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commit c18ae0fc93fd0ed6840b1ca8462863fe55703853 Author: Malihe Asemani <[email protected]> Date: Tue Sep 1 18:15:13 2015 +0000 Add manpage --- debian/king-probe.1 | 387 ++++++++++++++++++++++++++++++++++++++++++++++++++++ debian/links | 4 + 2 files changed, 391 insertions(+) diff --git a/debian/king-probe.1 b/debian/king-probe.1 new file mode 100644 index 0000000..7bc799b --- /dev/null +++ b/debian/king-probe.1 @@ -0,0 +1,387 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4. +.TH KING-PROBE "1" "September 2015" "king-probe 2.13.110909-1" "User Commands" +.SH NAME +king-probe \- Evaluate and visualize protein interatomic packing +.SH DESCRIPTION +Syntax: probe input.pdb >> out.kin +.IP +or: probe [flags] "src pattern" ["target pattern"] pdbfiles... >> out.kin +.SS "Flags:" +.TP +\fB\-SElf\fR +self intersection: src \-> src (default) +.TP +\fB\-Both\fR +intersect both ways: src <=> targ +.TP +\fB\-ONce\fR +single intersection: src \-> targ +.TP +\fB\-OUt\fR +external van der Waals surface of src (solvent contact surface) +.TP +\fB\-AUTObondrot\fR filename +read and process an autobondrot file +.IP +shortcuts: +.IP +<<NO FLAGS>>same as: \fB\-4H\fR \fB\-mc\fR \fB\-het\fR \fB\-self\fR "altA ogt33" +.TP +\fB\-DEFAULTs\fR +same as: <<NO FLAGS>>, but allows some other flags +.HP +\fB\-SCSurface\fR same as: \fB\-drop\fR \fB\-rad1\fR.4 \fB\-out\fR "not water" +.TP +\fB\-EXPOsed\fR +same as: \fB\-drop\fR \fB\-rad1\fR.4 \fB\-out\fR (note: user supplies pattern) +.TP +\fB\-ASurface\fR +same as: \fB\-drop\fR \fB\-rad0\fR.0 \fB\-add1\fR.4 \fB\-out\fR "not water" +.TP +\fB\-ACCESS\fR +same as: \fB\-drop\fR \fB\-rad0\fR.0 \fB\-add1\fR.4 \fB\-out\fR (note: user supplies pattern) +.HP +\fB\-SCAN0\fR same as: \fB\-4H\fR \fB\-mc\fR \fB\-self\fR "alta blt40 ogt33" +.HP +\fB\-SCAN1\fR same as: \fB\-4H\fR \fB\-once\fR "sc alta blt40 ogt33" "alta blt40 ogt65,(not water ogt33)" +.TP +\fB\-DUMPAtominfo\fR +count the atoms in the selection: src +.IP +(note that BOTH and ONCE require two patterns while +.IP +OUT, SELF and DUMPATOMINFO require just one pattern) +.TP +\fB\-Implicit\fR +implicit hydrogens +.TP +\fB\-Explicit\fR +explicit hydrogens (default) +.TP +\fB\-DEnsity\fR# +set dot density (default 16 dots/sq A) +.TP +\fB\-Radius\fR#.# +set probe radius (default 0.25 A) +.TP +\fB\-ADDvdw\fR#.# +offset added to Van der Waals radii (default 0.0) +.HP +\fB\-SCALEvdw\fR#.# scale factor for Van der Waals radii (default 1.0) +.TP +\fB\-COSCale\fR#.# +scale C=O carbon Van der Waals radii (default 0.94) +.TP +\fB\-SPike\fR +draw spike instead of dots (default) +.TP +\fB\-SPike\fR#.# +set spike scale (default=0.5) +.TP +\fB\-NOSpike\fR +draw only dots +.HP +\fB\-HBRegular\fR#.# max overlap for regular Hbonds(default=0.6) +.HP +\fB\-HBCharged\fR#.# max overlap for charged Hbonds(default=0.8) +.TP +\fB\-Keep\fR +keep nonselected atoms (default) +.TP +\fB\-DRop\fR +drop nonselected atoms +.TP +\fB\-LIMit\fR +limit bump dots to max dist when kissing (default) +.TP +\fB\-NOLIMit\fR +do not limit bump dots +.TP +\fB\-LENs\fR +add lens keyword to kin file +.TP +\fB\-NOLENs\fR +do not add lens keyword to kin file (default) +.TP +\fB\-MC\fR +include mainchain\->mainchain interactions +.TP +\fB\-HETs\fR +include dots to non\-water HET groups (default) +.TP +\fB\-NOHETs\fR +exclude dots to non\-water HET groups +.TP +\fB\-WATers\fR +include dots to water (default) +.TP +\fB\-NOWATers\fR +exclude dots to water +.TP +\fB\-WAT2wat\fR +show dots between waters +.TP +\fB\-DUMPH2O\fR +include water H? vectorlist in output +.TP +\fB\-4H\fR +extend bond chain dot removal to 4 for H (default) +.TP +\fB\-3\fR +limit bond chain dot removal to 3 +.TP +\fB\-2\fR +limit bond chain dot removal to 2 +.TP +\fB\-1\fR +limit bond chain dot removal to 1 +.HP +\fB\-IGNORE\fR "pattern" explicit drop: ignore atoms selected by pattern +.TP +\fB\-DOCHO\fR +recognize CH..O Hbonds +.TP +\fB\-CHO\fR#.# +scale factor for CH..O Hbond score (default=0.5) +.TP +\fB\-PolarH\fR +use short radii of polar hydrogens (default) +.TP +\fB\-NOPolarH\fR +do not shorten radii of polar hydrogens +.HP +\fB\-NOFACEhbond\fR do not identify HBonds to aromatic faces +.HP +\fB\-Name\fR "name" specify the group name (default "dots") +.TP +\fB\-DOTMASTER\fR +group name used as extra master={name} on lists +.TP +\fB\-NOGroup\fR +do not generate @group statement in .kin format output +.TP +\fB\-KINemage\fR +add @kinemage 1 statement to top of .kin format output +.TP +\fB\-Countdots\fR +produce a count of dots\-not a dotlist +.TP +\fB\-Unformated\fR +output raw dot info +.IP +name:pat:type:srcAtom:targAtom:mingap:gap:spX: +spY:spZ:spikeLen:score:stype:ttype:x:y:z:sBval:tBval: +.TP +\fB\-OFORMAT\fR +output dot info formatted for display in O +.TP +\fB\-XVFORMAT\fR +output dot info formatted for display in XtalView +.TP +\fB\-ONELINE\fR +output one line :contacts:by:severity:type: +.TP +\fB\-GAPcolor\fR +color dots by gap amount (default) +.TP +\fB\-ATOMcolor\fR +color dots by atom type +.TP +\fB\-BASEcolor\fR +color dots by nucleic acid base type +.TP +\fB\-COLORBase\fR +color dots by gap and nucleic acid base type +.HP +\fB\-OUTCOLor\fR "name" specify the point color for \fB\-OUT\fR (default "gray") +.TP +\fB\-GAPWeight\fR# +set weight for scoring gaps (default 0.25) +.HP +\fB\-BUMPWeight\fR# set relative scale for scoring bumps (default 10.0) +.TP +\fB\-HBWeight\fR# +set relative scale for scoring Hbonds (default 4.0) +.TP +\fB\-DIVLow\fR#.# +Division for Bump categories (default \fB\-0\fR.4) +.TP +\fB\-DIVHigh\fR#.# +Division for Contact categories (default 0.25) +.TP +\fB\-MINOCCupancy\fR#.# +Occupancy below this is same as zero (default 0.02) +.TP +\fB\-ELEMent\fR +add master buttons for different elements in kin output +.TP +\fB\-NOHBOUT\fR +do not output contacts for HBonds +.TP +\fB\-NOCLASHOUT\fR +do not output contacts for clashes +.TP +\fB\-NOVDWOUT\fR +do not output contacts for van der Waals interactions +.TP +\fB\-ONLYBADOUT\fR +onlybadout output bad clashes (severe overlap contacts) +.TP +\fB\-SUMMARY\fR +output summary list of contacts and clashes +.TP +\fB\-ONELINE\fR +output summary list on oneline +.TP +\fB\-NOTICKs\fR +do not display the residue name ticker during processing +.TP +\fB\-STDBONDs\fR +assume only standard bonding patterns in standard residues +.TP +\fB\-NOPARENT\fR +do not bond hydrogens based on table of parent heavy atoms +.TP +\fB\-SEGID\fR +use the PDB SegID field to descriminate between residues +.TP +\fB\-OLDU\fR +generate old style \fB\-u\fR output: kissEdge2BullsEye, etc +.TP +\fB\-VErbose\fR +verbose mode (default) +.TP +\fB\-REFerence\fR +display reference string +.TP +\fB\-CHANGEs\fR +display a list of program changes +.TP +\fB\-Quiet\fR +quiet mode +.TP +\fB\-Help\fR +show expanded help notice (includes other flags) +.TP +\fB\-VERSION\fR +one line version to stdout +.PP +Pattern elements: (should be put in quotes on the command line) +.TP +FILE# +within file # +.TP +MODEL# +within model # +.TP +CHAINaa +within chain a +.TP +SEGaaaa +segment identifier aaaa (where _ represents blank) +.TP +ALTa +alternate conformation a +.TP +ATOMaaaa +atom name aaaa (where _ represents blank) +(all 4 characters are used so H would be ATOM_H__) +.TP +RESaaa +residue aaa +.TP +# +residue # +.TP +#a +residue #, insert a +.TP +#\-# +residue range # (insert codes ignored) +.TP +a +residue type by one letter codes (eg. y) +.TP +aaa +residue type by three letter codes (eg. tyr) +.IP +ALL,PROTEIN,MC,SC,BASE,ALPHA,BETA,NITROGEN,CARBON, +OXYGEN,SULFUR,PHOSPHORUS,HYDROGEN,METAL,POLAR, +NONPOLAR,CHARGED,DONOR,ACCEPTOR,AROMATIC,METHYL, +HET,WATER,DNA,RNA +.IP +all or a subset of the atoms +.TP +OLT# +Occupancy less than # (integer percent) +.TP +OGT# +Occupancy greater than # (integer percent) +.TP +BLT# +B\-value less than # (integer) +.TP +BGT# +B\-value greater than # (integer) +.TP +INSa +Insert code a (where _ represents blank) +.TP +WITHIN #.# OF #.#, #.#, #.# +atoms within distance from point +.IP +Patterns can be combined into comma separated lists +such as "trp,phe,tyr" meaning TRP or PHE or TYR. +.IP +Patterns that are sepatated by blanks must all be true +such as "chainb 1\-5" meaning residues 1 to 5 in chain B. +.IP +You can also group patterns with parenthesis, separate +multiple patterns with | meaning 'or' and choose the +complement with NOT as in "not file1" meaning not in file 1. +.IP +An autobondrot file is similar to other PDB input files +but it includes information identifying atoms subject to rotations +and other transformations. +.IP +Example autobondrot file fragment showing Calpha\-Cbeta bond rotation +and a periodic torsion penalty function for this rotation +.TP +ATOM +1 CB TYR 61 34.219 17.937 4.659 1.00 0.00 +.TP +bondrot:chi1:78.7: +0:359:5:33.138:18.517: 5.531:34.219:17.937: 4.659 +.IP +cos:\-3:60:3: +ATOM 1 1HB TYR 61 34.766 18.777 4.206 1.00 0.00 +ATOM 1 2HB TYR 61 34.927 17.409 5.315 1.00 0.00 +ATOM 1 CG TYR 61 33.836 16.989 3.546 1.00 0.00 +\&... +.IP +Autobondrot commands use colons to separate values +Transformations: BONDROT:id:currAng:start:end:stepSz:x1:y1:z1:x2:y2:z2 +.TP +TRANS: +id:currpos:start:end:stepSz:x1:y1:z1:x2:y2:z2 +.TP +NULL +# dummy +.TP +Bias functions: +COS:scale:phaseOffset:frequency +POLY:scale:offset:polynomialDegree +CONST:value +.TP +Branching: +SAVE and RESTORE or "(" and ")" +.IP +(e.g. to rotate each Chi and the methyls for isoleucine the +.IP +sequence is: rotChi1/SAVE/rotChi2/rotCD1/RESTORE/rotCG2) +.IP +Set orientation: GO:angle1:angle2:... +Include files: @filename +Comments: # comment text +.PP +probe: version 2.13.110909, Copyright 1996\-2011, J. Michael Word diff --git a/debian/links b/debian/links index 4395a29..bec626d 100644 --- a/debian/links +++ b/debian/links @@ -1,2 +1,6 @@ # For compatibility reasons (i.e. scripts written using probe package <= 2.13.110909) usr/lib/debian-med/bin/probe usr/bin/king-probe + +# Also link the manpage to the Debian Med name space +usr/share/man/man1/king-probe.1.gz usr/lib/debian-med/share/man/man1/probe.1.gz + -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/king-probe.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
