align_hypoPair Command Help
Command: $SCHRODINGER/utilities/align_hypoPair
align_hypoPair - Aligns one hypothesis onto another based on least-squares
superposition of matching site points, considering all possible mappings.
Alignments are summarized to standard output in order of increasing RMSD, with
the lowest RMSD alignment being saved as a new hypothesis.
Usage: align_hypoPair -fixed <fixedHypoID>
-free <freeHypoID>
-new <newHypoID>
[-dtol <deltaDist>]
[-match <minSites>]
[-mix]
[-equiv <equivFile>]
[-merge <method>]
[-keep <maxAlign>]
[-rmsd <rmsdFile>]
[-sim <simFile> [-rmsdMax <rmsdMax>]]
[-fmt single|multi]
-fixed <fixedHypoID> - Hypothesis that will remain fixed when the alignment is
performed. If single-file format is used, <fixedHypoID>
should be the actual name of the hypothesis file, e.g.,
ADHHR.phypo. If multi-file format is used, <fixedHypoID>
should be the prefix of all hypothesis files (e.g., use
ADHHR if the files are ADHHR.def, ADHHR.mae, etc.).
Positional tolerances and site mask will be applied if
they are present in the hypothesis.
-free <freeHypoID> - Hypothesis that will be aligned to the fixed hypothesis.
The feature definitions in <freeHypoID> must be identical
to those in <fixedHypoID>.
-new <newHypoID> - Output hypothesis containing the aligned version of the
free hypothesis.
-dtol <deltaDist> - Intersite distance matching tolerance. The default is
2.0 angstroms.
-match <minSites> - The minimum number of sites that must match. The default
is 3.
-mix - Consider alignments involving different numbers of
matching sites. By default, only n-point matches are
retained and ranked by RMSD, where n is the greatest
number of sites that could be matched. But if -mix is
specified, matches involving fewer sites will be mixed
with the n-point matches. Beware that RMSD values are
generally smaller for matches with fewer sites, so using
-mix will tend to favor those alignments.
-equiv <equivFile> - A file that defines the allowed mappings between the
sites in the fixed and free hypotheses. This file
consists of two lines, each of which contains a string of
non-blank characters, with one character for each site in
the fixed and free hypotheses. For example, if the fixed
and free hypotheses contain 4 and 5 sites, respectively,
the following strings could be used to define the
allowed mappings:
abbc
ababc
This implies:
(1) The 1st site in the fixed hypothesis (denoted as "a")
can be matched to either the 1st or 3rd site of the
free hypothesis (because these are also denoted as
"a").
(2) The 2nd and 3rd sites of the fixed hypothesis
(denoted as "b") can be matched to the 2nd or 4th
sites of the free hypothesis.
(3) The 4th site of the fixed hypothesis (denoted as "c")
can be matched to only the 5th site of the free
hypothesis.
If this option is omitted, the feature types define the
allowed mappings, hence an acceptor can be mapped only to
another acceptor, a donor can be mapped only to another
donor, etc.
-merge <method> - The merging method. Allowed values are 1, 2, 3, 4. If
this option is used, the new hypothesis will be a union
of the sites in the fixed and aligned free hypotheses,
with matching sites merged/replaced as follows:
<method> Merged Site
-------- -----------
1 Fixed site type; fixed coordinates
2 Free site type; free coordinates
3 Fixed site type; average coordinates
4 Free site type; average coordinates
Note that when merging is done, the new hypothesis has no
reference ligand. Note also that the RMSD value is still
computed from the positions of the aligned free sites,
not from the positions of the merged sites.
-keep <maxAlign> - The maximum number of aligned hypotheses to keep. By
default, only a single hypothesis corresponding to the
smallest RMSD is created. However, if <maxAlign> is
greater than 1 and multiple alignments are possible, a
series of hypotheses <newHypoID>_1, <newHypoID>_2, etc.
will be created, with progressively larger RMSD values.
-rmsd <rmsdFile> - A file to which RMSD values should be written, one per
per line. The file will contain one value for each
hypothesis created (up to <maxAlign>).
-sim <simFile> - Use RMSD values to compute a similarity for each
alignment, according to the following formula:
Sim = max(0, (m/n)*(1 - RMSD/<rmsdMax>))
where
n = (1/2)*(#sites fixed + #sites free)
m = #sites matched
<rmsdMax> = User-defined parameter (default = 1.2)
Similarities will be written to <simFile>, one per line,
for each hypothesis created (up to <maxAlign>). Note that
RMSD is still used to rank the alignments.
-rmsdMax <rmsdMax> - Similarity parameter. The default is 1.2. Valid only in
combination with -sim <simFile>.
-trans <transFile> - Write least-squares transformation to a CSV file. The
file will contain a 3x4 matrix, where the first 3 columns
hold the rotation matrix R, and the last column holds the
translation vector T. The following operation should be
applied to transform a set of coordinates (x, y z):
x' r11 r12 r13 x t1
y' = r21 r22 r23 * y + t2
z' r31 r32 r33 z t3
If multiple hypotheses are created, <transFile> will
contain only the transformation for the first one (i.e.,
the hypothesis with the lowest RMSD).
-fmt single|multi - Specifies hypothesis format to read/write. The default is
"single".