项目目录结构：
BioShellHydrogenBondWithDriverProgram
│ heca_input.cc
│
├───core
│ │ BioShellEnvironment.cc
│ │ BioShellEnvironment.hh
│ │ index.hh
│ │
│ ├───algorithms
│ │ │ basic_algorithms.hh
│ │ │ Combinations.hh
│ │ │ GivenOrderIterator.hh
│ │ │ GraphWithData.hh
│ │ │ graph_algorithms.hh
│ │ │ IterateIJ.hh
│ │ │ predicates.hh
│ │ │ SimpleGraph.hh
│ │ │ UnionFind.hh
│ │ │
│ │ └───trees
│ │ algorithms.hh
│ │ BinaryTreeNode.hh
│ │ kd_tree.hh
│ │ TreeNode.hh
│ │ trees_io.hh
│ │
│ ├───alignment
│ │ │ AlignmentAnnotation.hh
│ │ │ AlignmentBlock.cc
│ │ │ AlignmentBlock.hh
│ │ │ AlignmentRow.hh
│ │ │ PairwiseAlignment.cc
│ │ │ PairwiseAlignment.fwd.hh
│ │ │ PairwiseAlignment.hh
│ │ │ PairwiseSequenceAlignment.cc
│ │ │ PairwiseSequenceAlignment.fwd.hh
│ │ │ PairwiseSequenceAlignment.hh
│ │ │
│ │ ├───scoring
│ │ │ k_tuples.hh
│ │ │
│ │ └───tasks
│ │ alignment_utility_tasks.cc
│ │ alignment_utility_tasks.hh
│ │
│ ├───calc
│ │ │ sse_math.cc
│ │ │ sse_math.hh
│ │ │
│ │ ├───numeric
│ │ │ basic_math.cc
│ │ │ basic_math.hh
│ │ │
│ │ └───structural
│ │ │ local_backbone_geometry.cc
│ │ │ local_backbone_geometry.hh
│ │ │
│ │ └───transformations
│ │ Rototranslation.cc
│ │ Rototranslation.fwd.hh
│ │ Rototranslation.hh
│ │ transformation_utils.cc
│ │ transformation_utils.hh
│ │
│ ├───chemical
│ │ AtomicElement.cc
│ │ AtomicElement.hh
│ │ Monomer.cc
│ │ Monomer.hh
│ │
│ ├───data
│ │ │ data_dummy.cpp
│ │ │
│ │ ├───basic
│ │ │ Array2D.hh
│ │ │ Vec3.cc
│ │ │ Vec3.fwd.hh
│ │ │ Vec3.hh
│ │ │ Vec3Cubic.cc
│ │ │ Vec3Cubic.hh
│ │ │ Vec3I.cc
│ │ │ Vec3I.fwd.hh
│ │ │ Vec3I.hh
│ │ │
│ │ ├───io
│ │ │ DataTable.cc
│ │ │ DataTable.hh
│ │ │ fasta_io.cc
│ │ │ fasta_io.hh
│ │ │ Pdb.cc
│ │ │ Pdb.fwd.hh
│ │ │ Pdb.hh
│ │ │ PdbField.hh
│ │ │ pir_io.cc
│ │ │ pir_io.hh
│ │ │ XML.cc
│ │ │ XML.hh
│ │ │ XMLElement.cc
│ │ │ XMLElement.hh
│ │ │
│ │ ├───sequence
│ │ │ PirEntry.cc
│ │ │ PirEntry.hh
│ │ │ ReduceSequenceAlphabet.cc
│ │ │ ReduceSequenceAlphabet.hh
│ │ │ SecondaryStructure.cc
│ │ │ SecondaryStructure.fwd.hh
│ │ │ SecondaryStructure.hh
│ │ │ SecondaryStructureAnnotation.hh
│ │ │ Sequence.cc
│ │ │ Sequence.fwd.hh
│ │ │ Sequence.hh
│ │ │ sequence_utils.cc
│ │ │ sequence_utils.hh
│ │ │
│ │ └───structural
│ │ │ Chain.cc
│ │ │ Chain.fwd.hh
│ │ │ Chain.hh
│ │ │ PdbAtom.cc
│ │ │ PdbAtom.fwd.hh
│ │ │ PdbAtom.hh
│ │ │ Residue.cc
│ │ │ Residue.fwd.hh
│ │ │ Residue.hh
│ │ │ ResidueSegment.cc
│ │ │ ResidueSegment.hh
│ │ │ ResidueSegmentProvider.cc
│ │ │ ResidueSegmentProvider.hh
│ │ │ SecondaryStructureElement.fwd.hh
│ │ │ Structure.cc
│ │ │ Structure.fwd.hh
│ │ │ Structure.hh
│ │ │
│ │ └───selectors
│ │ ResidueSegmentSelector.cc
│ │ ResidueSegmentSelector.hh
│ │ structure_selectors.cc
│ │ structure_selectors.fwd.hh
│ │ structure_selectors.hh
│ │
│ └───protocols
│ selection_protocols.cc
│ selection_protocols.hh
│
├───simulations
│ │ simulations_dummy.cpp
│ │
│ ├───forcefields
│ │ │ ByAtomEnergy.hh
│ │ │ Energy.hh
│ │ │ NeighborList.cc
│ │ │ NeighborList.hh
│ │ │
│ │ └───cartesian
│ │ CAHydrogenBond.cc
│ │ CAHydrogenBond.hh
│ │
│ │
│ └───systems
│ │ AtomRange.hh
│ │ AtomTypes.cc
│ │ AtomTypes.hh
│ │ AtomTypingInterface.hh
│ │ AtomTypingVariants.cc
│ │ AtomTypingVariants.hh
│ │ BuildFluidSystem.fwd.hh
│ │ CartesianAtoms.cc
│ │ CartesianAtoms.fwd.hh
│ │ CartesianAtoms.hh
│ │ CartesianChains.cc
│ │ CartesianChains.hh
│ │ SimpleAtomTyping.cc
│ │ SimpleAtomTyping.hh
│ │
│ └───surpass
│ SurpassAlfaAtomTyping.cc
│ SurpassAlfaAtomTyping.hh
│ SurpassAlfaChains.cc
│ SurpassAlfaChains.hh
│
├───ui
│ │
│ │
│ ├───pipelines
│ │ GenericProvider.hh
│ │
│ └───tasks
│ Task.cc
│ Task.hh
│
└───utils
│ exit.cc
│ exit.hh
│ io_utils.cc
│ io_utils.hh
│ Logger.cc
│ Logger.hh
│ LogManager.cc
│ LogManager.hh
│ string_utils.cc
│ string_utils.hh
│
├───exceptions
│ AtomNotFound.hh
│ NoSuchFile.hh
│
└───options
input_options.hh
Option.cc
Option.hh
OptionParser.cc
OptionParser.hh
structures_from_cmdline.cc
structures_from_cmdline.hh
CMakeLists.txt
cmake_minimum_required(VERSION 3.12)
project(BioShellHydrogenBondWithDriverProgram)
set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
add_executable(heca_input heca_input.cc)
set(SOURCE_FILES
core/BioShellEnvironment.cc
core/BioShellEnvironment.hh
core/index.hh
core/algorithms/basic_algorithms.hh
core/algorithms/Combinations.hh
core/algorithms/GivenOrderIterator.hh
core/algorithms/GraphWithData.hh
core/algorithms/graph_algorithms.hh
core/algorithms/IterateIJ.hh
core/algorithms/predicates.hh
core/algorithms/SimpleGraph.hh
core/algorithms/UnionFind.hh
core/algorithms/trees/algorithms.hh
core/algorithms/trees/BinaryTreeNode.hh
core/algorithms/trees/kd_tree.hh
core/algorithms/trees/TreeNode.hh
core/algorithms/trees/trees_io.hh
core/alignment/AlignmentAnnotation.hh
core/alignment/AlignmentBlock.cc
core/alignment/AlignmentBlock.hh
core/alignment/AlignmentRow.hh
core/alignment/PairwiseAlignment.cc
core/alignment/PairwiseAlignment.fwd.hh
core/alignment/PairwiseAlignment.hh
core/alignment/PairwiseSequenceAlignment.cc
core/alignment/PairwiseSequenceAlignment.fwd.hh
core/alignment/PairwiseSequenceAlignment.hh
core/alignment/scoring/k_tuples.hh
core/alignment/tasks/alignment_utility_tasks.cc
core/alignment/tasks/alignment_utility_tasks.hh
core/calc/sse_math.cc
core/calc/sse_math.hh
core/calc/numeric/basic_math.cc
core/calc/numeric/basic_math.hh
core/calc/structural/local_backbone_geometry.cc
core/calc/structural/local_backbone_geometry.hh
core/calc/structural/transformations/Rototranslation.cc
core/calc/structural/transformations/Rototranslation.fwd.hh
core/calc/structural/transformations/Rototranslation.hh
core/calc/structural/transformations/transformation_utils.cc
core/calc/structural/transformations/transformation_utils.hh
core/chemical/AtomicElement.cc
core/chemical/AtomicElement.hh
core/chemical/Monomer.cc
core/chemical/Monomer.hh
core/data/data_dummy.cpp
core/data/basic/Array2D.hh
core/data/basic/Vec3.cc
core/data/basic/Vec3.fwd.hh
core/data/basic/Vec3.hh
core/data/basic/Vec3Cubic.cc
core/data/basic/Vec3Cubic.hh
core/data/basic/Vec3I.cc
core/data/basic/Vec3I.fwd.hh
core/data/basic/Vec3I.hh
core/data/io/DataTable.cc
core/data/io/DataTable.hh
core/data/io/fasta_io.cc
core/data/io/fasta_io.hh
core/data/io/Pdb.cc
core/data/io/Pdb.fwd.hh
core/data/io/Pdb.hh
core/data/io/PdbField.hh
core/data/io/pir_io.cc
core/data/io/pir_io.hh
core/data/io/XML.cc
core/data/io/XML.hh
core/data/io/XMLElement.cc
core/data/io/XMLElement.hh
core/data/sequence/PirEntry.cc
core/data/sequence/PirEntry.hh
core/data/sequence/ReduceSequenceAlphabet.cc
core/data/sequence/ReduceSequenceAlphabet.hh
core/data/sequence/SecondaryStructure.cc
core/data/sequence/SecondaryStructure.fwd.hh
core/data/sequence/SecondaryStructure.hh
core/data/sequence/SecondaryStructureAnnotation.hh
core/data/sequence/Sequence.cc
core/data/sequence/Sequence.fwd.hh
core/data/sequence/Sequence.hh
core/data/sequence/sequence_utils.cc
core/data/sequence/sequence_utils.hh
core/data/structural/Chain.cc
core/data/structural/Chain.fwd.hh
core/data/structural/Chain.hh
core/data/structural/PdbAtom.cc
core/data/structural/PdbAtom.fwd.hh
core/data/structural/PdbAtom.hh
core/data/structural/Residue.cc
core/data/structural/Residue.fwd.hh
core/data/structural/Residue.hh
core/data/structural/ResidueSegment.cc
core/data/structural/ResidueSegment.hh
core/data/structural/ResidueSegmentProvider.cc
core/data/structural/ResidueSegmentProvider.hh
core/data/structural/SecondaryStructureElement.fwd.hh
core/data/structural/Structure.cc
core/data/structural/Structure.fwd.hh
core/data/structural/Structure.hh
core/data/structural/selectors/ResidueSegmentSelector.cc
core/data/structural/selectors/ResidueSegmentSelector.hh
core/data/structural/selectors/structure_selectors.cc
core/data/structural/selectors/structure_selectors.fwd.hh
core/data/structural/selectors/structure_selectors.hh
core/protocols/selection_protocols.cc
core/protocols/selection_protocols.hh
simulations/simulations_dummy.cpp
simulations/forcefields/ByAtomEnergy.hh
simulations/forcefields/Energy.hh
simulations/forcefields/NeighborList.cc
simulations/forcefields/NeighborList.hh
simulations/forcefields/cartesian/CAHydrogenBond.cc
simulations/forcefields/cartesian/CAHydrogenBond.hh
simulations/systems/AtomRange.hh
simulations/systems/AtomTypes.cc
simulations/systems/AtomTypes.hh
simulations/systems/AtomTypingInterface.hh
simulations/systems/AtomTypingVariants.cc
simulations/systems/AtomTypingVariants.hh
simulations/systems/BuildFluidSystem.fwd.hh
simulations/systems/CartesianAtoms.cc
simulations/systems/CartesianAtoms.fwd.hh
simulations/systems/CartesianAtoms.hh
simulations/systems/CartesianChains.cc
simulations/systems/CartesianChains.hh
simulations/systems/SimpleAtomTyping.cc
simulations/systems/SimpleAtomTyping.hh
simulations/systems/surpass/SurpassAlfaAtomTyping.cc
simulations/systems/surpass/SurpassAlfaAtomTyping.hh
simulations/systems/surpass/SurpassAlfaChains.cc
simulations/systems/surpass/SurpassAlfaChains.hh
ui/pipelines/GenericProvider.hh
ui/tasks/Task.cc
ui/tasks/Task.hh
utils/exit.cc
utils/exit.hh
utils/io_utils.cc
utils/io_utils.hh
utils/Logger.cc
utils/Logger.hh
utils/LogManager.cc
utils/LogManager.hh
utils/string_utils.cc
utils/string_utils.hh
utils/exceptions/AtomNotFound.hh
utils/exceptions/NoSuchFile.hh
utils/options/input_options.hh
utils/options/Option.cc
utils/options/Option.hh
utils/options/OptionParser.cc
utils/options/OptionParser.hh
utils/options/structures_from_cmdline.cc
utils/options/structures_from_cmdline.hh
)
# Include directories
include_directories(core)
include_directories(core/algorithms)
include_directories(core/algorithms/trees)
include_directories(core/alignment)
include_directories(core/alignment/scoring)
include_directories(core/alignment/tasks)
include_directories(core/calc)
include_directories(core/calc/numeric)
include_directories(core/calc/structural)
include_directories(core/calc/structural/transformations)
include_directories(core/chemical)
include_directories(core/data)
include_directories(core/data/basic)
include_directories(core/data/io)
include_directories(core/data/sequence)
include_directories(core/data/structural)
include_directories(core/data/structural/selectors)
include_directories(core/protocols)
include_directories(simulations)
include_directories(simulations/forcefields)
include_directories(simulations/forcefields/cartesian)
include_directories(simulations/systems)
include_directories(simulations/systems/surpass)
include_directories(ui)
include_directories(ui/pipelines)
include_directories(ui/tasks)
include_directories(utils)
include_directories(utils/exceptions)
include_directories(utils/options)
# Add the source files to the executable
target_sources(heca_input PRIVATE ${SOURCE_FILES})
输出
====================[ Clean | Debug ]===========================================
"C:\Users\pc\AppData\Local\JetBrains\CLion 2022.1.3\bin\cmake\win\bin\cmake.exe" --build "C:\Users\pc\Documents\__protein design\hydrogen bond\BioShellHydrogenBondWithDriverProgram - Copy\cmake-build-debug" --target clean -j 3
[1/1] Cleaning all built files...
Cleaning... 0 files.
Clean finished
====================[ Build | heca_input | Debug ]==============================
"C:\Users\pc\AppData\Local\JetBrains\CLion 2022.1.3\bin\cmake\win\bin\cmake.exe" --build "C:\Users\pc\Documents\__protein design\hydrogen bond\BioShellHydrogenBondWithDriverProgram - Copy\cmake-build-debug" --target heca_input -j 3
[1/57] Building CXX object CMakeFiles/heca_input.dir/core/alignment/AlignmentBlock.cc.obj
FAILED: CMakeFiles/heca_input.dir/core/alignment/AlignmentBlock.cc.obj
"C:\Users\pc\AppData\Local\JetBrains\CLion 2022.1.3\bin\mingw\bin\g++.exe" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/algorithms" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/algorithms/trees" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/alignment" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/alignment/scoring" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/alignment/tasks" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/calc" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/calc/numeric" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/calc/structural" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/calc/structural/transformations" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/chemical" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/data" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/data/basic" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/data/io" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/data/sequence" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/data/structural" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/data/structural/selectors" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/protocols" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/simulations" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/simulations/forcefields" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/simulations/forcefields/cartesian" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/simulations/systems" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/simulations/systems/surpass" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/ui" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/ui/pipelines" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/ui/tasks" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/utils" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/utils/exceptions" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/utils/options" -g -std=gnu++11 -MD -MT CMakeFiles/heca_input.dir/core/alignment/AlignmentBlock.cc.obj -MF CMakeFiles\heca_input.dir\core\alignment\AlignmentBlock.cc.obj.d -o CMakeFiles/heca_input.dir/core/alignment/AlignmentBlock.cc.obj -c "C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/alignment/AlignmentBlock.cc"
C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/alignment/AlignmentBlock.cc:1:10: fatal error: core/index.hh: No such file or directory
1 | #include <core/index.hh>
| ^~~~~~~~~~~~~~~
compilation terminated.
[2/57] Building CXX object CMakeFiles/heca_input.dir/core/alignment/tasks/alignment_utility_tasks.cc.obj
FAILED: CMakeFiles/heca_input.dir/core/alignment/tasks/alignment_utility_tasks.cc.obj
"C:\Users\pc\AppData\Local\JetBrains\CLion 2022.1.3\bin\mingw\bin\g++.exe" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/algorithms" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/algorithms/trees" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/alignment" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/alignment/scoring" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/alignment/tasks" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/calc" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/calc/numeric" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/calc/structural" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/calc/structural/transformations" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/chemical" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/data" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/data/basic" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/data/io" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/data/sequence" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/data/structural" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/data/structural/selectors" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/protocols" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/simulations" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/simulations/forcefields" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/simulations/forcefields/cartesian" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/simulations/systems" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/simulations/systems/surpass" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/ui" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/ui/pipelines" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/ui/tasks" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/utils" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/utils/exceptions" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/utils/options" -g -std=gnu++11 -MD -MT CMakeFiles/heca_input.dir/core/alignment/tasks/alignment_utility_tasks.cc.obj -MF CMakeFiles\heca_input.dir\core\alignment\tasks\alignment_utility_tasks.cc.obj.d -o CMakeFiles/heca_input.dir/core/alignment/tasks/alignment_utility_tasks.cc.obj -c "C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/alignment/tasks/alignment_utility_tasks.cc"
C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/alignment/tasks/alignment_utility_tasks.cc:1:10: fatal error: core/data/io/pir_io.hh: No such file or directory
1 | #include <core/data/io/pir_io.hh>
| ^~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
[3/57] Building CXX object CMakeFiles/heca_input.dir/core/alignment/PairwiseAlignment.cc.obj
FAILED: CMakeFiles/heca_input.dir/core/alignment/PairwiseAlignment.cc.obj
"C:\Users\pc\AppData\Local\JetBrains\CLion 2022.1.3\bin\mingw\bin\g++.exe" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/algorithms" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/algorithms/trees" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/alignment" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/alignment/scoring" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/alignment/tasks" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/calc" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/calc/numeric" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/calc/structural" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/calc/structural/transformations" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/chemical" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/data" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/data/basic" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/data/io" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/data/sequence" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/data/structural" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/data/structural/selectors" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/protocols" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/simulations" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/simulations/forcefields" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/simulations/forcefields/cartesian" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/simulations/systems" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/simulations/systems/surpass" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/ui" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/ui/pipelines" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/ui/tasks" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/utils" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/utils/exceptions" -I"C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/utils/options" -g -std=gnu++11 -MD -MT CMakeFiles/heca_input.dir/core/alignment/PairwiseAlignment.cc.obj -MF CMakeFiles\heca_input.dir\core\alignment\PairwiseAlignment.cc.obj.d -o CMakeFiles/heca_input.dir/core/alignment/PairwiseAlignment.cc.obj -c "C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/alignment/PairwiseAlignment.cc"
C:/Users/pc/Documents/__protein design/hydrogen bond/BioShellHydrogenBondWithDriverProgram - Copy/core/alignment/PairwiseAlignment.cc:5:10: fatal error: core/index.hh: No such file or directory
5 | #include <core/index.hh>
| ^~~~~~~~~~~~~~~
compilation terminated.
ninja: build stopped: subcommand failed.
更喜欢使用
target_include_directoriesinclude_directoriestarget_include_directories(heca_input PRIVATE
core
core/algorithms
core/algorithms/trees
core/alignment
core/alignment/scoring
core/alignment/tasks
core/calc
core/calc/numeric
core/calc/structural
core/calc/structural/transformations
core/chemical
core/data
core/data/basic
core/data/io
core/data/sequence
core/data/structural
core/data/structural/selectors
core/protocols
simulations
simulations/forcefields
simulations/forcefields/cartesian
simulations/systems
simulations/systems/surpass
ui
ui/pipelines
ui/tasks
utils
utils/exceptions
utils/options
)
然后考虑减少包含目录的数量。实际上，您不需要那么多包含目录。