Implementation of a generic docking algorithm #677
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Signed-off-by: cplett <[email protected]>
src/iff/calculator.f90
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| use xtb_docking_param | ||
| use xtb_type_environment, only : TEnvironment | ||
| use xtb_type_molecule, only : TMolecule | ||
| use xtb_iff_iffini, only : init_iff!, precomp | ||
| use xtb_iff_data, only : TIFFData |
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Import only in module scope, use public and private to limit reexports
src/iff/calculator.f90
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| type(TEnvironment), intent(inout) :: env | ||
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| type(TMolecule), intent(in) :: comb!Combined structure of molA and molB (molA has to be first) |
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| type(TMolecule), intent(in) :: comb!Combined structure of molA and molB (molA has to be first) | |
| !> Combined structure of molA and molB (molA has to be first) | |
| type(TMolecule), intent(in) :: comb |
src/iff/calculator.f90
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| fnam='xtblmoinfA' | ||
| call rd0(1,trim(fnam),calc%dat%n1,calc%dat%nlmo1) | ||
| call rd(trim(fnam),1,calc%dat%n1,calc%dat%xyz1,calc%dat%at1& | ||
| &,calc%dat%nlmo1,calc%dat%lmo1,calc%dat%rlmo1,calc%dat%q1,& | ||
| & calc%dat%qct1) | ||
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| fnam='xtblmoinfB' | ||
| call rd0(2,trim(fnam),calc%dat%n2,calc%dat%nlmo2) | ||
| call rd(trim(fnam),2,calc%dat%n2,calc%dat%xyz2,calc%dat%at2,& | ||
| & calc%dat%nlmo2,calc%dat%lmo2,calc%dat%rlmo2,calc%dat%q2,& | ||
| & calc%dat%qct2) |
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Can we use readMolecule provided by https://github.com/grimme-lab/xtb/blob/main/src/io/reader.f90
src/iff/iff_energy.f90
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| end if | ||
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| end subroutine |
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Always include the name of the subroutine in the end statement
src/iff/iff_energy.f90
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| end subroutine | ||
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| end module |
| use xtb_mctc_accuracy, only: wp | ||
| use xtb_docking_param | ||
| use xtb_iff_ifflmo | ||
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Use implicit none and explicit exports
| use xtb_splitparam | ||
| use xtb_iff_calculator, only: TIFFCalculator | ||
| implicit none | ||
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| case('--nat') | ||
| call args%nextArg(sec) | ||
| if (allocated(sec)) then | ||
| call set_natom(env,sec) | ||
| end if |
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This is required for setting the number of atoms of the first molecule in the input structure of a xtb-IFF single point calculation.
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Why a fixed range (1-n)? We have much more flexible input models for fragments available.
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That's a good point. I will change this.
Signed-off-by: cplett <[email protected]>
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Signed-off-by: cplett <[email protected]>
-the docking submodule was implemented
-it can add two molecules based on an interaction site screening with the xtbIFF energy
-geometry optimizations with a GFN method follow automatically
-it is executed with "xtb dock [options]"
-the resulting energetically lowest structure is on file best.xyz, the best 15 structures on file final_structures.xyz
-the documentation will follow later