>From scistra@frodo.cs.sandia.gov Fri Apr 12 18:51 EDT 1996 Received: from cs.sandia.gov for scistra@frodo.cs.sandia.gov by www.ccl.net (8.7.1/950822.1) id SAA16572; Fri, 12 Apr 1996 18:51:29 -0400 (EDT) Received: from frodo.cs.sandia.gov.noname by cs.sandia.gov with smtp (Smail3.1.28.1 #5) id m0u7rgC-000XQoC; Fri, 12 Apr 96 16:51 MDT Received: by frodo.cs.sandia.gov.noname (4.1/SMI-4.1) id AA02117; Fri, 12 Apr 96 16:50:58 MDT Date: Fri, 12 Apr 96 16:50:58 MDT From: scistra@cs.sandia.gov (Sorin C. Istrail) Message-Id: <9604122250.AA02117@frodo.cs.sandia.gov.noname> To: chemistry-request@www.ccl.net Subject: Call For Papers: Computational Molecular Biology ***CALL FOR PAPERS* CALL FOR PAPERS* CALL FOR PAPERS*** DISCRETE APPLIED MATHEMATICS Announcing a Second Special Issue on Computational Molecular Biology Guest Editors: Sorin Istrail, Pavel Pevzner, Ron Shamir Submission Deadline: August 1, 1996 Manuscripts are solicited for a special issue of Discrete Applied Mathematics on topics concerning the development of new combinatorial and algorithmic techniques in computational molecular biology. With this announcement Discrete Applied Mathematics continues the series of special issues devoted to computational molecular biology. The series publishes papers on the mathematical and algorithmic foundations of the inherently discrete aspects of computational biology. The traditional partnership of mathematics and physics has advanced and enriched both disciplines. In a similar partnership, mathematics and algorithms are becoming crucial tools in the rapid advancement of molecular biology. At the same time, the computational challenges of these biological disciplines raise exciting new problems in discrete mathematics and theoretical computer science. To paraphrase Stan Ulam, those challenges reflect "not only what mathematics can do for biology but what biology can do for mathematics." The following is a (nonexhaustive) list of possible topics of interest for the special issue: * DNA mapping * DNA sequencing * DNA/protein sequence comparison * molecular evolution * RNA/protein structure * gene/motif recognition Seven (7) copies of complete manuscripts should be sent to any of the Guest Editors indicated below by August 1, 1996. We expect this Second Special Issue to appear in the Fall 1997. Manuscripts must be prepared according to the normal submission requirements of Discrete Applied Mathematics, as described in each issue of the journal. The Guest Editors will make every possible effort to assure the timely completion of a thorough refereeing process. The Guest Editors are: Sorin Istrail Sandia National Laboratories Algorithms and Discrete Mathematics Department P.O.Box 5800, MS 1110 Albuquerque, NM 87185-5800 scistra@cs.sandia.gov Pavel Pevzner University of Southern California Department of Mathematics, DRB 155 Los Angeles, CA 90089-1113 ppevzner@hto.usc.edu Ron Shamir Dept. of Computer Science Tel Aviv University Tel Aviv 69978 ISRAEL shamir@math.tau.ac.il >From tim@mdli.com Sat Apr 13 19:19 EDT 1996 Received: from one.mind.net for tim@mdli.com by www.ccl.net (8.7.1/950822.1) id TAA23993; Sat, 13 Apr 1996 19:18:55 -0400 (EDT) Received: from nec.mentat.org ([206.101.74.4]) by one.mind.net (8.6.12/8.6.10) with SMTP id QAA16163; Sat, 13 Apr 1996 16:17:24 -0700 Message-Id: <2.2.32.19960413231800.00759004@mind.net> X-Sender: tim@mind.net X-Mailer: Windows Eudora Pro Version 2.2 (32) Mime-Version: 1.0 Date: Sat, 13 Apr 1996 16:18:00 -0700 To: Craig Taverner , Konrad HINSEN From: Tim Maffett Subject: Re: CCL:Chemistry, the WWW and Java Cc: chemistry@www.ccl.net Content-Type: text/plain; charset="us-ascii" Content-Length: 2096 Status: RO At 06:52 PM 4/13/96 +0200, Craig Taverner wrote: > >To everyone discussing the Java and WWW developments issue > >This whole discussion is clearly something that the chemical community >needs to (and apparently wants to) discuss in detail. Since it is not >what is usually discussed in the CCL list, I wonder whether we should >consider having an alternative list service to discuss this topic itself. > >I personally am finding it very interesting and am completely happy with >it on the CCL, but am worried that there may be many who would like the >CCL to stick to CC, and cause this discussion to die. From the >discussion so far, I gather that there is reason to believe that it >should definitely continue. > >Should it be moved to a new list, another list, or just stay right here >at CCL? The chemweb mailing list has existed for some time, and it has proved to be a high content/low noise mailing list devoted to various uses of the net by/for chemist. The chemweb mailing list is problably better suited for this discussion, although I am another person that does not mind this topic in the CCL mailing list. I have included subscription info below for the chemweb list. -- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To subscribe, send to listserver@ic.ac.uk the following message; subscribe chemweb List coordinator, Henry Rzepa (rzepa@ic.ac.uk) > >Cheers, Craig > > >"Imagine if every Thursday your shoes exploded if you tied them the > usual way. This happens to us all the time with computers, and nobody > thinks of complaining." > -- Jeff Raskin, interviewed in Doctor Dobb's Journal > >Craig Taverner >Structural Chemistry, University of the Witwatersrand, South Africa >tel: +27-11-716-2290 fax: +27-11-716-3826 >email: craig@hobbes.gh.wits.ac.za >www: http://www.gh.wits.ac.za/craig > -tim Tim Maffett tim@mdli.com Architect, Internet Technologies MDL Information Systems, Inc. From craig@occam.gh.wits.ac.za Mon Apr 15 03:46:43 1996 Received: from occam.gh.wits.ac.za for craig@occam.gh.wits.ac.za by www.ccl.net (8.7.1/950822.1) id DAA05280; Mon, 15 Apr 1996 03:13:20 -0400 (EDT) Received: (from craig@localhost) by occam.gh.wits.ac.za (8.6.12/8.6.9) id JAA09672; Mon, 15 Apr 1996 09:13:23 +0200 Date: Mon, 15 Apr 1996 09:13:22 +0200 (GMT+0200) From: Craig Taverner X-Sender: craig@occam.gh.wits.ac.za To: Konrad HINSEN cc: h.rzepa@ic.ac.uk, chemistry@www.ccl.net Subject: Re: CCL:Java and other WWW developments In-Reply-To: <199604141718.NAA06294@cyclone.ERE.UMontreal.CA> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > specific needs (including e.g. chemistry-related Web applets), we can > very well choose not to follow the mass-market trends. We agree that we must make the most informed decision about what trends to follow, but we must also try and predict where we think the chemistry market is going to go. It would be foolish both to waite too long for the trends to become apparent, and get in just as the next wave comes, as well as to get into something new that never takes off. I think the work being put into Java is justified and it is going to have an impact in chemistry. We must be in a position to make the most of what does come out of the current situation. I beleive we must also be in a position to try and make sure that what might come out is something to our liking. In fact, we should stop discussing just whether we should discuss it, and get back to the original discussion of standards that we would like the developers to follow. > Enthusiasm about the possibilities, yes. But that's something else than > talking about a "new standard" and unavoidable developments that we > just have to follow. Java is an alternative development platform. We cannot touch that. But we can be involved in the Chemistry and Computational Chemistry standards or trends that might be implemented. > One of the problems with Java is, for example, that is not really > free. To make the most of Java applets (or even just classes), it > would be necessary to be able to integrate them with other code, which > is not necessarily Web-related. But this requires licensing the rather > expensive byte-code interpreter from Sun, which is a prohibitive cost > for small developers, including academic groups. A real standard for > computational science should be fully available to everyone at an > acceptable, preferably zero, cost. Java is free. You only have to pay the licence fee if you want to develope a byte-code interpreter yourself. This is not our market. In order to interface with other code, all we need to use is Java's interfacing code. I understand there are some bugs with it, but it will certainly be an option. Cheers, Craig "Imagine if every Thursday your shoes exploded if you tied them the usual way. This happens to us all the time with computers, and nobody thinks of complaining." -- Jeff Raskin, interviewed in Doctor Dobb's Journal Craig Taverner Structural Chemistry, University of the Witwatersrand, South Africa tel: +27-11-716-2290 fax: +27-11-716-3826 email: craig@hobbes.gh.wits.ac.za www: http://www.gh.wits.ac.za/craig From owner-chemistry@ccl.net Mon Apr 15 06:46:46 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id FAA08615; Mon, 15 Apr 1996 05:55:42 -0400 (EDT) Received: from goliat.ugr.es for aentrena@goliat.ugr.es by bedrock.ccl.net (8.7.1/950822.1) id FAA04914; Mon, 15 Apr 1996 05:55:36 -0400 (EDT) Received: from quimfarm2 (quimfarm2.ugr.es [150.214.65.52]) by goliat.ugr.es (8.6.10/8.6.12) with SMTP id LAA25400 for ; Mon, 15 Apr 1996 11:57:23 +0100 Date: Mon, 15 Apr 1996 11:57:23 +0100 Message-Id: <199604151057.LAA25400@goliat.ugr.es> X-Sender: aentrena@goliat.ugr.es Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: aentrena@goliat.ugr.es (Antonio Entrena Guadix ) Subject: phase angle X-Mailer: Dear CCl users: A while back I posted this question to the CCL: "I am loocking for a program to calculate the phase angle in a five- six or seven-membered rings. As a input data I would like to use the MM3 output coordinates." I am very grateful to Graig Taverner (Structural Chemistry, University of the Witwatersrand, South Africa) who answered to my question. I am waiting for more responses but the following is the only one that I have received. I regreet for the delay in the submition of the answer but I have been outside of Granada for a few days " Professor Jan Boeyens and Debora Evans wrote a program to do exactly this for any size ring. It is called conpuc. I takes it's own cartesian coordinate input, that I'm sure is easy to convert >from MM3. The reference is: D.G.Evans, J.C.A.Boeyens, "Conformational Analysis of Ring Pucker", Acta Cryst. (1989). B45, 581-590 and the program source is available at: ftp://hobbes.gh.wits.ac.za/pub/conpuc/ Cheers, Craig" Sincerely A. Entrena From radkie@mousy.chemie.unibas.ch Mon Apr 15 07:46:46 1996 Received: from mousy.chemie.unibas.ch for radkie@mousy.chemie.unibas.ch by www.ccl.net (8.7.1/950822.1) id HAA09062; Mon, 15 Apr 1996 07:35:34 -0400 (EDT) From: Received: by mousy.chemie.unibas.ch (AIX 3.2/UCB 5.64/4.03) id AA17125; Mon, 15 Apr 1996 13:36:21 +0200 Message-Id: <9604151136.AA17125@mousy.chemie.unibas.ch> Subject: IPCM and SCIPCM To: chemistry@www.ccl.net (Computational Chem. List) Date: Mon, 15 Apr 1996 13:36:21 +0200 (DFT) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear members, Could someone please explain to me the difference between the IPCM and SCIPCM solvation models in Gaussian94, or could someone please give me references that explain this difference? I have read the Gaussian manual which states that IPCM uses the isodensity surface for the cavity, while SCIPCM uses a self-consistent cavity based on the isodensity surface, but I am not sure what this means, nor why the single point calculation outputs for these two models are so very different. Also, I have only been able to optimize anionic structures at dielectrics of 5 or less using the SCIPCM model. I would appreciate it if someone could suggest ways to get these calculations to optimize at higher dielectric constants. Many thanks, Jen -- Jennifer Radkiewicz Department of Chemistry University of California, Los Angeles email: jlr@chem.ucla.edu From arthur@csb0.IPC.PKU.EDU.CN Mon Apr 15 09:46:47 1996 Received: from csb0.IPC.PKU.EDU.CN for arthur@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.7.1/950822.1) id IAA10180; Mon, 15 Apr 1996 08:48:10 -0400 (EDT) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA21247; Mon, 15 Apr 96 20:44:39 -0700 Date: Mon, 15 Apr 1996 20:44:37 -0700 (PDT) From: Arthur Wang To: CCL mailing list Subject: Quantative prediction of binding affinities Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, In structure-based drug design, maybe the real problem lies in scoring the candidates, i.e. predicting the binding affinities to find the promising ones among the potential ligands. Obviously if the score relates directly to the free energy changes upon the binding process, designers will be lent much convenience. Many approaches have focused on this problem. Some use rule-based energy functions (e.g. J.Comp.-Aided Molecular Design, 1994, 8, 243-256), some use force field to evaluate the energies (e.g. GRID, DOCK, & J.Comp.Chem., 1995, 16, 454-464). For some reasons, we prefer force field method. (Any comments on the comparison of these two methods are welcome! :-) In such a energy function, these terms are usually included: E = E(vdW) + E(electrostatic) + E(desolvation) + E(H-bond) + ... Different force fields often have different forms. So here comes my question: Are there anyone who has checked the validities of these force fields? Which one is more reasonable and which is less reasonable? Usually a few crystal structures of complex are rebuilt by using a specific method, but so far I have not seen any attempts to predict quantitatively the experimentally determined binding constants or free energy changes. This is critical. Because we will probably yield nothing valuable by using a false energy estimation. Any comments? Any clues? I would like to calculate the binding energies for a series of complexes by using current force fields. In this case, I need a list of complex PDB entries which have reliable determined binding constants. Anyone maintains such a list? Answers will be summaried. Thanks in advance. Arthur _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Arthur Wang Doctoral Candidate _/ _/ Molecular Design Lab _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-2751490 Fax: 86-10-2751725 _/ _/ WWW: http://www.ipc.pku.edu.cn/moldes/arthur/home.html _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From robert@tocsy.utmb.edu Mon Apr 15 10:46:55 1996 Received: from tocsy.utmb.edu for robert@tocsy.utmb.edu by www.ccl.net (8.7.1/950822.1) id KAA12645; Mon, 15 Apr 1996 10:15:08 -0400 (EDT) Received: by tocsy.utmb.edu (940816.SGI.8.6.9/930416.SGI.AUTO) id JAA19062; Mon, 15 Apr 1996 09:17:20 -0500 Date: Mon, 15 Apr 1996 09:17:05 +0059 (CDT) From: Robert Fraczkiewicz Subject: Inside or outside of a polyhedron To: chemistry@www.ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, Suppose you have given N arbitrary points (in 3D space) that are vertices of a polyhedron: (x1,y1,z1),.....,(xN,yN,zN). What is the fastest algorithm for determining if a given point (x,y,z) is inside or outside of this polyhedron? (Calculating distances to every vertex is not a good idea). I will post summary to the net. Best regards, Robert Fraczkiewicz UT Medical Branch From hinsenk@ERE.UMontreal.CA Mon Apr 15 10:55:26 1996 Received: from harfang.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.7.1/950822.1) id JAA11429; Mon, 15 Apr 1996 09:50:03 -0400 (EDT) Received: from eole.ERE.UMontreal.CA (eole.ERE.UMontreal.CA [132.204.10.20]) by harfang.CC.UMontreal.CA with ESMTP id JAA24516 (8.6.11/IDA-1.6); Mon, 15 Apr 1996 09:40:52 -0400 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (951211.SGI.8.6.12.PATCH1042/5.17) id JAA03987; Mon, 15 Apr 1996 09:40:51 -0400 Received: by cyclone.ERE.UMontreal.CA (951211.SGI.8.6.12.PATCH1042/5.17) id JAA14619; Mon, 15 Apr 1996 09:40:49 -0400 Date: Mon, 15 Apr 1996 09:40:49 -0400 Message-Id: <199604151340.JAA14619@cyclone.ERE.UMontreal.CA> To: craig@hobbes.gh.wits.ac.za CC: h.rzepa@ic.ac.uk, chemistry@www.ccl.net In-reply-to: (message from Craig Taverner on Mon, 15 Apr 1996 09:13:22 +0200 (GMT+0200)) Subject: Re: CCL:Java and other WWW developments From: hinsenk@ERE.UMontreal.CA (Konrad HINSEN) > Java is free. You only have to pay the licence fee if you want to > develope a byte-code interpreter yourself. This is not our market. In You can develop your own bytecode interpreter for free, and in fact there are projects for alternative interpreters at various stages of completion. It remains to be seen whether these clones together with Sun's original can be used interchangeably and thus form an open standard, or whether each version will try to attract programmers by special noncompatible features, the way Netscape is about to destroy the HTML standard. > order to interface with other code, all we need to use is Java's > interfacing code. I understand there are some bugs with it, but it will > certainly be an option. But a very limited one, even if it works as advertised. With the interfacing code, all you will be able to do is to call non-Java code >from a Java applet. You will *not* be able to run Java code outside your Web browser. If someone invests a significant amount of time to develop Java code for visualization, access to chemical databases, etc., to make these things available in Web pages, it makes sense to use the same code for other applications *outside* of Web pages. But that requires the integration of the bytecode interpreter into whatever other system wants to use Java code. Another point worth considering is that Java-capable Web browsers are not available to everyone. Although everyone talks about Netscape 2.0 as "the" Web browser, it isn't available for some widely used systems (e.g. SGI Irix 4.0, or MIPS-based DECStations). And this situation may become worse in the future. Suppose you develop lots of interesting chemical software in Java, for use in special Web pages constructed for Netscape. Then a new machine appears on the market that is just perfect for computational chemistry: very fast, lots of memory, and very cheap. But Netscape won't port its browser, because this machine is not terribly interesting from a global market perspective. What do you do? ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. Centre-Ville | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From rmuller@invitro.usc.edu Mon Apr 15 15:46:51 1996 Received: from usc.edu for rmuller@invitro.usc.edu by www.ccl.net (8.7.1/950822.1) id PAA18105; Mon, 15 Apr 1996 15:31:22 -0400 (EDT) Received: from invitro.usc.edu (invitro.usc.edu [128.125.14.34]) by usc.edu (8.7.2/8.7.2/usc) with ESMTP id MAA10501 for ; Mon, 15 Apr 1996 12:31:19 -0700 (PDT) Received: (rmuller@localhost) by invitro.usc.edu (8.6.12/8.6.7+ucs) id MAA27227; Mon, 15 Apr 1996 12:31:19 -0700 Date: Mon, 15 Apr 1996 12:31:19 -0700 Message-Id: <199604151931.MAA27227@invitro.usc.edu> From: "Richard P. Muller" To: chemistry@www.ccl.net Subject: CCL:Macintosh XMol I have used the XMol program from the Minnesota Supercomputer Center for several years now and have been very happy with it. Does anyone know of a version that has ported to the Macintosh or PowerMacintosh computers? Thanks in advance. Reply to me and I'll summerize if there's interest. Rick Muller From rui@iris6.carb.nist.gov.carb.nist.gov Mon Apr 15 18:46:50 1996 Received: from ENH.NIST.GOV for rui@iris6.carb.nist.gov.carb.nist.gov by www.ccl.net (8.7.1/950822.1) id SAA19221; Mon, 15 Apr 1996 18:14:51 -0400 (EDT) Received: from iris6.carb.nist.gov.carb.nist.gov (iris6.carb.nist.gov) by ENH.NIST.GOV (PMDF V5.0-5 #10952) id <01I3KW144HY8010JNN@ENH.NIST.GOV>; Mon, 15 Apr 1996 18:16:28 -0400 (EDT) Received: by iris6.carb.nist.gov.carb.nist.gov (920330.SGI/920502.SGI) for @enh.nist.gov:chemistry@www.ccl.net id AA15988; Mon, 15 Apr 1996 18:11:39 -0400 Date: Mon, 15 Apr 1996 18:11:38 +30000 From: Rui Luo Subject: Re: CCL:Inside or outside of a polyhedron In-reply-to: To: Robert Fraczkiewicz Cc: chemistry@www.ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT On Mon, 15 Apr 1996, Robert Fraczkiewicz wrote: > > Dear Netters, > > Suppose you have given N arbitrary points (in 3D space) that are vertices > of a polyhedron: (x1,y1,z1),.....,(xN,yN,zN). What is the fastest > algorithm for determining if a given point (x,y,z) is inside or outside of > this polyhedron? (Calculating distances to every vertex is not a good > idea). I will post summary to the net. > > Best regards, > > Robert Fraczkiewicz > UT Medical Branch > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: robert@tocsy.utmb.edu > -- Original Sender From: Address: robert@tocsy.utmb.edu > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > Just an idea. It's very efficient, but not sure it's right. First transform the current coordinate system to one with the given point (x,y,z) as the origin. I.e. subtrate (xi,yi,zi), where i=1,...,N, by (x,y,z). This can be done very fast. Second look at the sign of the transformed coordinates of all vertices. If all xi's, where i=1,...,N, have the same sign, the point is outside of the polyhedron. The statement holds for all yi's or all zi's. So if any one of the three conditions holds, the point will be outside. Otherwise if none of the conditions hold, it's inside. Good Luck! Rui Luo CARB, UMBI 04/15 From carlos@hugin.ucsf.EDU Mon Apr 15 20:47:02 1996 Received: from hugin.ucsf.EDU for carlos@hugin.ucsf.EDU by www.ccl.net (8.7.1/950822.1) id UAA20023; Mon, 15 Apr 1996 20:23:38 -0400 (EDT) Received: by hugin.ucsf.EDU (931110.SGI/GSC4.24) id AA12890; Mon, 15 Apr 96 17:23:37 -0700 Date: Mon, 15 Apr 96 17:23:37 -0700 From: carlos@hugin.ucsf.EDU (Carlos Simmerling) Message-Id: <9604160023.AA12890@hugin.ucsf.EDU> To: chemistry@www.ccl.net Subject: Re: CCL:Inside or outside of a polyhedron > Just an idea. It's very efficient, but not sure it's right. > > First transform the current coordinate system to one with the given point > (x,y,z) as the origin. I.e. subtrate (xi,yi,zi), where i=1,...,N, by > (x,y,z). This can be done very fast. > > Second look at the sign of the transformed coordinates of all vertices. > If all xi's, where i=1,...,N, have the same sign, the point is outside > of the polyhedron. The statement holds for all yi's or all zi's. So if any > one of the three conditions holds, the point will be outside. Otherwise if > none of the conditions hold, it's inside. > > > Good Luck! > > Rui Luo > While this is a necessary condition for the point to be inside the polyhedron, it isn't sufficient. A polyhedron that has a concave portion may span both side of the point without actually enclosing it. ============================================================================= Carlos L. Simmerling, Ph.D. Department of Pharmaceutical Chemistry Phone: (415) 476-7985 Box 0446, Room S-926 Fax: (415) 476-0688 University of California San Francisco, CA 94143 E-mail: carlos@cgl.ucsf.edu ============================================================================= From Harry_Johnson@avanticorp.com Mon Apr 15 20:53:53 1996 Received: from dns2.avanticorp.com for Harry_Johnson@avanticorp.com by www.ccl.net (8.7.1/950822.1) id UAA19880; Mon, 15 Apr 1996 20:03:02 -0400 (EDT) Received: from sarah.rtp.avanticorp.com (sarah.rtp.avanticorp.com [192.160.17.207]) by dns2.avanticorp.com (8.7.4/8.7.3) with ESMTP id UAA13707; Mon, 15 Apr 1996 20:02:43 -0400 (EDT) Received: (from harry@localhost) by sarah.rtp.avanticorp.com (8.7.2/8.7.2) id UAA00634; Mon, 15 Apr 1996 20:02:42 -0400 (EDT) Date: Mon, 15 Apr 1996 20:02:42 -0400 (EDT) Message-Id: <199604160002.UAA00634@sarah.rtp.avanticorp.com> From: Harry Johnson To: rui@iris6.carb.nist.gov CC: robert@tocsy.utmb.edu, chemistry@www.ccl.net In-reply-to: (message from Rui Luo on Mon, 15 Apr 1996 18:11:38 +30000) Subject: Re: CCL:Inside or outside of a polyhedron >>>>> "Rui" == Rui Luo writes: Rui> Second look at the sign of the transformed coordinates of all Rui> vertices. If all xi's, where i=1,...,N, have the same sign, Rui> the point is outside of the polyhedron. The statement holds Rui> for all yi's or all zi's. So if any one of the three Rui> conditions holds, the point will be outside. Otherwise if Rui> none of the conditions hold, it's inside. Your last statement is incorrect. Consider the 2D case: ---- / / +/ / / / / / --- If the point '+' is the origin, then all of the Xi's do not have the same sign, nor do all of the Yi's, so none of the above conditions hold, yet the point is still outside the polygon. Your method is another implementation of a bounding box. Usually, however, it is done by simply finding the maximum and minimum value of each coordinate, x, y, and z, and checking to see whether the point's coordinates lie within the extrema of the polyhedrons coordinates. If most of the points of interest likely lie outside the polyhedron this is a quick initial screening method. -Harry ______________________________________________________________________ Avant! Harry C. Johnson IV harry@avanticorp.com 1101 Slater Rd Software Engineer Phone: (919)941-6726 RTP, NC 27703 FAX: (919)941-6700 ______________________________________________________________________ From WILLSD@conrad.appstate.edu Mon Apr 15 21:47:21 1996 Received: from listserv.appstate.edu for WILLSD@conrad.appstate.edu by www.ccl.net (8.7.1/950822.1) id VAA20767; Mon, 15 Apr 1996 21:09:03 -0400 (EDT) Received: from spd.appstate.edu ([152.10.1.23]) by listserv.appstate.edu with ESMTP id <13800-149>; Mon, 15 Apr 1996 21:08:50 -0500 Received: from conrad.appstate.edu by conrad.appstate.edu (PMDF V5.0-6 #8642) id <01I3L21K9M9CAXBM3A@conrad.appstate.edu>; Mon, 15 Apr 1996 21:08:37 -0400 (EDT) Date: Mon, 15 Apr 1996 21:08:36 -0400 (EDT) From: willsd@conrad.appstate.edu Subject: Re: CCL:Inside or outside of a polyhedron In-reply-to: To: Rui Luo Cc: Robert Fraczkiewicz , chemistry@www.ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT On Mon, 15 Apr 1996, Rui Luo wrote: > On Mon, 15 Apr 1996, Robert Fraczkiewicz wrote: > > > > > Dear Netters, > > > > Suppose you have given N arbitrary points (in 3D space) that are vertices > > of a polyhedron: (x1,y1,z1),.....,(xN,yN,zN). What is the fastest snip... > > Just an idea. It's very efficient, but not sure it's right. > > First transform the current coordinate system to one with the given point > (x,y,z) as the origin. I.e. subtrate (xi,yi,zi), where i=1,...,N, by > (x,y,z). This can be done very fast. > > Second look at the sign of the transformed coordinates of all vertices. > If all xi's, where i=1,...,N, have the same sign, the point is outside > of the polyhedron. The statement holds for all yi's or all zi's. So if any > one of the three conditions holds, the point will be outside. Otherwise if > none of the conditions hold, it's inside. > > It seems to me that this test will be reliable if the polyhedron is known to be convex, but other wise might be easily fooled: ___ \ \ \ \ \ \ *| | / / / / / / ---- Steve Williams Chemistry, ASU Boone, NC USA snip