
{
|
||||
public:
|
||||
File();
|
||||
File(const std::filesystem::path &path);
|
||||
File(const char *data, size_t length); // good luck trying to find out what it is...
|
||||
~File();
|
||||
File() {}
|
||||
|
||||
File(const std::filesystem::path &path)
|
||||
{
|
||||
load(path);
|
||||
}
|
||||
|
||||
File(const char *data, size_t length)
|
||||
{
|
||||
load(data, length);
|
||||
}
|
||||
|
||||
File(const File &) = delete;
|
||||
File &operator=(const File &) = delete;
|
||||
|
||||
cif::Datablock& createDatablock(const std::string_view name);
|
||||
void load(const std::filesystem::path &p) override;
|
||||
void save(const std::filesystem::path &p) override;
|
||||
|
||||
void load(const std::filesystem::path &path);
|
||||
void save(const std::filesystem::path &path);
|
||||
void load(std::istream &is) override;
|
||||
|
||||
Structure *model(size_t nr = 1);
|
||||
using cif::File::load;
|
||||
using cif::File::save;
|
||||
|
||||
struct FileImpl &impl() const { return *mImpl; }
|
||||
|
||||
cif::Datablock &data();
|
||||
cif::File &file();
|
||||
|
||||
private:
|
||||
struct FileImpl *mImpl;
|
||||
cif::Datablock &data() { return front(); }
|
||||
};
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
@@ -531,25 +616,46 @@ inline bool operator&(StructureOpenOptions a, StructureOpenOptions b)
|
||||
class Structure
|
||||
{
|
||||
public:
|
||||
Structure(File &p, size_t modelNr = 1, StructureOpenOptions options = {});
|
||||
Structure &operator=(const Structure &) = delete;
|
||||
~Structure();
|
||||
Structure(cif::File &p, size_t modelNr = 1, StructureOpenOptions options = {})
|
||||
: Structure(p.front(), modelNr, options)
|
||||
{
|
||||
}
|
||||
|
||||
Structure(cif::Datablock &db, size_t modelNr = 1, StructureOpenOptions options = {});
|
||||
|
||||
// Create a read-only clone of the current structure (for multithreaded calculations that move atoms)
|
||||
Structure(const Structure &);
|
||||
|
||||
File &getFile() const;
|
||||
Structure &operator=(const Structure &) = delete;
|
||||
~Structure();
|
||||
|
||||
const AtomView &atoms() const { return mAtoms; }
|
||||
// AtomView &atoms() { return mAtoms; }
|
||||
|
||||
EntityType getEntityTypeForEntityID(const std::string entityID) const;
|
||||
EntityType getEntityTypeForAsymID(const std::string asymID) const;
|
||||
|
||||
AtomView waters() const;
|
||||
|
||||
const std::list<Polymer> &polymers() const { return mPolymers; }
|
||||
std::list<Polymer> &polymers() { return mPolymers; }
|
||||
|
||||
const std::vector<Residue> &nonPolymers() const { return mNonPolymers; }
|
||||
const std::vector<Residue> &branchResidues() const { return mBranchResidues; }
|
||||
Polymer &getPolymerByAsymID(const std::string &asymID);
|
||||
|
||||
Atom getAtomByID(std::string id) const;
|
||||
const Polymer &getPolymerByAsymID(const std::string &asymID) const
|
||||
{
|
||||
return const_cast<Structure *>(this)->getPolymerByAsymID(asymID);
|
||||
}
|
||||
|
||||
const std::list<Branch> &branches() const { return mBranches; }
|
||||
std::list<Branch> &branches() { return mBranches; }
|
||||
|
||||
Branch &getBranchByAsymID(const std::string &asymID);
|
||||
const Branch &getBranchByAsymID(const std::string &asymID) const;
|
||||
|
||||
const std::vector<Residue> &nonPolymers() const { return mNonPolymers; }
|
||||
|
||||
Atom getAtomByID(const std::string &id) const;
|
||||
// Atom getAtomByLocation(Point pt, float maxDistance) const;
|
||||
|
||||
Atom getAtomByLabel(const std::string &atomID, const std::string &asymID,
|
||||
@@ -561,51 +667,64 @@ class Structure
|
||||
/// \brief Return the atom closest to point \a p with atom type \a type in a residue of type \a res_type
|
||||
Atom getAtomByPositionAndType(Point p, std::string_view type, std::string_view res_type) const;
|
||||
|
||||
/// \brief Get a residue, if \a seqID is zero, the non-polymers are searched
|
||||
const Residue &getResidue(const std::string &asymID, const std::string &compID, int seqID = 0) const;
|
||||
/// \brief Get a non-poly residue for an asym with id \a asymID
|
||||
Residue &getResidue(const std::string &asymID)
|
||||
{
|
||||
return getResidue(asymID, 0, "");
|
||||
}
|
||||
|
||||
/// \brief Get a residue, if \a seqID is zero, the non-polymers are searched
|
||||
Residue &getResidue(const std::string &asymID, const std::string &compID, int seqID = 0);
|
||||
/// \brief Get a non-poly residue for an asym with id \a asymID
|
||||
const Residue &getResidue(const std::string &asymID) const
|
||||
{
|
||||
return getResidue(asymID, 0, "");
|
||||
}
|
||||
|
||||
/// \brief Get a the single residue for an asym with id \a asymID
|
||||
const Residue &getResidue(const std::string &asymID) const;
|
||||
/// \brief Get a residue for an asym with id \a asymID seq id \a seqID and authSeqID \a authSeqID
|
||||
Residue &getResidue(const std::string &asymID, int seqID, const std::string &authSeqID);
|
||||
|
||||
/// \brief Get a the single residue for an asym with id \a asymID
|
||||
Residue &getResidue(const std::string &asymID);
|
||||
/// \brief Get a the single residue for an asym with id \a asymID seq id \a seqID and authSeqID \a authSeqID
|
||||
const Residue &getResidue(const std::string &asymID, int seqID, const std::string &authSeqID) const
|
||||
{
|
||||
return const_cast<Structure *>(this)->getResidue(asymID, seqID, authSeqID);
|
||||
}
|
||||
|
||||
/// \brief Get a residue for an asym with id \a asymID, compound id \a compID, seq id \a seqID and authSeqID \a authSeqID
|
||||
Residue &getResidue(const std::string &asymID, const std::string &compID, int seqID, const std::string &authSeqID);
|
||||
|
||||
/// \brief Get a residue for an asym with id \a asymID, compound id \a compID, seq id \a seqID and authSeqID \a authSeqID
|
||||
const Residue &getResidue(const std::string &asymID, const std::string &compID, int seqID, const std::string &authSeqID) const
|
||||
{
|
||||
return const_cast<Structure *>(this)->getResidue(asymID, compID, seqID, authSeqID);
|
||||
}
|
||||
|
||||
/// \brief Get a the residue for atom \a atom
|
||||
Residue &getResidue(const mmcif::Atom &atom);
|
||||
Residue &getResidue(const mmcif::Atom &atom)
|
||||
{
|
||||
return getResidue(atom.labelAsymID(), atom.labelCompID(), atom.labelSeqID(), atom.authSeqID());
|
||||
}
|
||||
|
||||
/// \brief Get a the residue for atom \a atom
|
||||
const Residue &getResidue(const mmcif::Atom &atom) const;
|
||||
|
||||
// map between auth and label locations
|
||||
|
||||
std::tuple<std::string, int, std::string> MapAuthToLabel(const std::string &asymID,
|
||||
const std::string &seqID, const std::string &compID, const std::string &insCode = "");
|
||||
|
||||
std::tuple<std::string, std::string, std::string, std::string> MapLabelToAuth(
|
||||
const std::string &asymID, int seqID, const std::string &compID);
|
||||
|
||||
// returns chain, seqnr, icode
|
||||
std::tuple<char, int, char> MapLabelToAuth(
|
||||
const std::string &asymID, int seqID) const;
|
||||
|
||||
// returns chain,seqnr,comp,iCode
|
||||
std::tuple<std::string, int, std::string, std::string> MapLabelToPDB(
|
||||
const std::string &asymID, int seqID, const std::string &compID,
|
||||
const std::string &authSeqID) const;
|
||||
|
||||
std::tuple<std::string, int, std::string> MapPDBToLabel(
|
||||
const std::string &asymID, int seqID, const std::string &compID, const std::string &iCode) const;
|
||||
const Residue &getResidue(const mmcif::Atom &atom) const
|
||||
{
|
||||
return getResidue(atom.labelAsymID(), atom.labelCompID(), atom.labelSeqID(), atom.authSeqID());
|
||||
}
|
||||
|
||||
// Actions
|
||||
void removeAtom(Atom &a);
|
||||
void swapAtoms(Atom &a1, Atom &a2); // swap the labels for these atoms
|
||||
void moveAtom(Atom &a, Point p); // move atom to a new location
|
||||
void swapAtoms(Atom a1, Atom a2); // swap the labels for these atoms
|
||||
void moveAtom(Atom a, Point p); // move atom to a new location
|
||||
void changeResidue(Residue &res, const std::string &newCompound,
|
||||
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 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
|
||||
/// \return The ID of the created entity
|
||||
@@ -627,9 +746,25 @@ class Structure
|
||||
/// \return The newly create asym ID
|
||||
std::string createNonpoly(const std::string &entity_id, std::vector<std::vector<cif::Item>> &atom_info);
|
||||
|
||||
/// \brief To sort the atoms in order of model > asym-id > res-id > atom-id
|
||||
/// Will asssign new atom_id's to all atoms. Be carefull
|
||||
void sortAtoms();
|
||||
/// \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_atom_info);
|
||||
|
||||
/// \brief Extend an existing (sugar) branch identified by \a asymID with one sugar containing atoms constructed from \a atom_info
|
||||
///
|
||||
/// \param asym_id The asym id of the branch to extend
|
||||
/// \param atom_info Array containing the info for the atoms to construct for the new sugar
|
||||
/// \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
|
||||
///
|
||||
/// \param res The residue to remove
|
||||
void removeResidue(mmcif::Residue &res);
|
||||
|
||||
/// \brief Translate the coordinates of all atoms in the structure by \a t
|
||||
void translate(Point t);
|
||||
@@ -644,33 +779,49 @@ class Structure
|
||||
void translateRotateAndTranslate(Point t1, Quaternion q, Point t2);
|
||||
|
||||
const std::vector<Residue> &getNonPolymers() const { return mNonPolymers; }
|
||||
const std::vector<Residue> &getBranchResidues() const { return mBranchResidues; }
|
||||
|
||||
void cleanupEmptyCategories();
|
||||
|
||||
/// \brief Direct access to underlying data
|
||||
cif::Category &category(std::string_view name) const;
|
||||
cif::Datablock &datablock() const;
|
||||
cif::Category &category(std::string_view name) const
|
||||
{
|
||||
return mDb[name];
|
||||
}
|
||||
|
||||
cif::Datablock &datablock() const
|
||||
{
|
||||
return mDb;
|
||||
}
|
||||
|
||||
void validateAtoms() const;
|
||||
|
||||
private:
|
||||
friend Polymer;
|
||||
friend Residue;
|
||||
// friend residue_view;
|
||||
// friend residue_iterator;
|
||||
|
||||
std::string insertCompound(const std::string &compoundID, bool isEntity);
|
||||
|
||||
std::string createEntityForBranch(Branch &branch);
|
||||
|
||||
void loadData();
|
||||
void updateAtomIndex();
|
||||
|
||||
void loadAtomsForModel(StructureOpenOptions options);
|
||||
|
||||
File &mFile;
|
||||
template<typename... Args>
|
||||
Atom& emplace_atom(Args ...args)
|
||||
{
|
||||
return emplace_atom(Atom{std::forward<Args>(args)...});
|
||||
}
|
||||
|
||||
Atom &emplace_atom(Atom &&atom);
|
||||
|
||||
cif::Datablock &mDb;
|
||||
size_t mModelNr;
|
||||
AtomView mAtoms;
|
||||
std::vector<size_t> mAtomIndex;
|
||||
std::list<Polymer> mPolymers;
|
||||
std::vector<Residue> mNonPolymers, mBranchResidues;
|
||||
std::list<Branch> mBranches;
|
||||
std::vector<Residue> mNonPolymers;
|
||||
};
|
||||
|
||||
} // namespace mmcif
|
||||
|
||||
254
src/AtomType.cpp
254
src/AtomType.cpp
@@ -159,11 +159,221 @@ const AtomTypeInfo kKnownAtoms[] =
|
||||
{ Ts, "Tennessine", "Ts", 294, true, { kNA, kNA, kNA, 165, kNA, kNA, kNA } }, // 117 Ts Tennessine
|
||||
{ Og, "Oganesson", "Og", 294, true, { kNA, kNA, kNA, 157, kNA, kNA, kNA } }, // 118 Og Oganesson
|
||||
|
||||
{ D, "Deuterium", "D", 2.014f, false, { 53, 25, 37, 32, kNA, kNA, 120 } }, // 1 D Deuterium
|
||||
{ D, "Deuterium", "D", 2.014f, false, { 53, 25, 37, 32, kNA, kNA, 120 } }, // 1 D Deuterium
|
||||
};
|
||||
|
||||
uint32_t kKnownAtomsCount = sizeof(kKnownAtoms) / sizeof(AtomTypeInfo);
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
// Crystal ionic radii, as taken from Wikipedia (https://en.m.wikipedia.org/wiki/Ionic_radius)
|
||||
|
||||
const struct IonicRadii
|
||||
{
|
||||
AtomType type;
|
||||
float radii[11];
|
||||
} kCrystalIonicRadii[] = {
|
||||
{ H, { kNA, kNA, 208, -4, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Hydrogen
|
||||
{ Li, { kNA, kNA, kNA, 90, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Lithium
|
||||
{ Be, { kNA, kNA, kNA, kNA, 59, kNA, kNA, kNA, kNA, kNA, kNA } }, // Beryllium
|
||||
{ B, { kNA, kNA, kNA, kNA, kNA, 41, kNA, kNA, kNA, kNA, kNA } }, // Boron
|
||||
{ C, { kNA, kNA, kNA, kNA, kNA, kNA, 30, kNA, kNA, kNA, kNA } }, // Carbon
|
||||
{ N, { 132, kNA, kNA, kNA, kNA, 30, kNA, 27, kNA, kNA, kNA } }, // Nitrogen
|
||||
{ O, { kNA, 126, kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Oxygen
|
||||
{ F, { kNA, kNA, 119, kNA, kNA, kNA, kNA, kNA, kNA, 22, kNA } }, // Fluorine
|
||||
{ Na, { kNA, kNA, kNA, 116, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Sodium
|
||||
{ Mg, { kNA, kNA, kNA, kNA, 86, kNA, kNA, kNA, kNA, kNA, kNA } }, // Magnesium
|
||||
{ Al, { kNA, kNA, kNA, kNA, kNA, 67.5, kNA, kNA, kNA, kNA, kNA } }, // Aluminium
|
||||
{ Si, { kNA, kNA, kNA, kNA, kNA, kNA, 54, kNA, kNA, kNA, kNA } }, // Silicon
|
||||
{ P, { kNA, kNA, kNA, kNA, kNA, 58, kNA, 52, kNA, kNA, kNA } }, // Phosphorus
|
||||
{ S, { kNA, 170, kNA, kNA, kNA, kNA, 51, kNA, 43, kNA, kNA } }, // Sulfur
|
||||
{ Cl, { kNA, kNA, 181, kNA, kNA, kNA, kNA, 26, kNA, 41, kNA } }, // Chlorine
|
||||
{ K, { kNA, kNA, kNA, 152, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Potassium
|
||||
{ Ca, { kNA, kNA, kNA, kNA, 114, kNA, kNA, kNA, kNA, kNA, kNA } }, // Calcium
|
||||
{ Sc, { kNA, kNA, kNA, kNA, kNA, 88.5, kNA, kNA, kNA, kNA, kNA } }, // Scandium
|
||||
{ Ti, { kNA, kNA, kNA, kNA, 100, 81, 74.5, kNA, kNA, kNA, kNA } }, // Titanium
|
||||
{ V, { kNA, kNA, kNA, kNA, 93, 78, 72, 68, kNA, kNA, kNA } }, // Vanadium
|
||||
{ Cr, { kNA, kNA, kNA, kNA, 87, 75.5, 69, 63, 58, kNA, kNA } }, // Chromium ls
|
||||
// { Cr,{ kNA, kNA, kNA, kNA, 94, kNA, kNA, kNA, kNA, kNA, kNA } }, // Chromium hs
|
||||
{ Mn, { kNA, kNA, kNA, kNA, 81, 72, 67, 47, 39.5, 60, kNA } }, // Manganese ls
|
||||
// { Mn,{ kNA, kNA, kNA, kNA, 97, 78.5, kNA, kNA, kNA, kNA, kNA } }, // Manganese hs
|
||||
{ Fe, { kNA, kNA, kNA, kNA, 75, 69, 72.5, kNA, 39, kNA, kNA } }, // Iron ls
|
||||
// { Fe,{ kNA, kNA, kNA, kNA, 92, 78.5, kNA, kNA, kNA, kNA, kNA } }, // Iron hs
|
||||
{ Co, { kNA, kNA, kNA, kNA, 79, 68.5, kNA, kNA, kNA, kNA, kNA } }, // Cobalt ls
|
||||
// { Co,{ kNA, kNA, kNA, kNA, 88.5, 75, 67, kNA, kNA, kNA, kNA } }, // Cobalt hs
|
||||
{ Ni, { kNA, kNA, kNA, kNA, 83, 70, 62, kNA, kNA, kNA, kNA } }, // Nickel ls
|
||||
// { Ni,{ kNA, kNA, kNA, kNA, kNA, 74, kNA, kNA, kNA, kNA, kNA } }, // Nickel hs
|
||||
{ Cu, { kNA, kNA, kNA, 91, 87, 68, kNA, kNA, kNA, kNA, kNA } }, // Copper
|
||||
{ Zn, { kNA, kNA, kNA, kNA, 88 , kNA, kNA, kNA, kNA, kNA, kNA } }, // Zinc
|
||||
{ Ga, { kNA, kNA, kNA, kNA, kNA, 76, kNA, kNA, kNA, kNA, kNA } }, // Gallium
|
||||
{ Ge, { kNA, kNA, kNA, kNA, 87, kNA, 67, kNA, kNA, kNA, kNA } }, // Germanium
|
||||
{ As, { kNA, kNA, kNA, kNA, kNA, 72, kNA, 60, kNA, kNA, kNA } }, // Arsenic
|
||||
{ Se, { kNA, 184, kNA, kNA, kNA, kNA, 64, kNA, 56, kNA, kNA } }, // Selenium
|
||||
{ Br, { kNA, kNA, 182, kNA, kNA, 73, kNA, 45, kNA, 53, kNA } }, // Bromine
|
||||
{ Rb, { kNA, kNA, kNA, 166, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Rubidium
|
||||
{ Sr, { kNA, kNA, kNA, kNA, 132, kNA, kNA, kNA, kNA, kNA, kNA } }, // Strontium
|
||||
{ Y, { kNA, kNA, kNA, kNA, kNA, 104, kNA, kNA, kNA, kNA, kNA } }, // Yttrium
|
||||
{ Zr, { kNA, kNA, kNA, kNA, kNA, kNA, 86, kNA, kNA, kNA, kNA } }, // Zirconium
|
||||
{ Nb, { kNA, kNA, kNA, kNA, kNA, 86, 82, 78, kNA, kNA, kNA } }, // Niobium
|
||||
{ Mo, { kNA, kNA, kNA, kNA, kNA, 83, 79, 75, 73, kNA, kNA } }, // Molybdenum
|
||||
{ Tc, { kNA, kNA, kNA, kNA, kNA, kNA, 78.5, 74, kNA, 70, kNA } }, // Technetium
|
||||
{ Ru, { kNA, kNA, kNA, kNA, kNA, 82, 76, 70.5, kNA, 52, 150 } }, // Ruthenium
|
||||
{ Rh, { kNA, kNA, kNA, kNA, kNA, 80.5, 74, 69, kNA, kNA, kNA } }, // Rhodium
|
||||
{ Pd, { kNA, kNA, kNA, 73, 100, 90, 75.5, kNA, kNA, kNA, kNA } }, // Palladium
|
||||
{ Ag, { kNA, kNA, kNA, 129, 108, 89, kNA, kNA, kNA, kNA, kNA } }, // Silver
|
||||
{ Cd, { kNA, kNA, kNA, kNA, 109, kNA, kNA, kNA, kNA, kNA, kNA } }, // Cadmium
|
||||
{ In, { kNA, kNA, kNA, kNA, kNA, 94, kNA, kNA, kNA, kNA, kNA } }, // Indium
|
||||
{ Sn, { kNA, kNA, kNA, kNA, kNA, kNA, 83, kNA, kNA, kNA, kNA } }, // Tin
|
||||
{ Sb, { kNA, kNA, kNA, kNA, kNA, 90, kNA, 74, kNA, kNA, kNA } }, // Antimony
|
||||
{ Te, { kNA, 207, kNA, kNA, kNA, kNA, 111, kNA, 70, kNA, kNA } }, // Tellurium
|
||||
{ I, { kNA, kNA, 206, kNA, kNA, kNA, kNA, 109, kNA, 67, kNA } }, // Iodine
|
||||
{ Xe, { kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, 62 } }, // Xenon
|
||||
{ Cs, { kNA, kNA, kNA, 167, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Caesium
|
||||
{ Ba, { kNA, kNA, kNA, kNA, 149, kNA, kNA, kNA, kNA, kNA, kNA } }, // Barium
|
||||
{ La, { kNA, kNA, kNA, kNA, kNA, 117.2, kNA, kNA, kNA, kNA, kNA } }, // Lanthanum
|
||||
{ Ce, { kNA, kNA, kNA, kNA, kNA, 115, 101, kNA, kNA, kNA, kNA } }, // Cerium
|
||||
{ Pr, { kNA, kNA, kNA, kNA, kNA, 113, 99, kNA, kNA, kNA, kNA } }, // Praseodymium
|
||||
{ Nd, { kNA, kNA, kNA, kNA, 143, 112.3, kNA, kNA, kNA, kNA, kNA } }, // Neodymium
|
||||
{ Pm, { kNA, kNA, kNA, kNA, kNA, 111, kNA, kNA, kNA, kNA, kNA } }, // Promethium
|
||||
{ Sm, { kNA, kNA, kNA, kNA, 136, 109.8, kNA, kNA, kNA, kNA, kNA } }, // Samarium
|
||||
{ Eu, { kNA, kNA, kNA, kNA, 131, 108.7, kNA, kNA, kNA, kNA, kNA } }, // Europium
|
||||
{ Gd, { kNA, kNA, kNA, kNA, kNA, 107.8, kNA, kNA, kNA, kNA, kNA } }, // Gadolinium
|
||||
{ Tb, { kNA, kNA, kNA, kNA, kNA, 106.3, 90, kNA, kNA, kNA, kNA } }, // Terbium
|
||||
{ Dy, { kNA, kNA, kNA, kNA, 121, 105.2, kNA, kNA, kNA, kNA, kNA } }, // Dysprosium
|
||||
{ Ho, { kNA, kNA, kNA, kNA, kNA, 104.1, kNA, kNA, kNA, kNA, kNA } }, // Holmium
|
||||
{ Er, { kNA, kNA, kNA, kNA, kNA, 103, kNA, kNA, kNA, kNA, kNA } }, // Erbium
|
||||
{ Tm, { kNA, kNA, kNA, kNA, 117, 102, kNA, kNA, kNA, kNA, kNA } }, // Thulium
|
||||
{ Yb, { kNA, kNA, kNA, kNA, 116, 100.8, kNA, kNA, kNA, kNA, kNA } }, // Ytterbium
|
||||
{ Lu, { kNA, kNA, kNA, kNA, kNA, 100.1, kNA, kNA, kNA, kNA, kNA } }, // Lutetium
|
||||
{ Hf, { kNA, kNA, kNA, kNA, kNA, kNA, 85, kNA, kNA, kNA, kNA } }, // Hafnium
|
||||
{ Ta, { kNA, kNA, kNA, kNA, kNA, 86, 82, 78, kNA, kNA, kNA } }, // Tantalum
|
||||
{ W, { kNA, kNA, kNA, kNA, kNA, kNA, 80, 76, 74, kNA, kNA } }, // Tungsten
|
||||
{ Re, { kNA, kNA, kNA, kNA, kNA, kNA, 77, 72, 69, 67, kNA } }, // Rhenium
|
||||
{ Os, { kNA, kNA, kNA, kNA, kNA, kNA, 77, 71.5, 68.5, 66.5, 53 } }, // Osmium
|
||||
{ Ir, { kNA, kNA, kNA, kNA, kNA, 82, 76.5, 71, kNA, kNA, kNA } }, // Iridium
|
||||
{ Pt, { kNA, kNA, kNA, kNA, 94, kNA, 76.5, 71, kNA, kNA, kNA } }, // Platinum
|
||||
{ Au, { kNA, kNA, kNA, 151, kNA, 99, kNA, 71, kNA, kNA, kNA } }, // Gold
|
||||
{ Hg, { kNA, kNA, kNA, 133, 116, kNA, kNA, kNA, kNA, kNA, kNA } }, // Mercury
|
||||
{ Tl, { kNA, kNA, kNA, 164, kNA, 102.5, kNA, kNA, kNA, kNA, kNA } }, // Thallium
|
||||
{ Pb, { kNA, kNA, kNA, kNA, 133, kNA, 91.5, kNA, kNA, kNA, kNA } }, // Lead
|
||||
{ Bi, { kNA, kNA, kNA, kNA, kNA, 117, kNA, 90, kNA, kNA, kNA } }, // Bismuth
|
||||
{ Po, { kNA, kNA, kNA, kNA, kNA, kNA, 108, kNA, 81, kNA, kNA } }, // Polonium
|
||||
{ At, { kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, 76, kNA } }, // Astatine
|
||||
{ Fr, { kNA, kNA, kNA, 194, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Francium
|
||||
{ Ra, { kNA, kNA, kNA, kNA, 162, kNA, kNA, kNA, kNA, kNA, kNA } }, // Radium
|
||||
{ Ac, { kNA, kNA, kNA, kNA, kNA, 126, kNA, kNA, kNA, kNA, kNA } }, // Actinium
|
||||
{ Th, { kNA, kNA, kNA, kNA, kNA, kNA, 108, kNA, kNA, kNA, kNA } }, // Thorium
|
||||
{ Pa, { kNA, kNA, kNA, kNA, kNA, 116, 104, 92, kNA, kNA, kNA } }, // Protactinium
|
||||
{ U, { kNA, kNA, kNA, kNA, kNA, 116.5, 103, 90, 87, kNA, kNA } }, // Uranium
|
||||
{ Np, { kNA, kNA, kNA, kNA, 124, 115, 101, 89, 86, 85, kNA } }, // Neptunium
|
||||
{ Pu, { kNA, kNA, kNA, kNA, kNA, 114, 100, 88, 85, kNA, kNA } }, // Plutonium
|
||||
{ Am, { kNA, kNA, kNA, kNA, 140, 111.5, 99, kNA, kNA, kNA, kNA } }, // Americium
|
||||
{ Cm, { kNA, kNA, kNA, kNA, kNA, 111, 99, kNA, kNA, kNA, kNA } }, // Curium
|
||||
{ Bk, { kNA, kNA, kNA, kNA, kNA, 110, 97, kNA, kNA, kNA, kNA } }, // Berkelium
|
||||
{ Cf, { kNA, kNA, kNA, kNA, kNA, 109, 96.1, kNA, kNA, kNA, kNA } }, // Californium
|
||||
{ Es, { kNA, kNA, kNA, kNA, kNA, 92.8, kNA, kNA, kNA, kNA, kNA } }, // Einsteinium
|
||||
}, kEffectiveIonicRadii[] = {
|
||||
{ H, { kNA, kNA, 139.9, -18, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Hydrogen
|
||||
{ Li, { kNA, kNA, kNA, 76, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Lithium
|
||||
{ Be, { kNA, kNA, kNA, kNA, 45, kNA, kNA, kNA, kNA, kNA, kNA } }, // Beryllium
|
||||
{ B, { kNA, kNA, kNA, kNA, kNA, 27, kNA, kNA, kNA, kNA, kNA } }, // Boron
|
||||
{ C, { kNA, kNA, kNA, kNA, kNA, kNA, 16, kNA, kNA, kNA, kNA } }, // Carbon
|
||||
{ N, { 146, kNA, kNA, kNA, kNA, 16, kNA, 13, kNA, kNA, kNA } }, // Nitrogen
|
||||
{ O, { kNA, 140, kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Oxygen
|
||||
{ F, { kNA, kNA, 133, kNA, kNA, kNA, kNA, kNA, kNA, 8, kNA } }, // Fluorine
|
||||
{ Na, { kNA, kNA, kNA, 102, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Sodium
|
||||
{ Mg, { kNA, kNA, kNA, kNA, 72, kNA, kNA, kNA, kNA, kNA, kNA } }, // Magnesium
|
||||
{ Al, { kNA, kNA, kNA, kNA, kNA, 53.5, kNA, kNA, kNA, kNA, kNA } }, // Aluminium
|
||||
{ Si, { kNA, kNA, kNA, kNA, kNA, kNA, 40, kNA, kNA, kNA, kNA } }, // Silicon
|
||||
{ P, { 212, kNA, kNA, kNA, kNA, 44, kNA, 38, kNA, kNA, kNA } }, // Phosphorus
|
||||
{ S, { kNA, 184, kNA, kNA, kNA, kNA, 37, kNA, 29, kNA, kNA } }, // Sulfur
|
||||
{ Cl, { kNA, kNA, 181, kNA, kNA, kNA, kNA, 12, kNA, 27, kNA } }, // Chlorine
|
||||
{ K, { kNA, kNA, kNA, 138, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Potassium
|
||||
{ Ca, { kNA, kNA, kNA, kNA, 100, kNA, kNA, kNA, kNA, kNA, kNA } }, // Calcium
|
||||
{ Sc, { kNA, kNA, kNA, kNA, kNA, 74.5, kNA, kNA, kNA, kNA, kNA } }, // Scandium
|
||||
{ Ti, { kNA, kNA, kNA, kNA, 86, 67, 60.5, kNA, kNA, kNA, kNA } }, // Titanium
|
||||
{ V, { kNA, kNA, kNA, kNA, 79, 64, 58, 54, kNA, kNA, kNA } }, // Vanadium
|
||||
{ Cr, { kNA, kNA, kNA, kNA, 73, 61.5, 55, 49, 44, kNA, kNA } }, // Chromium ls
|
||||
{ Cr, { kNA, kNA, kNA, kNA, 80, kNA, kNA, kNA, kNA, kNA, kNA } }, // Chromium hs
|
||||
{ Mn, { kNA, kNA, kNA, kNA, 67, 58, 53, 33, 25.5, 46, kNA } }, // Manganese ls
|
||||
{ Mn, { kNA, kNA, kNA, kNA, 83, 64.5, kNA, kNA, kNA, kNA, kNA } }, // Manganese hs
|
||||
{ Fe, { kNA, kNA, kNA, kNA, 61, 55, 58.5, kNA, 25, kNA, kNA } }, // Iron ls
|
||||
{ Fe, { kNA, kNA, kNA, kNA, 78, 64.5, kNA, kNA, kNA, kNA, kNA } }, // Iron hs
|
||||
{ Co, { kNA, kNA, kNA, kNA, 65, 54.5, kNA, kNA, kNA, kNA, kNA } }, // Cobalt ls
|
||||
{ Co, { kNA, kNA, kNA, kNA, 74.5, 61, 53, kNA, kNA, kNA, kNA } }, // Cobalt hs
|
||||
{ Ni, { kNA, kNA, kNA, kNA, 69, 56, 48, kNA, kNA, kNA, kNA } }, // Nickel ls
|
||||
{ Ni, { kNA, kNA, kNA, kNA, kNA, 60, kNA, kNA, kNA, kNA, kNA } }, // Nickel hs
|
||||
{ Cu, { kNA, kNA, kNA, 77, 73, 54, kNA, kNA, kNA, kNA, kNA } }, // Copper
|
||||
{ Zn, { kNA, kNA, kNA, kNA, 74, kNA, kNA, kNA, kNA, kNA, kNA } }, // Zinc
|
||||
{ Ga, { kNA, kNA, kNA, kNA, kNA, 62, kNA, kNA, kNA, kNA, kNA } }, // Gallium
|
||||
{ Ge, { kNA, kNA, kNA, kNA, 73, kNA, 53, kNA, kNA, kNA, kNA } }, // Germanium
|
||||
{ As, { kNA, kNA, kNA, kNA, kNA, 58, kNA, 46, kNA, kNA, kNA } }, // Arsenic
|
||||
{ Se, { kNA, 198, kNA, kNA, kNA, kNA, 50, kNA, 42, kNA, kNA } }, // Selenium
|
||||
{ Br, { kNA, kNA, 196, kNA, kNA, 59, kNA, 31, kNA, 39, kNA } }, // Bromine
|
||||
{ Rb, { kNA, kNA, kNA, 152, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Rubidium
|
||||
{ Sr, { kNA, kNA, kNA, kNA, 118, kNA, kNA, kNA, kNA, kNA, kNA } }, // Strontium
|
||||
{ Y, { kNA, kNA, kNA, kNA, kNA, 90, kNA, kNA, kNA, kNA, kNA } }, // Yttrium
|
||||
{ Zr, { kNA, kNA, kNA, kNA, kNA, kNA, 72, kNA, kNA, kNA, kNA } }, // Zirconium
|
||||
{ Nb, { kNA, kNA, kNA, kNA, kNA, 72, 68, 64, kNA, kNA, kNA } }, // Niobium
|
||||
{ Mo, { kNA, kNA, kNA, kNA, kNA, 69, 65, 61, 59, kNA, kNA } }, // Molybdenum
|
||||
{ Tc, { kNA, kNA, kNA, kNA, kNA, kNA, 64.5, 60, kNA, 56, kNA } }, // Technetium
|
||||
{ Ru, { kNA, kNA, kNA, kNA, kNA, 68, 62, 56.5, kNA, 38, 36 } }, // Ruthenium
|
||||
{ Rh, { kNA, kNA, kNA, kNA, kNA, 66.5, 60, 55, kNA, kNA, kNA } }, // Rhodium
|
||||
{ Pd, { kNA, kNA, kNA, 59, 86, 76, 61.5, kNA, kNA, kNA, kNA } }, // Palladium
|
||||
{ Ag, { kNA, kNA, kNA, 115, 94, 75, kNA, kNA, kNA, kNA, kNA } }, // Silver
|
||||
{ Cd, { kNA, kNA, kNA, kNA, 95, kNA, kNA, kNA, kNA, kNA, kNA } }, // Cadmium
|
||||
{ In, { kNA, kNA, kNA, kNA, kNA, 80, kNA, kNA, kNA, kNA, kNA } }, // Indium
|
||||
{ Sn, { kNA, kNA, kNA, kNA, 118, kNA, 69, kNA, kNA, kNA, kNA } }, // Tin
|
||||
{ Sb, { kNA, kNA, kNA, kNA, kNA, 76, kNA, 60, kNA, kNA, kNA } }, // Antimony
|
||||
{ Te, { kNA, 221, kNA, kNA, kNA, kNA, 97, kNA, 56, kNA, kNA } }, // Tellurium
|
||||
{ I, { kNA, kNA, 220, kNA, kNA, kNA, kNA, 95, kNA, 53, kNA } }, // Iodine
|
||||
{ Xe, { kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, 48 } }, // Xenon
|
||||
{ Cs, { kNA, kNA, kNA, 167, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Caesium
|
||||
{ Ba, { kNA, kNA, kNA, kNA, 135, kNA, kNA, kNA, kNA, kNA, kNA } }, // Barium
|
||||
{ La, { kNA, kNA, kNA, kNA, kNA, 103.2, kNA, kNA, kNA, kNA, kNA } }, // Lanthanum
|
||||
{ Ce, { kNA, kNA, kNA, kNA, kNA, 101, 87, kNA, kNA, kNA, kNA } }, // Cerium
|
||||
{ Pr, { kNA, kNA, kNA, kNA, kNA, 99, 85, kNA, kNA, kNA, kNA } }, // Praseodymium
|
||||
{ Nd, { kNA, kNA, kNA, kNA, 129, 98.3, kNA, kNA, kNA, kNA, kNA } }, // Neodymium
|
||||
{ Pm, { kNA, kNA, kNA, kNA, kNA, 97, kNA, kNA, kNA, kNA, kNA } }, // Promethium
|
||||
{ Sm, { kNA, kNA, kNA, kNA, 122, 95.8, kNA, kNA, kNA, kNA, kNA } }, // Samarium
|
||||
{ Eu, { kNA, kNA, kNA, kNA, 117, 94.7, kNA, kNA, kNA, kNA, kNA } }, // Europium
|
||||
{ Gd, { kNA, kNA, kNA, kNA, kNA, 93.5, kNA, kNA, kNA, kNA, kNA } }, // Gadolinium
|
||||
{ Tb, { kNA, kNA, kNA, kNA, kNA, 92.3, 76, kNA, kNA, kNA, kNA } }, // Terbium
|
||||
{ Dy, { kNA, kNA, kNA, kNA, 107, 91.2, kNA, kNA, kNA, kNA, kNA } }, // Dysprosium
|
||||
{ Ho, { kNA, kNA, kNA, kNA, kNA, 90.1, kNA, kNA, kNA, kNA, kNA } }, // Holmium
|
||||
{ Er, { kNA, kNA, kNA, kNA, kNA, 89, kNA, kNA, kNA, kNA, kNA } }, // Erbium
|
||||
{ Tm, { kNA, kNA, kNA, kNA, 103, 88, kNA, kNA, kNA, kNA, kNA } }, // Thulium
|
||||
{ Yb, { kNA, kNA, kNA, kNA, 102, 86.8, kNA, kNA, kNA, kNA, kNA } }, // Ytterbium
|
||||
{ Lu, { kNA, kNA, kNA, kNA, kNA, 86.1, kNA, kNA, kNA, kNA, kNA } }, // Lutetium
|
||||
{ Hf, { kNA, kNA, kNA, kNA, kNA, kNA, 71, kNA, kNA, kNA, kNA } }, // Hafnium
|
||||
{ Ta, { kNA, kNA, kNA, kNA, kNA, 72, 68, 64, kNA, kNA, kNA } }, // Tantalum
|
||||
{ W, { kNA, kNA, kNA, kNA, kNA, kNA, 66, 62, 60, kNA, kNA } }, // Tungsten
|
||||
{ Re, { kNA, kNA, kNA, kNA, kNA, kNA, 63, 58, 55, 53, kNA } }, // Rhenium
|
||||
{ Os, { kNA, kNA, kNA, kNA, kNA, kNA, 63, 57.5, 54.5, 52.5, 39 } }, // Osmium
|
||||
{ Ir, { kNA, kNA, kNA, kNA, kNA, 68, 62.5, 57, kNA, kNA, kNA } }, // Iridium
|
||||
{ Pt, { kNA, kNA, kNA, kNA, 80, kNA, 62.5, 57, kNA, kNA, kNA } }, // Platinum
|
||||
{ Au, { kNA, kNA, kNA, 137, kNA, 85, kNA, 57, kNA, kNA, kNA } }, // Gold
|
||||
{ Hg, { kNA, kNA, kNA, 119, 102, kNA, kNA, kNA, kNA, kNA, kNA } }, // Mercury
|
||||
{ Tl, { kNA, kNA, kNA, 150, kNA, 88.5, kNA, kNA, kNA, kNA, kNA } }, // Thallium
|
||||
{ Pb, { kNA, kNA, kNA, kNA, 119, kNA, 77.5, kNA, kNA, kNA, kNA } }, // Lead
|
||||
{ Bi, { kNA, kNA, kNA, kNA, kNA, 103, kNA, 76, kNA, kNA, kNA } }, // Bismuth
|
||||
{ Po, { kNA, 223, kNA, kNA, kNA, kNA, 94, kNA, 67, kNA, kNA } }, // Polonium
|
||||
{ At, { kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, 62, kNA } }, // Astatine
|
||||
{ Fr, { kNA, kNA, kNA, 180, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Francium
|
||||
{ Ra, { kNA, kNA, kNA, kNA, 148, kNA, kNA, kNA, kNA, kNA, kNA } }, // Radium
|
||||
{ Ac, { kNA, kNA, kNA, kNA, kNA, 106.5, kNA, kNA, kNA, kNA, kNA } }, // Actinium
|
||||
{ Th, { kNA, kNA, kNA, kNA, kNA, kNA, 94, kNA, kNA, kNA, kNA } }, // Thorium
|
||||
{ Pa, { kNA, kNA, kNA, kNA, kNA, 104, 90, 78, kNA, kNA, kNA } }, // Protactinium
|
||||
{ U, { kNA, kNA, kNA, kNA, kNA, 102.5, 89, 76, 73, kNA, kNA } }, // Uranium
|
||||
{ Np, { kNA, kNA, kNA, kNA, 110, 101, 87, 75, 72, 71, kNA } }, // Neptunium
|
||||
{ Pu, { kNA, kNA, kNA, kNA, kNA, 100, 86, 74, 71, kNA, kNA } }, // Plutonium
|
||||
{ Am, { kNA, kNA, kNA, kNA, 126, 97.5, 85, kNA, kNA, kNA, kNA } }, // Americium
|
||||
{ Cm, { kNA, kNA, kNA, kNA, kNA, 97, 85, kNA, kNA, kNA, kNA } }, // Curium
|
||||
{ Bk, { kNA, kNA, kNA, kNA, kNA, 96, 83, kNA, kNA, kNA, kNA } }, // Berkelium
|
||||
{ Cf, { kNA, kNA, kNA, kNA, kNA, 95, 82.1, kNA, kNA, kNA, kNA } }, // Californium
|
||||
{ Es, { kNA, kNA, kNA, kNA, kNA, 83.5, kNA, kNA, kNA, kNA, kNA } }, // Einsteinium
|
||||
};
|
||||
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
// The coefficients from Waasmaier & Kirfel (1995), Acta Cryst. A51, 416-431.
|
||||
|
||||
@@ -886,5 +1096,45 @@ auto AtomTypeTraits::elsf() const -> const SFData&
|
||||
|
||||
throw std::runtime_error("No scattering factor found for " + name());
|
||||
}
|
||||
|
||||
|
||||
// ionic radii
|
||||
|
||||
float AtomTypeTraits::crystal_ionic_radius(int charge) const
|
||||
{
|
||||
float result = data::kNA;
|
||||
|
||||
if (charge >= -3 and charge <= 8)
|
||||
{
|
||||
for (auto &r : data::kCrystalIonicRadii)
|
||||
{
|
||||
if (r.type != mInfo->type)
|
||||
continue;
|
||||
|
||||
result = r.radii[charge < 0 ? charge + 3 : charge + 2] / 100.0f;
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
return result;
|
||||
}
|
||||
|
||||
float AtomTypeTraits::effective_ionic_radius(int charge) const
|
||||
{
|
||||
float result = data::kNA;
|
||||
|
||||
if (charge >= -3 and charge <= 8)
|
||||
{
|
||||
for (auto &r : data::kEffectiveIonicRadii)
|
||||
{
|
||||
if (r.type != mInfo->type)
|
||||
continue;
|
||||
|
||||
result = r.radii[charge < 0 ? charge + 3 : charge + 2] / 100.0f;
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
return result;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@@ -233,7 +233,7 @@ BondMap::BondMap(const Structure &p)
|
||||
link[b].insert(a);
|
||||
};
|
||||
|
||||
cif::Datablock &db = p.getFile().data();
|
||||
cif::Datablock &db = p.datablock();
|
||||
|
||||
// collect all compounds first
|
||||
std::set<std::string> compounds;
|
||||
@@ -255,54 +255,70 @@ BondMap::BondMap(const Structure &p)
|
||||
cif::Progress progress(compounds.size(), "Creating bond map");
|
||||
|
||||
// some helper indices to speed things up a bit
|
||||
std::map<std::tuple<std::string, int, std::string>, std::string> atomMapByAsymSeqAndAtom;
|
||||
std::map<std::tuple<std::string, int, std::string, std::string>, std::string> atomMapByAsymSeqAndAtom;
|
||||
for (auto &a : p.atoms())
|
||||
{
|
||||
auto key = make_tuple(a.labelAsymID(), a.labelSeqID(), a.labelAtomID());
|
||||
auto key = make_tuple(a.labelAsymID(), a.labelSeqID(), a.labelAtomID(), a.authSeqID());
|
||||
atomMapByAsymSeqAndAtom[key] = a.id();
|
||||
}
|
||||
|
||||
// first link all residues in a polyseq
|
||||
|
||||
std::string lastAsymID;
|
||||
std::string lastAsymID, lastAuthSeqID;
|
||||
int lastSeqID = 0;
|
||||
for (auto r : db["pdbx_poly_seq_scheme"])
|
||||
for (const auto &[asymID, seqID, authSeqID] : db["pdbx_poly_seq_scheme"].rows<std::string,int,std::string>("asym_id", "seq_id", "pdb_seq_num"))
|
||||
{
|
||||
std::string asymID;
|
||||
int seqID;
|
||||
|
||||
cif::tie(asymID, seqID) = r.get("asym_id", "seq_id");
|
||||
|
||||
if (asymID != lastAsymID) // first in a new sequece
|
||||
{
|
||||
lastAsymID = asymID;
|
||||
lastSeqID = seqID;
|
||||
lastAuthSeqID = authSeqID;
|
||||
continue;
|
||||
}
|
||||
|
||||
auto c = atomMapByAsymSeqAndAtom[make_tuple(asymID, lastSeqID, "C")];
|
||||
auto n = atomMapByAsymSeqAndAtom[make_tuple(asymID, seqID, "N")];
|
||||
auto kc = make_tuple(asymID, lastSeqID, "C", lastAuthSeqID);
|
||||
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);
|
||||
}
|
||||
// if (not(c.empty() or n.empty()))
|
||||
|
||||
lastSeqID = seqID;
|
||||
lastAuthSeqID = authSeqID;
|
||||
}
|
||||
|
||||
for (auto l : db["struct_conn"])
|
||||
{
|
||||
std::string asym1, asym2, atomId1, atomId2;
|
||||
int seqId1 = 0, seqId2 = 0;
|
||||
cif::tie(asym1, asym2, atomId1, atomId2, seqId1, seqId2) =
|
||||
std::string authSeqId1, authSeqId2;
|
||||
|
||||
cif::tie(asym1, asym2, atomId1, atomId2, seqId1, seqId2, authSeqId1, authSeqId2) =
|
||||
l.get("ptnr1_label_asym_id", "ptnr2_label_asym_id",
|
||||
"ptnr1_label_atom_id", "ptnr2_label_atom_id",
|
||||
"ptnr1_label_seq_id", "ptnr2_label_seq_id");
|
||||
"ptnr1_label_seq_id", "ptnr2_label_seq_id",
|
||||
"ptnr1_auth_seq_id", "ptnr2_auth_seq_id");
|
||||
|
||||
std::string a = atomMapByAsymSeqAndAtom[make_tuple(asym1, seqId1, atomId1)];
|
||||
std::string b = atomMapByAsymSeqAndAtom[make_tuple(asym2, seqId2, atomId2)];
|
||||
auto ka = make_tuple(asym1, seqId1, atomId1, authSeqId1);
|
||||
auto kb = make_tuple(asym2, seqId2, atomId2, authSeqId2);
|
||||
|
||||
if (atomMapByAsymSeqAndAtom.count(ka) and atomMapByAsymSeqAndAtom.count(kb))
|
||||
{
|
||||
auto a = atomMapByAsymSeqAndAtom.at(ka);
|
||||
auto b = atomMapByAsymSeqAndAtom.at(kb);
|
||||
|
||||
if (not(a.empty() or b.empty()))
|
||||
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
|
||||
@@ -373,15 +389,12 @@ BondMap::BondMap(const Structure &p)
|
||||
}
|
||||
|
||||
// loop over pdbx_branch_scheme
|
||||
for (auto r : db["pdbx_branch_scheme"].find(cif::Key("mon_id") == c))
|
||||
for (const auto &[asym_id, pdb_seq_num] : db["pdbx_branch_scheme"].find<std::string,std::string>(cif::Key("mon_id") == c, "asym_id", "pdb_seq_num"))
|
||||
{
|
||||
std::string asymID;
|
||||
cif::tie(asymID) = r.get("asym_id");
|
||||
|
||||
std::vector<Atom> rAtoms;
|
||||
copy_if(atoms.begin(), atoms.end(), back_inserter(rAtoms),
|
||||
[&](auto &a)
|
||||
{ return a.labelAsymID() == asymID; });
|
||||
[&](const Atom &a)
|
||||
{ return a.labelAsymID() == asym_id and a.authSeqID() == pdb_seq_num; });
|
||||
|
||||
for (uint32_t i = 0; i + 1 < rAtoms.size(); ++i)
|
||||
{
|
||||
|
||||
@@ -613,20 +613,12 @@ bool operator==(const cif::Datablock &dbA, const cif::Datablock &dbB)
|
||||
int d = nA.compare(nB);
|
||||
if (d > 0)
|
||||
{
|
||||
auto cat = dbB.get(*catB_i);
|
||||
|
||||
if (cat == nullptr)
|
||||
missingA.push_back(*catB_i);
|
||||
|
||||
missingA.push_back(*catB_i);
|
||||
++catB_i;
|
||||
}
|
||||
else if (d < 0)
|
||||
{
|
||||
auto cat = dbA.get(*catA_i);
|
||||
|
||||
if (cat == nullptr)
|
||||
missingB.push_back(*catA_i);
|
||||
|
||||
missingB.push_back(*catA_i);
|
||||
++catA_i;
|
||||
}
|
||||
else
|
||||
@@ -1908,11 +1900,16 @@ bool Category::hasParent(Row r, const Category &parentCat, const ValidateLink &l
|
||||
if (mCatValidator->mMandatoryFields.count(name) and field.is_null())
|
||||
cond = std::move(cond) and (Key(link.mParentKeys[ix]) == Empty());
|
||||
}
|
||||
else
|
||||
else if (parentCat.mCatValidator->mMandatoryFields.count(link.mParentKeys[ix]))
|
||||
{
|
||||
const char *value = field.c_str();
|
||||
cond = std::move(cond) and (Key(link.mParentKeys[ix]) == value);
|
||||
}
|
||||
else
|
||||
{
|
||||
const char *value = field.c_str();
|
||||
cond = std::move(cond) and (Key(link.mParentKeys[ix]) == value or Key(link.mParentKeys[ix]) == Empty());
|
||||
}
|
||||
}
|
||||
|
||||
if (result and not cond.empty())
|
||||
@@ -2209,9 +2206,27 @@ void Category::validateLinks() const
|
||||
size_t missing = 0;
|
||||
for (auto r : *this)
|
||||
if (not hasParent(r, *parentCat, *link))
|
||||
{
|
||||
if (cif::VERBOSE > 1)
|
||||
{
|
||||
if (missing == 0)
|
||||
{
|
||||
std::cerr << "Links for " << link->mLinkGroupLabel << " are incomplete" << std::endl
|
||||
<< " These are the items in " << mName << " that don't have matching parent items in " << parentCat->mName << std::endl
|
||||
<< std::endl;
|
||||
}
|
||||
|
||||
for (auto k : link->mChildKeys)
|
||||
std::cerr << k << ": " << r[k].as<std::string>() << std::endl;
|
||||
|
||||
std::cerr << std::endl;
|
||||
}
|
||||
|
||||
++missing;
|
||||
|
||||
if (missing and VERBOSE >= 0)
|
||||
}
|
||||
|
||||
if (missing and VERBOSE == 1)
|
||||
{
|
||||
std::cerr << "Links for " << link->mLinkGroupLabel << " are incomplete" << std::endl
|
||||
<< " There are " << missing << " items in " << mName << " that don't have matching parent items in " << parentCat->mName << std::endl;
|
||||
@@ -2408,7 +2423,7 @@ namespace detail
|
||||
|
||||
size_t writeValue(std::ostream &os, std::string value, size_t offset, size_t width)
|
||||
{
|
||||
if (value.find('\n') != std::string::npos or width == 0 or value.length() >= 132) // write as text field
|
||||
if (value.find('\n') != std::string::npos or width == 0 or value.length() > 132) // write as text field
|
||||
{
|
||||
ba::replace_all(value, "\n;", "\n\\;");
|
||||
|
||||
@@ -2511,7 +2526,7 @@ void Category::write(std::ostream &os, const std::vector<size_t> &order, bool in
|
||||
if (not isUnquotedString(v->mText))
|
||||
l += 2;
|
||||
|
||||
if (l >= 132)
|
||||
if (l > 132)
|
||||
continue;
|
||||
|
||||
if (columnWidths[v->mColumnIndex] < l + 1)
|
||||
@@ -2547,7 +2562,7 @@ void Category::write(std::ostream &os, const std::vector<size_t> &order, bool in
|
||||
if (l < w)
|
||||
l = w;
|
||||
|
||||
if (offset + l >= 132 and offset > 0)
|
||||
if (offset + l > 132 and offset > 0)
|
||||
{
|
||||
os << std::endl;
|
||||
offset = 0;
|
||||
@@ -2555,7 +2570,7 @@ void Category::write(std::ostream &os, const std::vector<size_t> &order, bool in
|
||||
|
||||
offset = detail::writeValue(os, s, offset, w);
|
||||
|
||||
if (offset >= 132)
|
||||
if (offset > 132)
|
||||
{
|
||||
os << std::endl;
|
||||
offset = 0;
|
||||
@@ -3367,6 +3382,11 @@ File::File(const std::filesystem::path &path, bool validate)
|
||||
}
|
||||
}
|
||||
|
||||
File::File(const char *data, std::size_t length)
|
||||
{
|
||||
load(data, length);
|
||||
}
|
||||
|
||||
File::File(File &&rhs)
|
||||
: mHead(nullptr)
|
||||
, mValidator(nullptr)
|
||||
@@ -3483,6 +3503,25 @@ void File::load(std::istream &is, const std::string &datablock)
|
||||
}
|
||||
}
|
||||
|
||||
void File::load(const char *data, std::size_t length)
|
||||
{
|
||||
bool gzipped = length > 2 and data[0] == static_cast<char>(0x1f) and data[1] == static_cast<char>(0x8b);
|
||||
|
||||
struct membuf : public std::streambuf
|
||||
{
|
||||
membuf(char *data, size_t length) { this->setg(data, data, data + length); }
|
||||
} buffer(const_cast<char *>(data), length);
|
||||
|
||||
std::istream is(&buffer);
|
||||
|
||||
io::filtering_stream<io::input> in;
|
||||
if (gzipped)
|
||||
in.push(io::gzip_decompressor());
|
||||
in.push(is);
|
||||
|
||||
load(is);
|
||||
}
|
||||
|
||||
void File::save(std::ostream &os)
|
||||
{
|
||||
Datablock *e = mHead;
|
||||
@@ -3523,6 +3562,21 @@ Datablock &File::operator[](std::string_view name)
|
||||
return *result;
|
||||
}
|
||||
|
||||
Datablock &File::front()
|
||||
{
|
||||
assert(mHead);
|
||||
return *mHead;
|
||||
}
|
||||
|
||||
Datablock &File::back()
|
||||
{
|
||||
assert(mHead);
|
||||
auto *block = mHead;
|
||||
while (block->mNext != nullptr)
|
||||
block = block->mNext;
|
||||
return *block;
|
||||
}
|
||||
|
||||
bool File::isValid()
|
||||
{
|
||||
if (mValidator == nullptr)
|
||||
|
||||
@@ -1,17 +1,17 @@
|
||||
/*-
|
||||
* SPDX-License-Identifier: BSD-2-Clause
|
||||
*
|
||||
*
|
||||
* Copyright (c) 2020 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
|
||||
@@ -42,7 +42,7 @@ namespace cif
|
||||
const uint32_t kMaxLineLength = 132;
|
||||
|
||||
const uint8_t kCharTraitsTable[128] = {
|
||||
// 0 1 2 3 4 5 6 7 8 9 a b c d e f
|
||||
// 0 1 2 3 4 5 6 7 8 9 a b c d e f
|
||||
14, 15, 14, 14, 14, 15, 15, 14, 15, 15, 15, 15, 15, 15, 15, 15, // 2
|
||||
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 15, 15, 15, 15, // 3
|
||||
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, // 4
|
||||
@@ -82,6 +82,29 @@ const char *SacParser::kValueName[] = {
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
bool isUnquotedString(const char *s)
|
||||
{
|
||||
auto ss = s;
|
||||
|
||||
bool result = isOrdinary(*s++);
|
||||
while (result and *s != 0)
|
||||
{
|
||||
result = isNonBlank(*s);
|
||||
++s;
|
||||
}
|
||||
|
||||
// but be careful it does not contain e.g. stop_
|
||||
if (result)
|
||||
{
|
||||
static const std::regex reservedRx(R"((^(?:data|save)|.*(?:loop|stop|global))_.+)", std::regex_constants::icase);
|
||||
result = not std::regex_match(ss, reservedRx);
|
||||
}
|
||||
|
||||
return result;
|
||||
}
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
SacParser::SacParser(std::istream &is, bool init)
|
||||
: mData(is)
|
||||
{
|
||||
@@ -151,23 +174,26 @@ void SacParser::retract()
|
||||
mTokenValue.pop_back();
|
||||
}
|
||||
|
||||
void SacParser::restart()
|
||||
|
||||
int SacParser::restart(int start)
|
||||
{
|
||||
int result = 0;
|
||||
|
||||
while (not mTokenValue.empty())
|
||||
retract();
|
||||
|
||||
switch (mStart)
|
||||
switch (start)
|
||||
{
|
||||
case eStateStart:
|
||||
mState = mStart = eStateFloat;
|
||||
result = eStateFloat;
|
||||
break;
|
||||
|
||||
case eStateFloat:
|
||||
mState = mStart = eStateInt;
|
||||
result = eStateInt;
|
||||
break;
|
||||
|
||||
case eStateInt:
|
||||
mState = mStart = eStateValue;
|
||||
result = eStateValue;
|
||||
break;
|
||||
|
||||
default:
|
||||
@@ -175,6 +201,8 @@ void SacParser::restart()
|
||||
}
|
||||
|
||||
mBol = false;
|
||||
|
||||
return result;
|
||||
}
|
||||
|
||||
void SacParser::match(SacParser::CIFToken t)
|
||||
@@ -191,7 +219,7 @@ SacParser::CIFToken SacParser::getNextToken()
|
||||
|
||||
CIFToken result = eCIFTokenUnknown;
|
||||
int quoteChar = 0;
|
||||
mState = mStart = eStateStart;
|
||||
int state = eStateStart, start = eStateStart;
|
||||
mBol = false;
|
||||
|
||||
mTokenValue.clear();
|
||||
@@ -201,7 +229,7 @@ SacParser::CIFToken SacParser::getNextToken()
|
||||
{
|
||||
auto ch = getNextChar();
|
||||
|
||||
switch (mState)
|
||||
switch (state)
|
||||
{
|
||||
case eStateStart:
|
||||
if (ch == kEOF)
|
||||
@@ -209,27 +237,23 @@ SacParser::CIFToken SacParser::getNextToken()
|
||||
else if (ch == '\n')
|
||||
{
|
||||
mBol = true;
|
||||
mState = eStateWhite;
|
||||
state = eStateWhite;
|
||||
}
|
||||
else if (ch == ' ' or ch == '\t')
|
||||
mState = eStateWhite;
|
||||
state = eStateWhite;
|
||||
else if (ch == '#')
|
||||
mState = eStateComment;
|
||||
else if (ch == '.')
|
||||
mState = eStateDot;
|
||||
state = eStateComment;
|
||||
else if (ch == '_')
|
||||
mState = eStateTag;
|
||||
state = eStateTag;
|
||||
else if (ch == ';' and mBol)
|
||||
mState = eStateTextField;
|
||||
state = eStateTextField;
|
||||
else if (ch == '\'' or ch == '"')
|
||||
{
|
||||
quoteChar = ch;
|
||||
mState = eStateQuotedString;
|
||||
state = eStateQuotedString;
|
||||
}
|
||||
else if (ch == '?')
|
||||
mState = eStateQuestionMark;
|
||||
else
|
||||
restart();
|
||||
state = start = restart(start);
|
||||
break;
|
||||
|
||||
case eStateWhite:
|
||||
@@ -237,7 +261,7 @@ SacParser::CIFToken SacParser::getNextToken()
|
||||
result = eCIFTokenEOF;
|
||||
else if (not isspace(ch))
|
||||
{
|
||||
mState = eStateStart;
|
||||
state = eStateStart;
|
||||
retract();
|
||||
mTokenValue.clear();
|
||||
}
|
||||
@@ -248,7 +272,7 @@ SacParser::CIFToken SacParser::getNextToken()
|
||||
case eStateComment:
|
||||
if (ch == '\n')
|
||||
{
|
||||
mState = eStateStart;
|
||||
state = eStateStart;
|
||||
mBol = true;
|
||||
mTokenValue.clear();
|
||||
}
|
||||
@@ -258,44 +282,19 @@ SacParser::CIFToken SacParser::getNextToken()
|
||||
error("invalid character in comment");
|
||||
break;
|
||||
|
||||
case eStateQuestionMark:
|
||||
if (isNonBlank(ch))
|
||||
mState = eStateValue;
|
||||
else
|
||||
{
|
||||
retract();
|
||||
result = eCIFTokenValue;
|
||||
mTokenValue.clear();
|
||||
mTokenType = eCIFValueUnknown;
|
||||
}
|
||||
break;
|
||||
|
||||
case eStateDot:
|
||||
if (isdigit(ch))
|
||||
mState = eStateFloat + 2;
|
||||
else if (isspace(ch))
|
||||
{
|
||||
retract();
|
||||
result = eCIFTokenValue;
|
||||
mTokenType = eCIFValueInapplicable;
|
||||
}
|
||||
else
|
||||
mState = eStateValue;
|
||||
break;
|
||||
|
||||
case eStateTextField:
|
||||
if (ch == '\n')
|
||||
mState = eStateTextField + 1;
|
||||
state = eStateTextField + 1;
|
||||
else if (ch == kEOF)
|
||||
error("unterminated textfield");
|
||||
else if (not isAnyPrint(ch) and cif::VERBOSE >= 0)
|
||||
else if (not isAnyPrint(ch))
|
||||
// error("invalid character in text field '" + string({ static_cast<char>(ch) }) + "' (" + to_string((int)ch) + ")");
|
||||
std::cerr << "invalid character in text field '" << std::string({static_cast<char>(ch)}) << "' (" << ch << ") line: " << mLineNr << std::endl;
|
||||
break;
|
||||
|
||||
case eStateTextField + 1:
|
||||
if (isTextLead(ch) or ch == ' ' or ch == '\t')
|
||||
mState = eStateTextField;
|
||||
state = eStateTextField;
|
||||
else if (ch == ';')
|
||||
{
|
||||
assert(mTokenValue.length() >= 2);
|
||||
@@ -313,9 +312,10 @@ SacParser::CIFToken SacParser::getNextToken()
|
||||
if (ch == kEOF)
|
||||
error("unterminated quoted string");
|
||||
else if (ch == quoteChar)
|
||||
mState = eStateQuotedStringQuote;
|
||||
state = eStateQuotedStringQuote;
|
||||
else if (not isAnyPrint(ch))
|
||||
error("invalid character in quoted string");
|
||||
std::cerr << "invalid character in quoted string '" << std::string({static_cast<char>(ch)}) << "' (" << ch << ") line: " << mLineNr << std::endl;
|
||||
// error("invalid character in quoted string");
|
||||
break;
|
||||
|
||||
case eStateQuotedStringQuote:
|
||||
@@ -331,7 +331,7 @@ SacParser::CIFToken SacParser::getNextToken()
|
||||
else if (ch == quoteChar)
|
||||
;
|
||||
else if (isAnyPrint(ch))
|
||||
mState = eStateQuotedString;
|
||||
state = eStateQuotedString;
|
||||
else if (ch == kEOF)
|
||||
error("unterminated quoted string");
|
||||
else
|
||||
@@ -349,12 +349,12 @@ SacParser::CIFToken SacParser::getNextToken()
|
||||
case eStateFloat:
|
||||
if (ch == '+' or ch == '-')
|
||||
{
|
||||
mState = eStateFloat + 1;
|
||||
state = eStateFloat + 1;
|
||||
}
|
||||
else if (isdigit(ch))
|
||||
mState = eStateFloat + 1;
|
||||
state = eStateFloat + 1;
|
||||
else
|
||||
restart();
|
||||
state = start = restart(start);
|
||||
break;
|
||||
|
||||
case eStateFloat + 1:
|
||||
@@ -362,9 +362,9 @@ SacParser::CIFToken SacParser::getNextToken()
|
||||
// mState = eStateNumericSuffix;
|
||||
// else
|
||||
if (ch == '.')
|
||||
mState = eStateFloat + 2;
|
||||
state = eStateFloat + 2;
|
||||
else if (tolower(ch) == 'e')
|
||||
mState = eStateFloat + 3;
|
||||
state = eStateFloat + 3;
|
||||
else if (isWhite(ch) or ch == kEOF)
|
||||
{
|
||||
retract();
|
||||
@@ -372,16 +372,13 @@ SacParser::CIFToken SacParser::getNextToken()
|
||||
mTokenType = eCIFValueInt;
|
||||
}
|
||||
else
|
||||
restart();
|
||||
state = start = restart(start);
|
||||
break;
|
||||
|
||||
// parsed '.'
|
||||
case eStateFloat + 2:
|
||||
// if (ch == '(') // numeric???
|
||||
// mState = eStateNumericSuffix;
|
||||
// else
|
||||
if (tolower(ch) == 'e')
|
||||
mState = eStateFloat + 3;
|
||||
state = eStateFloat + 3;
|
||||
else if (isWhite(ch) or ch == kEOF)
|
||||
{
|
||||
retract();
|
||||
@@ -389,30 +386,27 @@ SacParser::CIFToken SacParser::getNextToken()
|
||||
mTokenType = eCIFValueFloat;
|
||||
}
|
||||
else
|
||||
restart();
|
||||
state = start = restart(start);
|
||||
break;
|
||||
|
||||
// parsed 'e'
|
||||
case eStateFloat + 3:
|
||||
if (ch == '-' or ch == '+')
|
||||
mState = eStateFloat + 4;
|
||||
state = eStateFloat + 4;
|
||||
else if (isdigit(ch))
|
||||
mState = eStateFloat + 5;
|
||||
state = eStateFloat + 5;
|
||||
else
|
||||
restart();
|
||||
state = start = restart(start);
|
||||
break;
|
||||
|
||||
case eStateFloat + 4:
|
||||
if (isdigit(ch))
|
||||
mState = eStateFloat + 5;
|
||||
state = eStateFloat + 5;
|
||||
else
|
||||
restart();
|
||||
state = start = restart(start);
|
||||
break;
|
||||
|
||||
case eStateFloat + 5:
|
||||
// if (ch == '(')
|
||||
// mState = eStateNumericSuffix;
|
||||
// else
|
||||
if (isWhite(ch) or ch == kEOF)
|
||||
{
|
||||
retract();
|
||||
@@ -420,14 +414,14 @@ SacParser::CIFToken SacParser::getNextToken()
|
||||
mTokenType = eCIFValueFloat;
|
||||
}
|
||||
else
|
||||
restart();
|
||||
state = start = restart(start);
|
||||
break;
|
||||
|
||||
case eStateInt:
|
||||
if (isdigit(ch) or ch == '+' or ch == '-')
|
||||
mState = eStateInt + 1;
|
||||
state = eStateInt + 1;
|
||||
else
|
||||
restart();
|
||||
state = start = restart(start);
|
||||
break;
|
||||
|
||||
case eStateInt + 1:
|
||||
@@ -438,35 +432,11 @@ SacParser::CIFToken SacParser::getNextToken()
|
||||
mTokenType = eCIFValueInt;
|
||||
}
|
||||
else
|
||||
restart();
|
||||
state = start = restart(start);
|
||||
break;
|
||||
|
||||
// case eStateNumericSuffix:
|
||||
// if (isdigit(ch))
|
||||
// mState = eStateNumericSuffix + 1;
|
||||
// else
|
||||
// restart();
|
||||
// break;
|
||||
//
|
||||
// case eStateNumericSuffix + 1:
|
||||
// if (ch == ')')
|
||||
// {
|
||||
// result = eCIFTokenValue;
|
||||
// mTokenType = eCIFValueNumeric;
|
||||
// }
|
||||
// else if (not isdigit(ch))
|
||||
// restart();
|
||||
// break;
|
||||
|
||||
case eStateValue:
|
||||
if (isNonBlank(ch))
|
||||
mState = eStateValue + 1;
|
||||
else
|
||||
error("invalid character at this position");
|
||||
break;
|
||||
|
||||
case eStateValue + 1:
|
||||
if (ch == '_') // first _, check for keywords
|
||||
if (ch == '_')
|
||||
{
|
||||
std::string s = toLowerCopy(mTokenValue);
|
||||
|
||||
@@ -476,23 +446,40 @@ SacParser::CIFToken SacParser::getNextToken()
|
||||
result = eCIFTokenSTOP;
|
||||
else if (s == "loop_")
|
||||
result = eCIFTokenLOOP;
|
||||
else if (s == "data_" or s == "save_")
|
||||
mState = eStateValue + 2;
|
||||
else if (s == "data_")
|
||||
{
|
||||
state = eStateDATA;
|
||||
continue;
|
||||
}
|
||||
else if (s == "save_")
|
||||
{
|
||||
state = eStateSAVE;
|
||||
continue;
|
||||
}
|
||||
}
|
||||
else if (not isNonBlank(ch))
|
||||
|
||||
if (result == eCIFTokenUnknown and not isNonBlank(ch))
|
||||
{
|
||||
retract();
|
||||
result = eCIFTokenValue;
|
||||
mTokenType = eCIFValueString;
|
||||
|
||||
if (mTokenValue == ".")
|
||||
mTokenType = eCIFValueInapplicable;
|
||||
else if (mTokenValue == "?")
|
||||
{
|
||||
mTokenType = eCIFValueUnknown;
|
||||
mTokenValue.clear();
|
||||
}
|
||||
}
|
||||
break;
|
||||
|
||||
case eStateValue + 2:
|
||||
case eStateDATA:
|
||||
case eStateSAVE:
|
||||
if (not isNonBlank(ch))
|
||||
{
|
||||
retract();
|
||||
|
||||
if (tolower(mTokenValue[0]) == 'd')
|
||||
if (state == eStateDATA)
|
||||
result = eCIFTokenDATA;
|
||||
else
|
||||
result = eCIFTokenSAVE;
|
||||
@@ -521,6 +508,7 @@ SacParser::CIFToken SacParser::getNextToken()
|
||||
return result;
|
||||
}
|
||||
|
||||
|
||||
DatablockIndex SacParser::indexDatablocks()
|
||||
{
|
||||
DatablockIndex index;
|
||||
|
||||
@@ -27,6 +27,7 @@
|
||||
#include <atomic>
|
||||
#include <cmath>
|
||||
#include <fstream>
|
||||
#include <iomanip>
|
||||
#include <iostream>
|
||||
#include <map>
|
||||
#include <mutex>
|
||||
@@ -642,7 +643,6 @@ void ProgressImpl::PrintProgress()
|
||||
|
||||
msg.append("| ");
|
||||
|
||||
// const char kSpinner[] = { '|', '/', '-', '\\' };
|
||||
const char kSpinner[] = {' ', '.', 'o', 'O', '0', 'O', 'o', '.'};
|
||||
const size_t kSpinnerCount = sizeof(kSpinner);
|
||||
|
||||
@@ -1251,6 +1251,19 @@ std::unique_ptr<std::istream> loadResource(std::filesystem::path name)
|
||||
}
|
||||
#endif
|
||||
|
||||
#if defined(CCP4) and CCP4
|
||||
if (not result and not fs::exists(p))
|
||||
{
|
||||
const char* CCP4_DIR = getenv("CCP4");
|
||||
if (CCP4_DIR != nullptr and fs::exists(CCP4_DIR))
|
||||
{
|
||||
auto p2 = fs::path(DATA_DIR) / p;
|
||||
if (fs::exists(p2))
|
||||
swap(p, p2);
|
||||
}
|
||||
}
|
||||
#endif
|
||||
|
||||
if (not result and fs::exists(p))
|
||||
{
|
||||
std::unique_ptr<std::ifstream> file(new std::ifstream(p, std::ios::binary));
|
||||
|
||||
@@ -295,13 +295,27 @@ Quaternion Normalize(Quaternion q)
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
Quaternion ConstructFromAngleAxis(float angle, Point axis)
|
||||
{
|
||||
auto q = std::cos((angle * mmcif::kPI / 180) / 2);
|
||||
auto s = std::sqrt(1 - q * q);
|
||||
|
||||
axis.normalize();
|
||||
|
||||
return Normalize(Quaternion{
|
||||
static_cast<float>(q),
|
||||
static_cast<float>(s * axis.mX),
|
||||
static_cast<float>(s * axis.mY),
|
||||
static_cast<float>(s * axis.mZ)});
|
||||
}
|
||||
|
||||
std::tuple<double,Point> QuaternionToAngleAxis(Quaternion q)
|
||||
{
|
||||
if (q.R_component_1() > 1)
|
||||
q = Normalize(q);
|
||||
|
||||
// angle:
|
||||
double angle = 2 * acos(q.R_component_1());
|
||||
double angle = 2 * std::acos(q.R_component_1());
|
||||
angle = angle * 180 / kPI;
|
||||
|
||||
// axis:
|
||||
|
||||
@@ -535,7 +535,7 @@ double CalculateHBondEnergy(Res &inDonor, Res &inAcceptor)
|
||||
result = kCouplingConstant / distanceHO - kCouplingConstant / distanceHC + kCouplingConstant / distanceNC - kCouplingConstant / distanceNO;
|
||||
|
||||
// DSSP compatibility mode:
|
||||
result = round(result * 1000) / 1000;
|
||||
result = std::round(result * 1000) / 1000;
|
||||
|
||||
if (result < kMinHBondEnergy)
|
||||
result = kMinHBondEnergy;
|
||||
@@ -1230,7 +1230,7 @@ DSSPImpl::DSSPImpl(const Structure &s, int min_poly_proline_stretch_length)
|
||||
|
||||
void DSSPImpl::calculateSecondaryStructure()
|
||||
{
|
||||
auto &db = mStructure.getFile().data();
|
||||
auto &db = mStructure.datablock();
|
||||
for (auto r : db["struct_conn"].find(cif::Key("conn_type_id") == "disulf"))
|
||||
{
|
||||
std::string asym1, asym2;
|
||||
|
||||
1652
src/Structure.cpp
1652
src/Structure.cpp
File diff suppressed because it is too large
Load Diff
BIN
test/1juh.cif.gz
Normal file
BIN
test/1juh.cif.gz
Normal file
Binary file not shown.
@@ -32,12 +32,12 @@ int main(int argc, char* argv[])
|
||||
mmcif::File f(testdir / ".."/"examples"/"1cbs.cif.gz");
|
||||
mmcif::Structure structure(f);
|
||||
|
||||
auto &res = structure.getResidue("B", "REA");
|
||||
auto &res = structure.getResidue("B");
|
||||
structure.changeResidue(res, "RXA", {});
|
||||
|
||||
structure.cleanupEmptyCategories();
|
||||
|
||||
f.file().save(std::cout);
|
||||
f.save(std::cout);
|
||||
}
|
||||
catch (const std::exception& e)
|
||||
{
|
||||
|
||||
@@ -78,8 +78,8 @@ BOOST_AUTO_TEST_CASE(create_nonpoly_1)
|
||||
cif::VERBOSE = 1;
|
||||
|
||||
mmcif::File file;
|
||||
file.file().loadDictionary("mmcif_pdbx_v50.dic");
|
||||
file.createDatablock("TEST"); // create a datablock
|
||||
file.loadDictionary("mmcif_pdbx_v50.dic");
|
||||
file.emplace("TEST"); // create a datablock
|
||||
|
||||
mmcif::Structure structure(file);
|
||||
|
||||
@@ -118,6 +118,17 @@ HETATM C CHD . ? -4.342 36.262 -3.536 1.00 8.00 ?
|
||||
|
||||
auto expected = R"(
|
||||
data_TEST
|
||||
#
|
||||
_pdbx_nonpoly_scheme.asym_id A
|
||||
_pdbx_nonpoly_scheme.ndb_seq_num 1
|
||||
_pdbx_nonpoly_scheme.entity_id 1
|
||||
_pdbx_nonpoly_scheme.mon_id HEM
|
||||
_pdbx_nonpoly_scheme.pdb_seq_num 1
|
||||
_pdbx_nonpoly_scheme.auth_seq_num 1
|
||||
_pdbx_nonpoly_scheme.pdb_mon_id HEM
|
||||
_pdbx_nonpoly_scheme.auth_mon_id HEM
|
||||
_pdbx_nonpoly_scheme.pdb_strand_id A
|
||||
_pdbx_nonpoly_scheme.pdb_ins_code .
|
||||
#
|
||||
loop_
|
||||
_atom_site.id
|
||||
@@ -141,10 +152,10 @@ _atom_site.auth_seq_id
|
||||
_atom_site.auth_comp_id
|
||||
_atom_site.auth_atom_id
|
||||
_atom_site.pdbx_PDB_model_num
|
||||
1 A ? A CHA HEM 1 . C HETATM ? -5.248 39.769 -0.250 1.00 7.67 ? ? HEM CHA 1
|
||||
2 A ? A CHB HEM 1 . C HETATM ? -3.774 36.790 3.280 1.00 7.05 ? ? HEM CHB 1
|
||||
3 A ? A CHC HEM 1 . C HETATM ? -2.879 33.328 0.013 1.00 7.69 ? ? HEM CHC 1
|
||||
4 A ? A CHD HEM 1 . C HETATM ? -4.342 36.262 -3.536 1.00 8.00 ? ? HEM CHD 1
|
||||
1 A ? A CHA HEM 1 . C HETATM ? -5.248 39.769 -0.250 1.00 7.67 ? 1 HEM CHA 1
|
||||
2 A ? A CHB HEM 1 . C HETATM ? -3.774 36.790 3.280 1.00 7.05 ? 1 HEM CHB 1
|
||||
3 A ? A CHC HEM 1 . C HETATM ? -2.879 33.328 0.013 1.00 7.69 ? 1 HEM CHC 1
|
||||
4 A ? A CHD HEM 1 . C HETATM ? -4.342 36.262 -3.536 1.00 8.00 ? 1 HEM CHD 1
|
||||
#
|
||||
_chem_comp.id HEM
|
||||
_chem_comp.type NON-POLYMER
|
||||
@@ -171,12 +182,12 @@ _struct_asym.details ?
|
||||
|
||||
expected.loadDictionary("mmcif_pdbx_v50.dic");
|
||||
|
||||
if (not (expected.firstDatablock() == structure.getFile().data()))
|
||||
if (not (expected.firstDatablock() == structure.datablock()))
|
||||
{
|
||||
BOOST_TEST(false);
|
||||
std::cout << expected.firstDatablock() << std::endl
|
||||
<< std::endl
|
||||
<< structure.getFile().data() << std::endl;
|
||||
<< structure.datablock() << std::endl;
|
||||
}
|
||||
}
|
||||
|
||||
@@ -199,3 +210,150 @@ _struct_asym.details ?
|
||||
// }
|
||||
// }
|
||||
// }
|
||||
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
BOOST_AUTO_TEST_CASE(test_atom_id)
|
||||
{
|
||||
auto data = R"(
|
||||
data_TEST
|
||||
#
|
||||
_pdbx_nonpoly_scheme.asym_id A
|
||||
_pdbx_nonpoly_scheme.ndb_seq_num 1
|
||||
_pdbx_nonpoly_scheme.entity_id 1
|
||||
_pdbx_nonpoly_scheme.mon_id HEM
|
||||
_pdbx_nonpoly_scheme.pdb_seq_num 1
|
||||
_pdbx_nonpoly_scheme.auth_seq_num 1
|
||||
_pdbx_nonpoly_scheme.pdb_mon_id HEM
|
||||
_pdbx_nonpoly_scheme.auth_mon_id HEM
|
||||
_pdbx_nonpoly_scheme.pdb_strand_id A
|
||||
_pdbx_nonpoly_scheme.pdb_ins_code .
|
||||
#
|
||||
loop_
|
||||
_atom_site.id
|
||||
_atom_site.auth_asym_id
|
||||
_atom_site.label_alt_id
|
||||
_atom_site.label_asym_id
|
||||
_atom_site.label_atom_id
|
||||
_atom_site.label_comp_id
|
||||
_atom_site.label_entity_id
|
||||
_atom_site.label_seq_id
|
||||
_atom_site.type_symbol
|
||||
_atom_site.group_PDB
|
||||
_atom_site.pdbx_PDB_ins_code
|
||||
_atom_site.Cartn_x
|
||||
_atom_site.Cartn_y
|
||||
_atom_site.Cartn_z
|
||||
_atom_site.occupancy
|
||||
_atom_site.B_iso_or_equiv
|
||||
_atom_site.pdbx_formal_charge
|
||||
_atom_site.auth_seq_id
|
||||
_atom_site.auth_comp_id
|
||||
_atom_site.auth_atom_id
|
||||
_atom_site.pdbx_PDB_model_num
|
||||
1 A ? A CHA HEM 1 . C HETATM ? -5.248 39.769 -0.250 1.00 7.67 ? 1 HEM CHA 1
|
||||
3 A ? A CHB HEM 1 . C HETATM ? -3.774 36.790 3.280 1.00 7.05 ? 1 HEM CHB 1
|
||||
2 A ? A CHC HEM 1 . C HETATM ? -2.879 33.328 0.013 1.00 7.69 ? 1 HEM CHC 1
|
||||
4 A ? A CHD HEM 1 . C HETATM ? -4.342 36.262 -3.536 1.00 8.00 ? 1 HEM CHD 1
|
||||
#
|
||||
_chem_comp.id HEM
|
||||
_chem_comp.type NON-POLYMER
|
||||
_chem_comp.name 'PROTOPORPHYRIN IX CONTAINING FE'
|
||||
_chem_comp.formula 'C34 H32 Fe N4 O4'
|
||||
_chem_comp.formula_weight 616.487000
|
||||
#
|
||||
_pdbx_entity_nonpoly.entity_id 1
|
||||
_pdbx_entity_nonpoly.name 'PROTOPORPHYRIN IX CONTAINING FE'
|
||||
_pdbx_entity_nonpoly.comp_id HEM
|
||||
#
|
||||
_entity.id 1
|
||||
_entity.type non-polymer
|
||||
_entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE'
|
||||
_entity.formula_weight 616.487000
|
||||
#
|
||||
_struct_asym.id A
|
||||
_struct_asym.entity_id 1
|
||||
_struct_asym.pdbx_blank_PDB_chainid_flag N
|
||||
_struct_asym.pdbx_modified N
|
||||
_struct_asym.details ?
|
||||
#
|
||||
)"_cf;
|
||||
|
||||
data.loadDictionary("mmcif_pdbx_v50.dic");
|
||||
|
||||
mmcif::Structure s(data);
|
||||
|
||||
BOOST_CHECK_EQUAL(s.getAtomByID("1").authAtomID(), "CHA");
|
||||
BOOST_CHECK_EQUAL(s.getAtomByID("2").authAtomID(), "CHC");
|
||||
BOOST_CHECK_EQUAL(s.getAtomByID("3").authAtomID(), "CHB");
|
||||
BOOST_CHECK_EQUAL(s.getAtomByID("4").authAtomID(), "CHD");
|
||||
}
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
BOOST_AUTO_TEST_CASE(atom_numbers_1)
|
||||
{
|
||||
const std::filesystem::path test1(gTestDir / ".." / "examples" / "1cbs.cif.gz");
|
||||
mmcif::File file(test1.string());
|
||||
mmcif::Structure structure(file);
|
||||
|
||||
auto &db = file.data();
|
||||
|
||||
auto &atoms = structure.atoms();
|
||||
auto ai = atoms.begin();
|
||||
|
||||
for (const auto &[id, label_asym_id, label_seq_id, label_atom_id, auth_seq_id, label_comp_id] :
|
||||
db["atom_site"].rows<std::string,std::string,int,std::string,std::string,std::string>("id", "label_asym_id", "label_seq_id", "label_atom_id", "auth_seq_id", "label_comp_id"))
|
||||
{
|
||||
auto atom = structure.getAtomByID(id);
|
||||
|
||||
BOOST_CHECK_EQUAL(atom.labelAsymID(), label_asym_id);
|
||||
BOOST_CHECK_EQUAL(atom.labelSeqID(), label_seq_id);
|
||||
BOOST_CHECK_EQUAL(atom.labelAtomID(), label_atom_id);
|
||||
BOOST_CHECK_EQUAL(atom.authSeqID(), auth_seq_id);
|
||||
BOOST_CHECK_EQUAL(atom.labelCompID(), label_comp_id);
|
||||
|
||||
BOOST_ASSERT(ai != atoms.end());
|
||||
|
||||
BOOST_CHECK_EQUAL(ai->id(), id);
|
||||
++ai;
|
||||
}
|
||||
|
||||
BOOST_ASSERT(ai == atoms.end());
|
||||
}
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
BOOST_AUTO_TEST_CASE(test_load_1)
|
||||
{
|
||||
using namespace cif::literals;
|
||||
|
||||
const std::filesystem::path example(gTestDir / ".." / "examples" / "1cbs.cif.gz");
|
||||
mmcif::File file(example.string());
|
||||
|
||||
auto &db = file.data();
|
||||
|
||||
mmcif::Structure s(file);
|
||||
|
||||
BOOST_CHECK(s.polymers().size() == 1);
|
||||
|
||||
auto &pdbx_poly_seq_scheme = db["pdbx_poly_seq_scheme"];
|
||||
|
||||
for (auto &poly : s.polymers())
|
||||
{
|
||||
BOOST_CHECK_EQUAL(poly.size(), pdbx_poly_seq_scheme.find("asym_id"_key == poly.asymID()).size());
|
||||
}
|
||||
}
|
||||
|
||||
BOOST_AUTO_TEST_CASE(remove_residue_1)
|
||||
{
|
||||
using namespace cif::literals;
|
||||
|
||||
const std::filesystem::path example(gTestDir / ".." / "examples" / "1cbs.cif.gz");
|
||||
mmcif::File file(example.string());
|
||||
|
||||
mmcif::Structure s(file);
|
||||
s.removeResidue(s.getResidue("B"));
|
||||
|
||||
BOOST_CHECK_NO_THROW(s.validateAtoms());
|
||||
}
|
||||
|
||||
168
test/sugar-test.cpp
Normal file
168
test/sugar-test.cpp
Normal file
@@ -0,0 +1,168 @@
|
||||
/*-
|
||||
* 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();
|
||||
|
||||
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());
|
||||
|
||||
s.removeResidue(NAG);
|
||||
|
||||
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");
|
||||
}
|
||||
1163
test/unit-test.cpp
1163
test/unit-test.cpp
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user