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avoid fileexist on empty strings #995

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Merged
merged 2 commits into from
Sep 6, 2024
Merged

avoid fileexist on empty strings #995

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d4b5fdc
Address issue #993
amjjbonvin Sep 2, 2024
b7769a4
Merge branch 'main' into fileexist
amjjbonvin Sep 6, 2024
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39 changes: 24 additions & 15 deletions src/haddock/modules/refinement/emref/cns/read_data.cns
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@
! * as part of this package. *
! ***********************************************************************
!

! Ambiguous and unambiguous distance restraints, hbonds
noe
reset
Expand All @@ -23,22 +22,30 @@ fileexist $filenam0 end
if ($result eq false) then
evaluate ($filenam0 = $ambig_fname)
end if
fileexist $filenam0 end
if ($result eq true) then
noe class ambi @@$filenam0 end

if ($filenam0 # "") then
fileexist $filenam0 end
if ($result eq true) then
noe class ambi @@$filenam0 end
end if
end if

if ($Data.randremoval eq true) then
noe part $Data.npart end
end if

fileexist $unambig_fname end
if ($result eq true) then
noe class dist @@$unambig_fname end
if ($unambig_fname # "") then
fileexist $unambig_fname end
if ($result eq true) then
noe class dist @@$unambig_fname end
end if
end if

fileexist $hbond_fname end
if ($result eq true) then
noe @@$hbond_fname end
if ($hbond_fname # "") then
fileexist $hbond_fname end
if ($result eq true) then
noe @@$hbond_fname end
end if
end if

noe
Expand All @@ -63,11 +70,13 @@ restraints dihedral
reset
nassign 50000
end
fileexist $dihe_fname end
if ($result eq true) then
restraints dihedral
@@$dihe_fname
end
if ($dihe_fname # "") then
fileexist $dihe_fname end
if ($result eq true) then
restraints dihedral
@@$dihe_fname
end
end if
end if

restraints dihedral ? end
33 changes: 20 additions & 13 deletions src/haddock/modules/refinement/emref/cns/read_noes.cns
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
! read_data.cns
! read_noes.cns
! Read the various restraints data
! In this version only distance-based restraints
!
Expand All @@ -11,10 +11,10 @@
! * as part of this package. *
! ***********************************************************************
!
!NOEs, hbonds
! Ambiguous and unambiguous distance restraints, hbonds
noe
reset
nrestraints = 12000000 ! allocate space for NOEs
nrestraints = 12000000 ! allocate space for NOEs
ceiling 1000
end

Expand All @@ -23,22 +23,30 @@ fileexist $filenam0 end
if ($result eq false) then
evaluate ($filenam0 = $ambig_fname)
end if
fileexist $filenam0 end
if ($result eq true) then
noe class ambi @@$filenam0 end

if ($filenam0 # "") then
fileexist $filenam0 end
if ($result eq true) then
noe class ambi @@$filenam0 end
end if
end if

if ($Data.randremoval eq true) then
noe part $Data.npart end
end if

fileexist $unambig_fname end
if ($result eq true) then
noe class dist @@$unambig_fname end
if ($unambig_fname # "") then
fileexist $unambig_fname end
if ($result eq true) then
noe class dist @@$unambig_fname end
end if
end if

fileexist $hbond_fname end
if ($result eq true) then
noe @@$hbond_fname end
if ($hbond_fname # "") then
fileexist $hbond_fname end
if ($result eq true) then
noe @@$hbond_fname end
end if
end if

noe
Expand All @@ -56,4 +64,3 @@ noe
mrswitch * 1.0
avexpo hbond 20
end

8 changes: 5 additions & 3 deletions src/haddock/modules/refinement/emref/cns/read_param.cns
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -46,9 +46,11 @@ parameter
@@$cofac_parameter_infile
@@$heme_parameter_infile
@@$shape_parameter_infile
fileexist $ligand_param_fname end
if ($result eq true) then
@@$ligand_param_fname
if ($ligand_param_fname # "") then
fileexist $ligand_param_fname end
if ($result eq true) then
@@$ligand_param_fname
end if
end if
end

Expand Down
39 changes: 24 additions & 15 deletions src/haddock/modules/refinement/flexref/cns/read_data.cns
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@
! * as part of this package. *
! ***********************************************************************
!

! Ambiguous and unambiguous distance restraints, hbonds
noe
reset
Expand All @@ -23,22 +22,30 @@ fileexist $filenam0 end
if ($result eq false) then
evaluate ($filenam0 = $ambig_fname)
end if
fileexist $filenam0 end
if ($result eq true) then
noe class ambi @@$filenam0 end

if ($filenam0 # "") then
fileexist $filenam0 end
if ($result eq true) then
noe class ambi @@$filenam0 end
end if
end if

if ($Data.randremoval eq true) then
noe part $Data.npart end
end if

fileexist $unambig_fname end
if ($result eq true) then
noe class dist @@$unambig_fname end
if ($unambig_fname # "") then
fileexist $unambig_fname end
if ($result eq true) then
noe class dist @@$unambig_fname end
end if
end if

fileexist $hbond_fname end
if ($result eq true) then
noe @@$hbond_fname end
if ($hbond_fname # "") then
fileexist $hbond_fname end
if ($result eq true) then
noe @@$hbond_fname end
end if
end if

noe
Expand All @@ -63,11 +70,13 @@ restraints dihedral
reset
nassign 50000
end
fileexist $dihe_fname end
if ($result eq true) then
restraints dihedral
@@$dihe_fname
end
if ($dihe_fname # "") then
fileexist $dihe_fname end
if ($result eq true) then
restraints dihedral
@@$dihe_fname
end
end if
end if

restraints dihedral ? end
33 changes: 20 additions & 13 deletions src/haddock/modules/refinement/flexref/cns/read_noes.cns
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
! read_data.cns
! read_noes.cns
! Read the various restraints data
! In this version only distance-based restraints
!
Expand All @@ -11,10 +11,10 @@
! * as part of this package. *
! ***********************************************************************
!
!NOEs, hbonds
! Ambiguous and unambiguous distance restraints, hbonds
noe
reset
nrestraints = 12000000 ! allocate space for NOEs
nrestraints = 12000000 ! allocate space for NOEs
ceiling 1000
end

Expand All @@ -23,22 +23,30 @@ fileexist $filenam0 end
if ($result eq false) then
evaluate ($filenam0 = $ambig_fname)
end if
fileexist $filenam0 end
if ($result eq true) then
noe class ambi @@$filenam0 end

if ($filenam0 # "") then
fileexist $filenam0 end
if ($result eq true) then
noe class ambi @@$filenam0 end
end if
end if

if ($Data.randremoval eq true) then
noe part $Data.npart end
end if

fileexist $unambig_fname end
if ($result eq true) then
noe class dist @@$unambig_fname end
if ($unambig_fname # "") then
fileexist $unambig_fname end
if ($result eq true) then
noe class dist @@$unambig_fname end
end if
end if

fileexist $hbond_fname end
if ($result eq true) then
noe @@$hbond_fname end
if ($hbond_fname # "") then
fileexist $hbond_fname end
if ($result eq true) then
noe @@$hbond_fname end
end if
end if

noe
Expand All @@ -56,4 +64,3 @@ noe
mrswitch * 1.0
avexpo hbond 20
end

8 changes: 5 additions & 3 deletions src/haddock/modules/refinement/flexref/cns/read_param.cns
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -46,9 +46,11 @@ parameter
@@$cofac_parameter_infile
@@$heme_parameter_infile
@@$shape_parameter_infile
fileexist $ligand_param_fname end
if ($result eq true) then
@@$ligand_param_fname
if ($ligand_param_fname # "") then
fileexist $ligand_param_fname end
if ($result eq true) then
@@$ligand_param_fname
end if
end if
end

Expand Down
39 changes: 24 additions & 15 deletions src/haddock/modules/refinement/mdref/cns/read_data.cns
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@
! * as part of this package. *
! ***********************************************************************
!

! Ambiguous and unambiguous distance restraints, hbonds
noe
reset
Expand All @@ -23,22 +22,30 @@ fileexist $filenam0 end
if ($result eq false) then
evaluate ($filenam0 = $ambig_fname)
end if
fileexist $filenam0 end
if ($result eq true) then
noe class ambi @@$filenam0 end

if ($filenam0 # "") then
fileexist $filenam0 end
if ($result eq true) then
noe class ambi @@$filenam0 end
end if
end if

if ($Data.randremoval eq true) then
noe part $Data.npart end
end if

fileexist $unambig_fname end
if ($result eq true) then
noe class dist @@$unambig_fname end
if ($unambig_fname # "") then
fileexist $unambig_fname end
if ($result eq true) then
noe class dist @@$unambig_fname end
end if
end if

fileexist $hbond_fname end
if ($result eq true) then
noe @@$hbond_fname end
if ($hbond_fname # "") then
fileexist $hbond_fname end
if ($result eq true) then
noe @@$hbond_fname end
end if
end if

noe
Expand All @@ -63,11 +70,13 @@ restraints dihedral
reset
nassign 50000
end
fileexist $dihe_fname end
if ($result eq true) then
restraints dihedral
@@$dihe_fname
end
if ($dihe_fname # "") then
fileexist $dihe_fname end
if ($result eq true) then
restraints dihedral
@@$dihe_fname
end
end if
end if

restraints dihedral ? end
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