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                             find command
                        Leif Laaksonen CSC 2001
                        Eero Häkkinen  CSC 2002
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#
# Find S-S bonds in a structure
# Apply the search on all structures available or just to the structure
# with number "StructureNumber". It is also possible to give a distance
# Fbond inside which the S-S must be.
#

find   ssbo$nds   all             [Fbond]
                  StructureNumber [Fbond]

#
# Find hydrogen bonds (equivalent to calculate hydrogen bonds).
# Array "gomHydrogenBondingParams" can be used to customize hbond criteria.
# Following array elements are recognized:
#   Maximum distances:
#     d-a              Distance between donor and acceptor
#     d-a_nohydrogens  Distance between donor and acceptor
#                      (used then "nohy$drogens" is applied)
#     h-a              Distance between hydrogen and acceptor
#     d-h              Distance between donor and hydrogen
#   Minimum angles:
#     d-h-a            donor-hydrogen-acceptor
#     d-a-aa           donor-acceptor-<atom bonded to acceptor>
#     h-a-aa           hydrogen-acceptor-<atom bonded to acceptor>
#   Maximum angles:
#     aromatic         Angle between aromatic plane and vector donor-hydrogen
#

       hbon$ds    Seg Res Atm
       hbon$ds    Seg Res Atm  nohy$drogens
      -hbo$nds

#
# Find protein chains in a structure.
# Returns a list of two items lists. First item is segment name and the
# second item is a residue number ranges in form
# ResN11[-ResN12][,ResN21[-ResN22][,...]]
#

       chain$s     Seg Res IStruct
                           all
                           sele$cted

#
# Find atoms around other atoms or around coordinate point.
# Return atom or residue number ranges in form
# Num11[-Num12][,Num21[-Num22][,...]]
# Return segment names as comma separated list.
# Return selection list as list of segment names, residue number ranges and
# atom number ranges.
# Structure index "IStruct" can also be "all" or "sele$cted".
#

       atom$s     around  Seg1 Res1 Atm1 FRad Seg2 Res2 Atm2 IStruct
                                         FRad FXc FYc FZc    IStruct
       resi$due   around  Seg1 Res1 Atm1 FRad Seg2 Res2 Atm2 IStruct
                                         FRad FXc FYc FZc    IStruct
       segm$ent   around  Seg1 Res1 Atm1 FRad Seg2 Res2 Atm2 IStruct
                                         FRad FXc FYc FZc    IStruct
       sel$list   around  Seg1 Res1 Atm1 FRad Seg2 Res2 Atm2 IStruct
                                         FRad FXc FYc FZc    IStruct

#
# Search for atoms using multiple selection lists.
# Return atom or residue number ranges in form
# Num11[-Num12][,Num21[-Num22][,...]]
# Return segment names as comma separated list.
# Return selection list as list of segment names, residue number ranges and
# atom number ranges.
# Structure index "IStruct" can also be "all" or "sele$cted".
#

       atom$s     join
                         Seg1 Res1 Atm1 IStruct
                         Seg1 Res1 Atm1 Seg2 Res2 Atm2 IStruct
                         Seg1 Res1 Atm1 Seg2 Res2 Atm2 Seg3 Res3 Atm3 IStruct
                         ...
       resi$due   join
                         Seg1 Res1 Atm1 IStruct
                         Seg1 Res1 Atm1 Seg2 Res2 Atm2 IStruct
                         Seg1 Res1 Atm1 Seg2 Res2 Atm2 Seg3 Res3 Atm3 IStruct
                         ...
       segm$ent   join
                         Seg1 Res1 Atm1 IStruct
                         Seg1 Res1 Atm1 Seg2 Res2 Atm2 IStruct
                         Seg1 Res1 Atm1 Seg2 Res2 Atm2 Seg3 Res3 Atm3 IStruct
                         ...
       sel$list   join
                         Seg1 Res1 Atm1 IStruct
                         Seg1 Res1 Atm1 Seg2 Res2 Atm2 IStruct
                         Seg1 Res1 Atm1 Seg2 Res2 Atm2 Seg3 Res3 Atm3 IStruct
                         ...

**************************************************************************
LUL/2002
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