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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML EXPERIMENTAL 970324//EN"><HTML><HEAD><META NAME="GENERATOR" CONTENT="Adobe FrameMaker 5.5/HTML Export Filter"><LINK REL="STYLESHEET" HREF="Manual.css"><TITLE> PTR format</TITLE></HEAD><BODY BGCOLOR="#ffffff"><H2 CLASS="Heading-3"><A NAME="pgfId=12669"> </A><A NAME="52195"> </A>PTR format</H2><DIV><H3 CLASS="Heading-4"><A NAME="pgfId=16664"> </A>Specification</H3><P CLASS="Body"><A NAME="pgfId=16649"> </A>PTR (or pointer) format is a compact representation for molecules which does not actually contain coordinates. Instead, it contains the transformations to the coordinates and "points" back to a source file where the untransformed coordinates reside.</P><P CLASS="Body"><A NAME="pgfId=16655"> </A>All information about a molecule is packed into one line. Each item of data is identified by a field name. Some fields are required, like the molecule source information. Some are optional, like the coordinate transformation information. All others are considered comments and are ignored, like the molecule name and score information.</P><H3 CLASS="Table"><A NAME="pgfId=16680"> </A>Table 6. PTR Format Data Fields</H3><TABLE><CAPTION><H3 CLASS="Table-Sub"><A NAME="pgfId=16683"> </A>6A: Required PTR Fields </H3></CAPTION><TR><TH ROWSPAN="1" COLSPAN="3"><P CLASS="Normal"><A NAME="pgfId=16689"> </A>These fields must be present in every PTR record.</P></TH></TR><TR><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17067"> </A>Field</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17069"> </A>Type</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17071"> </A>Description</P></TH></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16695"> </A><FILE></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16697"> </A>String</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16699"> </A>Directory path and name of file which contains molecule.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16701"> </A><FPOS></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16703"> </A>Integer</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16705"> </A>Byte position in file of molecule.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16928"> </A><END></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16930"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16932"> </A>End of record flag.</P></TD></TR></TABLE><P CLASS="Body"><A NAME="pgfId=16725"> </A> </P><TABLE><CAPTION><H3 CLASS="Table-Sub"><A NAME="pgfId=17800"> </A>6B: Optional PTR Fields1 of 2</H3></CAPTION><TR><TH ROWSPAN="1" COLSPAN="3"><P CLASS="Normal"><A NAME="pgfId=17854"> </A>If these fields are present, they will be read and used to update the molecule. The transformation fields will modify the position or conformation of the molecule.</P></TH></TR><TR><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17806"> </A>Field</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17808"> </A>Type</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17810"> </A>Description</P></TH></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17812"> </A><TRANS></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17814"> </A>Real[3]</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17816"> </A>XYZ translation vector in Angstroms.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17818"> </A><ROT></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17820"> </A>Real[3]</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17822"> </A>Quaternion rotation vector (unitless, range 0-1).</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17824"> </A><TORS></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17826"> </A>Integer</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17828"> </A>Number of rotatable torsions.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17830"> </A><REFL></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17832"> </A>Integer</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17834"> </A>Flag for chiral reflection (0 or 1).</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17836"> </A><T1>,<T2>, ...</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17838"> </A>Integer, Real</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17840"> </A>Bond identifier and torsion angle.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17842"> </A><KEY><A HREF="Manual.43.html#17886" CLASS="XRef">c</A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17844"> </A>Integer</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17846"> </A>Number of chemical keys.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17904"> </A><KFOLD><A HREF="Manual.43.html#17886" CLASS="XRef">c</A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17906"> </A>Integer</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17908"> </A>Flag for folded chemical keys.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17925"> </A><KI1>,<KI2>, ...<A HREF="Manual.43.html#17886" CLASS="XRef">c</A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17927"> </A>Integer</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17929"> </A>Chemical key label and distance fingerprint</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="3"><OL><LI CLASS="TableFootnote"><A NAME="pgfId=17940"> </A><A NAME="17886"> </A>This field is only read during a chemical screening run.</LI></OL></TD></TR></TABLE><P CLASS="Body"><A NAME="pgfId=16815"> </A> </P><TABLE><CAPTION><H3 CLASS="Table-Sub"><A NAME="pgfId=16819"> </A>6C: Comment PTR Fields </H3></CAPTION><TR><TH ROWSPAN="1" COLSPAN="3"><P CLASS="Normal"><A NAME="pgfId=17880"> </A>These fields are generated for output only. They are completely ignored during input. </P></TH></TR><TR><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17785"> </A>Field</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17787"> </A>Type</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17789"> </A>Description</P></TH></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17894"> </A><ID></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17896"> </A>Integer</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17898"> </A>Line position in ptr file.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16837"> </A><SRC_ID></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16839"> </A>Integer</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16841"> </A>Line position in input ptr file.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16843"> </A><NAME></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16845"> </A>String</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16847"> </A>Molecule name.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16849"> </A><DESCR></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16851"> </A>String</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16853"> </A>Molecule description.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16855"> </A><BMP></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16857"> </A>Integer</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16859"> </A>Number of bumps.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16861"> </A><CNT></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16863"> </A>Real</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16865"> </A>Contact score.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16978"> </A><CHM></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16980"> </A>Real</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16982"> </A>Chemical score.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17749"> </A><NRG></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17751"> </A>Real</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17753"> </A>Total energy score.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17767"> </A><INTRA></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17769"> </A>Real</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17771"> </A>Intramolecular component of score.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17773"> </A><INTER></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17775"> </A>Real</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17777"> </A>Intermolecular component of score.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17028"> </A><VDW></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17030"> </A>Real</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17036"> </A>VDW component of score.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17032"> </A><ELE></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17034"> </A>Real</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17038"> </A>Electrostatic component of score.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16954"> </A><RMSD></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16956"> </A>Real</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=16958"> </A>RMS deviation of current orientation from input.</P></TD></TR></TABLE></DIV><DIV><H3 CLASS="Heading-4"><A NAME="pgfId=16650"> </A>Example</H3><DIV><H6 CLASS="Heading-5"><A NAME="pgfId=22178"> </A>Database Entry</H6><TABLE><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=22181"> </A><ID> 10 <NAME> CAMYLOFIN_C00000105 <DESCR> **** <FILE> /marco/db/mol2.95.1/cmc/cmc.2.mol2 <FPOS> 46204 <END></P></TD></TR></TABLE></DIV><DIV><H6 CLASS="Heading-5"><A NAME="pgfId=22191"> </A>Flexible Docking Output</H6><TABLE><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=22190"> </A><ID> 5 <SRCID> 5 <NAME> DANAZOL_C00002993 <DESCR> **** <FILE> db/db3.mol2 <FPOS> 14144 <TRANS> 5.00991 29.9234 16.2096 <ROT> 0.270641 1.05337 0.0158567 <TORS> 2 <TANCHOR> 1 <T1> 20 153.624 <T2> 21 -28.0673 <REFL> 0 <BMP> 2 <NRG> -32.43 <INTRA> -0.48 <INTER> -31.95 <VDW> -32.53 <ELECTRO> 0.09 <RMSD> 34.95 <END></P></TD></TR></TABLE></DIV><DIV><H6 CLASS="Heading-5"><A NAME="pgfId=22196"> </A>Chemical Screen Database Entry</H6><TABLE><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=22195"> </A><ID> 1 <NAME> DAZOQUINAST_C00005118 <DESCR> **** <FILE> /marco/db/mol2.95.1/cmc/cmc.1.mol2 <FPOS> 9689688 <KEY> 5 <KFOLD> 1 <KI1> 0 <KJ1> 10 2d7 <KJ2> 35 3fff <KJ3> 0 0 <KJ4> 20 f65 <KJ5> 0 0 <KI2> 1 <KJ2> 21 fd <KJ3> 0 0 <KJ4> 28 ab7e <KJ5> 0 0 <KI3> 2 <KJ3> 0 0 <KJ4> 0 0 <KJ5> 0 0 <KI4> 3 <KJ4> 6 c1a <KJ5> 0 0 <KI5> 4 <KJ5> 0 0 <END></P></TD></TR></TABLE></DIV></DIV><DIV><H3 CLASS="Heading-4"><A NAME="pgfId=22284"> </A>Usage</H3><P CLASS="Body"><A NAME="pgfId=22285"> </A>Check out the <A HREF="Manual.37.html#97443" CLASS="XRef">ptrentry</A> and <A HREF="Manual.38.html#75291" CLASS="XRef">ptrfield</A> utilities to help manipulate PTR files.</P><P CLASS="Body"><A NAME="pgfId=22296"> </A>The <FILE> field can contain the relative path or absolute path of a filename. If you use the absolute path, then the ptr file can be used in any other directory. Otherwise, the ptr file is only useful in the idrectory in which it was originally made.</P></DIV><CENTER><P>⌨️ 快捷键说明
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